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Biomedical subjects

Y T Lu

Publications and source records attributed to Y T Lu.

14 recordsLinked to original sources
PubMed2003

The UCSC Genome Browser Database.

The University of California Santa Cruz (UCSC) Genome Browser Database is an up to date source for genome sequence data integrated with a large collection of related annotations. The database is optimized to support fast interactive performance with the web-based UCSC Genome Browser, a tool built on top of the database for rapid visualization and querying of the data at many levels. The annotations for a given genome are displayed in the browser as a series of tracks aligned with the genomic sequence. Sequence data and annotations may also be viewed in a text-based tabular format or downloaded as tab-delimited flat files. The Genome Browser Database, browsing tools and downloadable data files can all be found on the UCSC Genome Bioinformatics website (http://genome.ucsc.edu), which also contains links to documentation and related technical information.

Animals↗
PubMed2001

Pharmaceutical-induced cell apoptosis characterized by capillary zone electrophoresis.

Capillary zone electrophoresis (CZE) with a non-gel-sieving system was employed to characterize actinomycin D-induced cell apoptosis by measuring cellular DNA damage, termed DNA ladder, which proved to be thoroughly different from the DNA damage pattern of cell necrosis. The results by CZE analyses were identical to those obtained by conventional slab gel electrophoresis, demonstrating that CZE would be a reliable and more convenient technique for the identification of cell death with advantages of higher performance, high-speed, minute sample requirement, and advanced automation.

Animals↗
PubMed2001

Characterization of phosphorylation of a novel protein kinase in rice cells by capillary electrophoresis.

It was demonstrated that a separation of 20 amino acids constituting a protein and three phosphoamino acids that mostly frequently occur in eukaryotes was achieved within 15 min by capillary electrophoresis coupled with lamp-induced fluorescence detection. Fluorescein isothiocyanate was employed as the fluorescence label to facilitate the fluorescence detection of the 23 amino acid species. The fluorescent derivatization conditions and separation parameters including concentration of electrolyte, surfactant in buffer, applied voltage and sample injection were investigated in detail and optimized. The influence of buffer additives such as methanol, acetone and polyvinylpyrrolidone on separation selectivity and sensitivity were discussed. We showed that addition of 2% polyvinylpyrrolidone into the running buffer could dramatically enhance the separation selectivity of amino acids at the expense of a decrease of sensitivity of phosphoamino acids. Under the optimized conditions, the detection limits (S/N=2) ranged from 1.90 x 10(-8) M to 5.66 x 10(-8) M with an average efficiency of 620,000/m. The method was applied to characterization of the phosphorylation of a novel protein kinase RCaMBP (calcium/calmodulin-binding protein kinase) encoded by a cDNA newly isolated and cloned from rice. We verified that RCaMBP belonged to a type of Ser/Thr kinase, providing insight into its function in signal transduction.

Electrophoresis, Capillary↗
PubMed2001

Characterization, physical location and expression of the genes encoding calcium/calmodulin-dependent protein kinases in maize (Zea mays L.).

The maize genomic sequence and cDNA encoding a calcium/calmodulin-dependent protein kinase homolog were isolated and identified. The deduced peptide (MCK2) from this cDNA shared high amino acid identity (91.2%) with maize MCK1. These two genes were physically mapped onto chromosomes by fluorescence in situ hybridization using the first introns of the genes as gene-specific probes. While the MCK1 gene was assigned to a locus on the long arm of chromosome 9, the MCK2 gene was localized to a locus on the long arm of chromosome 1. Both of these genes were expressed in roots, leaves, stems and flowers, and the expression patterns of MCK were verified by RNA in situ hybridization. These results indicated that MCK expression is temporally and spatially regulated during maize growth and development.

Amino Acid Sequence↗
PubMed2001

Identifying the orientation of DNA fragment in recombinant plasmid by capillary electrophoresis with a non-gel sieving solution.

