DETAILED ACTION
Applicant's response, filed 22 October 2025, has been fully considered. Rejections and/or objections not reiterated from previous Office Actions are hereby withdrawn. The following rejections and/or objections are either reiterated or newly applied. They constitute the complete set presently being applied to the instant application.
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 88-95 and 98-119 are currently pending.
Claims 88-95, 98-115, and 118-119 are examined herein.
Claims 116 and 117 are withdrawn.
Claims 118-119 are newly added.
Claims 1-87 and 96-97 have been cancelled.
Drawings
The Replacement Drawings submitted 22 October 2025 are accepted.
Specification
Note: All references to the Specification herein pertain to the PG publication: US20210319279.
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.
1. Claims 88-93 and 98-99 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Blagovic et al. (Current Opinion in Biotechnology (2013) Vol. 24:940-947).
Claim 88 is directed to:
A system for biological computing, comprising:
(a) one or more computing units (CUs), wherein the one or more CUs comprises one or more genetically engineered cells and
(b) one or more sample objects derived from an input sample, wherein the one or more sample objects comprise one or more cells or clusters of cells;
wherein the one or more CUs interact with the one or more sample objects through one or more surface-bound entities (SBEs) associated with the one or more CUs and generate an output signal in response to a transfer of signal objects (SOs) produced inside one of the one or more CUs to the outside of the one or more CUs.
The prior art to Blagovic et al. disclose engineered cell-cell interactions modeling juxtacrine signaling. Blagovic et al. disclose, “an approach to directly tune cell–cell signals utilizes material scaffolds that are normally used to present adhesive matrix cues, such as the short peptide RGD. Proteins or peptides involved in juxtacrine signaling are immobilized on the scaffold to mimic cues that would otherwise be presented by adjacent cells (p. 940, col. 2; Figure 1). Figure 1 includes (a)-a cell; (b) cell sample object and surface bound entities associated with (a) cells. And transfer of signal objects inside of the cell.
With respect to claim 89, Blagovic et al. disclose independent cells which meet the definition of a computational cluster as being “one or more CUs and one or more sample objects” (see p. 940, Figure 1).
With respect to claim 90, Blagovic et al. disclose cells capable of recognition of a signal object (p. 940, Figure 1).
With respect to claim 91, Blagovic et al. disclose SBE comprising an SO at Figure 1 (p. 940).
With respect to claim 92, Blagovic et al. disclose attachment at the surface of the cell (Figure 1, p. 940; p. 943, col. 1- A non-genetic approach is to induce interactions between T cells and their target cells by exogenously introducing cell–cell bridging molecules, such as antibodies or its fragments).
With respect to claim 93, Blagovic et al. disclose said SO production at Figure 1 (p. 940).
With respect to claim 98, Blagovic et al. disclose a sample object (cell) that is associated with an SBE, for example (Figure 1).
With respect to claim 99, Blagovic et al. disclose recognition of SO to induce another SO (see eph/ephrin interaction in Figrue 1).
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.
1. Claims 94-95, 107-109 and 111-115 are rejected under 35 U.S.C. 103 as being unpatentable over Blagovic et al. (Current Opinion in Biotechnology (2013) Vol. 24:940-947), as applied to claims 88 and 90 above.
Claim 88 is directed to:
A system for biological computing, comprising:
(a) one or more computing units (CUs), wherein the one or more CUs comprises one or more genetically engineered cells and
(b) one or more sample objects derived from an input sample, wherein the one or more sample objects comprise one or more cells or clusters of cells;
wherein the one or more CUs interact with the one or more sample objects through one or more surface-bound entities (SBEs) associated with the one or more CUs and generate an output signal in response to a transfer of signal objects (SOs) produced inside one of the one or more CUs to the outside of the one or more CUs.
The prior art to Blagovic et al. disclose engineered cell-cell interactions modeling juxtacrine signaling. Blagovic et al. disclose, “an approach to directly tune cell–cell signals utilizes material scaffolds that are normally used to present adhesive matrix cues, such as the short peptide RGD. Proteins or peptides involved in juxtacrine signaling are immobilized on the scaffold to mimic cues that would otherwise be presented by adjacent cells (p. 940, col. 2; Figure 1). Figure 1 includes (a)-a cell; (b) cell sample object and surface bound entities associated with (a) cells. And transfer of signal objects inside of the cell.
With respect to claim 90, Blagovic et al. disclose cells capable of recognition of a signal object (p. 940, Figure 1).
Blagovic et al. do not specifically disclose elements as in claims 94-95, 107-109 and 111-115 which each include desired results of a cell to produce a first signaling object as being enhanced and/or attenuated or of a generation to include presence or absence of features. However, the system of claims 88 and 90, that includes cells that comprise surface bound entities that produce signal are disclosed in Blagovic et al. The desired programming for either attenuation or enhancement would have been prima facie obvious as a mere design choice of said system and the “capability” of the cell in the system to do so is not claimed beyond said wishful operation. Further, desired results of the particular “generation” of the output are also a design feature wherein there are no components of a system as to said particular embodiments. As such, the “wherein” clause is not limiting to the system as claimed and is obvious herein, as signals in cellular interactions operate to either enhance or degrade. It is suggested that said components be claimed as those of the system components only.
