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Biomedical subjects

J Tsai

Publications and source records attributed to J Tsai.

At least 19 recordsLinked to original sources
PubMed2006

Evaluation of the Cepheid GeneXpert system for detecting Bacillus anthracis.

AIMS: The Cepheid GeneXpert is a four-site, automated sample preparation and real-time PCR detection system. In this study, the capability of the GeneXpert to isolate and detect nucleic acid from Bacillus anthracis Ames spores was assessed. METHODS AND RESULTS: A four-plex, dried-down bead cartridge containing PCR reagents specific for the pXO1 and pXO2 plasmids as well as sample processing and inhibition controls was evaluated. For B. anthracis Ames spores harbouring pXO1 and pXO2, samples containing 68 CFU per ml (148 spores per ml) were positive in all four replicates. A limited cross-reactivity panel, which included closely related Bacillus species, was also tested to determine the specificity of the pXO1 and pXO2 assays. No cross-reactivity occurred. Further, B. anthracis Sterne spore samples were analysed to compare results when processed using the GeneXpert to those run directly on the Cepheid SmartCycler without sample processing. The GeneXpert detection capability was three logs lower than the SmartCycler indicating the benefit of incorporating a nucleic acid extraction procedure. CONCLUSIONS: This study demonstrates that the GeneXpert is a rapid and reliable system for simultaneously detecting the B. anthracis virulence plasmids pXO1 and pXO2. SIGNIFICANCE AND IMPACT OF THE STUDY: The GeneXpert is the only platform currently available that is capable of both nucleic acid purification and real-time PCR detection enclosed within a single system. Further, all sample manipulations are automated, thus reducing errors associated with manual processing.

Bacillus anthracis↗
PubMed2005

The TIGR Gene Indices: clustering and assembling EST and known genes and integration with eukaryotic genomes.

Although the list of completed genome sequencing projects has expanded rapidly, sequencing and analysis of expressed sequence tags (ESTs) remain a primary tool for discovery of novel genes in many eukaryotes and a key element in genome annotation. The TIGR Gene Indices (http://www.tigr.org/tdb/tgi) are a collection of 77 species-specific databases that use a highly refined protocol to analyze gene and EST sequences in an attempt to identify and characterize expressed transcripts and to present them on the Web in a user-friendly, consistent fashion. A Gene Index database is constructed for each selected organism by first clustering, then assembling EST and annotated cDNA and gene sequences from GenBank. This process produces a set of unique, high-fidelity virtual transcripts, or tentative consensus (TC) sequences. The TC sequences can be used to provide putative genes with functional annotation, to link the transcripts to genetic and physical maps, to provide links to orthologous and paralogous genes, and as a resource for comparative and functional genomic analysis.

Animals↗
PubMed2003

The binding interface database (BID): a compilation of amino acid hot spots in protein interfaces.

SUMMARY: To make information about protein interactive function easily accessible, we are mining the primary scientific literature for detailed data about protein interfaces. The Binding Interface Database (BID) organizes the vast amount of protein interaction information into tables, graphical contact maps and descriptive functional profiles. Currently data on 170 interacting protein pairs are available with over 1300 mutations described. AVAILABILITY: The BID database is freely available at http://tsailab.org/BID/ To have your protein of interest entered, contact Tiffany Fischer (tiffbrink@neo.tamu.edu) or Jerry Tsai at the email below

Amino Acid Sequence↗
PubMed2002

Ex vivo bioadhesion and in vivo testosterone bioavailability study of different bioadhesive formulations based on starch-g-poly(acrylic acid) copolymers and starch/poly(acrylic acid) mixtures.

Starch-g-poly(acrylic acid) copolymers or grafted starches synthesized by 60Co irradiation or chemical modification and co-freeze-dried starch/poly(acrylic acid) mixtures were evaluated on their ex vivo bioadhesion capacity. The buccal absorption of testosterone from a bioadhesive tablet formulated with the grafted starches or starch/poly(acrylic acid) mixtures was investigated. The results were compared to a reference formulation (physical mixture of 5% Carbopol 974P and 95% Drum Dried Waxy Maize). Rice starch-based irradiated grafted starches showed the best bioadhesion results. Partial neutralization of the acrylic acid with Ca(2+) ions resulted in significantly higher bioadhesion values compared to the reference. Ca(2+) and Mg(2+) partially neutralized maltodextrin-based irradiated grafted starches showed significantly higher bioadhesion values compared to the reference formulation. The chemically modified grafted starches showed significantly higher adhesion force values than for the reference tablet. None of the co-freeze-dried starch/poly(acrylic acid) mixtures showed significantly higher bioadhesion results than the reference (Bonferroni test, P<0.05). A chemically modified grafted starch could sustain the 3 ng/ml plasma testosterone target concentration during +/- 8 h (T(>3 ng/ml)). By lyophilization of a partially neutralized irradiated grafted starch, the in vivo adhesion time (22.0 +/- 7.2 h) and the T(>3 ng/ml) (13.5 +/- 1.3 h) could be increased. The absolute bioavailability of the lyophilized formulation approached the reference formulation. Some of the grafted starches showed to be promising buccal bioadhesive drug carriers for systemic delivery.

