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 1-20 are examined on the merits.
Claim Rejections - 35 USC § 112
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 19 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 19 is rejected as indefinite for the recitation “The method of claim 18….culturing the transformed organogenic callus or the modified organogenic callus”, but in claim 18 provides antecedent basis only for “modified organogenic callus”. It is unclear what “transformed organogenic callus” refers to in claim 19 and/or whether claim 19 improperly introduces an alternative limitation outside the scope of the claim from which it depends.
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.
Claims 1, 2, 4-8, 11-13 and 20 are rejected under 35 U.S.C. §103 as being unpatentable over Feeney (Mistianne Feeney et. al., Plant Cell Tiss Organ Cult (2007) 90:201–214) in view of Matt (Andrea Matt et. al., Plant Cell Rep (2005) 24: 468–476) and Shestibratov (Konstantin Aleksandrovich Shestibratov et.al., US20070124835A1 , Application 2003-10-15, Publication of 2007-05-31).
Claim 1 is drawn to a method of producing an organogenic callus, the method comprising: wounding a plant or plant part comprising stem tissue including a node to provide a wounded tissue; and culturing the wounded tissue on media comprising thidiazuron (TDZ) at a concentration of at least about 5 mg/L of the media, thereby producing the organogenic callus.
Feeney teaches using Prunus avium explants derived from shoot/stem tissues: “Leaves and petioles were removed from shoots with a scalpel. Shoots were then divided into three explant types: apical tips, stems, and shoot bases. Explants of each type were collected and pooled”(page 203, In-vitro explants), which inherently include stem tissue and node, and are handled as explants (cut sections= wounded tissue) for in vitro culture and regeneration callus responses. Feeney further teaches “explants forming organogenic callus was recorded after 3 months” (page 203, In-vitro explants).
Feeney does not teach culturing the wounded tissue on media comprising thidiazuron (TDZ) at a concentration of at least about 5 mg/L of the media.
Matt teaches TDZ-containing media as a cytokinin-like growth regulator used to induce organogenic response/shoot regeneration from explants (page 469, paragraph 3), supporting TDZ use for organogenic callus/shoot induction in Prunus avium.
Shestibratov teaches culture on media including TDZ and explicitly teaches TDZ concentration ranges that include ≥5 mg/L (e.g., TDZ 1-10 mg/L and 5 mg/L) (page 6, line 39-46). Shestibratov further teaches that morphogenic tissues/callus/regenerants form predominantly at wounding sites (page 16, line 1-5), consistent with “ wounding…..then culturing”.
Claim 2 is drawn to the method of claim 1, wherein the stem tissue comprises meristem tissue.
Feeney teaches use of shoot tips/shoot base (apical/lateral shoot tissues) as explants (page 203, In-vitro explants), these explants are understood to include meristematic regions or meristem-adjacent tissue (i.e., meristem tissue present within the stem/shoot explant context).
Claim 4 is drawn to the method of any preceding claim 1, wherein the media comprises TDZ in an amount of about 5 mg/L to about 15 mg/L of the media.
Because Matt establishes TDZ use in Prunus avium, and Shestibratov shows TDZ routinely used at 1-10 mg/L across other plants, a POSITA would have reasonably explored concentrations beyond a single working point (including 15 mg/L) through routine experimentation to optimize regeneration outcomes.
Claim 5 is drawn to the method of claim 1, wherein the media further comprises a sugar.
Feeney teaches plant tissue culture on basal media (MS) formulations that include a carbohydrate source (commonly sucrose/glucose) as a routine component for explant survival and morphogenesis (page 203, in-vitro explants).
Claim 6 is drawn to the method of claim 1, wherein culturing the wounded tissue comprises culturing the wounded tissue in the dark at a temperature of about 20°C to about 30°C.
Matt teaches “The Petri dishes were kept in a growth chamber at 24±2 ◦C either in complete darkness or in a 16h:8h light: dark photoperiod …. were evaluated”.
Claim 7 is drawn to the method of claim 1, wherein culturing the wounded tissue comprises culturing the wounded tissue on the media for about 4 weeks to about 15 weeks.
Feeney teaches “Explants were subcultured at 4-week intervals. The number of explants forming organogenic callus was recorded after 3 months.”(page 205, last paragraph).
Claim 8 is drawn to the method of claim 1, wherein the plant or plant part is or is from a plant that is an out-crossing species.
