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 .
DETAILED ACTION
Claims 1-19 are pending.
During a preliminary amendment of this application, the applicant, on date 11/10/2025 elected with traverse Group I (claims 1-14, 19 ), drawn to magnetic reagent comprised of a recombinant yeast cell having a CCC1 gene including the following genetic modifications :a) impairment of the CCC1 gene ;b) addition of at least one copy of a human ferritin gene complex; c) addition of at least one copy of a TC089 gene; and d) addition of at least one copy of a mineral- or metal ion- adsorbing target peptide, and wherein the magnetic susceptibility or mass magnetization of said recombinant yeast cell is increased and species selection of SEQ ID NO: 25, 296, 416, 482, 541, 548, 569, 585, 868 and 869; traversal on the ground that examiner will have no serious burden to examine all the groups. Applicants argument is considered but found unpersuasive because group I and group II claims belong two different type of invention searching one class will not encompass the other class; furthermore restriction requirement explained that if the claims of group I is allowable then the method claims of group II will be rejoined. In the meantime the restriction is remain applied, group II claims 15-18 of election/restriction-office action of date 5/8/2025 is withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions. Claims 1-14, 19 are for examination.
The requirement is therefore made FINAL.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 6/12/2023, 10/11/2024 in compliance with the provisions of 37 CFR 1.97. Accordingly, the examiner has considered the IDS statements .
Claim Objection
Claim 8-9 are objected for improperly multiple depended claims.
Appropriate correction is required.
.Specification objection
The Specification is objected for non-compliant of sequence requirement , see page 3 lines 26-27 for example.
Claim Rejections
35 USC 112(b) Rejection
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.
Claims 8 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.
Claim 8 is rejected for reciting “derived from Saccharomyces cerevisiae”. It is unclear the yeast cell is Saccharomyces cerevisiae or some other such as mutant or recombinant form obtained from Saccharomyces cerevisiae.
Claim 13-14 are rejected for reciting “amino acid sequence DSQKTNPS ( claim 13 and amino acid sequence MHGKTQATSGTIQS”. Amino acid sequence must be assigned SEQ ID NO:. Appropriate correction is required
Claim Rejections, 35 U.S.C 112 (a)
The following is a quotation of the first paragraph of 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 1-14 and 19 are rejected under 35 U.S.C. 112(a), as containing 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(s), at the time the application was filed, had possession of the claimed invention.
It is noted that MPEP 2111.01 states that "[d]uring examination, the claims must be interpreted as broadly as their terms reasonably allow." recombinant yeast cell having CCC1 gene including the following genetic modifications :a) impairment of the CCC1 gene having any structure ;b) addition of at least one copy of a human ferritin gene complex having any structure ; c) addition of at least one copy of a TC089 gene having any structure ; and d) addition of at least one copy of a mineral- or metal ion- adsorbing target peptide “ can be a genus of recombinant yeast cell having a) impairment of the CCC1 gene having any structure ;b) addition of at least one copy of a human ferritin gene complex; c) addition of at least one copy of a TC089 gene; and d) addition of at least one copy of a mineral- or metal ion- adsorbing target peptide so that the magnetic susceptibility or mass magnetization of said recombinant yeast cell is increased. Therefore in light of the specification, claims are broadly interpreted to comprise a genus of recombinant yeast cell expressing target peptide or polypeptide having any structure.
The Court of Appeals for the Federal Circuit has recently held that a "written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." University of California v. Eli Lilly and Co., 1997 U.S. App. LEXIS 18221, at *23, quoting Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993). To fully describe a genus of genetic material, which is a chemical compound, applicants must (1) fully describe at least one species of the claimed genus sufficient to represent said genus whereby a skilled artisan, in view of the prior art, could predict the structure of other species encompassed by the claimed genus and (2) identify the common characteristics of the claimed molecules, e.g., structure, physical and/or chemical characteristics, functional characteristics when coupled with a known or disclosed correlation between function and structure, or a combination of these (paraphrased from Enzo Biochemical).University of Rochester v. G.D. Searle & Co. (69 USPQ2d 1886 (2004)) specifically points to the applicability of both Lilly and Enzo Biochemical to methods of using products, wherein said products lack adequate written description. While in University of Rochester v. G.D. Searle & Co. the methods were held to lack written description because not a single example of the product used in the claimed methods was described, the same analysis applies wherein the product, used in the claimed methods, must have adequate written description (see Enzo paraphrased above).
