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 .
Claim Status
Claims 1-20 are pending.
Claims 13-14 and 19-20 are withdrawn.
Claims 1-12, and 15-18 are under examination.
Claim Interpretation
It is noted that instant claims recite “a” nucleic acid sequence (“a nucleotide sequence of SEQ ID NO: 11”).
The broadest reasonable interpretation “a” nucleic acid sequence is a nucleic acid sequence of two nucleotides or more that otherwise meets the recited claim limitations.
In the instant case, claim limitations are met by fragments of 2 nucleotides or more contained by SEQ ID NO: 11.
Instant claims recite “one or more elements capable of being tuned to modulate recombinase translation.” The instant specification is silent to a definition of “one or more elements capable of being tuned to modulate recombinase translation.” Therefore, this interpreted to include all possible elements that are capable of being operably linked to all possible elements which modulate translation.
Examiner’s Remark
If Applicant does not want the claim language to include fragments of SEQ ID NO: 11 (“a nucleotide sequence of SEQ ID NO: 11; see claim interpretation above), it is recommended that Applicant amend to “the nucleotide sequence of SEQ ID NO: 11.”
Claim Rejections - 35 USC § 112(a)
Written Description
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.
Claims 1-12, and 15-18 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.
The purpose of the written description requirement is to ‘ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor’s contribution to the field of art as described in the patent specification.” Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1353-54 (Fed. Cir. 2010) (en banc) (quoting Univ. of Rochester v. G.D. Searle & Co., 358 F.3d 916, 920 (Fed. Cir. 2004)). To satisfy the written description requirement, the specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. Vas-Cath, Inc. v. Mahurkar, 935 F.2d 1555, 1562-63, 19 USPQ2d 1111 (Fed. Cir. 1991). See also MPEP 2163.04.
For a claim to a genus, a generic statement that defines a genus of substances by only their functional activity does not provide an adequate written description of the genus. Reagents of the University of California v. Eli Lilly, 43 USPQ2d 1398 (CAFC 1997).
To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include a disclosure of a representative number of species to describe the complete structure of the claimed genus and/or disclosure of a complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, and any combination thereof.
Scope of the Invention
In the instant case, the genera are:
Temperature-sensitive terminators comprising “a nucleotide sequence of SEQ ID NO:11” (claim 1 and dependents).
The broadest reasonable interpretation of the scope of this genus includes all possible temperature-sensitive terminators comprising a nucleotide sequence of 2 nucleotides or more of SEQ ID NO: 11 (see also claim interpretation above) which encompasses a very large number of structurally and functionally distinct fragments of lengths from 2 nucleotides up to the full length 45 nucleotide SED ID NO:11. Since instant claims “comprise” the nucleotide sequences, the claims further encompass larger fragments that may include all possible additional elements.
Temperature-sensitive terminators comprising a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11 (claim 1 and dependents)
The broadest reasonable interpretation of the scope of this genus is all possible sequences of all possible lengths that comprise a sequence having one or two mismatches relative to SEQ ID NO:11. Since instant SEQ ID NO: 11 is 45 base pairs, 2 mismatches is 95.55% identical and 1 mismatch is 97.77% identical. Since instant claims “comprise” the nucleotide sequences, the claims further encompass larger fragments that may include all possible additional elements. For embodiments with one mismatch, this encompasses 135 structurally distinct sequences that may or may not function as required as part of a temperature-sensitive terminator. For 2 mismatches, the mismatches can occur at all possible locations and all possible combinations of locations in the 45 bp sequence, which is 990 possible locations. Accounting for a change of either of the two mismatches to one of the 3 other base pairs, this encompasses thousands of structurally and functionally distinct sequences that may or may not function as required as part of a temperature-sensitive terminator.
Disclosure of Structure
SEQ ID NO: 11
Regarding the nucleotide sequences of SEQ ID NO: 11, and the nucleotide sequences having one or two mismatches relative to SEQ ID NO: 11, Applicant discloses the sequence of SEQ ID NO:11. Sequences with less than 100% homology to SEQ ID NO: 11 are contemplated (para. [0013]), but no specific sequences with less than 100% homology to SEQ ID NO: 11 are disclosed.
Structure/Function Relationship
SEQ ID NO: 11
Regarding the nucleotide sequences of SEQ ID NO: 11, and the nucleotide sequences having one or two mismatches relative to SEQ ID NO: 11, SEQ ID NO:11 is a temperature-sensitive terminator.
Applicant is directed to the art of Krajewski et al. (Biochim Biophys Acta . 2014 Oct;1839(10):978-988. Epub 2014 Mar 21.; henceforth “Krajewski”). Krajewski evidences temperature-sensitive terminators are made up of 2-4 hairpin structures (Figure 1). Applicant is additionally directed to the art of Miladi et al. (Nucleic Acids Res. 2020 Jul 2;48(W1):W287-W291. Henceforth “Miladi”). Miladi evidences that single nucleotide variations can affect RNA secondary structures including hairpin structures. Specifically, Miladi evidences point mutations in a hairpin RNA structure can completely abolish the formation of the hairpin (pg. W290 col. 1 3rd para.). Accordingly, one or two mismatches in the temperature-sensitive terminator, encompassed by Applicant’s claim, could completely abolish the hairpin structure of the temperature-sensitive terminator. Furthermore, fragments of SEQ ID NO: 11 encompassed by instant claim may not be predictably functional.
Furthermore, it is noted that SEQ ID NO: 11 appears to be a novel sequence, and therefore the art is also silent to which mismatches may or may not be made in this sequence and result in the claimed function of temperature sensitivity and further the art is silent to which specific fragments of the sequence are required for function because SEQ ID NO: 11 appears to be a novel sequence.
Written Description - Conclusion
Therefore, the examiner concludes there is insufficient written description support for the instantly claimed genera of nucleotide sequences of SEQ ID NO: 11 and nucleotide sequences having one or two mismatches relative to SEQ ID NO: 11. One species example is not representative of the complete structure of the such a diverse genus as the fragments encompassed by “nucleotide sequences of” SEQ ID NO: 11 and is not representative of such a diverse genus as sequences with one or two mismatches relative to SEQ ID NO: 11. Because the breadth of the claims encompasses many sequences, and the specification has not provided sufficient structural-functional relationship between the sequences and the function of the temperature-sensitive terminator, a person of ordinary skill in the art cannot envision such sequences from the instant disclosure. Accordingly, the sequences have not been described in sufficient detail, and Applicant has not shown possession of the claimed invention at the time of effective filing
The examiner concludes that there is insufficient written description of the instantly claimed genus. Only sequences 100% identical to SEQ ID NO:11, and not the fill breadth of the claims, is supported by Applicant’s disclosure.
