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 .
DETAILED ACTION
Claims 1-19, 21-24, 29-30, 32-33, and 35-36 are pending. Claims 20, 25-28, 31, and 34 are cancelled.
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-19 and 21-24, and the species of azide, TAMRA, and DBCO in the reply filed on 4/14/2026 is acknowledged.
Claims 11, 18-19, 21-23, 29-30, 32-33, and 35-36 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention or species, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 4/14/2026.
Claims 1-10, 12-17 and 24 are examined herein.
Drawings
The drawings are objected to because the resolution of Figures 30-34 is too poor for printing and legibility. 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.
Specification
The use of the terms AF488, AF647, BODIPY,Cy5, Cy5., Cy7, Cy7.5, and TAMRA, which are trade names or marks used in commerce, has been noted in this application. The term should be accompanied by the generic terminology; furthermore the term should be capitalized wherever it appears or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 1-2 are objected to because of the following informalities:
Claim 1 and claim 2, line 8, “where the cells where not contacted” is a typographical error and should read “where the cells were not contacted.” Additionally, Applicant should consider amending the active method step, “providing” rather than “provide” to reflect continuous action in the process. The term “bacteria cell” in the preamble and step a), which should be corrected to “bacterial cells.”
Appropriate correction is required.
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.
Claims 1-10, 12-17 and 23-24 are 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 1 is indefinite for the limitation “wherein an increase in reporter molecule levels as compared to a control where the cells [were] not contacted with the test molecule correlates with permeation of said one or more test molecules to and/or within the PG scaffold.” It is unclear what the required method steps are for the testing of the control, when the testing of the control is performed in relation to a)-c), what materials are used in each step, and whether the testing of the control is required to be performed in parallel with the live cell assay. In addition, “control” has multiple reasonable interpretations as this limitation can be reasonably interpreted as referring to the cells (i.e. comparing permeable bacterial cells to impermeable bacterial cells) or to the molecules (i.e. comparing test molecules to control molecules in the same live bacterial cells). It is further unclear how a comparison of reporter levels can be performed while only the test molecule has a reporter molecule as recited in step b) and a control is not contacted with the test molecule.
Claim 2 is indefinite for “wherein a decrease in reporter molecule levels as compared to a control where the cells where not contacted with the test molecule correlates with permeation of said one or more test molecules to and/or within the PG scaffold” for the same reasons discussed above with respect to claim 1.
Claim 7 recites the limitation "the PG-reactive epitope" in line 3. There is insufficient antecedent basis for this limitation in the claim.
Claim 8 recites “wherein the reactive epitope is part of a stem peptide for culturing with said cells” and claim 9 recites “wherein the stem peptide can be used as a PG building block by the cells.” Claims 8-9 ultimately depend from claim 1, which recites a) provide live bacteria cells that comprise PG with a reactive epitope). It is unclear whether the method further comprises culturing live bacteria cells with the stem peptide in order for the live cells to use the stem peptide as a PG building block.
Claim 13 recites the limitation "test compound" in line 3. There is insufficient antecedent basis for this limitation in the claim.
Claim 16 contains the trademark/trade name AF488, AF647, BODIPY,Cy5, Cy5.5, Cy7, Cy7.5, and TAMRA. Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph. See Ex parte Simpson, 218 USPQ 1020 (Bd. App. 1982). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe specific fluorescent chemical dyes and, accordingly, the identification/description is indefinite.
Claims 3-10, 12-17 and 23-24 are rejected for depending from a rejected base claim and not rectifying the source of indefiniteness discussed 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.
Claims 1-2, 6-10, 12, 16, and 24 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liechti et al. (Nature 506.7489 (2014): 507-510).
Regarding claims 1 and 12, Liechti teaches live cell experiments in which exponentially growing cells are cultured in media containing azide-modified D-alanine or dipeptide analogues in order to incorporate the azide label into the PG, subsequently cross-linked via copper-free click chemistry to Alexa Fluor 488 DIBO Alkyne, and imaged (page 511, left column, Methods, Labelling E. coli, B. subtilis, and S. pneumoniae PG; Fig. 1a and b). Thus, Liechti teaches a test molecule (Alexa Fluor 488 DIBO Alkyne) comprising both a reporter molecule (the fluorophore) and a reactive handle (DIBO Alkyne), live cells that comprise peptidoglycan (PG) with a reactive epitope (the azide), and measuring the amount of reporter molecule (measuring fluorescence during image acquisition: see page 512, left column, Image acquisition and analysis). An increase in reporter molecule levels as compared to a control necessarily correlates with an increase in permeation of the test molecule to and/or within the PG scaffold after excess reporter molecule is washed away.
Regarding claim 2¸ in the absence of any special definition, correlate is given its broadest reasonable interpretation as requiring that a change in one parameter generally implies a similar or opposite change in another parameter.
