Charm Sciences, Inc.

Patent Trials and Appeals Board

Jan 19, 2021

2020003410 (P.T.A.B. Jan. 19, 2021)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
14/372,088 07/14/2014 John Jabour 9175-113 2171
4678 7590 01/19/2021
MACCORD MASON PLLC
2733 Horse Pen Creek Road, Suite 101
GREENSBORO, NC 27410
EXAMINER
MARCSISIN, ELLEN JEAN
ART UNIT PAPER NUMBER
1641
MAIL DATE DELIVERY MODE
01/19/2021 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte JOHN JABOUR, STEVEN J. SAUL, and MARK E. TESS
__________

Appeal 2020-003410
Application 14/372,088
Technology Center 1600
__________

Before FRANCISCO C. PRATS, JEFFREY N. FREDMAN, and
TAWEN CHANG, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims to a method
for extracting one or more small molecules from a dry test sample. The
Examiner rejected the claims as anticipated and as obvious. We have
jurisdiction under 35 U.S.C. § 6(b). We affirm-in-part.

1 We use the word “Appellant” to refer to “applicant” as defined in 37
C.F.R. § 1.42. Appellant identifies the Real Party in Interest as Charm
Sciences, Inc. (see Appeal Br. 2). We have considered the Specification of
July 14, 2014 (“Spec.”); Final Office Action of May 23, 2019 (“Final
Action”); Appeal Brief of July 19, 2019 (“Appeal Br.”); and Examiner’s
Answer of Dec. 23, 2019 (“Ans.”).
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Statement of the Case
Background
“When chromatographic test strips, such as lateral flow test strips, are
the testing medium, many sample matrices, such as solid or granular
materials, require extraction of analyte into a liquid matrix prior to testing”
(Spec. 1:16–18). The samples may be extracted with solvents but “such
solvents can be relatively hazardous and costly. In addition, such solvents
may require further dilution or buffering . . . Dilution can affect test
sensitivity and, therefore, when higher sensitivity is desired . . . dilution can
be undesirable” (id. at 1:20–27).
The Specification teaches “methods and compositions for performing
relatively non-hazardous extractions of a variety of toxins, such as
mycotoxins, from a sample” (id. at 1:31–33).
The Claims
Claims 1–5, 12, 13, 16–18, 20, and 24–27 are on appeal.2
Independent claim 1 is the sole independent claim, is representative and
reads as follows:
1. A method for extracting one or more small molecules
from a dry test sample comprising the steps of:
a) mixing the sample with a composition comprising a
protein in water to form an admixture;
b) separating said admixture between a settled layer and a
distinct water layer comprising small molecules, and
c) collecting at least a portion of said water layer,
wherein said at least a portion of said water layer is an extract
containing said one or more small molecules.

2 The Examiner states that claim 6–11, 14, 15, 19, 21–23, and 28–31 are
withdrawn from consideration (see Final Act 2).
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The issues3
A. The Examiner rejected claims 1, 17, and 20 under 35 U.S.C. § 102(b)
as anticipated by Cookman4 as evidenced by Aflatoxin,5 Ochratoxin,6
Fumonisin,7 and Markel8 (Final Act. 2–6).
B. The Examiner rejected claims 1, 3–5, 12, 13, and 16–18 under 35
U.S.C. § 103(a) as obvious over Saul,9 Nasir,10 and Blankfard11 (Final Act.
6–10).
C. The Examiner rejected claims 1 and 20 under 35 U.S.C. § 103(a) as
obvious over Saul, Nasir, Blankfard, and Garcia12 (Final Act. 10–11).
D. The Examiner rejected claims 1, 2, and 24 under 35 U.S.C. § 103(a)
as obvious over Saul, Nasir, Blankfard, and Danko13 (Final Act. 11–13).