Hence, there is insufficient written description support for instant claims.
Response to Arguments
Applicant’s arguments, filed 25th, September, 2025, have been fully considered but are not found persuasive.
Applicant argues “consistent with Example 11 of the Written Description Training Materials (Revision 1, March 25, 2008), those of skill in the art could readily envision all of the nucleotide sequences encompassed by presently amended claim 1. With the aid of a computer, one could list all of the nucleic acid sequences having one or two mismatches relative to SEQ ID NO: 11. As described in the
specification, temperature-sensitive terminators:
have been engineered to mimic temperature-modulated structures known as RNA
thermometers that are found in the 5' untranslated region of microbial mRNAs
and play an important role in regulating microbial gene expression in response to
temperature changes.
Specification at paragraph [0196]. Furthermore, the concepts of nucleic acid thermodynamics and intramolecular base pairing is known and studied in the art, and tools exist to predict the effect of nucleic acid sequence changes on nucleic acid structure. Indeed, in the Office Action, Miladi et al. (Nucleic Acids Res. 2020 Jul 2;48(Wl):W287-W291; henceforth "Miladi") was cited for teaching that "point mutations in a hairpin RNA structure can completely abolish the formation of the hairpin." Office Action at p. 4. However, this refers to a specific 5'UTR element that is "a classic example of mutations which affect RNA structure." Miladi at p. W290, 3rd paragraph. Furthermore, Miladi provides a tool to predict RNA structure changes when positions are mutated” (pg. 8-9).
Applicant argues “the claims as amended are adequately described based the specification in
combination with the knowledge available to one of skill in the art” (pg. 9).
In response, first, Applicant’s amendment to “a nucleotide sequence of SEQ ID NO: 11” broadens the claims to encompass a large number of structurally distinct sequences comprising fragments of SEQ ID NO: 11. Because SEQ ID NO: 11 appears to be a novel sequence, and the state of the art above indicates that even a single nucleotide change can alter the function of the nucleotide, one or ordinary skill could not envision which fragments of SEQ ID NO: 11 encompasses by instant claims are functional.
Regarding the embodiments of “one or two mismatches” relative to SEQ ID NO: 11, as discussed above, this encompasses thousands of structurally distinct sequences. As discussed above, Miladi evidences single nucleotide changes can affect RNA structure. Although Miladi does not refer to transcription factors specifically, Miladi evidences the concept that a single nucleotide change can alter the structure and function of RNA, which is applicable to transcription factors. As discussed above, SEQ ID NO: 11 is a novel sequence, and Applicant has not provided information on which regions of the sequence may or may not be altered to result in the required function of a temperature sensitive terminator.
Although RNA folding tools are available in the art, this does not support possession of the full breadth of Applicant’s claims which encompass a very large number of structurally and functionally distinct fragments of SEQ ID NO:11 and further specifically encompasses thousands of structurally distinct sequences with one or two mismatches relative to SEQ ID NO:11. Applicant is directed to MPEP 2163.02 which states that to satisfy the written description requirement, an applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, the inventor was in possession of the invention, and that the invention, in that context, is whatever is now claimed. The test for sufficiency of support in a parent application is whether the disclosure of the application relied upon "reasonably conveys to the artisan that the inventor had possession at that time of the later claimed subject matter." Ralston Purina Co. v. Far-Mar-Co., Inc., 772 F.2d 1570, 1575, 227 USPQ 177, 179 (Fed. Cir. 1985) (quoting In re Kaslow, 707 F.2d 1366, 1375, 217 USPQ 1089, 1096 (Fed. Cir. 1983)). In the instant case, Applicant discloses only one specific sequence of SEQ ID NO:11, and Applicant does not provide guidance on how this sequence could be modified to arrive at other functional sequence. This does not reasonably convey to the artisan that the inventor had possession of the unfathomably large number of sequences of fragments of SEQ ID NO:11 or the more specific thousands of sequences with one or two mismatches relative to SEQ ID NO:11 encompassed by instant claims because Applicant has not provided a nexus between the required function of the temperature sensitive terminator and the required structure of the fragments or sequences with mismatches relative to SEQ ID NO:11. As stated above, SEQ ID NO:11 is a novel sequence and as such one of ordinary skill would not be able to envision the requisite structural elements that the fragments encompassed by instant claims or the more specific thousands of sequences with one or two mismatches relative to SEQ ID NO:11 encompassed by instant claims.
New Claim Rejections - 35 USC § 112(a)
Written Description
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.
In the amendment filed on 25th, September, 2025, claim 1 was amended to recite the following new limitations:
“a nucleotide sequence of SEQ ID NO: 11”
“a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11”
These new limitations appear to be new matter.
A review of the originally filed specification by the Examiner did NOT find any specific basis for the recited limitations. The disclosure (including the specification, claims and sequence listing) as originally filed, does not contain a specific recitation of the limitations.
The closest support for the new limitation of “a nucleotide sequence of SEQ ID NO: 11” is the disclosure of SEQ ID NO:11, as well as the general disclosure of sequences 90%, 95%, 98% or 99% identical to SEQ ID NO: 11 (see original claim 15 and also para. [0013]). The disclosure of one specific full length fragment of SEQ ID NO:11 does not provide support for the full breadth of sequences encompassed by “a nucleotide sequence of SEQ ID NO: 11” which encompasses all possible fragments of 2 nucleotides or more included by SEQ ID NO: 11. The general disclosure of sequences 90%, 95%, 98% or 99% does not provide specific structures or species to support the full breadth of “a nucleotide sequence of SEQ ID NO: 11.”
The closest support for the new limitation of “a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11” is the disclosure of SEQ ID NO:11, as well as the general disclosure of sequences 90%, 95%, 98% or 99% identical to SEQ ID NO: 11 (see original claim 15 and also para. [0013]). SEQ ID NO:11 is 45 bp, so one or two mismatches would be a 44/45 or 43/45 match, which is a 95.55% or 97.77% match to SEQ ID NO: 11. There is no guidance in the specification that would lead one of ordinary skill to arrive at 95.55% or 97.77% identity from the broader disclosed percentages of 90% or the different percentages of 95%, 98%, 99% or 100%.
As noted by MPEP 608.04(a), new matter includes not only the addition of wholly unsupported subject matter, but may also include adding specific percentages or compounds after a broader original disclosure, or even the omission of a step from a method.
In the instant case one skilled in the art would NOT consider the genus of fragments of SEQ ID NO: 11 or the sequences with one or two mismatches relative to SEQ ID NO: 11 to be explicitly, implicitly, or inherently supported by Applicant’s disclosure.
