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 .
Claim Status
Claims 1-20 are currently pending.
Claims 15-20 are withdrawn, as being drawn to a nonelected invention.
Claims 1-14 under examination herein.
Claims 1-14 are rejected.
Election/Restrictions
The Applicant’s election without traverse of Group I: claims 1-14 in the reply filed on 05292026 is acknowledged.
Group II: claims 15-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 05292026.
Priority
Domestic Priority data as claimed by applicant is acknowledged. This application is a CON of US Patent No. 11,492,672 (15/779,531, filed 05/28/2018) which is a 371 of PCT/US16/64984, filed 12/05/2016, which claims benefit of 62/263,488, filed 12/04/2015.
In this action, all claims 1-14 are examined for an effective filing date of 12/04/2015. In future actions, the effective filing date of one or more claims may change, due to amendments to the claims, or further analysis of the disclosure(s) of the priority application(s).
Information Disclosure Statement
Information Disclosure Statement, filed 08/31/2022, has been considered. Signed copies of the IDS are included with this Office Action.
.
Drawings
The Drawings submitted 08/30/2022 are accepted. The drawings as filed are suitable to the Examiner. Applicant is encouraged to review the submission in PAIR to ensure all details are readable, particularly FIGs 3-4.
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
This application includes one or more claim limitations that do not use the word “means,” but are nonetheless being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because the claim limitation(s) uses a generic placeholder that is coupled with functional language without reciting sufficient structure to perform the recited function and the generic placeholder is not preceded by a structural modifier.
Such claim limitation(s) is/are:
“a barcoding process configured to correct sequencing errors and detect multi-bit errors and increase sequencing depth performance;” in claim 1.
“the personalized product prescription configured to improve production of an agricultural product associated with the set of samples. …” in claim 3;
“the personalized product prescription is configured to improve characteristics of at least one of nitrogen fixation and carbon fixation in an environment associated with the set of samples …” in claim 4;
Said barcoding process/ personalized product prescriptions are the generic placeholders, and each respective function is the specialized function:
“to correct sequencing errors and detect multi-bit errors and increase sequencing depth performance;” in claim 1.
“to improve production of an agricultural product associated with the set of samples. …” in claim 3;
“to improve characteristics of at least one of nitrogen fixation and carbon fixation in an environment associated with the set of samples …” in claim 4.
Because this/these claim limitation(s) is/are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are being interpreted to cover the corresponding structure described in the specification as performing the claimed function, and equivalents thereof.
If applicant does not intend to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (e.g., by reciting sufficient structure to perform the claimed function); or (2) present a sufficient showing that the claim limitation(s) recite(s) sufficient structure to perform the claimed function so as to avoid it/them being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
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, and 3-4 are rejected under 35 USC 112 2nd or 112(b) as failing to particularly point out and distinctly claim the invention. Claims 3-4 fail to particularly point out and distinctly claim the subject matter which applicant regards as his invention.
Claim limitation “a barcoding process configured to correct sequencing errors and detect multi-bit errors and increase sequencing depth performance;” in claim 1 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description, while discussing the definitions and options for barcoding [0027, 00128-00135], fails to disclose the instant corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claim fails to particularly set forth and distinctly claim the structures/ particular barcoding techniques, parameters, or system required to perform barcoding process. The dependent claims 11 and 14 recite employing a long-read sequencing platform and a double-index barcoding process implementing tagging with a first class of Hamming codes and a second class of Golay codes, and yet does not detail the active steps for combining said different barcoding techniques (are the two codes classes applied serially or nested, or with separate adapters) with the sequencing platform. The claim fails to set forth using barcoding process to achieve to correct[ion of] sequencing errors and detect multi-bit errors and increase sequencing depth performance. A reading of the specification provides a variety of possibilities, however no specific active steps of barcoding process which is necessary and sufficient for the stated goals of double-index barcoding is provided. While the claims are read in light of the specification, limitations from the specification cannot be read into the claims.