3 We note that US application 16/176,189 currently is in abandoned status
and therefore provisional obviousness-type double patenting rejections based
on the ’189 application are moot.
4 Cookman et al., Extraction of protein from distiller’s grain, 100
Bioresource Technology 2012–17 (2009).
5 Aflatoxin B1, https://pubchem.ncbi.nlm.nih.gov/compound/186907,
PubChem CID: 186907, (Accessed Aug. 17, 2017).
6 Ochratoxin, https://pubchem.ncbi.nlm.nih.gov/compound/442530
PubChem ID: 442530, (accessed Aug. 17, 2017).
7 Fumonisin, https://pubchem.ncbi.nlm.nih.gov/compound/2733487,
PubChem ID: 2733487 (accessed Aug.17, 2017).
8 Markel, G., US 2007/0293416 A1, published Dec. 20, 2007.
9 Saul et al., US 2010/0285610 A1, published Nov. 11, 2010.
10 Nasir et al., US 6,482,601 B1, issued Nov. 19, 2002.
11 Blankfard et al., US 2006/0275841 A1, published Dec. 7, 2006.
12 Garcia et al., Mycotoxins in Corn Distillers Grains A Concern in
Ruminants?, South Dakota Cooperative Extension Service (2008)
(http://agbiopubs.sdstate.edu/articles/ExEx4038.pdf).
13 Danko et al., US 2002/0004478 A1, published Jan. 10, 2002.
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E. The Examiner rejected claims 1 and 25 under 35 U.S.C. § 103(a) as
obvious over Saul, Nasir, Blankfard, Danks,14 and Joerger15 (Final Act. 13–
14).
F. The Examiner rejected claims 1, 26, and 27 under 35 U.S.C. § 103(a)
as obvious over Saul, Nasir, Blankfard, Danks, Joerger, and Sabucedo16
(Final Act. 14–16).
G. The Examiner provisionally rejected claims 1–5, 12, 13, 16–18, 20,
24, and 27 on the ground of nonstatutory double patenting as being
unpatentable over claims 1–52 of copending Application No. 15/068,341
(Final Act. 17–18).
H. The Examiner provisionally rejected claims 1, 25, and 26 on the
ground of nonstatutory double patenting as being unpatentable over claims
1–52 of copending Application No. 15/068,341, Danks, Joerger, and
Sabucedo (Final Act. 19–20).

A. 35 U.S.C. § 102(b) over Cookman as evidenced by Aflatoxin,
Ochratoxin, Fumonisin, and Markel
The issues with respect to this rejection are: When interpreted using
the broadest reasonable interpretation consistent with the Specification and
usages in the art, does the term “small molecule” recited in claim 1
encompass the peptides disclosed in Cookman? If so, does Cookman
anticipate claim 1?

14 Danks et al., US 2009/0098560 A1, published Apr. 16, 2009.
15 Joerger et al., US 2008/0176957 A1, published July 24, 2008.
16 Sabucedo et al., US 2002/0197741 A1, published Dec. 26, 2002.
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Findings of Fact
1. The Specification teaches “facilitating the extraction of small
molecules, such as mycotoxins, from agricultural products such as a variety
of grains, corns and feeds” (Spec. 5:4–6).
2. The Specification teaches that “[a]lthough, many of the herein
examples and descriptions refer to detecting mycotoxins such as aflatoxin,
zearalanone, patulin, DON, fumonisin and ochratoxin, other analytes can be
detected and quantified in a variety of matrices” (Spec. 10:31–33).
3. The Specification explains that “[o]ther possible target analytes
include hormones, vitamins, drugs, metabolites and their receptors and
binding materials, antibodies, peptides, protein” (Spec. 11:1–2).
4. Cookman teaches, regarding the preamble of claim 1, that
“[t]wo methods have been developed capable of successfully extracting
proteins from DDDG [dried, defatted distiller’s grain], following oil
recovery from DG [distiller’s grain]. These methods are an aqueous enzyme
extraction and an alkaline-ethanol extraction” (Cookman 2016, col. 1).
5. Cookman teaches, regarding step a) of claim 1, that a “mixture
of 10 g of DDDG, 1 ml Protex 6L and 150 mL deionized water was stirred at
520 rpm for 2 h at pH 8.0 in a 50 °C water bath” (Cookman 2013, col. 2).
6. Cookman teaches “Protex 6L (an alkaline serine-
endopeptidase,” demonstrating that Protex 6L is a protein (Cookman 2013,
col. 1).
7. Cookman teaches, regarding step b) of claim 1, that the “solids
and extract were separated by centrifugation in 50 mL centrifuge bottles at
3000g for 20 min and 25 °C” (Cookman 2013, col. 2).
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8. Cookman teaches, regarding step c) of claim 1, that the “size of
the proteins in the extract were analyzed using size exclusion
chromatography (SEC) and the solid fraction was analyzed for crude protein
content” (Cookman 2013, col. 2).
9. Figure 4 of Cookman is reproduced below:

“Fig. 4. Protein molecular weight distribution from SEC of the aqueous
enzyme extract. Results are averages of three replicates” (Cookman 2015,
col. 2).
10. Markel teaches:
The antipathogen agents of the present invention include but are
not limited to protein, polypeptide, peptide, nucleic acid, large
molecule, small molecule, derivatives and/or fragments thereof,
and combinations thereof. The term “large molecule”, as used
herein, refers to organic or inorganic molecules either
synthesized or found in nature, generally having a molecular
weight greater than 1000, however the definition of large
molecule is not limited by this number. The term “small
molecule”, as used herein, refers to organic or inorganic
molecules either synthesized or found in nature, generally
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having a molecular weight equal to or less than 1000, however
the definition of small molecule is not limited by this number.
(Markel ¶ 21).
Principles of Law
“[D]uring patent prosecution when claims can be amended,
ambiguities should be recognized, scope and breadth of language explored,
and clarification imposed.” In re Zletz, 893 F.2d 319, 321 (Fed. Cir. 1989).
Anticipation under 35 U.S.C. § 102 requires that “‘each and every
element as set forth in the claim is found, either expressly or inherently
described, in a single prior art reference.”’ In re Robertson, 169 F.3d 743,
745 (Fed. Cir. 1999).
Analysis
Claim Interpretation
We begin with claim construction because before a claim is properly
interpreted, its scope cannot be compared to the prior art. During
prosecution, we interpret terms in a claim using the broadest reasonable
interpretation in light of the Specification. Morris, 127 F.3d at 1054.
We first turn to the Specification which is, “[i]n most cases, the best
source for discerning the proper context of claim terms.” Metabolite Labs.,
Inc. v. Lab. Corp. of Am. Holdings, 370 F.3d 1354, 1360 (Fed. Cir. 2004).
The Specification uses, but does not define, the term “small molecule” (FF
1). The Specification does teach, however, that in addition to detecting
compounds such as mycotoxins, “other analytes can be detected and
quantified” (FF 2). The Specification teaches that these “[o]ther possible
analytes include . . . peptides, protein” (FF 3). Thus, the Specification
expressly encompasses detection of peptides and protein using the assays,
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and provides no guidance to exclude peptides or proteins of less than 900
daltons from detection as “small molecules.”
Next, we turn to the extrinsic evidence. The Examiner cites to two
prior art references to support the interpretation of “small molecule” as
encompassing peptides. Markel, in the context of antibacterial agents, states
the agents include “protein, polypeptide, peptide . . . small molecule” and
broadly defines “‘small molecule’, as used [t]herein, [to] refer[] to organic or
inorganic molecules either synthesized or found in nature, generally having a
molecular weight equal to or less than 1000” (FF 10). Jou17 is more
supportive of the Examiner’s position, stating the “specific binding member
can be a small molecule, such as a hapten or small peptide” (Jou 10:21–22).
Thus, there is evidence that the term “small molecule” may encompass
peptides, which like proteins are composed of chains of amino acids,
differing only in that peptides are usually shorter amino acid polymer chains
while proteins are polypeptides with longer amino acid polymer chains.
Appellant contends the “Office’s interpretation of the term ‘small
molecules’ is unreasonably broad. The Office attempts to encompass any
molecule that has a molecular weight less than 1000 Daltons” (Appeal Br.
6). Appellant cites the Saul Declaration,18 where Dr. Saul states
unless referring to their constituent monomers, polymers such
as proteins, DNA, and RNA are not considered “small
molecules” even if their molecular weights are under 1000 Da.
See Exhibit A. At best, an amino acid may be considered a
“small molecule” but not a polypeptide. For many in the art,
the term “small molecule” refers to a molecule that is capable
of binding to a specific biological target- such as a protein.