Hence, there is insufficient written descriptions support for the instantly claimed limitation of and Applicant has not shown possession of the invention.
Response to Arguments
Applicant’s arguments, filed 25th, September, 2025, have been fully considered but are not found persuasive.
Applicant argues “The amendments to the claims are fully supported by the specification and claims as originally filed. Accordingly, no new matter has been added by the claim amendments “ (pg. 7).
In response, Applicant has not provided the location of support for this amendment. When filing an amendment an applicant should show support in the original disclosure for new or amended claims. See MPEP §§ 714.02 and 2163.06 ("Applicant should ... specifically point out the support for any amendments made to the disclosure.") The claim is a new or amended claim, the support for the limitation is not apparent, and applicant has not pointed out where the limitation is supported (see MPEP 2163 (I), and therefore the claim is rejected under 35 U.S.C. 112a above.
New Claim Rejections - 35 USC § 112
Improper Markush
Claims 1 and 12 are rejected on the basis that they contain an improper Markush grouping of alternatives. Claims 2-12 and 15-18 are rejected by nature of their ultimate dependency on claim 1. 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.
Regarding claim 1, the Markush grouping of “a non-canonical start codon and a temperature-sensitive terminator comprising a nucleotide sequence of SEQ ID NO: 11 or a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11” 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: “a non-canonical start codon” does not share a single structural similarity with “a temperature-sensitive terminator comprising a nucleotide sequence of SEQ IS NO: 11 or a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11.”
Regarding claim 12, the Markush grouping of “a ribosomal binding sequence (RBS), the temperature-sensitive terminator, the non-canonical start codon, and a degradation tag” 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: a ribosomal binding sequence (RBS), the temperature-sensitive terminator, the non-canonical start codon, and a degradation tag do not share a single structural similarity with each other.
Furthermore, the recitation of “comprise one or more of” includes open language and is improper Markush language. Applicant is directed to MPEP 2117 which states claim language defined by a Markush grouping requires selection from a closed group "consisting of" the alternative members. Id. at 1280, 67 USPQ2d at 1196.
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 § 112(b)
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 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 12 is 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 12 recites “the first polynucleotide, recombinase transcript, and/or recombinase comprises one or more elements capable of being tuned to modulate recombinase translation and stability, and wherein the one or more elements comprise one or more of a ribosomal binding sequence (RBS), the temperature-sensitive terminator, the non-canonical start codon, and a degradation tag.” However, claim 1, upon which claim 12 depends, already recites the first polynucleotide and/or recombinase transcript comprises one or more elements capable of being tuned to modulate recombinase translation selected from the group comprising a non-canonical start codon and a temperature-sensitive terminator comprising a nucleotide sequence or SEQ ID NO: 11 or a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11. Therefore, the claim is unclear for several reasons. First, claim 12 recites “the temperature-sensitive terminator, the non-canonical start codon” as options which are already recited in claim 1, and it is unclear how these options, which are already structurally defined in claim 1 can further limit dependent claim 12. Further, claim 1, already recites a more specific temperature specific terminator of a sequence of SEQ ID NO: 11 or a sequence with one or two mismatches relative to SEQ ID NO: 11. Claim 12 is also unclear because it recites alternative embodiments of a ribosomal binding sequence (RBS) and a degradation tag. Because claim 1 already recites the elements are a non-canonical start codon, a temperature-sensitive terminator comprising a nucleotide sequence or SEQ ID NO: 11 or a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11, it is therefore unclear how the options of a ribosomal binding sequence (RBS) and a degradation tag can further limit the claim because they are not are a non-canonical start codon, a temperature-sensitive terminator comprising a nucleotide sequence or SEQ ID NO: 11 or a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11.
Generally, when the claims are indefinite, vague or unclear, they cannot be construed without speculation or conjecture; therefore, the indefinite claims are not treated on the merits with respect to prior art. See In re Steele, 305 F.2d 859, 862 (CCPA 1962) (A prior art rejection cannot be sustained if the hypothetical person of ordinary skill in the art would have to make speculative assumptions concerning the meaning of claim language.); see also In re Wilson, 424 F.2d 1382, 1385 (CCPA 1970) ("If no reasonably definite meaning can be ascribed to certain terms in the claim, the subject matter does not become obvious-the claim becomes indefinite."). Notwithstanding Steele, the Office has made every attempt to construe the claims in what the Office believes is the intent of the Applicants in the interest of compact prosecution.
New Claim Rejections - 35 USC § 112(d)
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 pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], 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.
Claim 12 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th 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.
Claim 12 recites ““the first polynucleotide, recombinase transcript, and/or recombinase comprises one or more elements capable of being tuned to modulate recombinase translation and stability, and wherein the one or more elements comprise one or more of a ribosomal binding sequence (RBS), the temperature-sensitive terminator, the non-canonical start codon, and a degradation tag.” However, claim 1, upon which claim 12 depends, already recites the first polynucleotide and/or recombinase transcript comprises one or more elements capable of being tuned to modulate recombinase translation selected from the group comprising a non-canonical start codon and a temperature-sensitive terminator comprising a nucleotide sequence or SEQ ID NO: 11 or a nucleotide sequence having one or two mismatches relative to the sequence of SEQ ID NO: 11. Therefore, claim 12 cannot further limit claim 1 because the embodiments of the temperature-sensitive terminator and the non-canonical start codon are already recited and defined in claim 1, and claim 12 also cannot further limit claim 1 because the recited elements of a ribosomal binding sequence(RBS) and a degradation tag are not recited in claim 1, and therefore these embodiments cant further limit because the elements capable of being tuned to modulate recombinase translation have already been structurally defined in claim 1 as the temperature-sensitive terminator or the non-canonical start codon.
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.
New 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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claims 1-3, 11-12 and 15 are rejected under 35 U.S.C. 103 as being unpatentable over Kotula et al. (WO-2016/210373-A2; see IDS filed 20th, January, 2023; henceforth “Kotula”) in view of Rossmanith et al. (ACS Synth Biol. 2018 Feb 16;7(2):613-621.; see IDS filed 20th, January, 2023; henceforth “Rossmanith”) and Shapiro et al. (US-20170298425-A1; see IDS filed 20th, January, 2023; henceforth “Shapiro”).
