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 .
Applicant’s response filed 04/20/2026 has been received and considered entered. This is a response to amendments and arguments filed 04/20/2026.
Election/Restrictions
Claims 22-24, 28, 34, 38, 42, 49, and 51 stand withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 09/08/2025.
Claims Status
Claims 64-65 are newly added. Claims 2-4, 8-9, 11-12, 14-16, 18, 20-21, 25-27, 29-33, 35-37, 39-41, 43-48, 50, 52, 54, 57-59, 61-63 is/are cancelled. Claims 1, 5-7, 10, 13, 17, 19, 22-24, 28, 34, 38, 42, 49, 51, 53, 55-56, 60, 64-65 is/are currently pending with claims 22-24, 28, 34, 38, 42, 49, and 51 withdrawn. Claims 1, 5-7, 10, 13, 17, 19, 53, 55-56, 60, 64-65 is/are under examination.
Claim Interpretation
The claims contain limitations preceded by the term “optional”. All claim limitations recited as “optional” are interpreted as not required. As such, prior art can be applied to teach these limitations, but does not need to be applied.
Claim Rejections - 35 USC § 112
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.
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, 5-7, 10, 13, 17, 19, 53, 55-56, 60, and 64-65 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. This rejection is amended as necessitated by amendment and is maintained.
To satisfy the written description requirement, a patent 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. See, e.g., Moba, B.V, v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. Possession may be shown in a variety of ways including description of an actual reduction to practice, or by showing that the invention was "ready for patenting" such as by the disclosure of drawings or structural chemical formulas that show that the invention was complete, or by describing distinguishing identifying characteristics sufficient to show that the applicant was in possession of the claimed invention. See, e.g., Pfaff v. Wells Eiees., Inc., 525 U.S. 55, 68, 119 S.Ct. 304, 312, 48 USPQ2d 1641,1647 (1998); Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406; Amgen, Inc. v. Chugai Pharm., 927 F. 2d 1200, 1206, 18 USPQ2d 1016, 1021 (Fed. Cir. 1991) (one must define a compound by "whatever characteristics sufficiently distinguish it”).
According to the MPEP § 2163, "The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice (see i)(A) above), reduction to drawings (see i)(B) above), or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus (see i)(C) above). See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406. A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutsch land GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014) (Claims directed to a functionally defined genus of antibodies were not supported by a disclosure that "only describe[d] one type of structurally similar antibodies" that "are not representative of the full variety or scope of the genus.")."
Claims 1, 53, and 55 recite hyperspectral reporters comprising any target input, any regulatory element, and any signaling protein. These are enormous genera of regulatory elements, inputs, and signaling proteins.
The specification teaches that the signaling protein can be an enzyme or a regulator of an enzyme (pages 17-18). The broad categories of “enzyme” and “regulator of an enzyme” are not limiting definitions of a signaling protein. As such, “signaling protein” is sufficiently broad to encompass any protein which can itself produce a hyperspectral signal or which through the function of the protein can result in the production of a hyperspectral signal by a molecule, compound, or different protein downstream of the activity of the protein. The disclosure does not describe a number of species representative of the full scope of the genus of “signaling protein”.
Claim 13, dependent on claim 1, recites particular species and types of target inputs, but fails to fulfill the written description requirement for the following reasons. Claim 13 recites “E. coli metabolites” and “volatile metabolites” which produce detectable signals with unique hyperspectral signatures. However, no specific E. coli metabolites or volatile metabolites are described in the claim or specification, nor are any such metabolites described through structural characteristics. The functional limitation that the metabolites produce a detectable signal with a unique hyperspectral signature, and that the metabolites have 6 or more conjugated π bonds or produce a detectable signal which absorbs light at 290-460nm or 790-810nm do not sufficiently describe the E. coli metabolites and volatile metabolites, as by Applicant’s own definition of these genera, all species would have this functional characteristic. An artisan would not be able to determine, based on the information provided in the disclosure, that the applicants were in possession of hyperspectral reporter cells comprising E. coli metabolites or volatile metabolites which produce a detectable signal with a unique hyperspectral signature.
