`
`Claims 1, 109, 155-182, 184, and 186 are amended, claims 188 is canceled, and claim
`
`190 is added herein. Claims 1-182, 184, 186, and 187 remain pending in the captioned case.
`
`Claims 4-32, 36-64, 69, 74, 76, 83-93, 96, 99-104, 109-112, 116, 117, 124, 125, 131, 140-142,
`
`144-154, 157, 159-168, 170-172 and 174-182 remain withdrawn. Further examination and
`
`reconsideration of the presently claimed application are respectfully requested.
`
`Specific support for the amendments to claims 1, 109, 155-182 and 184 and added claim
`
`189 may be found in the specification as filed, with particular support found at 1H] 0548 and
`
`0554, and in the sequence listing. Accordingly, these amendments does not add new matter.
`
`Priority
`
`The Office Action dated April 28, 2010 only granted priority to the claims for the elected
`
`species "lysozyme" as being disclosed in US Provisional Application No. 60/976,676 filed on
`
`10/01/2007. However, the instant application is a Continuation in Part of US Patent Application
`
`10/655,345 filed on 09/04/2003, which discloses the enzyme, lysozyme, at paragraph [0273].
`
`That the composition of the claims comprises an enzyme is disclosed throughout the
`
`specification of US Patent Application 10/655,345, such as at paragraphs [0120] and [0127]
`
`to [0132]. Applicants respectfully request that priority for "lysozyme" be corrected to at least the
`
`filing date of 09/04/2003 for US Patent Application 10/655,345.
`
`Objection to the Specification
`
`The specification was objected to for containing embedded hyperlinks at
`
`paragraph [0430]. The specification has been searched for any embedded hyperlinks and/or
`
`other form of browser-executable code, and found only the hyperlinks identified by this
`
`objection. The specification has been corrected by the submitted amendment replacing
`
`paragraph [0430] with a substitute paragraph deleting the cited hyperlinks. Accordingly, this
`
`33/61
`
`
`
`amendment constitutes no new matter. Applicants respectfully request that this objection be
`
`withdrawn.
`
`Double Patenting Rejection
`
`Claims 1-3, 35, 65-68, 70, 73, 75, 77-82, 94, 95, 97, 98, 105-108, 113-115, 118-123, 126-
`
`130, 132-139, 143, 155, 156, 158, 169, 173, 184 and 186-188 were provisionally rejected under
`
`the judicially created doctrine of obviousness-type double patenting as being unpatentable over
`
`claims 1-98 of McDaniel et al., (US Application No.: 12/696,651). In addition, claim 188 is
`
`canceled herein rendering rejection thereto moot. Applicants respectfully note the provisional
`
`rejection and will file a terminal disclaimer to obviate the rejection upon receiving notice that
`
`some or all of the claims in the captioned application are allowed.
`
`Section 112, lst Paragraph, Rejection for Written Description
`
`Claims 1-3, 35, 65-68, 70-73, 75, 77-82, 94, 97, 98, 105-108, 113-115, 118-123, 126-
`
`130, 132-139, 143, 155, 156, 158, 169, 173, 184 and 186-187 were rejected under 35 U.S.C.§
`
`112, first paragraph, for containing subject matter which was not described in the specification in
`
`such a way to reasonably convey to one skilled in the art that the inventors had possession of the
`
`claimed invention. Applicants respectfully traverse this rejection.
`
`The Examiner argues that there is no structure associated with function with regard to the
`
`claimed members of the "genus of coating compositions or paints comprising: i) any protein,
`
`having any structure and having enzymatic activities like lipase, lysozyme, libiase, esterase,
`
`hydrolase. . .from any source inclosing variants, mutants, and recombinants of undefined
`
`structure and ii) any antimicrobial peptide from any source including variants, mutants and
`
`recombinants of undefined structure having antimicrobial activity against any undefined
`
`microorganism and said coating composition or paint having the recited functional limitations."
