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 .
Amendment Entry
Applicant’s response to the Non-Final Action dated 8/14/25 is acknowledged (reply filed 9/15/25). In the amendment filed therein claims 21, 25-28, and 31 were modified. New claims 32-34 were added. While claims 1, 21-23, and 30 are canceled without prejudice or disclaimer.
Claims 2-20 and 24 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 7/8/25.
Currently, claims 25-29 and 31-34 are under consideration.
Rejections and/or objections of record not reiterated herein have been withdrawn.
Priority
5. This application has a priority date of July 9, 2020: This application is a continuation of U.S. Patent Application Serial No. 18/004,790, which is a national stage application under 35 U.S.C. § 371 of International Application No. PCT/FI2021/050529, filed July 7, 2021, which claims priority benefit to Finland Application No. 20205738, filed July 9, 2020.
New GROUNDS OF REJECTIONS NECESSITATED BY AMENDMENTS
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.
6. Claims 26-27 and 34 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.
A. Claims 26-27 and 34 are vague and indefinite because they recite the term “alcohol solution”. Claims 26-27 and 34 are dependent on claim 25 which reads on non-buffered alcohol solution. It is suggested that claims 26-27 and 34 use consistent terminology “non-buffered alcohol solution” to remove ambiguity. Appropriate correction is required.
Claim Rejections - 35 USC § 103
7. 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.
8. Claim(s) 25-29 and 31-34 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gowda et al. (Anal. Chem. 2017 April 18; 89(8):4620-4627) in view of Gonzalez et al. (Yeast, Vol.14, pages 1347-1355, 1997) and Sellick et al. (Metabolomics, 18 May 2010; Vol.6, pages 427-438).
Gowda et al. disclose a simple 1H NMR experiment that can simultaneously measure coenzymes and antioxidants in extracts of whole human blood, in addition to the nearly 70 metabolites that were previously shown to be quantitated in serum/plasma. Coenzymes of redox reactions: oxidized/reduced nicotinamide adenine dinucleotide (NAD+ and NADH) and nicotinamide adenine dinucleotide phosphate (NADP+ and NADPH); coenzymes of energy including adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP); and antioxidants, the sum of oxidized and reduced glutathione (GSSG and GSH) can be measured with essentially no additional effort. A new method was developed for detecting many of these unstable species without affecting other blood/blood plasma metabolites. The identities of coenzymes and antioxidants in blood NMR spectra were established combining 1D/2D NMR techniques, chemical shift databases, pH measurements and, finally, spiking with authentic compounds. See abstract.
Gowda et al. demonstrate that their quantitative serum/plasma-based approach can be extended to whole blood metabolomics to expand the metabolite pool and encompass physiologically sensitive coenzymes of redox reactions and energy, as well as antioxidants, in addition to the nearly 70 blood metabolites that were quantified in serum/plasma. See page 3.
Each protein precipitation/metabolite extraction method used 200 to 400 μL of whole blood, plasma, or RBCs. The biospecimens were mixed with cold methanol in a 1:2 sample/methanol (v/v) ratio, 55% methanol in a 1:9 ratio, methanol/chloroform in a 1:2:2 or 1:3.3:6.6 ratio or 4% trichloroacetic acid in a 1:5 ratio (Table S1). All sample solutions were then vortexed for 30 s, sonicated for 2 min at 4 °C, and incubated at −20 °C for 20 min. The mixtures were centrifuged at 13 400 rcf for 30 min to pellet proteins and cell debris. Clear aqueous solutions were transferred to fresh vials and dried using an Eppendorf Vacufuge-Plus vacuum concentrator for 5 h. Dried samples were mixed with 600 μL phosphate buffer containing 25 μM TSP, spun to sediment any residue, and the supernatants were transferred to 5 mm NMR tubes for analysis. See page 4.
Gowda et al. differ from the instant invention in not specifically teaching an incubation at high temperatures of 40-80°C for 10sec-10min.
However, Gonzalez et al. teach a simple and reliable method for the efficient inactivation of metabolism and for quantitative metabolite extraction from yeast cells.
The method is based on the use of a boiling solution made of 75% ethanol (volume/final volume) buffered with 70 mM-Hepes (final concentration), pH 7.5, to guarantee the stability throughout the whole procedure of a large variety of metabolites, including all glycolytic intermediates, nucleotides, pyridine nucleotides and organic acids compounds. The extraction is fast, requiring only 3 min incubation of yeast cells in the ethanol-buffered mixture maintained at 80 degrees C. It can be carried out either directly by spraying the cells into the boiling mixture, or after quenching the whole culture in 60% methanol kept at -40 degrees C.
Extracts are subsequently concentrated by evaporation under partial vacuum and the residue is resuspended in a small volume of water. This concentration step and the use of a highly sensitive analytical method allow us to quantify metabolites in less than 10 mg dry weight cells. This method, which can be applied to other fungi, could be very helpful for the determination of true metabolites in mutants and for metabolic flux analysis. See abstract.
While, Sellick et al. disclose methods of optimizing extraction procedures for metabolite targets. The extraction methods tested included cold methanol, hot ethanol, acid, alkali and methanol/chloroform plus combinations thereof. The extraction of metabolites using two 100% methanol extractions followed by a final water extraction recovered the largest range of metabolites. For the majority of metabolites, extracts generated in this manner exhibited the greatest recovery with high reproducibility. Therefore, this was the best extraction method for attaining a global metabolic profile from a single sample. However, another parallel extraction method (e.g. alkali) may also be required to maximize the range of metabolites recovered (e.g. non-polar metabolites). See abstract.
