Submarine Applications

Submarine patent applications are applications that pend secretly for an extended amount of time before becoming disclosed to the public by publication. “Classic” submarine patent applications, which were kept pending for years or even decades by filing multiple continuation applications, are generally no longer possible due to the implementation of a publication policy at the USPTO. In addition, the USPTO has changed its policy regarding the term of a patent. Formerly the term of a patent was 17 years calculated from the issue date. Now, applications filed on or after 8 June 1995 have a term that is 20 years from the earliest filing date. This makes the submarine patent applications less likely to have major impact because the extended length of pendency decreases the number of years that the granted patent is enforceable.

In general, U.S. applications filed on or after 29 November 2000 are published 18 months after the priority date, unless a non-publication request is filed. Non-publication is only allowed for applications that have not been filed in a jurisdiction that publishes applications.  This means that most, if not all, unpublished applications have been filed only in the U.S., because essentially all other countries publish patent applications.  Despite the publication rule, some applications can fail to publish in a timely manner. In other cases, the disclosure was made initially in a parent application that was filed before 29 November 2000, but did not publish until 18 months after a continuation was filed. In still other cases, the application was filed with a non-publication request, which was later rescinded.

The following eight applications, all assigned to Monsanto, might be considered “submarine” applications because the subject matter disclosed in the application pended in the patent office for extended periods of time before being published.

Patent Publication No. 20060236419

Length of pendency before publication: approximately 6 years 5 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20060236419

  • Earliest priority – 6 May 1999
  • Filed – 2 Jul 2003
  • Publication – 19 Oct 06
Title – Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

Claim 1A recombinant DNA construct comprising a polynucleotide selected from the group consisting of a polynucleotide comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1-3549.
Claim 2A recombinant DNA construct comprising a polynucleotide selected from the group consisting of a polynucleotide encoding a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 3550-7098.
Claim 3A method of producing a plant having an improved property, wherein said method comprises transforming a plant with a recombinant construct comprising a promoter region functional in a plant cell operably joined to a polynucleotide comprising coding sequence for a polypeptide associated with said property, and growing said transformed plant, wherein said polypeptide is selected from the group consisting of: a) a polypeptide useful for improving plant cold tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; b) a polypeptide useful for manipulating growth rate in plant cells by modification of the cell cycle pathway, wherein said polypeptide comprises a sequence identified as such in Table 1; c) a polypeptide useful for improving plant drought tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; d) a polypeptide useful for providing increased resistance to plant disease, wherein said polypeptide comprises a sequence identified as such in Table 1; e) a polypeptide useful for galactomannan production, wherein said polynucleotide comprises a sequence identified as such in Table 1; f) a polypeptide useful for production of plant growth regulators, wherein said polypeptide comprises a sequence identified as such in Table 1; g) a polypeptide useful for improving plant heat tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; h) a polypeptide useful for improving plant tolerance to herbicides, wherein said polypeptide comprises a sequence identified as such in Table 1; i) a polypeptide useful for increasing the rate of homologous recombination in plants, wherein said polypeptide comprises a sequence identified as such in Table 1; j) a polypeptide useful for lignin production, wherein said polypeptide comprises a sequence identified as such in Table 1; k) a polypeptide useful for improving plant tolerance to extreme osmotic conditions, wherein said polypeptide comprises a sequence identified as such in Table 1; l) a polypeptide useful for improving plant tolerance to pathogens or pests, wherein said polypeptide comprises a sequence identified as such in Table 1; m) a polypeptide useful for yield improvement by modification of photosynthesis, wherein said polynucleotide comprises a sequence identified as such in Table 1; n) a polypeptide useful for modifying seed oil yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; o) a polypeptide useful for modifying seed protein yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; p) a polypeptide encoding a plant transcription factor, wherein said polypeptide comprises a sequence identified as such in Table 1; q) a polypeptide useful for yield improvement by modification of carbohydrate use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; r) a polypeptide useful for yield improvement by modification of nitrogen use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; s) a polypeptide useful for yield improvement by modification of phosphorus use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; and t) a polypeptide useful for yield improvement by providing improved plant growth and development under at least one stress condition, wherein said polypeptide comprises a sequence identified as such in Table 1.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070016974

Length of pendency before publication: approximately 7 years 4 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20070016974A1

  • Earliest priority – 30 Sep 1999
  • Filed – 15 Sep 2006
  • Publication – 18 Jan 07
Title – Nucleic acid molecules and other molecules associated with plants

