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 claims 1-28 in the reply filed on 16 April 2026 is acknowledged.
Claims 29-34 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 16 April 2026.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Information Disclosure Statement
The information disclosure statement (IDS) filed 14 November 2023 is considered, initialed, and attached hereto.
Claim Status
Claims 1-34 are pending.
Claims 29-34 are withdrawn.
Claims 1-28 are under examination.
Nucleotide and/or Amino Acid Sequence Disclosures
Applicant’s amendment to the Specification, filed 16 April 2026, brings the sequence disclosure into compliance. Therefore, the objection to the sequence disclosure in the Requirement for Restriction mailed 18 February 2026 is withdrawn.
Specification
The use of terms including FluoSphere, CountBright, Roche, and LightCycler, which are trade names or marks used in commerce, has been noted in this application. The above terms are examples of trade names or marks used in commerce present in this application and are not an exhaustive list. These terms and other trade names or marks used in commerce present in this application should be accompanied by the generic terminology; furthermore the terms should be capitalized wherever they appear or, where appropriate, include a proper symbol indicating use in commerce such as ™, SM , or ® following the term.
Although the use of trade names and marks used in commerce (i.e., trademarks, service marks, certification marks, and collective marks) are permissible in patent applications, the proprietary nature of the marks should be respected and every effort made to prevent their use in any manner which might adversely affect their validity as commercial marks.
Claim Objections
Claims 6 and 18 are objected to because of the following informalities:
In claim 6, line 5, the phrase “semipermeable” should be corrected to “semi-permeable” to retain the same spelling as in claim 5, line 2.
In claim 18, line 4, the phrase “emit first light” should have an article (such as ‘a’, ‘an’, or ‘the’) inserted between ‘emit’ and ‘first’
In claim 18, line 6, the phrase “emit second light” should have an article (such as ‘a’, ‘an’, or ‘the’) inserted between ‘emit’ and ‘second.
Appropriate correction is required.
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 limitations use 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 limitations are:
“a computing device that is configured to: determine that the pathogen is aerosolizable based on the presence of the pathogens having been detected, the pathogen having been previously unknown of being aerosolizable; and notify a user based on the determination that the pathogen is aerosolizable” in claim 12
“a computing device in communication with the detection system, and wherein the computing device is configured to: cause the light source to emit first light towards the detection chamber, the first light interacting with a molecule that interacts with the genetic material of the pathogens to emit second light; receive optical data from the photodetector indicative of the second light interacting with the photodetector; and determine a presence of the pathogen, based on the optical data” in claim 18 (and inherited in claims 19-23 via their dependency on claim 18)
“the computing device is further configured to: determine an initial amount of the genetic material in the detection chamber before amplification, based on the optical data; and determine a concentration of the pathogen in the enclosed volume, based on the initial amount of genetic material and the total volume of the enclosed volume” in claim 24 (and inherited in claim 25 via its dependency on claim 24)
“the computing device is further configured to determine a concentration of the pathogen in the enclosed volume, based on the initial amount of genetic material, the total volume of the enclosed volume, and an efficiency ratio of the collection rate of the pathogens in the surrounding volume to the pathogens collected on the probe” in claim 25.
Because these claim limitations are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, they 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 these limitations interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitations to avoid 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 limitations recite sufficient structure to perform the claimed function so as to avoid 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(b) - Indefiniteness
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 12 and 17-25 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 limitations “a computing device that is configured to: determine that the pathogen […] determination that the pathogen is aerosolizable” in lines 1-6 of claim 12, “a computing device in communication with the detection system, and wherein the computing device is configured to: cause the light source […] based on the optical data” in lines 1-9 of claim 18, “the computing device is further configured to: determine an initial amount […] total volume of the enclosed volume” in lines 1-6 of claim 24, and “the computing device is further configured to determine the concentration […] collected on the probe” in lines 1-5 of claim 25 invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph (see Claim Interpretation section above). 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. No structure is taught in the specification that performs any of the functions in claims 12, 18, 24, and 25 above. The specification merely teaches a computing device that can be implemented in a variety of ways ([00136]) and general descriptions of computers and computer programs ([00260-00261]), without teaching any algorithm for performing the claimed specific computer functions. MPEP §2181(II)(B) recites: “For a computer-implemented 35 U.S.C. 112(f) claim limitation, the specification must disclose an algorithm for performing the claimed specific computer function, or else the claim is indefinite under 35 U.S.C. 112(b)”. Therefore, the claim is 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 19-23 are also rejected based on their dependency on claim 18, and claim 25 is further rejected based on its dependency on claim 24.
Claim 17 recites the limitations "the one or more cycles that define the PCR" in line 2, “the PCR” in line 2, “the one or more reagents” in line 3, “the one or more cycles that define the fast PCR” in line 4, and “the one or more cycles” in line 6. There is insufficient antecedent basis for these limitations in the claim.
Claim 18 recites the limitations "the light source" in line 4, “the detection chamber” in line 4, and “the photodetector” in lines 7 and 8. There is insufficient antecedent basis for these limitations in the claim. Claims 19-23 are also rejected based on their dependency on claim 18. For the purpose of examination, claim 18 is interpreted as depending upon claim 9 instead of claim 8, since claim 9 provides antecedent basis for all of these terms.
Claim 21 recites the limitation “the detection chamber” in line 3. There is insufficient antecedent basis for this limitation in the claim. Claims 22-23 are also rejected based on their dependency on claim 21.
Claim 24 recites the limitations “the computing device” in line 1, “the detection chamber” in line 3, “the optical data” in line 4, and “the enclosed volume” in lines 5 and 6. There is insufficient antecedent basis for these limitations in the claim. Claim 25 is also rejected based on its dependency on claim 24. For the purpose of examination, “the enclosed volume” is interpreted based on recitations in the instant specification (such as in [0005], [00121], [00130], and [00165]) as referring to an enclosed volume that contains the surrounding fluid of claim 1 (e.g. if the fluid is the fluidic contents of a tube, the enclosed volume is the volume of the fluidic contents in the tube, if the fluid is the air in a room, the enclosed volume is the volume of the air in the room).
Claim 25 recites the limitation "the surrounding volume" in line 4. There is insufficient antecedent basis for this limitation in the claim. It is unclear whether this refers to the enclosed volume recited in claims 24 and 25 or an inherent volume of the surrounding fluid recited in claim 1.
Claim Rejections - 35 USC § 112(a) - Written Description
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.
Claims 12 and 18-25 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.
Claims 12, 18 (and 19-23 via their dependency on claim 18), 24 (and 25 via its dependency on claim 24), and 25 have been rejected under 35 U.S.C. 112(b) as indefinite for failing to disclosed sufficient corresponding structure, materials, or acts that perform the entire claimed function that invokes 112(f) (see Claim Interpretation section and rejections under 35 U.S.C. 112(b) above). As such, they also lack adequate written description because an indefinite, unbounded functional limitation would cover all ways of performing a function and indicates that the inventor has not provided sufficient disclosure to show possession of the invention (see MPEP §2163.03(VI)). Therefore, claims 12 and 18-25 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement.
Claim Rejections - 35 USC § 112(a) - Scope of Enablement
Claims 1-28 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a collecting system comprising a heater configured to lyse pathogens, such as bacteria and viruses, to release genetic material, does not reasonably provide enablement for a collecting system comprising a heater configured . Claim 12 is further rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a collecting system comprising a computing device that is configured to determine that a pathogen is aerosolizable in the case that the probe configured to collect pathogens from a surrounding fluid collected pathogens from an air sample, does not reasonably provide enablement for computing device that is configured to determine that a pathogen is aerosolizable in the case that the probe configured to collect pathogens from a surrounding fluid collected pathogens from a non-air fluid, such as soup or saliva. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
Scope of the Claims/Nature of the Invention
Claims 1-28 are drawn to a collecting system comprising a heater configured to lyse pathogens to release the genetic material of the pathogens. In view of the recitation of “pathogens” (claim 1 lines 2, 4, 5, and 6) and the lack of any limiting definition in the instant specification of pathogens, claims 1-28 encompass a collecting system comprising a heater configured to lyse any pathogen, such as bacteria, viruses, and prions, to release genetic material of the pathogen. The nature of the invention is a system capable of lysing ANY pathogen to release genetic material.