In the hot ethanol procedure, a cell pellet was resuspended in 1 ml 90°C 100% ethanol and incubated at 90°C for 10 min. The samples were cooled on ice for 5 min, centrifuged at 15,000×g for 1 min and the supernatant removed and lyophilized. See section 2.4.3 The extraction with hot ethanol provided excellent recovery of fatty acids (e.g. stearic acid and palmitic acid). It is likely that this was due to the combination of heat and organic solvent increasing the solubility of the fatty acids.
As with cholesterol detection, decreasing the methanol:water ratio significantly decreased the recovery of fatty acids (see Fig. 7a). These data highlight the importance of using appropriate extraction processes for targeted analysis of specific metabolic pathway components.
Gonzalez et al. teach extraction procedure in yeast cell, while Sellick et al. teach extraction in mammalian cells (CHO cells).
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 incorporate the hot ethanol or boiling solution extract procedure taught by Gonzalez et al. and Sellick et al. into the method of Gowda et al. as a means for generating stable metabolites, allowing for complete permeabilization (including fatty acids) for total and reproductible release of the metabolites, with accurate and valid results. See Gonzalez et al. -page 1350, 1st column, Results and Discussion. And Sellick et al. -page 435.
One skilled in the art would have been motivated to employ the boiling extraction of Gonzalez et al. and Sellick et al. to guarantee the stability throughout the whole procedure of a large variety of metabolites, including all glycolytic intermediates, nucleotides, pyridine nucleotides and organic acids compounds with quick extraction, requiring only 3 min incubation in an ethanol-buffered mixture maintained at 80 degrees C. See abstract of Gonzalez et al. and abstract, section 2.4.3, and page 435 of Sellick et al.
It is noted that KSR forecloses the argument that a specific teaching, suggestion, or motivation is required to support a finding of obviousness. See recent Board decision Ex parte Smith,— USPQ2d—, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007)(citing KSR, 82 USPQ2d at 1396).
Response to Arguments
9. Applicants arguments and amendments dated 9/15/25 have been carefully considered and new rejections are presented herein.
Applicant contends that the reference to Lazzarino et al. teach tissue samples that include homogenized liver, brain or heart tissue, and the extraction medium (prior to HPLC analysis) is buffered acetonitrile. Accordingly, the reference to Gowda et al. (Anal. Chem., 2017 April 18; 89(8), pages 4620-4627) has been introduced to teach extraction in whole blood.
Gonzalez et al. demonstrate the utility of the heat extraction in yeast cells while Sellick et al. employ hot ethanol with temperatures as high as 90°C to release fatty acids for metabolite measurements. Absent evidence to the contrary it would have been mere optimization to include a heat extraction as demonstrated by the prior art teachings in the whole blood extraction procedures of Gowda et al.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986).
Double Patenting
10. The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used.
A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
11. Claims 25-29 and 31-34 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 7, 15, 16, 21, 22, 24, 25, 26, 27, 49, 50, 51, 53, 55, 56, 57, 58, 59, 61, and 69 of copending Application No. 18/004,790 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other because the claims are drawn to methods of preparing an extract comprising metabolites from a sample of a subject, wherein the method comprises: allowing the sample to contact with a non-buffered alcohol solution, with an alcohol concentration of about 30-80% at a high temperature of about 40 — 80 °C to obtain a mixture of the sample and the alcohol solution. The instantly claimed method is encompassed in the method claims of application number 18/004,790. For example, see claims 1 step A and 49 in the ‘790 Patent.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Response to Arguments
12. Applicant traverses the provisional rejection of the instant claims for non-statutory double patenting over claims 1, 2, 7, 15, 16, 21, 22, 24, 25, 26, 27, 49, 50, 51, 53, 55, 56, 57, 58, 59, 61 and 69 of co-pending Application No. 18/004,790 in view of the amendments presented herein. Examiner has carefully considered the amendments but the claims remain provisionally rejected because the invention of claims 25-29 and 31-34 are encompassed by the claims in the ‘790 Patent (see claims 1 step A and claim 49).
13. For reasons aforementioned, no claims are allowed.
14. 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.
Remarks
15. Prior art made of record and not relied upon is considered pertinent to the applicant’s disclosure:
A. Kamlage et al. (WO2015/145387A1) disclose blood sampling for metabolite measurements.
16. Any inquiry concerning this communication or earlier communications from the examiner should be directed to LISA V COOK whose telephone number is (571)272-0816. The examiner works a flexible schedule but can normally be reached on Monday-Friday from 9am to 5pm.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Samira Jean-Louis, can be reached on 571-270-3503. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of an application may be obtained from the Patent Application Information Retrieval (PAIR) system. Status information for published applications may be obtained from either Private PAIR or Public PAIR. Status information for unpublished applications is available through Private PAIR only.
For more information about the PAIR system, see http://portal.uspto.gov/external/portal. Should you have questions about access to the Private PAIR system, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free).
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.
Lisa V. Cook
Patent Examiner
Art Unit 1642
Hoteling
10/22/25
/LISA V COOK/Primary Examiner, Art Unit 1642
Prosecution Insights