DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Status of the Claims
Claims 1-20 are pending.
Claims 1-20 are examined herein.
Claims 1-20 are rejected.
Priority
Application no. 19/305,739 filed on 08/20/2025 is a divisional of application no. 17/927,082 filed on 11/22/2022, which is a 371 of PCT application no. PCT/US21/33799 filed on 05/22/2021, which claims benefit to provisional application no. 63/106,408 filed on 10/28/2020 and provisional application no. 63/028,970 filed on 05/22/2020.
Claim Objections
Claim 20 recites “A method of applying nutrients and/or a fertilizer to a soil, the method comprising: applying an amount of biomass from an engineered plant comprising a heterologous Diadenosine and Diphosphoinositol Polyphosphate Phosphohydrolase (DDP1), a biochar produced therefrom to the soil”.
The claim appears to have grammatical errors and is interpreted to require the step of applying an amount of biomass from an engineered plant comprising a heterologous Diadenosine and Diphosphoinositol Polyphosphate Phosphohydrolase (DDP1), or a biochar produced therefrom, to the soil.
If this interpretation is appropriate, Applicant should amend the claim to include “or” before “a biochar” and include a comma after “therefrom”.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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.
Written Description
Claims 1-20 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-20 are broadly drawn to “A method of removing Pi from a soil or water, comprising: growing, propagating, harvesting, cultivating, or any combination thereof a plant comprising a heterologous Diadenosine and Diphosphoinositol Polyphosphate Phosphohydrolase (DDP1) polypeptide, a heterologous DDP1 encoding polynucleotide, a vector or vector system comprising a heterologous DDP1 encoding polynucleotide, or a combination thereof in the soil or water” as recited in claim 1, and “wherein (a) the DDP1 polypeptide is about 50-100% identical to SEQ ID NO: 1, (b) wherein the DDP1 encoding polynucleotide is about 50-100% identical to SEQ ID NO: 2, or both (a) and (b)” as recited in claim 7. Additionally, because claim 7 depends from claim 1, claim 1 is interpreted to encompass polypeptides with as low as 50% sequence identity to SEQ ID NO: 1 or 2. Claim 1 and depending claims 2-6 and 8-20 are therefore also rejected for this reason.
Applicant describes in working examples overexpression of DDP1 gene from Saccharomyces cerevisiae, which is a polynucleotide sequence with 100% identity to instant SEQ ID NO: 2 and encodes a polypeptide sequence with 100% identity to instant SEQ ID NO: 1 (¶0242), in stably transformed Arabidopsis thaliana and Thlaspi arvense (Pennycress) and transiently transformed Nicotiana benthamiana (specification, examples 1-6, ¶0234-0259).
Applicant does not describe or reduce to practice any example of a DDP1 nucleotide or polypeptide, wherein the polypeptide has below 100% sequence identity, let alone a sequence identity as low as 50%, to SEQ ID NOs: 1 and 2 as recited in claim 7. Applicant does not provide any description of the structure-function relationship with respect to the recited sequences, DDP1 nucleotides and proteins, and the recited functions.
The prior art does not remedy this deficiency. A review of sequences that share identity with SEQ ID NO: 1 show that amino acid sequences encoding DDP1 proteins in the prior art tend to have varying degrees of identity to SEQ ID NO: 1, with identity gaps between sequences searches. For example, there is an extensive gap exhibited below in two sequential sequence search results, showing one sequence with 100% identity, and the next most similar sequence search showing 59.5% identity. It also appears the sequence with 59.5% is not a gene from the species Saccharomyces cerevisiae, and is not described by the art to have DDP1 function or activity.
RESULT 1
US-13-510-783A-151863
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
Sequence 151863, US/13510783A
Publication No. US20140259212A1
GENERAL INFORMATION
APPLICANT: Plesch, Gunnar
APPLICANT: Blau, Astrid
APPLICANT: Herold, Michael M.