Claim 12 is further drawn to a collecting system further comprising a computing device configured to determine that a pathogen is aerosolizable based on the presence of the pathogen having been detected by the collecting system. In view of the recitation “fluid” (claim 1, line 2) and the lack of any limiting definition in the specification of fluids, claim 12 encompasses a computing device configured to determine that a pathogen is aerosolizable based on the presence of the pathogens having been detected when the pathogens were collected from any fluid, such as air, soup, or saliva. The nature of the invention in claim 12 is a system further capable of determining that a detected pathogen is aersolizable when the pathogen was collected by the probe from ANY fluid.
Teachings in the Specification and Examples
In the Examples section, the instant specification teaches heating at 90°C to extract RNA from RNA viruses ([00201], [00203], [00219], [00244]). However, this does not teach a heater configured to lyse prions to release genetic material. The instant specification teaches that a heater can lyse pathogens by rupturing a membrane or capsid that encapsulates genetic material ([00126]) and that pathogens may include bacteria, viruses, other microorganisms that are not virulent towards a particular species, and spores ([00139]). The instant specification also teaches that a collecting system of the specification can collect “other airborne particulates”, which potentially could include prions, but does not teach how a heater can be configured to lyse prions to release genetic material.
The Examples section does not contain any teachings of how a computing device can be configured to determine that a pathogen is aersolizable. The instant specification teaches that the disclosed process “can include a computing device determining that a pathogen is capable of being aerosolized that has previously been unknown to be capable of being aerosolized, based on the computer device determining a presence of the pathogen” ([00187]). However, this does not teach one of ordinary skill in the art to configure a computing device to do so when the pathogen is collected from a non-aerosol fluid.
State of the Art and Unpredictability of the Art
Claims 1-28 broadly encompass a collecting system comprising a heater configured to lyse any pathogen, such as bacteria, viruses, and prions, to release genetic material of the pathogen. However, the specification only provides support for a heater configured to lyse bacteria, viruses, spores, and other genetic material-containing microorganisms to release genetic material. The prior art teaches that prions do not contain genetic material: “Unlike other infectious agents, such as bacteria, viruses, and fungi, prions do not contain genetic materials such as DNA or RNA” (Das et al., “Prions: Beyond a Single Protein” Clin Microbiol Rev 29(3), pages 633-658 (2016); Summary, page 633). This teaching of Das et al. supports the finding that there is no predictable means for one of ordinary skill in the art to configure a heater to lyse prions to release genetic material.
Claim 12 broadly encompasses a computing device configured to determine that a pathogen is aerosolizable based on the presence of the pathogens having been detected when the pathogens were collected from any fluid, such as air, soup, or saliva. While the specification does not present specific teachings on how this can be done, one of ordinary skill in the art could see a correlation between the presence of the pathogen having been detected when the pathogen was collected from the air and determine that the pathogen is aerosolizable, and thus configure a computing device to make the same determination. However, the prior art teaches that determining the biological plausibility of aerosol transmission of a pathogen requires weighing three main conditions, Aerosol generation, Viability in environment, and Access to target tissue, for which detection of a pathogen collected from a non-aerosol fluid would give little to no information on Aerosol generation (Jones et al., “Aerosol transmission of infectious disease” J Occup Environ Med 67(5), pages 501-508 (2015); Table 2, section on Establishing Biological Plausibility).
Quantity of Experimentation
The quantity of experimentation necessary to enable the full scope of claims 1-28 is undue. In support of this position, it is noted that the claimed systems encompass a collecting system comprising a heater configured to lyse any pathogen, such as bacteria, viruses, and prions, to release genetic material of the pathogen. In order to practice the breadth of the claimed invention, one of ordinary skill in the art would need to discover a way to lyse prions such that they release genetic material. As prions are not known in the art to contain any genetic material, being proteinaceous infectious material, this would require extensive experimentation necessary to force a paradigm shift in the field by demonstrating that all prions contain genetic material that can be released from the prions. The specification has not done any of the above. The results of such experimentation are highly unpredictable and achieving the enabling result of obtaining genetic material from all prions may even be impossible. The amount of experimentation that would be required to practice the full scope of the claimed invention and the amount of time and cost this experimentation would take supports the position that such experimentation is undue (see MPEP §2164.06).
The quantity of experimentation necessary to enable the full scope of claim 12 is undue. In support of this position, it is noted that the claimed system encompasses a computing device configured to determine that a pathogen is aerosolizable based on the presence of the pathogens having been detected when the pathogens were collected from any fluid, such as air, soup, or saliva. In order to practice the breadth of the claimed invention, one of ordinary skill in the art would need to discover a way to correlate the detection of a pathogen collected from any fluid sample, regardless of the fluid’s relation to an aerosol, with the ability for the pathogen to be aerosolized. The specification has not done any of the above. The results of such experimentation are highly unpredictable with no guarantee of eventual success. The amount of experimentation that would be required to practice the full scope of the claimed invention and the amount of time and cost this experimentation would take supports the position that such experimentation is undue (see MPEP §2164.06).
Conclusions
Herein, although the level of ordinary skill in the art is high, given the lack of disclosure in the specification and in the prior art and the unpredictability of the art, it would require undue experimentation for one of ordinary skill in the art to make and use the full scope of the invention as broadly claimed in claims 1-28. Similarly, it would require undue experimentation for one of ordinary skill in the art to make and use the full scope of the invention as broadly claimed in claim 12.
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 12 and 24-25 are rejected under 35 U.S.C. 101 because the claimed inventions are directed to a natural phenomenon and an abstract idea, respectively, without significantly more.
Step 1: is the claim to a process, machine, manufacture, or composition of matter? Yes, claims 12 and 24-25 are for a collecting system, which is a machine.
Step 2A, Prong One: does the claim recite an abstract idea, law of nature, or natural phenomenon (judicial exceptions)? Yes, claim 12 in lines 3-4 recites "determine that the pathogen is aerosolizable based on the presence of the pathogens having been detected, which is a natural phenomenon because it recites a natural correlation between the presence of a pathogen being detected (presumably having been collected from the air) and the pathogen being aerosolizable. Claim 24 in lines 3-4 recites “determine an initial amount of the genetic material in the detection chamber before amplification, based on the optical data; and determine a concentration of the pathogen in the enclosed volume, based on the initial amount of genetic material and the total volume of the enclosed volume” and claim 25, dependent on claim 24, in lines 2-5 recites “determine the concentration of the pathogen in the enclosed volume, based on the initial amount of genetic material, the total volume of the enclosed volume, and an efficiency ratio of the collection rate of the pathogens in the surrounding volume to the pathogens collected on the probe”, which are abstract ideas because they are merely the mental process of a calculation that could be done in the mind or by hand.