Adhesives↗
PubMed2002

Comparison between urban Toronto PM and selected materials: aerosol characterization using laser ablation/ionization mass spectrometry (LAMS).

Laser ablation/ionization mass spectrometry (LAMS) of particulate matter (PM) was undertaken on-line in order to extend and contrast PM characterization. Qualitative on-line LAMS results for certified materials and Toronto source materials demonstrated the versatility and limitations of the technique. The observation of organic and inorganic components of certified materials verified the proper working condition of the in-house on-line LAMS. Organic and inorganic components of Toronto source materials were also observed with the on-line LAMS. Common components identified from both types of materials were Na, Al, Ca, Fe, and K. Other recognized components were compared with marker elements reported for some common PM emission sources. An in-house off-line LAMS was used to analyze urban Toronto PM deposited on glass substrates, while the on-line LAMS analyzed individual urban Toronto PM particles that were introduced directly into the instrument. Scanning electron microscopy (SEM), X-ray spectrometry and inductively coupled plasma atomic emission spectrometry (ICP-AES) were used for confirmatory purposes. Organic and inorganic components of urban Toronto PM at their typical ng/m3 concentrations were successfully observed in mass spectra using both off-line LAMS and on-line LAMS. Identified ions unique to each analyzed material were compared to identified ions of urban Toronto PM. The ability of LAMS to analyze individual respirable PM particles (viz. < 2 microns), both for inorganic trace elements and for organic components, greatly extended our capability to characterize PM and also to achieve estimates of concentration contributions of each material.

Aerosols↗
PubMed2001

Molecular dynamics in the endgame of protein structure prediction.

In order adequately to sample conformational space, methods for protein structure prediction make necessary simplifications that also prevent them from being as accurate as desired. Thus, the idea of feeding them, hierarchically, into a more accurate method that samples less effectively was introduced a decade ago but has not met with more than limited success in a few isolated instances. Ideally, the final stages should be able to identify the native state, show a good correlation with native similarity in order to add value to the selection process, and refine the structures even further. In this work, we explore the possibility of using state-of-the-art explicit solvent molecular dynamics and implicit solvent free energy calculations to accomplish all three of those objectives on 12 small, single-domain proteins, four each of alpha, beta and mixed topologies. We find that this approach is very successful in ranking the native and also enhances the structure selection of predictions generated from the Rosetta method.

Automation↗
PubMed2001

Trypsin inhibition, calcium and zinc ion binding of starch-g-poly(acrylic acid) copolymers and starch/poly(acrylic acid) mixtures for peroral peptide drug delivery.

Newly synthesised starch-g-poly(acrylic acid) copolymers and starch/poly(acrylic acid) mixtures were evaluated for their in vitro inhibition potency towards the proteolytic enzyme trypsin. Their Ca2+ and Zn2+ binding capacity was measured. Carbopol 934P was used as reference polymer. Starch-g-poly(acrylic acid) copolymers were prepared by chemical grafting and 60Co irradiation, the starch/poly(acrylic acid) mixtures by freeze-drying. The influence of preparation method, the ratio starch:acrylic acid, the neutralisation degree and for the freeze-dried polymers the influence of heat treatment after freeze-drying was investigated. All freeze-dried polymers showed a higher inhibition factor (IF) than the chemically grafted and 60Co irradiated starches, which all showed significantly lower IF than Carbopol 934P. The heat treated freeze-dried polymer Amioca/poly(acrylic acid) (1:1) showed a significantly higher IF than the reference polymer (Mann-Whitney test, p<0.05). The Ca2+ and Zn2+ binding capacity of all chemically grafted starches was much lower than for Carbopol 934P. Only the 60Co irradiated starches and freeze-dried polymers with ratio 1:3 approached the binding capacity of the reference polymer. The freeze-dried polymers showed the highest proteolytic enzyme inhibition potency. Freeze-drying and 60Co irradiation could result in the highest ion binding capacity. This combination of proteolytic enzyme inhibition activity and ion binding capacity makes these polymers hopeful excipients for successful oral peptide delivery.