Claim limitation “the personalized product prescription configured to improve production of an agricultural product associated with the set of samples. …” in claim 3 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description fails to disclose the corresponding structure, material, or acts for performing the entire claimed function and to clearly link the structure, material, or acts to the function. The claim is purely functional and fails to particularly set forth and distinctly claim the standard for personaliz[ation] or “improve”, nor the differentiation of said prescription the state of the art required to improve production. The claim fails to identify what system components are relevant, necessary, and sufficient for the stated goals. The claim fails to particularly set forth how to incorporate the generically recited prescription for improv[ing] production. A reading of the specification provides a possibility regarding wine production/characteristics, however no specificity to provide said personalized or prescription [00521: Example 14 for a personalized product prescription as target flavor microbiome profile for a wine consumer in precision enology] which is necessary and sufficient is provided for any agricultural sample or bio-process. While the claims are read in light of the specification, limitations from the specification cannot be read into the claims. This applies equally to dependent claim 4.
Claim limitation ““the personalized product prescription is configured to improve characteristics of at least one of nitrogen fixation and carbon fixation in an environment associated with the set of samples …” in claim 4 invokes 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. However, the written description [0020: As used herein, the term "the personalized product prescription" refers to a that fails to disclose the corresponding structure, material, or acts for performing the entire claimed function improve characteristics and to clearly link the structure, material, or acts to the function. The claim fails to particularly set forth and distinctly claim the standard for personaliz[ation] or “improve”, nor the differentiation of said prescription from the state of the art required to improve characteristics. The claim fails to identify what system components are relevant, necessary, and sufficient for the stated goals. The claim fails to particularly set forth how to incorporate the generically recited prescription for improv[ing] characteristics. A reading of the specification provides a possibility regarding wine production/characteristics, however no specificity to provide said personalized or prescription [00521] which is necessary and sufficient is provided for any agricultural sample or bio-process. While the claims are read in light of the specification, limitations from the specification cannot be read into the claims.
Therefore, claims 3-4 are indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
Applicant may:
(a) Amend the claim so that the claim limitation will no longer be interpreted as a limitation under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph;
(b) Amend the written description of the specification such that it expressly recites what structure, material, or acts perform the entire claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(c) Amend the written description of the specification such that it clearly links the structure, material, or acts disclosed therein to the function recited in the claim, without introducing any new matter (35 U.S.C. 132(a)).
If applicant is of the opinion that the written description of the specification already implicitly or inherently discloses the corresponding structure, material, or acts and clearly links them to the function so that one of ordinary skill in the art would recognize what structure, material, or acts perform the claimed function, applicant should clarify the record by either:
(a) Amending the written description of the specification such that it expressly recites the corresponding structure, material, or acts for performing the claimed function and clearly links or associates the structure, material, or acts to the claimed function, without introducing any new matter (35 U.S.C. 132(a)); or
(b) Stating on the record what the corresponding structure, material, or acts, which are implicitly or inherently set forth in the written description of the specification, perform the claimed function. For more information, see 37 CFR 1.75(d) and MPEP §§ 608.01(o) and 2181.
Claims 3-4 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a WRITTEN DESCRIPTION rejection.
As set forth above, the claims invoke 112 6th paragraph for the above steps related to correct sequencing errors and detect multi-bit errors and increase sequencing depth performance… to improve production/characteristics. The specification fails to specifically disclose the necessary and sufficient step-by-step procedures or structures required to compute or generate each specialized function and fails to specifically link those structures to the specialized functions of the claims. Merely stating the desired goal of the step is not a written description of the actual steps required to achieve the goal. The claim fails to particularly set forth and distinctly claim the structures required for correcting/detecting/increasing…improving.… on the broadly claimed agricultural data. A reading of the specification provides a variety of possibilities for barcoding for barcoding [0027, 00128-00135], or prescription [00521], however without specific steps or parameters which is necessary and sufficient is provided for one of skill to achieve the instant invention and would need additional information. While the specification recites a variety of figures [0043-0045] of resulting microbiome profiles, they do not disclose a specific linkage of a particular set of steps and features which are necessary and sufficient to achieve each specialized function.