APPLICANT: Kamlage, Beate
APPLICANT: Wendel, Birgit
APPLICANT: Puzio, Piotr
APPLICANT: Henkes, Stefan
APPLICANT: Haake, Volker
APPLICANT: Van Camp, Wim
APPLICANT: Fahnenstich, Holger
APPLICANT: McKersie, Bryan
APPLICANT: Bruce, Wesley
APPLICANT: Christiansen, Nicole
TITLE OF INVENTION: PROCESS FOR THE PRODUCTION OF FINE CHEMICALS
FILE REFERENCE: 13311-00084-US
CURRENT APPLICATION NUMBER: US/13/510,783A
CURRENT FILING DATE: 2012-05-18
PRIOR APPLICATION NUMBER: PCT/EP2010/006988
PRIOR FILING DATE: 2010-11-18
PRIOR APPLICATION NUMBER: EP 09014472.6
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09176396.1
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09181052.3
PRIOR FILING DATE: 2009-12-22
PRIOR APPLICATION NUMBER: EP 10186930.3
PRIOR FILING DATE: 2010-10-08
PRIOR APPLICATION NUMBER: EP 10188863.4
PRIOR FILING DATE: 2010-10-26
PRIOR APPLICATION NUMBER: EP 10189169.5
PRIOR FILING DATE: 2010-10-28
PRIOR APPLICATION NUMBER: EP 10189358.4
PRIOR FILING DATE: 2010-10-29
PRIOR APPLICATION NUMBER: EP 10189943.3
PRIOR FILING DATE: 2010-11-04
PRIOR APPLICATION NUMBER: EP 10190115.5
PRIOR FILING DATE: 2010-11-05
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 158060
SEQ ID NO 151863
LENGTH: 188
TYPE: PRT
ORGANISM: Saccharomyces cerevisiae
Query Match 100.0%; Score 1005; Length 188;
Best Local Similarity 100.0%;
Matches 188; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MGKTADNHGPVRSETAREGRENQVYSPVTGARLVAGCICLTPDKKQVLMITSSAHKKRWI 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MGKTADNHGPVRSETAREGRENQVYSPVTGARLVAGCICLTPDKKQVLMITSSAHKKRWI 60
Qy 61 VPKGGVEKDEPNYETTAQRETWEEAGCIGKIVANLGTVEDMRPPKDWNKDIKQFENSRKD 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 VPKGGVEKDEPNYETTAQRETWEEAGCIGKIVANLGTVEDMRPPKDWNKDIKQFENSRKD 120
Qy 121 SEVAKHPPRTEFHFYELEIENLLDKFPECHKRHRKLYSYTEAKQNLIDAKRPELLEALNR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SEVAKHPPRTEFHFYELEIENLLDKFPECHKRHRKLYSYTEAKQNLIDAKRPELLEALNR 180
Qy 181 SAIIKDDK 188
||||||||
Db 181 SAIIKDDK 188
RESULT 2
US-13-510-783A-151875
Sequence 151875, US/13510783A
Publication No. US20140259212A1
GENERAL INFORMATION
APPLICANT: Plesch, Gunnar
APPLICANT: Blau, Astrid
APPLICANT: Herold, Michael M.
APPLICANT: Kamlage, Beate
APPLICANT: Wendel, Birgit
APPLICANT: Puzio, Piotr
APPLICANT: Henkes, Stefan
APPLICANT: Haake, Volker
APPLICANT: Van Camp, Wim
APPLICANT: Fahnenstich, Holger
APPLICANT: McKersie, Bryan
APPLICANT: Bruce, Wesley
APPLICANT: Christiansen, Nicole
TITLE OF INVENTION: PROCESS FOR THE PRODUCTION OF FINE CHEMICALS
FILE REFERENCE: 13311-00084-US
CURRENT APPLICATION NUMBER: US/13/510,783A
CURRENT FILING DATE: 2012-05-18
PRIOR APPLICATION NUMBER: PCT/EP2010/006988
PRIOR FILING DATE: 2010-11-18
PRIOR APPLICATION NUMBER: EP 09014472.6
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09176396.1
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09181052.3
PRIOR FILING DATE: 2009-12-22
PRIOR APPLICATION NUMBER: EP 10186930.3
PRIOR FILING DATE: 2010-10-08
PRIOR APPLICATION NUMBER: EP 10188863.4
PRIOR FILING DATE: 2010-10-26
PRIOR APPLICATION NUMBER: EP 10189169.5
PRIOR FILING DATE: 2010-10-28
PRIOR APPLICATION NUMBER: EP 10189358.4
PRIOR FILING DATE: 2010-10-29
PRIOR APPLICATION NUMBER: EP 10189943.3
PRIOR FILING DATE: 2010-11-04
PRIOR APPLICATION NUMBER: EP 10190115.5
PRIOR FILING DATE: 2010-11-05
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 158060
SEQ ID NO 151875
LENGTH: 176
TYPE: PRT
ORGANISM: Candida glabrata CBS 138
Query Match 59.5%; Score 597.5; Length 176;
Best Local Similarity 65.5%;
Matches 114; Conservative 24; Mismatches 35; Indels 1; Gaps 1;
Qy 13 SETAREGRENQVYSPVTGARLVAGCICLTPDKKQVLMITSSAHKKRWIVPKGGVEKDEPN 72
| || || |||| ||||||||:||| |: ||||:|||:: :||:||||:| |||:
Db 4 SMEARSGRANQVYGE-DGARLVAGCVCLTSDRHHVLMISSSANRNKWILPKGGIETDEPD 62
Qy 73 YETTAQRETWEEAGCIGKIVANLGTVEDMRPPKDWNKDIKQFENSRKDSEVAKHPPRTEF 132
|: || ||||||||| |:||::|| |:|||||| | || :: |:|| |:|||:||
Db 63 YKQTAIRETWEEAGCTGEIVSSLGVVKDMRPPKAKTMDRATFERAKSDAEVNKNPPRSEF 122
Qy 133 HFYELEIENLLDKFPECHKRHRKLYSYTEAKQNLIDAKRPELLEALNRSAIIKD 186
||||| | | | ||| ||| |||::| ||||||::|||||||||| ||:||||
Db 123 HFYELIIGKLEDNFPEMHKRDRKLFTYREAKQNLVEAKRPELLEALTRSSIIKD 176
The instant specification does not provide enough sequences to describe the genus of amino acid sequences encoding DDP1 proteins below 100%. There appears to be a dearth of description of amino sequences encoding DDP1 proteins that would be expected to have the required function when expressed in a plant (that function being a DDP1 function) below 100% identity.
