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 .
Response to Arguments
Applicant’s arguments with respect to claim(s) 1-20 have been considered but are moot because the new ground of rejection does not rely on the combination of references applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
With respect to the rejections under 35 U.S.C. 112(b), the Examiner notes that Applicant has amended the claims, and provided sufficient arguments to overcome the rejections. As such, the rejections under 35 U.S.C. 112(b) have been removed.
With respect to the prior art rejections, Applicant has amended the claims the recite first and second centrifuge plates or tubes not comprising membranes or spin columns, and argued that reference to Wang et al., teach utilizing spin columns and therefore cannot anticipate the claims. After reviewing reference to Wang et al., the Examiner contends that the reference no longer anticipates independent claim 1 as the reference does teach utilizing spin columns. However, as detailed below, the claims now stand rejected under 35 U.S.C. 103 as being obvious over the combination of Wang et al., in view of Sagova-Mareckova et al., wherein reference to Sagova Mareckova et al., teach a method of soil DNA extraction that does not utilize spin columns or membranes. Because reference to Sagova-Mareckova et al., is newly cited, the Examiner will not argue the merits of its teachings here, but will instead rely on the rejection detailed below. Therefore, in light of the teachings of the prior art, the Examiner contends that the limitations of the instant claims are taught by the references cited below, thus the claims are not in condition for allowance.
Claim Interpretation
Content of Specification
(k) CLAIM OR CLAIMS: See 37 CFR 1.75 and MPEP § 608.01(m). The claim or claims must commence on a separate sheet or electronic page (37 CFR 1.52(b)(3)). Where a claim sets forth a plurality of elements or steps, each element or step of the claim should be separated by a line indentation. There may be plural indentations to further segregate subcombinations or related steps. See 37 CFR 1.75 and MPEP 608.01(i)-(p).
The claimed invention is defined by the positively claimed steps, the process steps listed on separate indented lines listed in the body of the claim after the transitional phrase, “comprising”.
For claim 18, the Examiner suggests that Applicant amend the claims such that the full name of the compounds are recited prior to the abbreviation. For example, the claims should recite “sodium chloride (NaCl)” “Tris-EDTA (TE) and “centrimonium bromide (cTAB)”.
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.
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) 1-3, and 6-10 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al., (CN 1990863) in view of Sagova-Mareckova et al., (Appl. Environ. Microbiol. Vol 74, May 2008).
Regarding claims 1 and 10, Wang et al., teach a process for extracting DNA from soil comprising lysing cells in a buffer comprising centrimonium bromide(page 2 paragraph 4, page 3 paragraph 2), washing and re-suspending quartz sand and silica powder in water (page 3 paragraph 1), binding the released DNA to a silica substrate (page 2 paragraph 4, page 3 paragraphs 5 and 6), washing non-DNA from the substrate (page 4 paragraph 2), and eluting DNA in an elution buffer(page 4 paragraph 4). With respect to the first and second centrifuge plates or tubes, the Examiner notes that claim 1 is drafted with open-ended language (comprising) that does not preclude utilizing any number of centrifuge plates or tubes. As such, the Examiner contends that the number of centrifuge tubes taught by Wang et al., is within the scope of the claim. Wang et al., do not teach a process that does not comprise membranes or spin columns.
Sagova-Mareckova et al., teach a method of extracting soil DNA wherein the method does not require the use of membranes or spin columns (Experimental design, page 2903). Sagova-Mareckova et al., teach that extraction methods with spin columns gave the lowest yield of DNA, thereby providing an advantage of increased DNA yield in processes that do not require spin columns (Results, page 2904, first full paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., wherein spin columns are not utilized in order to provide for increased yields of DNA as taught by Sagova-Mareckova et al.
Regarding claim 2, Wang et al., teach extraction from 0.5g of soil, whereas Sagova-Mareckova et al., teach 250g of soil, but do not explicitly teach the sample ranging from 250 to 750 µg of soil. The Examiner is reading this limitation as optimization through routine experimentation which would have been obvious to one of ordinary skill in the art (MPEP 2144.05 II A). The MPEP states that where the general conditions of a claim are disclosed in the prior art, itis not inventive to discover the optimum or workable ranges by routine experimentation. One of ordinary skill in the art would have been motivated to discover the smallest sample size that yields a suitable amount of DNA in order to reduce the amount of reagents required for the extraction process. Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., in view of Sagova-Mareckova et al., wherein the sample size is reduced from 0.5g to a range of 250 µg to 750 µg as optimization requires only routine skill in the art
Regarding claim 3, Wang et al., teach mixing the soil sample and lysis buffer in a 2 ml centrifuge tube (page 3 paragraphs 1 and 2), thus the volume of the sample mixed with lysis buffer meets the limitation of about 2 ml as the 2 ml is the maximum volume of the vessel holding the sample and lysis buffer.