`
`34/61
`
`
`
`The Examiner argues the "Practical Limits of Function Prediction": 1. Devos et al.,
`
`(Proteins, Structure, Function and Genetics, 2000, Vol. 41: 98-107; known herein as "Devos et
`
`al.") teaches at the abstract (p. 98) that different aspects of protein filnction such as "(i)
`
`enzymatic function classification, (ii) filnctional annotations in the form of key words, (iii)
`
`classes of cellular filnction, and (iv) conservation of binding sites can only be reliably transferred
`
`between similar sequences to a modest degree. The reason for this difficulty is a combination of
`
`the unavoidable database inaccuracies and plasticity of proteins." The Examiner further quotes
`
`sections of Devos et al. that "questions about the current function prediction exercises and the
`
`intrinsic limitation of protein prediction" (column 1, 1] 3, p. 99) and "...the results here illustrate
`
`that transfer of function between similar sequences involves more difficulties than commonly
`
`believed. Our data show that even true pair-wise sequence relations, identified by their
`
`structural similarity, correspond in many cases to different functions" (column 2, 1] 2, p. 105) and
`
`further directs Applicant's attention to sections of pages 101-102 and Fig. 2a)-b) as "highlighting
`
`the structural and functional heterogeneity based on EC Classification numbers."
`
`Applicants have reviewed the cited reference and sections, and finds that, though
`
`increasing variations in sequences are correlated with change in function, the data of Devos et al.
`
`demonstrates that similar enzymatic sequences retain the same enzymatic activity for most
`
`species of sequences in the genera evaluated. Specifically, at the cited Fig 2b, which addresses
`
`the relationship between functional classification and sequence identity, it is stated "In (b) the
`
`proportion of pairs with both proteins assigned to the same functional class only reaches 70%
`
`when sequence identity is between 30 and 70%." Applicants submit that this statement of data
`
`demonstrates that the majority probability (70%) is that the evaluated protein's are assigned the
`
`samefunctional class when the sequence identity is in the minority — going as low as 30%. The
`
`data this reference presents is strongly indicative of conservation of filnction even with a
`
`minority sequence identity.
`
`The Examiner cites Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36(3):
`
`307-340; known herein as "Whisstock et al.") at p. 309,114 "to reason from sequence and
`
`structure to function is to step onto much shakier ground"..."assignment of function on the basis
`
`of homology, in the absence of direct experimental evidence, will give the wrong answer"; at p.
`
`35/61
`
`
`
`312, 1] 5 "it is difficult to state criteria for successful prediction of function, since function is in
`
`principle a fuzzy concept. Given three protein functions, it would be more difficult to choose the
`
`pair with most similar filnction, although it is possible to define metrics for quantitative
`
`comparisons of different protein sequences and structures, this is more difficult for proteins of
`
`different functions"; at p. 3 l3, 1] 4 "in families of closely related proteins, mutations usually
`
`conserve fianction but modulate specificity"; and at p. 323,1] 1 "substitutions of a single,
`
`critically placed amino acid in an active-site residue may be sufficient to alter a protein's role
`
`fundamentally. "
`
`Applicants have reviewed Whisstock et al., and the specific sections cited by the
`
`Examiner. In regards to the assertion made at based on the quote from page 309, paragraph 4 of
`
`Whisstock et al., Applicants find that the context the preceding sentences provide for this quote
`
`supports Applicants point regarding Devos et al. above that similar sequences often have the
`
`same function, contrary to the Examiner's concerns:
`
`"It is indeed true that manyfamilies ofproteins contain homologues with the
`samefunction, widely distributed among species; for these, reasoningfrom
`homology does assign function correctly. However, the assumption that
`homologues share function is less and less safe as the sequences progressively
`diverge. Moreover, even closely related proteins can change function, either
`through divergence to a related filnction or by recruitment for a very different
`function (Ganfomina & Sa'nchez, 1999). In such cases, assignment of function on
`the basis of homology, in the absence of direct experimental evidence, will give
`the wrong answer, leading to misannotations in databanks." (Emphasis added)
`
`In regards to the quote from p. 312, 1b", this statement only asserts that there is more
`
`difficulty in selecting pairs of proteins on the basis of function, though that level of success is
`
`still great in light of the data provided by Devos et al. noted in Applicants arguments above. The
`
`Examiner also cites that p. 3 13, 1% regarding sequence changes that may alter specificity, but as
`
`stated "in families of closely related proteins, mutations usually conserve function by modulate
`
`specificity" again supporting Applicant's point that sequences that are related (i.e., similar, but
`
`not necessarily identical) can undergo additional mutation and retain function. The quote from
`
`p. 323, 1] 1 notes that substitution of a single, critical amino acid in an active site may alter a
`
`protein's role, and the Examiner filrther argues this point based on one or few amino acid
`
`36/61
`
`
`
`substitutions or a few percent difference in sequence identity affecting function of specific
`
`enzymes described in Witkowski et al., (Biochemistry 38: 1 1643-1 1650, 1999), Seffemick et al.
