| 1. |
- Imanishi, T., et al.
(författare)
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Integrative annotation of 21,037 human genes validated by full-length cDNA clones
- 2004
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Ingår i: PLoS biology. - : Public Library of Science (PLoS). - 1544-9173 .- 1545-7885. ; 2:6, s. 856-875
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Tidskriftsartikel (refereegranskat)abstract
- The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates (1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for non-protein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
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| 2. |
- Buyanova, Irina, 1960-, et al.
(författare)
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Optical study of spin injection dynamics in InGaN/GaN quantum wells with GaMnN injection layers
- 2004
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Ingår i: Journal of Vacuum Science & Technology B. - : American Vacuum Society. - 1071-1023 .- 1520-8567. ; 22:6, s. 2668-2672
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Tidskriftsartikel (refereegranskat)abstract
- The spin injection dynamics of GaMnN/InGaN multiquantum well (MQW) light emitting diodes (LEDs) grown by molecular beam epitaxy were examined using picosecond-transient and circularly polarized photoluminescence (PL) measurements. Even with the presence of a room temperature ferromagnetic GaMnN spin injector, the LEDs are shown to exhibit very low efficiency of spin injection. Based on resonant optical orientation spectroscopy, the spin loss in the structures is shown to be largely due to fast spin relaxation within the InGaN MQW, which itself destroys any spin polarization generated by optical spin orientation or electrical spin injection. Typical photoluminescence decay times were 20-40 ns in both commercial GaN MQW LEDs with emission wavelengths between 420-470 nm and in the GaMnN/InGaN multi-quantum well MQW LEDs. In the wurtzite InGaN/GaN system, biaxial strain at the interfaces give rise to large piezoelectric fields directed along the growth axis. This built-in piezofield breaks the reflection symmetry of confining potential leading to the presence of a large Rashba term in the conduction band Hamiltonian which is responsible for the short spin relaxation times.
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| 3. |
- Buyanova, Irina, 1960-, et al.
(författare)
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On spin injection in GaMnN/InGaN Light-Emitting Diodes
- 2004
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Ingår i: 3rd International Conference on Physics and Applications of Spin-Related Phenomena in Semiconductors PASPS III,2004.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)
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| 4. |
- Buyanova, Irina, 1960-, et al.
(författare)
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On the origin of spin loss in GaMnN/InGaN Light-Emitting Diodes
- 2004
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 84, s. 2599-
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Tidskriftsartikel (refereegranskat)abstract
- Spin polarization of GaMnN/InGaN light-emitting diodes grown by molecular beam epitaxy is analyzed. In spite of the ferromagnetic behavior of the GaMnN spin injector, the diodes are shown to exhibit very low efficiency of spin injection. Based on resonant optical orientation spectroscopy, the spin loss in the structures is shown to be largely due to fast spin relaxation within the InGaN spin detector, which itself destroys any spin polarization generated by optical spin orientation or electrical spin injection.
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| 5. |
- Buyanova, Irina, 1960-, et al.
(författare)
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Optical and electrical characterization of (Ga,Mn)N/InGaN multiquantum well light-emitting diodes
- 2004
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Ingår i: Journal of Electronic Materials. - : Springer Science and Business Media LLC. - 0361-5235 .- 1543-186X. ; 33:5, s. 467-471
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Tidskriftsartikel (refereegranskat)abstract
- (Ga,Mn)/N/InGaN multiquantum well (MQW) diodes were grown by molecular beam epitaxy (MBE). The current-voltage characteristics of the diodes show the presence of a parasitic junction between the (Ga,Mn)N and the n-GaN in the top contact layer due to the low conductivity of the former layer. Both the (Ga,Mn)N/InGaN diodes and control samples without Mn doping show no or very low (up to 10% at the lowest temperatures) optical (spin) polarization at zero field or 5 T, respectively. The observed polarization is shown to correspond to the intrinsic optical polarization of the InGaN MQW, due to population distribution between spin sublevels at low temperature, as separately studied by resonant optical excitation with a photon energy lower than the bandgap of both the GaN and (Ga,Mn)N. This indicates efficient losses in the studied structures of any spin polarization generated by optical spin orientation or electrical spin injection. The observed vanishing spin injection efficiency of the spin light-emitting diode (LED) is tentatively attributed to spin losses during the energy relaxation process to the ground state of the excitons giving rise to the light emission.
