What is claimed is:
1. A method of screening a human subject for an increased risk of developing a lymphatic disorder, comprising the steps of:
(a) assaying nucleic acid of a human subject to determine a presence or an absence of a mutation altering the sequence or expression of at least one VEGFR-3 allele; and
(b) screening for an increased risk of developing a lymphatic disorder from the presence or absence of said mutation, wherein the presence of a mutation altering the encoded amino acid sequence or expression of at least one VEGFR-3 allele in the nucleic acid correlates with an increased risk of developing a lymphatic disorder.
2. A method according to claim 1 wherein the assaying step comprises determining the presence or absence of a mutation altering a tyrosine kinase domain amino acid sequence of the protein encoded by the VEGFR-3 allele.
3. A method according to claim 1 wherein the assaying step comprises determining the presence or absence of a missense mutation in a VEGFR-3 allele at a position corresponding to one of codons 857, 1041, 1044 and 1049 of the VEGFR-3-encoding sequence set forth in SEQ ID NO: 1.
4. A method according to claim 1 wherein the assaying step comprises determining the presence or absence of a missense mutation in the VEGFR-3 allele at a position corresponding to codon 1114 of the VEGFR-3-encoding sequence set forth in SEQ ID NO: 1.
5. A method according to claim 1 wherein the assaying step comprises at least one procedure selected from the group consisting of:
(a) determining a nucleotide sequence of at least one codon of at least one VEGFR-3 allele of the human subject;
(b) performing a hybridization assay to determine whether nucleic acid from the human subject has a nucleotide sequence identical to or different from one or more reference sequences;
(c) performing a polynucleotide migration assay to determine whether nucleic acid from the human subject has a nucleotide sequence identical to or different from one or more reference sequences; and
(d) performing a restriction endonuclease digestion to determine whether nucleic acid from the human subject has a nucleotide sequence identical to or different from one or more reference sequences.
6. A method according to claim 1 wherein the assaying step comprises: performing a polymerase chain reaction (PCR) to amplify nucleic acid comprising VEGFR-3 coding sequence, and determining nucleotide sequence of the amplified lnucleic acid.
7. A method of screening for a VEGFR-3 hereditary lymphedema genotype in a human patient, comprising the steps of:
(a) providing a biological sample comprising nucleic acid from said patient, said nucleic acid including sequences corresponding to said patient’s VEGFR-3 alleles;
(b) analyzing said nucleic acid for the presence of a mutation or mutations;
(c) determining a VEGFR-3 genotype from said analyzing step; and
(d) correlating the presence of a mutation in a VEGFR-3 allele with a hereditary lymphedema genotype.
8. The method according to claim 7 wherein said biological sample is a cell sample.
9. The method according to claim 7 wherein said analyzing comprises sequencing a portion of said nucleic acid, said portion comprising at least one codon of said VEGFR-3 alleles.
10. The method according to claim 7 wherein said nucleic acid is DNA.
11. The method according to claim 7 wherein said nucleic acid is RNA.
12. A method of treatment for hereditary lymphedema, comprising the step of administering to a patient with hereditary lymphedema a therapeutically effective amount of a growth factor product selected from the group consisting of vascular endothelial growth factor C (VEGF-C) protein products, vascular endothelial growth factor D (VEGF-D) protein products, VEGF-C gene therapy products, and VEGF-D gene therapy protein products.
13. A therapeutic or prophylactic method of treating lymphedema, comprising the steps of:
providing isolated lymphatic endothelial cells or lymphatic endothelial progenitor cells;
transforming or transfecting the cells ex vivo with a polynucleotide comprising a nucleotide sequence that encodes a wild type VEGFR-3;
and administering the transformed or transfected cells to the mammalian subject.
14. An oligonucleotide useful as a probe for identifying polymorphisms in a human Flt4 receptor tyrosine kinase gene, the oligonucleotide comprising 6-50 nucleotides that have a sequence that is identical or exactly complementary to a portion of a wild type human VEGFR-3 gene sequence or VEGFR-3 coding sequence, except for one sequence difference selected from the group consisting of a nucleotide addition, a nucleotide deletion, or nucleotide substitution.
