DETAILED ACTION
Status of the Application
Claims 1-2, 16, 35, 45, 65, 68 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, 35, and cancellation of claims 29, 60 as submitted in a communication filed on 2/5/2026 is acknowledged.
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 2/5/2026 has been entered.
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Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.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 1-2, 16, 35, 45, 65, 68 remain 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. New grounds of rejection are necessitated by amendment.
Claims 1 and 35 (claims 2, 16, 45, 65, 68 dependent thereon) is indefinite in the recitation of “wherein the bovine IAP comprises an amino acid sequence having at least 99% identity with SEQ ID NO: 5, with deletion of the signal peptide of SEQ ID NO: 5” for the following reasons. It is unclear as to how the term “with deletion of the signal peptide of SEQ ID NO: 5” further limits the claim or the bovine IAP. Does the term intend to limit the bovine IAP to one that lacks a signal peptide? Does the term intend to limit the 99% sequence identity to the segment of SEQ ID NO: 5 that does not have a signal peptide (i.e., 99% sequence identity to amino acids X-Y of SEQ ID NO: 5, instead of 99% sequence identity to all of SEQ ID NO: 5). It should also be noted that it is unclear as to how a variant of the polypeptide of SEQ ID NO: 5 can have a deletion that has been made to another protein, namely the protein of SEQ ID NO: 5. Even if the argument is made that the recited bovine IAP is one that lacks the signal peptide of the polypeptide of SEQ ID NO: 5, the term is unclear because the claims fail to provide the specific amino acids in SEQ ID NO: 5 that are intended by the term “signal peptide of the polypeptide of SEQ ID NO: 5”. For examination purposes, no patentable weight will be given to the term “with deletion of the signal peptide of SEQ ID NO: 5”. Correction is required.
When amending the claims, applicant is advised to carefully review all examined claims and make the necessary changes to ensure proper antecedent basis and dependency.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 1-2, 16, 29, 35, 45, 60, 65, 68 were 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. In view of the amendment of claims 1 and 35, which no longer recite “wherein the yield of recombinant bovine IAP is at least 3 g/L”, this rejection is hereby withdrawn.
Claim Rejections - 35 USC § 103 (AIA )
Claims 1-2, 16, 29, 35, 45, 60, 68 were rejected under 35 U.S.C. 103 as being unpatentable over Jaluria et al. (WO 2017/031114 published 2/23/2017; cited in the IDS) in view of Weissig et al. (Biochem. J. 290:503-508, 1993; cited in the IDS), and further in view of Klanert et al. (Journal of Biotechnology 235:150-161, 2016) as evidenced by Ritacco et al. (Biotechnology Progress 34(6):1407-1426, 2018).
Clams 29 and 60 have been cancelled. Claims 1 and 35 have been amended to now require a method for producing a bovine intestinal alkaline phosphatase having at least 99% sequence identity to the polypeptide of SEQ ID NO: 5, wherein said method requires two temperature shifts, wherein the first temperature shift from 37 °C to 33 °C occurs at about 72 hours (3 days) after initiation of the culturing process, and the second temperature shift from 33 °C to 31 °C occurs at about 288 hours (12 days) after initiation of the culturing process. A polypeptide that comprises all of SEQ ID NO: 5 except for amino acids 1-19 and a method to produce said polypeptide have been disclosed by Mueller et al. (U.S. Patent No. 6,884,602 issued 4/26/2005), wherein the polypeptide has SEQ ID NO: 4, and is labeled bIAP-II (column 3, lines 45-50). See alignment below. The polypeptide of Weissig et al. is 95% sequence identical to the polypeptide of SEQ ID NO: 5 (95% = 481x100/506; SEQ ID NO: 5 has 506 amino acids). See alignment below. While Jaluria et al. teach a temperature shift, wherein a higher temperature is used for cell growth and a lower temperature is used for product synthesis, and states that more than one temperature shift may be applied, such as from 37 °C first to 33 °C and then further to 30 °C, neither Jaluria et al, Weissig et al. nor Klanert et al. teach or suggest alone, or in combination, a method that requires two temperature shifts at days 3 and 12 of culturing as currently recited in claims 1 and 35. Therefore, the rejection of claims 1-2, 16, 35, 45, 65, 68 over the teachings of Jaluria et al, Weissig et al. and Klanert et al. as evidenced by Ritacco et al. is hereby withdrawn.