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| 6. |
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| 7. |
- Polyakov, A. Y., et al.
(författare)
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Electrical and luminescent properties and the spectra of deep centers in GaMnN/InGaN light-emitting diodes
- 2004
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Ingår i: Journal of Electronic Materials. - : Springer Science and Business Media LLC. - 0361-5235 .- 1543-186X. ; 33:3, s. 241-247
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Tidskriftsartikel (refereegranskat)abstract
- Electrical and electroluminescent properties were studied for GaN/InGaN light-emitting diodes (LEDs) with the n-GaN layer up and with the top portion of the n layer made of undoped GaMnN to allow polarization modulation by applying an external magnetic field (so-called -spin-LEDs-). The contact annealing temperature was kept to 750°C, which is the thermal stability limit for retaining room-temperature magnetic ordering in the GaMnN layer. Measurable electroluminescence (EL) was obtained in these structures at threshold voltages of ∼15 V, with a lower EL signal compared to control LEDs without Mn. This is related to the existence of two parasitic junctions between the metal and the lower contact p-type layer and between the GaMnN and the n-GaN in the top contact layer.
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| 8. |
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| 11. |
- Jimenez, A, et al.
(författare)
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Human spermatid-specific thioredoxin-1 (Sptrx-1) is a two-domain protein with oxidizing activity
- 2002
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Ingår i: FEBS Letters. - 0014-5793 .- 1873-3468. ; 530:1-3, s. 79-84
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Tidskriftsartikel (refereegranskat)abstract
- Spermatid-specific thioredoxin-1 (Sptrx-1) is the first member of the thioredoxin family of proteins with a tissue-specific expression pattern, found exclusively in the tail of elongating spermatids and spermatozoa. We describe here further biochemical characterization of human Sptrx-1 protein structure and enzymatic activity. In gel filtration chromatography human Sptrx-1 eluates as a 400 kDa protein consistent with either an oligomeric form, not maintained by intermolecular disulfide bonding, and/or a highly asymmetrical structure. Analysis of circular dichroism spectra of fragments 1-360 and 361-469 and comparison to spectra of full-length Sptrx-1 supports a two-domain organization with a largely unstructured N-terminal domain and a folded thioredoxin-like C-terminal domain. Functionally, Sptrx-1 behaves as an oxidant in vitro when using selenite, but not oxidized glutathione, as electron acceptor. This oxidizing enzymatic activity suggests that Sptrx-1 might govern the stabilization (by disulfide cross-linking) of the different structures in the developing tail of spermatids and spermatozoa.
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| 12. |
- Martinez, J, et al.
(författare)
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A 54-kDa fragment of the Poly(A)-specific ribonuclease is an oligomeric, processive, and cap-interacting Poly(A)-specific 3' exonuclease.
- 2000
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Ingår i: Journal of Biological Chemistry. - 0021-9258 .- 1083-351X. ; 275:31, s. 24222-24230
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Tidskriftsartikel (refereegranskat)abstract
- We have previously identified a HeLa cell 3' exonuclease specific for degrading poly(A) tails ofmRNAs, Here we report on the purification and identification of a calf thymus 54-kDa polypeptide associated witha similar 3' exonuclease activity. The 54-kDa polypeptide was shown to be a fragment of the poly(A)-specificribonuclease 74-kDa polypeptide. The native molecular mass of the nuclease activity was estimated to be 180-220 kDa, Protein/protein cross-linking revealed an oligomeric structure, most likely consisting of three subunits.The purified nuclease activity released 5'-AMP as the reaction product and degraded poly(A) in a highlyprocessive fashion. The activity required monovalent cations and was dependent on divalent metal ions. TheRNA substrate requirement was investigated, and it was found that the nuclease was highly poly(A)-specific and that only 3' end-located poly(A) was degraded by the activity. RNA substrates capped with m(7)G(5')ppp(5')G were more efficiently degraded than noncapped RNA substrates. Addition of free m7G(5')ppp(5')G cap analogue inhibited poly(A) degradation in vitro, suggesting a functional link between the RNA 5' end cap structure andpoly(A) degradation at the 3' end of the RNA.