15. An oligonucleotide according to claim 14 wherein the nucleotide sequence is exactly identical or exactly complementary to a portion of the human VEGFR-3 coding sequence set forth in SEQ ID NO: 1, except for a nucleotide substitution at a position corresponding to a nucleotide selected from the group consisting of bases 2546 through 2848 and bases 3044 through 3514.
16. An oligonucleotide according to claim 14 wherein the nucleotide sequence is exactly identical or exactly complementary to a portion of the human VEGFR-3 coding sequence set forth in SEQ ID NO: 1, except for a nucleotide substitution at a position corresponding to nucleotide 3360 of SEQ ID NO: 1.
17. An oligonucleotide according to claim 14 wherein the nucleotide sequence is exactly identical or exactly complementary to a portion of the human VEGFR-3 coding sequence set forth in SEQ ID NO: 1, except for a nucleotide substitution at a position corresponding to a nucleotide selected from the group consisting of position 2588, position 3141, position 3150 and position 3164 of SEQ ID NO: 1.
18. A kit comprising at least two oligonucleotides of the formula XnYZm or its complement;
where n and m are integers from 0 to 49;
where 5(nm)49;
where Xn is a stretch of n nucleotides identical to a first portion of SEQ ID NO: 1, said first portion ending immediately upstream (5) of position 3360 of SEQ ID NO: 1; and
where Zm is a stretch of m nucleotides identical to a second portion of SEQ ID NO: 1, said second portion beginning immediately downstream (3) of position 3360 of SEQ ID NO: 1; and
wherein Y represents a nucleotide selected from the group consisting of adenine, guanine, cytosine, thymine, and uracil nucleotides.
19. A kit comprising at least two oligonucleotides of the formula XnYZm or its complement;
where n and m are integers from 0 to 49;
where 5(nm)49;
where Xn is a stretch of n nucleotides identical to a first portion of SEQ ID NO: 1, said first portion ending immediately upstream (5) of position W of SEQ ID NO: 1; and
where Zm is a stretch of m nucleotides identical to a second portion of SEQ ID NO: 1, said second portion beginning immediately downstream (3) of position W of SEQ ID NO: 1;
wherein position W of SEQ ID NO: 1 is selected from the group consisting of nucleotides 2588, 3141, 3150, and 3164 of SEQ ID NO: 1; and
wherein Y represents a nucleotide selected from the group consisting of adenine, guanine, cytosine, thymine, and uracil nucleotides.
20. An array of oligonucleotide probes immobilized on a solid support, wherein each probe occupies a separate known site in the array; and wherein the array includes at least one probe set comprising two to four probes, wherein one probe is exactly identical or exactly complementary to a wild type human VEGFR-3 coding sequence, and the other one to three members of the set are exactly identical to the first member, but for at least one different nucleotide, which different nucleotide is located in the same position in each of the one to three additional set members.
21. An array of oligonucleotide probes immobilized on a solid support according to claim 20, wherein each probe occupies a separate known site in the array; and wherein the array includes at least one probe set comprising two to four probes, wherein one probe is exactly identical or exactly complementary to a portion of a human VEGFR-3 coding sequence set forth in SEQ ID NO: 1, and the other one to three members of the set are exactly identical to the first member, but for at least one different nucleotide, which different nucleotide is located in the same position in each of the one to three additional set members, said position corresponding to a position selected from the group consisting of bases 2546 through 2848 and bases 3044 through 3514 of SEQ ID NO: 1.
22. A purified polynucleotide comprising a nucleotide sequence encoding a human VEGFR-3 protein variant, wherein said polynucleotide is capable of hybridizing to the complement of SEQ ID NO: 1 under the following hybridization conditions:
hybridization at 42 C. in 50% formamide, 5X SSC, 20 mM NaPO4, pH 6.8; and
washing in 0.2X SSC at 55 C.;
and wherein the encoded VEGFR-3 protein variant has an amino acid sequence that differs from the amino acid sequence set forth in SEQ ID NO: 2 at one or more positions selected from the group consisting of amino acids 843 to 943 of SEQ ID NO: 2 and amino acids 1009 to 1165 of SEQ ID NO: 2.
23. A purified polynucleotide according to claim 22, wherein the encoded VEGFR-3 protein variant has an amino acid sequence that differs at position 1114 from the amino acid sequence set forth in SEQ ID NO: 2.