Claim 1A substantially purified nucleic acid molecule that encodes a plant protein or fragment thereof comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO:43701.
Claim 3A substantially purified rice protein or fragment thereof, wherein said rice protein is encoded by a nucleic acid molecule that comprises a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO:43701.
Claim 4
A transformed plant having a nucleic acid molecule which comprises: (a) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; (b) a structural nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 43701 or complements thereof; (c) a 3′ non-translated sequence that functions in said plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of said mRNA molecule.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070020621

Length of pendency before publication: approximately 6 years 5 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20070020621

  • Earliest priority – 19 Jul 2000
  • Filed – 23 Mar 2001
  • Publication – 25 Jan 07
Title – Genomic plant sequences and uses thereof

Claim 1A substantially purified nucleic acid molecule comprising a nucleic acid sequence wherein the nucleic acid sequence: i) hybridizes under stringent conditions with a sequence selected from the group consisting of SEQ ID NO:1 through 57,467, and the complements thereof; or ii) exhibits an 85% or greater identity to a sequence selected from the group consisting of SEQ ID NO:1 through 57,467.
Claim 18A transgenic plant containing a nucleic acid molecule that comprises in the 5′ to 3′ direction: a nucleic acid sequence that: i) hybridizes under stringent conditions with a sequence selected from the group consisting of SEQ ID NO:1 through 57,467, and the complements thereof; or ii) exhibits an 85% or greater identity to a sequence selected from the group consisting of SEQ ID NO:1 through 57,467; operably linked to a structural nucleic acid sequence; wherein the nucleic acid sequence is heterologous with respect to the structural nucleic acid sequence.
Claim 36
A method of transforming a host cell comprising: a) providing a nucleic acid molecule that comprises in the 5′ to 3′ direction: a nucleic acid sequence that: i) hybridizes under stringent conditions with a sequence selected from the group consisting of SEQ ID NO:1 through 57,467, and the complements thereof; or ii) exhibits an 85% or greater identity to a sequence selected from the group consisting of SEQ ID NO:1 through 57,467; operably linked to a structural nucleic acid sequence; and b) transforming said plant with the nucleic acid molecule.

Monsanto

Remarks

This application was filed on 23 March 2001, but did not publish until 25 January 2007. In this case, it appears that the applicants initially filed a non-publication request, but later rescinded it in March of 2004. Theoretically, it should have pubished shortly after that, but it didn’t actually publish until January 2007. To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070039076

Length of pendency before publication: approximately 7 years 7 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20070039076

  • Earliest priority – 20 Jul 1999
  • Filed – 24 Jul 2006
  • Publication – 15 Feb 07
Title – Plant genome sequence and uses thereof

Claim 1A substantially purified nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 69652 or complements thereof.
Claim 2A substantially purified nucleic acid molecule, said nucleic acid molecule capable of specifically hybridizing to a second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 69652 or complements thereof.
Claim 5A substantially purified nucleic acid molecule encoding a protein or fragment thereof, wherein said protein or fragment thereof is selected from the group consisting of a rice protein or fragment thereof from Table 1.
Claim 10
A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; which is linked to (B) a structural nucleic acid molecule, wherein said structural nucleic acid molecule encodes a protein or fragment thereof selected from the group consisting of a rice protein homologue or fragment thereof in Table 1; which is linked to (C) a 3′ non-translated sequence that functions in a plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of said mRNA molecule.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070044171

Length of pendency before publication: approximately 7 years 2 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20070044171

  • Earliest priority – 14 Dec 2000
  • Filed – 6 Nov 2003
  • Publication – 22 Feb 07
Title – Nucleic acid molecules and other molecules associated with plants

