Biomedical subjects

Gang Pan

Publications and source records attributed to Gang Pan.

At least 19 recordsLinked to original sources

PubMed2025

TRAIT: A Comprehensive Database for T-cell Receptor-antigen Interactions.

Comprehensive and integrated resources on interactions between T-cell receptors (TCRs) and antigens are still lacking for adoptive T-cell-based immunotherapies, highlighting a significant gap that must be addressed to fully understand the mechanisms of antigen recognition by T cells. In this study, we present the T-cell receptor-antigen interaction database (TRAIT), a comprehensive database that profiles the interactions between TCRs and antigens. TRAIT stands out due to its comprehensive description of TCR-antigen interactions by integrating sequences, structures, and affinities. It provides millions of experimentally validated TCR-antigen pairs, resulting in an exhaustive landscape of antigen-specific TCRs. Notably, TRAIT emphasizes single-cell omics as a major reliable data source for TCR-antigen interactions and includes millions of reliable non-interactive TCRs. Additionally, it thoroughly demonstrates the interactions between mutations of TCRs and antigens, thereby benefiting affinity optimization of engineered TCRs as well as vaccine design. TCRs on clinical trials are innovatively provided. With the significant efforts made toward elucidating the complex interactions between TCRs and antigens, TRAIT is expected to ultimately contribute superior algorithms and substantial advancements in the field of T-cell-based immunotherapies. TRAIT is freely accessible at https://pgx.zju.edu.cn/traitdb.

Receptors, Antigen, T-Cell↗

PubMed2006

Map-based cloning of a novel rice cytochrome P450 gene CYP81A6 that confers resistance to two different classes of herbicides.

Development of hybrid rice has greatly contributed to increased yields during the past three decades. Two bentazon-lethal mutants 8077S and Norin8m are being utilized in developing new hybrid rice systems. When the male sterile lines are developed in such a mutant background, the problem of F1 seed contamination by self-seeds from the sterile lines can be solved by spraying bentazon at seedling stage. We first determined the sensitivity of the mutant plants to bentazon. Both mutants showed symptoms to bentazon starting from 100 mg/l, which was about 60-fold, lower than the sensitivity threshold of their wild-type controls. In addition, both mutants were sensitive to sulfonylurea-type herbicides. The locus for the mutant phenotype is bel for 8077S and bsl for Norin8m. Tests showed that the two loci are allelic to each other. The two genes were cloned by map-based cloning. Interestingly, both mutant alleles had a single-base deletion, which was confirmed by PCR-RFLP. The two loci are renamed bel ( a ) (for bel) and bel ( b ) (for bsl). The wild-type Bel gene encodes a novel cytochrome P450 monooxgenase, named CYP81A6. Analysis of the mutant protein sequence also revealed the reason for bel ( a ) being slightly tolerant than bel ( b ). Introduction of the wild-type Bel gene rescued the bentazon- and sulfonylurea-sensitive phenotype of bel ( a ) mutant. On the other hand, expression of antisense Bel in W6154S induced a mutant phenotype. Based on these results we conclude that the novel cytochrome P450 monooxygenase CYP81A6 encoded by Bel confers resistance to two different classes of herbicides.

Alleles↗

PubMed2005

Removal of cyanobacterial blooms in Taihu Lake using local soils. I. Equilibrium and kinetic screening on the flocculation of Microcystis aeruginosa using commercially available clays and minerals.

Algal removal abilities of 26 clays/minerals were classified into three categories according to the 8-h equilibrium removal efficiency (Q8h) and removal rate at a clay loading of 0.7 g/L. Type I clays (sepiolite, talc, ferric oxide, and kaolinite) had a Q8h > 90%, a t50 (time needed to remove 50% of the algae) < 15 min, and a t80 < 2.5 h. Type II clays (6 clays) had a Q8h 50-90%, a t50 < 2.5 h, and a t80 > 2.5 h. Type III clays (14 clays) with Q8h < 50%, t50 > 8 h and t80 > 14 h had no practical value in removal of algal blooms. When the clay loading was reduced to 0.2 g/L, Q8h for all the 25 materials decreased to below 60%, except for sepiolite whose Q8h remained about 97%. The high efficiency for sepiolite to flocculate M. aeruginosa cells in freshwaters was due to the mechanism of netting and bridging effect.