Regarding claims 1, 12 and 15, Kotula discloses a nucleic acid composition, comprising:
a first promoter operably linked to a first polynucleotide comprising a recombinase
gene (recombinase 1),
wherein the first promoter is capable of inducing transcription of the first
polynucleotide to generate a recombinase transcript upon stimulation (inducible promoter) in a bacterium
and wherein the recombinase transcript is capable of being translated to
generate a recombinase capable of catalyzing a recombination event (flipping of an inverted
heterologous gene encoding a bacterial toxin which is then constitutively expressed after it is
flipped by the first recombinase); and
a second promoter and a second polynucleotide comprising a payload gene (toxin),
wherein, in the absence of the recombination event, the second promoter and the second polynucleotide are not operably linked,
and
wherein the second promoter and the second polynucleotide are operably
linked after the recombination event such that the second promoter is capable of
inducing transcription of the second polynucleotide to generate a payload transcript.
(pg. 4-5, 41; Figure 2; Claim 1).
Regarding the limitation that the promoter is “capable of inducing transcription of the first polynucleotide to generate a recombinase transcript upon a thermal stimulation,” of claim 1, as stated above, Kotula discloses a promoter, which includes inducible, constitutive and/or tissue-specific promoter sequences (para. [010]). These promoter sequences transcribe for a range of temperatures and are therefore capable of meeting the contingent limitation of “generate a recombinase transcript upon a thermal stimulation.” Further, because the promoters as disclosed by Kotula are capable of being operably linked to temperature-sensitive transcription factors, they are further capable of meeting the contingent limitation of “generate a recombinase transcript upon a thermal stimulation” (see MPEP section 2111.04 (II))).
Regarding the limitation that the payload is “therapeutic,” of claim 1, as discussed above Kotula discloses a toxin as a payload. Kotula specifically discloses the toxins include “bacteriocins, lysins, and other molecules that cause cell death by lysing cell membranes, degrading cellular DNA, or other mechanisms” (para. [07]). Because molecules that cause cell death by lysing cell membranes, degrading cellular DNA, or other mechanisms are known as agents that relate to the treatment of diseases or disorders, the “toxin” of Kotula meets instant claims as a “therapeutic” payload.
However, regarding claims 1, 12 and 15, Kotula is silent to the first polynucleotide comprising a temperature-sensitive terminator comprising a nucleotide sequence of SEQ ID NO: 11.
Nevertheless, regarding claims 1, 12 and 15 , Rossmanith teaches a temperature responsive transcription terminator to regulate transcription in vivo that comprises a nucleotide sequence of SEQ ID NO: 11 (“TTTTTTT” which is a fragment of SEQ ID NO: 11 and is part of a temperature sensitive terminator; see claim interpretation above; ibpA Term-bgaB Title; abstract; pg. 614; Figure 1-2) upstream of the coding sequence (see figure 1). Rossmanith teaches the ibpA Term is the first temperature-controllable transcription terminator able to prematurely terminate transcription of various reporter genes at low temperatures and allowing read-throughout after a heat shock (pg. 617).
Therefore, regarding claims 1, 12 and 15 , it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the composition of Kotula and combine the known prior art element of the temperature specific terminator of Rossmanith upstream of the coding sequence (the recombinase coding sequence of Kotula; instant claim 15) to obtain the predictable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Rossmanith because to regulate transcription in vivo (pg. 614 col. 2 last para.). Regarding the reasonable expectation of success, Shapiro evidences transcription terminators can be included in thermal genetic circuits (Figure 2; para. [0046, 0052, 0054, 0374]; Example 4).
Regarding claim 2, further to the discussion of claim 1 above, the thermal stimulation is a contingent limitation. The nucleic acid composition suggested by Kotula in view of Rossmanith above meets the structural limitations of instant claims and is capable of generating a recombinase transcript upon a thermal stimulation in a bacterium as discussed above, where the thermal stimulation comprises heating to an activating temperature, and wherein the activating temperature is above a physiological temperature.
Regarding claim 3, further to the discussion of claims 1-2 above, as discussed above, the thermal stimulation is a contingent limitation. The nucleic acid composition suggested by Kotula in view of Rossmanith above meets the structural limitations of instant claims and is capable of generating a recombinase transcript upon a thermal stimulation in a bacterium as discussed above, with the recited activating temperatures and physiological temperatures.
Regarding claim 11, Kotula discloses the recombinase is Cre, and the recombination system is the Cre-lox system (para. [0337-0339]). The Cre-lox system is permanent and therefore meets the claimed limitation of “after the recombination event, the recombinase target sites are modified such that said modified recombinase target sites are not capable of interacting with the recombinase to yield another recombination event, thereby rendering the recombination event permanent.”
Hence, the claimed invention as a whole was prima facie obvious.
Claims 1-12, and 15-18 are rejected under 35 U.S.C. 103 as being unpatentable over Kotula et al. (WO-2016/210373-A2; see IDS filed 20th, January, 2023; henceforth “Kotula”) in view of Shapiro et al. (US-20170298425-A1; see IDS filed 20th, January, 2023; henceforth “Shapiro”) and Rossmanith et al. (ACS Synth Biol. 2018 Feb 16;7(2):613-621.; see IDS filed 20th, January, 2023; henceforth “Rossmanith”).
Regarding claims 1, 12 and 15, Kotula discloses a nucleic acid composition, comprising:
a first promoter operably linked to a first polynucleotide comprising a recombinase
gene (recombinase 1),
wherein the first promoter is capable of inducing transcription of the first
polynucleotide to generate a recombinase transcript upon stimulation (inducible promoter) in a bacterium
and wherein the recombinase transcript is capable of being translated to
generate a recombinase capable of catalyzing a recombination event (flipping of an inverted
heterologous gene encoding a bacterial toxin which is then constitutively expressed after it is
flipped by the first recombinase); and
a second promoter and a second polynucleotide comprising a payload gene (toxin),
wherein, in the absence of the recombination event, the second promoter and the second polynucleotide are not operably linked,
and
wherein the second promoter and the second polynucleotide are operably
linked after the recombination event such that the second promoter is capable of
inducing transcription of the second polynucleotide to generate a payload transcript.
(pg. 4-5, 41; Figure 2; Claim 1).
However, regarding claims 1, 12 and 15, although Kotula teaches inducible, constitutive and/or tissue-specific promoter sequences (para. [010]), Kotula does not teach the TlpA36 promoter.
Nevertheless, regarding claims 1, 12, and 15, Shapiro teaches the TlpA36 promoter as a thermal bioswitch to activate genes in microbes in vivo (para. [0375]) in recombinant bacterial cells to treat a disease or disorder (para. [0005]; Background; Summary). Shapiro teaches control of microbial gene activation with thermal bioswitches could be highly advantageous in applications where the activity of a systemically administered microbial therapy needs to be localized to a specific anatomical site, such as a deep-seated tumor or section of the gastrointestinal tract, which would be difficult to reach with optogenetic triggers (para. [00375-376]). Shapiro specifically teaches TlpA36 is a suitable bioswitch because its activation threshold because its activation threshold is approximately 4 °C above the typical mouse model temperature, which is a sufficient difference for site-specific ultrasound activation (Example 4; para. [0376]).
