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Biomedical subjects

Kun Yang

Publications and source records attributed to Kun Yang.

At least 37 records · Page 2Linked to original sources

Adsorption of polycyclic aromatic hydrocarbons by carbon nanomaterials.

Carbon nanomaterials are novel manufactured materials, having widespread potential applications. Adsorption of hydrophobic organic compounds (HOCs) by carbon nanomaterials may enhance their toxicity and affect the fate, transformation, and transport of HOCs in the environment. In this research, adsorption of naphthalene, phenanthrene, and pyrene onto six carbon nanomaterials, including fullerenes, single-walled carbon nanotubes, and multiwalled carbon nanotubes was investigated, which is the first systematic study on polycyclic aromatic hydrocarbons (PAHs) sorption by various carbon nanomaterials. All adsorption isotherms were nonlinear and were fitted well by the Polanyi-Manes model (PMM). Through both isotherm modeling and constructing "characteristic curve", Polanyi theory was useful to describe the adsorption process of PAHs by the carbon nanomaterials. The three fitted parameters (Q0, a, and b) of PMM depended on both PAH properties and the nature of carbon nanomaterials. For different PAHs, adsorption seems to relate with their molecular size, i.e., the larger the molecular size, the lower the adsorbed volume capacity (Q0), but higher a and b values. For different carbon nanomaterials, adsorption seems to relate with their surface area, micropore volume, and the volume ratios of mesopore to micropore. Quantitative relationships between these sorbent properties and the estimated parameters of PMM were obtained. These relationships may represent a first fundamental step toward establishing empirical equations for quantitative prediction of PAH adsorption by carbon nanomaterials and possibly other forms of carbonaceous (geo-) sorbents, and for evaluating their environmental impact. In addition, high adsorption capacity of PAHs by carbon nanotubes may add to their high environmental risks once released to the environment, and result in potential alteration of PAHs fate and bioavailability in the environment.

Adsorption↗

PSI-DOCK: towards highly efficient and accurate flexible ligand docking.

We have developed a new docking method, Pose-Sensitive Inclined (PSI)-DOCK, for flexible ligand docking. An improved SCORE function has been developed and used in PSI-DOCK for binding free energy evaluation. The improved SCORE function was able to reproduce the absolute binding free energies of a training set of 200 protein-ligand complexes with a correlation coefficient of 0.788 and a standard error of 8.13 kJ/mol. For ligand binding pose exploration, a unique searching strategy was designed in PSI-DOCK. In the first step, a tabu-enhanced genetic algorithm with a rapid shape-complementary scoring function is used to roughly explore and store potential binding poses of the ligand. Then, these predicted binding poses are optimized and compete against each other by using a genetic algorithm with the accurate SCORE function to determine the binding pose with the lowest docking energy. The PSI-DOCK 1.0 program is highly efficient in identifying the experimental binding pose. For a test dataset of 194 complexes, PSI-DOCK 1.0 achieved a 67% success rate (RMSD < 2.0 A) for only one run and a 74% success rate for 10 runs. PSI-DOCK can also predict the docking binding free energy with high accuracy. For a test set of 64 complexes, the correlation between the experimentally observed binding free energies and the docking binding free energies for 64 complexes is r = 0.777 with a standard deviation of 7.96 kJ/mol. Moreover, compared with other docking methods, PSI-DOCK 1.0 is extremely easy to use and requires minimum docking preparations. There is no requirement for the users to add hydrogen atoms to proteins because all protein hydrogen atoms and the flexibility of the terminal protein atoms are intrinsically taken into account in PSI-DOCK. There is also no requirement for the users to calculate partial atomic charges because PSI-DOCK does not calculate an electrostatic energy term. These features are not only convenient for the users but also help to avoid the influence of different preparation methods.

Algorithms↗

SARS coronavirus nucleocapsid immunodominant T-cell epitope cluster is common to both exogenous recombinant and endogenous DNA-encoded immunogens.

