Notice of Pre-AIA or AIA Status
Applicant’s election of Group III and species SEQ ID NO:97 in the replies filed on 6 April 2026 and 13 May 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 1-2 are withdrawn from consideration as being drawn to nonelected inventions. Claims 13-14 are drawn to nonelected species and are thus also withdrawn from consideration. Claims 3-12 are examined to the extent they read on SEQ ID NO:97.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claim Objections
Claims 4 and 6 are objected to because the “a” before “kinase” in line 1 of claim 4 and the “a” before “nucleic” in line 1 of claim 6 should be replaced with --the--.
Improper Markush Grouping
Claims 3-12 are rejected on the basis that they contain 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 groupings of SEQ ID NOs:92, 94-99, and 1-91 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use.
SEQ ID NOs: 92, 94-99, and 1-91 are all kinase-dead mutant proteins, that is, they are all inactivated kinases. While all the wild-type proteins these sequences are based on (SEQ ID NOs:15, 17, 49, 60, 66, 75, 83, and 91, respectively, Table 2) are kinases, they do not share a single structural similarity. For example, SEQ ID NO:s 97 and 57 have only 5.1% identity over the length of the 614-amino acid long SEQ ID NO:97:
Query Match 5.1%; Score 163; DB 1; Length 356;
Best Local Similarity 25.8%;
Matches 74; Conservative 39; Mismatches 106; Indels 68; Gaps 14;
Qy 307 IIGTGRTGTVYKAVLDDGTT----LMVRRLQESQYTEKEFMSEMGTLGTVKHRNLVPLLG 362
::| | | | : | |: | | :: : |: |: : : | :
Db 75 VVGKGNGGVV-QLVQHKWTSQFFALKVIQMNIEESMRKQIAQEL----KINQQAQCPYVV 129
Qy 363 FCMTKRERLLVYKNM-PNGNLHDQLHPADGVSTLDWTTRLK---------IAIGAAKGLA 412
| |:: || : | || | | ::| | |||
Db 130 VC---------YQSFYENGVISIILEYMDGGSLADLLKKVKTIPEDYLAAICKQVLKGLV 180
Qy 413 WLHHSCNPRIIHRNISSRCILLDADFEPKISDFGLARLMNPIDTHLSTFVNGEFGDLGYV 472
:||| ||||:: :|:: | ||:|||:: :| :||: | |:
Db 181 YLHH--EKHIIHRDLKPSNLLINHIGEVKITDFGVSAIMESTSGQANTFI----GTYNYM 234
Qy 473 APE--------YTRTLVATPKGDIYSFGTVLLELVTGERPTNVSKAPETFKGNLVEWITE 524
:|| | | ||:| | :||| | | ||: | | |
Db 235 SPERINGSQRGYNY------KSDIWSLGLILLECALGRFPYAPPDQSETW-----ESIFE 283
Qy 525 LTSNAKLHDAIDESLVRKD---VDSELF--QFLKVACNCVSPTPKER 566
| |::| | || | :| |: ||:|
Db 284 LI----------ETIVDKPPPIPPSEQFSTEFCSFISACLQKDPKDR 320
Further, plants contain large numbers of kinases, but only 10% of them are involved in signaling pathways in response to biotic or abiotic or hormonal or developmental signals (Colcombet et al, 2008, Biochem J. 413:217-226; see pg 217, left column, paragraph 2).
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.
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.
Claims 3 and 11-12 are rejected under 35 U.S.C. 101 because the claimed invention is not supported by either a specific and substantial asserted utility or a well-established utility.
Claim 3 and 11-12 are drawn to a kinase-dead mutant protein.
The specification describes no use for isolated kinase-dead mutant proteins. It only describes a use for nucleic acids that encode them and plants transformed with the nucleic acids.
There is no well-established utility for a kinase-dead mutant protein, as such proteins exhibit no or almost activity.
The specification describes no substantial utility for the claimed kinase-dead mutant protein, as such, further research required to determine how to use it.
It is apparent that extensive further research, not considered to be routine experimentation, would be required before one skilled in the art would know how to use the claimed invention. It has been established in the courts that a utility that requires or constitutes carrying out further research to identify or reasonably confirm a “real world” context of use is not a substantial utility:
The basic quid pro quo contemplated by the Constitution and the Congress for granting a patent monopoly is the benefit derived by the public from an invention with substantial utility. Unless and until a process is refined and developed to this point-where specific benefit exists in currently available form, there is insufficient justification for permitting an application to engross what may prove to be a broad field (Brenner v. Manson, 383 U.S. 519 (1966)).
Accordingly, the invention in claims 3 and 11-12 lacks a “real-world” use.