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| 13. |
- Cho, H., et al.
(författare)
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High density plasma via hole etching in SiC
- 2001
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Ingår i: Journal of Vacuum Science & Technology. A. Vacuum, Surfaces, and Films. - : American Vacuum Society. - 0734-2101 .- 1520-8559. ; 19:4, s. 1878-1881
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Tidskriftsartikel (refereegranskat)abstract
- Throughwafer vias up to 100 mum deep were formed in 4H-SiC substrates by inductively coupled plasma etching with SF6/O-2 at a controlled rate of similar to0.6 mum min(-1) and use of Al masks. Selectivities of > 50 for SiC over Al were achieved. Electrical (capacitance-voltage: current-voltage) and chemical (Auger electron spectroscopy) analysis techniques showed that the etching produced only minor changes in reverse breakdown voltage, Schottky barrier height, and near surface stoichiometry of the SiC and had high selectivity over common frontside metallization. The SiC etch rate was a strong function of the incident ion energy during plasma exposure. This process is attractive for power SiC transistors intended for high current, high temperature applications and also for SiC micromachining.
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| 14. |
- Cho, H., et al.
(författare)
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Ultradeep, low-damage dry etching of SiC
- 2000
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Ingår i: Applied Physics Letters. - : AIP Publishing. - 0003-6951 .- 1077-3118. ; 76:6, s. 739-741
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Tidskriftsartikel (refereegranskat)abstract
- The Schottky barrier height (Phi(B)) and reverse breakdown voltage (V-B) of Au/n-SiC diodes were used to examine the effect of inductively coupled plasma SF6/O-2 discharges on the near-surface electrical properties of SiC. For low ion energies (less than or equal to 60 eV) in the discharge, there is minimal change in Phi(B) and V-B, but both parameters degrade at higher energies. Highly anisotropic features typical of through-wafer via holes were formed in SiC using an Al mask.
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| 15. |
- Lee, K. P., et al.
(författare)
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Comparison of F2 plasma chemistries for deep etching of SiC
- 2001
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Ingår i: Materials Research Society Symposium - Proceedings. - Boston, MA. ; , s. H7.7.1-H7.7.6
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Konferensbidrag (refereegranskat)abstract
- A number of F2-based plasma chemistries (NF3, SF6, PF5 and BF3) were investigated for high rate etching of SiC. The most advantageous of these is SF6, based on the high rate (0.6 Όm·min-) it achieves and its relatively low cost compared to NF3. The changes in electrical properties of the near-surface region are relatively minor when the incident ion energy is kept below approximately 75 eV. At a process pressure of 5 m Torr, the SiC etch rate falls-off by ∌15% in 30 Όm diameter via holes compared to larger diameter holes (> 60 Όm diameter) or open areas on the mask.
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| 16. |
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| 17. |
- Ren, J, et al.
(författare)
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Expression of sphingosine kinase gene in the interactions between human gastric carcinoma cell and vascular endothelial cell
- 2002
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Ingår i: World Journal of Gastroenterology. - 1007-9327. ; 8:4, s. 602-607
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Tidskriftsartikel (refereegranskat)abstract
- AIM: To study the interactions between human gastric carcinoma cell (HGCC) and human vascular endothelial cell (HVEC), and if the expression of sphingosine kinase (SPK) gene was involved in these interactions. METHODS: The specific inhibitor to SPK, dimethyl sphingosine (DMS), was added acting on HGCC and HVEC, then the cell proliferation was measured by MTT. The conditioned mediums (CMs) of HGCC and HVEC were prepared. The CM of one kind of cell was added to the other kind of cell, and the cell proliferation was measured by MTT. After the action of CM, the cellular expression of SPK gene in mRNA level was detected with in situ hybridization (ISH). RESULTS: DMS could almost completely inhibit the proliferation of HGCC and HVEC. The growth inhibitory rates could amount to 97.21%, 83.42%, respectively (P<0.01). The CM of HGCC could stimulate the growth of HVEC (2.70 +/- 0.01, P<0.01) while the CM of HVEC could inhibit the growth of HGCC (52.97 +/- 0.01%, P<0.01). There was no significant change in the mRNA level of SPK gene in one kind of cell after the action of the CM of the other kind of cell. CONCLUSION: SPK plays a key role in regulating the proliferation of HGCC and HVEC. There exist complicated interactions between HGCC and HVEC. HGCC can significantly stimulate the growth of HVEC while HVEC can significantly inhibit the growth of HGCC. The expression of SPK gene is not involved in the interactions.
