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 .
Continued Examination Under 37 CFR 1.114
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 response filed 6/11/2026 has been received and entered into the application file. All arguments have been fully considered.
Claims 1-2, 8, 11, 17, 20, 23, 26, 29, and 62-63 from the claim set filed 6/11/2026 are pending. Examiner acknowledges claims 3-7, 9-10, 12-16, 18-19, 21-22, 24-25, 27-28, and 30-61 are canceled.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 4/8/2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Examiner’s Note
Examiner respectfully notes the claim set and remarks filed 6/11/2026 are identical to the claim set and remarks filed 10/20/2025 in response to the non-final office action filed 4/18/2025. Examiner respectfully notes the final office action filed 12/12/2025 withdrew the previously filed improper Markush rejection of claim 17, the claim interpretation of SEQ ID NO: 14, the 112b rejection of claim 17, the 112a rejection of claims 1 and 62, the 102 rejection of claims 1, 26, and 29, and the 103 rejection of claims 2, 14, 8, 62-63, 11, 17, 20, and 23. Further, Examiner respectfully notes the final office action filed 12/12/2025 maintained the improper Markush grouping rejection of claims 8, 11, 20, and 62, as well as comprised new grounds of rejection in regards to 35 USC 103 in regards to claims 1-2, 26, and 29, as well as claims 8, 11, 17, 20, and 23.
As the claims and remarks filed 6/11/2026 do not address the rejections at issue, as filed in the final office action dated 12/12/2025, all rejections have thus been maintained.
Examiner spoke with the attorney of record, David Kerr, Registration No. 64,447, on 6/23/2026 to verify the claims and remarks filed 6/11/2026 were the intended claims and remarks to be filed. David Kerr authorized that the filed claims and remarks dated 6/11/2026 were the intended claims/remarks.
Thus, Examiner respectfully reiterates, the rejections of record, as filed in the final office action dated 12/12/2025 are maintained as Applicant remarks do not address the rejections at issue. Said rejections are incorporated below for ease of viewing.
REJECTION(S) MAINTAINED
Improper Markush Grouping
As noted supra, Applicant remarks filed 6/11/2026 do not address the improper Markush grouping rejection filed in the final office action dated 12/12/2025. As such, said rejection is maintained and incorporated herein for ease of viewing.
Claims 8, 11, 20, and 62 are rejected on the basis that they contain an improper Markush grouping of alternatives.
As was noted in the final office action filed 12/12/2025:
Applicant remarks (i.e., filed in response to the non-final office action) have been considered but have not been found persuasive in regards to the improper Markush groupings found in claims 8, 11, 20, and 62. Examiner notes Applicant argues the enzymes claimed must be considered as a whole, and not broken down into elements or compounds. Examiner notes however, that the sequences provided in said claims have been considered as a whole, as the full sequences provided were searched and used to compare homology.
As noted in the previously filed non-final rejection, “…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 grouping of claims 8, 11, 20, and 62 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons:
As can be seen by the sequence alignment for claims 8, 11, 20, and 62, the Markush groupings do not share a single structural similarity (please see the previously filed non-final rejection for sequence alignments).
Thus, the previously filed rejections of claims 8, 11, 20 and 62 are maintained.
As was noted in the previously filed final office action:
An examiner's interview was conducted 12/2/2025 with the attorney of record to discuss the Applicant's response to the non-final office action, specifically regarding the improper Markush groupings rejection and a potential species election. The examiner inquired if the applicant wished to elect different sequences than those previously searched; the attorney confirmed the applicant would proceed with the sequences previously searched during the non-final examination (i.e., SEQ ID NOs: 2, 8, and 26). Thus, the species election due to the improper Markush groupings of claims 8, 11, 29, and 62 are:
SEQ ID NO:2 for species of IF (claim 8 and 62), SEQ ID NO: 8 for species of EF (claim 11 and 62), SEQ ID NO: 26 for species of RS (claim 20 and 62).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
As was noted supra in the Examiner’s note, the remarks and claims filed 6/11/2026 do not address the 103 rejections filed in the final office action dated 12/12/2025. As such, the previously filed rejections are maintained.