“When a claim containing a computer-implemented 35 U.S.C. 112(f) claim limitation is found to be indefinite under 35 U.S.C. 112(b) for failure to disclose sufficient corresponding structure (e.g., the computer and the algorithm) in the specification that performs the entire claimed function, it will also lack written description under 35 U.S.C. 112(a). See MPEP § 2163.03, subsection VI.”
Claim 9 is 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.
The metes and bounds of claim 9 are unclear. Claim 9 recites “microorganisms from the group consisting essentially of: a single-celled organism, a bacteria, an archaea, a protozoan, a unicellular fungus and a protist”, which is unclear as to how “essentially” is intended and as to whether the group from which to select is complete and closed.
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-14 are rejected under 35 U.S.C. 101 because the claimed invention is directed to abstract ideas without significantly more.
The instant rejection reflects the framework as outlined in the MPEP at 2106.04:
Framework with which to Evaluate Subject Matter Eligibility:
(1) Are the claims directed to a process, machine, manufacture, or composition of matter;
(2A) Prong One: Do the claims recite a judicially recognized exception, i.e. a law of nature, a natural phenomenon, or an abstract idea;
Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application (Prong Two); and
(2B) If the claims do not integrate the judicial exception, do the claims provide an inventive concept.
Framework Analysis as Pertains to the Instant Claims:
With respect to step (1): yes, the claims 1-14 are directed to a method for multiplex barcoded sequencing and profiling target agricultural microbiomes, the answer is "yes".
With respect to step (2A)(1), the claims recite abstract ideas. To determine if the claims recite any concepts that equate to an abstract idea, law of nature, or natural phenomenon, MPEP at 2106.03 teaches abstract ideas include mathematical concepts (mathematical formulas or equations, mathematical relationships, and mathematical calculations), certain methods of organizing human activity, and mental processes (including procedures for collecting, observing, evaluating, and organizing information (see MPEP 2106.04(a)(2)). In the instant application, the claims recite the following limitations that equate to an abstract idea with mental steps and natural correlations.
Abstract ideas include mathematical concepts, (mathematical formulas or equations, mathematical relationships and mathematical calculations), certain methods of organizing human activity, and mental processes (procedures for observing, evaluating, analyzing/ judging and organizing information) (MPEP 2106.04(a)(2). Laws of nature or natural phenomena include naturally occurring principles/ relations and nature-based products that are naturally occurring or that do not have markedly different characteristics compared to what occurs in nature (MPEP2106(b)).
The claims directing to judicial exceptions are as follows:
Mental processes:
Claim 1: to correct sequencing errors and detect multi-bit errors (mental process of judging);…generating one or more clusters upon clustering reads of the set of nucleic acid sequence reads (mental process of organizing information); selecting a representative sequence from each of the one or more clusters to return a characterization of bacterial and fungal microorganism abundances for each of the set of samples (mental process of analyzing).
Claim 2: returning a report characterizing a microbiome profile… (mental process of organizing information);
Claim 3: returning a personalized product prescription…… (mental process of organizing information);
Claim 10: clustering sequences exhibiting a threshold level of similarity, and selecting a representative sequence for each cluster for taxonomic assignment (mental process of analyzing/organizing information).
Natural phenomenon:
Claim 1, and 3-4: obtaining a set of nucleic acid sequence reads of 16S and ITS genes of microorganisms represented in the set of samples; and generating one or more clusters upon clustering reads of the set of nucleic acid sequence reads; and selecting a representative sequence from each of the one or more clusters to return a characterization of bacterial and fungal microorganism abundances for each of the set of samples… characterization… to improve production/characteristics (natural correlation between agricultural traits and sample material genetic material and abundance).
Hence, the claims explicitly recite elements that, individually and in combination, constitute abstract ideas and natural phenomenon.