Claim Rejections - 35 USC § 112
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 3 and 11-12 are also rejected under 35 U.S.C. 112(a) or pre-AIA 35 U.S.C. 112, first paragraph. Specifically, because the claimed invention is not supported by either a specific and substantial asserted utility or a well-established utility for the reasons set forth above, one skilled in the art clearly would not know how to use the claimed invention.
Claims 6 and 8-9 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 plant cell comprising a nucleic acid encoding SEQ ID NO:97, where the cell is soybean or another cyst nematode host, does not reasonably provide enablement for a plant cell comprising a nucleic acid encoding SEQ ID NO:97, where the cell is not a cyst nematode host. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
The claims are drawn to a plant cell comprising a nucleic acid encoding SEQ ID NO:97.
SEQ ID NO:97 is a mutant kinase in which a lysine in each of the ATP-binding pocket and the substrate binding pocket has been replaced with arginines (pg 30, lines 20-33). Soybean plants transformed with a nucleic acid encoding SEQ ID NO:97 have resistance to soybean cyst nematode (example 5).
However, not all plants are susceptible to soybean cyst nematode.
The instant specification fails to provide guidance for how to use such plant cells (or plants regenerated from them), where the original plant was not susceptible to soybean cyst nematode.
Given the nature of the invention and lack of guidance as discussed above, undue experimentation would have been required by one skilled in the art to develop and evaluate a use for such plant cells.
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.
The following is a quotation of the second paragraph of 35 U.S.C. 112:
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 3-12 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 that the inventor or a joint inventor, or for pre-AIA the applicant, regards as the invention. Dependent claims are included in all rejections.
Claim 3 is indefinite in its recitation of “comprising … SEQ ID NO:94-99”. It is unclear if the mutant protein comprises each of SEQ ID NO:94-99 or only one of them. The language of the claim implies that the mutant comprises each of SEQ ID NO:94-99; however, dependent claim 12, which recites that the mutant comprises SEQ ID NO:97, implies that the mutant of claim 3 comprises only one of SEQ ID NO:94-99. The metes and bounds of the claims are thus unclear.
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 35 U.S.C. 112 (pre-AIA ), fourth paragraph:
Subject to the [fifth paragraph of 35 U.S.C. 112 (pre-AIA )], 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 11-12 are rejected under 35 U.S.C. 112(d) or 35 U.S.C. 112(pre-AIA ), fourth paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Parent claim 3 recites “a kinase-dead mutant protein comprising … SEQ ID NO:94-99”. Dependent claims 11-12 recite that the kinase-dead mutant protein is SEQ ID NO:97. These claims fail to include all the limitations of the claim upon which they depend.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claims 4-5, 7 and 10 would be allowable if rewritten to overcome the objection and the rejection(s) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), 2nd paragraph, set forth in this Office action and to include all of the limitations of the base claim and any intervening claims.
The closest prior art to SEQ ID NO:97 is the wild-type kinase, taught in GenBank: KHN16981 (2014, www.ncbi.nlm.nih.gov/protein/KHN16981) and thought to be inactive:
A0A0B2Q607_GLYSO
ID A0A0B2Q607_GLYSO Unreviewed; 614 AA.
AC A0A0B2Q607;
DT 04-MAR-2015, integrated into UniProtKB/TrEMBL.
DT 04-MAR-2015, sequence version 1.
DT 28-JAN-2026, entry version 43.
DE SubName: Full=Inactive leucine-rich repeat receptor-like protein kinase {ECO:0000313|EMBL:KHN16981.1, ECO:0000313|EMBL:RZB60075.1};
DE EC=2.7.10.1 {ECO:0000313|EMBL:KHN16981.1};
DE EC=2.7.11.25 {ECO:0000313|EMBL:KHN16981.1};
GN ORFNames=D0Y65_043016 {ECO:0000313|EMBL:RZB60075.1}, glysoja_035832
GN {ECO:0000313|EMBL:KHN16981.1};
OS Glycine soja (Wild soybean).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Glycine;
OC Glycine subgen. Soja.
OX NCBI_TaxID=3848 {ECO:0000313|EMBL:KHN16981.1};
RN [1] {ECO:0000313|EMBL:KHN16981.1}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC TISSUE=Root {ECO:0000313|EMBL:KHN16981.1};
RA Lam H.-M., Qi X., Li M.-W., Liu X., Xie M., Ni M., Xu X.;
RT "Identification of a novel salt tolerance gene in wild soybean by whole-
RT genome sequencing.";
RL Submitted (JUL-2014) to the EMBL/GenBank/DDBJ databases.