Acrylic Resins↗
PubMed2001

Quantification of the hydrophobic interaction by simulations of the aggregation of small hydrophobic solutes in water.

The hydrophobic interaction, the tendency for nonpolar molecules to aggregate in solution, is a major driving force in biology. In a direct approach to the physical basis of the hydrophobic effect, nanosecond molecular dynamics simulations were performed on increasing numbers of hydrocarbon solute molecules in water-filled boxes of different sizes. The intermittent formation of solute clusters gives a free energy that is proportional to the loss in exposed molecular surface area with a constant of proportionality of 45 +/- 6 cal/mol A(2). The molecular surface area is the envelope of the solute cluster that is impenetrable by solvent and is somewhat smaller than the more traditional solvent-accessible surface area, which is the area transcribed by the radius of a solvent molecule rolled over the surface of the cluster. When we apply a factor relating molecular surface area to solvent-accessible surface area, we obtain 24 cal/mol A(2). Ours is the first direct calculation, to our knowledge, of the hydrophobic interaction from molecular dynamics simulations; the excellent qualitative and quantitative agreement with experiment proves that simple van der Waals interactions and atomic point-charge electrostatics account for the most important driving force in biology.

Computer Simulation↗
PubMed2001

The role of aldose reductase in sugar cataract formation: aldose reductase plays a key role in lens epithelial cell death (apoptosis).

Since aldose reductase is localized primarily in lens epithelial cells, osmotic insults induced by the accumulation of sugar alcohols occur first in these cells. To determine whether the accumulation of sugar alcohols can induce lens epithelial cell death, galactose-induced apoptosis has been investigated in dog lens epithelial cells. Dog lens epithelial cells were cultured in Dulbecco's modified Eagle's mimimum essential medium (DMEM) supplemented with 20% fetal calf serum (FCS). After reaching confluence at fifth passage, the medium was replaced with the same DMEM medium containing 50 mM D-galactose and the cells were cultured for an additional 2 weeks. Almost all of the cells cultured in galactose medium were stained positively for apoptosis with the terminal deoxynucleotidyl transferance-mediated biotin-dUTP nick end labeling (TUNEL) technique. Agarose gel electrophoresis of these cells displayed obvious DNA fragmentation, known as a ladder formation. All of these apoptotic changes were absent in similar cells cultured in galactose medium containing 1 microM of the aldose reductase inhibitor AL 1576. Addition of AL 1576 also reduced the cellular galactitol levels from 123+/-10 microgram/10(6) cells (n=5) to 3.9+/-1.9 microgram/10(6) cells (n=5). These observations confirm that galactose induced apoptosis occurs in dog lens epithelial cells. Furthermore, the prevention of apoptosis by an aldose reductase inhibitor suggests that this apoptosis is linked to the accumulation of sugar alcohols.

Aldehyde Reductase↗
PubMed2001

Cancer of retromolar trigone: long-term radiation therapy outcome.

BACKGROUND: Cancer of the retromolar trigone is an uncommon head and neck cancer. In this retrospective study, we identified the prognostic factors and evaluated the therapeutic outcomes of patients treated with preoperative radiation therapy (RT), postoperative RT, and RT alone. METHODS: Between 1971 and 1994, 65 patients with histologically proven epidermoid carcinoma of the retromolar trigone were treated at the Mallinckrodt Institute of Radiology; 10 patients received preoperative RT (30-55.2 Gy), 39 received postoperative RT (46-66.6 Gy), and 15 were treated with RT alone (63-74 Gy). Surgery included 44 composite resections and 7 wide excisions. The minimum follow-up was 5 years. RESULTS: The 5-year disease-free survival rates were 90% with preoperative RT, 63% with postoperative RT, and 31% with RT alone. The 5-year disease-free survival rates were 76% for patients with T1 disease, 50% for T2, 72% for T3, and 54% for T4. The 5-year disease-free survival rates were 69% for patients with NO disease, 56% for N1, and 26% for N2. The locoregional recurrence rates were 10% (1 of 10) for preoperative RT, 23% (9 of 39) for postoperative RT, and 44% (7 of 16) for RT alone. On multivariate analysis, the significant factors for disease-free survival were treatment modality (p =.002) and N stage (p =.012); for locoregional control it was treatment modality (p =.046); and for distant metastasis it was N stage (p =.002). The incidence of bone necrosis, soft tissue necrosis, and severe trismus was 12% with postoperative RT, 11% with RT alone, and none with preoperative RT. CONCLUSIONS: Combination surgery with postoperative or preoperative RT offers better locoregional control and disease-free survival than RT alone for epidermoid carcinoma of the retromolar trigone. Lymph node status significantly influences the disease-free survival and distant metastasis rates.