It was demonstrated that a capillary electrophoresis (CE) method with a non-gel sieving solution has been developed to identify the orientation of DNA fragments in recombinant plasmids in molecular biology. The influences of the concentration of sieving polymer HEC, the applied electric field strength and sampling on CE separation were analyzed concerning the optimization of separation. YO-PRO-1 was used as a DNA intercalating reagent to facilitate fluorescence detection. Under the chosen conditions (buffer, 1 x TBE containing 1 microM YO-PRO-1 and 1.2% HEC; applied electric field strength, 200 V/cm; electrokinetic sampling: time, 5 s; voltage, -6 kV), three DNA markers (phi 174/HaeIII, pBR322/HaeIII and lambda DNA/HindIII) were tested for further evaluating the relationship between the DNA size and the mobility. The established CE method conjugated with the enzymatic approach was successfully applied to identifying the DNA orientation of recombinant plasmid in transgene operations of a newly cloned gene from Arabidopsis Thaliana.

DNA, Recombinant↗
PubMed2001

[Identification of medicinal plant Xanthium L. produced in China].

OBJECTIVE: To gain a clear idea on the resources and pharmacognostic identification of medicinal plant Xanthium in China. METHOD: Identification of botanical origin, analysis of fruit shapes and properties, microscopic characteristics, TLC and UV. RESULT: Identification criteria have been worked out for Xanthium and its confused species. CONCLUSION: The resources of medicinal plant Xanthium may be appropriately expanded.

Drug Contamination↗
PubMed1999

Microscopic methods for distinguishing among three cell types in TOL plasmid-carrying Pseudomonas putida cultures.

Microscopic methods were developed that enable the sensitive quantification of different cell types that are generated by plasmid instability processes when Pseudomonas putida PaW164 (X+), which carries a TOL plasmid (pWW0-164), is grown in chemostat culture. Cells that have lost the structural TOL genes (X-) or the entire TOL plasmid (X0) can be quantified in a background of 6000 X+ cells using catechol agarose miniplates. X0 cells can be quantified in a background of 3500 X+ or X- cells using carbenicillin agarose miniplates. These methods represent significant improvements in sensitivity over conventional plating methods.

Benzoates↗
PubMed1998

The role of endogenous nitric oxide in modulating ischemia-reperfusion injury in the isolated, blood-perfused rat lung.

Ischemia-reperfusion (IR) lung injury occurs after various clinical procedures, including cardiopulmonary bypass. It is not clear whether endogenous nitric oxide (NO) is protective or injurious in lungs subjected to IR. Thus, in this study we examined the contribution of endogenous NO to IR injury in isolated, blood-perfused rat lungs. Lungs of male Wistar rats (300 g) were subjected to 30 min ischemia and 180 min reperfusion (I30R180). Lungs were sampled for inducible nitric oxide synthase (i-NOS) mRNA expression (each n = 3) and NOS enzyme activity (each n = 4) at different time points. NOS inhibitors NG-nitro-L-arginine-methyl ester (10[-4] M) and aminoguanidine (10[-4] M) were used to study the contribution of NO to IR injury in lungs subjected to I30R30 and I30R180. The contribution of i-NOS to IR lung injury was studied by inducing i-NOS enzyme with Salmonella lipopolysaccharide, followed by I30R30. We found that ischemia-reperfusion alone can upregulate i-NOS mRNA and i-NOS enzyme activity (p < 0.05, ANOVA), but downregulate constitutive NOS enzyme activity over 180 min reperfusion. Endogenously produced NO is protective against lung injury in I30R180 in normal rats and lung injury in I30R30 in septic rats. NO is also pivotal in maintaining pulmonary vascular homeostasis in septic rat lungs undergoing IR.

Animals↗
PubMed1997

Light-regulated root gravitropism: a role for, and characterization of, a calcium/calmodulin-dependent protein kinase homolog.

Roots of many species grow downward (orthogravitropism) only when illuminated. Previous work suggests that this is a calcium-regulated response and that both calmodulin and calcium/calmodulin-dependent kinases participate in transducing gravity and light stimuli. A genomic sequence has been obtained for a calcium/calmodulin-dependent kinase homolog (MCK1) expressed in root caps, the site of perception for both light and gravity. This homolog consists of 7265 base pairs and contains 11 exons and 10 introns. Since MCK1 is expressed constitutively in both light and dark, it is unlikely that the light directly affects MCK1 expression, though the activity of the protein may be affected by light. In cultivars showing light-regulated gravitropism, we hypothesize that MCK1, or a homolog, functions in establishing the auxin asymmetry necessary for orthogravitropism.