Aluminum Silicates↗

PubMed2005

Removal of harmful cyanobacterial blooms in Taihu Lake using local soils. III. Factors affecting the removal efficiency and an in situ field experiment using chitosan-modified local soils.

Effects of ionic strength, pH, organic content, cell concentration, and growth phase on the removal of MA cells using chitosan-modified sepiolite were studied in the laboratory. The MA removal efficiency increased with the increase of salinity for normal clay flocculation. In contrast, for chitosan-modified clays/soils, MA removal efficiency increased with the decrease of salinity. The removal efficiency of chitosan-modified sepiolite was not significantly affected by pH (6-9), but dropped dramatically beyond pH 10. Humic acid had a small negative effect on the removal of MA cells. Cells were removed more effectively by clays around the early senescence growth phase than other growth stages. The removal efficiency increased as the cell concentration increased. In a field enclosure of Taihu Lake, a loading of 0.025 g/L chitosan-modified local soils removed 99% algal cells and no increase of chlorophyll-a was observed during the following one month's monitoring process.

Aluminum Silicates↗

PubMed2005

Removal of cyanobacterial blooms in Taihu Lake using local soils. II. Effective removal of Microcystis aeruginosa using local soils and sediments modified by chitosan.

After sepiolite was modified with Fe3+ to increase its surface charge, the initial algal removal rate increased significantly, but its Q8h was not improved substantially at clay loadings below 0.1 g/L. Modification on netting and bridging properties of clays by either chitosan or polyacrylamide (PAM) dramatically increased flocculation (Q8h) of MA cells in freshwaters. Algal removal efficiencies of different solids, including Type III clays, local soils and sediments, were all improved to a similar level of >90% at a total loading of 0.011 g/L (contained 0.001 g/L chitosan) after they were modified with chitosan, making the idea of clearing up algal blooms using local soils/sediments possible. The mechanism of netting and bridging was confirmed to be the most important factor in improving the removal efficiency of cells, whereas clays also played important roles in the sedimentation of the floc.

Acrylic Resins↗

PubMed2005

Quantum chemical studies of mononuclear zinc species of hydration and hydrolysis.

Optimal geometries, charge distributions, bond analysis, changes of Gibbs free energy, entropies and enthalpies of hydration, and hydrolysis reactions for mononuclear species of Zn(2+) including hydrated and hydrolysis complexes were investigated using quantum chemical calculations in the gas phase. Optimized geometrical structures showed that the stable hydrated and hydrolysis zinc species without outer-sphere water molecules were Zn(H(2)O)(6)(2+), Zn(OH)(H(2)O)(3)(+), Zn(OH)(2)(H(2)O)(2), Zn(OH)(3)(-), and Zn(OH)(4)(2-). Results of NPA (Natural Population Analysis) indicated that the charge on the Zn atom of the hydrated ions decreased but the charge on the zinc atom of the hydrolysis species increased with the increase of inner-sphere water molecules. NBO (Natural Bond Orbital) analyses demonstrated that hydrated and hydrolysis species of zinc were mainly electrostatic bonding compounds. Calculations of reaction energies indicated that inner-sphere water molecules became more unfavorable as the hydrolysis increased. Stepwise hydrolysis equilibrium constants decreased successively and the order remained unchanged when the inner-sphere dehydration occurred.

Hydrolysis↗

PubMed2005

Surgeon offsets and dynamic eye movements in laser refractive surgery.

PURPOSE: To determine the amount of static and dynamic pupil decentrations that occur during laser refractive surgery. SETTING: The Center of Visual Science and the Department of Ophthalmology, University of Rochester, Rochester, New York, USA. METHODS: The surgeon's accuracy in aligning the pupil center with the laser center axis was measured when engaging the eye-tracker in 17 eyes receiving conventional laser in situ keratomileusis (LASIK) procedures (Technolas 217z; Bausch & Lomb). Eye movements were measured subsequently during the treatment in 10 eyes using a pupil camera operating at 50 Hz. Temporal power spectra were calculated from the eye movement measurements. RESULTS: The mean pupil misalignment by the surgeon at the beginning of the procedure was 206.1 microm +/- 80.99 (SD) (with respect to the laser center). The laser center was typically misaligned below (inferiorly) and to the left (nasally and temporally in left and right eyes, respectively) of the pupil [corrected] center. Small amounts of cyclotorsion were observed during the ablation (<2 degrees). The mean magnitude of dynamic pupil decentration from the laser center during treatment was 227.0 +/- 44.07 microm. The mean standard deviation of eye movements was 65.7 +/- 25.64 microm. Temporal power spectra calculated from the horizontal and vertical changes in eye position during the ablation were similar. Ninety-five percent of the total power of the eye movements was contained in temporal frequencies up to 1 Hz, on average, in both directions. CONCLUSIONS: Most eye movements during LASIK are slow drifts in fixation. An eye-tracker with a 1.4 Hz closed-loop bandwidth could compensate for most eye movements in conventional or customized ablations.