Correspondence between the T-cell epitope responses of vaccine immunogens and those of pathogen antigens is critical to vaccine efficacy. In the present study, we analyzed the spectrum of immune responses of mice to three different forms of the SARS coronavirus nucleocapsid (N): (1) exogenous recombinant protein (N-GST) with Freund's adjuvant; (2) DNA encoding unmodified N as an endogenous cytoplasmic protein (pN); and (3) DNA encoding N as a LAMP-1 chimera targeted to the lysosomal MHC II compartment (p-LAMP-N). Lysosomal trafficking of the LAMP/N chimera in transfected cells was documented by both confocal and immunoelectron microscopy. The responses of the immunized mice differed markedly. The strongest T-cell IFN-gamma and CTL responses were to the LAMP-N chimera followed by the pN immunogen. In contrast, N-GST elicited strong T cell IL-4 but minimal IFN-gamma responses and a much greater antibody response. Despite these differences, however, the immunodominant T-cell ELISpot responses to each of the three immunogens were elicited by the same N peptides, with the greatest responses being generated by a cluster of five overlapping peptides, N76-114, each of which contained nonameric H2d binding domains with high binding scores for both class I and, except for N76-93, class II alleles. These results demonstrate that processing and presentation of N, whether exogenously or endogenously derived, resulted in common immunodominant epitopes, supporting the usefulness of modified antigen delivery and trafficking forms and, in particular, LAMP chimeras as vaccine candidates. Nevertheless, the profiles of T-cell responses were distinctly different. The pronounced Th-2 and humoral response to N protein plus adjuvant are in contrast to the balanced IFN-gamma and IL-4 responses and strong memory CTL responses to the LAMP-N chimera.

Amino Acid Sequence↗

Localization of S genes on extended DNA fibers (EDFs) in Brassica oleracea by high-resolution FISH.

The compactness of plant chromosome and the structures of plant cell wall and cytoplasm pose a great resistance to fluorescence in situ hybridization (FISH), and consequently many new methods for improving spatial resolution are being exploited to overcome these problems. However, for plants with small chromosomes like rice and Brassica, there are still many difficulties. In this article a new and effective technique for preparation of extended DNA fibers (EDFs), using a series of treatments to prophase I chromosomes of Brassica oleracea PMCs, is presented. This technique allows longitudinal extension of the chromosomes 30-107 times longer than those of their metaphase counterparts. The length of the extended DNA fibers is between 89 microm and 273 microm, and the space resolution is 42.8-53.0 kb. Stretching ratios were assessed in a number of FISH experiments with super-stretched chromosomes from meiotic prophase I nuclei of B. olerecea. Through FISH to EDFs of pachytene chromosomes hybridized in situ with SRK (S-locus receptor kinase) and SPII (S-locus protein II) probes, for the first time we localized the accurate positions of S-locus and quantitatively analyzed the features of S genes in B. oleracea genome to show all S genes were single-copied. In addition, the length between two linked genes was measured to be about one micron. As a result, the highest space resolution which was about 4 kb was obtained.

Brassica↗

Crystal structure of a type III pantothenate kinase: insight into the mechanism of an essential coenzyme A biosynthetic enzyme universally distributed in bacteria.

Pantothenate kinase (PanK) catalyzes the first step in the five-step universal pathway of coenzyme A (CoA) biosynthesis, a key transformation that generally also regulates the intracellular concentration of CoA through feedback inhibition. A novel PanK protein encoded by the gene coaX was recently identified that is distinct from the previously characterized type I PanK (exemplified by the Escherichia coli coaA-encoded PanK protein) and type II eukaryotic PanKs and is not inhibited by CoA or its thioesters. This type III PanK, or PanK-III, is widely distributed in the bacterial kingdom and accounts for the only known PanK in many pathogenic species, such as Helicobacter pylori, Bordetella pertussis, and Pseudomonas aeruginosa. Here we report the first crystal structure of a type III PanK, the enzyme from Thermotoga maritima (PanK(Tm)), solved at 2.0-A resolution. The structure of PanK(Tm) reveals that type III PanKs belong to the acetate and sugar kinase/heat shock protein 70/actin (ASKHA) protein superfamily and that they retain the highly conserved active site motifs common to all members of this superfamily. Comparative structural analysis of the PanK(Tm) active site configuration and mutagenesis of three highly conserved active site aspartates identify these residues as critical for PanK-III catalysis. Furthermore, the analysis also provides an explanation for the lack of CoA feedback inhibition by the enzyme. Since PanK-III adopts a different structural fold from that of the E. coli PanK -- which is a member of the "P-loop kinase"superfamily -- this finding represents yet another example of convergent evolution of the same biological function from a different protein ancestor.

