NOTE: This disposition is nonprecedential.

United States Court of Appeals 

for the Federal Circuit ______________________

IN RE: QAPSULE TECHNOLOGIES, INC.,

Appellant

______________________

2018-1772

______________________

Appeal from the United States Patent and Trademark 

Office, Patent Trial and Appeal Board in No. 13/882,773.

______________________

Decided: March 11, 2019

______________________

DONALD GEORGE LEWIS, Lewis Kohn & Walker LLP, 

San Diego, CA, for appellant. 

 THOMAS W. KRAUSE, Office of the Solicitor, United 

States Patent and Trademark Office, Alexandria, VA, for 

appellee Andrei Iancu. Also represented by SARAH E.

CRAVEN, FRANCES LYNCH. 

 ______________________

Before NEWMAN, CHEN, and STOLL, Circuit Judges.

NEWMAN, Circuit Judge.

Qapsule Technologies, Inc. (“Qapsule”) appeals from 

the Patent Trial and Appeal Board (“Board”) determination 

that claims 1, 2, 5, 7, 13–15, 31, 33–35, and 38 of U.S. Patent Application No. 13/882,773 (“the ’773 Application”) are 
2 IN RE: QAPSULE TECHNOLOGIES, INC.

anticipated by Perez1 as evidenced by Mair,2 Ye,3 and Gonzales.4 Because substantial evidence supports the Board’s 

determination, and we discern no legal error in its analysis, 

we affirm.5

THE ’773 APPLICATION

The ’773 Application relates to “encapsulating recombinant enzymes and other cargo proteins within the interior space of protein nanoparticles.” ’773 Appl. at p. 2, ll. 

32–34. The nanoparticles are assembled using shell proteins, such as viral coat proteins, in the presence of bifunctional polynucleotides and the desired cargo protein. Id. at 

p. 3, ll. 7–26. Claim 1 is representative:

1. A synthetic capsule construct for providing a protected chemical milieu, the construct comprising:

a shell having a plurality of shell proteins, said plurality of shell proteins being assembled with one 

another for forming said shell and defining an enclosure therein, each of said shell proteins, when 

 

1 Perez et al., Functional Analysis of PA Binding by 

Influenza A Virus PBJ: Effects on Polymerase Activity and 

Viral Infectivity, 75 J. VIROLOGY 8127–36 (2001).

2 Mair et al., Receptor binding and pH stability- How 

influenza A virus hemagglutinin affects host-specific virus 

infection, 1838 BIOCHIMICA ET BIOPHYSICA ACTA 1153–68 

(2014).

3 Ye et al., Association of Influenza Virus Matrix Protein with Ribonucleoproteins, 73 J. VIROLOGY 7467–73 

(1999).

4 Gonzalez et al., Characterization of Influenza Virus 

PBJ Protein Binding to Viral RNA: Two Separate Regions 

of the Protein Contribute to the Interaction Domain, 73 J.

VIROLOGY 631–37 (1999).

5 Ex Parte Finn et al., No. 2017-001118, 2017 WL 

6055117 (P.T.A.B. Nov. 27, 2017) (“Bd. Op.”).
IN RE: QAPSULE TECHNOLOGIES, INC. 3

assembled for forming said shell, having an interior surface facing inwardly toward said enclosure 

and an exterior surface facing outwardly away 

from said enclosure, said shell serving to restrict 

permeability to and from said enclosure for providing the protected chemical milieu therein, said 

shell proteins being recombinant;

a cargo protein, said cargo protein being recombinant and optionally including a peptide tag; and

a bifunctional polynucleotide having both a first 

aptameric activity for binding said cargo protein 

and a second aptameric activity for retaining said 

bifunctional polynucleotide within said enclosure 

by assembly with the interior surface of said shell 

protein,

said bifunctional polynucleotide being non-naturally occurring; said bifunctional polynucleotide 

serving to link said cargo protein within said enclosure for providing the said cargo protein with the 

protected chemical milieu therein.

