DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
This action is in response to an amendment field 2/17/2026.
Claims 1, 3-5, 8, 9, 11 and 15-27 are pending. Claims 11, 15, 16, 18, 19, 26 and 27 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected subject matter, there being no allowable generic or linking claim. Rejoinder as requested is dependent on allowance of the product claims. The claims are not currently allowable.
This application claims priority under 35 U.S.C. 371 to PCT/PT2019/050035 filed 10/9/2019 which claims priority to Portuguese Patent Application No. 115073, filed on 10/9/2018.
Response to Amendment
Applicants amendment distinguishes the subject matter of claim 1 from that of claim 5 and 8 wherein claim 1 recites a nucleic acid consisting of SEQ ID NO:1 having restriction sequences at one or both end or consisting of a tandem repeat of SEQ ID NO:1. Claims 5 and 8 no longer depend from claim 1 but recite that constructs and cells comprise a nucleic acid sequence of SEQ ID NO:1. From this amendment and argument, it is to be understood that claim 1 is limited to this construct or one consisting of tandem repeats of SEQ ID NO:1 and claims 5 and 8 allow for additional sequence with this construct. It is noted that by amendment, these two claims recite that the sequence is a nucleic acid sequence of SEQ ID NO:1. This means it can be a portion thereof. It is believed that the intent is the entirety of SEQ ID NO:1 and hence, the objection below is meant to provide that distinction. However, the claims can be considered in their broadest reading (any sequence of SEQ ID NO:1). The amendments to separate the claims has led to a new consideration of the art necessitated by amendment.
The amendments are sufficient to overcome the rejection under 35 USC 112, fourth and first.
Claim Objections
Claim 1, 3, 5 and 8 are objected to because of the following informalities: claim 1 requires the term “isolated” prior to the second nucleic acid in line 3. This will provide the consistency to reflect applicants intent.
Claim 3, upon reconsideration, should amend “the isolated” in line 2 to “an isolated”. This provides consistency with the formatting of the other claims as well as in part
Claims 5 and 8 require the term “of the oligonucleotide sequence of” prior to SEQ ID NO:1. A SEQ ID NO: is a place holder but does not convey the full breadth of reciting whether the sequence is a nucleic acid sequence or the nucleic acid sequence of SEQ ID NO:1.
These are new objections. Appropriate correction is required.
Claim Rejections - 35 USC § 112, first paragraph
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.
Claims 3, 4 and 17 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 3 newly recites that the composition for increasing expressino0 f a protein of interest comprises an “isolated nucleic acid sequence consisting of the oligonucleotide sequence of SEQ ID NO: 1, or consisting of tandem repeats of the oligonucleotide sequence of SEQ ID NO: 1, or an isolated nucleic acid sequence consisting of the oligonucleotide sequence of SEQ ID NO: 1 having restriction enzyme recognition sequences upstream, downstream or at both ends of the oligonucleotide sequence of SEQ ID NO: 1; (ii) a buffer; and (iii) a divalent ion chelating agent”.
Applicants assert that claim 3 requires that the nucleic acid is isolated, that it is not part of a longer sequence. This is contrary to the description in the disclosure. The sequence in the disclosure is called iPLUS. This sequence only functions in cis and hence are part of a larger sequence. There is no demonstration in the disclosure that the sequence functions as a stand alone in trans.
[0046] In another embodiment of the invention, the iPLUS is subcloned downstream of GFP and the resultant construct (pucl9 miniTOL-GFP-iPLUS, FIG. 1A) is microinjected into zebrafish one cell stage embryos. A control construct is also made where the iPLUS sequence is mutated (pucl9 miniTOL-GFP-iPLUSmt). Notably, GFP protein production is increased in zebrafish embryos microinjected with the iPLUS in comparison to the iPLUS mutant control, visualized by fluorescence microscopy (FIG. 1B). Quantification of protein level clearly shows that the iPLUS enhances GFP production in contrast to control (FIG. 1C). Zebrafish where GFP-iPLUS and GFP-iPLUS mutant were randomly inserted into the genome confirm that the iPLUS acts as an activator for protein production (FIG. 1D).
[0047] In another embodiment of the invention, the iPLUS sequence (SEQ ID NO: 1) is sub-cloned downstream of the luciferase gene and the resultant construct (pLucDelSV40.iPLUS) is transfected into HeLa cells. A control construct was also designed where the iPLUS was mutated (pLucDelSV40.iPLUSmutant). Levels of Luciferase protein activity were quantified and results show that there is an eight-fold increase in cells transfected with the iPLUS in comparison to control (FIG. 2).