Calibration↗

PubMed2005

Quantitative detection of HIV-1 RNA using NucliSens EasyQ HIV-1 assay.

HIV-1 RNA viral load has become the major biological marker for disease prognosis and outcome of antiretroviral therapy in the treatment of HIV-infected individuals. The aim of this study was to compare the performance of the new CE marked NucliSens EasyQ HIV-1 assay with NucliSens HIV-1 QT assay (reference method). NucliSens EasyQ HIV-1 (EasyQ) couples nucleic acid sequence-based amplification (NASBA) with real-time detection using molecular beacons utilizing the NucliSens EasyQ analyzer. NASBA is a sensitive, isothermal, transcription-based amplification system designed specifically for the detection of RNA targets. There was significant correlation (r = 0.878, P < 0.0001) between the two different assays in the analysis of clinical samples and the frequency of concordant results (log difference <0.5) was 74%. The two assays detected HIV-1 RNA in 81 specimens, and neither detected (below the lower detection limit, 400 copies/ml for NucliSens HIV-1 QT and 500IU/ml for EasyQ) HIV-1 RNA in 12 specimens. Three clinical specimens had detectable HIV-1 RNA using the EasyQ only, and two specimens had detectable HIV-1 RNA using the NucliSens HIV-1 QT only. The EasyQ procedure can analyze 48 clinical samples within 6h. The coefficient of variation of EasyQ ranged from 3.0 to 9.5% (3% at 4.9 log; 5.7% at 3.7 log; 9.5% at 2.7 log). The new assay is shown to be a rapid, convenient, and reliable procedure for HIV-1 RNA viral load monitoring.

HIV Infections↗

PubMed2005

[Effects of ionic strength on the flocculation and removal of cyanobacterial cells of Microcystis aeruginosa by clays].

The effect of ionic strength on the flocculation and removal of Microcystis aeruginosa by clays and chitosan-modified clays were studied. High ionic strength was beneficial to the removal of algae cells by clays due to the reduction of the thickness of electrical double layer that enhanced the collision probability of the granules. In contrast to normal clays, chitosan-modified clays showed a higher removal efficiency of Microcystis aeruginosa cells under low ionic strength. The removal efficiency was reduced from more than 90% to 70% by sepiolite, but promoted from 70% to 95% by modified sepiolite when the ionic strength decreased from 0.17mol/L to 0 mol/L. This is because the repulsion of positive charged groups in chitosan molecule chain were shielded by large number of ions at higher ionic strength that reduce the extensibility of the chitosan molecule, leading to the reduction of bridging and netting between particles. Chitosan-modified clays were therefore suitable for removal cyanobacterial cells in fresh waters such as lakes, reservoirs and rivers.

Adsorption↗

PubMed2005

[Evaluating the harmfulness of copper in aquatic environment by measuring the supercoiled structure change of plasmid DNA].

The interaction of cupric ions with supercoiled DNA was investigated by agarose gel electrophoresis. Experimental results indicate that cupric ions could convert DNA structure from supercoiled to relaxed forms outside the cells in distilled water medium. At the levels of 10(-3) mol/L and 10(-4) mol/L copper, supercoiled DNA was totally converted into other forms of DNA after 24 hours. At a lower cupric level of 10(-6) mol/L, 52% supercoiled DNA was converted to other forms after 24 h and the relaxed form increased by 17% at 48h. Supercoiled form of DNA relaxed and gradually disappeared with the increase of incubation period of copper ions with the plasmid DNA. Supercoiled DNA degraded into other forms more rapidly at higher copper concentration. The percentages of different forms of DNA were related to copper concentration and incubation time. These results suggested that changes in supercoiled DNA structure may provide a rapid and sensitive method to assess the harmfulness of copper in aquatic environment.