Claim 17 recites multiple classes of target inputs: toxins, radiation, pollutants, nucleic acids, explosives, bacteria, fungi, viruses, and nutrients. However, in order for these to be target inputs, a corresponding regulatory element responsive, directly or indirectly, to the target input must exist. However, the disclosure only describes a limited number of species of cellular elements (regulatory sequences, receptors) which bind to a target input and produce a detectable signal or trigger a signaling cascade which downstream produces a detectable signal. The specification describes zinc-, dexamethasone-, tetracycline-, RU486-, and rapamycin-inducible promoters (page 15), and inducible promoters ParaBAD, PrhaBAD, Plac, Ptac, Plux, Ptet, Psa1, Ptrp, PA1lacO1, and Ppho (page16 lines 15-19). These inducible promoters are not representative of the entire scope of the genus of inducible promoters. The specification also describes that “the cell expresses a receptor capable of recognizing the target input” (page 2 lines 18-20). However, the disclosure does not provide a representative number of such receptors. These species of promoters and the broad description of receptors are not a representative number of species of cellular elements which are capable of binding or recognizing any target input selected from a toxin, radiation, pollutant, nucleic acid, explosive, bacterium, fungus, virus, and nutrient. As described above, a description of a representative number of species of such cellular elements is required in order to describe a representative number of species of target inputs as recited in claim 17. Furthermore, the disclosure does not describe a representative number of species of target inputs. The specification teaches the specific species of target inputs vanillate, IPTG, aTc, cuminic acid, DAPG, salicylic acid, 3,4-dihydroxybenzoic acid, 3OC6HSL, and 3OC14HSL (page 24 lines 5-7; page 30 “Example 1”). These are not representative of the full scope of the genera of toxins, radiation, pollutants, nucleic acids, explosives, bacteria, fungi, viruses, and nutrients.
Claim 60 recites a cell comprising a DNA molecule having a regulatory element responsive to a first target input, wherein the regulatory element is operatively linked to a DNA sequence encoding a first signaling protein, wherein the target input produces a physiological response (claim 55) which physiological response makes the cell responsive to a second target input (claim 60). However, the disclosure does not describe any target inputs or downstream structures (such as proteins activated or expressed because of the presence of the first target input) which render the cell responsive to a second target input. On page 15 lines 10-14, the specification teaches that “a first target may trigger the production of a sensor for a second target. Thus, a reporter cell can conditionally report on the presence of a second molecule only when a first molecule is present, thus increasing the complexity of the detection process.” However, no species of target inputs, sensors, or signaling proteins which could fulfill the functional requirements of claim 60 are described in the disclosure. As such, an artisan would not be able to determine, based on the disclosure, what structures could fulfill the required functions of claim 60 or that the applicants were in possession of structures which could fulfill the structural requirements of claim 60, and thus in possession of the hyperspectral reporter cell of claim 60.
Response to Arguments
Applicant's arguments filed 04/20/2026 have been fully considered but they are not persuasive.
Applicant argues that the “invention relates, at least in part to the discovery that unique hyperspectral signals may be produced and detected using hyperspectral cameras by selecting a target input and corresponding signaling protein for use in a cell…A wide range of target inputs, signaling proteins and regulatory elements can be used, as long as they produce the hyperspectral signal, following the guidance found in the specification. Each of target inputs, signaling proteins and regulatory elements are well known in the art…Using the guidance found in the specification, the skilled artisan could identify an appropriate target input and corresponding signaling protein and also select the appropriate regulatory element for controlling expression of the protein and depending on the cell type” (page 12). Using the guidance in the specification, a skilled artisan would be able to identify corresponding target inputs, signaling proteins, and regulatory elements from those described; however, those described do not represent the complete genus of target inputs, signaling proteins, and regulatory elements, as described above.
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claim(s) 1, 5-7, 13, 17, 19, 55-56 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Maeda (JP2009159862A, English machine translation provided, obtained from J-PlatPat OPD machine translation function), as evidenced by Camara (2013). This rejection is maintained and modified as necessitated by amendment.
MPEP §2131.01 provides guidance as to 35 U.S.C. 102 rejections over multiple references. Such rejection has been held to be proper when the extra references are cited to: (C) Show that a characteristic not disclosed in the reference is inherent.
The MPEP states: “To serve as an anticipation when the reference is silent about the asserted inherent characteristic, such gap in the reference may be filled with recourse to extrinsic evidence. Such evidence must make clear that the missing descriptive matter is necessarily present in the thing described in the reference, and that it would be so recognized by persons of ordinary skill.” Continental Can Co. USA v. Monsanto Co., 948 F.2d 1264, 1268, 20 USPQ2d 1746, 1749 (Fed. Cir. 1991) (The court went on to explain that “this modest flexibility in the rule that 'anticipation' requires that every element of the claims appear in a single reference accommodates situations in which the common knowledge of technologists is not recorded in the reference; that is, where technological facts are known to those in the field of the invention, albeit not known to judges.” 948 F.2d at 1268, 20 USPQ at 1749-50.). Note that the critical date of extrinsic evidence showing a universal fact need not antedate the filing date. See MPEP §2124.