Said rejections are incorporated herein for ease of viewing.
Claims 1-2, 26, and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Shimizu, in view of Imanaka (WO 2006109751 A1, published 10/19/2006; PTO 892) and Grosjean (Grosjean et al., PLOS (2014) 10(5): 1-21; PTO 892).
In regards to claims 1 and 2, Shimizu teaches of a cell-free translation system termed the “protein synthesis using recombinant elements” (PURE) system which contains all necessary translation factors, purified with high specific activity, and allows efficient protein production (i.e., macromolecule synthesis). Shimizu further specifies said system comprises reaction mixtures (p751, Col 2, paragraph 1-2; p754, Col 2, paragraph 3).
In more detail, Shimizu teaches protein biosynthesis proceeds in three steps: initiation, elongation, and termination. In E. coli, the translation factors responsible for completing these steps are three initiation factors, three elongation factors, and three release factors, as well as ribosome recycling factor (RRF) for termination. Shimizu teaches the PURE system includes 32 components (i.e., “the factor mix”) that have been purified individually, to include: IF1, IF2, IF3, EF-G, EF-Tu, EF-Ts, RF1, RF3, RRF, 20 aminoacyl-tRNA synthetases (ARSs), and methionyl-tRNA transformylase (MTF) (p751, Col 2, paragraph 2). Shimizu teaches the standard translation mixtures (i.e., reaction mixtures). Shimizu teaches of template plasmids used for translation (i.e., nucleic acid synthesis template) (p754, 2nd column, paragraphs 2-3) and teaches of using mRNA template sequences (p752, 2nd column, 1st paragraph; p753, 1st column, last paragraph). Lastly, Shimizu teaches said reaction mixture (i.e., the translation reaction mixture and the factor mix) was incubated (i.e., an incubator reads on a bioreactor) at 37 degrees, template was added and the reaction was incubated again until being terminated (i.e., after protein synthesis had taken place).
Therefore, Shimizu teaches a system for recombinant cell-free expression comprising: a core recombinant protein mixture with the limitations required by claim 1, a nucleic acid synthesis template, and a reaction mixture having cell-free reaction components necessary for in vitro macromolecule synthesis, wherein the above components are situated in a bioreactor configured for cell-free expression of macromolecules.
Shimizu does not teach of thermophilic bacteria but rather teaches of E. coli. Thus, Shimizu does not teach “wherein at least one of the components of said core recombinant protein mixture is derived from thermophilic Bacillaceae bacteria or thermophilic Geobacillus bacteria.”
Imanaka teaches a method for producing a protein using a cell-free protein translation system, in which the mRNA encoding the target protein is translated under high temperature conditions in a cell-free protein translation system containing a cell extract derived from hyperthermophilic bacteria [0008]. Imanaka teaches
the term "hyperthermophilic bacterium" used in the present invention refers to a thermophilic bacterium or thermophilic progenitor that grows at 60 ° C or higher, preferably 90 ° C or higher. Imanaka teaches the hyperthermophilic bacterium applicable to the present invention is not particularly limited as long as it meets the above definition. Imanaka teaches at present, more than 100 types of hyperthermophilic bacteria have been isolated and identified, and any of these can be applied to the present invention, such as Geobacillus kaustophilus, Geobacillus thermocatenulatus, Geobacillus thermodenitrifics, Geobacillus thermoglucosidasius, Geobacillus stearothermophilus, and Geobacillus thermoleovorans [0015] (i.e., claim 2 of the instant application). Imanaka additionally teaches the cell extract refers to an extract of a hyperthermophilic bacterium containing components necessary for protein synthesis such as ribosome and tRNA. This cell extract can be prepared by the method of Pratt et al [0018].
Thus, Imanaka teaches using cell extracts from Geobacillus for cell free protein synthesis and notes said cell extracts contain the necessary components for protein synthesis.
Imanaka does not per se teach the specific components required for protein translation. Rather, Imanaka simply states the cell extract contains the necessary components for protein synthesis.