[0048] Thus, in the preferred embodiment of the present invention comprises the expression vectors in which iPLUS (SEQ ID NO: 1) is inserted downstream of the encoded gene of interest (LUC or GFP in the former case).
To this end, the MPEP provides such guidance (emphasis added). If the application as filed does not disclose the complete structure (or acts of a process) of the claimed invention as a whole, determine whether the specification discloses other relevant identifying characteristics sufficient to describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize applicant was in possession of the claimed invention. For example, if the art has established a strong correlation between structure and function, one skilled in the art would be able to predict with a reasonable degree of confidence the structure of the claimed invention from a recitation of its function. Thus, the written description requirement may be satisfied through disclosure of function and minimal structure when there is a well-established correlation between structure and function. In contrast, without such a correlation, the capability to recognize or understand the structure from the mere recitation of function and minimal structure is highly unlikely. In this latter case, disclosure of function alone is little more than a wish for possession; it does not satisfy the written description requirement. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (written description requirement not satisfied by merely providing "a result that one might achieve if one made that invention"); In re Wilder, 736 F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming a rejection for lack of written description because the specification does "little more than outline goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate"). Compare Fonar, 107 F.3d at 1549, 41 USPQ2d at 1805 (disclosure of software function adequate in that art).
In this case, the disclosure does not provide for an isolated sequence that can mediate an increase in expression of a protein of interest. Rather, it is a sequence that is inserted into a vector that mediates the increase in expression of the protein. Hence, while the art has been overcome by indication that the sequence is isolated, it is not clear that the art as cited differed from that of the intent of the sequence as set forth in the disclosure. The subject matter of claim 5 and 8 reflect this scope.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 5, 8, 9, 17 and 20-25 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pinto, 2008, Dissertation, pages 1-174. This rejection is reworded based upon applicants amendment.
As to claim 5, the claim is (as amended) drawn to an expression vector comprising a nucleic acid sequence of SEQ ID NO:1. It no longer depends from claim 5 and hence the ambiguities of its placement in a larger sequence is overcome, it is in a larger sequence and the expression vector comprises the sequence. To this end, Pinto teaches at least three genetic construct that is express sequences and comprises USE 1. Applicants seem to argue that the constructs are not expression vectors. However, two of those mentioned explicitly indicate they are expression vectors and the first shown below even though it is used to make transgenes, it is a vector that expresses.
This vector was used to transform flies,
This transgene was constructed using a 7 kb genomic fragment that contains the
polo gene and its promoter and was shown to be sufficient for complementation of polo1 and polo2 mutant alleles (Llamazares et al., 1991). By PCR mutagenesis, a GFP coding sequence was fused with the polo initiation codon. This fragment was then subcloned into a pW8 plasmid and the resulting construct used for P-element-mediated germ line transformation (Fig. 9B).
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The second was used in HeLa and expresses polo as recited in claim 21 and the second in Drosophila.
In order to conduct a study of each USE, we proceeded to study these elements in
vivo. To this end, mini-genes were constructed in which each USE was deleted. These
mini-genes were used to transfect HeLa cells and the produced mRNAs analysed by S1
nuclease..
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Using the Drosophila expression vector pAc5.1-V5/His A, a wild-type mini-gene
was constructed under the actin promoter (Fig. 41A).
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The number 1 in both of the above is USE 1. The construct is modified to comprise mutations in each of 1, 2 and 3 independently. It is shown that the USE 2 mt which comprises a nucleic acid sequence of SEQ ID NO:1 leads to increased mRNA expression. This is demonstrated by S1 nuclease analysis which demonstrates the level of mRNA which inherently will be translated and demonstrates sources of increased protein (see Figure 41). The results, “supports a role for USE 1 in the synthesis of the longer polo mRNA in abdominal histoblast, most likely through down-regulation of the proximal poly(A) site.” Page 91, first sentence.
As to claim 8 and 9 which recite a cell for increased protein expression, the requirement is now that the cell comprise a nucleic acid sequence of SEQ ID NO:1. Pinto teaches a number of cells comprising a nucleic acid sequence of SEQ ID NO:1 as well as the entirety and these are discussed above.
As to claims 20 and 22-25, this is only a sufficient limitation if the host cell is limited to one of the cell types as claim 8 provides options as host cells. Hence, the claim does not recite wherein the cell is a mammalian host cell and the mammalian host cell is. Rather, the claims are all drawn to potential types of host cells. Hence, the disclosure of HeLa and drosophila provide coverage for all the claims.