Therefore, regarding claims 1, 12, and 15 , it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the nucleic acid composition of Kotula and combine the known prior art element of the TlpA36 promoter of Shapiro to obtain the predictable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Shapiro so that the composition could be used to activate genes in microbes in vivo (para. [0375]) in recombinant bacterial cells to treat a disease or disorder (para. [0005]; Background; Summary), which would be advantageous in applications where the activity of a systemically administered microbial therapy needs to be localized to a specific anatomical site, such as a deep-seated tumor or section of the gastrointestinal tract, which would be difficult to reach with optogenetic triggers (para. [00375-376]). Regarding the reasonable expectation of success, Shapiro evidences preparation of nucleic acids that are thermal bioswitches with the TlpA36 promoter (Example 4; para. [0376]).
Regarding the limitation that the payload is “therapeutic,” of claim 1, as discussed above Kotula discloses a toxin as a payload. Kotula specifically discloses the toxins include “bacteriocins, lysins, and other molecules that cause cell death by lysing cell membranes, degrading cellular DNA, or other mechanisms” (para. [07]). Because molecules that cause cell death by lysing cell membranes, degrading cellular DNA, or other mechanisms are known as agents that relate to the treatment of diseases or disorders, the “toxin” of Kotula meets instant claims as a “therapeutic” payload.
However, regarding claims 1, 12 and 15, Kotula is silent to the first polynucleotide comprising a temperature-sensitive terminator comprising a nucleotide sequence of SEQ ID NO: 11.
Nevertheless, regarding claims 1, 12 and 15 , Rossmanith teaches a temperature responsive transcription terminator to regulate transcription in vivo that comprises a nucleotide sequence of SEQ ID NO: 11 (“TTTTTTT” which is a fragment of SEQ ID NO: 11 and is part of a temperature sensitive terminator; see claim interpretation above; ibpA Term-bgaB Title; abstract; pg. 614; Figure 1-2) upstream of the coding sequence (see figure 1). Rossmanith teaches the ibpA Term is the first temperature-controllable transcription terminator able to prematurely terminate transcription of various reporter genes at low temperatures and allowing read-throughout after a heat shock (pg. 617).
Therefore, regarding claims 1, 12 and 15 , it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the composition of Kotula and combine the known prior art element of the temperature specific terminator of Rossmanith upstream of the coding sequence (the recombinase coding sequence of Kotula; instant claim 15) to obtain the predictable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Rossmanith because to regulate transcription in vivo (pg. 614 col. 2 last para.). Regarding the reasonable expectation of success, Shapiro evidences transcription terminators can be included in thermal genetic circuits (Figure 2; para. [0046, 0052, 0054, 0374]; Example 4).
Regarding claims 2-3, further to the discussion of claim 1 above, Shapiro teaches the thermal stimulation for the TlpA promoter comprises heating to an activating temperature, and wherein the activating temperature is above a physiological temperature (4 °C above the typical mouse model temperature; para. [0376]; Example 4, also see mouse models of Kotula) (instant claim 2). 4 °C above the typical mouse model temperature taught by Shapiro is an activating temperature of about 40.0 °C (Shapiro-4 °C above the typical mouse model temperature; para. [0376]; Examples 3-4)(instant claim 3).
Regarding claim 4, it is noted that the wherein clause recites a contingent limitation (i.e. “in the absence of the thermal stimulation, the recombinase reaches steady state protein levels in a probiotic cell insufficient to catalyze the recombination event”). The broadest reasonable interpretation of a system (or apparatus or product) claim having structure that performs a function, which only needs to occur if a condition precedent is met, requires structure for performing the function should the condition occur (see MPEP section 2111.04 (II)). In the instant case, the structure of the nucleic acid composition as suggested by Kotula in view of Shapiro and Rossmanith includes the TlpA promoter of Shapiro, which is not activated in the absence of thermal stimulation (transcript expression after thermal stimulation; abstract; Summary; para. [0010, 0046, 0313, 0322]; Figure 2A and 8f), and it therefore capable of meeting the contingent limitation of “in the absence of the thermal stimulation, the recombinase reaches steady state protein levels in a probiotic cell insufficient to catalyze the recombination event.”
Regarding claim 5, further to the discussion of claim 1 above, Kotula and Rossmanith are silent to a third promoter operably linked to a third polynucleotide encoding a temperature sensitive transcription factor.
Nevertheless, regarding claim 5, Shapiro teaches a promoter(pLacI) operably linked to a polynucleotide encoding a temperature sensitive transcription factor (temperature sensitive repressor/TSR) (Figure 2A, 21-22; para. [0046-49, 0051-52, 0065-66, 0076, 0082, 0089, 0091, 0093, 0145-146, 0148, 0170, 0171, 0244, 0249, 0268, 0289, 0306, 0312-314, 0316, 0322, 0324-330, 0344, 0337; Examples 1-3). Shapiro teaches the temperature sensitive repressor derepresses after the temperature increase (de-repression of a thermally gated promoter; Figure 2; para. [0046]). Shapiro teaches including a copy of the temperature sensitive repressor itself creates a negative feedback loop such that if there is any leaky expression due to the low concentration of repressor protein, it will lead to a buildup in the concentration of that protein and restore repression (para. [0313, 0322]; Figure 2A and 8f). Shapiro teaches for this reason, the temperature the temperature-sensitive repressor is driven by its own operator and a constitutively active (i.e. always on) promoter (pLacI) (para. [0313, 0322]; Figure 2A and 8f).
Therefore, regarding claim 5, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the nucleic acid composition of Kotula in view of Shapiro and Rossmanith, and combine the known prior art element of the temperature sensitive transcription factor (repressor) with its own promoter of Shapiro to obtain the predicable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Shapiro because having a separate segment with a constitutively promoter and the repressor would reduce leaky expression of the temperature sensitive promoter at the non-activating temperature, providing further precision of the thermal genetic circuit. Regarding the reasonable expectation of success, Shapiro evidences preparation of a nucleic acid comprising a promoter(pLacI) operably linked to a polynucleotide encoding a temperature sensitive transcription factor (temperature sensitive repressor/TSR) (Figure 2A, 21-22; para. [0046-49, 0051-52, 0065-66, 0076, 0082, 0089, 0091, 0093, 0145-146, 0148, 0170, 0171, 0244, 0249, 0268, 0289, 0306, 0312-314, 0316, 0322, 0324-330, 0344, 0337; Examples 1-3).