Claim 1A recombinant polynucleotide selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 105,582.
Claim 2A recombinant polypeptide selected from the group consisting of SEQ ID NO: 105,583 through SEQ ID NO: 211,164.
Claim 3
A method of producing a plant having an improved property, wherein said method comprises transforming a plant with a recombinant construct comprising a promoter region functional in a plant cell operably joined to a polynucleotide comprising a coding sequence for a polypeptide associated with said property, and growing said transformed plant, wherein said polypeptide is selected from the group consisting of: a) a polypeptide useful for improving plant cold tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; b) a polypeptide useful for manipulating growth rate in plant cells by modification of the cell cycle pathway, wherein said polypeptide comprises a sequence identified as such in Table 1; c) a polypeptide useful for improving plant drought tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; d) a polypeptide useful for providing increased resistance to plant disease, wherein said polypeptide comprises a sequence identified as such in Table 1; e) a polypeptide useful for galactomannan production, wherein said polynucleotide comprises a sequence identified as such in Table 1; f) a polypeptide useful for production of plant growth regulators, wherein said polypeptide comprises a sequence identified as such in Table 1; g) a polypeptide useful for improving plant heat tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; h) a polypeptide useful for improving plant tolerance to herbicides, wherein said polypeptide comprises a sequence identified as such in Table 1; i) a polypeptide useful for increasing the rate of homologous recombination in plants, wherein said polypeptide comprises a sequence identified as such in Table 1; j) a polypeptide useful for lignin production, wherein said polypeptide comprises a sequence identified as such in Table 1; k) a polypeptide useful for improving plant tolerance to extreme osmotic conditions, wherein said polypeptide comprises a sequence identified as such in Table 1; l) a polypeptide useful for improving plant tolerance to pathogens or pests, wherein said polypeptide comprises a sequence identified as such in Table 1; m) a polypeptide useful for yield improvement by modification of photosynthesis, wherein said polynucleotide comprises a sequence identified as such in Table 1; n) a polypeptide useful for modifying seed oil yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; o) a polypeptide useful for modifying seed protein yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; p) a polypeptide encoding a plant transcription factor, wherein said polypeptide comprises a sequence identified as such in Table 1; q) a polypeptide useful for yield improvement by modification of carbohydrate use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; r) a polypeptide useful for yield improvement by modification of nitrogen use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; s) a polypeptide useful for yield improvement by modification of phosphorus use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; and t) a polypeptide useful for yield improvement by providing improved plant growth and development under at least one stress condition, wherein said polypeptide comprises a sequence identified as such in Table 1.

Monsanto

Remarks

The corresponding patent (US 7214786) has been issued, which has two claims left that are drawn to two sequences: a recombinant polynucleotide of SEQ ID NO: 28,864 and a recombinant polypeptide of SEQ ID NO: 134,446. We have no information that a corresponding patent application has been filed in any other country besides the USA.

Patent Publication No. 200700661916

Length of pendency before publication: approximately 5 years 9 Months

 Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20070061916

  • Earliest priority – 7 May 2001
  • Filed – 14 Jul 2006
  • Publication – 15 Mar 07
Title -Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

Claim 1A recombinant polynucleotide selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 58,798.
Claim 2A recombinant polypeptide selected from the group consisting of SEQ ID NO: 58,799 through SEQ ID NO: 117,596.
Claim 3
A method of producing a plant having an improved property, wherein said method comprises transforming a plant with a recombinant construct comprising a promoter region functional in a plant cell operably joined to a polynucleotide comprising a coding sequence for a polypeptide associated with said property, and growing said transformed plant, wherein said polypeptide is selected from the group consisting of: a) a polypeptide useful for improving plant cold tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; b) a polypeptide useful for manipulating growth rate in plant cells by modification of the cell cycle pathway, wherein said polypeptide comprises a sequence identified as such in Table 1; c) a polypeptide useful for improving plant drought tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; d) a polypeptide useful for providing increased resistance to plant disease, wherein said polypeptide comprises a sequence identified as such in Table 1; e) a polypeptide useful for galactomannan production, wherein said polynucleotide comprises a sequence identified as such in Table 1; f) a polypeptide useful for production of plant growth regulators, wherein said polypeptide comprises a sequence identified as such in Table 1; g) a polypeptide useful for improving plant heat tolerance, wherein said polypeptide comprises a sequence identified as such in Table 1; h) a polypeptide useful for improving plant tolerance to herbicides, wherein said polypeptide comprises a sequence identified as such in Table 1; i) a polypeptide useful for increasing the rate of homologous recombination in plants, wherein said polypeptide comprises a sequence identified as such in Table 1; j) a polypeptide useful for lignin production, wherein said polypeptide comprises a sequence identified as such in Table 1; k) a polypeptide useful for improving plant tolerance to extreme osmotic conditions, wherein said polypeptide comprises a sequence identified as such in Table 1; l) a polypeptide useful for improving plant tolerance to pathogens or pests, wherein said polypeptide comprises a sequence identified as such in Table 1; m) a polypeptide useful for yield improvement by modification of photosynthesis, wherein said polynucleotide comprises a sequence identified as such in Table 1; n) a polypeptide useful for modifying seed oil yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; o) a polypeptide useful for modifying seed protein yield and/or content, wherein said polypeptide comprises a sequence identified as such in Table 1; p) a polypeptide encoding a plant transcription factor, wherein said polypeptide comprises a sequence identified as such in Table 1; q) a polypeptide useful for yield improvement by modification of carbohydrate use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; r) a polypeptide useful for yield improvement by modification of nitrogen use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; s) a polypeptide useful for yield improvement by modification of phosphorus use and/or uptake, wherein said polypeptide comprises a sequence identified as such in Table 1; and t) a polypeptide useful for yield improvement by providing improved plant growth and development under at least one stress condition, wherein said polypeptide comprises a sequence identified as such in Table 1.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.