As a POSITA will appreciate, and as is taught by Grosjean, the majority of genes coding for the ribosomal proteins, aminoacyl-tRNA synthetases, translation factors and ribosome biogenesis/maturation enzymes are universal and essential (p2, 1st column, last paragraph). Thus, it is reasonable to conclude that the cell extracts from the Geobacillus bacterium taught by Imanaka comprise initiation factors, elongation factors, ribosome recycling factors, aminoacyl-tRNA synthetases and methionyl-tRNA transformylases.
Thus, it would have been obvious to a POSITA, before the effective filing date of the claimed invention, to combine the teachings of Shimizu and Imanaka, as there existed a motivation to do so. Specifically, the known universality of the bacterial translational apparatus would have provided the requisite rationale for a skilled artisan to integrate Shimizu’s “ingredients” for a core recombinant protein mixture with Imanaka’s high-temperature cell-free translation system from Geobacillus, i.e., the cell extracts from said bacterium, in order to have a system in which protein translation could occur at high temperatures. The skilled artisan would have had a reasonable expectation of success in combining said teachings due to all working in the field of cell-free protein translation in bacteria.
Thus, the claims are obvious and are properly rejected.
In regards to claim 26, the above cited references teach the system of claim 1. Further, Shimizu teaches wherein said nucleic acid synthesis template comprises a DNA template (p754, 2nd column, “Measurement of energy charge”).
Thus, the claim is obvious and is properly rejected.
In regards to claim 29, the above cited references teach the system of claim 1. Further, Shimizu teaches wherein said reaction mixture comprises (1) a quantity of ribosomes; (2) a quantity of T7 RNA polymerase; (3) a quantity of tRNAs; (4) a quantity of amino acids; (5) and a buffer (p751, Results 1st paragraph; p754, 2nd column, Translation reaction).
Thus, the claim is obvious and is properly rejected.
Claim 8 is rejected under 35 U.S.C. 103 as being unpatentable over Shimizu in view of Imanaka and Grosjean, and further in view of UniProt A0A087LHL7 · A0A087LHL7_GEOSE (https://www.uniprot.org/uniprotkb/A0A087LHL7/entry (2014); retrieved from the internet 12/4/2025; PTO 892).
In regards to claim 8, the above cited references teach the system of claim 1. Additionally, and as noted in the rejection of claim 1, Shimizu teaches of Initiation Factor 1, of E. coli.
As noted above in regards to the improper Markush groupings, claim 8 is such an improper grouping. As such, and as noted above, Applicant has selected SEQ ID NO: 2 as the species of IF.
Examiner notes SEQ ID NO: 2 has 100% identity to UniProt A0A087LHL7 · A0A087LHL7_GEOSE, which is noted as being translation initiation factor 1 from Geobacillus stearothermophilus and was entered into UniProt 10/29/2014.
As discussed supra in regards to claim 2, Imanaka teaches of Geobacillus bacteria.
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Therefore, it would have been obvious to a POSITA, before the effective filing date of the claimed invention, to do a simple substitution of one known element for another to obtain predictable results. It would have been obvious to substitute the IF of E. coli as taught by Shimizu for the IF of Geobacillus as taught by Imanaka and UniProt. The skilled artisan would have had a reasonable expectation of successfully substituting said IFs, due to the translational machinery of bacteria being universal. The skilled artisan would have been so motivated to perform said substitution in order to have a cell free translation system operable at high temperatures. Substitution of one element for another known in the field is considered to be obvious, absent a showing that the result of the substitution yields more than predictable results. See KSR International Co. v Teleflex Inc 82 USPQ2d 1385 (US 2007) at page 1395.
Thus, the claim is obvious and is properly rejected.
Claim 11 is rejected under 35 U.S.C. 103 as being unpatentable over Shimizu in view of Imanaka and Grosjean, and further in view of UniProt ID A0A063YXQ5_9BACI.
In regards to claim 11, the above cited references the system of claim 1. As noted above in regards to the improper Markush groupings, claim 11 is such an improper grouping. As such, and as noted above, Applicant has selected SEQ ID NO: 8 to be the species of EF.
As discussed supra in regards to claim 2, Imanaka teaches of Geobacillus bacteria.
