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 .
Election/Restrictions
Applicant’s election without traverse of Group I, species
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in the reply filed on 2/24/25 is acknowledged.
Upon further consideration, the species 5-bromo-2’deoxyuridine and 5-ethynyl-uridine are REJOINED to the elected 5-ethynyl-2’-deoxyuridine because prior art was identified that reads on the rejoined species during search, and thus no burden remained to search the species. Additionally, for the same reason, claims 19, 20, and 31 are rejoined. Claim 1 has been considered for 5-bromo-2’deoxyuridine, 5-ethynyl-uridine or 5-ethynyl-2’deoxyuridine.
Applicant asserted that claim 23 reads on the elected species of “labelling reagent comprising a biotin group” but it does not because the elected species does not have an alkynyl group. Rejoinder will be considered upon a finding of allowable subject matter.
Therefore, claims 23 and 41 are the only remaining withdrawn claims.
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.
Claim(s) 1, 6, 9, 17, 21, 22, 25, 26, 32, 37, and 40 is/are rejected under 35 U.S.C. 103 as being unpatentable over Baretto. (Click Chemistry Labeling of Rna: A New Tool for Microbial Biology. 2015. https://doi.org/10.17615/e32g-2071) in view of Lin et al. (IDS; Journal of Proteome Research, 2014, 13, 3523-3529).
Baretto teaches a method for the identification and analysis of viable and/or proliferating microorganisms in a sample comprising obtaining a sample having or suspected of having one or more types of microorganism, incubating the sample in the presence of 5-ethenyl uridine (methods, Figure 2 and throughout), labelling newly synthesized microbial nucleic acids by contacting them with a labeling reagent that selectively binds to or with the nucleoside or nucleotide analog (via click chemistry addition of capture tag (biotin); methods Figure 2 and throughout), isolating or purifying the labelled microbial nucleic acids (labeled nucleic acids were captured with paramagnetic beads (methods Figure 2 and throughout) and determining the identity of the microorganisms in the sample based on sequencing or determining the identity of the isolated or purified newly synthesized microbial nucleic acid (methods; PDF page 9-10). A pull-down agent (paramagnetic beads) is used to isolate the labeled newly synthesized nucleic acids (Figure 2; p. 8).
With regard to claim 6, the reference teaches carrying out this process on natural sediment samples, which are an environmental sample obtained from an environmental test site (PDF p. 10-11).
With regard to claim 9, the reference teaches detecting and sequencing E. coli RNA (p. 11).
With regard to claim 17, the reference teaches incubating the sample with EU for 2 hours and 38 minutes before isolating labeled RNA.
With regard to claim 21, the labeling reagent binds to the EU via click chemistry (Figure 2, and p. 9).
With regard to claim 22, the labeling reagent binds to the EU via azide click chemistry, wherein the azide group is on the capture group and binds do an alkynyl group on the EU via click chemistry (Figure 1).
With regard to claim 37, the identity of the newly synthesized nucleic acids was obtained via sequencing (p. 10).
With regard to claim 40, the newly synthesized nucleic acids are RNA, they are reverse transcribed and then sequenced (p. 10).
Baretto teaches that desthiobiotin was used instead of biotin to allow the release of RNA from the beads (p. 9). Baretto does not teach a method wherein the labelling reagent comprises a biotin group, and particularly does not teach one of the biotin groups recited in claim 25. Baretto does not teach wherein the labelling reagent comprises a chemically or enzymatically cleavable linker.
Lin teaches a method for removable biotin addition to a moiety using click chemistry. Lin exemplifies attachment of biotin via azide functionalized biotinyl linkers, which can be removed to elute the desired moiety. The labeling reagent taught by Lin is an azide-linker-biotin labelling reagent. The reference teaches an enrichment workflow using click chemistry and cleavage of the disulfide linker to release the desired moiety from the pull down reagent an biotin (abstract, Figure 2, throughout). The azide biotin structure containing a chemically cleavable disulfide bond is showing in figure 1(a) and is identical to the instantly elected structure.
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It would have been prima facie obvious to one having ordinary skill in the art to have substituted the labelling reagent taught by Baretto with the reagent taught by Lin. Because both Baretto and Lin are concerned with labeling and enriching moieties using labels added by click chemistry, it would have been obvious to substitute one label for another to achieve the predictable result of providing a functional enrichment scheme for isolating the target nucleic acids of Baretto. All the claimed elements were known in the art and one skilled in the art could have combined them with no change in their respective functions, and the combination would have yielded predictable results to one of ordinary skill in the art at the time of the invention.
Claim(s) 2, 7 and 8 is/are rejected under 35 U.S.C. 103 as being unpatentable over Baretto in view of Lin as applied to claims 1, 6, 9, 17, 21, 22, 25, 26, 32, 37, and 40 above, and further in view of Saha (US 2014/0228248).
The teachings of Baretto in view of Lin as they pertain to claim 1 and 6, from which claims 2, 7, and 8 depend are given previously in this Office action and fully incorporated here. Baretto in view of Lin does not teach a method wherein the sample is from a subject suspected of having a microbial infection or a foodstuff suspected of microbial contamination, or where an environmental sample is tested for contamination.
Saha teaches a similar method that includes steps of incubating a test sample from a subject suspected of having an infection with labeled nucleotide analog, allowing the analog to be incorporated and detecting the nucleic acids with incorporated nucleotides (p. 3, p. 7). The sample can be from an individual suspected of having bacterial disease or from a foodstuff (para 93). The foodstuff can include natural sources of drinking water such as fresh water springs, rivers, lakes, aquifers and the like (para 135), which in the context of Saha are environmental test sites being tested for microbial contamination.
