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Biomedical subjects

D Qi

Publications and source records attributed to D Qi.

At least 19 recordsLinked to original sources
PubMed2006

Metformin influences cardiomyocyte cell death by pathways that are dependent and independent of caspase-3.

AIMS/HYPOTHESIS: Metformin has been shown to increase fatty acid oxidation, an effect mediated by AMP activated protein kinase (AMPK). We hypothesised that metformin could prevent both caspase-3 activation and apoptosis when induced by palmitic acid. MATERIALS AND METHODS: Cardiomyocytes were incubated with 1 mmol/l palmitic acid, in the absence or presence of metformin (1-5 mmol/l). Following 1 to 16 h, cell damage was evaluated by measuring lactate dehydrogenase released into the incubation medium, and Hoechst staining. To investigate the mechanism of metformin's effect on cardiomyocytes, substrate utilisation and phosphorylation of AMPK and acetyl-CoA carboxylase were measured. Intracellular mediators of apoptosis were also evaluated. RESULTS: Incubation of myocytes with palmitic acid for 16 h increased apoptosis, an effect that was partly blunted by 1 and 2 mmol/l metformin. This beneficial effect of metformin was associated with increased AMPK phosphorylation, palmitic acid oxidation and suppression of high-fat-induced increases in (1) long chain base biosynthesis protein 1 levels, (2) ceramide levels, and (3) caspase-3 activity. Unexpectedly, 5 mmol/l metformin dramatically increased apoptosis in myocytes incubated with high fat. This effect was associated with a robust increase in glycolysis, lactate accumulation, and a significant drop of pH in the myocyte incubation medium. CONCLUSIONS/INTERPRETATION: Our study demonstrates that metformin reduces high-fat-induced cardiac cell death, probably through inhibition of ceramide synthesis. However, at high concentrations, metformin causes proton and lactate accumulation, leading to cell damage that is independent of caspase-3.

Acetyl-CoA Carboxylase↗
PubMed2005

The Mouse Genome Database (MGD): from genes to mice--a community resource for mouse biology.

The Mouse Genome Database (MGD) forms the core of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a model organism database resource for the laboratory mouse. MGD provides essential integration of experimental knowledge for the mouse system with information annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genotype (sequence) through phenotype information, including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships among genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent improvements in MGD discussed here include the enhancement of phenotype resources, the re-development of the International Mouse Strain Resource, IMSR, the update of mammalian orthology datasets and the electronic publication of classic books in mouse genetics.

Animals↗
PubMed2004

The Mouse Genome Database (MGD): integrating biology with the genome.

The Mouse Genome Database (MGD) is one component of the Mouse Genome Informatics (MGI) system (http://www.informatics.jax.org), a community database resource for the laboratory mouse. MGD strives to provide a comprehensive knowledgebase about the mouse with experiments and data annotated from both literature and online sources. MGD curates and presents consensus and experimental data representations of genetic, genotype (sequence) and phenotype information including highly detailed reports about genes and gene products. Primary foci of integration are through representations of relationships between genes, sequences and phenotypes. MGD collaborates with other bioinformatics groups to curate a definitive set of information about the laboratory mouse and to build and implement the data and semantic standards that are essential for comparative genome analysis. Recent developments in MGD discussed here include an extensive integration of the mouse sequence data and substantial revisions in the presentation, query and visualization of sequence data.

Animals↗
PubMed2002

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs.

Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There is an international collaborative effort to identify all full-length mRNA transcripts from the mouse, and to ensure that each is represented in a physical collection of clones. Here we report the manual annotation of 60,770 full-length mouse complementary DNA sequences. These are clustered into 33,409 'transcriptional units', contributing 90.1% of a newly established mouse transcriptome database. Of these transcriptional units, 4,258 are new protein-coding and 11,665 are new non-coding messages, indicating that non-coding RNA is a major component of the transcriptome. 41% of all transcriptional units showed evidence of alternative splicing. In protein-coding transcripts, 79% of splice variations altered the protein product. Whole-transcriptome analyses resulted in the identification of 2,431 sense-antisense pairs. The present work, completely supported by physical clones, provides the most comprehensive survey of a mammalian transcriptome so far, and is a valuable resource for functional genomics.

Alternative Splicing↗
PubMed2002

Myosin light chain phosphorylation facilitates in vivo myosin filament reassembly after mechanical perturbation.

Phosphorylation of the 20-kDa regulatory myosin light chain (MLC) of smooth muscle is known to cause monomeric myosins in solution to self-assemble into thick filaments. The role of MLC phosphorylation in thick filament formation in intact muscle, however, is not clear. It is not known whether the phosphorylation is necessary to initiate thick filament assembly in vivo. Here we show, by using a potent inhibitor of MLC kinase (wortmannin), that the MLC phosphorylation and isometric force in trachealis muscle could be abolished without affecting calcium transients. By measuring cross-sectional densities of the thick filaments electron microscopically, we also show that inhibition of MLC phosphorylation alone did not cause disassembly of the filaments. The unphosphorylated thick filaments, however, partially dissolved when the muscle was subjected to oscillatory strains (which caused a 25% decrease in the thick filament density). The postoscillation filament density recovered to the preoscillation level only when wortmannin was removed and the muscle was stimulated. The data suggest that in vivo thick filament reassembly after mechanical perturbation is facilitated by the cyclic MLC phosphorylation associated with repeated stimulation.