Step 2A, Prong Two: does the claim recite additional elements that integrate the judicial exception into a practical application? No. In addition to the judicial exception, claim 12 recites “a computer device that is configured to”, followed by the judicial exception that it implements, and claims 24 and 25 recite “wherein the computer device is configured to”, followed by the judicial exception that it implements. In all cases, the computer is a general machine, not a particular machine, so these recitations do not integrate the judicial exceptions of claims 12 and 24-25 into practical applications (see MPEP §2106.05(b): “a general purpose computer that applies a judicial exception, such as an abstract idea, by use of conventional computer functions does not qualify as a particular machine”). Claims 12 and 24-25 depend on claims 1 and 8, which recite a collecting system comprising a probe to collect pathogens, an elution chamber containing a liquid solvent and configured to receive the probe, a heater configured to lyse the pathogens, and a detection system that is configured to detect a presence of the pathogens. Claim 12 further depends on claim 11, which recites that the detection system is configured to detect the presence of a pathogen by detecting the genetic material of the lysed pathogens, and claim 12 also recites that the computing device is configured to notify a user based on the determination that the pathogen is aerosolizable. Claims 24 and 25 further depend on claim 15, which recites that the collecting system further comprises a thermocycler configured to cycle the temperature of the liquid solvent and genetic material. All of these additional limitations are considered insignificant extra-solution activity, because they amount to merely a system for gathering and outputting the data (the presence or lack thereof of the pathogen for claim 15, the initial amount of genetic material in claim 25) that is used in the application of the respective judicial exception (see MPEP §2106.05(g), insignificant extra-solution activity includes limitations amounting to necessary data gathering and outputting).
Step 2B: does the claim recite additional elements that amount to significantly more than the judicial exception? No. The additional elements (as listed in the discussion of Step 1B, Prong Two above) were well known prior to the effective filing date of the claimed invention, and therefore are considered well-understood, routine, conventional activity that do not amount to significantly more than the judicial exception (see MPEP §2106.05(d)). This is seen in the prior art of Philips (EP 2198965, published 23 June 2010) as well as Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020)(both discussed at length in below section on 35 U.S.C. 102 rejections), which both teach separate systems comprising a probe configured to collect pathogens, an elution chamber containing a liquid solvent and configured to receive the probe, a heater configured to lyse the pathogens, and a detection system. Additionally, both Philips and Rothberg amplify nucleic acids for detection, in the case of Philips using a thermocycler configured to cycle the temperature of a liquid solvent with genetic material to amplify the genetic material (Rothberg, though not using temperature cycling for amplification, also discloses the inclusion of a thermocycler and the use of thermocyclers for PCR is well known in the art, such as in Philips).
Therefore, claims 12 and 24-25 are rejected under 35 U.S.C. 101.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1, 8, 11, 13-14, and 28 are rejected under 35 U.S.C. 102(a)(2) as being anticipated by Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg.
Regarding claim 1, Rothberg teaches a collecting system (“In FIG. 1A, diagnostic system 100 comprises sample-collecting component 110, reaction tube 120, readout device 130, and heater 140” [0049]) comprising: a probe configured to collect pathogens from a surrounding fluid (“sample-collecting components (e.g., swabs) for collecting a sample from a subject” [0048], sample-collecting component is the probe; “In some embodiments, the sample comprises a mucus (e.g., nasal secretion), sputum (e.g., a mixture of saliva and mucus), or saliva (e.g., spit) sample or specimen. However, other sample types are envisioned, including, for example, bodily fluids (e.g. blood, serum, plasma, amniotic fluid, urine, cerebrospinal fluid, lymph, tear fluid, feces, or gastric fluid), […] exhaled breath particles, tissue extracts, culture media” [0072], teaching various fluids being sampled that the probe is surrounded by during sampling; “systems provided herein can include the components needed to detect one or more target nucleic acid sequences (e.g., from one or more pathogens of interest)” [0045]); an elution chamber containing a liquid solvent and configured to receive the probe to elute the pathogens collected on the probe using the liquid solvent (“After collecting a sample with swab element 110A, first cap 120B may be removed from tube 120A, and swab element 110A may be inserted into the fluidic contents of tube 120A” [0050], the reaction tube is the elution chamber, which is configured for the swab/probe to be received and has fluidic contents for eluting the sample on the swab/probe); and a heater configured to lyse the pathogens to release the genetic material of the pathogens into the liquid solvent (“reaction tube 120 may be inserted into heater 140. Heater 140 may heat reaction tube 120 […] heating reaction tube 120 according to a first heating protocol (e.g., a first set of temperature(s) and time period(s)) may […] facilitate lysis of cells within the collected sample” [0052]; “In some embodiments, cell lysis is performed by thermal lysis […] exposure of cells to high temperatures can damage the cellular membrane by denaturing membrane proteins, resulting in cell lysis and the release of intracellular material” [0144]).
Regarding claims 8 and 11, Rothberg teaches the collecting system of claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), further comprising a detection system that is configured to detect a presence of the pathogens by detecting the genetic material of the lysed pathogens (“reaction tube 120 may be inserted into readout device 130” [0053]; “a readout device comprising a detection component” [0048]; “system described herein is configured to detect one or more target nucleic acids in a sample” [0065]; “target nucleic acid sequences may, in some embodiments, be a nucleic acid sequence of a pathogen” [0041]).
Regarding claims 13-14, Rothberg teaches the collecting system of claim 8 (see 35 U.S.C. 102 rejection of claim 8 above), wherein the genetic material is amplified without the use of a thermocycler and the collecting system does not use a thermocycler ([0315] teaches various alternatives options for the heater, which while including a thermocycler as one option, allows one of skill in the art to immediately understand embodiments lacking a thermocycler, such as using “a hot water bath”; “In some embodiments, a diagnostic method comprises performing an isothermal nucleic acid amplification reaction configured to amplify one or more target nucleic acids” [0069], teaching the system amplifying genetic material with a method amenable to the non-thermocycler options like the hot water bath).
Regarding claim 28, Rothberg teaches the collecting system of claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), wherein the volume of the liquid solvent is less than or equal to 12.5 µL (“In some embodiments, the fluidic contents of the reaction tube have an initial volume in a range from 5 μL to 10 μL” [0304]).
Therefore, claims 1, 8, 11, 13-14, and 28 are anticipated by Rothberg.
Claims 1, 8-9, 11, 15-16, and 26 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Philips (EP 2198965, published 23 June 2010).
Regarding claim 1, Philips teaches a collecting system comprising: a probe configured to collect pathogens from a surrounding fluid (Fig. 1; “1 - sampler attached to screw-cap” [0006]; “A "sample" in the meaning of the invention is a sample comprised in a medical swab which has been collected from a patient suffering from an infection or being suspected of suffering from an infection. The sample may be collected from various sources of the patient's body, such as the oral or nasal cavity” [0051], since disclosed oral and nasal cavities contain fluids such as saliva and mucus, the sampler is configured to collect from a surrounding fluid); an elution chamber containing a liquid solvent and configured to receive the probe to elute the pathogens collected on the probe using the liquid solvent (Fig. 1; “Providing the sample to a sample receptacle unit Generating a crude lysate fluid” [0014]; “2 - lysis chamber with lysis buffer” [0006]; “In a particular embodiment the sample receptacle unit and the sample lysis unit are within the same chamber. In another particular embodiment the lysis of the sample takes place in the sample receptacle unit, which thus is at the same time the sample lysis unit” [0008]; since the lysis chamber is also the sample receptacle chamber, it is considered the elution chamber and the lysis buffer considered the liquid solvent, such as in Fig. 1; “Pathogens are then eluted from the swab and a crude lysate is generated in the lysis unit” [0023]); and a heater configured to lyse the pathogens to release the genetic material of the pathogens into the liquid solvent (“3 - heater for lysis chamber” [0006]).
Regarding claims 8, Philips teaches the collecting system of claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), further comprising a detection system that is configured to detect a presence of the pathogens (Fig. 1; “8 - hybridization array on top of optically transparent surface; 9 - optically transparent surface; 10 - heater for hybridization compartment; 11 - confocal scanning optics” [0006]; “Pushing or pulling the sample out of the PCR chamber into the said low-density flow-over hybridization array Detection either by a scanning fluorescence optical system or an evanescent wave illumination and image detection system” [0014]).
