Biomedical subjects

Yong Ran

Publications and source records attributed to Yong Ran.

11 recordsLinked to original sources

PubMed2006

Predicting organic contaminant concentrations in sediment porewater using solid-phase microextraction.

Because of its cost and time saving features, solid-phase microextraction (SPME) is a leading candidate as a biomimic technique in assessing the bioavailable fraction of hydrophobic organic contaminants (HOCs) in sediment porewater. However, no predictive modeling framework in which to systematically address the effect of key parameters on SPME performance for this application exists. In this study, we derived two governing equations to predict (1) the minimum sediment volume (V(s)min) required to achieve non-depletive conditions, and (2) dissolved phase HOC porewater concentrations (C(pw)) as functions of HOC- and sediment specific characteristics in a conceptual three compartment system. The resulting model predicted that V(s)min was independent of HOC concentrations both in sediment and porewater, but did vary with hydrophobicity (characterized by logK(ow)), the fraction of sediment porewater (f(pw)), and the volume (V(f)) of the SPME sorbent phase. Moreover, the effects of these parameters were minimized (i.e., V(s)min reached plateaus) as logK(ow) approached 4-5. Model predictions of C(pw), a surrogate for SPME-based detection limits in porewater, decreased with increasing sediment volume (V(s)) at low V(s) values, but rapidly leveled off as V(s) increased. A third result suggested that the sediment HOC concentration required for SPME is completely independent of K(ow). These results suggest that relatively small sediment volumes participate in exchange equilibria among sediment, porewater and the SPME fiber, and that large sediment HOC reservoirs are not needed to improve the detection sensitivity of SPME-based porewater samplers. The ultimate utility of this modeling framework will be to assist future experimental designs and help predict in situ bioavailability of sediment-associated HOCs.

Algorithms↗

PubMed2006

Concentration levels, compositional profiles, and gas-particle partitioning of polybrominated diphenyl ethers in the atmosphere of an urban city in South China.

Air samples were collected in June of 2004 from four sites in the city of Guangzhou, a typical urban center in South China, to determine the levels, compositional profiles, and gas-particle distribution of 11 polybrominated diphenyl ether (PBDE) congeners (BDE-28, -47, -66, -100, -99, -85, -154, -153, -138, -183, and -209). The arithmetic mean atmospheric concentrations of sigmaPBDEs (sum of all target PBDE congeners except for BDE-209) in samples from the urban and city background sites were comparable to or slightly higher than those from other places around the world. The arithmetic mean atmospheric concentrations of BDE-209, however, were higherthan those in North America and Europe, and similar to the values from Japan. Congener compositions were dominated by BDE-209 in all (>70%) but an industrial site, with an average abundance of 48% for BDE-209. The PBDE patterns were generally similar to that in the technical penta-BDE mixture, Bromkal 70-5DE. Partitioning of PBDEs between the gas and particle phases (Kp) was well correlated with the subcooled liquid vapor pressure (PLO) for all of the samples, but the relationship differed between samples from different sites. The measured fractions of PBDEs in the particulate phase were compared to the predictions from the Junge-Pankow adsorption and KOA-based absorption models. The results indicated that the KOA-based model worked better than the Junge-Pankow model that tended to overestimate the particulate fractions for most PBDE congeners.

Adsorption↗

PubMed2005

Sorption kinetics of organic contaminants by sandy aquifer and its kerogen isolate.

Long-term sorption behaviors of phenanthrene (Phen) on the Borden sand from 1 min to 365 days and of Phen and 1,2-dichlorobenzene (DCB) on the isolated kerogen from 1 to 120 days were characterized by examining the time dependence of solute phase distribution relationships (PDRs) and compared with the prior reported sorption of tetrachlorobenzene (TeCB) and tetrachloroethene (PCE) on the pulverized and/or acid-treated bulk sand and size fractions. The sorption kinetics for Phen on the bulk sand and its kerogen isolate can well be described by the fractional power kinetics equation (q(e) = kt(b)). The similar rate parameter b for q(e)(t) vs t at 5-7 levels of initial concentrations of Phen on the two sorbents, respectively, ranging from 0.077 to 0.099 and from 0.072 to 0.086, indicates the similar sorption kinetics rate. The modified-Freundlich parameters of TeCB on the pulverized or acid-treated 0.3-mm size fraction match those of Phen on the isolated kerogen, suggesting the same natural organic matter (NOM) property of the two sorbents. As the prior investigation underestimated the Koc value for the TeCB sorption on the acid-treated 0.3-mm size fraction by a factor of 1.76, the estimated time to reach 95% of sorption equilibrium is much longer than the prior estimation (over 10 years vs about 2.5 years). The estimated times to reach 95% of sorption equilibrium at three levels of relative solubility for Phen on the bulk sand and its isolated kerogen are, respectively, longer than one decade, demonstrating the similar diffusion length for Phen on the two sorbents. The observed slow sorption kinetics is related to nanometer-pore diffusion within kerogen matrix. The investigation supplies new clues for explaining the often observed much longer persistence of organic contaminants in soils and sediments than the prediction based on the short-term laboratory experiment.