Amino Acid Sequence↗

[Predation and dispersal of Lithocarpus glaber seeds by rodents in Tiantong National Forest Park, Zhejiang Province].

This paper studied the predation and dispersal of Lithocarps glaber seeds by rodents in the Tiantong National Forest Park (29 degrees 48'N, 121 degrees 47'E) of Ningbo City, Zhejiang Province. Five seeds release transects (three in evergreen broad-leaved forest, one in Pinus messoniana forest, and one in shrub), and two seeds release states (covered/uncovered and tagged/untagged) were set up. Iron snare traps were baited to determine the effects of rodents on seeds disappearance. The results showed that two species of rodents, Niviventer confucianus and N. fulvescensi, were the potential predators and dispersers of the seeds. The lost seeds labeled with small piece of tintags could be classified into three categories, i. e., 1) seeds consumed by rodents, with tags stuck seed fragments; 2) seeds cut off from tags, with tags kept only; and 3) both seeds and tags disappeared. The loss rate of seeds was high at the beginning of the observation, and then decreased gradually. The daily seeds disappearance rate (DS-DR) was variable in different habitats, with the highest (1.03%) in evergreen broad-leaved forest and the lowest (0.32%) in shrub. The proportion of these three categories was different, and related with habitat types. The difference of DSDR between covered and uncovered states was statistically significant (P < 0.05), with a higher DSDR under uncovered state. No significant difference was observed between the DSDR of tagged and untagged. The distance of seeds dispersal by rodents was within 6.7 m.

Animals↗

[Establishment of chemiluminescence immunoassay for detecting Staphylococcal enterotoxin B and C1].

AIM: To establish chemiluminescence immunoassay (CLIA) for detecting staphylococcal enterotoxin B (SEB) and C1 (SEC1) and compare its sensitivity and stability with ELISA. METHODS: The anti-SEB and SEC1 monoclonal antibodies (mAb) were purified by Q Sepharose Fast Flow chromatographic column. The alkaline phosphatase (AP) conjugated mAbs FMMU-SEB.D6 and FMMU-SEC1.C4 were used as detecting antibodies and the FMMU-SEB.B4 and FMMU-SEC1.G8 mAbs were used as coating antibodies in both methods. Phenolphthalein monophosphate (PMP) and lumigen APS-5 were employed as substrates for AP in ELISA and CLIA, respectively. The light was detected and measured by the GENios analyzer (TECAN Group Ltd.). The sensitivities and detect ranges of CLIA and ELISA methods were compared. RESULTS: Compared with ELISA, CLIA was more sensitive (0.1 ng/mL vs 0.39 ng/mL) and timesaving. Furthermore, the liner range of CLIA was broader than that of ELISA (0.78-50 ng/mL vs 3.125-50 ng/mL). CONCLUSION: CLIA for detecting SEB and SEC1 are established successfully which may be useful in food monitoring, epidemiology survey and detecting SE contaminated samples in environment.

Animals↗

[Forest biomass carbon storage and its dynamics in Tanjiang River basin].

Based on an improved estimation method of forest carbon storage and the inventory of forest resources, this paper estimated the forest carbon storage and its dynamic changes in Tanjiang River basin, and analyzed the relationships of the carbon storage and its density with the increase of population density and GDP during the urbanization in 1990-2001. The results showed that the forest carbon storage in Tanjiang River basin increased from 5.906 x 10(6) t in 1990 to 7.852 x 10(6) t in 2001, with an annual average accumulation amount of 0.18 x 10(6) t or an annual average accumulation rate of 3.05%, and playing a role of carbon sink. The rapid increase of population density and GDP didn't influence the increase of forest carbon storage and density, but the development of forestry was far lower than that of economy. To have a better service function of forest ecosystem in the process of urbanization, and to promote the sustainable development of regional ecological environment, the key point is the reasonable coordination of forestry management with the development of economy.

Biomass↗

Septicemia without sepsis: inherited disorders of nuclear factor-kappa B-mediated inflammation.