2. Claim 100 is rejected under 35 U.S.C. 103 as being unpatentable over Blagovic et al. (Current Opinion in Biotechnology (2013) Vol. 24:940-947), as applied to claims 88 and 90 above, in view of Brownlee (CIS Technical Report 070427A (April 2007): 5 pages).
Blagovic et al. (Current Opinion in Biotechnology (2013) Vol. 24:940-947), disclose the limitations as applied to claims 88 and 90 above. With respect to the sample object being a cell and the SBE associated with the cell comprising an antigen, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to engineer said design, as it is well-known in the art of immunology, as disclosed, for example, in a review of Brownlee that antigens interact with antibodies on cell surfaces (Figure 1). One would have been motivated to provide such in cell-cell interaction systems such as those in Blagovic et al. wherein Blagovic et al. teach that strategies from immune system regulation are integral to understanding cell-cell interaction signaling in the context, for example, of cell surface manipulations (page 943, col. 1).
3. Claims 101-106 and 118-119 are rejected under 35 U.S.C. 103 as being unpatentable over Blagovic et al. (Current Opinion in Biotechnology (2013) Vol. 24:940-947), as applied to claim 88 above, in view of Weiss et al. (Natural Computing (2003) Vol. 2:47-84).
Blagovic et al. disclose the limitations as applied to claims 88 above. With respect to disclosure of the operation of the system in the context of an AND, OR and/or NOT gate as in claims 101-106, the prior art to Weiss et al. disclose programmed cellular behaviors that are operational in computations, communication and signal processing (abstract). The processes as disclosed include those in circuit design and are applied to biological computing (abstract). Specifically, operational design includes those based in logic gate operation, which include, for example AND, OR and NOT gating (pp. 48-55).
With respect to claims 118-119, Weiss et al. disclose that cell-cell communication is important in both eukaryotic and prokaryotic cell systems, thus making obvious the inclusion of said logic gate operation in the context of E. coli (prokaryote that is specifically disclosed in Weiss et al., for example at p. 71-74) and as would also be obvious in yeast systems (which are eukaryotes).
As such, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized the cell-cell communication units as in Blagovic et al. with the detailed gate operations as disclosed in Weiss et al., as Weiss et al. describe specific operations for cell-cell and multi-cell signal procedures (starting p. 71) and wherein both references are in the same field of endeavor thus lending a reasonable expectation of success.
4. Claim 110 is rejected under 35 U.S.C. 103 as being unpatentable over Blagovic et al. (Current Opinion in Biotechnology (2013) Vol. 24:940-947), as applied to claim 88 above, in view of Khorshid (Proc. 2nd Saudi Sci. Conl, Fac. Sci., KAU; 15-17 March 2004, Part I. pp.67-98 (2005).
Blagovic et al. disclose the limitations as applied to claims 88 above. Blagovic et al. do not specifically include viscosity discussions.
However, with respect to disclosure of a system that has an agent to increase viscosity of a medium, the prior art to Khorshid discloses that a cellular medium viscosity can alter the cellular reactions to topography and can affect cellular interactions and growth as demonstrated by cells in the presence of a variety of concentrations of macromolecules (p. 67 at abstract).
As such it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have utilized the cell-cell communication units as in Blagovic et al. with the ideal medium conditions that include viscosity agents as described in Khorshid. One would have been motivated to do so because Khorshid discloses that an elevated medium viscosity is pertinent to biochemical and cellular functions (abstract).
Conclusion
No claims are allowed.
It is suggested that the inventive features as discussed in the Interview conducted on 7 October 2025, be more specifically claimed herein, such as those directed to the aspects that would distinguish the recitations from cell-cell mechanisms as disclosed in the prior art. This might include, for example, the yeast strains and binders as scaffolded to said strains that also include pheromone signal objects that act to activate cells/reporters.
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.
Inquiries
Papers related to this application may be submitted to Technical Center 1600 by facsimile transmission. Papers should be faxed to Technical Center 1600 via the PTO Fax Center. The faxing of such papers must conform to the notices published in the Official Gazette, 1096 OG 30 (November 15, 1988), 1156 OG 61 (November 16, 1993), and 1157 OG 94 (December 28, 1993) (See 37 CFR § 1.6(d)). The Central Fax Center Number is (571) 273-8300.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Lori A. Clow, whose telephone number is (571) 272-0715. The examiner can normally be reached on Monday-Thursday from 11:00AM to 9:00PM ET.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Karlheinz Skowronek can be reached on (571) 272-9047.
Any inquiry of a general nature or relating to the status of this application or proceeding should be directed to (571) 272-0547.
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/Lori A. Clow/Primary Examiner, Art Unit 1687
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