Adult↗
PubMed2001

Rosetta in CASP4: progress in ab initio protein structure prediction.

Rosetta ab initio protein structure predictions in CASP4 were considerably more consistent and more accurate than previous ab initio structure predictions. Large segments were correctly predicted (>50 residues superimposed within an RMSD of 6.5 A) for 16 of the 21 domains under 300 residues for which models were submitted. Models with the global fold largely correct were produced for several targets with new folds, and for several difficult fold recognition targets, the Rosetta models were more accurate than those produced with traditional fold recognition models. These promising results suggest that Rosetta may soon be able to contribute to the interpretation of genome sequence information.

Protein Conformation↗
PubMed2001

Determining the minimum number of types necessary to represent the sizes of protein atoms.

MOTIVATION: Traditionally, for packing calculations people have collected atoms together into a number of distinct 'types'. These, in fact, often represent a heavy atom and its associated hydrogens (i.e. a united atom). Also, atom typing is usually done according to basic chemistry, giving rise to 20-30 protein atom types, such as carbonyl carbons, methyl groups, and hydroxyl groups. No one has yet investigated how similar in packing these chemically derived types are. Here we address this question in detail, using Voronoi volume calculations on a set of high-resolution crystal structures. RESULTS: We perform a rigorous clustering analysis with cross-validation on tens of thousands of atom volumes and attempt to compile them into types based purely on packing. From our analysis, we are able to determine a 'minimal' set of 18 atom types that most efficiently represent the spectrum of packing in proteins. Furthermore, we are able to uncover a number of inconsistencies in traditional chemical typing schemes, where differently typed atoms have almost the same effective size. In particular, we find that tetrahedral carbons with two hydrogens are almost identical in size to many aromatic carbons with a single hydrogen. AVAILABILITY: Programs available from http://geometry.molmovdb.org. CONTACT: JerryTsai@TAMU.edu; neil.voss@yale.edu; Mark.Gerstein@yale.edu SUPPLEMENTARY INFORMATION: Available at http://geometry.molmovdb.org.

Carbon↗
PubMed2001

Susceptibilities of Eikenella corrodens, Prevotella intermedia, and Prevotella nigrescens clinical isolates to amoxicillin and tetracycline.

The AB Biodisk Etest showed that 106 (100%) and 98 (92%) isolates of Eikenella corrodens were susceptible to amoxicillin and tetracycline, respectively. Twenty-three (68%) Prevotella intermedia isolates and 14 (67%) Prevotella nigrescens isolates were susceptible to amoxicillin. Seventy-nine percent of the P. intermedia isolates and 67% of the P. nigrescens isolates were susceptible to tetracycline. A higher percentage of beta-lactamase-producing isolates of P. intermedia and P. nigrescens were identified with selective agar containing amoxicillin than with nonselective agar.

Amoxicillin↗
PubMed2001

Activation of purified cardiac ryanodine receptors by dihydropyridine agonists.

Prior observations have raised the possibility that dihydropyridine (DHP) agonists directly affect the sarcoplasmic reticulum (SR) cardiac Ca(2+) release channel [i.e., ryanodine receptor (RyR)]. In single-channel recordings of purified canine cardiac RyR, both DHP agonists (-)-BAY K 8644 and (+)-SDZ202-791 increased the open probability of the RyR when added to the cytoplasmic face of the channel. Importantly, the DHP antagonists nifedipine and (-)-SDZ202-791 had no competitive blocking effects either alone or after channel activation with agonist. Thus there is a stereospecific effect of SDZ202-791, such that the agonist activates the channel, whereas the antagonist has little effect on channel activity. Further experiments showed that DHP agonists changed RyR activation by suppressing Ca(2+)-induced inactivation of the channel. We concluded that DHP agonists can also influence RyR single-channel activity directly at a unique allosteric site located on the cytoplasmic face of the channel. Similar results were obtained in human purified cardiac RyR. An implication of these data is that RyR activation by DHP agonists is likely to cause a loss of Ca(2+) from the SR and to contribute to the negative inotropic effects of these agents reported by other investigators. Our results support this notion that the negative inotropic effects of DHP agonists result in part from direct alteration in the activity of RyRs.