Instant application recites “For example, the out-crossing species sweet cherry (Prunus avium) is often referred to…” (paragraph 0003).
Feeney teaches shoot regeneration from organogenic callus of sweet cherry (Prunus avium); and Matt teaches In vitro plant regeneration from leaves and internode sections of sweet cherry cultivars (Prunus avium L.).
Claim 11 is drawn to the method of claim 1, further comprising forming a plurality of organogenic calluses from a plurality of wounded tissues.
Feeney teaches processing multiple wounded explants on regeneration medium and obtaining callus and shoot regeneration responses from the explants (page 201, abstract), which inherently results in the formation of a plurality of organogenic calluses from a plurality of wounded tissues.
Claim 12 is drawn to the method of claim 11, wherein an organogenic callus is formed on at least about 80% of the plurality of wounded tissues.
Feeney teaches “Shoot regeneration on callus explants was almost 100% after 2 weeks on W3B medium. By 4 weeks, all explants had formed shoots in both trials, with 7 - 17 shoots forming per callus explant (Fig. 2d)” (page209, paragraph 3).
Claim 13 is drawn to the method of claim 1, further comprising exposing the wounded tissue to an antibiotic.
Shestibratov explicitly teaches antibiotic use during culture/selection/ regeneration (e. g., cefotaxime and kanamycin used on media; antibiotic exposure is part of the protocol) (paragraph 0125).
Claim 20 is draw to the method of claim 1,wherein the plant is or the plant part is from Prunus avium.
A person of ordinary skill in the art would have been motivated to modify the Prunus avium explant culture system of Feeney by employing the TDZ-containing regeneration media taught by Matt and the TDZ concentration ranges expressly disclosed in Shestibratov, with a reasonable expectation of success.
A POSITA, seeking to improve or reliably induce organogenic callus formation from Prunus avium stem/shoot explants as taught by Feeney, would have been motivated to employ a TDZ-based culture regime at concentrations known in the art to promote organogenesis, including concentrations as or above about 5 mg/L as expressly taught by Shestibratov. Adjustment of TDZ concentration within known workable ranges would have been a routine optimization of a result-effective viable to achieve robust callus induction and regeneration.
Because Feeney and Matt provides the species (Prunus avium) and competent stem/short explants, Matt teaches TDZ-driven organogenic induction from stem tissues, Shestibratov provides explicit mg/L TDZ concentration ranges and confirms callus formation at wound sites.
The combination merely applies a known growth regulator system at known effective concentrations to a known explant system in the same technical field (woody fruit tissue culture), which would have yielded predictable organogenic callus formation.
The claimed invention in claims 1, 2, 4-8, 11-13 and 20 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Claim 3 is drawn to the method of claim, wherein the stem tissue is present in a mixture with other plant tissue and the wounding comprises wounding the plant tissue present in the mixture and the culturing comprises culturing the wounded tissue from the mixture.
Feeney teaches preparing and culturing three explant types: apical tips, stems, and shoot bases, and collecting /pooling together (page 203, In-vitro explants) for in vitro culture and regeneration/callus formation. All of the tissues are wounded together and plated together, and that culturing wounded tissue fragments from such mixed plant material is routine explant plant-handling practice.
Claim 9 is drawn to the method of claim 1,wherein the organogenic callus is not a cotyledon-derived organogenic callus and/or the wounded tissue is devoid of a cotyledon.
Feeney teaches using vegetative stem/shoot-derived explants (including node-associated tissues) as starting material for in vitro culture and regeneration/callus formation (page 203, In-vitro explants). Such stem/shoot explants are not cotyledons and are therefore devoid of cotyledon, and any callus produced therefrom is necessarily not cotyledon-derived. Matt and Shestibratov further support that organogenic callus induction from vegetative explants under TDZ-containing media is a conventional and predictable approach.
Claim 10 is drawn to the method of claim 1, wherein the organogenic callus is true-to-type relative to the plant or plant part from which the wounded stem tissue was obtained.
Under BRI, the “organogenesis callus” is the callus induced from the wounded stem tissue in the culturing /organogenesis steps of claim 1, and “true-to -type relative to the plant or plant part from which the wounded stem tissue was obtained” means the callus (and the shoot/organs regenerated from it) retains the donor plant’s type/identity and does not exhibit an off-type phenotype relative to the source plant/plant part. The callus is required to be genetically/phenotypically consistent with the donor plant/plant part from which the wounded stem tissue explant was taken, as supported by applicant’s definition of “true-to-type” set forth in the specification.