Septicemia is a life-threatening condition that may lead to sepsis and even septic shock. This cascade is usually accompanied by a pronounced inflammatory response, leading to high body temperature and elevated levels of laboratory markers of inflammation. However, this response can be significantly diminished in children with inherited disorders of nuclear factor (NF)-kappa B-mediated immunity. Three disease-causing genes involved in NF-kappa B activation have been identified: NEMO, IKBA, and IRAK4. Patients with anhidrotic ectodermal dysplasia and immunodeficiency, which is caused by mutations in NEMO and IKBA, have sparse hair, dry skin, and conical teeth and are at increased risk of severe infections caused by pyogenic bacteria and atypical mycobacteria. Patients with interleukin-1 receptor-associated kinase-4 deficiency are at increased risk of invasive disease due to pyogenic bacteria. An underlying defect in NF- kappa B activation should be suspected in children with bacterial septicemia accompanied by mild signs of inflammation.

Ectodermal Dysplasia↗

Minimizing losses of nonionic and anionic surfactants to a montmorillonite saturated with calcium using their mixtures.

Losses of surfactants through sorption to soils/sediments, especially to clay minerals, by various chemical interactions such as sorption and precipitation threaten the success of surfactant in enhancing remediation of contaminated soil and groundwater. In this study, the behavior of mixtures of a nonionic surfactant (TX-100) and an anionic surfactant (SDBS) sorbed to a montmorillonite saturated with calcium (Ca-montmorillonite) was investigated, and compared with that of individual surfactants. It is shown that the amounts of both TX-100 and SDBS sorbed to Ca-montmorillonite are significant. However, the amount of either TX-100 or SDBS sorbed can be decreased and minimized when they are mixed with each other. Mixed micelle formation, which causes negative deviation of critical micelle concentrations (CMCs) from the ideal, is responsible for the decrease in sorbed TX-100 and sorbed SDBS in their mixtures. Because of their ability to minimize their amounts sorbed and thus enhance their active concentrations, as observed in mixed TX-100 and SDBS systems, mixed anionic-nonionic surfactants exhibit potential advantages in the area of enhanced soil and groundwater remediation.

Adsorption↗

Solubilization of DNAPLs by mixed surfactant: reduction in partitioning losses of nonionic surfactant.

Efforts to remediate the dense nonaqueous phase liquids (DNAPLs) by mobilizing them face with risks of driving the contaminants deeper into aquifer zones. This spurs research for modifying the approach for in situ remediation. In this paper, a novel solubilization of DNAPLs by mixed nonionic and anionic surfactant, Triton X-100 (TX100) and sodium dodecylbenzene sulfonate (SDBS), was presented and compared with those by single ones. Given 1:40 phase ratio of DNAPL:water (v/v) and the total surfactant concentration from 0.2 to 10gl(-1), mixed TX100-SDBS at the total mass ratios of 3:1, 1:1 and 1:3 exhibited significant solubilization for the DNAPLs, trichloroethene (TCE), chlorobenzene (CB) and 1,2-dichlorobenzene (1,2-DCB). The solubilization extent by mixed TX100-SDBS was much larger than by single TX100 and even larger than by single SDBS at the ratios of 1:1 and 1:3, respectively. TX100 partitioning into the organic phase dictated the solubilization extent. The TX100 losses into TCE, CB and 1,2-DCB phases were more than 99%, 97% and 97% when single TX100 was used. With SDBS alone, no SDBS partitioned into DNAPLs was observed and in mixed systems, SDBS decreased greatly the partition loss of TX100 into DNAPLs. The extent of TX100 partition decreased with increasing the amount of SDBS. The mechanism for reduction of TX100 partition was discussed. TX100 and SDBS formed mixed micelles in the solution phase. The inability of SDBS to partition into DNAPLs and the mutual affinity of SDBS and TX100 in the mixed micelle controlled the partitioning of TX100 into DNAPL phase. The work presented here demonstrates that mixed nonionic-anionic surfactants would be preferred over single surfactants for solubilization remediation of DNAPLs, which could avoid risks of driving the contaminants deeper into aquifers and decrease the surfactant loss and remediation cost.

Benzenesulfonates↗

Gains of glycosylation comprise an unexpectedly large group of pathogenic mutations.