`
`(J. Bacteriol. 183(8):2405-2410, 2001), and Broun et al. (Science 282: 13 15-13 17, 1998). While
`
`in some cases, such as, for example, active site mutations, a limited number of amino acid
`
`changes may produce enzymes of different function, knowledge of such a limited number or
`
`percentage of variations is either available in the art, such as by previous active site analysis,
`
`sequence alignments, or other techniques, or readily contemplated by a skilled artisan, given that
`
`a limited number of changes are being considered.
`
`The Examiner cites Kisselev L. (Structure, 2002, Vol. 10:8-9) as teaching "functionally
`
`similar molecules have different structures." While certain species of some enzymes produced
`
`by convergent evolution may have differing sequences and similar function, Applicants submits
`
`that one or more sub-genera of enzymes in a fianctional classification does not show a lack of
`
`written description for the claimed enzymes when the written description requirement is met for
`
`each of the sub-genera, and that the Examiner has failed to relate the species of enzymes in
`
`Kisselev L. as somehow showing a lack of written description in the instant application.
`
`Finally, the Examiner refers the Applicants to the "revised guidelines concerning
`
`compliance with the written description requirement of U.S.C. 112, f1rstparagraph." Applicants
`
`have reviewed the "Written Description Training Materials: Revision 1 March 25, 2008" by the
`
`United States Patent and Trademark Office, Department of Commerce, and finds that Examples
`
`4 to7, 9, 11A, 11B, and 15 being most related to claims involving amino acid or nucleotide
`
`sequences, and thus are discussed below. Applicants have included an evaluation of the
`
`examples in this document directed to nucleotide sequences, given some similarity to the issues
`
`involved with amino acid sequences.
`
`Example 4 is directed to a DNA sequence comprising single disclosed nucleotide
`
`sequence (See claim 1, p. 13) which "the claimed DNAs may also include additional DNA
`
`sequences attached to either end of the sequence" and that claim 1 is found to meet the 35 U.S.C.
`
`112, 1st paragraph written description requirement (p. 13, under "Conclusion"). This example
`
`supports variations in size by the additional sequences incorporated to the ends of a nucleotide or
`
`37/61
`
`
`
`amino acid sequence, as a nucleotide or amino acid sequence. Applicants argue that such a
`
`sequence, whether it is novel and disclosed in an instant application or known in the art, may
`
`include additional sequences and meet the written description requirement.