Regarding claim 9, Philips teaches the collecting system of claim 8 (see 35 U.S.C. 102 rejection of claim 8 above), wherein the detection system includes: a detection chamber; a light source optically coupled to the detection chamber; a photodetector optically coupled to the detection chamber (in Fig. 1, the chamber containing “8 - hybridization array on top of optically transparent surface” is the detection chamber and the “11 - confocal scanning optics”, inherently having a light source and photodetector, is optically coupled to the detection chamber by “9 - optically transparent surface” [0006]).
Regarding claim 11, Philips teaches the collecting system of claim 8 (see 35 U.S.C. 102 rejection of claim 8 above), wherein the detection system is configured to detect the presence of a pathogen by detecting the genetic material of the lysed pathogens (“"target DNA" specifies a DNA of interest which is to be detected and/or quantified in a sample by use of the devices and by the methods of the present invention. This may for instance be the DNA of one of the pathogens” [0058]; also see full method of [0014] and pathogens taught in [0017-0022]).
Regarding claim 15, Philips teaches the collecting system of claim 8 (see 35 U.S.C. 102 rejection of claim 8 above), further comprising a thermocycler that is configured to cycle the temperature of the liquid solvent and the genetic material to amplify the genetic material (Fig. 1; “6 - rotary PCR assembly; 7 - PCR heaters (set at a fixed temperature)” [0006]; “At least one closed PCR reaction chamber repeatedly movable over areas with at least three different temperatures to perform thermocycling or a circuit of at least three closed PCR reaction chambers, wherein each chamber has a different temperature and wherein the fluid comprising the sample is sequentially and repeatedly pumped through said PCR reaction chambers” [0007]; see also [0052]).
Regarding claim 16, Philips teaches the collecting system of claim 15 (see 35 U.S.C. 102 rejection of claim 15 above), further comprising one or more reagents that are configured to implement a PCR on the genetic material to amplify the genetic material (“In the PCR chamber, appropriate labeled multiplex primers are preferably pre-deposited together with PCR buffer mastermix” [0028]).
Regarding claim 26, Philips teaches the collecting system of claim 9 (see 35 U.S.C. 102 rejection of claim 9 above), further comprising a pump that is configured to move the genetic material from the elution chamber and to the detection chamber (Fig. 1; “A indicates the part of the device wherein pumping is carried out by an active pumping device as described herein” [0006], note that this refers to the label ‘A’ in Fig. 1, which encompasses the portion of the device from the sample receptacle/lysis/elution chamber to the entrance of the detection chamber; “A pumping unit for pumping the amplification unit over the low-density flow-over hybridization array” [0007], since the hybridization array is in the detection chamber this teaches that the pumping unit pumps into the detection chamber).
Therefore, claims 1, 8-9, 11, 15-16, and 26 are anticipated by Philips.
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.
Claims 2 and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg, as applied to claims 1, 8, 11, 13-14, and 28 above, in view of Dohale et al. (US 2017/0327867, published 16 November 2017, effectively filed 22 December 2015), herein Dohale.
Regarding claim 2, Rothberg teaches the collecting system of claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), further comprising an elution device configured to elute the pathogens collected on the probe into the liquid solvent, wherein the elution device includes: a container that defines the elution chamber (the combination of the heater and the reaction tube, discussed in the 35 U.S.C. 102 rejection of claim 1 above, is considered the elution device). However, while Rothberg teaches various options for heaters ([0315-01316]), they do not specifically teach a heat block in thermal communication with the heater and the elution chamber, the heater being configured to heat the heat block thereby heating the liquid solvent to lyse the pathogens. This deficiency is made up for in the teachings of Dohale.
Regarding claim 2, Dohale teaches a sample-to-answer system wherein a heat block is in thermal communication with a heater and a sample chamber, the heater configured to heat the heat block thereby heating the contents of the sample chamber (“resistive heaters are used to rapidly heat the filter and lyse the bacteria in the biological sample. At least one of the resistive heaters is attached to a heat block. The heat block is configured to have the same interior shape as the outer shape of the sample chamber” [0117], the sample chamber is equivalent to the claimed elution chamber since both contain the sample for thermal lysis).
Regarding claim 4, Dohale teaches using a concentrator in a sample-to-answer system to concentrate the genetic material of a pathogen (“a sample-to-answer process featuring sample enrichment” [0026], “enrichment of the target of interest may include concentrating the targets of interest within the sample. Enrichment may include separating the targets of interest from a portion of the sample by methods including filtering, centrifugation, sedimentation and other methods whereby non-target fluid and/or other sample components are removed from the targets of interest” [0101]; “targets of interest […] include […] influenza”; “the target may be amplified by amplification techniques known in the art, and specifically by nucleic acid amplification reactions”). Dohale also teaches that enriching a sample for a target of interest is advantageous because processing time can be shortened (“Causative microorganisms are often present in sufficient numbers in samples but generally are present at low concentration. As a result, effective POC or PON systems need to consider enrichment of target microorganisms by a process that concentrates the targets to facilitate rapid detection. When sample enrichment is used, processing time can be shortened” [0005]).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the heat block in thermal communication with the heater and the elution chamber taught by Dohale for the heater configured to lyse pathogens in the system taught by Rothberg (MPEP §2143 I. B.). Additionally, one of ordinary skill in the art would be motivated to combine Dohale with Rothberg in order to obtain the system of Rothberg with the advantage of shortened processing time obtained by the target enrichment taught by Rothberg. One of ordinary skill in the art could have performed this substitution and would have found the results of this combination predictable because both Rothberg and Dohale are concerned with art pertaining to processing a sample for analysis, both use the heaters taught for thermal lysis, and exchanging one heater that uses a heat block for another heater when both are intended to heat a sample would not be expected to negate the ability of the system to heat a sample. Similarly, the addition of an enrichment step would not be expected to negate the ability of the system to collect and lyse samples. Therefore, the invention as a whole of claims 2 and 4 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 5-6 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg, as applied to claims 1, 8, 11, 13-14, and 28 above, in view of Dohale et al. (US 2017/0327867, published 16 November 2017, effectively filed 22 December 2015), herein Dohale, as applied to claims 2 and 4 above, and further in view of Khandurina et al. (Non-Patent Literature Documents Cite No 6 in IDS filed 14 November 2023)(“Microfabricated Porous Membrane Structure for Sample Concentration and Electrophoretic Analysis”, Anal Chem 71(9), pages 1815-1819 (1999)), herein Khandurina.
Regarding claim 5, the combination of Rothberg and Dohale teaches the collecting system of claim 4 (see 35 U.S.C. 103 rejection of claim 4 over Rothberg and Dohale above). However, neither Rothberg nor Dohale teach the system, wherein the concentrator includes a semi-permeable barrier positioned within a flow path of the genetic material of the pathogens and an electrode that is configured to be positively or negatively charged to direct the genetic material of the pathogens towards the semi-permeable barrier to concentrate the genetic material. This deficiency is made up for in the teachings of Khandurina.