Copper↗

PubMed2004

An efficient method for flow cytometric analysis of pollen and detection of 2n nuclei in Brassica napus pollen.

A simple and reliable method was developed for isolating pollen nuclei from Brassica napus and Triticum aestivum for DNA analysis using flow cytometry. The nuclei were released from pollen by ultrasonic treatment. The isolated nuclei following filtration through nylon mesh and a purification procedure were suitable for flow cytometric analysis as well as for isolating genomic DNA. Ultrasonic treatment time was optimized for B. napus pollen at different developmental stages. The method is effective and suitable for the preparation of many samples. We analyzed the nuclear DNA levels in pollen of B. napus at three major developmental stages as well as in mature wheat pollen. Only a single 1C peak representing the haploid DNA level was detected in the nuclei isolated from Brassica uninucleate microspores as well as in mature Triticum pollen. Interestingly, diploid nuclei were detected in both binucleate and mature pollen of B. napus. The possible origins of the diploid nuclei are discussed.

Brassica napus↗

PubMed2004

EXAFS studies on adsorption-desorption reversibility at manganese oxides-water interfaces. I. Irreversible adsorption of zinc onto manganite (gamma-MnOOH).

Microscopic structures of Zn(II) surface complexes adsorbed at the manganite (gamma-MnOOH)-water interface were studied using extended X-ray absorption fine structure (EXAFS) spectroscopy. Quantitative analysis of the first sphere showed that, in a 0.1 M NaNO(3) solution of pH 7.5, Zn(II) was adsorbed as a mixture of tetrahedral and octahedral structure (ZnO(4,6) polyhedra) and the average Zn-O distance was 2.00+/-0.01 A. EXAFS analysis of the second sphere showed that two typical atomic Zn-Mn distances of 3.07+/-0.01 and 3.52+/-0.02 A existed in the surface complexes, indicating that there were two types of linkage, i.e., the edge-linkage of high affinity and the corner-linkage of low affinity, between the ZnO(4,6) polyhedra and the MnO(6) octahedra of the manganite. Macroscopic adsorption-desorption experiments showed that adsorption of Zn(II) onto manganite was largely irreversible and the stronger edge-linkage mode was found to be responsible for the adsorption irreversibility. This result provided direct evidence from the molecular level for the basic hypothesis of the metastable-equilibrium adsorption (MEA) theory that adsorption density is not a thermodynamic state variable because a given value of adsorption density could have different values of chemical potential, depending on the proportion between the edge and corner linkage modes.

Journal Article↗

PubMed2004

EXAFS studies on adsorption-desorption reversibility at manganese oxide-water interfaces. II. Reversible adsorption of zinc on delta-MnO2.

Microscopic structures of Zn(II) adsorbed at delta-MnO(2)-water interfaces were studied using extended X-ray absorption fine structure (EXAFS) spectroscopy. In a 0.1 M NaNO(3) solution of pH 5.50, hydrous Zn(II) was adsorbed onto the solid surface in the form of octahedral coordination. Adsorbed octahedral Zn(II) was located above and below the vacancy sites of delta-MnO(2). Each Zn was coordinated on one side to H(2)O molecules forming an H(2)O sheet and on the other side to oxygen atoms shared with layer MnO(6) octahedra forming a corner-sharing octahedral interlayer complex. The average Zn-O and Zn-Mn distances were 2.07+/-0.01 and 3.52+/-0.01 A, respectively. Macroscopic adsorption-desorption isotherms showed that, in contrast to that of the Zn-gamma-MnOOH system, adsorption of Zn(II) on delta-MnO(2) was highly reversible. EXAFS results indicated that the highly reversible adsorption was due to the weak adsorption mode of the corner-sharing linkage between the adsorbate and adsorbent polyhedra.

Journal Article↗

PubMed2004

Increase in biodegradation of dimethyl phthalate by Closterium lunula using inorganic carbon.