Regarding claim 6, Wang et al., do not teach a buffer comprising proteinase K, thus the Examiner contends that the prior art buffer does not comprise proteinase K.
Regarding claim 7, Wang et al., do not teach a buffer comprising sodium dodecyl sulfate, lysozymes, and glusulase, thus the Examiner contends that the prior art buffer does not comprise the components of claim 7.
Regarding claim 8, Wang et al., teach a solution comprising diatomaceous earth and water (paragraph 0015).
Regarding claim 9, Wang et al., do not teach the silica solution comprising potassium iodide, thus the Examiner contends that the prior art buffer does not comprise potassium iodide.
Claim(s) 4 and 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al., (CN 1990863) in view of Sagova-Mareckova et al., (Appl. Environ. Microbiol. Vol 74, May 2008) as applied to claim 1 above, and further in view of Reed et al., (US 2009/0215125).
Regarding claim 4, Wang et al., in view of Sagova-Mareckova et al., do not teach a silica solution comprising 6M guanidine thiocyanate.
Reed et al., teach that it is advantageous to provide 6M guanidine thiocyanate as a means of facilitating release and binding of nucleic acids to glass surfaces (paragraph 0086).
Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., to include 6M guanidine thiocyanate in a silica solution in order to facilitate the release and binding of nucleic acids as taught by Reed et al.
Regarding claim 5, Wang et al., in view of Sagova-Mareckova et al., do not teach utilizing sonication to lyse cells.
Reed et al, teach a process of nucleic acid extraction wherein cells are lysed by sonication (paragraph 0087). Reed et al., teach that lysing cells by sonication is well known and routinely utilized in the art (paragraph 0087). The Examiner is reading this combination as combining prior art elements according to known methods to yield predictable results (see MPEP2141 II A) which would have been obvious to one of ordinary skill in the art. The Examiner contends that based on the teachings of Reed et al., one of ordinary skill in the art would have found it obvious to utilize sonication to lyse cells as sonication is recognized as a routine technique for lysing cells. Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., in view of Sagova-Mareckova et al., to utilize a sonication buffer as combining prior art elements according to known methods to yield predictable results requires only routine skill in the art.
Claim(s) 11, 13, and 14 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al., (CN 1990863) in view of Sagova-Mareckova et al., (Appl. Environ. Microbiol. Vol 74, May 2008) and further in view of MoBio PowerSoil Extraction Method (March 2012).
Regarding claims 11 and 14, Wang et al., teach a process for extracting DNA from soil comprising lysing cells in a buffer comprising centrimonium bromide(page 2 paragraph 4, page 3 paragraph 2), washing and re-suspending quartz sand and silica powder in water (page 3 paragraph 1), binding the released DNA to a silica substrate (page 2 paragraph 4, page 3 paragraphs 5 and 6), washing non-DNA from the substrate (page 4 paragraph 2), and eluting DNA in an elution buffer(page 4 paragraph 4). With respect to the first and second centrifuge plates or tubes, the Examiner notes that claim 1 is drafted with open-ended language (comprising) that does not preclude utilizing any number of centrifuge plates or tubes. As such, the Examiner contends that the number of centrifuge tubes taught by Wang et al., is within the scope of the claim. Wang et al., do not teach a process that does not comprise membranes or spin columns.
Sagova-Mareckova et al., teach a method of extracting soil DNA wherein the method does not require the use of membranes or spin columns (Experimental design, page 2903). Sagova-Mareckova et al., teach that extraction methods with spin columns gave the lowest yield of DNA, thereby providing an advantage of increased DNA yield in processes that do not require spin columns (Results, page 2904, first full paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., wherein spin columns are not utilized in order to provide for increased yields of DNA as taught by Sagova-Mareckova et al. Wang et al., in view of Sagova-Mareckova et al., do not teach utilizing first and second centrifuge plates.