Regarding claims 5-6, Khandurina teaches a system comprising a concentrator configured to concentrate a genetic material, wherein the concentrator includes a semi-permeable barrier positioned within a flow path of the genetic material, an electrode that is configured to be positively or negatively charged to direct the genetic material towards the semi-permeable barrier to concentrate the genetic material, a first electrode that is configured to be positively charged, a second electrode that is configured to be negatively charged, and the semi-permeable membrane is positioned between the first electrode and the second electrode (“During sample loading, the potentials at the analyte and side reservoirs were 0 and 1 kV, respectively, and the buffer and waste reservoirs had no potentials applied. DNA molecules accumulate in the tee region due to their hindered transport through the membrane, and the concentration, observed by monitoring the fluorescence intensity, increased with time” page 1817, left column, paragraph 2; “Schematic of porous membrane microchip for DNA concentration” Figure 1 legend, page 1816; Figure 1, page 1816; note that the analyte and side reservoirs are the positively and negatively charged first and second electrodes on opposite sides of the porous membrane). Khandurina also teaches that concentration technologies, such as the one they teach, are advantageous because detection capabilities are enhanced by increased sample concentration (“Detection capabilities can also be enhanced by sample concentration methods” page 1815, right column, paragraph 2) and that their teachings both substantially enhance DNA concentration and that the concentrated DNA can be then directed into a separate channel for detection (“This arrangement allowed substantial enhancement in DNA concentration […] Concentrated int his manner, the sample plug can then be injected into the separation channel and detected” page 1816, left column, paragraph 2).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the concentrator taught by Khandurina that operates by filtering nucleic acids that can’t pass through a membrane for the generic enrichment taught by Dohale that includes filtering methods (MPEP §2143 I. B.). One of ordinary skill in the art could have performed this substitution and would have found the results of this combination predictable because both Khandurina and the combination of Rothberg and Dohale are concerned with art pertaining to processing a sample for analysis and merely teach alternative filtering methods for increasing the concentration of nucleic acid, so exchanging one filtering method for another would not be expected to negatively impact the functioning of the system as a whole. Therefore, the invention as a whole of claims 5-6 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 7 and 10 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg, as applied to claims 1, 8, 11, 13-14, and 28 above, in view of Florian et al. (“Principles of computer-controlled linear motion applied to an open-source affordable liquid handler for automated micropipetting”, Sci Rep 10, 13663 (2020)), herein Florian.
Regarding claim 7, Rothberg teaches the collecting system of claim 1 (see 35 U.S.C. 102 rejection of claim 1 above). However, Rothberg does not teach the system further comprising at least one of: a robotic arm that is configured to selectively grasp the probe to place the probe into and out of the elution chamber; or an actuator that is coupled to the probe, the actuator being configured to be extended to place the probe into the elution chamber or retracted to remove the probe from the elution chamber. This deficiency is made up for in the teachings of Florian.
Regarding claim 7, Florian teaches an actuator that is coupled to a pipette, the actuator being configured to be extended to place the probe into a region or retracted to remove the probe from the region (“we designed an open-source liquid handler, known as OTTO” page 2, paragraph 2; “OTTO is a 3D linear motion platform […] that is capable of positioning a manual micropipette anywhere within its work envelope (Fig. 1A,D)” page 2, paragraph 5; “Bipolar hybrid stepper motors move the timing belt (X-axis) and lead screws (Y- and Z-axes)” page 3, paragraph 1; “the linear actuators are able to move the micropipette in the X-, Y-, and Z-directions” page 4, paragraph 1; note that the actuation in the Z-direction is what allows the tip to be extended into or retracted from a tube such as that taught by Rothberg). Florian also teaches that robot handlers such as OTTO are more precise and faster than human operation (“robotic liquid handlers that are more precise and faster than their human counterparts” page 1, body paragraph 1). In combination with Rothberg, by substituting the probe of Rothberg for the micropipette itself or the micropipette tip or even using the tip as the probe (a tip suspended in the air collects aerosolized pathogens that collide with it) and having the reaction tube of Rothberg in the working envelope of handler of Florian, the actuator would be configured to extend the probe into the elution chamber or retract the probe from the elution chamber, thereby providing the advantage of not involving a slower and less precise human in the insertion of the probe into the reaction tube.
Regarding claim 10, the combination of Rothberg and Florian teaches the collecting system of claim 7 (see 35 U.S.C. 103 rejection of claim 7 above), and Rothberg teaches a collecting system that is configured to amplify the amount of genetic material (“In some embodiments, a diagnostic method comprises performing an isothermal nucleic acid amplification reaction configured to amplify one or more target nucleic acids” [0069]).
One of ordinary skill in the art would be motivated to combine the collection system taught by Rothberg with the handler taught by Florian in order to gain the advantage of increased speed and precision compared to human operation as taught by Florian (MPEP §2143 I. G.). Additionally, the MPEP states: “In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958) (Appellant argued that claims to a permanent mold casting apparatus for molding trunk pistons were allowable over the prior art because the claimed invention combined "old permanent-mold structures together with a timer and solenoid which automatically actuates the known pressure valve system to release the inner core after a predetermined time has elapsed." The court held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art.)” (MPEP §2144.04 III.). This further supports that it would be obvious to use the mechanical means of Florian to replace manual activity in the system taught by Rothberg. One of ordinary skill in the art would have a reasonable expectation of success in this combination because the insertion and/or removal of a probe being accomplished by a human instead of an actuated robotic handler is not necessary for the sample collection, elution, and lysis capabilities of the system taught by Rothberg. Therefore, the invention as a whole of claims 7 and 10 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 9 and 18-23 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg, as applied to claims 1, 8, 11, 13-14, and 28 above, in view of Kalkum et al. (US 2022/0193658, effectively filed 23 December 2020), herein Kalkum.
Regarding claim 9, Rothberg teaches the collecting system of claim 8 (see 35 U.S.C. 102 rejection of claim 8 above) and that nucleic acid amplification of target nucleic acids by isothermal techniques such as LAMP (loop-mediated isothermal amplification) may allow small amounts of target nucleic acid to be detected by the detection system of the collecting system (“a diagnostic method comprises performing an isothermal nucleic acid amplification reaction configured to amplify one or more target nucleic acids. In certain cases, the nucleic acid amplification reaction may be a LAMP […] isothermal nucleic acid amplification may advantageously provide for accurate detection of the presence of small amounts of a target nucleic acid” [0069]). However, Rothberg does not teach the system specifically including a detection chamber; a light source optically coupled to the detection chamber; and a photodetector optically coupled to the detection chamber. This deficiency is made up for in the teachings of Kalkum.
Regarding claim 9, Kalkum teaches a LAMP device (“The LAMP device 100 may be housed inside an enclosure 105” [0047]; FIG. 1A) for detection of nucleic acids (“systems, methods, and computer program products described herein include and/or implement a loop-mediated isothermal amplification (LAMP) reactions for detecting the presence of genetic material” [0041]), wherein the LAMP device includes a detection chamber (“a reaction vessel 115 configured to support a sample for amplification” [0047], the reaction vessel where the nucleic acid amplification reaction occurs is considered the detection chamber, note that this is equivalent to the reaction tube of Rothberg); a light source optically coupled to the detection chamber (“The light emitter 125 may be configured to illuminate the reaction vessel 115” [0049]); and a photodetector optically coupled to the detection chamber (“The imaging device 120 may be configured to detect a fluorescence signal emitted from a reaction vessel 115 […] The imaging device 120 may be configured to obtain an image of the sample for determining a quantity of the fluorescence in the sample” [0051]).
Regarding claim 18, Rothberg teaches the collecting system of claim 8 (see 35 U.S.C. 102 rejection of claim 8 above) and the combination of Rothberg and Kalkum teach the collecting system of claim 9 (see 35 U.S.C. 103 rejection of claim 9 above). Kalkum also teaches the LAMP device further comprising a computing device in communication with the detection system (“the LAMP device 100 may further include or be coupled to a computer comprising a controller configured to control one or more aspects of the device. The controller may be communicatively coupled to the tray assembly, the plurality of light emitters, and the imaging device 120” [0053]), and wherein the computing device is configured to: cause the light source to emit first light towards the detection chamber, the first light interacting with a molecule that interacts with the genetic material of the pathogens to emit second light (“The light emitter 125 may be configured to illuminate the reaction vessel 115 for exciting a fluorescence of the sample in the reaction vessel 115” [0049]; “the controller may be configured to generate an instruction to the light emitter to illuminate thereby illuminating the reaction vessel 115. The controller may be configured to measure a fluorescence signal from the reaction vessel 115” [0055]); receive optical data from the photodetector indicative of the second light interacting with the photodetector (“The controller may be configured to measure a fluorescence signal from the reaction vessel 115” [0055], the measured fluorescence signal is optical data); and determine a presence of the pathogen, based on the optical data (“The controller may be configured to determine that a pathogenic material is present in the sample based on the fluorescence signal” [0055]).
