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 .
Election/Restrictions
Applicant’s election without traverse to Group I, encompassed in claims 89-90 and 92-96, in the reply filed 13 Feb 2026 is acknowledged.
Applicant’s species election without traverse to a nuclease, recited in claims 93, 108, and 122, in the reply filed 13 Feb 2026 is acknowledged.
Claims 95-98, 100, 108-111, 119-120, and 122-125 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions or species, there being no allowable generic or linking claims. Election was made without traverse in the replied filed 13 Feb 2026.
Claims 1-88, 91, 99, 101-107, 112-118, and 121 are canceled.
Claims 89-90 and 92-94 are pending and under consideration.
Drawings
The drawings are objected to because Fig. 4 is a duplicate of Fig. 3 and Fig. 5 is a duplicate of Fig. 1. Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - 35 USC § 112(a)
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 89-90 and 92-94 are rejected under 35 U.S.C. § 112(a) as failing to comply with the enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Enablement is considered in view of the Wands factors (MPEP 2164.01(a)). The court in Wands states, “Enablement is not precluded by the necessity for some experimentation such as routine screening. However, experimentation needed to practice the invention must not be undue experimentation. The key word ‘undue’, not ‘experimentation.’” (Wands, 8 USPQ2d 1404). Clearly, enablement of a claimed invention cannot be predicated on the basis of quantity of experimentation required to make or use the invention. "Whether undue experimentation is needed is not a single, simple factual determination, but rather is a conclusion reached by weighing many factual considerations." (Wands, 8 USPQ2d 1404). When determining whether a specification meets the enablement requirement, some of the factors to be analyzed are: (1) the breadth of the claims, (2) the nature of the invention, (3) the state of the prior art, (4) the level of one of ordinary skill in the art, (5) the level of predictability in the art, (6) the amount of direction provided by the inventor, (7) the existence of working examples, and (8) whether the quantity of any necessary experimentation to make and use the invention based on the content of the disclosure is undue (Wands). While all of these factors are considered, those sufficient for establishing a prima facie case are discussed below.
Nature of the invention
The claimed invention relates to a method of synthetic lethality to generate single sex progeny for uses in which a single sex is required or highly desired, such as in agriculture for dairy, egg, and meat production or in research for sex-specific physiology and disease. The claimed invention involves generating transgenic parents carrying nucleotide sequences encoding toxin fragments inherited in a sex-specific manner. Progeny of the transgenic parents are viable if they inherit a single toxin fragment but are not viable if they inherit both toxin fragments.
Breadth of the claims
Issue 1: The breadth of the claims with respect to “the non-human vertebrate animal” encompasses tens of thousands of vertebrate species and multiple sex-determining mechanisms, which include the XX/XY and the ZZ/ZW chromosome systems, temperature sensitivity, hormone sensitivity, epigenetic factors, and other environmental factors (B. Capel, Nat Rev Genetics, 2017, pp. 676-685, hereafter Capel). Most, but not all, mammals use the XX/XY chromosome system, in which XX individuals are female and XY individuals are male (Capel, pp. 676-677). Birds and snakes use the ZZ/ZW chromosome system, in which ZZ individuals are male and ZW individuals are female (Capel, p. 677). Other vertebrates, including fish, amphibians, turtles, and some lizards use the XX/XY or the ZZ/ZW system, but sex in those animals is additionally modified by, and can be overridden by, environmental factors, such as temperature (Capel, pp. 679-682). Other vertebrates, including crocodilians and the genus of lizards Tuatara, do not use chromosomal inheritance for sex determination (Capel, Fig. 2a).
Issue 2: The claims do not specify that the first and second non-human vertebrate are from the same species. While interspecific crosses can produce viable progeny, many hybridizations are known to be lethal, even for closely related species (S. Maheshwari and D.A. Barbash, Ann Rev Genet, 2011, Introduction, hereafter Maheshwari). Furthermore, the factors that cause interspecies crosses to be nonviable are highly pleiotropic and not fully understood (Maheshwari, p. 349).
Issue 3: The breadth of the claims with respect to the first and second toxin fragments encompasses any toxin, which represents a vast array of structurally and mechanistically diverse compounds. No sequence, structural component, or locus is recited for the first and second toxin fragments. The claims do not specify the relation between the first and second toxin fragments. The two toxin fragments may be identical, fragments of different portions of the same toxin, or from different toxins entirely. Furthermore, the nuclease recited in claim 93 and the Barnase, RNase, and restriction endonuclease recited in claim 94 are broad in these nucleases encompass toxic, but non-lethal nucleases.
