The gas phase sabinene þ OH reaction is studied both experimentally and theoretically. Product yi... more The gas phase sabinene þ OH reaction is studied both experimentally and theoretically. Product yields from the reaction of sabinene with OH radicals have been measured in the absence of NO x in the UCC chamber (Cork, Ireland) and in the presence of NO x in the LISA chamber. Three primary carbonyl compounds were observed and quantified: acetone in [(24 AE 6)%], formaldehyde in [(25 AE 6)%] and sabinaketone in [(20 AE 6)%]. The simultaneous quantification of these compounds is one of the major results of this work. The mechanism of product formation for this reaction has been studied using the quantum chemical DFT-B3LYP (6-31G(d,p) method. According to these calculations, the H-atom abstraction channel from sabinene by OH in the initial oxidation step may be taken into account to explain the acetone production. Sabinaketone and formaldehyde are mainly products of the addition channels of OH on the -CQCH 2 double bond of sabinene. This is the first theoretical work on the title reaction.
The human genome sequence defines our inherent biological potential; the realization of the biolo... more 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 nonprotein-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.
Proceedings of The National Academy of Sciences, 2008
Despite their potential to regulate approximately one-third of the whole genome, relatively few m... more Despite their potential to regulate approximately one-third of the whole genome, relatively few microRNA (miRNA) targets have been experimentally validated, particularly in stratified squamous epithelia. Here we demonstrate not only that the lipid phosphatase SHIP2 is a target of miRNA-205 (miR-205) in epithelial cells, but, more importantly, that the corneal epithelial-specific miR-184 can interfere with the ability of miR-205 to suppress SHIP2 levels. This is the first example of a miRNA negatively regulating another to maintain levels of a target protein. Interfering with miR-205 function by using a synthetic antagomir, or by the ectopic expression of miR-184, leads to a coordinated damping of the Akt signaling pathway via SHIP2 induction. This was associated with a marked increase in keratinocyte apoptosis and cell death. Aggressive squamous cell carcinoma (SCC) cells exhibited elevated levels of miR-205. This was associated with a concomitant reduction in SHIP2 levels. Partial knockdown of endogenous miR-205 in SCCs markedly decreased phosphorylated Akt and phosphorylated BAD levels and increased apoptosis. We were able to increase SHIP2 levels in SCC cells after inhibition of miR-205. Therefore, miR-205 might have diagnostic value in determining the aggressivity of SCCs. Blockage of miR-205 activity with an antagomir or via ectopic expression of miR-184 could be novel therapeutic approaches for treating aggressive SCCs.
1,4-benzenedicarboxylate; BDC-F 4 ) 2,3,5,6-tetrafluoro-1,4-benzenedicarboxylate or tetrafluorote... more 1,4-benzenedicarboxylate; BDC-F 4 ) 2,3,5,6-tetrafluoro-1,4-benzenedicarboxylate or tetrafluoroterephthalate; DMF ) dimethylformamide) have been synthesized and structurally characterized. Studies on thermal gravimetric analysis and the spectroscopic and luminescent properties of 1, 2, and their desolvated solid Er 2 (BDC) 3 (1a) and partially desolvated solid Er 2 (BDC-F 4 ) 3 (DMF)‚DMF (2a) indicate that fluorination can significantly improve the luminescence intensity of the Er ions by reducing the fluorescence quenching effect of the vibrational C−H bond; thus, the near-IR−luminescence intensity of 2a is 3 times higher than that of 1a.
Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
PLOS Biology, 2004
The human genome sequence defines our inherent biological potential; the realization of the biolo... more 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.
Direct synthesis of phosphinopeptides containing C-terminal α-aminoalkylphosphinic acids
Amino Acids, 2010
A series of phosphinopeptides containing C-terminal α-aminoalkylphosphinic acids were prepared in... more A series of phosphinopeptides containing C-terminal α-aminoalkylphosphinic acids were prepared in good yields directly in one-pot reactions of 2-(N-benzoxycarbonylamino)alkanamides/peptide amides, aldehydes, and aryldichlorophosphines, followed by hydrolysis. In the current method, the peptide bond was formed in a Mannich-type reaction.
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Papers by Jia Fatima