RN [2] {ECO:0000313|EMBL:RZB60075.1, ECO:0000313|Proteomes:UP000289340}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. W05 {ECO:0000313|Proteomes:UP000289340};
RC TISSUE=Hypocotyl of etiolated seedlings {ECO:0000313|EMBL:RZB60075.1};
RA Xie M., Chung C.Y.L., Li M.-W., Wong F.-L., Chan T.-F., Lam H.-M.;
RT "A high-quality reference genome of wild soybean provides a powerful tool
RT to mine soybean genomes.";
RL Submitted (SEP-2018) to the EMBL/GenBank/DDBJ databases.
CC -!- SUBCELLULAR LOCATION: Membrane {ECO:0000256|ARBA:ARBA00004170};
CC Peripheral membrane protein {ECO:0000256|ARBA:ARBA00004170}. Membrane
CC {ECO:0000256|ARBA:ARBA00004479}; Single-pass type I membrane protein
CC {ECO:0000256|ARBA:ARBA00004479}. Secreted, cell wall
CC {ECO:0000256|ARBA:ARBA00004191}.
CC -!- SIMILARITY: Belongs to the polygalacturonase-inhibiting protein family.
CC {ECO:0000256|ARBA:ARBA00038043}.
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DR EMBL; KN660432; KHN16981.1; -; Genomic_DNA.
DR EMBL; QZWG01000016; RZB60075.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A0B2Q607; -.
DR SMR; A0A0B2Q607; -.
DR Gramene; XM_028350480.1; XP_028206281.1; LOC114389732.
DR Proteomes; UP000053555; Unassembled WGS sequence.
DR Proteomes; UP000289340; Chromosome 16.
DR GO; GO:0016020; C:membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0004709; F:MAP kinase kinase kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0004714; F:transmembrane receptor protein tyrosine kinase activity; IEA:UniProtKB-EC.
DR GO; GO:0006952; P:defense response; IEA:UniProtKB-KW.
DR CDD; cd14066; STKc_IRAK; 1.
DR FunFam; 1.10.510.10:FF:000609; Inactive LRR receptor-like serine/threonine-protein kinase BIR2; 1.
DR FunFam; 3.30.200.20:FF:000428; Inactive LRR receptor-like serine/threonine-protein kinase BIR2; 1.
DR FunFam; 3.80.10.10:FF:000400; Nuclear pore complex protein NUP107; 1.
DR Gene3D; 3.30.200.20; Phosphorylase Kinase, domain 1; 1.
DR Gene3D; 3.80.10.10; Ribonuclease Inhibitor; 1.
DR Gene3D; 1.10.510.10; Transferase(Phosphotransferase) domain 1; 1.
DR InterPro; IPR011009; Kinase-like_dom_sf.
DR InterPro; IPR001611; Leu-rich_rpt.
DR InterPro; IPR032675; LRR_dom_sf.
DR InterPro; IPR013210; LRR_N_plant-typ.
DR InterPro; IPR051824; LRR_Rcpt-Like_S/T_Kinase.
DR InterPro; IPR000719; Prot_kinase_dom.
DR InterPro; IPR001245; Ser-Thr/Tyr_kinase_cat_dom.
DR PANTHER; PTHR48006; LEUCINE-RICH REPEAT-CONTAINING PROTEIN DDB_G0281931-RELATED; 1.
DR PANTHER; PTHR48006:SF88; LRR RECEPTOR-LIKE KINASE FAMILY PROTEIN; 1.
DR Pfam; PF00560; LRR_1; 2.
DR Pfam; PF08263; LRRNT_2; 1.
DR Pfam; PF07714; PK_Tyr_Ser-Thr; 1.
DR SUPFAM; SSF52058; L domain-like; 1.
DR SUPFAM; SSF56112; Protein kinase-like (PK-like); 1.
DR PROSITE; PS50011; PROTEIN_KINASE_DOM; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840};
KW Cell wall {ECO:0000256|ARBA:ARBA00022512};
KW Disulfide bond {ECO:0000256|ARBA:ARBA00023157};
KW Glycoprotein {ECO:0000256|ARBA:ARBA00023180};
KW Kinase {ECO:0000313|EMBL:KHN16981.1};
KW Leucine-rich repeat {ECO:0000256|ARBA:ARBA00022614};
KW Membrane {ECO:0000256|ARBA:ARBA00023136, ECO:0000256|SAM:Phobius};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741};
KW Phosphoprotein {ECO:0000256|ARBA:ARBA00022553};
KW Plant defense {ECO:0000256|ARBA:ARBA00022821};
KW Receptor {ECO:0000313|EMBL:KHN16981.1};
KW Reference proteome {ECO:0000313|Proteomes:UP000289340};
KW Repeat {ECO:0000256|ARBA:ARBA00022737};
KW Secreted {ECO:0000256|ARBA:ARBA00022525};
KW Signal {ECO:0000256|ARBA:ARBA00022729, ECO:0000256|SAM:SignalP};
KW Transferase {ECO:0000313|EMBL:KHN16981.1};
KW Transmembrane {ECO:0000256|ARBA:ARBA00022692, ECO:0000256|SAM:Phobius};
KW Transmembrane helix {ECO:0000256|ARBA:ARBA00022989,
KW ECO:0000256|SAM:Phobius}.