Examiner notes SEQ ID NO: 8 has 99.9% identity to ID A0A063YXQ5_9BACI (i.e., a sequence having at least 90% identity to SEQ ID NO: 8), which was integrated into UniProtKB/TrEMBL September 3, 2014 and is recognized as being Elongation Factor G from Geobacillus. A sample of the sequence alignment is included below for Applicant’s reference.
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383
759
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For ease of reference, the information included in DAV from the STIC sequence search results teaching the background information for the above posted sequence alignment is included below:
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615
895
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Therefore, it would have been obvious to a POSITA, before the effective filing date of the claimed invention, to do a simple substitution of one known element for another to obtain predictable results. It would have been obvious to substitute the EF of E. coli as taught by Shimizu for the EF of Geobacillus as taught by Imanaka and UniProt. The skilled artisan would have had a reasonable expectation of successfully substituting said EFs, due to the translational machinery of bacteria being universal. The skilled artisan would have been so motivated to perform said substitution in order to have a cell free translation system operable at high temperatures. Substitution of one element for another known in the field is considered to be obvious, absent a showing that the result of the substitution yields more than predictable results. See KSR International Co. v Teleflex Inc 82 USPQ2d 1385 (US 2007) at page 1395.
Thus, the claim is obvious and is properly rejected.
Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Shimizu in view of Imanaka and Grosjean, and further in view of UniProt A4IMC6 · RRF_GEOTN (retrieved from the internet 12/4/2025; https://www.uniprot.org/uniprotkb/A4IMC6/entry (2007); PTO 892).
In regards to claim 17, the above cited references teach the system of claim 1. Examiner notes as discussed supra, Imanaka teaches of Geobacillus.
Examiner notes SEQ ID NO: 90 has100% identity to UniProt A4IMC6 · RRF_GEOTN, which is noted as being a ribosome recycling factor from Geobacillus thermodenitrificans.
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Therefore, it would have been obvious to a POSITA, before the effective filing date of the claimed invention, to do a simple substitution of one known element for another to obtain predictable results. It would have been obvious to substitute the RRF of E. coli as taught by Shimizu for the RRF of Geobacillus as taught by Imanaka and UniProt. The skilled artisan would have had a reasonable expectation of successfully substituting said RRFs, due to the translational machinery of bacteria being universal. The skilled artisan would have been so motivated to perform said substitution in order to have a cell free translation system operable at high temperatures. Substitution of one element for another known in the field is considered to be obvious, absent a showing that the result of the substitution yields more than predictable results. See KSR International Co. v Teleflex Inc 82 USPQ2d 1385 (US 2007) at page 1395.
Thus, the claim is obvious and is properly rejected.
Claim 20 is rejected under 35 U.S.C. 103 as being unpatentable over Shimizu in view of Imanaka and Grosjean and further in view of UniProt A0A0E0TE69.
In regards to claim 20, the above cited references teach the system of claim 1. As noted above in regards to the improper Markush groupings, claim 20 is such an improper grouping. As such, and as noted above, Applicant has selected SEQ ID NO: 26 to be the species of RS.
Examiner notes as discussed above, Imanaka teaches of Geobacillus.
Examiner notes SEQ ID NO: 26 has 99.8% identity to ID A0A0E0TE69 (i.e., a sequence having at least 90% identity to SEQ ID NO: 26), which was integrated into UniProtKB/TrEMBL May 27, 2015 and is recognized as being alanine- tRNA ligase (i.e., alanine- tRNA synthetase, i.e., RS) from Geobacillus. A sample of the sequence alignment is included below for Applicant’s reference.
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455
760
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For ease of reference, the information included in DAV from the STIC sequence search results teaching the background information for the above posted sequence alignment is included below:
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365
846
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Therefore, it would have been obvious to a POSITA, before the effective filing date of the claimed invention, to do a simple substitution of one known element for another to obtain predictable results. It would have been obvious to substitute the RS of E. coli as taught by Shimizu for the RS of Geobacillus as taught by Imanaka and GenBank. The skilled artisan would have had a reasonable expectation of successfully substituting said RSs, due to the translational machinery of bacteria being universal. The skilled artisan would have been so motivated to perform said substitution in order to have a cell free translation system operable at high temperatures. Substitution of one element for another known in the field is considered to be obvious, absent a showing that the result of the substitution yields more than predictable results. See KSR International Co. v Teleflex Inc 82 USPQ2d 1385 (US 2007) at page 1395.