Regarding the wherein clauses of claim 5, Shapiro teaches two of the temperature-sensitive transcription factors are capable of associating to generate a temperature-sensitive transcription factor homodimer in the absence of the thermal stimulation and the two temperature-sensitive transcription factors are incapable of associating to generate a temperature-sensitive transcription factor homodimer in the presence of the thermal stimulation (para. [0010, 0313, 0322]; Figure 2A and 8f).
Regarding claim 6, further to the discussion of claims 1 and 5 above, as stated above (see claim 1 rejection above) Shapiro teaches and makes obvious the first promoter comprises the TlpA operator (Figure 4; para. [0048]). Shapiro teaches a temperature-sensitive transcription factor homodimer is capable of binding the operator (association of the dimer with the TlpA operator; and wherein, upon the temperature-sensitive transcription factor homodimer binding the one or more operators, the first promoter is incapable of inducing transcription of the first polynucleotide(para [0048]; Figure 4).
Regarding claim 7, further to the discussion of claims 1 and 5 above, as stated above, the first promoter in the composition as suggested by Kotula in view of Shapiro and Rossmanith is repressed by a constitutively active repressor that is unbound upon thermal stimulation. Therefore, the first promoter is incapable of inducing transcription of the first polynucleotide in the absence of the thermal stimulation due to the expression of the repressor, and Shapiro teaches the first promoter is capable of inducing transcription of the first polynucleotide in the absence of the temperature-sensitive transcription factor homodimer (transcript expression after thermal stimulation; abstract; Summary; para. [0010, 0046, 0313, 0322]; Figure 2A and 8f).
Regarding claim 8, further to the discussion of claims 1 and 5 above, the temperature sensitive transcription factor homodimerization in the composition as suggested and made obvious by Shapiro above occurs with a dissociation constant that is at least 1.1-fold lower in the presence of a physiological temperature as compared to in the presence of the thermal stimulation (Shapiro-Kds 100 nM in the DNA-bound state(physiological) and 10 uM in the DNA-unbound state (thermal stimulation); para. [0174]).
Regarding claim 9, further to the discussion of claims 1 and 5 above, as stated above (see claim 1 rejection above), Shapiro teaches and makes obvious the temperature sensitive transcription factor homodimerization in the composition comprises a temperature sensitive mutant of TlpA (Example 4-5). Additionally, Shapiro teaches a temperature sensitive mutant of TlpA36 or TlpA39 are options (Example 4-5).
Regarding claim 10, further to the discussion of claim 1 above, Kotula teaches the second polynucleotide is flanked by recombinase target sites, wherein the recombination event comprises an inversion of a sequence flanked by recombinase target sites (para. [0185, 0331, 0332, 0334, 0340, 0350]).
Regarding claim 11, Kotula discloses the recombinase is Cre, and the recombination system is the Cre-lox system (para. [0337-0339]). The Cre-lox system is permanent and therefore meets the claimed limitation of “after the recombination event, the recombinase target sites are modified such that said modified recombinase target sites are not capable of interacting with the recombinase to yield another recombination event, thereby rendering the recombination event permanent.”
Regarding claim 16, further to the discussion of claims 1, and 5-6 above, as stated above, Shapiro teaches the one or more operators is the TlpA operator/promoter ([0048, 0146, 174]; Examples 4-5).
Regarding claim 17, further to the discussion of claim 1 above, as stated above, Shapiro teaches and makes obvious a TlpA operator/promoter (Shapiro para. [0048, 0146, 0170, 0174]; Examples 4-5).
Regarding claim 18, further to the discussion of claim 1 above, although Kotula teaches a payload protein, Kotula is silent to a payload protein of a cytokine of IL-10 or IL-2.
Nevertheless, regarding claim 18, Shapiro teaches a payload protein (“therapeutic protein” or “therapeutic agent”; para. [0005, 0029, 0039, 0042, 0301, 0309, 0311, 0313, 0319-0320, 0324, 0326-0328, 0330, 0336] , wherein the payload protein comprises IL-10 or IL-2 (para. [0301]) to modulate the
immune response (para. [0301]) in in vivo microbial therapy scenarios (para. [0299]).
Therefore, regarding claim 18, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the nucleic acid composition suggested by Kotula in view of Shapiro and Rossmanith and simply substitute the payload protein or IL-10 or IL-2 of Shapiro for the toxin of Kotula to obtain the predictable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Shapiro to modulate the immune response (para. [0301]) in in vivo microbial therapy scenarios (para. [0299]). Regarding the reasonable expectation of success, Kotula evidences preparation of the composition with a payload protein and therefore one of ordinary skill would have had a reasonable expectation of success in preparing the composition with an alternative payload protein.
Hence, the claimed invention as a whole was prima facie obvious
New Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Non-Statutory Double Patenting
U.S. Co-pending Application No. 19235417
Claims 1-12, and 15-18 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 14-15, 19 and 52-64 of copending application No. 19235417 (claims filed 11th, June, 2025) in view of Shapiro et al. (US-20170298425-A1; see IDS filed 20th, January, 2023; henceforth “Shapiro”) and Rossmanith et al. (ACS Synth Biol. 2018 Feb 16;7(2):613-621.; see IDS filed 20th, January, 2023; henceforth “Rossmanith”).
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented
The subject matter claimed in the instant application is disclosed in the referenced application as follows: the nucleic acid composition makes obvious the nucleic acid composition of instant application.
Although the claims at issue are not identical, they are not patentably distinct for the reasons stated below.
Regarding claims 1, 12 and 15, U. S. Co-pending App ‘417 claims a nucleic acid composition, comprising:
a first promoter operably linked to a first polynucleotide comprising a recombinase gene,
wherein the first promoter is capable of inducing transcription of the first polynucleotide to generate a recombinase transcript upon a thermal stimulation, and
wherein the recombinase transcript is capable of being translated to generate a recombinase (recombinases, such as the claimed “Cre” of claim 19 are “capable of catalyzing a recombination event” as claimed),
a second promoter and a second polynucleotide comprising a therapeutic payload gene (a third promoter and a second polynucleotide comprising a payload gene” see claims 52-64 for therapeutic payload genes),
wherein, in the absence of the recombination event, the second promoter and the second polynucleotide are not operably linked,
and
wherein the second promoter and the second polynucleotide are operably linked after the recombination event such that the second promoter is capable of inducing transcription of the second polynucleotide to generate a therapeutic payload transcript (claim 14).
However, regarding claims 1, 12, and 15, U. S. Co-pending App ‘417 does not claim the promoter is a TlpA36 promoter that is capable of inducing transcription of the first polynucleotide to generate a transcript upon a thermal stimulation in a bacterium.