Existence of working examples
The specification provides Example 1 and Example 2 as prophetic examples (pp. 32-33). However, both Example 1 and Example 2 are drawn to non-elected inventions. No working example, prophetic or otherwise, is provided for the elected invention. No indication is given that any part of the claimed invention has been attempted.
Amount of direction provided by the inventor
The specification only discloses a generic approach to producing a single sex population of non-human vertebrates via first and second toxin fragments. The specification does not provide direction related to the missing elements noted above discussed under Breadth of the claims.
Issue 4: The claims do not include active steps or structural elements to suggest how the first and second toxin fragments result in a non-viable progeny. No steps or structural elements are recited in the claims that suggest how inheriting both toxin fragments leads to lethal toxicity in a manner that differs from having a single toxin fragment. The only direction given for how two non-lethal toxin fragments might give rise to lethal toxicity relate to a non-elected invention. Presumably, the first and second toxin fragments are not toxic when expressed in isolation, otherwise the parents would not be viable, nor would progeny that inherit a single toxin fragment. No other direction is provided as to how two non-lethal toxin fragments suddenly given rise to lethal toxicity given that there is no recited promoter for the nucleotide sequence to express an RNA or protein and no recited mechanism by which the two toxin fragments interact, effect cells in tandem, or some other mode of action. Additionally, for a toxin to lead to lethality, there must be sufficient dosing in the correct context to produce nonviable progeny. No direction is provided for the timing, gene dosage, or expression pattern required to achieve lethal toxicity.
State of the prior art
As of the earliest effective filing date of the immediate application, 16 Sep 2022, the art teaches genetic methods for synthetic lethality to generate single sex progeny (C. Douglas and J.M.A. Turner, PLOS Genet, 2020, cited in IDS, hereafter Douglas 2020). The most relevant of such methods involve splitting the genetic components required for synthetic lethality onto chromosomes separately inherited from both parents (Douglas 2020, Fig. 1c and pp. 4-12). However, such methods are based on knocking out or mutating genes required for development rather than expressing a toxin (Douglas 2020, pp. 4,6 and Fig.1). Methods of expressing a transgene to generate a toxin has been limited to use in insects (Douglas 2020, pp. 4,6 and Fig. 1). The art does not teach splitting induced toxins into fragments. Therefore, a skilled artisan attempting to make or use the claimed invention would have to translate methods practiced in insects to a vast number of vertebrate species without direction from the art or from the inventor. Particularly, the art does not teach how two separate, non-lethal toxin fragments can become lethal just because the nucleic acids encoding two toxin fragments are found within the same animal.
Unpredictability in the prior art
The art teaches challenges in practicing the invention as claimed. To achieve single sex offspring when practicing the claimed invention, at least one of the toxin fragments must be on a sex chromosome; an embodiment in which both the first and second toxin fragments are both on autosomes cannot produce a single sex population of progeny because the first and second toxin fragments would be passed on at approximately equal distribution to male and female progeny. Douglas 2021 (C. Douglas, et al., Nat Commun, 2021) teaches two major hurdles when practicing the claimed invention in mammals. First, “transgenes on the X chromosome are susceptible to silencing”. (Douglas 2021, p. 2). Second, transgenes “on the Y chromosome are repressed by its heterochromatic state” (Douglas 2021, p. 2).
With respect to Issue 1, for the method to only generate a single sex population, or even to skew the population of progeny toward a single sex, inheritance of the first and second toxin fragments must occur in a sex-specific manner. The current art does not contemplate heritable methods for producing single sex progeny without at least one on a sex chromosome (Douglas 2020 p. 2). A skilled artisan would expect that the method could not generate single sex progeny in species in which factors determining sex are not inherited or in which the action of sex chromosomes can be overridden by environmental factors (Capel Fig. 2).