Response to Arguments
Applicants argue with regard to claim 5, that Pinto does not disclose an expression vector comprising SEQ ID NO:1. However, the previous construct does constitute a recombinant eukaryotic plasmid vector.
This transgene was constructed using a 7 kb genomic fragment that contains the
polo gene and its promoter and was shown to be sufficient for complementation of polo1
and polo2 mutant alleles (Llamazares et al., 1991). By PCR mutagenesis, a GFP coding
sequence was fused with the polo initiation codon. This fragment was then subcloned into
a pW8 plasmid and the resulting construct used for P-element-mediated germ line
transformation (Fig. 9B).
By inclusion of the promoter from polo, the vector expresses polo and is therefore regardless of location an expression vector. There is no explicit definition that does not allow cloning plasmids to be modified into expression plasmid vectors. An expression plasmid vector is one that comprises a promoter and allows for expression of sequences. The figure demonstrates that all of these components are met.
Applicants argue that Pinto does not teach GFP or polo transgenes with a nucleic acid sequence of SEQ ID NO:1 downstream. The above description in the rejection demonstrates that in fact Pinto does even aside from the semantics of whether the GFP-polo construct ius a plasmid expression vector or not. It is noted that contrary to applicants arguments the claim does not recite “the nucleic acid sequence of claim 1 introduced downstream of the gfp protein”. However, if it did, it is not clear how the three diagrams do not reflect this. A polyA tail in some cases with USE 1 is introduced downstream of any of polo and GFP-polo.
As to increased protein expression, it is clear that introducing a nucleic acid sequence of SEQ ID NO:1 and deleting USE 2 leads to increased expression. IN fact page 107 indicates that the effect is higher stability (experimental evid3ence stars on page 85). Increased stability leads to improved expression. Every indication from the Pinto thesis is that prior to the instant invention, USE 1 which is the nucleic acid sequence of SEQ ID NO:1 was know and isolated. The sequence was assayed as to function and found to mediate mRNA stability and expression of alternative polo mRNA. The results as a whole indicate that USE 1 is critical for mRNA expression and mediates regulation thus of heterologous sequences.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 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.
Claim 1 is rejected under 35 U.S.C. 103 as being unpatentable over Pinto, 2008, Dissertation, pages 1-174 in view of Zimmerman et al ( Benchmarks, 1998, pages 582-4). This is a new rejection necessitated by amendment.
As recited in claim 1, Pinto teaches a nucleic acid sequence that is SEQ ID NO:1, it is USE 1. USE 1 consists of SEQ ID NO:1. As shown on page 60.
Aatttatttgtttttgccccttcccctt
Applicants argue that it is not isolated. However, the sequence is shown as a PCR product in Table AII, page 133, last entry, col 1. Hence, the sequence has been PCR amplified and as such is isolated (see heading of column associated with the fragment, it states “isolated fragment size”).
It is distinct from the claimed sequence by lacking restriction sites at one or both ends. The art teaches that restriction sites are added to PCR products so that they can be cloned into other sequences. This process leads to the oligo and the RXN site as well as an Xnt (extra nucleotides) this is removed leaving the oligo and restriction site in the end as displayed in figure 1. Hence, this will lead to the restriction sites flanking the oligo that matches SEQ ID NO:1.
Based on such teachings, it would have prima facie been obvious to one of ordinary skill in the art at the time the invention was made that the sequence as intended and as shown in the insertion and use methods of Pinto to be the sequence of USE 1 as dictated by Pinto (see e.g. page 60, top line that demonstrates that USE 1 has the sequence (consists of the sequence) of SEQ ID NO:1. In order to incorporate sequences such as USE 1, one would add restriction sites. Hence, the combination of references lead to the invention claimed in claim 1. To add restriction sites would lead to the invention of claim 1. Thus, a person of ordinary skill in the art, absent evidence to the contrary, would have reasonably expected that he use of restriction sites would allow cloning using the engineered PCR product.
USE 1 consisting of SEQ ID NO:1 of claim 3 is used in in vitro transcription reactions. This is shown to use EDTA and buffer which can absent evidence to the contrary can be kit (see page 121). Subsequently protein levels were measured (figure 22) and shows that the presence of USE 1 increases protein levels (asterisk are protein levels that changed).
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Conclusion
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARIA MARVICH whose telephone number is (571)272-0774. The examiner can normally be reached 8 am - 5 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Maria Leavitt can be reached on 571-272-1085. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/MARIA MARVICH/ Primary Examiner, Art Unit 1631
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