With respect to step 2A(2): The claims must therefore be examined further to determine whether they integrate that abstract idea into a practical application (MPEP 2106.04(d). A claim that integrates a judicial exception into a practical application will apply, rely on, or use the judicial exception in a manner that imposes a meaningful limit on the judicial exception. The claimed additional elements are analyzed to determine if the abstract idea is integrated into a practical application (MPEP 2106.04(d).I.; MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the abstract idea, the claim fails to integrate the abstract idea into a practical application (MPEP 2106.04(d).III).
With respect to the instant recitations, the claims recite the following additional elements considered for practical application:
Claim 1: receiving a set of samples… agricultural material; extracting nucleic acid material…bead-beating homogenization process; barcoding said nucleic acid material… increase sequencing depth performance …amplifying said nucleic acid material …to generate a 16S library and an internal transcribed spacer (ITS) library…pooling material of the 16S library with material of the ITS library…to generate a pooled library; sequencing the pooled library…high-throughput sequencer, thereby obtaining a set of nucleic acid sequence reads of 16S and ITS genes of microorganisms…
Claim 3: to improve production of an agricultural product associated with the set…
Claim 4: configured to improve characteristics of at least one of nitrogen fixation and carbon fixation…
Claim 5: sugar crop and a starch-producing crop.
Claim 6: soil
Claim 7: a plant part… leaf part, a stem part, a root part, and a seed.
Claim 8: material of a food production process.…
Claim 9: microorganisms from the group…a single-celled organism, a bacteria, an archaea, a protozoan, a unicellular fungus and a protist.
Claim 11: employing a long-read sequencing platform.
Claim 12: kit…containers for sample reception, reagents for sample reception…a computer-readable medium.
Claim 13: representative sequences and auxiliary data comprising: geographical information and climate.
Claim 14: double-index barcoding process… tagging with a first class of Hamming codes and a second class of Golay codes.
Claims 1 do not utilize the representative sequence in any real world or practical application, only to characterize more agricultural data (return a characterization of bacterial and fungal microorganism abundances for each of the set of samples).
Claims 1-14 recite conventional laboratory steps of receiving a set of samples… agricultural material; extracting nucleic acid material…bead-beating homogenization process; barcoding said nucleic acid material…amplifying said nucleic acid material …to generate a 16S library and an internal transcribed spacer (ITS) library…pooling material of the 16S library with material of the ITS library…to generate a pooled library; sequencing the pooled library…high-throughput sequencer, thereby obtaining a set of nucleic acid sequence reads of 16S and ITS genes of microorganisms… employing a long-read sequencing platform… kit…containers for sample reception, reagents for sample reception … double-index barcoding process… tagging with a first class of Hamming codes and a second class of Golay codes. (Oh J (2015) Human, Bacterial and Fungal Amplicon Collection and Processing for Sequencing; Salipante SJ et al (2014) Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling; Fadrosh DW et al (2014) An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform).
Claims 1 and 13 recite additional elements that are not an abstract idea but are receiving a set of samples… to generate a 16S library and an internal transcribed spacer (ITS) library… to generate a pooled library... representative sequences and auxiliary data comprising: geographical information and climate. Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering steps are not sufficient to integrate an abstract idea into a practical application. (MPEP 2106.05(g).
Claims 1-6, and 13 also recite the additional non-abstract elements: kit…containers for sample reception, reagents for sample reception…a computer-readable medium… a long-read sequencing platform.. The claims do not describe any specific laboratory steps by which the kit, the CRM, the platform perform or carry out the abstract idea, nor do they provide any details of how specific structures of the computer- readable medium are used to implement these functions. The claims require nothing more than a minimally described, generic CRM [0063: A "computer-readable medium", is an information storage medium that can be accessed by a computer using a commercially available or custom-made interface. Exemplary computer-readable media include… or other commercially available media.] and a nonspecific kit [0039: provides a kit, comprising: one or more compositions for use in measuring a microbiome profile in a fermentation sample obtained from fermentation process or environment thereof, wherein the microbiome profile comprises at least one marker and preferably two markers to at least one microbe; and instructions for performing any of the preceding methods. In some embodiments, a kit can further comprise a computer readable medium.] to perform the functions that constitute the abstract idea Hence, these are mere instructions to apply the abstract idea using a computer, and therefore the claim does not recite integrate that abstract idea into a practical application. (see MPEP 2106.05(f)).