As relevant herein, the limitations of claim 1 include 

an enclosure made of recombinant “shell proteins,” a recombinant “cargo protein,” and a “bifunctional polynucleotide” having the function of linking the cargo protein within 

the enclosure. The ’773 Application defines “shell protein” 

as “any protein or set of proteins capable of self-assembly 

or directed-assembly to form a ‘shell,’” including viral and 

non-viral proteins. ’773 Appl. at p. 40, ll. 26–30. The Application defines “cargo protein” as “any recombinant protein capable of being incorporated into a synthetic capsule 

construct.” Id. at p. 42, ll. 1–3. And “bifunctional polynucleotide” is defined as a “polynucleotide having two or more 

aptameric activities,” id. at p. 41, ll. 20–22, or “binding affinit[ies] . . . for a protein tag or protein binding site,” id. at 

p. 39, ll. 23–25.
4 IN RE: QAPSULE TECHNOLOGIES, INC.

PROCEDURAL HISTORY

The ’773 Application’s claims were initially rejected as 

anticipated and/or obvious in view of a set of references not 

relevant to the present appeal. In view of the initial 

grounds of rejection, Qapsule appealed to the Board and 

obtained reversal of the examiner’s rejections for want of 

reference disclosure of the claimed “aptameric activity for 

binding.”

The Board, however, entered a new ground of rejection 

for claims 1, 2, 5, 7, 13–15, 31, 33–35, and 38 as anticipated 

by Perez as evidenced by Mair, Ye, and Gonzalez. Bd. Op. 

at *4.

The Board found that Perez discloses a recombinant influenza A virus and relied upon Mair as evidence of the inherent structural features of such a virus:

Bd. Op. at *5 (citing Mair at 1155, Figure 1). The Board 

found that the “M1” protein met the claim 1 limitation of

“shell protein,” that the mutated “PB1” protein of Perez 

met the limitation of a recombinant “cargo protein,” and 

the mutated viral RNA of the “RNPs” constituted the “bifunctional polynucleotide” of claim 1, for it was non-naturally occurring and was capable of binding both the M1 

shell protein and the PB1 protein. See Bd. Op. at *6–7.
IN RE: QAPSULE TECHNOLOGIES, INC. 5

The Board relied on Ye for teaching that the M1 protein 

binds to viral RNA. See Bd. Op. at *5 (citing Ye at p. 7467, 

col. 2 (“Two domains in M1 have been shown to affect the 

disposition of RNA. One domain residing in a palindromic 

stretch of basic amino acids (101RKLKR105) has been 

shown to bind vRNA . . . .”)). And the Board relied on Gonzalez as teaching that the PB1 protein binds to the viral 

RNA. See Bd. Op. at *5 (citing Gonzalez at p. 636, col. 2 

(“Since we show that PB1 protein on its own binds preferentially the 5′-terminal sequence of vRNA . . . .”)). Accordingly, the Board concluded that “the influenza virus 

particles of Perez with mutated PB1 protein and vRNA inherently anticipate the requirements of claim 1.” Bd. Op. 

at *7.

Faced with the new ground of rejection, Qapsule had 

the option of reopening prosecution before the examiner, or 

requesting rehearing. See 37 C.F.R. § 41.50(B)(2). Qapsule 

chose the rehearing route. Treating claim 1 as representative, Qapsule argued that “Claim 1 includes a limitation 

that the shell proteins are recombinant” whereas the shell 

proteins identified by the Board in Perez “are not recombinant.” ’773 Application, Request for Rehearing, filed Jan. 

22, 2018, at 3 (J.A.64). Qapsule stated in its request for 

rehearing that Ye disclosed recombinant shell proteins, but 

not in combination with recombinant proteins as claimed. 

See id. But Qapsule acknowledged that the Board’s new 

ground of rejection was for anticipation by Perez and not 

Ye. See id. Accordingly, Qapsule argued that Perez did not 

anticipate the rejected claims.

The Board determined that Qapsule’s reliance on the 

term “recombinant” was an attempt to impose a method 

step into a claim for a product, that pursuant to In re 

Dilnot, 300 F.2d 945, 950 (CCPA 1962), “addition of a 

method step in a product claim, which product is not patentably distinguishable from the prior art, cannot impart 
6 IN RE: QAPSULE TECHNOLOGIES, INC.

patentability to the old product.”6 The Board concluded 

that “whether the shell proteins were produced in a ‘recombinant’ eukaryotic expression system in MDCK cells or produced as taught by Perez by virus infection in the MDCK 

cells, the final constructs including the shell proteins would 

be expected to be structurally identical because they would 

share the same amino acid sequence, same glycosylation 

patterns (if any), as they were produced by the same cell.” 