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| 18. |
- Ren, J, et al.
(författare)
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The role of KDR in the interactions between human gastric carcinoma cell and vascular endothelial cell
- 2002
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Ingår i: World Journal of Gastroenterology. - 1007-9327. ; 8:4, s. 596-601
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Tidskriftsartikel (refereegranskat)abstract
- AIM:To study the interactions between human gastric carcinoma cell (HGCC) and human vascular endothelial cell (HVEC), and the role of KDR in these interactions. METHODS:Antisense oligodexynucleotide(ASODN) specific to KDR gene was devised and added to the culture medium of HGCC and HVEC. After the action of ASODN, the proliferation of two cells was measured by MTT method. The role of KDR in regulating the proliferation of two kinds of cells was known through observing the effect of ASODN on them. The conditioned mediums (CMs) of HGCC and HVEC were prepared. The CM of one kind of cell was added acting on the other kind of cell, then the cell proliferation was measured by MTT. After the action of ASODN or CM, the cellular expression of KDR gene was detected with in situ hybridization(ISH) for mRNA level and with immunohistochemical staining for protein level. ABC-ELISA was used to detect hVEGF in the CMs of two cells. RESULTS: KDR ASODN could specifically inhibit the proliferation of HGCC and HVEC significantly. The growth inhibitory rate amounted to 55.35 % and 54.83 %, respectively (P <0.01). HGCC and HVEC could secret a certain level of hVEGF(92.06 +/- 1.69 ng/L, 77.70 +/- 8.04 ng/L. The CM of HGCC could significantly stimulate the growth(2.70 +/- 0.01 times) and KDR gene expression of HVEC( P<0.01) while the CM of HVEC could significantly inhibit the growth(52.97 +/- 0.01%) and KDR gene expression of HGCC (P <0.01). CONCLUSION: KDR plays a key role in regulating the proliferation of HGCC and HVEC. There exist complicated interactions between HGCC and HVEC. HGCC can significantly stimulate the growth of HVEC while HVEC can significantly inhibit the growth of HGCC. KDR is involved in the interactions between them.
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| 23. |
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| 24. |
- Yan, Mingdi, et al.
(författare)
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Covalent immobilization of ultrathin polymer films by thermal activation of perfluorophenyl azide
- 2004
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Ingår i: Chemistry of Materials. - : American Chemical Society (ACS). - 0897-4756 .- 1520-5002. ; 16:9, s. 1627-1632
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Tidskriftsartikel (refereegranskat)abstract
- The attachment of thin films on solid materials is an effective way to tailor the chemical and physical properties of the surface layer. In this article, we report an alternative approach to the covalent immobilization of ultrathin polymer films. The immobilization chemistry is based on the C-H/N-H insertion reaction of perfluorophenyl nitrenes that were generated by the thermal activation of perfluorophenyl azides (PFPAs). In the process, a silicon wafer was treated with PFPA-silane 1 to give a monolayer of azido groups on the surface. A polymer was then spin coated on the functionalized wafer and the sample was heated. Thermolysis produced perfluorophenyl nitrenes which underwent insertion reactions with the neighboring polymer chains. Removal of the excess polymer by solvent extraction resulted in nanometer-thick polymer thin films covalently attached to the wafer surface. Using polystyrene and poly(2-ethyl-2-oxazoline) as examples, covalently immobilized thin films with thicknesses ranging from a few to over a hundred A were obtained. The thickness of the film could be controlled by the type and the molecular weight of the polymer. Patterned polymer films were also fabricated using this method.
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| 25. |
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