DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on June 8, 2026, has been entered.
Claims 8 and 10 are cancelled.
Claims 1-7, 9, 11, and 12 are pending and 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.
Claims 1-7, 9, 11, and 12 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 rendered indefinite by the recitation “a second tray of a second shaker” in the second line of step (b). The recitation implies that the second shaker has a first tray. It is unclear whether the second shaker comprises two trays, and a first tray of the second shaker lacks antecedent basis. Since claim 1 is indefinite, then the claims incorporating claim 1, claims 2-12, are rendered indefinite. Thus, claims 1-12 are rejected under 35 U.S.C. 112(b). For the purpose of applying prior art, the “second tray” of the second shaker is being interpreted as the only tray of the second shaker.
Notice Re: Prior Art Available Under Both Pre-AIA and AIA
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.
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.
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.
Claims 1-7, 9, 11, and 12 are rejected under 35 U.S.C. 103 as being unpatentable over Ma (CN 103525866. Listed on IDS filed 12/5/24. Translation cited below, annexed to the Extended European Search Report of EP 21867584 of patent family of instant application) in view of Lewcock (Biocompare [online], December 13, 2013 [retrieved on 2026-09-16]. Retrieved from the Internet: <URL: https://www.biocompare.com/Editorial-Articles/151873-Get-Your-Samples-Moving-with-Laboratory-Rockers-and-Shakers/>. Reading mode pages of website cited below), Honig (WO 2017/112454), Engebrecht (Current Protocols in Immunology. 1998. Chapter 10: Unit 10.3. pages 10.3.1-10.3.10. Previously cited), and Ciccolini (Biotechnology and Bioengineering. 1998. 60(6): 768-770. Previously cited)
Ma discloses a method for preparing a plasmid (paragraph [0014] of Translation). The method comprises lysing a suspension of Escherichia coli to obtain an E. coli lysate, wherein the E. coli contains a plasmid (paragraphs [0015] and [0017] of Translation). The lysing of the E. coli suspension comprises mixing the E. coli suspension with a lysis solution containing 0.2 M NaOH and 1% SDS at 15-30 rpm (paragraphs [0017] and [0033] of Translation). This meets limitations of step (a) of instant claim 1 since it is directed to adding a lysis solution to a bacterial cell suspension to obtain a first mixture. The treated bacterial cell suspension is directed to the ‘preliminary bacterial cell lysate’ of instant claim 1. Further still, the lysis solution containing 0.2 M NaOH and 1% SDS of Ma is an ‘alkaline lysis buffer’ as instantly claimed because this same solution is taught in Engebrecht, specifically a 0.2 M NaOH solution containing 1% (w/v) SDS, for alkaline lysis (page 768, right column, first paragraph; page 769, left column, third paragraph of Engebrecht).
Then, the E. coli suspension treated by the lysis solution is mixed with a potassium acetate solution and stirred at 15-30 rpm in order to obtain the E. coli lysate (paragraphs [0017] and [0034] of Translation). Potassium acetate is directed to an acetate buffer, meeting the buffer limitations of instant claims 1 and 11. Therefore, this step of the lysing taught in Ma meets limitations of step (b) of instant claim 1 since it is directed to adding an acetate buffer (the potassium acetate solution) to the preliminary bacterial cell lysate to obtain a second mixture.
The mixing steps of Ma differ from the claimed invention in that they are accomplished by stirring, as opposed to shaking using a first shaker (for mixing the E. coli suspension with the lysis solution) and a second shaker (for mixing the lysis solution-treated E. coli suspension with the potassium acetate solution), as claimed. Further regarding the mixing, Ma differs from the claimed invention in that Ma does not expressly disclose that the combination of the E. coli suspension and the lysis solution (directed to the claimed ‘first mixture’) is placed on the first tray of a first 3D shaker and the combination of lysis solution-treated E. coli suspension and the potassium acetate solution (directed to the claimed ‘second mixture’) is placed on a ‘second tray’ (interpreted as the only tray) of a second 3D shaker, wherein the first tray and the second tray each forms an angle of about 10 degrees to about 20 degrees with respect to a horizontal plane.