24. A purified polynucleotide according to claim 22 wherein the encoded VEGFR-3 protein variant has an amino acid sequence that differs from the amino acid sequence set forth in SEQ ID NO: 2 at position selected from the group consisting of residues 857, 1041, 1044 and 1049 of SEQ ID NO: 2.
25. A purified polynucleotide comprising a nucleotide sequence encoding a VEGFR-3 protein of a human that is affected with heritable lymphedema;
wherein said polynucleotide is capable of hybridizing to the complement of SEQ ID NO: 1 under the following hybridization conditions: hybridization at 42 C. in 50% formamide, 5X SSC, 20 mMNa-PO4, pH 6.8; and washing in 0.2X SSC at 55 C.;
and wherein the polynucleotide encodes a VEGFR-3 amino acid sequence that differs from SEQ ID NO: 2 at at least one residue.
26. A purified polynucleotide according to claim 25 wherein the polynucleotide encodes an amino acid sequence that differs from SEQ ID NO: 2 at at least one residue selected from the group consisting of residues 843 to 943 and 1009 to 1165 of SEQ ID NO: 2.
27. A vector comprising a polynucleotide according to claim 25.
28. A host cell that has been transformed or transfected with a polynucleotide according to claim 25 and that expresses the VEGFR-3 protein encoded by the polynucleotide.
29. A host cell according to claim 28 that has been co-transfected with a polynucleotide encoding the VEGFR-3 amino acid sequence set forth in SEQ ID NO: 2 and that expresses the VEGFR-3 protein having the amino acid sequence set forth in SEQ ID NO: 2.
30. A method for identifying a modulator of intracellular VEGFR-3 signaling, comprising the steps of:
a) contacting a cell expressing at least one mutant mammalian VEGFR-3 polypeptide in the presence and in the absence of a putative modulator compound;
b) detecting VEGFR-3 signaling in the cell; and
c) identifying a putative modulator compound in view of decreased or increased signaling in the presence of the putative modulator, as compared to signaling in the absence of the putative modulator.
31. A method according to claim 30 wherein the cell expresses the mutant mammalian VEGFR-3 polypeptide and a wildtype mammalian VEGFR-3 polypeptide.
32. A method according to claim 31 wherein the mutant and wildtype VEGFR-3 polypeptides are human.
33. A method according to claim 32 wherein said mutant VEGFR-3 polypeptide is characterized by a substitution or deletion mutation in a kinase domain of the VEGFR-3 polypeptide.
34. A method according to claim 32 wherein said mutant VEGFR-3 polypeptide is characterized by at least one substitution or deletion of the wild type VEGFR-3 amino acid sequence set forth in SEQ ID NO: 2, said at least one substitution or deletion occurring at a position corresponding to a residue selected from positions 843 to 943 and positions 1009 to 1165 of SEQ ID NO: 2.
35. A method according to claim 32 wherein the mutant VEGFR-3 polypeptide comprises a leucine amino acid at the position corresponding to position 1114 of SEQ ID NO: 2.
36. A method according to claim 32 wherein said mutant VEGFR-3 polypeptide is characterized by at least one substitution or deletion of the wild type VEGFR-3 amino acid sequence set forth in SEQ ID NO: 2, said at least one substitution or deletion occurring at a position corresponding to a residue selected from positions 857, 1041, 1044 and 1049, and 1114 of SEQ ID NO: 2.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
What is claimed is:
1. A semiconductor device structure, comprising:
a first structure comprising conductive or semiconductive material;
at least one hydrogen species adsorbed to a surface of said first structure; and
a second structure comprising dielectric material adjacent to said surface of said first structure.
2. The semiconductor device structure of claim 1, wherein said first structure comprises a bottom electrode of a capacitor structure.
3. The semiconductor device structure of claim 1, wherein said second structure comprises a dielectric layer of a capacitor structure.
4. The semiconductor device structure of claim 1, wherein said second structure is substantially free of voids and defects.
5. The semiconductor device structure of claim 1, wherein said first structure comprises at least one of ruthenium, ruthenium oxide, platinum, titanium nitride, tungsten, tungsten nitride, cobalt, and polysilicon.