Nevertheless, regarding claims 1, 12, and 15, Shapiro teaches the TlpA36 promoter as a thermal bioswitch to activate genes in microbes in vivo (para. [0375]) in recombinant bacterial cells to treat a disease or disorder (para. [0005]; Background; Summary). Shapiro teaches control of microbial gene activation with thermal bioswitches could be highly advantageous in applications where the activity of a systemically administered microbial therapy needs to be localized to a specific anatomical site, such as a deep-seated tumor or section of the gastrointestinal tract, which would be difficult to reach with optogenetic triggers (para. [00375-376]). Shapiro specifically teaches TlpA36 is a suitable bioswitch because its activation threshold because its activation threshold is approximately 4 °C above the typical mouse model temperature, which is a sufficient difference for site-specific ultrasound activation (Example 4; para. [0376]).
Therefore, regarding claims 1, 12, and 15 , it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the nucleic acid composition as claimed by U. S. Co-pending App ‘417 and combine the known prior art element of the TlpA36 promoter of Shapiro to obtain the predictable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Shapiro so that the composition could be used to activate genes in microbes in vivo (para. [0375]) in recombinant bacterial cells to treat a disease or disorder (para. [0005]; Background; Summary), which would be advantageous in applications where the activity of a systemically administered microbial therapy needs to be localized to a specific anatomical site, such as a deep-seated tumor or section of the gastrointestinal tract, which would be difficult to reach with optogenetic triggers (para. [00375-376]). Regarding the reasonable expectation of success, Shapiro evidences preparation of nucleic acids that are thermal bioswitches with the TlpA36 promoter (Example 4; para. [0376]).
However, regarding claims 1, 12 and 15, U. S. Co-pending App ‘417 does not claim and Shapiro is silent to the first polynucleotide comprising a temperature-sensitive terminator comprising a nucleotide sequence of SEQ ID NO: 11 upstream of the coding sequence.
Nevertheless, regarding claims 1, 12 and 15 , Rossmanith teaches a temperature responsive transcription terminator to regulate transcription in vivo that comprises a nucleotide sequence of SEQ ID NO: 11 (“TTTTTTT” which is a fragment of SEQ ID NO: 11 and is part of a temperature sensitive terminator; see claim interpretation above; ibpA Term-bgaB Title; abstract; pg. 614; Figure 1-2) upstream of the coding sequence (see figure 1). Rossmanith teaches the ibpA Term is the first temperature-controllable transcription terminator able to prematurely terminate transcription of various reporter genes at low temperatures and allowing read-throughout after a heat shock (pg. 617).
Therefore, regarding claims 1, 12 and 15 , it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the composition as claimed by U. S. Co-pending App ‘417 in view of Shapiro, and combine the known prior art element of the temperature specific terminator of Rossmanith upstream of the coding sequence to obtain the predictable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Rossmanith because to regulate transcription in vivo (pg. 614 col. 2 last para.). Regarding the reasonable expectation of success, Shapiro evidences transcription terminators can be included in thermal genetic circuits (Figure 2; para. [0046, 0052, 0054, 0374]; Example 4).
Regarding claims 2-3, further to the discussion of claim 1 above, Shapiro teaches the thermal stimulation for the TlpA promoter comprises heating to an activating temperature, and wherein the activating temperature is above a physiological temperature (4 °C above the typical mouse model temperature; para. [0376]; Example 4) (instant claim 2). 4 °C above the typical mouse model temperature taught by Shapiro is an activating temperature of about 40.0 °C (Shapiro-4 °C above the typical mouse model temperature; para. [0376]; Examples 3-4)(instant claim 3).
Regarding claim 4, it is noted that the wherein clause recites a contingent limitation (i.e. “in the absence of the thermal stimulation, the recombinase reaches steady state protein levels in a probiotic cell insufficient to catalyze the recombination event”). The broadest reasonable interpretation of a system (or apparatus or product) claim having structure that performs a function, which only needs to occur if a condition precedent is met, requires structure for performing the function should the condition occur (see MPEP section 2111.04 (II)). In the instant case, the structure of the nucleic acid composition as claimed by U. S. Co-pending App ‘417 in view of Shapiro and Rossmanith includes the TlpA promoter of Shapiro, which is not activated in the absence of thermal stimulation (transcript expression after thermal stimulation; abstract; Summary; para. [0010, 0046, 0313, 0322]; Figure 2A and 8f), and it therefore capable of meeting the contingent limitation of “in the absence of the thermal stimulation, the recombinase reaches steady state protein levels in a probiotic cell insufficient to catalyze the recombination event.”
Regarding claim 5, further to the discussion of claim 1 above, U. S. Co-pending App ‘417 does not claim and Rossmanith is silent to a third promoter operably linked to a third polynucleotide encoding a temperature sensitive transcription factor.
Nevertheless, regarding claim 5, Shapiro teaches a promoter(pLacI) operably linked to a polynucleotide encoding a temperature sensitive transcription factor (temperature sensitive repressor/TSR) (Figure 2A, 21-22; para. [0046-49, 0051-52, 0065-66, 0076, 0082, 0089, 0091, 0093, 0145-146, 0148, 0170, 0171, 0244, 0249, 0268, 0289, 0306, 0312-314, 0316, 0322, 0324-330, 0344, 0337; Examples 1-3). Shapiro teaches the temperature sensitive repressor derepresses after the temperature increase (de-repression of a thermally gated promoter; Figure 2; para. [0046]). Shapiro teaches including a copy of the temperature sensitive repressor itself creates a negative feedback loop such that if there is any leaky expression due to the low concentration of repressor protein, it will lead to a buildup in the concentration of that protein and restore repression (para. [0313, 0322]; Figure 2A and 8f). Shapiro teaches for this reason, the temperature the temperature-sensitive repressor is driven by its own operator and a constitutively active (i.e. always on) promoter (pLacI) (para. [0313, 0322]; Figure 2A and 8f).
Therefore, regarding claim 5, it would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to prepare the nucleic acid composition as claimed by as claimed by U. S. Co-pending App ‘417 in view of Shapiro and Rossmanith, and combine the known prior art element of the temperature sensitive transcription factor (repressor) with its own promoter of Shapiro to obtain the predicable result of a nucleic acid composition. One of ordinary skill would have been motivated to do so as taught by Shapiro because having a separate segment with a constitutively promoter and the repressor would reduce leaky expression of the temperature sensitive promoter at the non-activating temperature, providing further precision of the thermal genetic circuit. Regarding the reasonable expectation of success, Shapiro evidences preparation of a nucleic acid comprising a promoter(pLacI) operably linked to a polynucleotide encoding a temperature sensitive transcription factor (temperature sensitive repressor/TSR) (Figure 2A, 21-22; para. [0046-49, 0051-52, 0065-66, 0076, 0082, 0089, 0091, 0093, 0145-146, 0148, 0170, 0171, 0244, 0249, 0268, 0289, 0306, 0312-314, 0316, 0322, 0324-330, 0344, 0337; Examples 1-3).