Claims 1-14 recite no additional element/limitation related to the natural law and so do not provide a particular limitation which would integrate the natural law into a practical application. To integrate a judicial exception into a practical application, the additional limitation must be specifically identified, and not merely instructions to apply the judicial exception. The additional limitation must have more than a nominal or insignificant relationship to the identified judicial exception. (MPEP 2106.04(d)(2))
Remaining dependent claims have been analyzed. These further limitations are sample materials that provide data, are field of use limitations (employing a long-read sequencing platform), or intended use limitations in claims 3-4 (to improve production of an agricultural product associated with the set… to improve characteristics of at least one of nitrogen fixation and carbon fixation…)
None of these dependent claims recite additional elements which would integrate a judicial exception into a practical application.
Finally, the (2B) analysis. Because the claims recite an abstract idea, and do not integrate that abstract idea into a practical application, the claims lack a specific inventive concept. The judicial exception alone cannot provide that inventive concept or practical application (MPEP 2106.05). Identifying whether the additional elements beyond the abstract idea amount to such an inventive concept requires considering the additional elements individually and in combination to determine if they provide significantly more than the judicial exception. (MPEP 2106.05.A i-vi).
With respect to the instant claims, the additional elements of data gathering, instructions, and field of use limitations described above do not rise to the level of significantly more than the judicial exception. As directed in the Berkheimer memorandum of 19 April 2018 and set forth in the MPEP, determinations of whether or not additional elements (or a combination of additional elements) may provide significantly more and/or an inventive concept rest in whether or not the additional elements (or combination of elements) represent well-understood, routine, conventional activity. Said assessment is made by a factual determination stemming from a conclusion that an element (or combination of elements) is widely prevalent or in common use in the relevant industry, which is determined by either a citation to an express statement in the specification or to a statement made by an applicant during prosecution that demonstrates a well-understood, routine or conventional nature of the additional element(s); a citation to one or more of the court decisions as discussed in MPEP 2106(d)(II) as noting the well-understood, routine, conventional nature of the additional element(s); a citation to a publication that demonstrates the well-understood, routine, conventional nature of the additional element(s); and/or a statement that the examiner is taking official notice with respect to the well-understood, routine, conventional nature of the additional element(s).
With respect to the instant recitations, the claims recite the following additional elements considered for inventive concept:
Claim 1: receiving a set of samples… agricultural material; extracting nucleic acid material…bead-beating homogenization process; barcoding said nucleic acid material… increase sequencing depth performance …amplifying said nucleic acid material …to generate a 16S library and an internal transcribed spacer (ITS) library…pooling material of the 16S library with material of the ITS library…to generate a pooled library; sequencing the pooled library…high-throughput sequencer, thereby obtaining a set of nucleic acid sequence reads of 16S and ITS genes of microorganisms…
Claim 3: to improve production of an agricultural product associated with the set…
Claim 4: configured to improve characteristics of at least one of nitrogen fixation and carbon fixation…
Claim 5: sugar crop and a starch-producing crop.
Claim 6: soil
Claim 7: a plant part… leaf part, a stem part, a root part, and a seed.
Claim 8: material of a food production process.…
Claim 9: microorganisms from the group…a single-celled organism, a bacteria, an archaea, a protozoan, a unicellular fungus and a protist.
Claim 11: employing a long-read sequencing platform.
Claim 12: kit…containers for sample reception, reagents for sample reception…a computer-readable medium.
Claim 13: representative sequences and auxiliary data comprising: geographical information and climate.
Claim 14: double-index barcoding process… tagging with a first class of Hamming codes and a second class of Golay codes.