Patent Publication No. 20070067865

Length of pendency before publication: approximately 6 years 10 Months

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20070067865

  • Earliest priority – 5 Sep 2000
  • Filed – 14 Aug 2006
  • Publication – 22 Jul 07
Title – Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement

Claim 1A substantially purified nucleic acid molecule comprising a nucleic sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173 or complements thereof or fragments of either.
Claim 2A substantially purified first nucleic acid molecule, wherein the first nucleic molecule specifically hybridizes to a second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173 complements thereof.
Claim 3
A substantially purified protein or fragment thereof encoded by a first nucleic acid molecule which specifically hybridizes to a second nucleic acid molecule, the second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of a complement of SEQ ID NO: 1 through SEQ ID NO: 463,173.
Claim 5
A purified antibody or fragment thereof which is capable of specifically binding to a protein or fragment thereof, wherein the protein or fragment thereof is encoded by a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting SEQ ID NO: 1 through SEQ ID NO: 463,173.
Claim 6
A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; (B) a structural nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173; and (C) a 3′ non-translated sequence that functions in the plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of the mRNA molecule.
Claim 8
A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; which is linked to (B) a transcribed nucleic acid molecule with a transcribed strand and a non-transcribed strand, wherein the transcribed strand is complementary to a nucleic acid molecule comprising a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 463,173 or fragment thereof; which is linked to (C) a 3′ non-translated sequence that functions in plant cells to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of the mRNA molecule.
Claim 10
A method for determining a level or pattern of a protein in a plant cell or plant tissue under evaluation which comprises assaying the concentration of a molecule, whose concentration is dependent upon the expression of a gene, the gene specifically hybridizes to a nucleic acid molecule having a nucleic acid sequence selected from the group consisting of a complement of SEQ ID NO: 1 through SEQ ID NO: 463,173, in comparison to the concentration of that molecule present in a reference plant cell or a reference plant tissue with a known level or pattern of the protein, wherein the assayed concentration of the molecule is compared to the assayed concentration of the molecule in the reference plant cell or reference plant tissue with the known level or pattern of the protein.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one. This application is a continuation of US Patent Application 09/654,617, which was filed on 5 September 2000, and subsequently abandoned. The parent application was never published. In effect, the subject matter of Application No. US 2007/67865 A1 pended in secret for more than 6.5 years before it was published.

Patent Publication No. 20070083945

Length of pendency before publication: approximately 7 years 1 Month

Publication No.

Title, Independent Claims and Summary

Assignee and licensing information
20070083945

  • Earliest priority – 10 Mar 2000
  • Filed – 2 Aug 2006
  • Publication – 12 Apr 07
Title – Nucleic acid molecules and other molecules associated with plants

Claim 1A substantially purified nucleic acid molecule, said nucleic acid molecule capable of specifically hybridizing to a second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO: 1 through SEQ ID NO: 304905 or complement or fragment thereof.
Claim 8A substantially purified nucleic acid molecule comprising a nucleic acid molecule or fragment thereof having a pair of defined ends, wherein said pair of defined ends are selected from the defined ends in Table A.
Claim 11
A substantially purified protein or fragment thereof encoded by a first nucleic acid molecule which specifically hybridizes to a second nucleic acid molecule, said second nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NO:1 through SEQ ID NO:304905 or complements thereof.
Claim 12
A transformed plant having a nucleic acid molecule which comprises: (A) an exogenous promoter region which functions in a plant cell to cause the production of a mRNA molecule; which is linked to (B) a structural nucleic acid molecule, wherein said structural nucleic acid molecule is selected from the group consisting of SEQ ID NO:1 through SEQ ID NO:304905 or complements thereof or fragment of either; which is linked to (C) a 3′ non-translated sequence that functions in a plant cell to cause termination of transcription and addition of polyadenylated ribonucleotides to a 3′ end of said mRNA molecule.

Monsanto

Remarks

To the best of our knowledge, there are no foreign-filed applications corresponding to this one.