3-Pyridinecarboxylic acid, 1,4-dihydro-2,6-dimethy↗
PubMed2001

RESOURCERER: a database for annotating and linking microarray resources within and across species.

Microarray expression analysis is providing unprecedented data on gene expression in humans and mammalian model systems. Although such studies provide a tremendous resource for understanding human disease states, one of the significant challenges is cross-referencing the data derived from different species, across diverse expression analysis platforms, in order to properly derive inferences regarding gene expression and disease state. To address this problem, we have developed RESOURCERER, a microarray-resource annotation and cross-reference database built using the analysis of expressed sequence tags (ESTs) and gene sequences provided by the TIGR Gene Index (TGI) and TIGR Orthologous Gene Alignment (TOGA) databases [now called Eukaryotic Gene Orthologs (EGO)].

Animals↗
PubMed2001

Sterols in blood of normal and Smith-Lemli-Opitz subjects.

Smith-Lemli-Opitz syndrome (SLOS) is a hereditary disorder in which a defective gene encoding 7-dehydrocholesterol reductase causes the accumulation of noncholesterol sterols, such as 7- and 8-dehydrocholesterol. Using rigorous analytical methods in conjunction with a large collection of authentic standards, we unequivocally identified numerous noncholesterol sterols in 6 normal and 17 SLOS blood samples. Plasma or erythrocytes were saponified under oxygen-free conditions, followed by multiple chromatographic separations. Individual sterols were identified and quantitated by high performance liquid chromatography (HPLC), Ag(+)-HPLC, gas chromatography (GC), GC-mass spectrometry, and nuclear magnetic resonance. As a percentage of total sterol content, the major C(27) sterols observed in the SLOS blood samples were cholesterol (12;-98%), 7-dehydrocholesterol (0.4;-44%), 8-dehydrocholesterol (0.5;-22%), and cholesta-5,7,9(11)-trien-3beta-ol (0.02;-5%), whereas the normal blood samples contained <0.03% each of the three noncholesterol sterols. SLOS and normal blood contained similar amounts of lathosterol (0.05;-0.6%) and cholestanol (0.1;-0.4%) and approximately 0.003;-0.1% each of the Delta(8), Delta(8(14)), Delta(5,8(14)), Delta(5,24), Delta(6,8), Delta(6,8(14)), and Delta(7,24) sterols. The results are consistent with the hypothesis that the Delta(8(14)) sterol is an intermediate of cholesterol synthesis and indicate the existence of undescribed aberrant pathways that may explain the formation of the Delta(5,7,9(11)) sterol. 19-Norcholesta-5,7,9-trien-3beta-ol was absent in both SLOS and normal blood, although it was routinely observed as a GC artifact in fractions containing 8-dehydrocholesterol. The overall findings advance the understanding of SLOS and provide a methodological model for studying other metabolic disorders of cholesterol synthesis.

Adult↗
PubMed2000

Leucine 42 in the fibronectin motif of streptokinase plays a critical role in fibrin-independent plasminogen activation.

The NH(2) terminus (residues 1-59) of streptokinase (SK) is a molecular switch that permits fibrin-independent plasminogen activation. Targeted mutations were made in recombinant (r) SK1-59 to identify structural interactions required for this process. Mutagenesis established the functional roles of Phe-37and Glu-39, which were projected to interact with microplasmin in the activator complex. Mutation of Leu-42 (rSK1-59(L42A)), a conserved residue in the SK fibronectin motif that lacks interactions with microplasmin, strongly reduced plasminogen activation (k(cat) decreased 50-fold) but not amidolysis (k(cat) decreased 1.5-fold). Otherwise rSK1-59(L42A) and native rSK1-59 were indistinguishable in several parameters. Both displayed saturable and specific binding to Glu-plasminogen or the remaining SK fragment (rSKDelta59). Similarly rSK1-59 and rSK1-59(L42A) bound simultaneously to two different plasminogen molecules, indicating that both plasminogen binding sites were intact. However, when bound to SKDelta59, rSK1-59(L42A) was less effective than rSK1-59 in restructuring the native conformation of the SK A domain, as detected by conformation-dependent monoclonal antibodies. In the light of previous studies, these data provide evidence that SK1-59 contributes to fibrin-independent plasminogen activation through 1) intermolecular interactions with the plasmin in the activator complex, 2) binding interactions with the plasminogen substrate, and 3) intramolecular interactions that structure the A domain of SK for Pg substrate processing.

Base Sequence↗