MoBio teaches a process for extracting DNA from soil wherein centrifuge plates are utilized lyse, wash, and elute DNA from soil samples (page 2 steps 2 and 5, pages 3-4 steps 11 30, page 4 step 31). With respect to claim 14, the Examiner contends that any centrifuge plate can be reusable provided that it is cleaned prior to any additional uses. As such, the centrifuge plates of MoBio are considered as reusable. The Examiner is reading this combination as combining prior art elements according to known methods to yield predictable results which would have been obvious to one of ordinary skill in the art (MPEP 2141 III). Reference to MoBio clearly teaches utilizing centrifuge plates for extracting DNA from soil samples, thus one of ordinary skill in the art would have found it obvious to utilize the process of Wang et al., in view of Sagova-Mareckova et al., with a centrifuge plate as combining prior art elements according to known methods to yield predictable results requires only routine skill in the art.
Regarding claim 13, Wang et al., teach mixing the soil sample and lysis buffer in a 2 ml centrifuge tube (page 3 paragraphs 1 and 2), thus the volume of the sample mixed with lysis buffer meets the limitation of about 2 ml as the 2 ml is the maximum volume of the vessel holding the sample and lysis buffer.
Claim(s) 12 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al., (CN 1990863) in view of Sagova-Mareckova et al., (Appl. Environ. Microbiol. Vol 74, May 2008) in view of MoBio PowerSoil Extraction Method (March 2012), and further in view of Kappel et al., (US 2004/0259162).
Regarding claim 12, Wang et al., in view of Sagova-Mareckova et al., in view of MoBio do not teach a centrifuge plate having a capacity of abut 8 mL or about 10 mL.
Kappel et al., teach a solid phase cell lysis and capture platform wherein a 7.5ml container (paragraph 0135) is utilized for cell lysis and nucleic acid capture (paragraph 0007). Kappel et al., teach that the containers may hold a volume of about 100ml (paragraph 0026). Kappel et al., also teach that the containers can be in the format of a multi-well plate (paragraph 0028). Kappel et al., teach that utilizing the container or multi-well plate provides the advantage of eliminating the need to centrifuge the solution to remove insoluble material (paragraph 0007).
Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., in view of Sagova-Mareckova et al., in view of MoBio, to utilize a container or multi well plate as taught by Kappel et al., in order to eliminate the need to centrifuge a solution to remove insoluble material as taught by Kappel et al.
Claim(s) 15, 16, 19, and 20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al., (CN 1990863) in view of Sagova-Mareckova et al., (Appl. Environ. Microbiol. Vol 74, May 2008) and further in view of Reed et al., (US 2009/0215125).
Regarding claims 15 and 20, Wang et al., teach a process for extracting DNA from soil comprising lysing cells in a buffer comprising centrimonium bromide (page 2 paragraph 4, page 3 paragraph 2), washing and re-suspending quartz sand and silica powder in water (page 3 paragraph 1), binding the released DNA to a silica substrate (page 2 paragraph 4, page 3 paragraphs 5 and 6), washing non-DNA from the substrate (page 4 paragraph 2), and eluting DNA in an elution buffer(page 4 paragraph 4). With respect to the first and second centrifuge plates or tubes, the Examiner notes that claim 1 is drafted with open-ended language (comprising) that does not preclude utilizing any number of centrifuge plates or tubes. As such, the Examiner contends that the number of centrifuge tubes taught by Wang et al., is within the scope of the claim. Wang et al., also teach the components of the extraction process can be formed into a kit (paragraph 0006). Wang et al., do not teach a process that does not comprise membranes or spin columns.
Sagova-Mareckova et al., teach a method of extracting soil DNA wherein the method does not require the use of membranes or spin columns (Experimental design, page 2903). Sagova-Mareckova et al., teach that extraction methods with spin columns gave the lowest yield of DNA, thereby providing an advantage of increased DNA yield in processes that do not require spin columns (Results, page 2904, first full paragraph).
Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., wherein spin columns are not utilized in order to provide for increased yields of DNA as taught by Sagova-Mareckova et al. Wang et al., in view of Sagova-Mareckova et al., do not teach a sonication buffer.