17 Jou et al., US 5,670,381, issued Sept. 23, 1997.
18 Declaration by Dr. Steve Saul, Ph.D., dated Nov. 10, 2017.
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Small molecules and proteins are considered separate classes
of compounds, and interchanging the two would be confusing.
See Exhibits B and C for examples of the terms “small
molecule” and “protein” being treated as distinct.
(Saul Decl. ¶ 9).
Dr. Saul cites three exhibits in support of his position. Exhibits B and
C use both terms “small molecules” and “peptides”, suggesting that at least
sometimes these terms are intended to represent distinct entities. However,
Exhibit A, drawn to a definition of the term “small molecule”, contradicts
Dr. Saul, stating “[v]ery small oligomers are also usually considered small
molecules, such as . . . peptides such as the antioxidant glutathione” (Exhibit
A, page 1).
As we balance the evidence as a whole, there is evidence showing that
the term “small molecule” is sometimes treated as distinct from proteins or
peptides and sometimes treated, as in Jou and Exhibit A of the Saul
Declaration, as expressly encompassing small peptides. “Absent an express
definition in their specification, the fact that appellants can point to
definitions or usages that conform to their interpretation does not make the
PTO’s definition unreasonable when the PTO can point to other sources that
support its interpretation.” In re Morris, 127 F.3d 1048, 1056 (Fed. Cir.
1997).
In this case, we find the Examiner’s interpretation of “small
molecule” as broadly encompassing peptides is reasonable and consistent
with at least some of the prior art, particularly as the Specification
recognizes peptides as analytes (FF 3) in the small molecule assay (FF 1)
and does not define the term “small molecule in a way that excludes
peptides. “An essential purpose of patent examination is to fashion claims
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that are precise, clear, correct, and unambiguous. Only in this way can
uncertainties of claim scope be removed, as much as possible, during the
administrative process.” Zletz, 893 F.2d at 322.
Anticipation
The Examiner finds that Cookman teaches “methods have been
developed capable of successfully extracting proteins from DDDG [dried,
defatted distiller’s grain]” (FF 4) which comprises the steps of (a) mixing
“DDDG, 1 ml Protex 6L and 150 mL deionized water” (FF 5) where protex
is a protein (FF 6). Cookman teaches a step (b) where the “solids and
extract were separated by centrifugation (FF 7) and a step (c) collecting the
water layer where the “size of the proteins in the extract were analyzed using
size exclusion chromatography (SEC)” (FF 8).
Cookman showed that a portion of the proteins in the extract were
peptides smaller than 0.9 kDa (FF 9). Thus, Cookman teaches all the
required elements of claim 1. In particular, Cookman teaches peptides that
were smaller than 900 daltons, and were therefore “small molecules” under
our claim interpretation above.
Conclusion of Law
The term “small molecule” recited in claim 1 encompasses the
peptides disclosed in Cookman and Cookman anticipates claim 1.