Regarding claim 1, Maeda teaches an engineered cell (a freshwater purple bacterium) comprising a DNA molecule having a regulatory element (promoter Pars) responsive to a target input (arsenic), wherein the promoter is operatively linked to a DNA sequence encoding a signaling protein (phytoene desaturase CrtI), wherein the cell produces a detectable signal in response to the target input by producing the signaling protein, and wherein the detectable signal features a unique hyperspectral signature (claims 1-9). Maeda teaches that activation of expression of CrtI in response to arsenic results in production of red lycopene from colorless phytoene, wherein red lycopene produces a unique hyperspectral signature (paragraph [0010]; claim 6). Camara teaches that lycopene produces a detectable signal with more than one detectable peak in its spectrum between 400 and 1000nm (three peaks) (Fig. 4 of Camara).
Regarding claim 5, Maeda teaches that the promoter is an inducible promoter (claims 1, 5-6, 8-9).
Regarding claim 6, Maeda teaches that activation of expression of CrtI in response to arsenic results in production of red lycopene from colorless phytoene, wherein red lycopene produces a unique hyperspectral signature (paragraph [0010]; claim 6).
Regarding claim 7, Maeda teaches that the signaling protein is an enzyme (phytoene desaturase, CrtI), which catalyzes the production of a metabolite (red lycopene) which produces a unique hyperspectral signature, and wherein the metabolite is produced from a substrate that is naturally occurring in the cell (phytoene) (paragraph [0010]; claim 6).
Regarding claim 17, Maeda teaches that the target input is a toxin (arsenic) (claims 5-6, 8).
Regarding claim 19, Maeda teaches that the cell comprises one sensor plasmid (transducer) (paragraph [0043]).
Regarding claims 55-56, Maeda teaches an engineered cell (bacterial cell) comprising a DNA molecule having a regulatory element (promoter Pars) responsive to a target input (arsenic), wherein the regulatory element is operatively linked to a DNA sequence encoding a signaling protein (CrtI, arsR, see Fig. 4), wherein the cell produces a detectable signal in response to the target input by producing the signaling protein (claims 1-9). The signaling protein CrtI is an enzyme which produces a physiological response; this physiological response consists of the production of carotenoids in the spirilloxanthin pathway, which produce a detectable signal (paragraph [0017]; claim 6). Maeda teaches that activation of expression of CrtI in response to arsenic results in production of red lycopene from colorless phytoene, wherein red lycopene produces a unique hyperspectral signature (paragraph [0010]; claim 6). Camara teaches that lycopene produces a detectable signal with more than one detectable peak in its spectrum between 400 and 1000nm (three peaks) (Fig. 4 of Camara).
Response to Arguments
Applicant's arguments filed 04/20/2026 have been fully considered but they are not persuasive. Applicant argues that the system of Maeda differs in strength and proximity from the inventions disclosed in the specification (pages 12-13). However, the limitations of the claims rejected above under 35 USC 102 do not differ structurally from the system described in Maeda. There are no functional or structural limitations which distinguish the instant claimed invention from the system of Maeda. As such, the rejection is maintained.
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 (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 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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 5-7, 13, 17, 19, 55-56 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Maeda (JP2009159862A, English machine translation provided, obtained from J-PlatPat OPD machine translation function), as evidenced by Camara (2013), in view of Suyama (1999). This rejection is maintained and modified as necessitated by amendment.
Regarding claim 1, Maeda teaches an engineered cell (a freshwater purple bacterium) comprising a DNA molecule having a regulatory element (promoter Pars) responsive to a target input (arsenic), wherein the promoter is operatively linked to a DNA sequence encoding a signaling protein (phytoene desaturase CrtI), wherein the cell produces a detectable signal in response to the target input by producing the signaling protein, and wherein the detectable signal features a unique hyperspectral signature (claims 1-9). Maeda teaches that activation of expression of CrtI in response to arsenic results in production of red lycopene from colorless phytoene, wherein red lycopene produces a unique hyperspectral signature (paragraph [0010]; claim 6). Camara teaches that lycopene produces a detectable signal with more than one detectable peak in its spectrum between 400 and 1000nm (three peaks) (Fig. 4 of Camara).
Regarding claim 5, Maeda teaches that the promoter is an inducible promoter (claims 1, 5-6, 8-9).