`
`Example 5 is directed to an isolated protein comprising a partial amino acid sequence and
`
`further identified by other characteristics of the protein related to the protein purification (See
`
`claim 1, p. 17), which is taught as meeting the 35 U.S.C. 112, 1st paragraph written description
`
`requirement (p. 18, under "Conclusion"). Claim 2 (p. 17) is directed to a nucleic acid encoding
`
`the protein, and it is taught (p. 19, 3rd complete paragraph) that claim 2 does not meet the 35
`
`U.S.C. 112, 1st paragraph written description requirement because "the specification fails to
`
`support even one species of DNA in the claimed genus." Example 6 describes claims to an
`
`isolated nucleic acid encoding a protein with receptor binding and stimulates tyrosine kinase
`
`activity (claim 1, p. 21), a SEQ ID No for such a nucleic acid (claim 2, p. 21), and a nucleic acid
`
`encoding a protein with the activity of the protein of claim 1 that hybridizes to the sequence of
`
`claim 2 (claim 3, p. 21). Claims 1 and 3 are taught (p. 23, 2Ild complete paragraph; p. 22, 4th
`
`complete paragraph) as not meeting the written description requirement as "those of ordinary
`
`skill in the art would not consider the applicant to have been in possession of the entire breadth
`
`of the claimed genus of nucleic acids based on the single species disclosed." Example 7
`
`describes a DNA encoding a protein's amino acid sequence of a SEQ ID No. (claim 1, p. 25), an
`
`isolated allele of the DNA encoding the same amino acid sequence (claim 2, p. 25), and an
`
`isolated allele of another DNA sequence of a SEQ ID no. (claim 3, p. 25). Claims 2 and 3 are
`
`taught (p. 27, 1st complete paragraph; p. 28, 1St incomplete paragraph) as not meeting the 35
`
`U.S.C. 112, 1St paragraph written description requirement again on the basis of "a description of
`
`only one member of this genus is not representative of the variants of the genus and is
`
`insufficient to support the claim."
`
`In direct contrast to these examples' teachings of failure to meet the written description
`
`requirement due to a "single species,
`
`one member of a genus," etc., the specification clearly
`
`delineates specific antimicrobial enzymes that have been isolated and characterized, and thus
`
`usable in the claimed compositions and methods in light of the disclosures therein, such as
`
`described for lysozyme at 1111 [0438]—[0442], including exemplary (i.e., non-limiting to other
`
`38/61
`
`
`
`sequences known and available in the art) nucleic and protein sequences referenced at 1]1] [0441]-
`
`[0442]; lysostaphin at 1]1] [0443]-[0444], including exemplary nucleic and protein sequences
`
`referenced at 1] [0444]; libiase at 1] [0445]; lysyl endopeptidase at 1]1] [0446]-[0447], including
`
`exemplary nucleic and protein sequences referenced at 1] [0447]; mutanolysin at 1]1] [0448]-
`
`[0449]; cellulase at 1]1] [0450]-[0451], including exemplary nucleic and protein sequences
`
`referenced at 1] [0451]; chitinase at 1]1] [0452]-[0453], including exemplary nucleic and protein
`
`sequences referenced at 1] [0453]; u-agarase at 1] [0454]; B-agarase at 1] [0455], including
`
`exemplary nucleic and protein sequences referenced at 1] [0455]; N—acetylmuramoyl-L-alanine
`
`amidase at 1] [0456], including exemplary nucleic and protein sequences referenced at 1] [0456];
`
`lytic transglycosylase at 1]1] [0457]-[0458], including exemplary nucleic and protein sequences
`
`referenced at 1] [0458]; glucan endo-1,3-B-D-glucosidase at 1] [0459], including exemplary
`
`nucleic and protein sequences referenced at 1] [0459]; endo-1,3(4)-B-gluscanase at 1] [0460],
`
`including exemplary nucleic and protein sequences referenced at 1] [0460]; B-lytic
`
`metalloendopeptidase at 1] [0461]; 3-deoxy-2-octulosonidase at 1] [0462]; peptide-N4-(N—acetyl-
`
`B-glucosaminyl)asparagine amidase at 1] [0463], including exemplary nucleic and protein
`
`sequences referenced at 1] [0463]; mannosyl-glycoprotein endo-B-N—acetylglucosaminidase at