Base Sequence↗
PubMed1997

Ischemia-reperfusion lung injury: contribution of ischemia, neutrophils, and hydrostatic pressure.

We used an isolated, blood-perfused rat lung model to evaluate the separate roles of ischemia and reperfusion time, the changes in pulmonary artery pressure (Ppa), and the circulating neutrophil number in mediating ischemia-reperfusion lung injury. Extravascular albumin accumulation was used to quantify changes in the permeability of the alveolar capillary membranes. In animals subjected to 30 and 45 min of ischemia without reperfusion, extravascular albumin accumulation was significantly higher than in controls subjected to continuous perfusion (P < 0.05). Albumin accumulation in animals subjected to 45 min of ischemia was greater compared with those undergoing 30 min of ischemia followed by 30 min of reperfusion (P < 0.05). In animals undergoing 45 min of ischemia followed by 30 min of reperfusion, a linear relationship was demonstrated between changes in Ppa and extravascular albumin accumulation. Reducing Ppa with a thromboxane antagonist (ICI-192605) and a smooth muscle relaxant (papaverine) produced, in both cases, a significant decrease in albumin extravasation (P < 0.05). No significant difference in extravascular albumin accumulation or change in Ppa was shown in neutrophil-depleted animals compared with nondepleted animals. We conclude that ischemia time contributes significantly to ischemia-reperfusion lung injury and that transient changes in Ppa after reperfusion exacerbate and injury in this model. This early injury demonstrated here was neutrophil dependent.

Animals↗
PubMed1996

Characterization of a calcium/calmodulin-dependent protein kinase homolog from maize roots showing light-regulated gravitropism.

Roots of many species respond to gravity (gravitropism) and grow downward only if illuminated. This light-regulated root gravitropism is phytochrome-dependent, mediated by calcium, and inhibited by KN-93, a specific inhibitor of calcium/calmodulin-dependent protein kinase II (CaMK II). A cDNA encoding MCK1, a maize homolog of mammalian CaMK, has been isolated from roots of maize (Zea mays L.). The MCK1 gene is expressed in root tips, the site of perception for both light and gravity. Using the [35S]CaM gel-overlay assay we showed that calmodulin-binding activity of the MCK1 is abolished by 50 microM KN-93, but binding is not affected by 5 microM KN-93, paralleling physiological findings that light-regulated root gravitropism is inhibited by 50 microM KN-93, but not by 5 microM KN-93. KN-93 inhibits light-regulated gravitropism by interrupting transduction of the light signal, not light perception, suggesting that MCK1 may play a role in transducing light. This is the first report suggesting a physiological function for a CaMK homolog in light signal transduction.

Amino Acid Sequence↗
PubMed1995

Characterization of a cDNA encoding a novel heat-shock protein that binds to calmodulin.

A cDNA clone (pTCB48) encoding a calmodulin-binding protein was isolated by screening a lambda ZAPII cDNA expression library constructed from cell cultures of heat-shocked tobacco (Nicotiana tabacum L. cv Wisconsin-38) with metabolically labeled [35S]calmodulin. Calmodulin gel overlay analysis indicated that pTCB48 generated major peptides of 53, 36, and 22 kD and two minor peptides of 37 and 16 kD that bound calmodulin in a Ca(2+)-dependent manner. Deletion analysis of pTCB48 indicated that these and the minor calmodulin-binding proteins resulted from the insert. A probe made from the cDNA insert recognized two bands with sizes of 2.1 and 1.8 kb on northern blot analysis. Both species of RNAs were undetectable in the control and were induced after 15 min of heat-shock treatment at 38 degrees C. The intensity of the two bands reached maximum after 1.5 h of heat-shock treatment. The cDNA clone was not full length; however, the complete sequence was determined by 5' rapid amplification of cDNA ends using nested antisense primers. The full-length cDNA contains 1648 bp and a single open reading frame of 1347 bp and is expected to encode a protein of approximately 50 kD. No significant homology with other reported genes and proteins was found. Structural predictions, deletion analysis, and gel overlay analysis suggested that the calmodulin-binding domain was a basic amphiphilic alpha-helix near the C terminus of the protein. The strong induction of the mRNA for this protein suggests a role for Ca2+/calmodulin-mediated process in the heat-shock response.

Amino Acid Sequence↗