B. 35 U.S.C. § 103(a) over Saul, Nasir, Blankfard
The issue with respect to this rejection is: Does a preponderance of the
evidence of record support the Examiner’s conclusion that the combination
of Saul, Nasir, and Blankfard render the claims obvious?
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Findings of Fact
11. Saul teaches, regarding the preamble of claim 1, that “[m]any
sample matrices, such as solid or granular materials, require an extraction of
analyte into a liquid matrix before application to a solid support such as a
test strip” (Saul ¶ 50).
12. Saul teaches, regarding step a) of claim 1, that “ground sample,
for example 10 grams (g) or 50 g, can be extracted with 70% methanol” and
that “extraction can take place using a variety of methods including . . .
mixing the sample with a stirrer” (Saul ¶¶ 50–51).
13. Saul teaches, regarding step b) of claim 1, that “[a]n extract can
be obtained also by using a variety of methods including filtering to collect
the extract, allowing sample to sit to form an extract layer above the ground
sample, or centrifuging a portion of the sample to obtain an extract layer and
sample layer” (Saul ¶ 52).
14. Saul teaches, regarding step c) of claim 1, that “the sample
extract, can be mixed with a dilution buffer . . . The dilution buffer can
consist of, for example, BSA [bovine serum albumin] solution” (Saul ¶ 53).
15. Saul teaches that the process functions to detect aflatoxin, a
“small molecule” (see Saul, Example 1, ¶¶ 56–69).
16. The Examiner finds that “Saul does not specifically teach that
the solvent (i.e. composition for achieving/promoting extraction) comprises
a proteinaceous material” (Final Act. 6).
17. Nasir teaches “a homogeneous assay that uses changes in
fluorescence polarization to detect the presence of fumonisin in grains”
(Nasir 1:9–11).
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18. Nasir teaches “Fumonisin has been historically extracted from
corn using mixtures of CH3OH:H2O (3:1) or CH3CN:H2O (1:1). All of these
methods require relatively long and extensive shaking or stirring time”
(Nasir 9:21–24 (citations omitted)).
19. Nasir teaches “it is preferable to use water or water solutions
substantially free of organic solvents, for extraction of fumonisin. This
minimizes the problem of extracting side colored products during fumonisin
extraction in grains” (Nasir 9:32–35).
20. Blankfard teaches the “term ‘extraction buffer’ refers to a
composition used to reduce non-specific binding between an analyte or
analog of an analyte and the sample matrix” (Blankfard ¶ 73).
21. Blankfard teaches the “recovery and detection of an analyte
from a sample containing an interfering matrix can be increased by the use
of appropriate extraction buffers” (Blankfard ¶ 99).
22. Blankfard teaches “the extraction buffer can comprise a
blocking agent . . . Exemplary blocking agents include serum and serum
albumins, such as animal serum (e.g., goat serum), bovine serum albumin
(BSA), gelatin, biotin, and milk proteins (‘blotto’)” (Blankfard ¶ 108).
Principles of Law
A prima facie case for obviousness “requires a suggestion of all
limitations in a claim,” CFMT, Inc. v. Yieldup Int’l Corp., 349 F.3d 1333,
1342 (Fed. Cir. 2003) and “a reason that would have prompted a person of
ordinary skill in the relevant field to combine the elements in the way the
claimed new invention does.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398,
418 (2007).

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Analysis
The Examiner finds it obvious
to have modified the extraction/dilution steps of the method as
taught by Saul and Nasir, in order to combine the reagent
components (namely, combine the extraction solvent and the
BSA blocking agent) into a single step, because Blankfard et al.
specifically teach extraction buffers, used for the purpose of
separating analyte from matrix (i,e. all other non-analyte
components of a sample), comprising blocking agent such as
BSA, the modification thereby making integral what was
separable (i.e. integrating the separate solution steps of Saul to
provide a single extraction/dilution step).
(Ans. 9–10). The Examiner finds “one of ordinary skill in the art would
expect that the presence of BSA would not interfere with extraction” (id.).
Appellant contends the Examiner’s “rationale mistakenly assumes that
a PHOSITA would have looked to Blankfard for a compatible solvent to be
used in an aqueous extraction. As discussed above, Blankfard’s ‘extraction
buffer’ is not analogous to the extraction performed by Saul and claimed by
Applicant” (Appeal Br. 10). Appellant also contends “[w]hile Nasir teaches
a method of phase extraction using water, neither Nasir nor Saul teaches
separating analytes in a test sample using filtration. Because of the different
separation techniques, a PHOSITA would not have been motivated to
combine the teachings of Blankfard with Nasir and Saul” (id.).
We agree with Appellant that the rejection does not provide a
persuasive reason to include a protein in the buffer used to extract the small
molecules prior to separation. Neither Saul nor Nasir provide any reason to
incorporate a protein into step a). While Saul and Blankfard do teach
diluting the extracted and separated solution of step c) with blocking
proteins such as BSA or Blotto (FF 14, 22) before application to a solid
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support (FF 11), neither reference provides any reason to add the proteins
prior to extraction as required by claim 1.
We are not persuaded by the Examiner’s reliance on the legal theory
that it would have been obvious to perform the step a) extraction and post
step c) dilution steps of the prior art into a single step because this fails to
allow step b) to occur. The grammar and logic of claim 1 requires that the
steps occur in the particular order recited, and is not open to any order of
steps. “[A] process claim is properly limited to a certain order of steps
‘when the claim language, as a matter of logic or grammar, requires that the
steps be performed in the order written, or the specification directly or
implicitly requires’ an order of steps.” Amgen Inc. v. Sandoz Inc., 923 F.3d
1023, 1028 (Fed. Cir. 2019) (citing Mformation Technologies, Inc. v.
Research in Motion Ltd., 764 F.3d 1392, 1398–1400 (Fed. Cir. 2014)).
Moreover, to the extent that the Examiner finds that “BSA would not
interfere with extraction” (Ans. 10), the Examiner has not supported that
finding with persuasive evidence. Blankfard, however, states that in
“addition to ionic interactions, hydrophobic interactions can reduce analyte
recovery” (Blankfard ¶ 101). Addition of a protein molecule to the extract
of claim 1 might reasonably be expected to reduce small molecule recovery
due to ionic or hydrophobic interactions.19
Also, addition of proteins like BSA to matrices prior to interactions is
typically understood as function to block parts of the matrices that would
non-specifically bind analyte (see Jou 51:30–32 “heparin was included as a