Said steps that are “in addition” to the recited judicial exception in the instant claims represent those of mere data handling instructions (receiving a set of samples… to generate a 16S library and an internal transcribed spacer (ITS) library… to generate a pooled library... representative sequences and auxiliary data comprising: geographical information and climate), or field of use and intended use limitations (employing a long-read sequencing platform…to improve production of an agricultural product associated with the set… to improve characteristics of at least one of nitrogen fixation and carbon fixation…) to implement in the recited judicial exception and do not impart meaning to said recited judicial exception, such that is applied in a practical manner. Further with respect to the additional elements in the instant claims, these steps direct to mere data gathering and handling (receive an input) to carry out the abstract idea without imposing any meaningful limitation on the abstract idea and is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
With respect to claim 1: The additional element of data gathering does not rise to the level of significantly more than the judicial exception. Steps of “receiving a set of samples” are merely steps of obtaining samples from which to extract data.
Claims 1-14 recite conventional laboratory steps of receiving a set of samples… agricultural material; extracting nucleic acid material…bead-beating homogenization process; barcoding said nucleic acid material…amplifying said nucleic acid material …to generate a 16S library and an internal transcribed spacer (ITS) library…pooling material of the 16S library with material of the ITS library…to generate a pooled library; sequencing the pooled library…high-throughput sequencer, thereby obtaining a set of nucleic acid sequence reads of 16S and ITS genes of microorganisms… employing a long-read sequencing platform… kit…containers for sample reception, reagents for sample reception … double-index barcoding process… tagging with a first class of Hamming codes and a second class of Golay codes. (Oh J (2015) Human, Bacterial and Fungal Amplicon Collection and Processing for Sequencing; Salipante SJ et al (2014) Performance comparison of Illumina and ion torrent next-generation sequencing platforms for 16S rRNA-based bacterial community profiling; Fadrosh DW et al (2014) An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform). Activities such as routine laboratory steps to produce data, followed by data gathering, do not improve the functioning of a computer, or comprise an improvement to any other technical field, they do not require or set forth a particular machine, they do not effect a transformation of matter, nor do they provide a non-conventional or unconventional step. Data gathering steps constitute a general link to a technological environment which is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
Claims 1 and 13 recite additional elements that are not an abstract idea but are receiving a set of samples… to generate a 16S library and an internal transcribed spacer (ITS) library… to generate a pooled library... representative sequences and auxiliary data comprising: geographical information and climate. Data gathering steps are not an abstract idea, they are extra-solution activity, as they collect the data needed to carry out the abstract idea. Data gathering does not impose any meaningful limitation on the abstract idea, or how the abstract idea is performed. Data gathering and handling (generate…) to carry out the abstract idea without imposing any meaningful limitation on the abstract idea and is insufficient to constitute an inventive concept which would render the claims significantly more than the judicial exception (MPEP2106.05(g)&(h)).
Claims 1-6, and 13 also recite the additional non-abstract elements: kit…containers for sample reception, reagents for sample reception…a computer-readable medium… a long-read sequencing platform.. The claims do not describe any specific laboratory steps by which the kit, the CRM, the platform perform or carry out the abstract idea, nor do they provide any details of how specific structures of the kit or computer- readable medium are used to implement these functions. The claims require nothing more than a minimally described, generic CRM [0063: A "computer-readable medium", is an information storage medium that can be accessed by a computer using a commercially available or custom-made interface. Exemplary computer-readable media include… or other commercially available media.] and a nonspecific kit [0039: provides a kit, comprising: one or more compositions for use in measuring a microbiome profile in a fermentation sample obtained from fermentation process or environment thereof, wherein the microbiome profile comprises at least one marker and preferably two markers to at least one microbe; and instructions for performing any of the preceding methods. In some embodiments, a kit can further comprise a computer readable medium.] to perform the functions that constitute the abstract idea Hence, these are mere instructions to apply the abstract idea using a computer, and are set forth at such a high level of generality that they can be met by a general purpose computer or sampling kit. Therefore, these tangible components constitute no more than a general link to a technological environment, which is insufficient to constitute an inventive concept that would render the claims significantly more than an abstract idea (see MPEP 2106.05(b)I-III).