Adsorption↗

PubMed2005

Contents and sources of polycyclic aromatic hydrocarbons and organochlorine pesticides in vegetable soils of Guangzhou, China.

We investigated contents, distribution and possible sources of PAHs and organochlorine pesticides (Ops) in 43 surface and subsurface soils around the urban Guangzhou where variable kinds of vegetables are grown. The results indicate that the contents of PAHs (16 US EPA priority PAHs) range from 42 to 3077 microg/kg and the pollution extent is classified as a moderate level in comparison with other investigations and soil quality standards. The ratios of methylphenanthrenes to phenanthrene(MP/P), anthracene to anthracene plus phenanthrene (An/178), benz[a]anthracene to benz[a]anthracene plus chrysene (BaA/228), indeno[1,2,3-cd]pyrene to indeno[1,2,3-cd]pyrene plus benzo[ghi]perylene (In/In+BP) suggest that the sources of PAHs in the soil samples are mixed with a dominant contribution from petroleum and combustion of fossil fuel. The correlation analysis shows that the PAHs contents are significantly related to total organic carbon contents (TOC) (R2=0.75) and black carbon contents (BC) (R2=0.62) in the soil samples. Dichlorodiphenyltrichloroethane and metabolites (DDTs) and hexachlorocyclohexanes and metabolites (HCHs) account largely for the contaminants of OPs. The concentrations of DDTs range from 3.58 to 831 microg/kg and the ratios for DDT/(DDD+DDE) are higher than 2 in some soil samples, suggesting that DDT contamination still exists and may be caused by its persistence in soils and/or impurity in the pesticide dicofol. The concentrations of HCHs are 0.19-42.3 microg/kg.

Carbon↗

PubMed2004

Photochromic biliproteins from the cyanobacterium Anabaena sp. PCC 7120: lyase activities, chromophore exchange, and photochromism in phytochrome AphA.

Photochromic biliproteins can be switched by light between two states, initiated by Z/E photoisomerization of the linear tetrapyrrole chromophore. The cyanobacterium Anabaena sp. PCC 7120 contains three genes coding for such biliproteins, two coding for phytochromes (aphA/B) and one for the alpha subunit of phycoerythrocyanin (pecA). (a) aphA was overexpressed in Escherichia coli with N-terminal His and S tags, and the protein was reconstituted by an optimized protocol with phycocyanobilin (PCB), to yield the photochromic chromoprotein, PCB-AphA, carrying the PCB chromophore. (b) AphA chromophorylation is autocatalytic such as in other phytochromes. (c) AphA chromophorylation is also possible by chromophore transfer from the PCB-carrying biliprotein, phycocyanin (CPC). The autocatalytic transfer is very slow, and it is enhanced more than 100-fold by catalysis of PCB:CpcA lyase and alpha-CPC as donor. (d) Through deletion mutations of aphA, a short sequence IQPHGV [amino acids (aa) 26-31] was found essential for the lyase activity of AphA, indicating an interaction of the N terminus with the chromophore-binding domain around cysteine 259. (e) A motif of at least 23 aa, starting with this sequence and located approximately 250 aa N terminal of the chromophore-binding cysteine, is proposed to relate to the lyase function in plant and most prokaryotic phytochromes. (f) Long-range interactions in AphA are further supported by blue-shifted absorptions (<or=12 nm) of both the Pr and Pfr forms of truncated chromoproteins.

Amino Acid Motifs↗

PubMed2004

Importance of adsorption (hole-filling) mechanism for hydrophobic organic contaminants on an aquifer kerogen isolate.