Lewcock discloses laboratory rockers and shakers as labor-saving devices saving hours of manual mixing time (page 1, first paragraph of Reading mode). Results can be optimized by picking a device with motions and speeds specific to an application (page 1, third paragraph of Reading mode). For instance, similar results can be achieved with both a 2D (see-saw) and 3D (nutating) rocker by adjusting speed and tilt angle (page 1, third paragraph of Reading mode). Factors in selecting a particular model include the speed and orbit/tilt needed (page 1, last paragraph of Reading mode). 3D rockers move in a circular up and down motion, so that the wave generated moves around the vessel from corner to corner (page 2, first paragraph of Reading mode). For a shaker, considerations include the speed and shaking orbit that are needed (page 2, third paragraph of Reading mode).
Honig discloses a nutating mixer that has an angle adjustment mechanism that operates without the use of a tool (paragraph [0002]). Nutating mixers are used to mix samples for a broad range of molecular and biological mixing applications (paragraph [0003]). The nutating mixer of Honig includes a tray defined by a tray plane that is at a tilt angle relative to an axis perpendicular to a surface upon which the nutating mixer rests (paragraph [0005]). See Figure 1, showing the nutating mixer comprising a tray 30 capable of both nutating and supporting a sample container (paragraph [0017]). As shown in Figure 4, the tilt angle of the tray plane may be defined as the angle between a vertical axis 27 and a predetermined angle perpendicular to the tray plane (paragraph [0020]). The vertical axis 27 is the axis perpendicular to the surface upon which the nutating mixer 10 is resting (paragraph [0020]). The tilt angle, i.e., the angle between the vertical axis 27 and a predetermined axis 24, may be z (paragraph [0020]). The angle z may be between about 0 and about 30 degrees, or between about 15 and about 25 degrees, or may be about 20 degrees (paragraph [0020]). It is obvious, through applying geometry, that the angle of the tray (surface perpendicular to the predetermined axis 24 of Figure 4) to a horizontal plane (e.g., the surface upon which the nutating mixer 10 is resting) is the same as the z angle, i.e. between about 0 and about 30 degrees, or between about 15 and 25 degrees, or about 20 degrees.
Before the effective filing date of the claimed invention, it would have been obvious to the person of ordinary skill in the art to perform shaking using a 3D shaker (i.e. nutating mixer) comprising a tray having a tilt angle of between about 0 and about 30 degrees, instead of stirring, for each of the treatments with the lysis solution and the potassium acetate solution, such that a first 3D shaker is used for shaking with the lysis solution and a second 3D shaker is used for shaking with the potassium acetate solution, when performing the method of Ma for the predictable result of mixing the lysis solution with the E. coli suspension and mixing the potassium acetate solution with the E. coli suspension that had been treated with the lysis solution. It would have been a matter of simple substitution of one technique for another of mixing solutions with a cell suspension for the purpose of preparing a plasmid from bacterial cells, wherein the substitution is using a known 3D shaker as disclosed in Honig which has a tilt angle of between about 0 and about 30 degrees. As indicated in Lewcock and Honig, 3D shakers are known laboratory devices for mixing that are labor-saving (as pointed out in Lewcock) and have biological mixing applications. Additionally, a 3D shaker comprising a tray having a tilt angle of between about 0 and about 30 degrees is known in the art, specifically in Honig, and thus it would have been obvious to the skilled artisan to use such a 3D shaker to perform the mixing of Ma. A tilt angle as disclosed in Honig of between about 0 and about 30 degrees, such as 20 degrees, then signifies that the tray of the 3D shaker forms an angle with respect to a horizontal plane of between about 0 and about 30 degrees, such as 20 degrees. That angle range overlaps the claimed range of ‘about 10 degrees to about 20 degrees,’ thereby rendering obvious the claimed angle limitation. Further still, the angle of 20 degrees falls within the claimed range, thus meeting the claimed angle limitation. Moreover, it would have an obvious matter of routine optimization to have selected a tilt angle of between about 10 degrees to about 20 degrees because the selection and adjustment of tilt angle is recognized for rockers and shakers in laboratory applications, as indicated in Lewcock and Honig, and because those tilt angles are within the range of tilt angles recognized for 3D shakers such as the 3D shaker of Honig. It is noted that “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