Regarding claim 6, Maeda teaches that activation of expression of CrtI in response to arsenic results in production of red lycopene from colorless phytoene, wherein red lycopene produces a unique hyperspectral signature (paragraph [0010]; claim 6).
Regarding claim 7, Maeda teaches that the signaling protein is an enzyme (phytoene desaturase, CrtI), which catalyzes the production of a metabolite (red lycopene) which produces a unique hyperspectral signature, and wherein the metabolite is produced from a substrate that is naturally occurring in the cell (phytoene) (paragraph [0010]; claim 6).
Regarding claim 13, Maeda teaches that the detectable unique hyperspectral signal produced by the engineered cell is produced by the combined hyperspectral signatures produced by bacteriochlorophyll (paragraphs [0010], [0017], [0026], [0027]) and the carotenoids lycopene, dehydrorhodopin, anhydrorhodovibrin, rhodovibrin, hydroxyspirilloxanthin, and spirilloxanthin (paragraph [0010]; Fig. 1). Maeda teaches that the cell is a bacterium (claims 1-9), and optionally Rubrivivax gelatinosus (paragraph [0017]). As the bacteriochlorophyll synthesis pathway is endogenous (Maeda teaches that the freshwater purple bacterium “has a spirilloxanthin pathway and a bacteriochlorophyll synthesis pathway”, paragraph [0017]), the bacteriochlorophyll produced by Rubrivivax gelatinosus is bacteriochlorophyll a (Suyama, page 49). It would have been obvious to an artisan, based on the information provided by Maeda and Suyama regarding the spirilloxanthin synthesis pathway and bacteriochlorophyll a synthesis pathway, that the reporter cell of Maeda could be modified such that the Bchl gene was placed under the control of the inducible promoter, instead of the Crtl gene. In such a modified cell, the unique hyperspectral signature produced by the products of the endogenous spirilloxanthin pathway would be constant (whereas the cell as described by Maeda constantly produces the hyperspectral signature of bacteriochlorophyll a), and the unique hyperspectral signature of the endogenously-synthesized bacteriochlorophyll a would be produced in the presence of a target input (whereas the cell as described by Maeda produces the hyperspectral signature of spirilloxanthin synthesis pathway products in response to the presence of a target input).
Regarding claim 17, Maeda teaches that the target input is a toxin (arsenic) (claims 5-6, 8).
Regarding claim 19, Maeda teaches that the cell comprises one sensor plasmid (transducer) (paragraph [0043]).
Regarding claims 55-56, Maeda teaches an engineered cell (bacterial cell) comprising a DNA molecule having a regulatory element (promoter Pars) responsive to a target input (arsenic), wherein the regulatory element is operatively linked to a DNA sequence encoding a signaling protein (CrtI, arsR, see Fig. 4), wherein the cell produces a detectable signal in response to the target input by producing the signaling protein (claims 1-9). The signaling protein CrtI is an enzyme which produces a physiological response; this physiological response consists of the production of carotenoids in the spirilloxanthin pathway, which produce a detectable signal (paragraph [0017]; claim 6). Maeda teaches that activation of expression of CrtI in response to arsenic results in production of red lycopene from colorless phytoene, wherein red lycopene produces a unique hyperspectral signature (paragraph [0010]; claim 6). Camara teaches that lycopene produces a detectable signal with more than one detectable peak in its spectrum between 400 and 1000nm (three peaks) (Fig. 4 of Camara).
Response to Arguments
Applicant's arguments filed 04/20/2026 have been fully considered but they are not persuasive. Applicant did not respond to the rejection of claims under 35 USC 103 over Maeda in view of Suyama. Applicant does argue that a 102(a)(1) rejection over Maeda as evidenced by Suyama should be withdrawn because “Maeda does not disclose that the hyperspectral reporter includes a DNA molecule which produces a signaling protein that can produce a signal having a unique hyperspectral signature which can be detected by a hyperspectral camera” (page 14). However, as described above, Maeda does teach a cell (a hyperspectral reporter) comprising a DNA molecule encoding a signaling protein (CrtI, arsR) which produces a signal having a unique hyperspectral signature. While Maeda does not disclose a hyperspectral camera itself, the ability for a hyperspectral camera to detect the hyperspectral signature of the engineered cells of Maeda is considered an inherent property of the engineered cells of Maeda, due to the wavelengths of light absorbed by the compounds in the cells.
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.
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/AFRICA M MCLEOD/ Examiner, Art Unit 1635
/KIMBERLY CHONG/ Primary Examiner, Art Unit 1636
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