Sorption and desorption behaviors of four hydrophobic organic compounds (HOCs) were investigated for an isolated kerogen material from Borden aquifer material with total organic carbon of 0.021%. The solubility-normalized modified Freundlich equation and the combined linear and Polanyi-Dubinin (PD) equation can quite well describe the sorption or desorption isotherms. The partition component is estimated and compared using desorption data, dual-mode modeling, and the reported partition coefficients. The result suggests that the dual-mode modeling and the combined linear and PD modeling may overestimate the partitioning component. The partition component is not so important as assumed before in sorption of HOCs for the studied sorbent. As the fitted PD equation has an exponent parameter b' approaching 1, it is equivalent to the modified Freundlich equation. The small molecules 1,2-dichlorobenzene (DCB) and naphthalene (Naph) have higher adsorption volumes. The lower adsorption volumes for 1,3,5-trichlorobenzene (TCB) and phenanthrene (Phen) suggest that accessibility to the holes of kerogen by large HOC molecules is reduced. The desorption hysteresis is approximately constant for DCB when the relative aqueous concentration ranges from 0.0007 to 0.6, but for Phen is only obvious at higher relative aqueous concentrations. The varied sorption and desorption behaviors for DCB and Phen are satisfactorily explained by an adsorption/ hole filling mechanism and entrapment of some adsorbates in the kerogen matrix and by possible pore deformation mechanism at high concentrations.

Adsorption↗

PubMed2004

[Study on the reconstitution in vitro and photochemical activities of phytochrome from the Synechocystis sp. PCC6803].

Genomic DNA sequence analysis of phytochrome like photoreceptors in a number of bacteria revealed several open reading frames (ORFs) encoding proteins with amino acid sequences homologous to plant phytochromes. The phytochrome like photoreceptors, collectively called bacteriophytochromes, contain an N-terminal domain homologous to the chromophore-binding domain (CBD) of higher plants and a C-terminal domain of histidine kinase domain( HKD). Due to their simple structure, bacteriophytochromes broaden the view of phytochrome evolution and provide us with a simple model to investigate phytochrome-mediated light signal in higher plants. In this report, the bacteriophytochromes from Synechocystis sp. PCC6803 were investigated. The gene cph1 and its fragment cph1 (C-435) were isolated from the Synechocystis sp. PCC6803 genomic DNA by polymerase chain reaction(PCR) using specific primers. Then, the genes were cloned with the vector pBluescript, yielding plasmids pBlu-cphl and pBlu-cph1 ( C-435), before they are subcloned with the vector pET30, using the EcoRV and Xho I restriction sites. pBlu-cph1, pBlu-cph1 (N-435) were cleaved with Sma I and Xho I, and the released genes were ligated to the pET30a fragment. The E. coli [strain BL21 (DE3)] cells containing recombinant pET30a were grown in medium RB at 20 degrees C, and harvested 6 h later after induction with isopropyl thio-beta-D-galactoside (IPTG). Then, reconstitution systems were employed to study the characteristics of the genes. In the reconstitution system, autoassembly of aprotein of phytochrome with PCB was investigated. The chromophore addition was an autocatalytic process. Reconstitution products were red/infrared (R/FR) photochromic, which was similar to that of the phytoehrome in higher plants. How ever, the spectral change ratios (deltaAmax/deltaAmin) of the two fragments differed from each other. It was also shown that PCB was covalently bound to apo-protein via Zn2+ fluoresc ence SDS-PAGE. After irradiation by light of 700 nm, the maximum absorption spectrum o f holo-Cphl was 650nm. The absorption of it after denaturatior in the dark with ur ea in the presence of hydrochloric acid (pH = 2) was 660nm, which was similar with th at of cis-PCB. In addition, after irradiation by light of 650nm, the maximum absorption spectrum of holo-Cph1 was 700nm. The absorption of it after denaturation in the dark with urea in the presence of hydrochloric acid (pH = 2) was 600nm, which was similar with that of trans-PCB. The result showed that the photochromism of phytochrome resulted from the isomerizaation of chromophore (PCB in this report). The reconstitution of Cph1 (C-435) under the same condition supported the conclusion. Fluorescence emission spectrum of the products suggested that bacteriophytochrom e structure with cis-PCB was more stable than that with trans-PCB. The new reconstitution system in this report sets a base for the application of phytochrome as photochromic biomaterials in biosensors. In addition, phytochrome shows great potential in food, cosmetic and biological engineering, etc.

Bacterial Proteins↗

PubMed2003

Sorption and desorption hysteresis of organic contaminants by kerogen in a sandy aquifer material.