`
`1] [0464], including exemplary nucleic and protein sequences referenced at 1] [0464]; t-
`
`carrageenase at 1] [0465], including exemplary protein sequences referenced at 1] [0465]; k-
`
`carrageenase at 1] [0466], including exemplary nucleic and protein sequences referenced at
`
`1] [0466]; k—carrageenase at 1] [0467]; (x-neoararo-oligosacaride hydrolase at 1] [0468]; and
`
`additional antimicrobial enzymes are described at 1]1] [0469]-[0470]. Further, lipolytic enzymes
`
`are described at 1]1] [0472]-[0514]; describing, for example, carboxylesterase at 1] [0487],
`
`including exemplary nucleic acid and protein sequences referenced at 1] [0487] and at Table 85;
`
`lipase at 1]1] [0488]-[0491], including exemplary nucleic acid and protein sequences referenced at
`
`1] [0491] and at Table 85; lipoprotein lipase at 1] [0492], including exemplary nucleic and protein
`
`sequences referenced at Table 85; acylglycerol lipase at 1] [0493], including exemplary nucleic
`
`and protein sequences referenced at Table 85; hormone-sensitive lipase at 1] [0494], including
`
`exemplary nucleic and protein sequences referenced at Table 85; phospholipaseA1 at 1] [0495],
`
`including exemplary nucleic acid and protein sequences referenced at 1] [0495] and at Table 85;
`
`phospholipaseAz at 1] [0496], including exemplary nucleic acid and protein sequences referenced
`
`at 1] [0496]and at Table 85; phosphatidylinositol deacylase at 1] [0497], including exemplary
`
`39/61
`
`
`
`nucleic acid and protein sequences referenced at 1] [0497]; phospholipase C at 1] [0498],
`
`including exemplary nucleic and protein sequences referenced at 1] [0498] and at Table 85;
`
`phospholipase D at 1] [0499], including exemplary nucleic acid and protein sequences referenced
`
`at 1] [0499] and at Table 85; phosphoinositide phospholipase C at 1] [0500], including exemplary
`
`nucleic acid and protein sequences referenced at 1] [0500] and at Table 85; phosphatidate
`
`phosphatase at 1] [0501]; lysophospholipase at 1] [0502], including exemplary nucleic acid and
`
`protein sequences referenced at 1] [0502] at Table 85; sterol esterase at 1] [0503], including
`
`exemplary nucleic acid and protein sequences referenced at 1] [0503] and at Table 85;
`
`galactolipase at 1] [0504]; sphingomyelin phosphodiesterase at 1] [0505]; sphingomyelin
`
`phosphodiesterase D at 1] [0506]; ceramidase at 1] [0507]; wax-ester hydrolase at 1] [0508]; fatty-
`
`acyl-ethyl-ester synthase at 1] [0509]; retinyl-palmitate esterase at 1] [0510], including exemplary
`
`nucleic acid and protein sequences reference at Table 85; ll-cz's-retinyl-palmitate hydrolase at
`
`1] [05 l l]; All-trans-retinyl-palmitate hydrolase at 1] [05 12]; cutinase at 1] [05 13]; and acyloxyacyl
`
`hydrolase at 1] [05 14]. Additionally, phosphoric triester hydrolases are described at 1]1] [05 15]-
`
`[0540]; describing, organophosphorus hydrolase at 1]1] [0527]-[053 1], including exemplary
`
`nucleic and protein sequences referenced at 1] [0528]; paraoxonase at 1] [0532], including
`
`exemplary nucleic and protein sequences referenced at 1] [0532]; carboxylase at 1] [0533],
`
`including exemplary nucleic and protein sequences referenced at 1] [0533]; organophosphorus
`
`acid anhydrolase at 1] [0534]-[0535], including exemplary nucleic and protein sequences
`
`referenced at 1] [0534]; prolidase, PepQ and aminopeptidase P at 1] [0536], including exemplary
`
`nucleic and protein sequences referenced at 1] [0536]; squid-type DFPase at 1]1] [0537]-[0538],
`
`including exemplary nucleic and protein sequences referenced at 1] [0538]; mazur-type DFPase at
`
`1] [0539], including exemplary nucleic and protein sequences referenced at 1] [0539]; as well as a
`
`phosphoric triester hydrolase at 1] [0540], including exemplary nucleic and protein sequences
`
`referenced at 1] [0540]. Also, sulfuric ester hydrolase is described at 1] [0541]; peptidase is
`
`described at 1] [0542]; peroxidase is described at 1] [0543]; and typsin is described at 1] [0544].