FT SIGNAL 1..27
FT /evidence="ECO:0000256|SAM:SignalP"
FT CHAIN 28..614
FT /evidence="ECO:0000256|SAM:SignalP"
FT /id="PRO_5040666464"
FT TRANSMEM 225..251
FT /note="Helical"
FT /evidence="ECO:0000256|SAM:Phobius"
FT DOMAIN 302..586
FT /note="Protein kinase"
FT /evidence="ECO:0000259|PROSITE:PS50011"
SQ SEQUENCE 614 AA; 67863 MW; 4D8EC8A909220A44 CRC64;
Query Match 99.8%; Score 3206; Length 614;
Best Local Similarity 99.7%;
Matches 612; Conservative 2; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MVLHSWISSSHILVNFLLLLGCGITYGTDTDIFCLKSIKESLEDPYNYLKFSWDFNNKTE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MVLHSWISSSHILVNFLLLLGCGITYGTDTDIFCLKSIKESLEDPYNYLKFSWDFNNKTE 60
Qy 61 GYICRFNGVECWHPDENRVLNLKLSNMGLKGQFPRGIQNCSSLTGLDLSINKLSGTIPGD 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GYICRFNGVECWHPDENRVLNLKLSNMGLKGQFPRGIQNCSSLTGLDLSINKLSGTIPGD 120
Qy 121 ISTLIPFATSIDLSTNEFSGAIPVSLANCTFLNTLKLDQNRLTGQIPPQFGVLSRIKVFS 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ISTLIPFATSIDLSTNEFSGAIPVSLANCTFLNTLKLDQNRLTGQIPPQFGVLSRIKVFS 180
Qy 181 VSNNLLTGQVPIFRDGVELHYANNQGLCGGNTLAPCQATPSKSNMAVIAGAAAGGVTLAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 VSNNLLTGQVPIFRDGVELHYANNQGLCGGNTLAPCQATPSKSNMAVIAGAAAGGVTLAA 240
Qy 241 LGLGIGMFFFVRRVSFKKKEEDPEGNKWARSLKGTKRIKVSMFEKSISKMKLSDLMKATN 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 LGLGIGMFFFVRRVSFKKKEEDPEGNKWARSLKGTKRIKVSMFEKSISKMKLSDLMKATN 300
Qy 301 NFSNTNIIGTGRTGTVYKAVLDDGTTLMVRRLQESQYTEKEFMSEMGTLGTVKHRNLVPL 360
|||||||||||||||||||||||||||||:||||||||||||||||||||||||||||||
Db 301 NFSNTNIIGTGRTGTVYKAVLDDGTTLMVKRLQESQYTEKEFMSEMGTLGTVKHRNLVPL 360
Qy 361 LGFCMTKRERLLVYKNMPNGNLHDQLHPADGVSTLDWTTRLKIAIGAAKGLAWLHHSCNP 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 LGFCMTKRERLLVYKNMPNGNLHDQLHPADGVSTLDWTTRLKIAIGAAKGLAWLHHSCNP 420
Qy 421 RIIHRNISSRCILLDADFEPKISDFGLARLMNPIDTHLSTFVNGEFGDLGYVAPEYTRTL 480
|||||||||:||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 RIIHRNISSKCILLDADFEPKISDFGLARLMNPIDTHLSTFVNGEFGDLGYVAPEYTRTL 480
Qy 481 VATPKGDIYSFGTVLLELVTGERPTNVSKAPETFKGNLVEWITELTSNAKLHDAIDESLV 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 VATPKGDIYSFGTVLLELVTGERPTNVSKAPETFKGNLVEWITELTSNAKLHDAIDESLV 540
Qy 541 RKDVDSELFQFLKVACNCVSPTPKERPTMFEVYQLLRAIGGRYNFTTEDDILVPTDIGNT 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 RKDVDSELFQFLKVACNCVSPTPKERPTMFEVYQLLRAIGGRYNFTTEDDILVPTDIGNT 600
Qy 601 DNMQELIVAQEGSY 614
||||||||||||||
Db 601 DNMQELIVAQEGSY 614
It would not be obvious to one of ordinary skill in the art that further inactivation of this kinase would confer soybean cyst nematode resistance on a soybean plant.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Anne R. Kubelik, Ph.D., whose telephone number is (571) 272-0801. The examiner -+can normally be reached Monday through Friday, 9:00 am - 5:00 pm Eastern.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham, can be reached at (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Anne Kubelik/Primary Examiner, Art Unit 1663