Androstadienes↗
PubMed2001

Enzyme design by chemical modification of protein scaffolds.

Covalent modification methods allow an almost unlimited range of functionality to be introduced into proteins. In concert with genetic techniques, chemical strategies have had significant impact in the field of enzyme design. Major recent developments include introducing catalytic activity into inactive proteins, modifying the selectivity and/or reactivity of existing enzymes and designing novel enzyme-based biosensors. New chemical methods promise to further increase the range of functionality that can be incorporated into proteins. These results suggest that semi-synthetic methods will play a key role in the development of future biocatalysts.

Amino Acid Sequence↗
PubMed2000

An autosomal dominant congenital myopathy with cores and rods is associated with a neomutation in the RYR1 gene encoding the skeletal muscle ryanodine receptor.

Central core disease (CCD) and nemaline myopathy (NM) are congenital myopathies for which differential diagnosis is often based on the presence either of cores or rods. Missense mutations in the skeletal muscle ryanodine receptor gene (RYR1) have been identified in some families with CCD. Mutations in the alpha-tropomyosin and alpha-actin genes have been associated with most dominant forms of NM. Analysis of the RYR1 cDNA in a French family identified a novel Y4796C mutation that lies in the C-terminal channel-forming domain of the RyR1 protein. This mutation was linked not only to a severe and penetrant form of CCD, but also to the presence of rods in the muscle fibres and to the malignant hyperthermia susceptibility (MHS) phenotype. The Y4796C mutation was introduced into a rabbit RYR1 cDNA and expressed in HEK-293 cells. Expression of the mutant RYR1 cDNA produced channels with increased caffeine sensitivity and a significantly reduced maximal level of Ca(2+) release. Single-cell Ca(2+) analysis showed that the resting cytoplasmic level was increased by 60% in cells expressing the mutant channel. These data support the view that the rate of Ca(2+) leakage is increased in the mutant channel. The resulting chronic elevation in myoplasmic concentration is likely to be responsible for the severe expression of the disease. Haplotyping analysis indicated that the mutation arose as a neomutation in the proband. This first report of a neomutation in the RYR1 gene has strong implications for genetic linkage studies of MHS or CCD, two diseases characterized by a genetic heterogeneity.

Amino Acid Substitution↗
PubMed2000

Synthesis of a cationic pyridoxamine conjugation reagent and application to the mechanistic analysis of an artificial transaminase.

An N-methylated, cationic pyridoxamine conjugation reagent was synthesized and tethered via a disulfide bond to a cysteine residue inside the cavity of intestinal fatty acid binding protein. The conjugate was characterized and the kinetic parameters compared to its nonmethylated pyridoxamine analogue. Kinetic isotope effects were used for further mechanistic analysis. Taken together, these experiments suggest that a step distinct from deprotonation of the ketimine in the pyridoxamine to pyridoxal reaction is what limits the rate of the artificial transaminase IFABP-Px. However, the internal energetics of reactions catalyzed by the conjugate containing the N-methylated cofactor appear to be different suggesting that the MPx reagent will be useful in future experiments designed to alter the catalytic properties of semisynthetic transaminases.

Carrier Proteins↗
PubMed2000

Family, peer, and individual correlates of depressive symptomatology among U.S. and Chinese adolescents.

This study examined the correlates of symptoms of depressed mood among adolescents in 2 dramatically different cultures (n = 502 in Tianjin, People's Republic of China; n = 201 in greater Los Angeles). Gender, stressful life events, perceived parental warmth, and conflict with parents were associated in the expected direction with depressive symptoms in each cultural setting. As predicted, regression analyses showed that the quality of family relationships and grades in school had significantly stronger associations with depressive symptoms among Chinese youths than among U.S. youths, whereas gender differences in depressive symptoms were greater among the U.S. youths. Peer warmth moderated the effects of particular risk factors for depressive symptoms in each cultural setting.

Adolescent↗
PubMed2000

[The effects of experimental osteoporosis on bone tissues around hydroxyapatite implants].