With respect to Issue 2, given that there are tens of thousands of non-human vertebrate species, the claims encompass an incomprehensibly vast number of non-enabled embodiments of crosses between species that cannot produce viable progeny. The art does not contemplate crosses between highly unrelated vertebrate species, which a skilled artisan could reasonably predict to be non-enabled. However, crosses between closely related species can be viable, but predictability of viable progeny from interspecies crosses is complex and poorly understood (Maheshwari, p. 333). The presence of inoperative embodiments within the scope of a claim does not necessarily render a claim non-enabled. However, the standard is whether a skilled person could determine which embodiments that were conceived, but not yet made, would be inoperative or operative with expenditure of no more effort than is normally required in the art. Atlas Powder Co. v. E.I. du Pont de Nemours & Co., 750 F.2d 1569, 1577, 224 USPQ 409, 414 (Fed. Cir. 1984). Claims reading on significant numbers of inoperative embodiments render claims non-enabled when the specification does not clearly identify the operative embodiments and undue experimentation is involved in determining those that are operative. Atlas Powder Co. v. E.I. duPont de Nemours & Co., 750 F.2d 1569, 1577, 224 USPQ 409, 414 (Fed. Cir. 1984); In re Cook, 439 F.2d 730, 735, 169 USPQ 298, 302 (CCPA 1971). See MPEP 2164.08(b).
With respect to Issue 3, an example of a toxic nuclease encompassed by the breadth of the claims is zinc finger nucleases, which are artificial restriction endonucleases used for gene editing. Zinc finger nucleases have known genotoxicity due to cleavage at off-target sites in the genome (T.I. Cornu, Methods Mol Biol, 2010, p. 237, hereafter Cornu). However, even given this toxicity, zinc finger nucleases can be introduced to and expressed in cells without lethality (Cornu, p. 237). A toxin is not necessarily lethal, and toxins capable of inducing lethality are not lethal in all circumstances.
With respect to Issue 4, the claims do not include active steps or structural elements to suggest that the toxin fragments are expressed, or if so, under what conditions. For example, the toxin fragments may be under control of a promoter that limits expression to gonadal cells, which would only lead to lethality in cells not required for viability of the animal. Lethality of a toxin is determined by dosage, localization to cells and tissues required for survival, and insufficiency in homeostatic mechanisms to neutralize or excrete the toxin. Particularly for the present invention, lethality of the toxin(s) must also be limited in timing such that lethality is induced in early development before birth/hatching. When the claimed invention is practiced in vertebrates that gestate the fetus to term, such as mammals, the dosing and timing of lethal toxicity must also be limited so as to not kill littermates or the pregnant mother, which would render the claimed invention inoperable (Douglas 2020 p. 11 and Douglas 2021 p. 2). Achieving these limits on feasibility is further complicated by the requirement to achieve toxic lethality using two toxin fragments acting in concert, which is not taught in the art. This is particularly challenging because which it is unclear from the claims and the specification how the two toxin fragments interact with each other, if at all.
Quantity of experimentation required
As discussed above, the claims are broad with respect to species of both the first and second non-human vertebrate animal, the system of sex determination in the chosen species, the identity and relationship between the first and second toxin fragments, the mechanism by which the first and second toxin fragments induce lethality, and whether or how the toxin fragments are expressed and in what conditions. Furthermore, methods of synthetic lethality based on expression of a toxin has not been applied to vertebrates, much less methods based on toxin fragments. To make and use the claimed invention, a skilled artisan would have to test an incalculable number of combinations of embodiments, overcome barriers in multiple scientific fields, and translate findings from insects to vertebrate.
Conclusions
One of ordinary skill in the ordinary would be unable to make and use the claimed invention. There is no connection between the inheritance of the first and second toxin fragment and induced lethality. Furthermore, the claims are extremely broad and encompass a vast number of non-enabled embodiments, and the art teaches barriers to genetic methods of synthetic lethality. The specification fails provide direction or working examples of the claimed invention. Given the breadth of the claims and the lack of direction from the inventor and from the art, a skilled artisan would be faced with the burden of undue experimentation when attempting to make and use the claimed invention.
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.
Claim 90 is rejected under 35 U.S.C. § 112(d) 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. A chromosome is, by definition, always an allosome or an autosome, as noted in the specification (par 34). Therefore, elaboration, “the chromosome is an autosome or an allosome”, does not add limitations to claim 90 that are not already present in claim 89, from which claim 90 depends. Applicant may cancel the claim, amend the claim to place it in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Conclusion
No claim is allowed.
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/Eric B Wright/Examiner, Art Unit 1632
/PETER PARAS JR/Supervisory Patent Examiner, Art Unit 1632