Mutations involving gains of glycosylation have been considered rare, and the pathogenic role of the new carbohydrate chains has never been formally established. We identified three children with mendelian susceptibility to mycobacterial disease who were homozygous with respect to a missense mutation in IFNGR2 creating a new N-glycosylation site in the IFNgammaR2 chain. The resulting additional carbohydrate moiety was both necessary and sufficient to abolish the cellular response to IFNgamma. We then searched the Human Gene Mutation Database for potential gain-of-N-glycosylation missense mutations; of 10,047 mutations in 577 genes encoding proteins trafficked through the secretory pathway, we identified 142 candidate mutations ( approximately 1.4%) in 77 genes ( approximately 13.3%). Six mutant proteins bore new N-linked carbohydrate moieties. Thus, an unexpectedly high proportion of mutations that cause human genetic disease might lead to the creation of new N-glycosylation sites. Their pathogenic effects may be a direct consequence of the addition of N-linked carbohydrate.

Anti-Bacterial Agents↗

Correlations of nonlinear sorption of organic solutes with soil/sediment physicochemical properties.

The estimation of solute sorptive behaviors is essential when direct sorption data are unavailable and will provide a convenient way to assess the fate and the biological activity of organic solutes in soil/sediment environments. In this study, the sorption of 2,4-dichlorophenol (2,4-DCP) on 19 soil/sediment samples and the sorption of 13 organic solutes on one sediment were investigated. All sorption isotherms are nonlinear and can be described satisfactorily by a simple dual-mode model (DMM): q(e)=KpCe+Q0 . bCe/(1+bCe), where Kp (mlg(-1)) is the partition coefficient; Ce (microgml(-1)) is the equilibrium concentration; Q0 (microgg(-1)) is the maximum adsorption capacity; Q0 . b (mlg(-1)) is the Langmuir-type isotherm slope in the low concentration (Henry's law) range and b (mlmicrog(-1)) is a constant related to the affinity of the surface for the solute. Based on these nonlinear sorption isotherms and similar other nonlinear isotherms, it is observed that, for both polar 2,4-DCP and nonpolar phenanthrene, Kp, Q0 and Q0 . b are linearly correlated with soil/sediment organic carbon content (f(oc) in the range of 0.118-53.7%). The results indicate that the nonlinear sorption of organic solutes results primarily from interactions with soil/sediment organic matter. The K*oc K*oc=Kp/f(oc)), Qoc (Qoc=Q0/f(oc)), Loc (Loc=Q0 . b/f(oc)) and b for a given organic solute with different soils/sediments are largely invariant. Furthermore, logK*oc, logb and logLoc for various organic solutes are correlated significantly with the solute logKow or logSw (logKow in the range of 0.9 to 5.13 and logSw in the range of -6.176 to -0.070). A fundamental empirical equation was then established to calculate approximately the nonlinear sorption from soil/sediment f(oc) and solute Sw for a given solute equilibrium concentration.

Adsorption↗

Human TLR-7-, -8-, and -9-mediated induction of IFN-alpha/beta and -lambda Is IRAK-4 dependent and redundant for protective immunity to viruses.

Five TLRs are thought to play an important role in antiviral immunity, sensing viral products and inducing IFN-alpha/beta and -lambda. Surprisingly, patients with a defect of IRAK-4, a critical kinase downstream from TLRs, are resistant to common viruses. We show here that IFN-alpha/beta and -lambda induction via TLR-7, TLR-8, and TLR-9 was abolished in IRAK-4-deficient blood cells. In contrast, IFN-alpha/beta and -lambda were induced normally by TLR-3 and TLR-4 agonists. Moreover, IFN-beta and -lambda were normally induced by TLR-3 agonists and viruses in IRAK-4-deficient fibroblasts. We further show that IFN-alpha/beta and -lambda production in response to 9 of 11 viruses tested was normal or weakly affected in IRAK-4-deficient blood cells. Thus, IRAK-4-deficient patients may control viral infections by TLR-3- and TLR-4-dependent and/or TLR-independent production of IFNs. The TLR-7-, TLR-8-, and TLR-9-dependent induction of IFN-alpha/beta and -lambda is strictly IRAK-4 dependent and paradoxically redundant for protective immunity to most viruses in humans.

Fibroblasts↗

Inherited disorders of human Toll-like receptor signaling: immunological implications.