It would have been obvious before the effective filing date to have applied the method taught by Baretto in view of Lin for identifying microbes present in a test sample to the samples taught by Saha in order to achieve the predictable outcome of surveying the sample for living bacteria. One would have been motivated to test the samples of Saha in order to identify potential infections microbes, as taught by Saha, using the method taught by Baretto in view of Lin which was demonstrated to be able to detect a wide variety of bacterial components in a sample.
Claim(s) 4-5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Baretto in view of Lin as applied to claims 1, 6, 9, 17, 21, 22, 25, 26, 32, 37, and 40 above, and further in view of Blauwkamp (WO 2016187234).
The teachings of Baretto in view of Lin as they pertain to claim 1, from which claims 4 and 5 depend are given previously in this Office action and fully incorporated here. Baretto in view of Lin teaches methods for studying live microbial populations in environmental water samples. Baretto in view of Lin do not teach a method removing non-microbial DNA from the sample.
Blauwkamp et al. teaches a method which includes enriching non-host sequences by providing the sample wherein the sample from the host comprises host nucleic acids associated with nucleosomes. Nonmicrobial DNA is not associated with nucleosomes (para 148). The reference teaches that a population of interest may be bacterial nucleic acids present in a complex mixture of host and non-host nucleic acids (para 88). The reference teaches removing at least a portion of the host nucleic acids associated with the nucleosomes by using one or more antibodies that bind histones immobilized on a column (see claim 88, at least).
Therefore, it would have been obvious before the effective filing date to have modified the method taught by Baretto in view of Lin so as to have used the histone binding technique to remove the DNA from non-microbial organisms from the sample. One would have been motivated to do so because Blauwkamp teaches that by depleting histone bound DNA microbial DNA can be enriched in a sample.
Claim(s) 35-36 is/are rejected under 35 U.S.C. 103 as being unpatentable over Baretto in view of Lin as applied to claims 1, 6, 9, 17, 21, 22, 25, 26, 32, 37, and 40 above, and further in view of Peplies et al. (APPLIED AND ENVIRONMENTAL MICROBIOLOGY, Mar. 2003, p. 1397–1407).
The teachings of Baretto in view of Lin as they pertain to claim 1, from which claim 35 depends are given previously in this Office action and fully incorporated here. Baretto in view of Lin teaches methods for studying live microbial populations in environmental water samples. Baretto in view of Lin does not teach identifying microbial species using a microarray.
Peplies teaches DNA Microarray-Based detection of Bacteria with 16S rRNA targeting oligonucleotide probes. The method taught by the reference includes amplifying target DNA using 16S primers targeting conserved sequences where the primers contain a fluorescent dye, and then applying the amplified sample to a microarray to identify bacterial species present in the sample (methods).
It would have been obvious to have modified the methods taught by Baretto in view of Lin so as to have included a step of amplifying and applying nucleic acids to a microarray as taught by Peplies et al. because Peplies teaches “Our results show that, compared to standard hybridization formats such as fluorescence in situ hybridization, a large number of oligonucleotide probes with different characteristics can be applied in parallel in a highly specific way without extensive experimental effort (abstract).”
Claim(s) 38-39 is/are rejected under 35 U.S.C. 103 as being unpatentable over Baretto in view of Lin as applied to claims 1, 6, 9, 17, 21, 22, 25, 26, 32, 37, and 40 above, and further in view of Bruinsma et al. BMC Genomics (2018) 19:722; 16 pages.
The teachings of Baretto in view of Lin as they pertain to claim 1 and 37, from which claims 38 and 39 depend are given previously in this Office action and fully incorporated here. Baretto in view of Lin teaches methods for studying live microbial populations in water samples and sequencing nucleic acids. Baretto in view of Lin does not teach identifying microbial species using a using a transposome based sequencing method, and in particular a method that employs bead-linked transposomes.
Bruinsma teaches such a method. See Figure 7, which includes all of the steps recited in claim 39, see Figure 7 and p. 12.
It would have been obvious to have modified the method taught by Baretto in view of Lin so as to have used the sequencing protocol taught by Bruinsma because Bruinsma teaches “This methodology generates normalized libraries for sequencing to facilitate a quantification-free workflow, and expands the range of possible sample types, providing significant improvements in flexibility and performance over solution-based library preparation kits (p. 11).”
Response to Remarks
With regard to the previously set forth rejection using Baretto in view of Lin, applicant argues that these fail to teach or suggest the claimed labelling reagent or cleaving the linker. However, these elements are taught in the combined references, as discussed in the newly set forth rejection. All rejections were modified to address the amended claims.
Conclusion
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Smriga teaches labeling viable microbial cells in seawater using the thymidine analog 5-ethynyl-2’-deoxyuridine (EdU) and subsequent click chemistry labeling of synthesized nucleic acids (Aquat Microb Ecol 72: 269–280, 2014).
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 Juliet Switzer whose telephone number is (571)272-0753. The examiner can normally be reached Monday to Thursday, 8:00 AM-3:30 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Winston Shen can be reached at (571)-272-3157. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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Juliet Switzer
Primary Examiner
Art Unit 1682
/JULIET C SWITZER/Primary Examiner, Art Unit 1682