`
`Continuing in the evaluation of "Written Description Training Materials: Revision 1
`
`March 25, 2008" relationship to the current rejection, several examples teach that the written
`
`description requirement as not being meet due to a lack of sufficient structure and changes to that
`
`structure that may affect function. Example 9 is directed to a protein isolated from liver of an
`
`40/6l
`
`
`
`amino acid sequence of a SEQ ID No. (claim 1, p. 31) and an isolated variant of the protein
`
`(claim 2, p. 31). Claim 2 is taught (p. 32, 3rd paragraph) as not meeting the written description
`
`requirement:
`
`"the specification and claim do not describe any specific changes t be
`made. . .because the disclosure fails to describe the common attributes or
`
`characteristics that identify substitution, deletion and insertion variant members of
`the genus, and because the genus is highly variant, SEQ ID NO: 3 is insufficient
`to describe the genus, even when considered in light of the general knowledge in
`the art concerning fusion proteins... The claimed subject matter is not supported
`by an adequate written description because a representative number of species has
`not been described."
`
`Example 15 has similar teachings, as claim 1 (p. 51) is directed to an isolated nucleic acid
`
`encoding a mammalian protein. Claim 1 is not found to meet the written description requirement
`
`(p. 54, 4th complete paragraph) as:
`
`"the specification does not provide a representative number of species or
`sufficient common structural features to show that the applicant would have been
`in possession of the claimed genus as a whole at the time of filing."
`
`Example 10 describes an isolated protein of an amino acid sequence of a SEQ ID No.
`
`(claim 1, p. 33), an isolated variant of the protein of at least 95% identical to the SEQ ID No.
`
`(claim 2, p. 33), and an isolated variant of claim 2 that catalyzes a reaction (claim 3, p. 33). The
`
`variant of claim 3 having the catalytic activity is taught as not meeting the written description
`
`requirement (p. 35, paragraph 8), with factors for considerations (p. 35, paragraphs 5-6)
`
`including:
`
`"The specification discloses the reduction to practice of one species within
`the claimed genus; specifically, the protein having the amino acid sequence of
`SEQ ID NO: 3. There are no drawings or structural formulas disclosed of any
`other proteins that catalyze the reaction A->B.
`The recitation of a polypeptide with at least 95% amino acid sequence
`identity to SEQ ID NO: 3 represents a partial structure. That is, the claimed
`proteins share at least 95% of the structure of SEQ ID NO: 3, while 5% of the
`structure can vary. There is no teaching in the specification regarding which 5%
`of the structure can be varied while retaining the ability of the protein to catalyze
`the reaction A->B. Further, there is no art-recognized correlation between any
`structure (other than SEQ ID NO: 3) and the activity of catalyzing A->B, based
`
`41/61
`
`
`
`on which those of ordinary skill in the art could predict which amino acids can
`vary from SEQ ID NO: 3 without losing the catalytic activity. Consequently,
`there is no information about which amino acids can vary from SEQ ID NO: 3 in
`the claimed genus of proteins and still retain the catalytic activity."
`
`Further, example llA relates to "an isolated nucleic acid that encodes a polypeptide with
`
`at least 85% amino acid sequence identity to" a SEQ ID No. (claim 1, p. 37), and such a nucleic
`
`acid where the polypeptide has an activity (claim 2, p. 37). Similar to example 10, it is taught
`
`that the written description requirement is not meet for claim 2 (p. 39, lSt complete paragraph),
`
`stating :
`
`"However, if activity X is enzymatic, and there is no disclosure of the active site
`amino acid residues responsible for the catalytic activity, lack of that kind of
`correlating information may be a problem. Similarly, if activity X is as a ligand,
`and there is no disclosure of the domain(s) responsible for the ligand activity, the
`absence of information may be persuasive that those of skill in the art would not
`take the disclosure as generic."