Similarly, a review of sequences that share identity with SEQ ID NO: 2 reveals a dearth of description of sequences that encode DDP1 proteins, with extensive identity gap between 98% identity (and published even after instant filing date) to 70.1% identity. Furthermore, the sequences with either 98% or 70.1% identity fail to teach the sequence is a DDP1 protein or has any DDP1-related function or activity. The identity gap is exhibited below in two sequential sequence search results, showing one sequence with 98% identity and the next most similar sequence showing below 72% identity:
RESULT 4
US-18-286-611-10448
Sequence 10448, US/18286611
Publication No. US20240271122A1
GENERAL INFORMATION
APPLICANT: OPENTRONS LABWORKS INC.
APPLICANT: BADER, JOEL S.
TITLE OF INVENTION: METHODS FOR CODON OPTIMIZATION AND USES THEREOF
FILE REFERENCE: 59725-703.601
CURRENT APPLICATION NUMBER: US/18/286,611
CURRENT FILING DATE: 2023-10-12
PRIOR APPLICATION NUMBER: 63/174,823
PRIOR FILING DATE: 2021-04-14
NUMBER OF SEQ ID NOS: 11812
SEQ ID NO 10448
LENGTH: 567
TYPE: DNA
ORGANISM: Artificial Sequence
FEATURE:
OTHER INFORMATION: Description of Artificial Sequence: Synthetic
polynucleotide
Query Match 98.0%; Score 555.4; Length 567;
Best Local Similarity 98.9%;
Matches 559; Conservative 0; Mismatches 6; Indels 0; Gaps 0;
Qy 1 ATGGGCAAAACCGCGGATAATCATGGTCCAGTACGTTCTGAGACAGCACGTGAAGGAAGA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGGCAAAACCGCGGATAATCATGGTCCAGTACGTTCTGAGACAGCACGTGAAGGAAGA 60
Qy 61 GAAAACCAGGTTTACTCACCCGTTACAGGTGCAAGATTAGTTGCTGGCTGCATATGTTTA 120
||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Db 61 GAAAACCAGGTTTACTCTCCCGTTACAGGTGCAAGATTAGTTGCTGGCTGCATATGTTTA 120
Qy 121 ACACCCGACAAGAAGCAAGTTCTCATGATTACTTCTTCTGCACACAAGAAAAGATGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACACCCGACAAGAAGCAAGTTCTCATGATTACTTCTTCTGCACACAAGAAAAGATGGATT 180
Qy 181 GTCCCCAAAGGTGGCGTTGAGAAAGACGAGCCTAATTACGAGACGACTGCCCAACGAGAA 240
|||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||
Db 181 GTCCCCAAAGGTGGCGTTGAGAAAGACGAGCCTAATTACGAGACGACTGCCCAAAGAGAA 240
Qy 241 ACTTGGGAGGAAGCTGGTTGCATAGGTAAAATTGTCGCCAATTTGGGTACAGTTGAAGAC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 ACTTGGGAGGAAGCTGGTTGCATAGGTAAAATTGTCGCCAATTTGGGTACAGTTGAAGAC 300
Qy 301 ATGAGACCCCCTAAGGACTGGAACAAAGACATTAAGCAATTCGAGAACTCTCGAAAAGAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Db 301 ATGAGACCCCCTAAGGACTGGAACAAAGACATTAAGCAATTCGAGAACTCTAGAAAAGAT 360
Qy 361 TCAGAAGTAGCAAAGCACCCGCCAAGAACCGAATTTCATTTTTATGAATTAGAGATTGAA 420
|| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 TCTGAAGTAGCAAAGCACCCGCCAAGAACCGAATTTCATTTTTATGAATTAGAGATTGAA 420
Qy 421 AATCTCCTTGATAAATTTCCGGAATGTCACAAAAGACATAGAAAGCTATACTCTTATACA 480
||||||||||||||||||||||||||||||||||||||||||||| | ||||||||||||
Db 421 AATCTCCTTGATAAATTTCCGGAATGTCACAAAAGACATAGAAAGTTGTACTCTTATACA 480
Qy 481 GAAGCTAAACAAAACTTGATAGACGCCAAGAGGCCTGAATTGTTGGAGGCCCTTAATAGG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 GAAGCTAAACAAAACTTGATAGACGCCAAGAGGCCTGAATTGTTGGAGGCCCTTAATAGG 540
Qy 541 TCTGCTATCATTAAAGACGACAAAT 565
|||||||||||||||||||||||||
Db 541 TCTGCTATCATTAAAGACGACAAAT 565
RESULT 5
US-10-932-182A-5276
(NOTE: this sequence has 2 duplicates in the database searched.