Id. And the Board remarked that Qapsule had failed to 

provide any evidence rebutting the inherency ruling. See 

id.

Qapsule appeals, arguing that the Board erred in its 

factual findings and application of the law of inherent anticipation.

DISCUSSION

As to the Board’s factual findings, Qapsule argues that 

Perez does not inherently disclose the “bifunctional polynucleotide” claim limitation because Ye concluded that binding of the ribonucleoprotein to the viral shell proteins in 

influenza A requires the presence of nucleoproteins in addition to the viral RNA and the ribonucleoprotein. Qapsule 

asserts that the claimed synthetic capsule does not require 

ribonucleoprotein in order for binding to occur between M1 

and the viral RNA. And without the presence of ribonucleoproteins, Qapsule argues that “the Board’s proposed subset of elements drawn from Perez, viz. M1, vRNA, and PD1, 

would fail to assemble to form a virus particle.” Appellant

Reply Br. at 6. Accordingly, Qapsule contends that there 

are structural differences between the shell proteins and 

bifunctional polynucleotide as claimed, and those disclosed 

by Perez.

 

6 Ex Parte Finn et al., No. 2017-001118, 2018 WL 

799026, at *1 (P.T.A.B. Feb. 1, 2018).
IN RE: QAPSULE TECHNOLOGIES, INC. 7

A reference anticipates a patent claim under 35 U.S.C. 

§ 102(b) if every claim limitation is present in the reference. 

See Verizon Servs. Corp. v. Cox Fibernet Va., Inc., 602 F.3d 

1325, 1336–37 (Fed. Cir. 2010). A reference may anticipate 

inherently if a claim limitation that is not expressly described “is necessarily present, or inherent, in the single 

anticipating reference.” Id. at 1337 (quoting Schering 

Corp. v. Geneva Pharm., Inc., 339 F.3d 1373, 1377 (Fed.

Cir. 2003)).

“[A]nticipation is a question of fact, including whether 

an element is inherent in the prior art.” In re Gleave, 560 

F.3d 1331, 1334–35 (Fed. Cir. 2009). Thus we review the 

Board’s factual finding of inherent anticipation for support 

by substantial evidence. 5 U.S.C. § 706(2)(E); Dickinson v. 

Zurko, 527 U.S. 150, 152 (1999); In re Gartside, 203 F.3d 

1305, 1316 (Fed. Cir. 2000). “Substantial evidence is something less than the weight of the evidence but more than a 

mere scintilla of evidence,” In re Kotzab, 217 F.3d 1365, 

1369 (Fed. Cir. 2000), and “means such relevant evidence 

as a reasonable mind might accept as adequate to support 

a conclusion,” Consol. Edison Co. of New York v. NLRB, 305 

U.S. 197, 229 (1938).

A. Waiver

The PTO solicitor argues that Qapsule waived its present arguments by failing to present them at the Board 

hearing and rehearing. By electing rehearing under 37 

C.F.R. § 41.50(b)(2), Qapsule was required to “address any 

new ground of rejection and state with particularity the 

points believed to have been misapprehended or overlooked 

in entering the new ground of rejection and also state all 

other grounds upon which rehearing is sought.” The PTO 

states that Qapsule in its rehearing request only argued 

that Perez failed to disclose a recombinant “shell protein,” 

and that Qapsule’s new arguments about the binding of the 

“bifunctional polynucleotide” and the application of inherent anticipation are waived.
8 IN RE: QAPSULE TECHNOLOGIES, INC.

The court “retains case-by-case discretion over whether 

to apply waiver.” Harris Corp. v. Ericsson Inc., 417 F.3d 

1241, 1251 (Fed. Cir. 2005) (citing Singleton v. Wulff, 428 

U.S. 106, 120 (1976)). Here the issues of Perez’s disclosure 

of a shell protein binding to a bifunctional polynucleotide 

and the Board’s application of inherent anticipation are arguments about claim scope that are sufficiently developed 

in the record before us. Because no party will be prejudiced 

by our resolution of these issues, we proceed to the merits 

without applying waiver.