Regarding claim 19, the combination of Rothberg and Kalkum teach the collecting system of claim 18 (see 35 U.S.C. 103 rejection of claim 18 above). Rothberg further teaches the system wherein the system is configured to implement a reverse transcription loop mediated isothermal amplification (RT-LAMP) reaction on the genetic material from the pathogen to amplify the amount of genetic material (“Following cell lysis […] one or more target nucleic acids (e.g., a nucleic acid of a target pathogen) are amplified […] the target pathogen's RNA may need to be reverse transcribed to DNA prior to amplification” [0158], teaching the RT (reverse transcription) portion of RT-LAMP; “In some embodiments, the nucleic acid amplification method is an isothermal amplification method comprising loop-mediated isothermal amplification (LAMP)” [0162]).
Regarding claim 20, the combination of Rothberg and Kalkum teach the collecting system of claim 19 (see 35 U.S.C. 103 rejection of claim 19 above). Rothberg further teaches the system further comprising one or more reagents that include: a primer specific to a corresponding region on the genetic material of the pathogen; a reverse transcriptase; and a deoxyribonucleic acid ("DNA") polymerase (“In certain embodiments, the one or more reagents comprise isothermal nucleic acid amplification reagents (e.g., reagents for loop-mediated isothermal amplification (LAMP)” [0048]; “LAMP employs a primer set” [0163]; “reverse transcription is performed by exposing lysate to one or more reverse transcription reagents. In certain instances, the one or more reverse transcription reagents comprise a reverse transcriptase” [0159]; “the LAMP reagents comprise a DNA polymerase” [0175]).
Regarding claim 21, the combination of Rothberg and Kalkum teach the collecting system of claim 19 (see 35 U.S.C. 103 rejection of claim 19 above), further comprising one or more reagents that are configured to implement the RT-LAMP reaction, the one or more reagents being preloaded within the detection chamber (“In certain embodiments, the one or more reagents comprise isothermal nucleic acid amplification reagents (e.g., reagents for loop-mediated isothermal amplification (LAMP)” Rothberg [0048]; “a reaction vessel 115 configured to support a sample for amplification” Kalkum [0047], the reaction vessel where the nucleic acid amplification reaction occurs is considered the detection chamber, note that this is equivalent to the reaction tube 120 of Rothberg; “third cap 120D may be placed on tube 120A. In some embodiments, third cap 120D comprises one or more reagents (e.g., nucleic acid amplification reagents)” Rothberg [0055], when the third cap is placed on the reaction tube they are equivalent to the reaction vessel of Kalkum that supports amplification, therefore the detection chamber is considered preloaded with the reagents because the cap portion of the detection chamber is preloaded with the reagents).
Regarding claim 22, the combination of Rothberg and Kalkum teach the collecting system of claim 21 (see 35 U.S.C. 103 rejection of claim 21 above). Rothberg further teaches the system wherein the one or more reagents are lyophilized (“In certain embodiments, the one or more reagents are […] lyophilized” [0054]).
Regarding claim 23, the combination of Rothberg and Kalkum teach the collecting system of claim 21 (see 35 U.S.C. 103 rejection of claim 21 above). Rothberg further teaches the system wherein the heater or another heater is configured to heat the genetic material and the one or more reagents to a temperature that is greater than or equal to 65°C (“In some embodiments, the amplification reagents are present in the cap as an amplification pellet, and connecting the cap to the tube releases the pellet into the tube. The user then shakes the tube briefly to mix the components, and then places it back in the heating device […] if LAMP reagents are used, the heating device heats the sample to […] 65° C. for 40 minutes” [0354]).
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the LAMP device for detecting amplification of genetic material taught by Kalkum for the readout device in the system taught by Rothberg (MPEP §2143 I. B.). One of ordinary skill in the art would also be motivated to perform this combination because Kalkum teaches that their LAMP device has the advantage of using minimal consumables ([0097]), which would improve the system of Rothberg to require replacement of consumables less often and in lower quantity. One of ordinary skill in the art could have performed this substitution and would have found the results of this substitution predictable because it is merely the substitution of a device for reading out the result of a LAMP reaction for another device for reading out the result of a LAMP reaction, which both perform the same function. Therefore, the invention as a whole of claims 9 and 18-23 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 12, 15-17, and 24 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg, as applied to claims 1, 8, 11, 13-14, and 28 above, in view of Liu et al. (“Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals” Nature 582, pages 557-560 (2020)), herein Liu Main, and supplementary data of Liu Main, herein Liu Supplementary, and source data of Liu Main, herein Liu Source (annotated by Examiner with the formulas of the Concentration and Total Copies in Samples columns at the bottom of the document).
Regarding claim 12, Rothberg teaches the collecting system of claim 11 (see 35 U.S.C. 102 rejection of claim 11 above). However, Rothberg does not teach that the collecting system further comprises a computing device that is configured to: determine that the pathogen is aerosolizable based on the presence of the pathogens having been detected, the pathogen having been previously unknown of being aerosolizable; and notify a user based on the determination that the pathogen is aerosolizable. This deficiency is made up for in the teachings of Liu Main.
Regarding claim 12, Liu Main teaches the determination that a pathogen, SARS-CoV-2, is aerosolizable based on the presence of the pathogen having been detected by detecting the genetic material, the pathogen having been previously unknown of being aerosolizable, and notifying interested people that read the publication (equivalent to a user) based on the determination that the pathogen is aerosolizable (“Reported transmission pathways of SARS-CoV-2 in humans include the inhalation of virus-laden liquid droplets, close contact with infected individuals and contact with surfaces that are contaminated with SARS-CoV-2. Moreover, aerosol transmission has been suggested to be an additional, yet important pathway, on the basis of clinical observations in confined spaces” page 557, left column; “We analysed the occurrence of airborne SARS-CoV-2 and its aerosol deposition at 30 sites in two designated hospitals and public areas in Wuhan, China, and then quantified the copy counts of SARS-CoV-2 in aerosol samples using a robust droplet-digital-PCR-based detection method (ddPCR)” page 557, right column; “The concentrations of airborne SARS-CoV-2 at the different sites are shown in Table 1” page 559, left column, paragraph 1; Table 1; Fig. 1). Additionally, Liu Main teaches that in response to the notification of a pathogen being aerosolizable, various recommendations to reduce the risk of exposure can be taken (“The results of this study have important implications for the prevention of infection of the public and protection of medical staff. We call for particular attention to (1) the ventilation and sterilization of toilets as a potential source for the spreading of the virus; (2) personal protection measures for the general public, such as the wearing of masks and avoidance of busy crowds to reduce the risk of exposure to airborne virus” page 560, left column, paragraph 2).
Regarding claim 12, though neither Rothberg nor Liu Main teach that the determination and notification of Liu Main is done by a computing device configured to do the determination and notification, the recited computing device is merely a general recitation of an automatic or mechanical means to replace the manual activity of determining that the presence of the pathogens having been detected indicates that the pathogen is aerosolizable and notifying people based on the determination. The MPEP states: “In re Venner, 262 F.2d 91, 95, 120 USPQ 193, 194 (CCPA 1958) (Appellant argued that claims to a permanent mold casting apparatus for molding trunk pistons were allowable over the prior art because the claimed invention combined "old permanent-mold structures together with a timer and solenoid which automatically actuates the known pressure valve system to release the inner core after a predetermined time has elapsed." The court held that broadly providing an automatic or mechanical means to replace a manual activity which accomplished the same result is not sufficient to distinguish over the prior art.)” (MPEP §2144.04 III.). As the claim only recites a broad approach of automating a manual activity of the system, the automation does not distinguish the claimed invention over the prior art.