19 We are not suggesting that claim 1 lacks enablement, but simply that the
prior art does not unambiguously support proteins in an extraction step as
having no impact on extraction.
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nonspecific binding blocker”). This blocking is usually performed in order
to improve the signal to noise ratio (see Jou 51:3234 “The blocker was used
to enhance the signal-to-noise ratio by inhibiting the binding of the labeled
antibody to non-analyte.”). Similarly, Saul teaches the “nitrocellulose
membrane can also be pretreated and/or blocked” (Saul ¶ 54).
Thus, in addition to finding that the rejection lacks a persuasive reason
to put a protein into step a), we also find that there is some evidence that this
would not have been expected to improve analyte recovery and therefore
there is a reduced expectation of success in performing the method with a
protein in step a).
Conclusion of Law
A preponderance of the evidence of record does not support the
Examiner’s conclusion that the combination of Saul, Nasir, and Blankfard
render the claims obvious.

C.–F. 35 U.S.C. § 103(a) Rejections
Having reversed the obviousness rejection of claim 1 over Saul, Nasir,
and Blankfard for the reasons given above, we also find that the further
combinations do not provide reasons or motivation to include a protein in
step a). We therefore reverse these rejections for the same reasons as given
above.

G.–H.Provisional Obviousness-Type Double Patenting Rejections
We decline to reach these provisional rejections. See In re Moncla, 95
USPQ2d 1884, 1885 (BPAI 2010) (precedential). The rejections are
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provisional and US Application No. 15/068,341 remains copending and not
allowed; accordingly, the issues are not ripe for decision.

DECISION SUMMARY
In summary:
Claims
Rejected
35 U.S.C. § References/Basis Affirmed Reversed
1, 17, 20 102 Cookman, Aflatoxin,
Ochratoxin,
Fumonisin, Markel
1, 17, 20
1, 3–5, 12,
13, 16–18
103 Saul, Nasir, Blankfard, 1, 3–5,
12, 13,
16–18
1, 20 103 Saul, Nasir, Blankfard,
Garcia
1, 20
1, 2, 24 103 Saul, Nasir, Blankfard,
Danko
1, 2, 24
1, 25 103 Saul, Nasir, Blankfard,
Danks, Joerger
1, 25
1, 26, 27 103 Saul, Nasir, Blankfard,
Danks, Joerger,
Sabucedo
1, 26, 27
1–5, 12,
13, 16–18,
20, 24, 27
Nonstatutory Double
Patenting US
15/068,341

1, 25, 26 Nonstatutory Double
Patenting US
15/068,341, Danks,
Joerger, Sabucedo

Overall
Outcome
1, 17, 20 2–5, 12,
13, 16,
18, 24–
27
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No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a).

AFFIRMED-IN-PART