`
`However, example's llB teachings, by contrast to the previous examples 9, 15, 10, and
`
`11A described above, support that the instant application's claims meet the written description
`
`requirement. The claims relative to example llA are identical, but claim 2 (bridging paragraph
`
`pp. 41-42) is deemed to meet the written description requirement based upon disclosure of
`
`additional structural information:
`
`"the specification identifies two domains responsible for activity Y, z'.e., a binding
`domain and catalytic domain. The specification also predicts that conservative
`mutations in these domains will result in a protein having activity Y. Although all
`conservative amino acid substitutions in these domains will not necessarily result
`in a protein having activity Y, those of ordinary skill in the art would expect that
`many of these conservative substitutions would result in a protein having the
`required activity. Further, amino acid substitutions outside of the two identified
`functional domains are unlikely to greatly affect activity Y. Thus, a correlation
`exists between the fianction of the claimed protein and the structure of the
`disclosed binding and catalytic domains. Consequently, there is information about
`which nucleic acids can vary from SEQ ID NO: 1 in the claimed genus of nucleic
`acids and still encode a polypeptide having activity Y. Based on the applicant’s
`disclosure and the knowledge within the art, those of ordinary skill in the art
`would conclude that the applicant would have been in possession of the claimed
`
`42/61
`
`
`
`genus of nucleic acids based on the disclosure of the single species of SEQ ID
`NO: 1."
`
`In keeping with the teachings of these examples, the specification meets the written
`
`description requirement under 35 U.S.C. 112, 1St paragraph, as it clearly teaches numerous non-
`
`limiting examples of sequences available in the art, including various modifications incorporated
`
`in those sequences (e. g., active site mutated sequences), that may be used in conjunction with
`
`structural and sequence knowledge for various enzymes and their active site domains described
`
`in the specification or as would be know in the art. In particular, many of such enzyme
`
`sequences have been modeled and analyzed in the art to identify correlations between structure
`
`and enzymatic activity (e.g., important fianctional domains, active site residues, common
`
`structural features), with specific, but non-limiting, examples of such relationships described in
`
`the specification at the paragraphs cited above, and more specifically at paragraphs [0439],
`
`[0449], [0457], [0458], [0474], [0475], [0476], [0529], [0530], [0531], [0538], and [0559]-
`
`[0590].
`
`The Examiner's concerns regarding a lack of disclosure of structure is erroneous, as the
`
`specification provides overwhelming recitations of structures for most described species of
`
`antimicrobial enzymes and peptides, including numerous variant sequences, as well as coating
`
`and material types that can be combined with such enzymes and peptide sequences. Applicants
`
`note the Examiner's acknowledgement that the specification teaches in Examples 1-6 and 22 "a
`
`few well characterized coating compositions and paints comprising a few well characterized
`
`enzymes like known lipases and lysozyme. . .and said paint filrther comprising an anti-microbial
`
`polypeptide of SEQ ID NO:40 having anti-filngal activity." Applicants appreciate this
`
`acknowledgement of disclosures of the specification by the Examiner, but Applicants
`
`respectfully disagree that the specification are so limited, in light of the disclosures of structure
`
`and modifications described in the specification described above, coupled with additional
`
`knowledge of the claimed enzyme's structure and relations of that structure to function. Further,
`
`numerous specific working and prophetic examples of enzymes, peptides, specific material types
`
`(e.g., coatings) and assays for activity demonstrated at examples 7-21, and 23-48, including:
`
`lysozyme in combination with an antimicrobial peptide in an acrylic latex coating described in
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`example 7; lysozyme comprising coatings in examples 8, 9, 12, 15, 16 and 17; assays for
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`detection of the antimicrobial activity of a coating component such as an enzyme (e. g.,
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`lysozyme) and/or an antimicrobial peptide demonstrated in examples 10, 11, 13, 14, 16 and 17
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`and other examples; a sulfatase in latex coatings in example 18; phosphodiesterase I in acrylic
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`latex coatings and assays for activity in a coating demonstrated in examples 19 and 20; lipase in
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`an alkyd/oil solvent-bome coating and an acrylic latex coating demonstrated in examples 21, 23
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`and 24; recombinant and industrial scale preparation of an organophosphorus hydrolase and
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`coatings (e. g., paints) comprising the organophosphorus hydrolase and activity assays
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`demonstrated in examples 26-35 and 44-46; numerous sources organisms organophosphorus
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`degrading enzymes and nucleic acid sequences encoding lipolytic enzymes listed at examples 25
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`and 43; and various specific materials that may comprise enzyme(s) and peptide(s) (e.g.,
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`elastomers, fillers, adhesives, sealants, textile finishes, waxes) that are described at examples 37-
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`42 and 48.