In using 3D shakers, then the components that are to be mixed are necessarily placed on a tray of each 3D shaker since the tray of a 3D shaker is for nutating and supporting a sample container, as indicated in Honig (paragraph [0017]). Furthermore, it would have been an obvious matter of routine experimentation to vary the speed of the 3D shaker to a rotation speed ranging from about 10 rpm to about 30 rpm, from about 10 rpm to about 70 rpm, or from about 10 rpm to about 20 rpm (as in instant claim 2), when performing the method rendered obvious by Ma in view of Lewcock and Honig because the selection and adjustment of the speed is recognized for rockers and shakers in laboratory applications, as indicated in Lewcock which further recognizes that picking a device with specific speeds specific to the application will optimize results (page 1, third paragraph of Reading mode). The skilled artisan would have expected the rotation speed to be a results-effective optimizable parameter affecting the degree of mixing of components of a mixture. It is noted that “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Therefore, Ma in view of Lewcock and Honig renders obvious placing the ‘first mixture’ (resulting from adding the lysis solution to the E. coli cell suspension) on a first tray of a first 3D shaker, shaking without stirring the first mixture using the first 3D shaker at a rotation speed ranging from about 10 rpm to about 30 rpm (or from about 10 rpm to about 20 rpm) of step (a) of instant claim 1, as well as rendering obvious placing the ‘second mixture’ (resulting from adding the potassium acetate solution to the E. coli suspension treated with the lysis solution) on a ‘second tray’ (interpreted as the only tray) of a second 3D shaker, shaking without stirring the second mixture using the second 3D shaker at a rotation speed ranging from about 10 rpm to about 70 rpm of step (b) of instant claim 1, wherein the first tray and the second tray each forms an angle of about 0 degrees to about 30 degrees (overlaps the claimed range), about 10 degrees to about 20 degrees, or about 20 degrees (falls within the claimed range) with respect to a horizontal plane.
Ma in view of Lewcock and Honig differs from the claimed invention in that they do not expressly disclose that each of the shaking steps (the first shaking step at 10 rpm to about 30 rpm; the second shaking step at 10 rpm to about 70 rpm) is for about 1 minute to about 10 minutes, followed by incubation without shaking each mixture for about 1 minute to about 60 minutes (that is, incubation without shaking for about 1 minute to about 60 minutes after the shaking of the E. coli suspension and the lysis solution, and incubation without shaking for about 1 minute to about 60 minutes after the shaking of that suspension and the potassium acetate solution).
Engebrecht is a review of methods for preparing bacterial plasmid DNA free from chromosomal DNA (page 10.3.1, third paragraph). One method is a miniprep procedure in which plasmid-containing bacteria are lysed by treatment with a solution containing SDS, which denatures bacterial proteins, and NaOH, which denatures chromosomal and plasmid DNA (page 10.3.1, last paragraph). The mixture is neutralized with potassium acetate, causing the covalently closed plasmid DNA to reanneal rapidly, as well as causing the precipitation of most of the chromosomal DNA and bacterial proteins (page 10.3.1, last paragraph). The steps of the procedure are described on page 10.3.2, with the materials set forth in the paragraph bridging pages 10.3.1 and 10.3.2. In particular, an NaOH/SDS solution comprising 0.2 N NaOH and 1% SDS is added to a suspension of plasmid-bearing E. coli cells, mixed by tapping the tube with a finger, and placed on ice for 5 minutes. Placing the tube on ice for 5 minutes is directed to incubation without shaking. Then, a potassium acetate solution is added and vortexed at maximum speed for 2 seconds to mix. The mixture is then placed on ice for 5 minutes - this is directed to incubation without shaking.