Sorption and desorption hysteresis of 1,2-dichlorobenzene, 1,3,5-trichlorobenzene, naphthalene, and phenanthrene were investigated for the Borden aquifer material with total organic carbon of 0.021% and the isolated natural organic matter (NOM). The isolated NOM is a kerogen type of organic matter with relatively low maturation degree and contained many different types of organic matters including vitrinite particles. The modified Freundlich sorption capacities (logK(')(f) and logK(')(foc)) are very close for the sorption of the four solutes by the isolated NOM and the original sand, respectively. Isotherm non-linearity (n value) and hysteric behaviors are related to solute molecular properties (e.g. K(ow) and molecular size). Kerogen encapsulated by inorganic matrices in the original aquifer may not be accessed fully by solutes. The larger the hydrophobic organic chemical (HOC) (hydrophobic organic contaminant) molecule is, the lower accessibility of the HOC to kerogen. This study disputes widely held hypothesis that sorption to mineral surfaces may play a major role in the overall sorption by low TOC (e.g. 0.1% by mass) geomaterials such as Borden sand. It also demonstrates the importance of the condensed NOM domain, even at very low contents, in the sorption and desorption hysteresis of HOCs in groundwater systems.

Adsorption↗

PubMed2002

[Effect on trihalomethane forming for different molecular weight dissolved organic matter in water resource].

A raw water sample was collected from Guangzhou section of Pearl River to support experiment studies. The sample were passed through Amicon YC-05, YM-1, YM-3, YM-10, YM-30, YM-100 and ZM-500 series membranes after being pretreated. The molecular weight distribution of the isolate for each membranes were analyzed, and the isolates were disinfected by chlorine and chlorine dioxide. The results showed that the RO isolate was the main dissolved organic matter (DOM) in the water sample, which proved that the water was highly contaminated by human activities, and it was the main THMs precursor in the disinfection process with chlorine and chlorine dioxide for all the isolates. Meanwhile, the disinfection process for water sample contain DOM that its molecular smaller than 500 were very different from raw water.

Disinfection↗

PubMedDate not supplied

The role of condensed organic matter in the nonlinear sorption of hydrophobic organic contaminants by a peat and sediments.

This study examines the effect of soil organic matter heterogeneity on equilibrium sorption and desorption of phenanthrene, naphthalene, 1,3,5-trichlorobenzene (1,3,5-TCB), and 1,2-dichlorobenzene (1,2-DCB) by soils and sediments. Two estuary sediments, a Pahokee peat (PP; Euic, hyperthermic Lithic Haplosaprist), and two subsamples (base- and acid-treated peat [TP] and acid-treated peat [FP]) of the peat were used as the sorbents. The contents of black carbon particles were quantified with a chemical extraction method. Petrographical examinations revealed the presence of the condensed soil and sediment organic matter (SOM) in Pahokee peat. The Freundlich isotherm model in two different forms was used to fit both sorption and desorption data. The results show that the sorption and desorption isotherms are generally nonlinear and that the apparent sorption-desorption hysteresis is present for phenanthrene and TCB. Detailed analysis of sorption data for the tested sorbent-sorbate systems indicates that black carbon is probably responsible for sorption isotherm nonlinearity for the two sediments, whereas the humic substances and kerogen may play the dominant role in nonlinear sorption by the peat. This investigation suggests that the microporosity of SOM is important for the hydrophobic organic contaminant (HOC) sorption capacity on the peat.

Adsorption↗

PubMedDate not supplied

Kerogen in aquifer material and its strong sorption for nonionic organic pollutants.

Sorption of organic pollutants by subsurface materials has been found to not only correlate with the total organic carbon (TOC) content, but also depend on the types of soil and sediment organic matter (SOM). Characterization of geochemically heterogeneous SOM is key to elucidating sorption mechanisms and predicting pollutant transport in ground water systems. In this study, kerogen, a nonextractable organic material, was isolated with an acid demineralization procedure from a sandy aquifer material (Borden, Ontario, Canada) having a TOC content of approximately 0.021% (w/w). Petrographical examinations reveal that the kerogen has three major types of macerals including bituminite (Kerogen Type I and II), vitrinite (Type III), and fusinite (Type IV or charred kerogen). The solid-state 13C nuclear magnetic resonance (NMR) spectrum shows two dominant peaks, aliphatic and aromatic carbons, for the isolated material. Sorption isotherms measured using phenanthrene, naphthalene, 1,3,5-trichlorobenzene (TCB), and 1,2-dichlorobenzene (DCB) as sorbates showed that both the isolated kerogen and the original sand exhibited nonlinear sorption and that the phenanthrene and TCB isotherms measured for the kerogen material are more nonlinear than the respective isotherms for the original sand. The single-point organic carbon--normalized sorption capacity measured for the isolated kerogen can be several times greater than that measured for the original sand for a given sorbate. The study suggests that kerogen plays a major role in overall sorption isotherm nonlinearity and could yield higher-than-predicted sorption capacities for the subsurface material even though the content of this organic material is very low.

Adsorption↗