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`Further, the Examiner has not met the burden to show that the claims are not adequately
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`described or lack of enablement due to a "lack of specific sequence." This argument by the
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`Examiner is incorrect as a standard for the written description requirement, and consequentially,
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`enablement. The disclosure as originally filed need not provide "in haec verba support for the
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`claimed subject matter at issue," Purdue Pharma L.P. v. Faulding Pharmaceutical Co., 230 F.3d
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`1320, USPQ2d 1481, 1483 (Fed. Cir. 2000). In Capon v. Eshhar, 418 F.3d at 1349, 1358, 76
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`USPQ2d at 1084, the Federal Circuit held that the Board of Patent Appeals and Interferences
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`(BPAI):
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`erred in ruling that § 112 imposes a per se rule requiring recitation in the
`specification of the nucleotide sequence of the claimed DNA, when that sequence
`is already known in the field. at 1349
`The Board erred in holding that the specifications do not meet the written
`description requirement because they do not reiterate the structure or formula or
`chemical name for the nucleotide sequences of the claimed chimeric genes. at
`1 3 5 8
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`In Invitrogen Corp. v. Clontech Laboratories, Inc., 429 F.3d 1052,1073 (Fed. Cir. 2005)
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`the court upheld a district court decision that claims to a polypeptide encoded by a modified
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`reverse transcriptase nucleotide sequence were not invalid under the written description
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`requirement, even though the claims were not limited to sequences recited in the specification.
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`Applicants hold that the claims are not indefinite in light of the specifications written
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`description of enzymes in the art, and that this description further supports the enablement of the
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`claims. As described in Lizard Tech Inc, v. Earth Resource Mapping, Inc., 424 F.3d 1336, 1343,
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`76 USPQ2d 1724, 1732 (Fed. Cir. 2005):
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`a recitation of how to make and use an invention across the full breadth of the
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`claim is ordinarily sufficient to demonstrate that the inventor possesses the filll
`scope of the invention and vice versa. (emphasis added).
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`Further, the specification also meets the written description requirement in regards to
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`"antimicrobial peptides" by disclosure of nearly 200 species of antimicrobial peptide sequences
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`in the sequence listing. Written description support for all coatings and compositions are found
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`throughout the specification as filed.
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`However, merely to forward the case, Applicants have amended the independent claims
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`to specify "wherein the antimicrobial peptide comprises a peptide sequence of SEQ ID No. 40 or
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`a fianctionally equivalent conservative, common amino acid substituted peptide sequence
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`wherein any amino acid substitution has no more than a +/- 2 difference in hydropathic value of
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`the Kyte-Doolittle scale relative thereto." Additionally, Applicants have added independent
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`claim 189 with alternative language regarding the antimicrobial enzymes for the Examiner's
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`consideration.
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`For at least the reasons cited above, it is asserted that the specification conveys to one
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`skilled in the art that the inventor had possession of the claimed subject matter and, therefore, the
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`written description requirement is satisfied for the present claims. Accordingly, removal of this
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`35 U.S.C. § 112, first paragraph rejections of the claims is respectfully requested.
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`Section 112, 1st Paragraph, Rejection for Enablement
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`Claims 1-3, 35, 65-68, 70-73, 75, 77-82, 94, 97, 98, 105-108, 113-115, 118-123,