Ciccolini discloses the laboratory preparation of plasmid DNA from Escherichia coli carrying the plasmid vector (page 768, paragraph bridging left and right columns). It includes an alkaline lysis reaction which normally starts by addition and gentle shaking of a known volume of cell suspension with a solution of sodium hydroxide (NaOH) containing sodium dodecyl sulfate (SDS) (page 768, right column, first paragraph). The alkaline rich environment of the mixture causes the denaturation of low molecular weight plasmid DNA and high molecular weight chromosomal DNA (page 768, right column, first paragraph). Following a period of about 5 minutes, which is thought to be sufficient for the lysis reaction and denaturation to be complete, the mixture is neutralized by the addition of a concentrated, chilled solution of potassium acetate (page 768, right column, first paragraph).
The study of Ciccolini investigated the time course of the SDS-alkaline lysis of recombinant E. coli cell suspensions (abstract). The course of reaction was followed by carrying out the lysis operation in the cup of a coaxial cylinder rheometer (page 769, left column, second paragraph). In particular, the lysis reaction experiment was started by addition of 0.2 M NaOH containing 1% (w/V) SDS, and recording the viscosity continuously as a function of time for up to 10-12 minutes (page 769, paragraph bridging left and right columns). The increase in viscosity reached a peak value between 80 and 120 seconds, i.e. between about 1.3 and 2 minutes (paragraph bridging pages 769 and 770). Ciccolini states that the time required for viscosity to rise to its final peak value evidently corresponded to the time for the completion of chromosomal DNA denaturation and maximal entanglement (80-120 s), and the gradual decrease in viscosity following the peak reflected the expected shear degradation of the denatured chromosomal DNA (page 770, right column, third paragraph). Also, the apparent viscosity falls to a steady value after about 200-400 seconds, i.e. about 3.3-6.7 minutes (page 770, left column, first paragraph).
Before the effective filing date of the claimed invention, it would have been an obvious matter of routine optimization to vary the length of time of the shaking for each treatment with the lysis solution and the potassium acetate solution using the respective first and second 3D shakers when performing the method rendered obvious by Ma in view of Lewcock and Honig, specifically varying the shaking time to about 1 minutes to about 10 minutes, or about 3 minutes to about 8 minutes for the two treatments; also, varying the shaking time to about 1 minute to about 8 minutes for the treatment with the lysis solution. This would have been obvious because the skilled artisan would have recognized that the length of time of the shaking would have affected the extent of the denaturation of the chromosomal and plasmid DNA by the lysis solution, the neutralization by the potassium acetate for reannealing the covalently closed plasmid DNA, and the precipitation of the chromosomal DNA and bacteria, based on the teachings of Engebrecht and Ciccolini, including the teaching of a reaction time of 1.3-3 minutes in Ciccolini which would have served as a starting point for optimization of the shaking time for the treatment with the lysis solution. It is noted that “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955).
Further still, before the effective filing date of the claimed invention, it would have been obvious to the person of ordinary skill in the art to incubate without shaking for 5 minutes, specifically placing on ice for 5 minutes, the mixtures after each treatment with the lysis solution and the potassium acetate solution when performing the method rendered obvious by Ma in view of Lewcock, Honig, Engebrecht, and Ciccolini. One of ordinary skill in skill in the art would have been motivated to do this because such incubation (without mixing) after mixing were well known, as indicated in Engebrecht and Ciccolini, for a method of preparing plasmids from plasmid-containing E. coli using the same treatment with a lysis solution comprising 0.2 M NaOH and 1% (w/v) SDS with a later treatment with potassium acetate solution. There would have been a reasonable expectation of obtaining an E. coli lysate for plasmid preparation, as sought by Ma, by this modification because these incubation periods were included in treatment with the same chemicals for plasmid release and recovery in Engebrecht and Ciccolini. The incubation without shaking time period of 5 minutes falls within the claimed range of ‘about 1 minute to about 60 minutes,’ thereby rendering obvious the time limitation of the claimed incubation without shaking of steps (a) and (b) of instant claim 1.