B. Inherent Anticipation

The Board found that Ye discloses that the M1 protein 

(i.e., the recombinant “shell protein” as claimed) binds to 

viral RNA (the recombinant “bifunctional polynucleotide” 

as claimed). Bd. Op. at *5. The Board quoted Ye’s disclosure that “[t]wo domains in M1 have been shown to affect 

the disposition of RNA. One domain residing in a palindromic stretch of basic amino acids (101RKLKR105) has 

been shown to bind vRNA . . . .” Id. (quoting Ye at p. 7467, 

col. 2). This is substantial evidence supporting the Board’s 

conclusion that Perez inherently discloses “a bifunctional 

polynucleotide having . . . a second aptameric activity for 

retaining said bifunctional polynucleotide within said enclosure by assembly with the interior surface of said shell 

protein.”

Qapsule acknowledges that the Board’s understanding 

of Ye is correct. Appellant Reply Br. at 5 (“Although Ye 

teaches that vRNA binds to M1, Ye also teaches that ribonucleoproteins (RNP) also binds to M1 and that binding by 

both vRNA and ribonucleoproteins (RNP) are necessary for 

virus assembly . . . .”). Qapsule, however, attempts to differentiate the present claims by arguing that viral assembly in Ye occurs in the presence of ribonucleoprotein. 

However, the present claims use the open-ended term 

“comprising,” and do not exclude capsule assembly in the 

presence of ribonucleoprotein as long as the claimed 
IN RE: QAPSULE TECHNOLOGIES, INC. 9

“bifunctional polynucleotide” (here, the viral RNA) assembles with the interior surface of the “shell protein.” See 

Crystal Semiconductor Corp. v. TriTech Microelectronics 

Int’l, Inc., 246 F.3d 1336, 1348 (Fed. Cir. 2001):

When a patent claim uses the word “comprising” as 

its transitional phrase, the use of “comprising” creates a presumption that the body of the claim is 

open. In the parlance of patent law, the transition 

“comprising” creates a presumption that the recited elements are only a part of the device, that 

the claim does not exclude additional, unrecited elements.

Similarly, the word “having,” in the clause “a bifunctional 

polynucleotide having . . . a second aptameric activity for 

retaining said bifunctional polynucleotide within said enclosure by assembly with the interior surface of said shell 

protein” does not exclude additional, unrecited elements 

from participating in capsule assembly. See id.:

The transition “having” can also make a claim 

open. However, the term “having” does not convey 

the open-ended meaning as strongly as “comprising.” “Having,” for instance, does not create a presumption that the body of the claim is open. 

Therefore, this court examines the claim in its full 

context to determine whether [Applicant’s] use of 

“having” limits claim 1 to its recited elements.

(internal citation omitted).

Claim 1 does not require that the claim excludes capsule assembly in the presence of ribonucleoproteins, as 

Qapsule has argued. First, the whole of the claimed “synthetic capsule construct” is offset by the “comprising” transitional, signaling the intent to have an open-ended claim 

that would allow for additional, unrecited elements beyond 

the listed shell protein, cargo protein, and bifunctional polynucleotide. The specification defines “synthetic capsule 
10 IN RE: QAPSULE TECHNOLOGIES, INC.

construct” broadly to mean “a non-naturally occurring capsule,” ’773 Appl. at p. 39, ll. 19–20, and defines the term 

“capsule” in equally broad language to mean “a nanoparticle sized structure having a well organized outer layer that 

defines an enclosure . . . ,” id. at p. 39, ll. 14–16. Qapsule 

has not directed us to any language that would rebut the 

presumption that has arisen from its choice to use the 

“comprising” transitional.