SEQ ID NO: 5
RESULT 4
US-09-911-132A-4
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
Sequence 4, US/09911132A
Patent No. 6884602
GENERAL INFORMATION
APPLICANT: Roche Diagnostics GmbH
TITLE OF INVENTION: Expression of Alkaline Phosphatase in Yeast
FILE REFERENCE: RDID 0073US
CURRENT APPLICATION NUMBER: US/09/911,132A
CURRENT FILING DATE: 2002-08-28
NUMBER OF SEQ ID NOS: 38
SEQ ID NO 4
LENGTH: 487
TYPE: PRT
ORGANISM: Bovine
Query Match 96.5%; Score 2555; Length 487;
Best Local Similarity 100.0%;
Matches 487; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 20 LIPAEEENPAFWNRQAAQALDVAKKLQPIQTAAKNVILFLGDGMGVPTVTATRILKGQMN 79
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 LIPAEEENPAFWNRQAAQALDVAKKLQPIQTAAKNVILFLGDGMGVPTVTATRILKGQMN 60
Qy 80 GKLGPETPLAMDQFPYVALSKTYNVDRQVPDSAGTATAYLCGVKGNYRTIGVSAAARYNQ 139
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GKLGPETPLAMDQFPYVALSKTYNVDRQVPDSAGTATAYLCGVKGNYRTIGVSAAARYNQ 120
Qy 140 CNTTRGNEVTSVINRAKKAGKAVGVVTTTRVQHASPAGAYAHTVNRNWYSDADLPADAQK 199
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 CNTTRGNEVTSVINRAKKAGKAVGVVTTTRVQHASPAGAYAHTVNRNWYSDADLPADAQK 180
Qy 200 NGCQDIAAQLVYNMDIDVILGGGRMYMFPEGTPDPEYPDDASVNGVRKDKQNLVQEWQAK 259
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 NGCQDIAAQLVYNMDIDVILGGGRMYMFPEGTPDPEYPDDASVNGVRKDKQNLVQEWQAK 240
Qy 260 HQGAQYVWNRTALLQAADDSSVTHLMGLFEPADMKYNVQQDHTKDPTLAEMTEAALQVLS 319
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 HQGAQYVWNRTALLQAADDSSVTHLMGLFEPADMKYNVQQDHTKDPTLAEMTEAALQVLS 300
Qy 320 RNPRGFYLFVEGGRIDHGHHDGKAYMALTEAIMFDNAIA KANELTSELDTLILVTADHSH 379
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 RNPRGFYLFVEGGRIDHGHHDGKAYMALTEAIMFDNAIA KANELTSELDTLILVTADHSH 360
Qy 380 VFSFGGYTLRGTSIFGLAPGKALDSKSYTSILYGNGPGYALGGGSRPDVNGSTSEEPSYR 439
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 VFSFGGYTLRGTSIFGLAPGKALDSKSYTSILYGNGPGYALGGGSRPDVNGSTSEEPSYR 420
Qy 440 QQAAVPLASETHGGEDVAVFARGPQAHLVHGVQEETFVAHIMAFAGCVEPYTDCNLPAPA 499
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 QQAAVPLASETHGGEDVAVFARGPQAHLVHGVQEETFVAHIMAFAGCVEPYTDCNLPAPA 480
Qy 500 TATSIPD 506
|||||||
Db 481 TATSIPD 487
RESULT 8
PPBI_BOVIN
ID PPBI_BOVIN Reviewed; 533 AA.
AC P19111; Q28124;
DT 01-NOV-1990, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1997, sequence version 2.
DT 18-JUN-2025, entry version 153.
DE RecName: Full=Intestinal-type alkaline phosphatase;
DE Short=IAP;
DE Short=Intestinal alkaline phosphatase;
DE EC=3.1.3.1;
DE Flags: Precursor;
GN Name=ALPI;
OS Bos taurus (Bovine).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Laurasiatheria; Artiodactyla; Ruminantia; Pecora; Bovidae;
OC Bovinae; Bos.
OX NCBI_TaxID=9913;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC TISSUE=Liver;
RX PubMed=8452539; DOI=10.1042/bj2900503;
RA Weissig H., Schildge A., Hoylaerts M.F., Iqbal M., Millan J.L.;
RT "Cloning and expression of the bovine intestinal alkaline phosphatase gene:
RT biochemical characterization of the recombinant enzyme.";
RL Biochem. J. 290:503-508(1993).
RN [2]
RP PROTEIN SEQUENCE OF 20-35 AND 91-152, AND ACTIVE SITE.
RC TISSUE=Intestine;
RX PubMed=3902089; DOI=10.1016/0167-4838(85)90115-3;
RA Culp J.S., Hermodson M., Butler L.G.;
RT "The active-site and amino-terminal amino acid sequence of bovine
RT intestinal alkaline phosphatase.";
RL Biochim. Biophys. Acta 831:330-334(1985).
RN [3]
RP PROTEIN SEQUENCE OF 20-63.