Regarding steps b) and c) of claim 2, contacting cells of a) with one or more test molecules conjugated to a reporter molecule and a reactive epitope satisfies the contacting steps of both b) and c). Thus, Liechti’s live cell experiments in which exponentially growing cells are cultured in media containing azide-modified D-alanine or dipeptide analogues in order to incorporate the azide label (“reactive handle”) into the PG, subsequently cross-linked via copper-free click chemistry to Alexa Fluor 488 DIBO Alkyne (test molecule comprising a reporter molecule conjugated to a reactive epitope that binds with the reactive handle), and imaged via fluorescence microscopy (page 511, left column, Methods, Labelling E. coli, B. subtilis, and S. pneumoniae PG; Fig. 1a and b) also anticipates the process of claim 2. A decrease in reporter molecule levels necessarily correlates with the penetration of said one or more test molecules to and/or within the PG scaffold because a decrease in the reporter molecule levels reflects a decrease in the penetration of the test molecules to and/or within the PG scaffold after the excess reporter molecule is washed away.
Regarding claims 6 and 8-9, the PG is covalently linked to the reactive epitope because the azide-functionalized D-amino acids are incorporated into the stem peptide of peptidoglycan (Figure 1a, 1b). The stem peptide is a pentapeptide (Figure 1a).
Regarding claim 7, Liechti teaches that the cells are incubated in media containing azide-modified D-alanine or dipeptide analogues for 5 min or 60 min (page 511, left column, Methods, Labelling E. coli, B. subtilis, and S. pneumoniae PG; Fig. 1a and b).
Regarding claim 10, Liechti teaches that the stem peptide is N-terminally tagged with the azide-modified dipeptide (page 16, right column, line 1).
Regarding claim 16, Liechti’s reporter molecule is Alexa Fluor 488, which is AF488 (page 511, left column, Methods, Labelling E. coli, B. subtilis, and S. pneumoniae PG).
Regarding claim 24¸ Liechti labels E. coli (Gram negative), B. subtilis (Gram positive), and S. pneumoniae (Gram negative): see page 511, left column, Methods, Labelling E. coli, B. subtilis, and S. pneumoniae PG.
Claims 13, 15, and 17 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Liechti et al. (Nature 506.7489 (2014): 507-510), as applied to claims 1-2, 6-10, 12, 16, and 24 above, as evidenced by Thermo Fisher (2015, website).
See discussion of Liechti above, which is incorporated into this rejection as well.
Regarding claims 13 and 15, Liechti’s Alexa Fluor 488 DIBO Alkyne reporter molecule (a fluorophore) is conjugated via a linker to the reactive handle as evidenced by Thermo Fisher (Figure 3.1.3).
Regarding claims 17, Liechti’s DIBO is a synonym for dibenzocyclooctyne as evidenced by Thermo Fisher (page 4, Copper-Free Click Chemistry, paragraph 3).
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.
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.
Claims 3-4 are rejected under 35 U.S.C. 103 as being unpatentable over Shieh et al. (Proceedings of the National Academy of Sciences 111.15 (2014): 5456-5461) in view of Campbell et al. (ACS chemical biology 6.1 (2011): 106-116).
Shieh teaches incubating bacteria with endobcnDala 14 (cyclooctyne D-alanine analogue, see Fig. 7), washing away excess amino acid, and then incubating the bacteria with 11 (azido Si-rhodamines) for 1 h and measuring fluorescence (page 5459, right column, bottom paragraph). Shieh teaches that the cyclooctyne-functionalized D-amino acids (reactive epitope) and fluorogenic azides (reporter molecule with reactive handle) are suitable for imaging peptidoglycan in live cells (page 5459, right column, bottom paragraph). Shieh teaches that the platform facilitates the in vivo imaging of peptidoglycan in pathogenic bacteria (page 5460, left column, bottom paragraph). Shieh images peptidoglycan in three different species of bacteria: Gram-positive bacteria Mycobacterium smegmatis, Corynebacterium glutamicum, and Listeria monocytogenes (page 5459, right column, Copper-Free PG Imaging with Fluorogenic NIR Azide Probes and page 5459 left column, paragraph 3).
Shieh does not teach growing the bacterial cells in the presence of tunicamycin.
Campbell teaches growing S. aureus in the presence of concentrations of tunicamycin sufficient to abolish wall teichoic acid (WTA) biosynthesis but not affect growth (page 108, right column, bottom paragraph; Figure 2). Campbell Figure 1 illustrates that WTA are anchored to peptidoglycan in bacterial cell walls. Campbell teaches that the combination of tunicamycin and methicillin sensitizes MRSA strains to beta-lactams (page 109, paragraph bridging left and right columns). Campbell teaches that the synergy between TarO inhibition (via tunicamycin) of the native peptidoglycan transpeptidase in MRSA strains suggests that WTA biosynthesis is functionally coupled to PG biosynthesis in S. aureus (page 110, right column, paragraph 1). Campbell teaches that tunicamycin should provide a useful tool for efforts to identify the molecular mechanisms that link WTA and PG biosynthesis in S. aureus (page 114, right column, paragraph 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace Shieh’s bacteria with Campbell’s S. aureus cells, culture the cells in the presence of tunicamycin, and then fluorescently image the cells and their peptidoglycan via Shieh’s method in order to study the molecular mechanisms that link WTA and PG biosynthesis in S. aureus. The person of ordinary skill in the art would have had a reasonable expectation of success given that Campbell teaches that S. aureus is capable of growing in the presence of low concentrations of tunicamycin that inhibit WTA biosynthesis (Figure 2) and Shieh is able to fluorescently label and image three different strains of Gram positive bacteria.