See complete list at the end of this report)
Sequence 5276, US/10932182A
Publication No. US20060046253A1
GENERAL INFORMATION
APPLICANT: NAKAO, YOSHIHIRO
APPLICANT: NAKAMURA, NORIHISA
APPLICANT: KODAMA, YUKIKO
APPLICANT: FUJIMURA, TOMOKO
APPLICANT: ASHIKARI, TOSHIHIKO
TITLE OF INVENTION: METHODS FOR ANALYZING GENES OF INDUSTRIAL YEASTS
FILE REFERENCE: 030685-043
CURRENT APPLICATION NUMBER: US/10/932,182A
CURRENT FILING DATE: 2004-09-02
NUMBER OF SEQ ID NOS: 197023
SEQ ID NO 5276
LENGTH: 573
TYPE: DNA
ORGANISM: Saccharomyces pastorianus
Query Match 70.1%; Score 397.4; Length 573;
Best Local Similarity 81.9%;
Matches 458; Conservative 0; Mismatches 101; Indels 0; Gaps 0;
Qy 1 ATGGGCAAAACCGCGGATAATCATGGTCCAGTACGTTCTGAGACAGCACGTGAAGGAAGA 60
||| | ||| || | || ||||||| ||||||||||||||| ||||||||||||||
Db 1 ATGATCGAAAAGGCAGGTAGTCATGGTATAGTACGTTCTGAGACTGCACGTGAAGGAAGG 60
Qy 61 GAAAACCAGGTTTACTCACCCGTTACAGGTGCAAGATTAGTTGCTGGCTGCATATGTTTA 120
|| ||||| ||||| || || |||| ||||||||||| |||||||||||||| |||||
Db 61 GAGAACCAAGTTTATTCTGCCATTACTGGTGCAAGATTGGTTGCTGGCTGCATCTGTTTG 120
Qy 121 ACACCCGACAAGAAGCAAGTTCTCATGATTACTTCTTCTGCACACAAGAAAAGATGGATT 180
|| |||||||||||| ||||||| ||||| |||||||||||||| ||||| |||||||||
Db 121 ACTCCCGACAAGAAGGAAGTTCTTATGATCACTTCTTCTGCACATAAGAAGAGATGGATT 180
Qy 181 GTCCCCAAAGGTGGCGTTGAGAAAGACGAGCCTAATTACGAGACGACTGCCCAACGAGAA 240
|| || ||||| || ||||| ||||| || ||| |||| || ||||| || ||| |||||
Db 181 GTGCCTAAAGGAGGTGTTGAAAAAGATGAACCTGATTATGAAACGACGGCACAAAGAGAA 240
Qy 241 ACTTGGGAGGAAGCTGGTTGCATAGGTAAAATTGTCGCCAATTTGGGTACAGTTGAAGAC 300
|||||||| |||||||||||| | ||||||||||| ||||| |||||||| || |||||
Db 241 ACTTGGGAAGAAGCTGGTTGCGTGGGTAAAATTGTTGCCAACTTGGGTACGGTGGAAGAT 300
Qy 301 ATGAGACCCCCTAAGGACTGGAACAAAGACATTAAGCAATTCGAGAACTCTCGAAAAGAT 360
|||||||| || ||||| ||||||||||| || |||||||| |||| | | || | |||
Db 301 ATGAGACCTCCAAAGGATTGGAACAAAGATATAAAGCAATTTGAGACCGCAAGAGATGAT 360
Qy 361 TCAGAAGTAGCAAAGCACCCGCCAAGAACCGAATTTCATTTTTATGAATTAGAGATTGAA 420
| ||||||||||| || || || |||||||| ||||||||||| || || |||||||||
Db 361 CCTGAAGTAGCAAAACATCCACCTAGAACCGAGTTTCATTTTTACGAGTTGGAGATTGAA 420
Qy 421 AATCTCCTTGATAAATTTCCGGAATGTCACAAAAGACATAGAAAGCTATACTCTTATACA 480
|| ||| |||| || || || |||||||| |||||||| ||| | |||||||||||| |
Db 421 AAGCTCATTGAAAAGTTCCCTGAATGTCATAAAAGACACAGACAACTATACTCTTATGCG 480
Qy 481 GAAGCTAAACAAAACTTGATAGACGCCAAGAGGCCTGAATTGTTGGAGGCCCTTAATAGG 540
||||| ||| || |||||||| |||| || || || |||||| | || ||||| |||||
Db 481 GAAGCCAAAAAACACTTGATAAACGCAAAAAGACCCGAATTGCTAGAAGCCCTGGATAGG 540
Qy 541 TCTGCTATCATTAAAGACG 559
|| |||| ||||| || |
Db 541 TCCTCTATTATTAAGGATG 559
The instant specification does not provide enough sequences to describe the genus of nucleotide sequences encoding DDP1 proteins below 100% identity. There appears to be a dearth of description of nucleotide sequences encoding DDP1 proteins that would be expected to have the required function when expressed in a plant (that function being a DDP1 function) below 100% identity.