RX PubMed=3458202; DOI=10.1073/pnas.83.8.2368;
RA Hua J.-C., Berger J., Pan Y.C.E., Hulmes J.D., Udenfriend S.;
RT "Partial sequencing of human adult, human fetal, and bovine intestinal
RT alkaline phosphatases: comparison with the human placental and liver
RT isozymes.";
RL Proc. Natl. Acad. Sci. U.S.A. 83:2368-2372(1986).
CC -!- FUNCTION: Alkaline phosphatase that can hydrolyze various phosphate
CC compounds. {ECO:0000250|UniProtKB:P15693}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=a phosphate monoester + H2O = an alcohol + phosphate;
CC Xref=Rhea:RHEA:15017, ChEBI:CHEBI:15377, ChEBI:CHEBI:30879,
CC ChEBI:CHEBI:43474, ChEBI:CHEBI:67140; EC=3.1.3.1;
CC Evidence={ECO:0000250|UniProtKB:P15693, ECO:0000255|PROSITE-
CC ProRule:PRU10042};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000250|UniProtKB:P15693};
CC Note=Binds 1 Mg(2+) ion. {ECO:0000250|UniProtKB:P15693};
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000250|UniProtKB:P15693};
CC Note=Binds 2 Zn(2+) ions. {ECO:0000250|UniProtKB:P15693};
CC -!- COFACTOR:
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000250|UniProtKB:P05186};
CC -!- SUBUNIT: Homodimer. {ECO:0000250|UniProtKB:P15693}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000250|UniProtKB:P15693};
CC Lipid-anchor, GPI-anchor {ECO:0000250|UniProtKB:P15693}.
CC -!- MISCELLANEOUS: In most mammals there are four different isozymes:
CC placental (ALPP), germ cell (ALPG), intestinal (ALPI) and tissue non-
CC specific (liver/bone/kidney) (ALPL/TNAP).
CC -!- SIMILARITY: Belongs to the alkaline phosphatase family. {ECO:0000305}.
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DR EMBL; L07733; AAA30571.1; -; Genomic_DNA.
DR PIR; S30364; S30364.
DR AlphaFoldDB; P19111; -.
DR SMR; P19111; -.
DR FunCoup; P19111; 28.
DR IntAct; P19111; 2.
DR MINT; P19111; -.
DR STRING; 9913.ENSBTAP00000005937; -.
DR BindingDB; P19111; -.
DR ChEMBL; CHEMBL5695; -.
DR DrugCentral; P19111; -.
DR GlyCosmos; P19111; 2 sites, No reported glycans.
DR GlyGen; P19111; 2 sites.
DR PaxDb; 9913-ENSBTAP00000005937; -.
DR eggNOG; KOG4126; Eukaryota.
DR InParanoid; P19111; -.
DR BRENDA; 3.1.3.1; 908.
DR SABIO-RK; P19111; -.
DR STRENDA-DB; Y9CBQW; Alkaline phosphatase.
DR Proteomes; UP000009136; Unplaced.
DR GO; GO:0005886; C:plasma membrane; IBA:GO_Central.
DR GO; GO:0098552; C:side of membrane; IEA:UniProtKB-KW.
DR GO; GO:0004035; F:alkaline phosphatase activity; ISS:UniProtKB.
DR GO; GO:0000287; F:magnesium ion binding; ISS:UniProtKB.
DR GO; GO:0008270; F:zinc ion binding; ISS:UniProtKB.
DR GO; GO:0016311; P:dephosphorylation; ISS:UniProtKB.
DR CDD; cd16012; ALP; 1.
DR FunFam; 3.40.720.10:FF:000008; Alkaline phosphatase; 1.
DR Gene3D; 3.40.720.10; Alkaline Phosphatase, subunit A; 1.
DR InterPro; IPR001952; Alkaline_phosphatase.
DR InterPro; IPR018299; Alkaline_phosphatase_AS.
DR InterPro; IPR017850; Alkaline_phosphatase_core_sf.
DR PANTHER; PTHR11596; ALKALINE PHOSPHATASE; 1.
DR PANTHER; PTHR11596:SF30; INTESTINAL-TYPE ALKALINE PHOSPHATASE; 1.
DR Pfam; PF00245; Alk_phosphatase; 1.
DR PRINTS; PR00113; ALKPHPHTASE.
DR SMART; SM00098; alkPPc; 1.
DR SUPFAM; SSF53649; Alkaline phosphatase-like; 1.
DR PROSITE; PS00123; ALKALINE_PHOSPHATASE; 1.
PE 1: Evidence at protein level;
KW Calcium; Cell membrane; Direct protein sequencing; Disulfide bond;
KW Glycoprotein; GPI-anchor; Hydrolase; Lipoprotein; Magnesium; Membrane;
KW Metal-binding; Reference proteome; Signal; Zinc.