Regarding claim 15, Rothberg teaches the collecting system of claim 8 (see 35 U.S.C. 102 rejection of claim 8 above) and also teaches the system comprising a thermocycler being used as the heat source for lysis and amplification reactions (“In some embodiments, the heat source is a thermocycler” [0315]; “the heater is pre-programmed with a lysis heating protocol and/or an amplification heating protocol” [0321]). Liu Main with Liu Supplementary teaches amplifying genetic material using a thermocycler that is configured to cycle the temperature of a liquid solvent and the genetic material (“quantified the copy counts of SARS-CoV-2 in aerosol samples using a robust droplet-digital-PCR-based detection method (ddPCR)” Liu Main page 557, right column; “cycled in a T100 Thermal Cycler (Bio-Rad)” Liu Supplementary, page 5).
Regarding claim 16, the combination of Rothberg and Liu Main teach the collecting system of claim 15 (see 35 U.S.C. 103 rejection of claim 15 above), and Liu Main with Liu Supplementary further teaches the PCR reaction further comprising one or more reagents that are configured to implement a PCR on the genetic material to amplify the genetic material (“The ddPCR was performed according to the manufacturer’s instructions for the QX200 Droplet Digital PCR System (Bio-Rad) using supermix for probe (without dUTP) (Bio-Rad)” Liu Supplementary, page 5).
Regarding claim 17, the combination of Rothberg and Liu Main teach the collecting system of claim 15 (see 35 U.S.C. 103 rejection of claim 15 above), and Liu Main with Liu Supplementary further teaches the PCR reaction wherein the one or more cycles that define the PCR take less than 120 minutes; or the one or more reagents, the thermocycler, or both are configured to implement a fast PCR on the genetic material to amplify the genetic material, the one or more cycles that define the fast PCR being less than 3 minutes, and wherein the one or more cycles are at least one of greater than 30 cycles, greater than 35 cycles, or greater than 40 cycles (“40 cycles of 94 °C for 30 s (denaturation) and 60 °C for 1 min (annealing)” Liu Supplementary, page 5, note that the duration of a cycle is 90 seconds and the total duration is 70 minutes, even with a slower than normal ramp rate of 1C/s, the cycle duration would be 158 seconds and total duration under 116 minutes).
Regarding claim 24, the combination of Rothberg and Liu Main teach the collecting system of claim 15 (see 35 U.S.C. 103 rejection of claim 15 above), and Liu Main with Liu Supplementary and Liu Source teaches the determination of an initial amount of genetic material in a detection chamber before amplification based on optical data and the determination of a concentration of the pathogen in the enclosed volume it was sampled from based on the initial amount of genetic material and the total volume of the enclosed volume using a computing device (“In accordance with current clinical diagnosis of COVID-19 in China, primers and probes that targeted the ORF1ab and N genes of SARS-CoV-2 were used” Liu Supplementary, page 4; note that in Liu Source Concentration is column D, the ddPCR Raw Rep1 and Rep2 for ORFlab and N are columns G-J, and the Total Copies in Samples column is column K, so the initial amount of genetic material represented in the Total Copies in Samples column is calculated from the ddPCR optical data and the concentration of the pathogen is calculated based on the Total Copies in Samples and the Air Volume of where it was sampled; “Analysis of the ddPCR data was performed with QuantaSoft analysis software v.1.7.4.0917 (Bio-Rad) that accompanied the droplet reader to calculate the concentration of the target sequences” Liu Supplementary, page 5). Though it is unclear in the Liu references if the computing device was configured to perform all of the determinations or just the initial concentration calculation in columns G-J of Liu Source, the determinations could be done initial concentration calculations by hand. Even if the Liu references does not disclose the computing device as claimed, per MPEP §2144.04(III) (see 35 U.S.C. 103 rejection of claim 12 above), since the claim merely recites a broad approach of automating a manual activity of the system via a computing device, the automation does not distinguish the claimed invention over the prior art.
One of ordinary skill in the art would be motivated to combine the collection system taught by Rothberg with the determination and notification that a pathogen is aerosolizable taught by the Liu references in order to gain the advantage of allowing recommendations to reduce risk of exposure based on this determination to be taken, as taught by the Liu references (MPEP §2143 I. G.). One of ordinary skill in the art would have a reasonable expectation of success in this combination because the making a determination based off of data and notifying people of the determination does not impact the ability of the system to produce said data. One could also perform the simple substitution of the ddPCR detection system of the Liu references for the detection system of Rothberg, since both function by amplification of small amounts of input genetic material and Rothberg already discloses the system including a thermocycler. Therefore, the invention as a whole of claims 12, 15-17, and 24 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg, as applied to claims 1, 8, 11, 13-14, and 28 above, in view of Liu et al (“Aerodynamic analysis of SARS-CoV-2 in two Wuhan hospitals” Nature 582, pages 557-560 (2020)), herein Liu Main, and supplementary data of Liu Main, herein Liu Supplementary, and source data of Liu Main, herein Liu Source (annotated by Examiner with the formulas of the Concentration and Total Copies in Samples columns at the bottom of the document), as applied to claims 12, 15-17, and 24 above, and further in view of Mainelis (“Bioaerosol Sampling: Classical Approaches, Advances, and Perspectives” Aerosol Sci Technol 54(5), pages 496-519 (2019)).
Regarding claim 25, the combination of Rothberg and the Liu references teach the collecting system of claim 24 (see 35 U.S.C. 103 rejection of claim 24 above). However, though Liu teaches the determination of the concentration of the pathogen in the enclosed volume based on the initial amount of genetic material and the total volume of the enclosed volume (see 35 U.S.C. 103 rejection of claim 24 above), this calculation is not based on an efficiency ratio of the collection rate of the pathogens in the surrounding volume to the pathogens collected on the probe. This deficiency is made up for in the teachings of Mainelis.
Regarding claim 25, Mainelis teaches that the particle concentration in a liquid sample (which can be derived from the initial amount of genetic material in the sample divided by the volume of the sample) divided by the airborne particle concentration (the concentration of the pathogen in the enclosed volume, which is equivalent to the total pathogen in the enclosed volume divided by the total volume of the enclosed volume) is equivalent to the sampling flow rate multiplied by the collection efficiency (efficiency ratio of the collection rate) (page 503, right column, Equation 1 and paragraph 3). Therefore, one of ordinary skill in the art would by simple arithmetic be able to calculate the total pathogen in the enclosed volume based on the initial amount of genetic material, total volume of the enclosed volume, efficiency ratio, sampling flow rate, and volume of the sample, and to then calculate the concentration of the pathogen in the enclosed volume based on the obtained total pathogen in the enclosed volume and the total volume of the enclosed volume. Mainelis also teaches that that this mathematical relationship is useful for calculating the Concentration Rate, which is directly related to a sampler’s detection ability (the sampler being equivalent to the collecting system comprising a probe that is configured to collect, or sample, pathogens from a fluid), thereby teaching variables that may be modified to improve a sampler’s detection ability (“A sampler’s detection ability could be improved by increasing its Concentration Rate” page 503, right column, paragraph 3).
One of ordinary skill in the art would be motivated to combine the collection system taught by the combination of Rothberg and the Liu references with the equation for calculating concentration rate taught by Mainelis in order to gain the advantage of being able to improve the sampler’s detection ability using the parameters taught by Mainelis (MPEP §2143 I. G.). One of ordinary skill in the art would have a reasonable expectation of success in this combination because using an equation to analyze data from the system does not prevent the system from functioning or the data from being analyzed by other methods. Therefore, the invention as a whole of claim 25 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Claims 3 and 27 are rejected under 35 U.S.C. 103 as being unpatentable over Rothberg et al. (US 2021/0292825, effectively filed 17 March 2020), herein Rothberg, as applied to claims 1, 8, 11, 13-14, and 28 above, in view of Rufino de Sousa et al. (Non-Patent Literature Documents Cite No 19 in IDS filed 14 November 2023)(“A fieldable electrostatic air sampler enabling tuberculosis detection in bioaerosols” Tuberculosis (Edinb), 101896 (2019)), herein Rufino de Sousa, and in view of Altman et al. (US 2006/0130648, published 22 June 2006), herein Altman.