The effect and mechanism of inorganic carbon (IC) on the biodegradation of dimethyl phthalate (DMP) by a green microalga Closterium lunula was investigated. The growth of this microalga and the biodegradation of DMP were significantly enhanced when the initial IC was increased. An intermediate product of DMP biodegradation was identified as phthalic acid (PA) that was accumulated and caused a sharp decrease in pH of microalgal culture medium, which inhibited both the growth of microalga and the biodegradation of DMP. A suggested second-order kinetic equation of organic pollutant biodegradation by microalgae (-dC/dt = kNr) fitted well with the experimental data. The increase of IC caused a decline in biodegradation rate constant for organic carbon (k) and an increase in growth (N) by supplying a favorite carbon source and mitigating the decrease of pH. As the net effect, the overall biodegradation rate of DMP was promoted as IC increased, which was dominated by the increase of microalgal growth.

Biodegradation, Environmental↗

PubMed2004

Adsorption of zinc on manganite (gamma-MnOOH): particle concentration effect and adsorption reversibility.

The adsorption and desorption processes of Zn(II) on gamma-MnOOH as a function of particle concentrations (Cp) were studied. An obvious Cp effect was observed in this adsorption system. The degree of adsorption hysteresis increased greatly with the increasing of Cp, indicating that the extent of the real metastable-equilibrium states deviating from the ideal equilibrium state was enhanced with the increasing of Cp. The Cp-reversibility relationship confirmed the metastable-equilibrium adsorption (MEA) inequality (Pan, 1998a), which was the core formulation of the MEA theory. Because the MEA inequality was based on the basic hypothesis of MEA theory that adsorption density [see symbol in text] is not a state variable, the Cp-reversibility relationship gave indirect evidence to the basic hypothesis of MEA theory.

Adsorption↗

PubMed2004

A method to extract algae toxin of microcystin-LR.

A simple and low-cost method to obtain cyanobacterial toxin microcystin-LR (MC-LR) was developed. A new strain of Microcystis aeruginosa, named DC-1, producing microcystin-LR but not microcystin-RR, was separated from the field blooming algae samples of Dianchi Lake, in southwest of China. Following three times' freeze and thaw treatment, the cultivated DC-1 cells were extracted with 40% methanol in water. The extract was centrifuged and the supernatant applied to a Hydrophilic-Lipophilic Balance (HLB) SPE cartridge. Eluted impurities with a certain gradient from 30% to 50% methanol in water, MC-LR was finally eluted from the HLB cartridge with 60% methanol in water, and samples containing 3.85% to 14.8% of MC-LR were obtained. These MC-LR samples may be used in adsorption and biodegradation experiments instead of using expensive standard reagents.

Bacterial Toxins↗

PubMed2004

Effects of nitrogen forms on the production of cyanobacterial toxin microcystin-IR by an isolated Microcystis aeruginosa.

A cyanobacterial strain, which produced high content of microcystin-LR (MC-LR) but no microcystin-RR (MC-RR), was isolated from the hypertrophic Dianchi Lake in China and identified as Microcystis aeruginosa DC-1. Effects of nitrogen containing chemicals and trace elements on the growth and the production of MC-LR by this strain were studied. In the presence of bicine, compared with urea and ammonium, nitrate greatly promoted the growth and the production of MC-LR. However, leucine and arginine, which were the constitutional components in the molecular structure of MC-LR or RR, inhibited the production of MC-LR. Iron and silicon up to 10 mg/L had little effects on the growth of M. aeruginosa DC-1, but the production of MC-LR was apparently enhanced. Under all conditions studied here, only MC-LR but no RR was detected within the cells of M. aeruginosa DC-1. Thus, chemical forms of nitrogen, rather than the usually concerned the total nitrogen, and trace elements played important roles in the production of MC toxins during cyanobacterial blooms.

Amino Acids↗

PubMed2004

[Flocculation and removal of water bloom cells Microcystis aeruginosa by chitosan-modified clays].

The kinetics of flocculation and removal of Microcystis aeruginosa by chitosan-modified clays was studied. The efficiency of flocculating and removing of algal cells was greatly improved after the modification of the clays. About 80% of algae cell was removed in 0.5 hour, and 90% in 2 hours, when 11 mg/L modified sepiolite was added. Algae-removal capacities of different clays were all improved to a similar level of >90% at a total loading of 11 mg/L after being modified with chitosan. The efficiency of algae-removing was reduced when the clay loading was larger or smaller than the optimum loading.

Aluminum Silicates↗