FT SIGNAL 1..19
FT /evidence="ECO:0000269|PubMed:3458202,
FT ECO:0000269|PubMed:3902089"
FT CHAIN 20..506
FT /note="Intestinal-type alkaline phosphatase"
FT /id="PRO_0000024035"
FT PROPEP 507..533
FT /note="Removed in mature form"
FT /evidence="ECO:0000255"
FT /id="PRO_0000024036"
FT ACT_SITE 111
FT /note="Phosphoserine intermediate"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU10042,
FT ECO:0000269|PubMed:3902089"
FT BINDING 61
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 61
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 111
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 174
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 235
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:P05186"
FT BINDING 288
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:P05186"
FT BINDING 289
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:P05186"
FT BINDING 304
FT /ligand="Ca(2+)"
FT /ligand_id="ChEBI:CHEBI:29108"
FT /evidence="ECO:0000250|UniProtKB:P05186"
FT BINDING 330
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 335
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 339
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 376
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 377
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT BINDING 451
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /evidence="ECO:0000250|UniProtKB:P15693"
FT LIPID 506
FT /note="GPI-anchor amidated aspartate"
FT /evidence="ECO:0000255"
FT CARBOHYD 268
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 429
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 140..202
Query Match 95.2%; Score 2521; Length 533;
Best Local Similarity 95.1%;
Matches 481; Conservative 9; Mismatches 16; Indels 0; Gaps 0;
Qy 1 MQGACVLLLLGLHLQLSLGLIPAEEENPAFWNRQAAQALDVAKKLQPIQTAAKNVILFLG 60
||||||||||||||||||||:| |||:|||||||||||||||||||||||||||||||||
Db 1 MQGACVLLLLGLHLQLSLGLVPVEEEDPAFWNRQAAQALDVAKKLQPIQTAAKNVILFLG 60
Qy 61 DGMGVPTVTATRILKGQMNGKLGPETPLAMDQFPYVALSKTYNVDRQVPDSAGTATAYLC 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 DGMGVPTVTATRILKGQMNGKLGPETPLAMDQFPYVALSKTYNVDRQVPDSAGTATAYLC 120
Qy 121 GVKGNYRTIGVSAAARYNQCNTTRGNEVTSVINRAKKAGKAVGVVTTTRVQHASPAGAYA 180
|||||||||||||||||||| ||||||||||:||||||||:|||||||||||||||||||
Db 121 GVKGNYRTIGVSAAARYNQCKTTRGNEVTSVMNRAKKAGKSVGVVTTTRVQHASPAGAYA 180
Qy 181 HTVNRNWYSDADLPADAQKNGCQDIAAQLVYNMDIDVILGGGRMYMFPEGTPDPEYPDDA 240
|||||||||||||||||| ||||||||||| |||||||||||| |||| |||||||||||
Db 181 HTVNRNWYSDADLPADAQMNGCQDIAAQLVNNMDIDVILGGGRKYMFPVGTPDPEYPDDA 240
Qy 241 SVNGVRKDKQNLVQEWQAKHQGAQYVWNRTALLQAADDSSVTHLMGLFEPADMKYNVQQD 300
||||||| |||||| |||||||||||||||||||||||||||||||||||||||||||||
Db 241 SVNGVRKRKQNLVQAWQAKHQGAQYVWNRTALLQAADDSSVTHLMGLFEPADMKYNVQQD 300
Qy 301 HTKDPTLAEMTEAALQVLSRNPRGFYLFVEGGRIDHGHHDGKAYMALTEAIMFDNAIA KA 360
||||||| |||| ||:|:|||||||||||||||||||||| ||||||||| |||||||||
Db 301 HTKDPTLQEMTEVALRVVSRNPRGFYLFVEGGRIDHGHHDDKAYMALTEAGMFDNAIA KA 360
Qy 361 NELTSELDTLILVTADHSHVFSFGGYTLRGTSIFGLAPGKALDSKSYTSILYGNGPGYAL 420
|||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Db 361 NELTSELDTLILVTADHSHVFSFGGYTLRGTSIFGLAPSKALDSKSYTSILYGNGPGYAL 420
Qy 421 GGGSRPDVNGSTSEEPSYRQQAAVPLASETHGGEDVAVFARGPQAHLVHGVQEETFVAHI 480
||||||||| ||||:|||:|||||| |||||||||||||||||||||||||:||||||||
Db 421 GGGSRPDVNDSTSEDPSYQQQAAVPQASETHGGEDVAVFARGPQAHLVHGVEEETFVAHI 480
Qy 481 MAFAGCVEPYTDCNLPAPATATSIPD 506
|||||||||||||||||| |||||||
Db 481 MAFAGCVEPYTDCNLPAPTTATSIPD 506
Conclusion
No claim is in condition for allowance.
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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
May 15, 2026
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