Claims 1-14 recite no additional element/limitation related to the natural law and so do not provide a particular limitation which would integrate the natural law into a practical application. To integrate a judicial exception into a practical application, the additional limitation must be specifically identified, and not merely instructions to apply the judicial exception. The additional limitation must have more than a nominal or insignificant relationship to the identified judicial exception. (MPEP 2106.04(d)(2))
Remaining dependent claims have been analyzed. These further limitations are sample materials that provide data, are field of use limitations (employing a long-read sequencing platform), or intended use limitations in claims 3-4 (to improve production of an agricultural product associated with the set… to improve characteristics of at least one of nitrogen fixation and carbon fixation…). None of these claims provide a specific inventive concept, as they all fail to rise to the level of significantly more than the identified judicial exception.
For these reasons, the claims, when the limitations are considered individually and as a whole, are rejected under 35 USC § 101 as being directed to non-statutory subject matter (Step 2B: No). As such, claims 1-14 are not patent eligible.
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.
(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.
Note: citations from the instant application are italicized in the following section.
Claims 1-14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Embree M et al (2015) US Patent No. 9,938,558.
The independent claim is drawn to a method for multiplex barcoded sequencing and profiling target agricultural microbiomes from collected fermentation samples. Extracted nucleic acids, sequencing marker genes, and computationally converting the sequence data into microbiome profiles that can be used for target process control over production and characteristics. Instant techniques include bead beating, pairing 16S with ITS barcoding to correct errors, to multiplex pooled libraries, and to better distinguish strains for computational analysis.
With respect to claims 1-2, Embree provides a method:
“to improve at least one target biological property in a target biological environment comprises: (1) selecting at least two active microorganism strains, the at least two active microorganism strains including at least one active fungus strain and a least one active bacterium strain… samples collected from a sample population… determining a number of each detected microorganism type; measuring unique first markers and quantity thereof, each unique first marker (16S or ITS) being a marker of a microorganism strain (i.e. microbiome profiling);
determining an absolute cell count of each microorganism strain based on the number of each detected microorganism type and relative quantity of unique first markers (16S or ITS); determining an activity level for each microorganism strain based on at least one unique second marker(16S or ITS); filtering each microorganism strain by the determined activity level to provide a set of active microorganism strains and respective absolute cell counts (i.e returning a report characterizing a microbiome profile from the characterization);
(b) measuring at least one biological property (i.e. nitrogen/carbon fixation) for each sample of the plurality of samples collected from the sample population; and (c) analyzing the set of active microorganism strains and respective absolute cell counts of each sample of the plurality of samples with the at least one measured biological property of each sample of the plurality of samples to identify relationships between each active microorganism strain from the set of active microorganism strains and between each active microorganism strain from the set of active microorganism strains and the at least one measured biological property” [Col 7 L60-Col 8 L1-L55].
Specifically, Embree provides collecting fermentation-related material from animals, soil, plant/rhizosphere part, an agricultural product (i.e. crop), etc. [Col 2 L45] and extracts nucleic acids using disruption methods such as bead beating [Col 59 L 17; FIG 2 2003-2004]. The steps include 16S and ITS amplification as first/second markers for bacterial and fungal classification [Col 8 L60, Col 25 L20, Col 29 L41; FIG. 1B, 1003, FIG. 2, 2003] (i.e dual-marker profiling workflows). Pooled libraries [Col 43 L45] are multiplex sequenced together (i.e. single run) on a high-throughput platform [Col 54 L22], then clusters reads into OTUs/assigns taxonomy through clustering. Embree provides a cluster analysis [Col 36 L4-30] for taxonomy classification based on a threshold of marker expression greater than a specified threshold:
“calculating the absolute cell count of each detected active microorganism strain in each sample based upon the quantity of the one or more first markers and the absolute number of cells of the microorganism types from which the one or more microorganism strains is a subtaxon, the one or more active microorganism strains expressing one or more unique RNA markers above the specified threshold; analyzing the active microorganism strains of the two or more sample sets, the analyzing including conducting nonparametric network analysis of each of the active microorganism strains for each of the two or more sample sets, the at least one common environmental parameter, and the at least one different environmental parameter [Col 94 L50-65].”