Regarding the wherein clauses of claim 5, Shapiro teaches two of the temperature-sensitive transcription factors are capable of associating to generate a temperature-sensitive transcription factor homodimer in the absence of the thermal stimulation and the two temperature-sensitive transcription factors are incapable of associating to generate a temperature-sensitive transcription factor homodimer in the presence of the thermal stimulation (para. [0010, 0313, 0322]; Figure 2A and 8f).
Regarding claim 6, further to the discussion of claims 1 and 5 above, as stated above (see claim 1 rejection above) Shapiro teaches and makes obvious the first promoter comprises the TlpA operator (Figure 4; para. [0048]). Shapiro teaches a temperature-sensitive transcription factor homodimer is capable of binding the operator (association of the dimer with the TlpA operator; and wherein, upon the temperature-sensitive transcription factor homodimer binding the one or more operators, the first promoter is incapable of inducing transcription of the first polynucleotide(para [0048]; Figure 4).
Regarding claim 7, further to the discussion of claims 1 and 5 above, the first promoter of TlpA taught and made obvious by Shapiro above is capable of inducing transcription of the first polynucleotide in the absence of the temperature-sensitive transcription factor homodimer (transcript expression after thermal stimulation; abstract; Summary; para. [0010, 0046, 0313, 0322]; Figure 2A and 8f).
Regarding claim 8, further to the discussion of claims 1 and 5 above, the temperature sensitive transcription factor homodimerization in the composition as suggested and made obvious by Shapiro above occurs with a dissociation constant that is at least 1.1-fold lower in the presence of a physiological temperature as compared to in the presence of the thermal stimulation (Shapiro-Kds 100 nM in the DNA-bound state(physiological) and 10 uM in the DNA-unbound state (thermal stimulation); para. [0174]).
Regarding claim 9, further to the discussion of claims 1 and 5 above, as stated above (see claim 1 rejection above), Shapiro teaches and makes obvious the temperature sensitive transcription factor homodimerization in the composition comprises a temperature sensitive mutant of TlpA (Example 4-5). Additionally, Shapiro teaches a temperature sensitive mutant of TlpA36 or TlpA39 are options (Example 4-5).
Regarding claim 10, further to the discussion of claim 1 above, U. S. Co-pending App ‘417 claims the second polynucleotide is flanked by recombinase target sites, wherein the recombination event comprises an inversion of a sequence flanked by recombinase target sites (claim 15).
Regarding claim 11, U. S. Co-pending App ‘417 claims the recombinase is Cre (claim 19), and the recombination system is the Cre-lox system (para. [0337-0339]). The Cre-lox system is permanent and therefore meets the claimed limitation of “after the recombination event, the recombinase target sites are modified such that said modified recombinase target sites are not capable of interacting with the recombinase to yield another recombination event, thereby rendering the recombination event permanent.”
Regarding claim 16, further to the discussion of claims 1, and 5-6 above, as stated above, Shapiro teaches the one or more operators is the TlpA operator/promoter ([0048, 0146, 174]; Examples 4-5).
Regarding claim 17, further to the discussion of claim 1 above, as stated above, Shapiro teaches and makes obvious a TlpA operator/promoter (Shapiro para. [0048, 0146, 0170, 0174]; Examples 4-5).
Regarding claim 18, further to the discussion of claim 1 above, U. S. Co-pending App ‘417 claims the therapeutic payload transcript is capable of being translated to generate a therapeutic payload protein and therapeutic payload protein comprises a cytokine selected from the group consisting of interleukin-I (IL-1), IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, IL-8, IL-9, IL-10, IL-11, IL-12, IL-13, IL-14, IL-15, IL-16, IL-17, IL-18, IL-19, IL-20, IL-21, IL-22, IL-23, IL-24, IL-25, IL-26, IL-27, IL-28, IL-29, IL-30, IL-31, IL-32, IL-33, IL-34, IL-35, granulocyte macrophage colony stimulating factor (GM-CSF), M-CSF, SCF, TSLP, oncostatin M, leukemia-inhibitory factor (LIF), CNTF, Cardiotropin-1, NNT-l/BSF-3, growth hormone, Prolactin, Erythropoietin, Thrombopoietin, Leptin, and G-CSF;
a member of the TGF-β/BMP family selected from the group consisting of TGF β l, TGF- β 2, TGF- β 3, BMP-2, BMP-3a, BMP-3b, BMP-4, BMP-5, BMP-6, BMP-7, BMP-8a, BMP-8b, BMP-9, BMP-10, BMP-11, BMP-15, BMP-16, endometrial bleeding associated factor (EBAF), growth differentiation factor-I (GDF-I), GDF-2, GDF-3, GDF-5, GDF-6, GDF-7, GDF-8, GDF-9, GDF-12, GDF-14, mullerian inhibiting substance (MIS), activin-1, activin-2, activin-3, activin-4, and activin-5;
a member of the TNF family of cytokines selected from the group consisting of TNF-alpha, TNF-beta, LT-beta, CD40 ligand, Fas ligand, CD 27 ligand, CD 30 ligand, and 4-1 BBL;
a chemokine, optionally the chemokine is selected from CCLI, CCL2, CCL3, CCR4, CCL5, CCL7, CCL8/MCP-2, CCLll, CCL13/MCP-4, HCC- l/CCL14, CTAC/CCL17, CCL19, CCL22, CCL23, CCL24, CCL26, CCL27, VEGF, PDGF, lymphotactin (XCLI), Eotaxin, FGF, EGF, IP- 10, TRAIL, GCP-2/CXCL6, NAP-2/CXCL7, CXCL8, CXCLI0, ITAC/CXCLll, CXCL12, CXCL13, or CXCL15;
a interleukin, optionally the interleukin is selected from IL- 10, IL-12, IL-I, IL-6,IL-7, IL-15, IL-2, IL-18 or IL-21; or
a tumor necrosis factor (TNF) selected from the group comprising TNF-alpha, TNF-beta, TNF-gamma, CD252, CD154, CDI 78, CD70, CD153, and 4-IBBL (claim 53);
Since the instant application claims are anticipated by or obvious over cited application claims, in view of Shapiro and Rossmanith, said claims are not patentably distinct.
Conclusion
No claim is allowable.
Correspondence
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/BRIANA N EBBINGHAUS/Examiner, Art Unit 1632
/PETER PARAS JR/Supervisory Patent Examiner, Art Unit 1632