6. The semiconductor device structure of claim 1, wherein said first structure comprises a metallic catalyst for ammonia combustion.
7. The semiconductor device structure of claim 1, wherein said second structure comprises at least one of Ta2O5, barium strontium titanate, strontium titanate, barium titanate, lead zirconium titanate, strontium bismuth tantalate, a silicon nitride, and a silicon oxide.
8. The semiconductor device structure of claim 1, wherein said at least one hydrogen species is configured to substantially prevent an oxidant from diffusing into or through said first structure.
9. A semiconductor device structure, comprising:
a first structure comprising conductive or semiconductive material;
at least one species associated with a surface of said first structure, said at least one species configured to prevent an oxidant from passing through said first structure; and
a second structure comprising dielectric material adjacent to said surface of said first structure.
10. The semiconductor device structure of claim 9, wherein said first structure comprises a bottom electrode of a capacitor structure.
11. The semiconductor device structure of claim 9, wherein said second structure comprises a dielectric layer of a capacitor structure.
12. The semiconductor device structure of claim 9, wherein said second structure is substantially free of voids and defects.
13. The semiconductor device structure of claim 9, wherein said first structure comprises at least one of ruthenium, ruthenium oxide, platinum, titanium nitride, tungsten, tungsten nitride, cobalt, and polysilicon.
14. The semiconductor device structure of claim 9, wherein said first structure comprises a metallic catalyst for ammonia combustion.
15. The semiconductor device structure of claim 9, wherein said second structure comprises at least one of Ta2O5, barium strontium titanate, strontium titanate, barium titanate, lead zirconium titanate, strontium bismuth tantalate, a silicon nitride, and a silicon oxide.
16. The semiconductor device structure of claim 9, wherein said at least one species comprises at least one hydrogen species.
17. The semiconductor device structure of claim 9, wherein said at least one species is at least partially derived from ammonia.
18. The semiconductor device structure of claim 9, wherein said oxidant comprises at least one of H2O, H2O2, CO, CO2, NO and N2O.
19. The semiconductor device structure of claim 9, wherein said at least one species substantially prevents oxidation of said first structure.
20. A selective oxidation environment, comprising an oxidizing atmosphere comprising an oxidant and at least one species, said oxidizing atmosphere proximate a semiconductor device comprising a conductive or semiconductive layer adjacent a dielectric material, said at least one species adhered to a surface of said conductive or semiconductive layer and configured to prevent oxidation of said conductive or semiconductive layer.
21. The selective oxidation environment of claim 20, wherein said oxidizing atmosphere further comprises a nitrogen species.
22. The selective oxidation environment of claim 20, wherein said at least one species comprises a hydrogen species.
23. The selective oxidation environment of claim 20, wherein said at least one species is at least partially derived from ammonia.
24. The selective oxidation environment of claim 23, wherein said conductive or semiconductive layer comprises a metallic catalyst for ammonia combustion.
25. The selective oxidation environment of claim 20, wherein said oxidant comprises at least one of H2O, H2O2, CO, CO2, NO and N2O.
26. The selective oxidation environment of claim 20, wherein said conductive or semiconductive layer comprises a bottom electrode of a capacitor structure.
27. The selective oxidation environment of claim 20, wherein said dielectric material comprises a dielectric layer of a capacitor structure.
28. The selective oxidation environment of claim 20, wherein said dielectric material is substantially free of voids and defects.
29. The selective oxidation environment of claim 20, wherein said conductive or semiconductive layer comprises at least one of ruthenium, ruthenium oxide, platinum, titanium nitride, tungsten, tungsten nitride, cobalt, and polysilicon.
30. The selective oxidation environment of claim 20, wherein said conductive or semiconductive layer comprises a metallic catalyst for ammonia combustion.
31. The selective oxidation environment of claim 20, wherein said dielectric material comprises at least one of Ta2O5, barium strontium titanate, strontium titanate, barium titanate, lead zirconium titanate, strontium bismuth tantalate, a silicon nitride, and a silicon oxide.
32. The selective oxidation environment of claim 20, wherein said at least one hydrogen species is configured to substantially prevent said oxidant from diffusing into or through said conductive or semiconductive layer.