Matt teaches that explants are used for micropropagation/organogenesis (page 469, Material and methods) to maintain donor genotype/phenotype.
A POSITA would have been motivated to apply TDZ-based organogenic culture conditions (Matt and Shestibratov) to Feeney’s stem/shoot pooled explant system because stem/node-associated vegetative tissues are established explant source for regeneration and are routinely processed to generate large numbers of wound sites and explant fragments. Pooling together produces a mixture of plant tissues that are wounded tother and plated together, and competent cells within those fragments predictably respond to TDZ-containing media to form organogenic callus. Further, because Feeney’s explants are vegetative stem/shoot tissues rather than seed cotyledons, the resulting callus is inherently not cotyledon-derived and the wounded tissue is inherently devoid of cotyledon. Thus, the additional limitations of claims 3 and 9 represent routine explant selection/handling and /or inherent outcomes of practicing the comminated prior art.
A POSITA would have been motivated to generate organogenic callus from stem/modal/meristem-containing tissue with the expectation that regenerated plants (and the intermediated callus used for propagation) would be true-to-type relative to the donor plant, because nodal/meristem-based culture is a standard clonal propagation approach used specifically to preserve cultivar identity. A POSITA would have had a reasonable expectation of success because regeneration from vegetative meristematic tissues is widely used to maintain donor genotype/phenotype.
The claimed invention in claims 3, 9 and 10 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Claim 14 is drawn to a method of propagating a plant from an organogenic callus, the method comprising: culturing the organogenic callus of claim 1 on media in the presence of light.
Matt teaches that TDZ-based organogeneic culture systems yield regeneration-competent tissues and that regeneration is carried out by transferring organogenic tissues to regeneration conditions (…2 weeks…. internode sections were transferred ..under the same conditions in a 16h photoperiod (50µmols−1m−2)… Subculturing on fresh media … every 2 weeks. Following regeneration, new adventitious shoots …) (page 470, last paragraph). Therefore, it would have been obvious to culture an organogenic callus on regeneration media in the presence of light to propagated/regenerate a plant.
Claim 15 is drawn to the method of claim 14, wherein culturing the organogenic callus comprises culturing the organogenic callus on shoot regeneration media to form tissue comprising a shoot and then culturing the tissue comprising a shoot on root regeneration media.
Matt teaches that organogenic tissues induced in vitro can be regenerated into shoots (page 472, last two paragraphs), and routine tissue culture practice further includes transferring shoots to rooting conditions/media (page 473, Rooting conditions).
Claim 16 is drawn to a method of transforming an organogenic callus, the method comprising: contacting the organogenic callus of claim 1 and a bacterial cell, thereby transforming the organogenic callus with the bacterial cell to provide a transformed organogenic callus.
US20070124835A1 teaches Agrobacterium-mediated transformation of plant explants and recovery of transformed tissues via selection/regeneration culture steps (page 1, abstract).
Matt teaches that TDZ-induced organogenic tissues/calli are competent to regeneration and can be used as culture material in regeneration system (page 468-469, introduction). Feeney teaches handling/culturing plant tissues in vitro in regeneration contexts. Thus, it would have been obvious to contact an organogenic callus with Agrobacterium to produce a transformed organogenic callus, because Agrobacterium-mediated DNA delivery is routinely performed on cultured plant tissues/explants that are regeneration competent, with predictable recovery under standard culture conditions.
A person of ordinary skill in the art would have been motivated to apply established plant regeneration and transformation workflows to organogenic callus because organogenic callus is a regeneration-competent intermediate routinely used to recover whole plants. Feeney and Matt collectively support that organogenic tissues produced in vitro are routinely transferred to regeneration conditions (including light to obtain shoots and are further transferred to rooting conditions to form plantlets). Shestibratov provides additional evidence of conventional Agrobacterium-mediated transformation and recovery of cultured tissues using selection/regeneration media. Combining there teaches yields a predictable pathway to regenerate plants from organogenic callus under light and through shoot/root regeneration steps, and transform regeneration-competent cultured tissues using Agrobacterium with routine recovery in culture, with a reasonable expectation of success.
The claimed invention in claims 14-16 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Claims 17-19 are rejected under 35 U.S.C. §103 as being unpatentable over Feeney (2007) in view of Matt (2005), Shestibratov (2007-05-31) as applied on claim 1, and Clement (Erik William Clement et. al., US11168319B1, Application 2018-02-28, Publication: 2021-11-09).