There is no structure-function correlation with regard to the members of the genus of recombinant yeast cell having CCC1 gene including the following genetic modifications :a) impairment of the CCC1 gene having any structure ;b) addition of at least one copy of a human ferritin gene complex having any structure ; c) addition of at least one copy of a TC089 gene having any structure ; and d) addition of at least one copy of a mineral- or metal ion- adsorbing target peptide having any structure having magnetic susceptibility or mass magnetization of said recombinant yeast cell is increased. The specification discloses a modified Saccharomyces cerevisiae knockout strain BY4742 SOD1 expressing protein comprising the structure of SEQ ID NO: 25, 296, 416, 482, 541, 548, 569, 585, 868 and 869. Therefore one of skill in the art would not recognize from the disclosure that applicants were in possession of the claimed invention.
The genus of modified yeast strain expressing mineral- or metal ion- adsorbing target peptide or polypeptides required in the claimed invention is an extremely large structurally and functionally variable genus. An argument can be made that the recited genus of Saccharomyces cerevisiae knockout strain BY4742 SOD1 expressing metal adsorbing comprising the structure of SEQ ID NO: 25, 296, 416, 482, 541, 548, 569, 585, 868 and 869. However, the art clearly teaches there is a practical limits to predict function of a polypeptide based structural homology:
A. Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and 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 (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that "Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented 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, paragraph 2, and page 105).
B. Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340,) also highlight the difficulties associated with "Prediction of protein function from protein sequence and structure": "To reason from sequence and structure to function is to step onto much shakier ground", closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, 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 (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein's role fundamentally (page 323, paragraph 1).
C. This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polypeptides do not necessarily share the same function and many functionally similar proteins will have little or no structural homology to disclosed proteins. For example, proteins having similar structure have different activities (structure does not always correlate to function); Witkowski et al., (Biochemistry 38:11643-11650, 1999) teaches that one conservative amino acid substitution transforms a beta -ketoacyl synthase into a malonyl decarboxylase and completely eliminates beta-ketoacyl synthase activity. The art also teaches that functionally similar molecules have different structures; Kisselev L., (Structure, 2002, Vol. 10: 8-9) teach that polypeptide release factors in prokaryotes and eukaryotes have same function but different structures.
As stated above, no information beyond the characterization of a few species; such as Saccharomyces cerevisiae knockout strain BY4742 SOD1 expressing Saccharomyces cerevisiae knockout strain BY4742 SOD1 expressing metal adsorbing comprising the structure of SEQ ID NO: 25, 296, 416, 482, 541, 548, 569, 585, 868 and 869 respectively has been provided by the applicants’, which would indicate that they had the possession of the claimed genus yeast cell and expressing of polypeptides. The claimed genera of polypeptides and the encoding polynucleotides have widely variable structures and associated functions. As it is discussed above, a minor changes in structure may result in changes affecting function, since, the specification provided no additional information (species/variant/mutant) correlating structure with function, one skilled in the art cannot reasonably conclude that applicant had possession of the claimed invention at the time the instant application was filed. Furthermore, "Possession may not be shown by merely describing how to obtain possession of members of the claimed ,genus or how to identify their common structural features" (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895). A definition by function, as we have previously indicated, does not suffice to define the genus because it is only an indication of what the .gene does (function), rather what it is (structure), see University of California v. Eli Lilly & Co., 43 USPQ2d 1938, thus above claims lack adequate written description.
Conclusion
Claims 1-14 and 19 are rejected. No claim is allowed.
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examiner should be directed to Mohammad Meah whose telephone number is 571-272-
1261. The examiner can normally be reached on 8:30-5PM.
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supervisor, Robert Mondesi can be reached on 4089187584. The fax phone number
for the organization where this application or proceeding is assigned is 571-273-8300.
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/MOHAMMAD Y MEAH/Examiner, Art Unit 1652