Thus, the claim is obvious and is properly rejected.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Shimizu in view of Imanaka and Grosjean, and further in view of UniProt A0A0E0TA16_GEOS2.
In regards to claim 23, the above cited references teach the system of claim 1.
Examiner notes Imanaka teaches of Geobacillus.
Examiner notes SEQ ID NO: 68 has 100% identity to A0A0E0TA16_GEOS2 (i.e., a sequence having at least 90% identity to SEQ ID NO: 68), which was integrated into UniProtKB/TrEMBL May 27, 2015 and is recognized as being methionyl-tRNA formyltransferase (i.e., MTF) from Geobacillus. A sample of the sequence alignment is included below for Applicant’s reference.
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For ease of reference, the information included in DAV from the STIC sequence search results teaching the background information for the above posted sequence alignment is included below:
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Therefore, it would have been obvious to a POSITA, before the effective filing date of the claimed invention, to do a simple substitution of one known element for another to obtain predictable results. It would have been obvious to substitute the MTF of E. coli as taught by Shimizu for the MTF of Geobacillus as taught by Imanaka and GenBank. The skilled artisan would have had a reasonable expectation of successfully substituting said MTFs, due to the translational machinery of bacteria being universal. The skilled artisan would have been so motivated to perform said substitution in order to have a cell free translation system operable at high temperatures. Substitution of one element for another known in the field is considered to be obvious, absent a showing that the result of the substitution yields more than predictable results. See KSR International Co. v Teleflex Inc 82 USPQ2d 1385 (US 2007) at page 1395.
Thus, the claim is obvious and is properly rejected.
RESPONSE TO APPLICANT REMARKS
Applicant did not file remarks addressing the grounds of rejection noted in the final office action dated 12/12/2025.
Conclusion
(as was noted in the final office action dated 12/12/2025)
In regards to claim 62 (and dependent claim 63), Examiner refers Applicant to the Improper Markush Groupings discussion above and the subsequent species election. Examiner notes Applicant has selected, as stated supra: SEQ ID NO:2 for species of IF (claim 8 and 62), SEQ ID NO: 8 for species of EF (claim 11 and 62), SEQ ID NO: 26 for species of RS (claim 20 and 62). As such, due to the improper Markush groupings and subsequent election of species, Examiner notes there is not prior art for: A system for recombinant cell-free expression comprising:
-a core recombinant protein mixture [comprising] the following components:
-at least one initiation factor having an amino acid sequence selected from SEQ ID NO: 2 (i.e., Applicant elected species of IF);
- at least one elongation factor having an amino acid sequence selected from SEQ ID NO: 8 (i.e., Applicant elected species of EF);
- at least one peptide release factor having an amino acid sequence selected from SEQ ID NO: 18, 20, 22, 86, 88;
- at least one ribosome recycling factor having an amino acid sequence selected from SEQ ID NO: 90;
- at least one aminoacyl-tRNA-synthetase having an amino acid sequence selected from SEQ ID NO: 26 (i.e., Applicant elected species of RS); and
- at least one methionyl-tRNA transformylase having an amino acid sequence selected from SEQ ID NOs: 68 and 132.
The claim language requires each “category” of protein translation machinery to exhibit 100% identity to at least one of the listed sequences within that specific “category”.
Examiner notes, after a thorough sequence search, that the closest prior art for SEQ ID NO: 8 is 99.9% and for SEQ ID NO: 26 the closest prior art is 99.8%. As such, there is not prior art teaching the limitations of claim 62, and thus dependent claim 63.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KATHERINE R SMALL whose telephone number is (703)756-4783. The examiner can normally be reached Monday - Friday 8:30am-4pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Chris Babic can be reached on 571-272-8507. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KATHERINE R SMALL/Examiner, Art Unit 1633
/EVELYN Y PYLA/Primary Examiner, Art Unit 1633
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