OBJECTIVE: To investigate the effects of estrogen decreasing on bone tissues around implants in ovariectomized rats. METHOD: Forty-two female Wistar rats, aged 32 weeks, were used in this study. First, cylindrical hydroxyapatite-coated implants were planted in the proximal part of tibiae of the rats. Then, the rats in experimental group and control group were respectively performed ovariectomy and false surgery after 56 days, the rates were killed in 28, 84 and 168 days after operation, and tibiae were taken out to prepare undecalcified sections. The section were examined by routine histomorphometric measurement and the dynamic changes of trabecular bone and extent of contact between the implants and bone tissue around them. RESULTS: Twenty-eight days after operation, the density of trabecular bone around the implant in experiment group was found significantly reduced compared with the control group. In the area of cortical bone, no difference was found in the extent of implant-bone contact between two groups, while in the area of spongy bone the extent of contact was different obviously. CONCLUSION: Ovariectomy in Wistar rats can induce significant osteoporosis around implant, these finding suggest that menopause in women patients may also induce osteoporosis around implanted artificial teeth and affect the prognosis. Therefore, the patients should be carefully observed during the implant treatment course.

Animals↗
PubMed1999

Artificial metalloenzymes based on protein cavities: exploring the effect of altering the metal ligand attachment position by site directed mutagenesis.

In an effort to construct catalysts with enzyme-like properties, we are employing a small, cavity-containing protein as a scaffold for the attachment of catalytic groups. In earlier work we demonstrated that a phenanthroline ligand could be introduced into the cavity of the protein ALBP and used to catalyze ester hydrolysis. To examine the effect of positioning the phenanthroline catalyst at different locations within the protein cavity, three new constructs--Phen60, Phen72 and Phen104--were prepared. Each new conjugate was characterized by UV/vis spectroscopy, fluorescence spectroscopy, guanidine hydrochloride denaturation, gel filtration chromatography, and CD spectroscopy to confirm the preparation of the desired construct. Analysis of reactions containing Ala-OiPr showed that Phen60 catalyzed ester hydrolysis with less selectivity than ALBP-Phen while Phen72 promoted this same reaction with higher selectivity. Reactions with Tyr-OMe were catalyzed with higher selectivity by Phen60 and more rapidly by Phen104. These results demonstrate that both the rates and selectivities of hydrolysis reactions catalyzed by these constructs are dependent on the precise site of attachment of the metal ligand within the protein cavity.

Carrier Proteins↗
PubMed1998

Effects of metal ions on the rates and enantioselectivities of reactions catalyzed by a series of semisynthetic transaminases created by site directed mutagenesis.

Fatty acid binding proteins are a class of small 15 kDa proteins with a simple architecture that forms a large solvent sequestered cavity. In previous work, we demonstrated that reductive amination reactions could be performed in this cavity by covalent attachment of a pyridoxamine cofactor and that the rate, enantioselectivity and substrate specificity of these reactions could be altered by site directed mutagenesis. Herein, we show that the chemistry performed by these conjugates can be extended to include catalytic transamination and describe the effects of added metal ions on reaction rate and enantioselectivity. We conclude that metal ions can be used to increase the rate of reactions catalyzed by semisynthetic transaminases; however, the addition of metal ions can also retard the reaction rate. Furthermore, it appears that the presence of metal ions almost always results in an erosion of reaction enantioselectivity. This limits their utility as a practical means of increasing reaction rate. The results reported here, for four independent systems, should be considered in future designs of artificial transaminases.

Carrier Proteins↗
PubMed1998

The design of protein-based catalysts using semisynthetic methods.

The combination of site-directed mutagenesis and chemical modification has resulted in the preparation of protein conjugates with new and useful properties. Proteins modified with metal-chelating groups are proving useful for mapping tertiary and quaternary interactions using the technique of affinity cleavage. The attachment of cofactors, including pyridoxal and pyridoxamine, has resulted in the preparation of semisynthetic transaminases that display enzyme-like properties, including enantioselectivity, substrate specificity and reaction-rate acceleration.

Catalysis↗
PubMed1998

Antibiotic activities and affinities for bacterial cell wall analogue of N-demethylvancomycin and its derivatives.

N-Demethylvancomycin, which has been clinically used in China, is one member of vancomycin group (glycopeptide) antibiotics. It differs from vancomycin only in that methyl group on the amino group of the N-terminal residue of vancomycin has been replaced by H. By reductive alkylation of N-demethylvancomycin, we synthesized N-alkyl and N,N'-dialkyl N-demethylvancomycins, which closely correlated with vancomycin in structure. The association constants of the complexes of N-demethylvancomycin and its analogues with di-N-Ac-L-Lys-D-Ala-D-Ala and the antibiotic activity against Staphylococcus aureus of the glycopeptides were determined. Results showed that N-demethylvancomycin has higher affinity for bacterial cell wall analogue di-N-Ac-L-Lys-D-Ala-D-Ala and more potent antibiotic activity against Staphylococcus aureus than vancomycin. Both N-alkylation and N,N'-dialkylation of N-demethylvancomycin reduced the affinity and antibiotic activity. The longer the alkyl groups, the less potent antibiotic activities and lower affinities have the glycopeptides. The antibiotic activities against Staphylococcus aureus of N-demethylvancomycin and its analogues roughly parallel their affinities for di-N-Ac-L-Lys-D-Ala-D-Ala.

Alkylation↗