The specification fails to provide an adequate written description to support the sequences recited in claim 7 with as low as 50% identity are able to effectively confer the functions of a DDP1 polypeptide. The limited examples at 100% identity do not describe the claimed genus by virtue of example. Therefore, one of ordinary skill in the art would not have recognized the Applicant to be in possession of the claimed invention at the time the application was filed.
Enablement
Claim 19 is 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 wherein the biochar releases phosphorus at a rate of 1-3 times slower as compared to control, does not reasonably provide enablement for wherein the phosphorus is released at a rate of greater than 3 and up to 100 times slower. 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.
Claim 19 recites “The method of claim 18, wherein the biochar releases phosphorus at a rate 1-100 times slower as compared to biochar made from or comprising biomaterial from a wild-type plant or of non-DDP1 expressing control plant.”
The specification is not enabling for the claimed subject matter of wherein the biochar releases phosphorus at a rate of up to 100 times slower as compared to biochar made from or comprising biomaterial from a wild-type plant or of non-DDP1 expressing control plant.”
The specification is not enabling for wherein the biochar releases phosphorus at a rate of 100 times slower compared to a biochar produced from WT plants because it only provides a method of producing biochar from the claimed plants, wherein the biochar appears to release the phosphorus at a rate of approximately 3 times slower (See Fig. 21b). To achieve an increase from 3 times slower to 100 times slower phosphorus release from the plants in the claimed method would require undue experimentation by one of ordinary skill in the art given the dearth of evidence in the art teaching how this can be accomplished. Therefore, one of ordinary skill in the art would not have recognized the Applicant to be in possession of the claimed invention of wherein the biochar releases phosphorus at a rate of up to 100 times slower than biochar made from WT plants at the time the application was filed.
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 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)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-17 and 20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Plesch (US-20140259212-A1).
Regarding claim 1, Plesch discloses a plant cell transformed with a nucleic acid molecule encoding a polypeptide shown in Table Il of Plesch (claims 34, 33, and 29). Table Il teaches nucleic acid sequence of SEQ ID NO: 151862 which is 100% identical to instant SEQ ID NO: 2 (i.e. a polynucleotide encoding DDP1), and encodes polypeptide SEQ ID NO: 151863 which is 100% identical to instant SEQ ID NO: 1 (see alignment below). In another section of the disclosure, Plesch further discloses transforming a plant, plant cell or part thereof with SEQ ID NO: 151862 which encodes SEQ ID NO: 151863 which is a Yor163w polypeptide, which is also disclosed in the instant specification (see instant spec., ¶0216), and activity of the polypeptide with phosphohydrolase activity is increased in the plant, plant cell or part thereof (¶88569). Additionally, Plesch discloses growing the plant (¶85560), wherein growing is to be understood as meaning for example culturing the intact transgenic plant in hydroponic culture, potting compost, or on field soil (¶51312) (i.e. growing the plant comprising the heterologous DDP1 polynucleotide and encoded polypeptide in soil or water).
Regarding claim 2, Plesch discloses transforming a plant, plant cell or part thereof with SEQ ID NO: 151862 which encodes SEQ ID NO: 151863 which is a Yor163w polypeptide, which is also disclosed in the instant specification (see instant spec., ¶0216), and activity of the polypeptide with phosphohydrolase activity is increased in the plant, plant cell or part thereof (¶88569) (i.e. wherein the plant expresses the heterologous DDP1 polypeptide).