Claim 1 as the teachings of Feeney, Matt, and Shestibratov is discussed above.
Claim 17 is interpreted as dependent of claim 1.
Claim 17 is drawn to a method of modifying a target nucleic acid, the method comprising :contacting the organogenic callus of claim 1, and a bacterial cell, wherein the organogenic callus comprises the target nucleic acid and wherein the bacterial cell comprises and/or encodes an editing system and the editing system modifies the target nucleic acid, thereby providing a modified organogenic callus.
Clement teaches plant genome editing in plant cells/plant cell cultures and expressly includes embodiments in which callus is produced from the plant cell and plants/plantlets are regenerated from such callus, with seeds/plants having altered genetic sequences (column 1, summary). In this context, the callus (a mass of plant cells) inherently contains the plant genome, and thus comprises the target nucleic acid ( i. e., the endogenous genomic DNA sequence selected as the editing target) within those plant cells. Clement further teaches that the genome-editing components may be delivered by bacterially mediated transfection, including Agrobacterium species, i. e., using a bacterial cell carrying a polynucleotide that encodes the RNA-guide nuclease and/or gRNA (collum 37, line 35-45), which necessarily involves contacting the plant tissue/cells with the bacterial cells during inoculation/cocultivation to transfer the editing construct into the plant cell, thereby teaching a bacterial cell that comprises and /or encodes and editing system for modifying the target nucleic acid in the plant cells/callus by contacting the cell/callus.
Clement also teaches “the culture, methods, systems, and/or compositions provided herein includes plant cells (encompasses cells from any plant tissue and cell culture, including cells present in an explant-derived cell mass such as callus) obtained from or located in any monocot or dicot plant species of interest, for example… cherry (Prunus avium)”(collum 15, line 30-50).
Claim 18 is drawn to a method of propagating a plant from an organogenic callus, the method comprising: culturing the modified organogenic callus of claim 17 on media in the presence of light.
Claim 18 recites the same culturing limitation as claim 14 (culturing the organogenic callus of claim 17 on media in the presence of light). Therefore, for the same reason stated for claim 14, Matt teaches this limitation. The fact that claim 18 specifies the callus is “modified” (per claim 17) does not change the culturing condition; culturing callus (including edited/modified callus) on regeneration media under light is a routine propagation step, and Matt expressly teaches culturing callus under light to regenerate /propagate plants.
Claim 19 is drawn to the method of claim 18, wherein culturing the transformed organogenic callus or the modified organogenic callus comprises culturing the transformed organogenic callus or modified organogenic callus on shoot regeneration media to form tissue comprising a shoot and then culturing the tissue comprising the shoot on root regeneration media.
For the same reason set forth with respect to claim 15, Matt teaches regeneration of plants from callus by inducing shoots on shoot regeneration medium and subsequently inducing roots on root regeneration medium (i.e., a shoot induction step followed by a rooting step).
A POSITA would have been motivated to apply the genome editing system of Clement to the organogenic callus culture/regeneration framework taught by Feeney, Matt and Clement in order to obtain edited (modified) regenerable callus and to efficiently recover regenerated plants carrying the desired target nucleic acid modification. Combination of gene editing technology and organogenic callus culture/regeneration framework would have been a routine and predictable optimization to achieve the expected goal of producing plats regenerated from callus that carry a targeted genome edit, because Agrobacterium-mediated delivery of editing constructs into regenerable plants tissue/callus and subsequent regeneration on standard shoot/root media under light were well-known compatible steps in plant biotechnology.
Further, a person of ordinary skill in the art would have had a reasonable expectation of success in combing Clement with Feeney, Matt and Clement. Accordingly, the combination predictably yields (1) a modified organogenic callus produced by contacting organogenic callus with an Agrobacterium bacterial cell encoding an editing system to modify a target nucleic acid (claim 17), and (2) propagation/regeneration of plants from that modified callus by culturing on media in the presence of light (claim 18) and , as recited, by culturing on shoot regulation media to form shoot tissue followed by culturing on root regeneration media to induce rooting (claim 19).
The claimed invention in claims 17-19 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Conclusion
No claims are allowed.
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/YANXIN SHEN/ Examiner, Art Unit 1663
/WEIHUA FAN/ Primary Examiner, Art Unit 1663