Reed et al, teach a process of nucleic acid extraction wherein cells are lysed by sonication in a buffer comprising cTAB (paragraph 0087). Reed et al., also teach soil as a suitable sample from which nucleic acids may be extracted (paragraphs 0097, 0098). Reed et al., teach that lysing cells by sonication is well known and routinely utilized to lyse cells in a sample (paragraph 0087). Reed et al., also teach forming the components of the extraction process in a kit that includes various solutions and buffers (paragraph 0010). The Examiner is reading this combination as combining prior art elements according to known methods to yield predictable results (see MPEP 2141 II A) which would have been obvious to one of ordinary skill in the art. The Examiner contends that based on the teachings of Reed et al., one of ordinary skill in the art would have found it obvious to utilize sonication to lyse cells in a buffer comprising cTAB as both are routine techniques utilized in the art. Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., in view of Sagova-Mareckova et al., to utilize a sonication buffer comprising cTAB as combining prior art elements according to known methods to yield predictable results requires only routine skill in the art.
Regarding claim 16, Wang et al., do not teach the silica solution comprising potassium iodide, thus the Examiner contends that the prior art buffer does not comprise potassium iodide.
Regarding claim 19, Wang et al., in view of Sagova-Mareckova et al., in view of Reed et al., do not teach a buffer excluding proteinase K and sodium dodecyl sulfate, thus the Examiner contends that the prior art buffer does not comprise proteinase K and sodium dodecyl sulfate.
Regarding claim 20, Wang et al., do not teach a kit comprising metal beads, thus the Examiner contends that the prior art kit does not comprise metal beads.
Claim(s) 17 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al., (CN 1990863) in view of Sagova-Mareckova et al., (Appl. Environ. Microbiol. Vol 74, May 2008) in view of Reed et al., (US 2009/0215125), and further in view of Kappel et al., (US 2004/0259162).
Regarding claim 17, Wang et al., in view of Sagova-Mareckova et al., in view of Reed et al., do not teach a centrifuge plate comprising wells having a capacity of about 8 mL or about 10 mL.
Kappel et al., teach a solid phase cell lysis and capture platform wherein a 7.5ml container (paragraph 0135) is utilized for cell lysis and nucleic acid capture (paragraph 0007). Kappel et al., teach that the containers may hold a volume of about 100ml paragraph 0026). Kappel et al., also teach that the containers can be in the format of a multi-well plate (paragraph 0028). Kappel et al., teach that utilizing the container or multi-well plate provides the advantage of eliminating the need to centrifuge the solution to remove insoluble material (paragraph 0007).
Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., in view of Sagova-Mareckova et al., in view of Reed et al., to utilize a container or multi well plate as taught by Kappel et al., in order to eliminate the need to centrifuge a solution to remove insoluble material as taught by Kappel et al.
Claim(s) 18 is/are rejected under 35 U.S.C. 103 as being unpatentable over Wang et al., (CN 1990863) in view of Sagova-Mareckova et al., (Appl. Environ. Microbiol. Vol 74, May 2008) in view of Reed et al., (US 2009/0215125) as applied to claim 15 above, and further in view of Taguchi et al., (US 2009/0222941).
Regarding claim 18, Wang et al., in view of Sagova-Mareckova et al., in view of Reed et al., do not teach a buffer comprising NaCl, polyvinylpyrrolidine, TE, RNaseA, and cTAB.
Taguchi et al., teach a DNA extraction process (paragraph 0097) wherein a buffer comprising NaCl, polyvinylpyrrolidone, TE, RNaseA, and cTAB (paragraph 0099). Taguchi et al., also teach forming kits for DNA extraction (paragraph 0057). The Examiner is reading this combination as combining prior art elements according to known methods to yield predictable results which would have been obvious to one of ordinary skill in the art. Taguchi et al., clearly teach that a buffer comprising NaCl, polyvinylpyrrolidone, TE, RNaseA, and cTAB can be utilized in a DNA extraction process, thus one of ordinary skill in the art would have found it obvious to utilize the taught buffer in a DNA extraction process. Therefore, it would have been obvious to one of ordinary skill in the art at the time the invention was made to modify Wang et al., in view of Sagova-Mareckova et al., in view of Reed et al., wherein a buffer comprising NaCl, polyvinylpyrrolidone, TE, RNaseA, and cTAB is utilized as combining prior art elements according to known methods to yield predictable results requires only routine skill in the art.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DWAN A GERIDO whose telephone number is (571)270-3714. The examiner can normally be reached Mon-Fri 10-6.
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/DWAN A GERIDO/Examiner, Art Unit 1797 /LYLE ALEXANDER/Supervisory Patent Examiner, Art Unit 1797
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