Regarding claims 3-6, Plesch discloses SEQ ID NO: 151862 which encodes SEQ ID NO: 151863 which is a Yor163w polypeptide is from Saccharomyces cerevisiae (¶92329) (i.e. wherein the heterologous DDP1 is a fungi DDP1, a yeast DDP1, is from the genus Saccharomyces, and wherein the DDP1 is a Saccharomyces cerevisiae DDP1).
Regarding claim 7, the nucleotide and polypeptide sequences of DDP1 taught by Plesch (SEQ ID NOs: 151862 and 151863) are 100% identical to instant SEQ ID NOs: 2 and 1, respectively (see alignment below).
Regarding claims 12-13 and 15, Plesch discloses it is advantageous to use in the process of the invention transgenic microorganisms such as algae selected from a list of species including Chlorella (¶1052, 2548) (i.e. the phyla Chlorophyta and species Chlorella, and an algae).
Regarding claims 8-11 and 14, Plesch discloses particular preference is given to transgenic crop plants including especially monocotyledonous crop plants like corn, wheat or rice; or dicotyledonous crop plants like soy bean, oil seed rape (including canola and winter oil seed rape), and cotton (at least ¶2365-2366) (i.e. an engineered monocotyledonous plant or engineered dicotyledonous plant, wherein the engineered monocotyledonous is of the order Zea; wherein the engineered dicotyledonous is of the order Fabales; wherein the engineered plant is a species of Glycine; and wherein the engineered plant is soybean).
Regarding claim 16, Plesch discloses the plant cell or plant may be stably or transiently transformed (at least ¶1693, 2143, 2171, 2204, and 2530).
Regarding claim 17, Plesch discloses transforming a plant, plant cell or part thereof with SEQ ID NO: 151862 which encodes SEQ ID NO: 151863 which is a Yor163w polypeptide, which is also disclosed in the instant specification (see instant spec., ¶0216), and activity of the polypeptide with phosphohydrolase activity is increased in the plant, plant cell or part thereof as compared to corresponding non-transformed wild-type (¶88569) (i.e. reasonably interpreted as the engineered plant or cell has a modulated observable trait as compared to an unmodified plant, the observable trait being increased phosphohydrolase activity).
Regarding claim 20, Plesch discloses discloses transforming a plant, plant cell or part thereof with SEQ ID NO: 151862 which encodes SEQ ID NO: 151863 which has 100% identity to instant SEQ ID NOs: 2 and 1, respectively, and is a Yor163w polypeptide which is also disclosed in the instant specification (see instant spec., ¶0216). Plesch discloses growing the plant (¶85560), wherein growing is to be understood as meaning for example culturing the intact transgenic plant in hydroponic culture, potting compost, or on field soil (¶51312) (i.e. growing the plant comprising the heterologous DDP1 polynucleotide and encoded polypeptide in soil or water). Because Plesch discloses growing the plant comprising the heterologous DDP1 polynucleotide and encoded polypeptide in soil which is broadly interpreted as applying an amount of biomass from an engineered plant comprising a heterologous DDP1 to the soil, the method of claim 20 is anticipated by Plesch.
Closest Prior Art
Claims 18-19 appear free of the prior art.
Regarding claims 18-19, the closest prior art is Plesch (US-20140259212-A1). Plesch discloses a plant cell transformed with a nucleic acid molecule encoding a polypeptide shown in Table Il of Plesch (claims 34, 33, and 29). Table Il teaches nucleic acid sequence of SEQ ID NO: 151862 which is 100% identical to instant SEQ ID NO: 2 (i.e. a polynucleotide encoding DDP1), and encodes polypeptide SEQ ID NO: 151863 which is 100% identical to instant SEQ ID NO: 1. In another section of the disclosure, Plesch further discloses transforming a plant, plant cell or part thereof with SEQ ID NO: 151862 which encodes SEQ ID NO: 151863 which is a Yor163w polypeptide, which is also disclosed in the instant specification (see instant spec., ¶0216), and activity of the polypeptide with phosphohydrolase activity is increased in the plant, plant cell or part thereof (¶88569). Additionally, Plesch discloses growing the plant (¶85560), wherein growing is to be understood as meaning for example culturing the intact transgenic plant cells in hydroponic culture, potting compost, or on field soil (¶51312) (i.e. growing the plant comprising the heterologous DDP1 polynucleotide and encoded polypeptide in soil or water). Thus, Plesch discloses the limitations of claim 1 which claims 18-19 depend from.