Claim 5 is rejected under 35 U.S.C. 103 as being unpatentable over Shieh et al. (Proceedings of the National Academy of Sciences 111.15 (2014): 5456-5461) In view of Foxley et al. (ACS medicinal chemistry letters 8.10 (2017): 1083-1088).
Shieh teaches incubating bacteria with endobcnDala 14 (cyclooctyne D-alanine analogue, see Fig. 7), washing away excess amino acid, and then incubating the bacteria with compound 11 (an azido Si-rhodamine) for 1 h and measuring fluorescence (page 5459, right column, bottom paragraph). Shieh teaches that the cyclooctyne-functionalized D-amino acids and fluorogenic azides are suitable for imaging peptidoglycan in live cells (page 5459, right column, bottom paragraph). Shieh teaches that the platform facilitates the in vivo imaging of peptidoglycan in pathogenic bacteria (page 5460, left column, bottom paragraph). Shieh images peptidoglycan in three different species of bacteria: Gram-positive bacteria Mycobacterium smegmatis, Corynebacterium glutamicum, and Listeria monocytogenes (page 5459, right column, Copper-Free PG Imaging with Fluorogenic NIR Azide Probes and page 5459 left column, paragraph 3).
Shieh does not teach culturing the cells in the presence of positively charged, branched polyethylenimine (BPEI) prior to contacting the cells with one or more test molecules (Shieh’s azido Si-rhodamines).
Regarding claim 5, Foxley teaches that branched polyethylenimine restores susceptibility of methicillin-resistant Staphylococcus aureus (MRSA) to β-lactam antibiotics (Abstract). Foxley’s BPEI is positively charged because it is polycationic (page 1086, right column, line 3). Foxley teaches that autolysins are used by bacterial cells to lyse peptidoglycan strands during cell division, allowing separation of daughter cells (page 1086, right column, bottom paragraph). Foxley teaches that MRSA aggregates after BPEI exposure, possibly due to slowing of autolysis (page 1087, left column, paragraph 1). However, the origin of BPEI-induced slowing of autolysis is unknown (page 1087, left column, paragraph 1).
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace Shieh’s bacteria with Foxley’s S. aureus cells, culture the cells in the presence of BPEI, and then fluorescently image the cells and their peptidoglycan via Shieh’s method in order to study the effect of BPEI on cell wall peptidoglycan. The person of ordinary skill in the art would have had a reasonable expectation of success given that Foxley teaches that BPEI is non-toxic (page 1087, left column, bottom paragraph) and Shieh is able to fluorescently label and image three different strains of Gram positive bacteria (page 5459, right column, Copper-Free PG Imaging with Fluorogenic NIR Azide Probes and page left column, paragraph 3).
Claims 13-14 are rejected under 35 U.S.C. 103 as being unpatentable over Shieh et al. (Proceedings of the National Academy of Sciences 111.15 (2014): 5456-5461).
Shieh teaches incubating bacteria with endobcnDala 14 (cyclooctyne D-alanine analogue, see Fig. 7), washing away excess amino acid, and then incubating the bacteria with compound 11 (an azido Si-rhodamine) for 1 h and measuring fluorescence (page 5459, right column, bottom paragraph). Shieh teaches that the cyclooctyne-functionalized D-amino acids and fluorogenic azides are suitable for imaging peptidoglycan in live cells (page 5459, right column, bottom paragraph). Shieh teaches that the platform facilitates the in vivo imaging of peptidoglycan in pathogenic bacteria (page 5460, left column, bottom paragraph).
Shieh also teaches incorporating endobcnDala 14 (cyclooctyne D-alanine analogue, see Fig. 7) into the cell walls of Gram-positive bacteria and then reacting with commercially available azido-PEG-3-carboxyrhodamine (page 5459, left column, paragraph 3).
However, Shieh does not measure the fluorescence in live cells with the reporter molecule azido-PEG-3-carboxyrhodamine.
It would have been obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to replace azido Si-rhodamine with azido-PEG-3-carboxyrhodamine in the live cell assay of Shieh because azido-PEG-3-carboxyrhodamine is commercially available whereas azido Si-rhodamine is synthesized (page 5456, right column, bottom paragraph, Results and Discussion, Synthesis and Evaluation of Azido Si-Rhodamines). The person of ordinary skill in the art would have had a reasonable expectation of success in the replacement of azido Si-rhodamine with azido-PEG-3-carboxyrhodamine because both are fluorogenic azides.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CANDICE LEE SWIFT whose telephone number is (571)272-0177. The examiner can normally be reached M-F 8:00 AM-4:30 PM (Eastern).
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Louise Humphrey can be reached at (571)272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/CANDICE LEE SWIFT/Examiner, Art Unit 1657
Prosecution Insights