As such, Ma in view of Lewcock, Honig, Engebrecht, and Ciccolini renders obvious instant claims 1-4, 7, and 11.
Regarding instant claims 5 and 6, the references differ from the claimed invention in that they do not expressly disclose that the shaking using a second shaker of the E. coli suspension (which had been treated with the lysis solution) with the potassium acetate solution is at a rotation speed ranging from about 30 rpm to about 55 rpm as in instant claim 5, or from about 40 rpm to about 50 rpm as in instant claim 6. Engebrecht teaches mixing with the NaOH/SDS solution by tapping tube finger, whereas the mixing with the potassium acetate solution is by vortex at maximum speed (page 10.3.2). Before the effective filing date of the claimed invention, it would have been a matter of routine optimization to use a higher rotation speed of the shaking using the second 3D shaker of the potassium acetate solution with the E. coli suspension (that had been treated with the lysis solution), including optimization to a rotation speed ranging from about 30 rpm to about 55 rpm, or from about 40 rpm to about 50 rpm, when performing the method rendered obvious by Ma in view of Lewcock, Honig, Engebrecht, and Ciccolini, because the skilled artisan would have recognized that the rotation speed would have affected the mixing which is turn affects the extent of neutralization by the potassium acetate solution to cause the covalently closed plasmid DNA to reanneal and precipitation of the chromosomal DNA and bacterial proteins (see page 10.3.1, last paragraph of Engebrecht). Moreover, it would have been obvious to use a higher rotation speed of the shaking using a second shaker of the potassium acetate solution with the E. coli suspension because increased agitation was taught in Engebrecht for the treatment with potassium acetate solution as compared with the treatment with the lysis solution (solution containing SDA and NaOH). It is noted that “[W]here the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimum or workable ranges by routine experimentation.” In re Aller, 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955). Therefore, instant claims 5 and 6 are rendered obvious.
Regarding instant claim 9, as pointed out above, the lysis solution of Ma contains 0.2 M NaOH and 1% SDS (paragraphs [0017] and [0033] of Translation). This same solution is taught in Engebrecht, specifically a 0.2 M NaOH solution containing 1% (w/v) SDS, for alkaline lysis (page 768, right column, first paragraph; page 769, left column, third paragraph). Therefore, the lysis solution of Ma is directed to an alkaline lysis buffer comprising 1% (w/v) SDS and 200 mM NaOH. As such, instant claim 9 is rendered obvious.
Regarding instant claim 12, as pointed out above, the method of Ma is a method of preparing a plasmid. After obtaining the E. coli lysate through treatments with the lysis solution and the potassium acetate solution (paragraphs [0015] and [0017] of Translation), Ma teaches steps of microfiltration of the E. coli lysate to purify the E. coli lysate, subjecting the E. coli lysate to ultrafiltration, and isolating the plasmid from the ultrafiltrated lysate (paragraph [0015] of Translation). Thus, instant claim 12 is rendered obvious.
Response to Arguments
Applicant’s arguments, filed June 8, 2026, with respect to the rejection under 35 U.S.C. 103 of claims 1-7, 9, 11, and 12 as being unpatentable over Ma in view of Domanico, Engebrecht, and Ciccolini, have been fully considered and are persuasive. In particular, the amendment to claim 1 has overcome the rejection because the references do not expressly disclosing using 3D shakers wherein a tray of each 3D shaker forms an angle of about 10 degrees to about 20 degrees with respect to a horizontal plane.
Therefore, the rejection has been withdrawn. However, upon further consideration, a new ground(s) of rejection is made in view of the newly cited references Lewcock and Honig which are cited in combination with previously cited reference Ma as a primary reference and previously cited references Engebrecht and Ciccolini as secondary references.
Conclusion
No claims are allowed.
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/SUSAN E. FERNANDEZ/Examiner, Art Unit 1651
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