Further, Embree provides for high-throughput sequencing platform [Col 27 L30-35] with amplicon sequencing [Col 27 L33-35] and barcoded sample multiplexing [Col 28 L33-35].
With respect to claim 3, Embree provides improve milk fat production in cows [Col 10 FIGs. 2 and 4: in FIG 2: microbe interaction analysis and selection system 300, according to some embodiments, and FIG. 3B is example process flow for use with such a system. Systems and processes to determine multi-dimensional interspecies interactions and dependencies within natural microbial communities, identify active microbes, and select a plurality of active microbes to form an ensemble, aggregate or other synthetic grouping of microorganisms that will alter specified parameter(s) and/or related measures, is described with respect to FIGS. 3A and 3B].
With respect to claim 4, Embree teaches use of microbial biogeochemical cycling of essential elements, e.g., the cycling of carbon, oxygen, nitrogen, sulfur, phosphorus and various metals [Col 11 L2] with an embodiment targeted at carbon/ nitrogen fixation:
“subjected to DNA/RNA stable isotope probing (SIP) to determine the level of a second unique marker (FIG. 1B, 1004; FIG. 2, 2004). SIP enables determination of the microbial diversity associated with specific metabolic pathways and has been generally applied to study microorganisms involved in the utilization of carbon and nitrogen compounds. The substrate of interest is labelled with stable isotopes (such as 13C or 15N) and added to the sample. Only microorganisms able to metabolize the substrate will incorporate it into their cells. Subsequently, 13C-DNA and 15N-DNA can be isolated by density gradient centrifugation and used for metagenomic analysis. RNA-based SIP can be a responsive biomarker for use in SIP studies, since RNA itself is a reflection of cellular activity” [Col 32 L 24].
With respect to claims 5-9, Embree discloses using fungus and bacteria strains [Col 8 L60: “to improve at least one target biological property in a target biological environment comprises: (1) selecting at least two active microorganism strains, the at least two active microorganism strains including at least one active fungus strain and a least one active bacterium strain, the selected at least two active microorganism strains corresponding to at least two active microorganism strains identified by processing (i.e., prior processing) a plurality of samples collected from a sample population, the processing including: (a) for each sample of the plurality of samples: detecting the presence of one or more microorganism types and determining a number of each detected microorganism type”].
With respect to claim 10, Embree provides a cluster analysis [Col 36 L4-30] into taxonomy based on a threshold of marker expression greater than a specified threshold [Col 94 L50-65].
With respect to claim 11, Embree provides for high-throughput sequencing platform [Col 27 L30-35].
With respect to claim 12, Embree provides a kit [Col 22 16, Col 100 L 58] and CRM [Col 56 L18].
With respect to claim 13, Embree provides sample metadata, including incorporating target environment data [Col 3 L 35, Col 4 L12, Col 6 L46].
With respect to claim 14, Embree provides high-throughput sequencing platform [Col 27 L30-35] with amplicon sequencing [Col 27 L33-35] and barcoded sample multiplexing [Col 28 L33-35, Col 29 L19, Col 34 L42, Col 57 L28].
Double Patenting
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.
A. Instant claims 1-14 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-5, 7, 9, 12, and 29 of US Patent No. 11,492,672. Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims are generic to ‘672 which is a method and system for sequencing microbial marker genes combining 16S with ITS from fermentation-associated samples and converting the sequence data into microbiome profiles with addition of Hamming and Golay barcoding samples for pooling libraries.
Conclusion
No claims are allowed.
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/VR/
Examiner
Art Unit 1685
/MARY K ZEMAN/Primary Examiner, Art Unit 1686
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