However, Plesch does not disclose, teach, or otherwise render obvious further comprising, after harvesting, producing a biochar from a biomass comprising the engineered plant (claim 18); and wherein the biochar releases phosphorus at a rate 1-100 times slower as compared to biochar made from or comprising biomaterial from a wild-type plant or of non-DDP1 expressing control plant. This is because Plesch appears to express DDP1 to increase and produce glucose, and there is no apparent motivation in the art to produce biochar from the plant disclosed by Plesch.
Alignments
Alignment of instant SEQ ID NO: 1 with SEQ ID NO: 151863 of Plesch:
RESULT 1
US-13-510-783A-151863
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
Sequence 151863, US/13510783A
Publication No. US20140259212A1
GENERAL INFORMATION
APPLICANT: Plesch, Gunnar
APPLICANT: Blau, Astrid
APPLICANT: Herold, Michael M.
APPLICANT: Kamlage, Beate
APPLICANT: Wendel, Birgit
APPLICANT: Puzio, Piotr
APPLICANT: Henkes, Stefan
APPLICANT: Haake, Volker
APPLICANT: Van Camp, Wim
APPLICANT: Fahnenstich, Holger
APPLICANT: McKersie, Bryan
APPLICANT: Bruce, Wesley
APPLICANT: Christiansen, Nicole
TITLE OF INVENTION: PROCESS FOR THE PRODUCTION OF FINE CHEMICALS
FILE REFERENCE: 13311-00084-US
CURRENT APPLICATION NUMBER: US/13/510,783A
CURRENT FILING DATE: 2012-05-18
PRIOR APPLICATION NUMBER: PCT/EP2010/006988
PRIOR FILING DATE: 2010-11-18
PRIOR APPLICATION NUMBER: EP 09014472.6
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09176396.1
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09181052.3
PRIOR FILING DATE: 2009-12-22
PRIOR APPLICATION NUMBER: EP 10186930.3
PRIOR FILING DATE: 2010-10-08
PRIOR APPLICATION NUMBER: EP 10188863.4
PRIOR FILING DATE: 2010-10-26
PRIOR APPLICATION NUMBER: EP 10189169.5
PRIOR FILING DATE: 2010-10-28
PRIOR APPLICATION NUMBER: EP 10189358.4
PRIOR FILING DATE: 2010-10-29
PRIOR APPLICATION NUMBER: EP 10189943.3
PRIOR FILING DATE: 2010-11-04
PRIOR APPLICATION NUMBER: EP 10190115.5
PRIOR FILING DATE: 2010-11-05
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 158060
SEQ ID NO 151863
LENGTH: 188
TYPE: PRT
ORGANISM: Saccharomyces cerevisiae
Query Match 100.0%; Score 1005; Length 188;
Best Local Similarity 100.0%;
Matches 188; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MGKTADNHGPVRSETAREGRENQVYSPVTGARLVAGCICLTPDKKQVLMITSSAHKKRWI 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MGKTADNHGPVRSETAREGRENQVYSPVTGARLVAGCICLTPDKKQVLMITSSAHKKRWI 60
Qy 61 VPKGGVEKDEPNYETTAQRETWEEAGCIGKIVANLGTVEDMRPPKDWNKDIKQFENSRKD 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 VPKGGVEKDEPNYETTAQRETWEEAGCIGKIVANLGTVEDMRPPKDWNKDIKQFENSRKD 120
Qy 121 SEVAKHPPRTEFHFYELEIENLLDKFPECHKRHRKLYSYTEAKQNLIDAKRPELLEALNR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 SEVAKHPPRTEFHFYELEIENLLDKFPECHKRHRKLYSYTEAKQNLIDAKRPELLEALNR 180
Qy 181 SAIIKDDK 188
||||||||
Db 181 SAIIKDDK 188
Alignment of instant SEQ ID NO: 2 with SEQ ID NO: 151862 of Plesch:
RESULT 1
US-13-510-783A-151862
(NOTE: this sequence has 4 duplicates in the database searched.
See complete list at the end of this report)
Sequence 151862, US/13510783A
Publication No. US20140259212A1
GENERAL INFORMATION
APPLICANT: Plesch, Gunnar
APPLICANT: Blau, Astrid
APPLICANT: Herold, Michael M.