Regarding claim 27, Rothberg teaches the collecting system of claim 1 (see 35 U.S.C. 102 rejection of claim 1 above). However, Rothberg does not teach that the collecting system further comprises a power source in selective electrical communication with the probe, wherein the probe is in selective electrical communication with an electrical ground, wherein when the probe is electrically connected to the electrical ground, the probe attracts and collects aerosolized pathogens that have been ionized, and wherein when the probe is electrically connected to the power source, the power source charges the probe to repel the pathogens or the genetic materials of the pathogen away from the probe into the liquid solvent. This deficiency is made up for in the teachings of Rufino de Sousa and Altman.
Regarding claim 27, Rufino de Sousa teaches a collecting system comprising a probe in electrical communication with an electrical ground, wherein when the probe is electrically connected to the electrical ground, the probe attracts and collects aerosolized pathogens that have been ionized (“The collector piece is a 3.5 cm long and 0.88 cm in diameter stainless-steel rod designed to fit into a 2 mL microcentrifuge tube. It is magnetically attached and electrically connected to the grounded holder on the device” page 2, right column, paragraph 1, the collector piece is the probe; “THOR is activated by connecting it to power. It generates a strong electric field between the −20 kV ionizers and the grounded collector (Supplementary Fig. 1A). A corona discharge is formed at the small radius tips of the carbon brush fibers of the ionizers and emitted electrons ionize air molecules at the vicinity of the carbon brush tips. A Townsend avalanche generates a high number of ions that also ionize aerosol particles, which then accelerate in the electric field by electrostatic forces towards the collector where they impact and lose their charge” page 2, right column, paragraph 2, aerosol particles include pathogens, see Title and Abstract disclosing tuberculosis). Rufino de Sousa also teaches the elution of a sample from the probe (“After air sampling, the collector piece was transferred into a microcentrifuge tube […]. Thereafter, 0.5 mL PBS-0.05% Tween-80 (PBS-T80) was added to the microcentrifuge tube with the collector unit inside followed by incubation at room temperature for 2 min and then vortexing for 1 min. The collector unit was then removed using a magnet and the extracted sample in liquid left in the tube” page 3, left column, paragraph 4). However, neither Rothberg nor Rufino de Sousa teach a collecting system wherein the probe is in selective electrical communication with an electrical ground and when the probe is electrically connected to the power source, the power source charges the probe to repel the pathogens or the genetic material of the pathogens away from the probe into the liquid solvent. This deficiency is made up for in the teachings of Altman.
Regarding claim 27, Altman teaches an electrostatic precipitator wherein particles collected on a collector via electrostatic precipitation are repelled by reversing polarity by selectively applying voltage potentials of opposite polarity to the electrostatic precipitator (“a rapid impulse of reversed polarity will generate very consequential electrostatic force which repels the particulate from the collector plates” [0035]; “an electrostatic precipitator having at least one discharge electrode for charging particulates within a gas stream, at least one collector for attracting the newly charged particulates, a high voltage power source operatively and selectively able to apply a high voltage potential of a first polarity between discharge electrode and collector, […]. A second high voltage power source is operatively and selectively able to apply a high voltage potential of a second polarity opposite to the first polarity between discharge electrode and collector” [0020]; also see [0018-0019], [0028-0032], and FIG. 1). Altman teaches that the polarity reversal is advantageous because it allows for reliable cleaning of the collector electrode (“The electrical cleaning of precipitate is very rapid, and provides a reliable approach to the maintenance of an electrostatic precipitator” [0036]).
By combining Rothberg, Rufino de Sousa, and Altman, one of ordinary skill in the art would be able to substitute the collector of Rufino de Sousa that operates by electrostatic precipitation for the general sample-collecting component of the system of Rothberg, which would be improved by the teachings of Altman that inform one of ordinary skill in the art to use a circuit to selectively reverse the voltage potential of the electrostatic precipitator of Rufino de Sousa from the collecting state (charged ionizers and collector connected to ground) to a repelling state (collector charged by electrical connection to power source and ionizers connected to ground) so that the collector can be more easily cleaned. Because the claimed collecting system is an apparatus, the recitation in claim 27 “to repel the pathogens or the genetic material of the pathogens away from the probe into the liquid solvent” recites functional language that only limits the apparatus insofar as it limits the structure of the apparatus (see MPEP §2114 II.). As the combination of Rothberg, Rufino de Sousa, and Altman teach a collector that can be inserted into a tube for elution and that can have its collected particles repelled by charging the collector, this combination teaches a structure that is capable of the recited function and therefore teach a structure satisfying this limitation.
Regarding claim 3, Rothberg teaches the collecting system of claim 1 (see 35 U.S.C. 102 rejection of claim 1 above), Rufino de Sousa teaches using an electrostatic precipitator to collect pathogens from the air onto a collector (see 35 U.S.C. 103 rejection of claim 27 above, the collector being analogous to the claimed probe, the electrostatic precipitator is considered an elution device since it the samples on its collector are eluted into a tube), and Altman teaches a power source in selective electrical communication with the collector and configured to charge the collector to repel particles from the collector (see 35 U.S.C. 103 rejection of claim 27 above). The recitation “to repel the pathogens or the genetic material of the pathogens away from the probe into the liquid solvent” is identical the same recitation in claim 27, so the combination of Rothberg, Rufino de Sousa, and Altman teach this limitation for the same reasoning as discussed in the 35 U.S.C 103 rejection of claim 27 above.
It would have been obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention to perform the simple substitution of the electrostatic precipitator that collects pathogen samples from air on a collector, taught by Rufino de Sousa, for the sample-collecting component of the system taught by Rothberg (MPEP §2143 I. B.). One of ordinary skill in the art would also be motivated to perform this substitution because though Rothberg teaches that their system may be used with “environmental samples” ([0072]), they do not teach any particular manner of obtaining environmental samples suitable for elution in the reaction tube of the system, which Rufino de Sousa solves by teaching an apparatus for collecting bioaerosol samples on a collect that can be inserted into standard microcentrifuge tubes (MPEP §2143 I. G.). One of ordinary skill in the art could have performed this substitution and would have found the results of this substitution predictable because both the collector taught by Rufino de Sousa and the sample-collecting component taught by Rothberg are for collecting samples and being inserted into a tube for elution of the sample. One of ordinary skill in the art would be further motivated to combine the combination of Rothberg and Rufino de Sousa with Altman because Altman teaches that an electrostatic precipitator, such as that taught by Rufino de Sousa and used for collection in the combination of Rothberg and Rufino de Sousa, can be improved to be more easily cleaned by using a circuit that reverse the polarity of the voltage potential of the electrostatic precipitator (MPEP §2143 I. G.). One of ordinary skill in the art would have a reasonable expectation of success in this combination because both Altman and Rufino de Sousa are in the art of electrostatic precipitators and the inclusion of the ability to reverse polarity taught by Altman does not prevent the electrostatic precipitator of the combination of Rothberg and Rufino de Sousa from performing its primary function of collecting a sample. Therefore, the invention as a whole of claims 3 and 27 would have been prima facie obvious to one of ordinary skill in the art prior to the effective filing date of the claimed invention.
Conclusion
Claims 1-28 are pending and rejected. Claims 29-34 are pending and withdrawn.
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/JEFFREY BELLAH/Examiner, Art Unit 1683
/ANNE M. GUSSOW/Supervisory Patent Examiner, Art Unit 1683
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