Additionally, the use of the “having” transitional does 

not alter the construction, for it is specific to the recited 

“bifunctional polynucleotide” limitation and not the 

claimed “synthetic capsule construct” as a whole. The 

“having” transitional within this claim offsets two “aptameric activit[ies],”which the specification defines as 

“binding affinit[ies] . . . for a protein tag or protein binding 

site,” ’773 Appl. at p. 39, ll. 23–25. Although this usage, in 

conjunction with the “bifunctional” qualifier of nucleotide, 

could imply that the number of “aptameric affinities” of the 

polynucleotide should be limited, this does not restrict unrecited elements from participating in capsule assembly as

long as the “bifunctional polynucleotide” possesses the two 

recited aptameric affinities.

In sum, it does not affect the Board’s ground of rejection that Qapsule has purportedly created a capsule that 

will assemble in the presence of only a shell protein, cargo 

protein, and bifunctional polynucleotide, see Appellant Reply Br. at 6, for representative claim 1 is not so limited. 

Thus substantial evidence supports the Board’s conclusion 

that the Perez recombinant viral RNA inherently meets 

the “bifunctional polynucleotide” limitation in claim 1.

Qapsule further argues that the Board misapplied the 

requirement of structural identity for inherent anticipation 

under In re Best. 562 F.2d 1252, 1256 (CCPA 1977)

(“Where, as here, the claimed and prior art products are 

identical or substantially identical, or are produced by 

identical or substantially identical processes, the PTO can 
IN RE: QAPSULE TECHNOLOGIES, INC. 11

require an applicant to prove that the prior art products do 

not necessarily or inherently possess the characteristics of 

his claimed product.”). We find that the Board properly applied the concept of inherency on an element-by-element 

basis in order to establish that the M1 protein, viral RNA, 

and PB1 protein would meet the claimed “shell protein,” 

“bifunctional polynucleotide,” and “cargo protein” limitations, respectively.

On appeal, Qapsule points to the presence of additional 

elements in Perez, such as a lipid envelope and other proteins, as evidencing a structural difference between Perez’s 

influenza A disclosure and the recited limitations of representative claim 1. See Appellant Br. at 9–12. Qapsule contends that these structural differences negate anticipation. 

That is incorrect, as applied herein, for as discussed supra, 

Qapsule’s claims are not limited to the three recited components. The Board correctly found that the Examiner met 

his burden of establishing structural identity of the 

claimed synthetic capsule construct in view of the scope of 

representative claim 1, and that this prima facie case has 

not been rebutted by the Applicant. See In re Jung, 637 

F.3d 1356, 1362 (Fed. Cir. 2011) (explaining the burdenshifting framework during prosecution); In re Mousa, 479 

F. App’x 348, 352 (applying the same specifically to inherency). 

Qapsule also argues that unlike the influenza A of Perez, Qapsule’s synthetic capsule is functionally different 

because it is non-infective and has utility in the chemical 

industry. Appellant Reply Br. at 8 (“Appellant’s claimed 

synthetic capsule construct is a simple system with three 

components and is employable in industrial chemical processes; in contrast, Perez’s virus particles are complex with 

many components and lack industrial applicability, but 

they might be employable for germ warfare.”). However,

unclaimed functional distinctions or uses are insufficient 

to overcome anticipation. It is not before us to decide 
12 IN RE: QAPSULE TECHNOLOGIES, INC.

whether further specificity in the claims might distinguish 

these references.

“First, and most importantly, the language of the claim 

defines the scope of the protected invention.” Bell 

Commc’ns Research, Inc. v. Vitalink Commc’ns Corp., 55 

F.3d 615, 619 (Fed. Cir. 1995); see Yale Lock Mfg. Co. v. 

Greenleaf, 117 U.S. 554, 559 (1886) (“The scope of letterspatent must be limited to the invention covered by the 

claim, and while the claim may be illustrated it cannot be 

enlarged by language used in other parts of the specification.”). Unclaimed limitations cannot distinguish the 

claims. Ventana Med. Sys., Inc. v. Biogenex Labs., Inc., 473 

F.3d 1173, 1181 (Fed. Cir. 2006) (“[I]t is improper to limit 

the claim to other, unclaimed features.”).

The structures of Perez anticipate representative claim 

1. Unclaimed differences do not avoid anticipation, for 

claim 1 as written, in its breadth, reads on Perez. The 

Board correctly rejected claim 1 on this ground.

We have considered all of Qapsule’s arguments, and affirm the judgment of the Board.

AFFIRMED

No costs.