APPLICANT: Kamlage, Beate
APPLICANT: Wendel, Birgit
APPLICANT: Puzio, Piotr
APPLICANT: Henkes, Stefan
APPLICANT: Haake, Volker
APPLICANT: Van Camp, Wim
APPLICANT: Fahnenstich, Holger
APPLICANT: McKersie, Bryan
APPLICANT: Bruce, Wesley
APPLICANT: Christiansen, Nicole
TITLE OF INVENTION: PROCESS FOR THE PRODUCTION OF FINE CHEMICALS
FILE REFERENCE: 13311-00084-US
CURRENT APPLICATION NUMBER: US/13/510,783A
CURRENT FILING DATE: 2012-05-18
PRIOR APPLICATION NUMBER: PCT/EP2010/006988
PRIOR FILING DATE: 2010-11-18
PRIOR APPLICATION NUMBER: EP 09014472.6
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09176396.1
PRIOR FILING DATE: 2009-11-18
PRIOR APPLICATION NUMBER: EP 09181052.3
PRIOR FILING DATE: 2009-12-22
PRIOR APPLICATION NUMBER: EP 10186930.3
PRIOR FILING DATE: 2010-10-08
PRIOR APPLICATION NUMBER: EP 10188863.4
PRIOR FILING DATE: 2010-10-26
PRIOR APPLICATION NUMBER: EP 10189169.5
PRIOR FILING DATE: 2010-10-28
PRIOR APPLICATION NUMBER: EP 10189358.4
PRIOR FILING DATE: 2010-10-29
PRIOR APPLICATION NUMBER: EP 10189943.3
PRIOR FILING DATE: 2010-11-04
PRIOR APPLICATION NUMBER: EP 10190115.5
PRIOR FILING DATE: 2010-11-05
Remaining Prior Application data removed - See File Wrapper or PALM.
NUMBER OF SEQ ID NOS: 158060
SEQ ID NO 151862
LENGTH: 567
TYPE: DNA
ORGANISM: Saccharomyces cerevisiae
FEATURE:
NAME/KEY: CDS
LOCATION: (1)..(567)
Query Match 100.0%; Score 567; Length 567;
Best Local Similarity 100.0%;
Matches 567; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 ATGGGCAAAACCGCGGATAATCATGGTCCAGTACGTTCTGAGACAGCACGTGAAGGAAGA 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGGCAAAACCGCGGATAATCATGGTCCAGTACGTTCTGAGACAGCACGTGAAGGAAGA 60
Qy 61 GAAAACCAGGTTTACTCACCCGTTACAGGTGCAAGATTAGTTGCTGGCTGCATATGTTTA 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 GAAAACCAGGTTTACTCACCCGTTACAGGTGCAAGATTAGTTGCTGGCTGCATATGTTTA 120
Qy 121 ACACCCGACAAGAAGCAAGTTCTCATGATTACTTCTTCTGCACACAAGAAAAGATGGATT 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 ACACCCGACAAGAAGCAAGTTCTCATGATTACTTCTTCTGCACACAAGAAAAGATGGATT 180
Qy 181 GTCCCCAAAGGTGGCGTTGAGAAAGACGAGCCTAATTACGAGACGACTGCCCAACGAGAA 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 GTCCCCAAAGGTGGCGTTGAGAAAGACGAGCCTAATTACGAGACGACTGCCCAACGAGAA 240
Qy 241 ACTTGGGAGGAAGCTGGTTGCATAGGTAAAATTGTCGCCAATTTGGGTACAGTTGAAGAC 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 ACTTGGGAGGAAGCTGGTTGCATAGGTAAAATTGTCGCCAATTTGGGTACAGTTGAAGAC 300
Qy 301 ATGAGACCCCCTAAGGACTGGAACAAAGACATTAAGCAATTCGAGAACTCTCGAAAAGAT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 ATGAGACCCCCTAAGGACTGGAACAAAGACATTAAGCAATTCGAGAACTCTCGAAAAGAT 360
Qy 361 TCAGAAGTAGCAAAGCACCCGCCAAGAACCGAATTTCATTTTTATGAATTAGAGATTGAA 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 TCAGAAGTAGCAAAGCACCCGCCAAGAACCGAATTTCATTTTTATGAATTAGAGATTGAA 420
Qy 421 AATCTCCTTGATAAATTTCCGGAATGTCACAAAAGACATAGAAAGCTATACTCTTATACA 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 AATCTCCTTGATAAATTTCCGGAATGTCACAAAAGACATAGAAAGCTATACTCTTATACA 480
Qy 481 GAAGCTAAACAAAACTTGATAGACGCCAAGAGGCCTGAATTGTTGGAGGCCCTTAATAGG 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 GAAGCTAAACAAAACTTGATAGACGCCAAGAGGCCTGAATTGTTGGAGGCCCTTAATAGG 540
Qy 541 TCTGCTATCATTAAAGACGACAAATAG 567
|||||||||||||||||||||||||||
Db 541 TCTGCTATCATTAAAGACGACAAATAG 567
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA N STOCKDALE whose telephone number is (703)756-5395. The examiner can normally be reached M-F 8:30-5:00 CT.
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JESSICA N. STOCKDALE
Examiner
Art Unit 1663
/JESSICA NICOLE STOCKDALE/Examiner, Art Unit 1663
/CHARLES LOGSDON/Primary Examiner, Art Unit 1662
Prosecution Insights