In vitro nine of 10 known human Toll-like receptors (TLRs) are engaged by well-defined chemical agonists that mimic microbial compounds, raising the possibility that human TLRs play a critical role in protective immunity in vivo. We thus review here the recently described human primary immunodeficiencies caused by germline mutations in genes encoding molecules involved in cell signaling downstream from TLRs. Subjects with anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID) carry either X-linked recessive hypomorphic mutations in NEMO or autosomal dominant hypermorphic mutations in IKBA. Their cells show a broad defect in nuclear factor-kappaB (NF-kappaB) activation, with an impaired, but not abolished response to a large variety of stimuli including TLR agonists. EDA-ID patients show developmental anomalies of skin appendages and a broad spectrum of infectious diseases. Patients with autosomal recessive amorphic mutations in IRAK4 present a purely immunological syndrome and more restricted defects, with specific impairment of the Toll and interleukin-1 receptor (TIR)-interleukin-1 receptor-associated kinase (IRAK) signaling pathway. In these subjects, the NF-kappaB- and mitogen-activated protein kinase-mediated induction of inflammatory cytokines in response to TIR agonists is impaired. The patients present a narrow range of pyogenic bacterial infections that become increasingly rare with age. Altogether, these data suggest that human TLRs play a critical role in host defense. However, they do not provide compelling evidence, as even the infectious phenotype of patients with mutations in IRAK4 may result from impaired signaling via receptors other than TLRs. Paradoxically, these experiments of nature raise the possibility that the entire set of human TLRs is largely redundant in protective immunity in vivo.

Animals↗

Heritable defects of the human TLR signalling pathways.

Recently, three human primary immunodeficiencies associated with impaired TLR signalling were described. Anhidrotic ectodermal dysplasia with immunodeficiency (EDA-ID), either X-linked recessive or autosomal dominant, is caused by hypomorphic mutations in NEMO or hypermorphic mutation in IKBA, respectively, both involved in nuclear factor-kappaB (NF-kappaB) activation. These patients present with abnormal development of ectoderm-derived structures and suffer from a broad spectrum of infectious diseases. In vitro studies of the patients' cells showed an impaired, but not abolished, NF-kappaB activation in response to a large set of stimuli, including TLR agonists. More recently, patients with autosomal recessive amorphic mutations in IRAK4 have been reported, presenting no developmental defect and a more restricted spectrum of infectious diseases, mostly caused by pyogenic encapsulated bacteria, principally, but not exclusively Gram-positive. In vitro studies carried out with these patients' cells showed a specific impairment of the Toll-interleukin-1 receptor (TIR)-interleukin-1 receptor associated kinase (IRAK) signalling pathway. NF-kappaB- and mitogen activated protein kinase (MAPK) pathways are impaired in response to all TIR agonists tested. These data, therefore, suggest that TLRs play a critical role in host defence against pyogenic bacteria, but may be dispensable or redundant for immunity to most other infectious agents in humans.

Ectodermal Dysplasia↗

[Biocompatibility of polyester net in the cornea of rabbits].

OBJECTIVE: To explore biocompatibility and biohealing characteristics of a polyester net with cornea after the net implanted into the cornea lamina. METHODS: Twenty New Zealand rabbits weighing 2.0 - 2.5 kg were randomly divided into experimental and control group. Surgery was performed in right eye of all these animals and the left one as control. A square of implant of 5 - 6 mm in diameter was cut from polyester net (0.2 mm in thickness and 1 mm pore diameter) and implanted into the cornea lamina of experimental group; only a sack was made without implantation in control group. Cornea edema and growth status of new blood vessels were observed at scheduled times after operation; animals were sacrificed 2 weeks, 1, 3, 5 and 8 months after operation and their cornea was removed and examined under light microscopy. RESULTS: Different degrees of cornea edema and new vessels were revealed after surgery. The edema and neovascularization were all automatically disappeared in the period of post-operation or after suture removed. The implant was stable inside the cornea and lasted as longest as 8 months. The number of fibroblasts was markedly increased at the upper and bottom surface of the cornea lamina close to the implant and in the area of net pore particularly. And finally, a close connection of collagen fibers was formed. No serious complications such as necrosis, ulcer, as well as implant dislocation from cornea were seen. CONCLUSION: The polyester net possesses a well biocompatibility with the cornea tissue.

Animals↗