Parafilm® M and Strat-M® as skin simulants in in vitro permeation of dissolving microarray patches loaded with proteins

In vitro permeation studies play a crucial role in early formulation optimisation before extensive animal model investigations. Biological membranes are typically used in these studies to mimic human skin conditions accurately. However, when focusing on protein and peptide transdermal delivery, utilising biological membranes can complicate analysis and quantification processes. This study aims to explore Parafilm®M and Strat-M® as alternatives to dermatomed porcine skin for evaluating protein delivery from dissolving microarray patch (MAP) platforms. Initially, various MAPs loaded with different model proteins (ovalbumin, bovine serum albumin and amniotic mesenchymal stem cell metabolite products) were prepared. These dissolving MAPs underwent evaluation for insertion properties and in vitro permeation profiles when combined with different membranes, dermatomed porcine skin, Parafilm®M, and Strat-M®. Insertion profiles indicated that both Parafilm®M and Strat-M® showed comparable insertion depths to dermatomed porcine skin (in range of 360-430 µm), suggesting promise as membrane substitutes for insertion studies. In in vitro permeation studies, synthetic membranes such as Parafilm®M and Strat-M® demonstrated the ability to bypass protein-derived skin interference, providing more reliable results compared to dermatomed neonatal porcine skin. Consequently, these findings present valuable tools for preliminary screening across various MAP formulations, especially in the transdermal delivery of proteins and peptides.

[Relationship between epiphyllous bud of tropical waterlily (Brachyceras)umbilics and carbohydrate meta-bolism in different parts of leaves]

To understand the development mechanism of the epiphyllous bud of waterlily, we examined the morphological anatomy of the leaf-navel epiphyllous bud by paraffin section technique at four stages, and compared the differences of carbohydrate metabolism between viviparous and non-viviparous waterlily leaves. Three tropical waterlily cultivars of Brachyceras were used, including two viviparous cultivars Nymphaea 'Margaret Mary', Nymphaea 'Ruby', and a non-viviparous cultivar Nymphaea 'Pink Star'. The results showed that parenchyma cells below the epidermis of leaf-navel divided and grew continuously after the leaf unfolded, forming a closely arranged cell cluster in viviparous waterlily and raised upward to a spherical shape. In contrast, no change was observed in leaf-navel of non-viviparous waterlily with the expansion of leaves. With the development of leaves, the contents of all physiological variables except sucrose and enzyme activities in the leaves of viviparous waterlily showed a first increase and then a decrease, which was significantly higher than those of non-viviparous waterlily. The carbohydrate contents in different parts showed the order of leaf > leaf-navel > petiole (except for starch content, which was highest in the leaf-navel). The activities of sucrose synthase (SS) and acid invertase (AI) were higher than those of sucrose phosphate synthase (SPS) and neutral invertase (NI). The activities of SPS and NI in different tissues of viviparous waterlily were significantly higher than those in non-viviparous one, but SS and AI did not show pronounced cultivar advantage in viviparous cultivars. AI activity varied greatly among cultivars, whereas NI activity varied less and was at a low level in different tissues. The sucrose of Nymphaea 'Ruby' leaves was positively correlated with the SPS and AI, and significantly associated with NI. The accumulation of sucrose content increased the activities of SS and NI of waterlily leaves, which was conducive to promoting the formation of epiphyllous buds.

Short- and Medium-Chain Chlorinated Paraffins in Foods from the Sixth Chinese Total Diet Study: Occurrences and Estimates of Dietary Intakes in South China

Food consumption has been identified as a major pathway for human exposure to short-chain chlorinated paraffins (SCCPs) and medium-chain chlorinated paraffins (MCCPs), but evaluations of SCCP and MCCP intake from major dietary sources are limited. We used the sixth Chinese Total Diet Study to perform a comprehensive investigation of SCCPs and MCCPs in cereals, vegetables, potatoes, legumes, eggs, milk, meats, and aquatic foods from nine southern provinces. The geographical distribution of CP concentrations showed higher levels in Jiangsu, Hubei, and Zhejiang provinces. The CP concentrations in most animal-origin foods were higher than those in foods of plant origin. The total estimated daily intakes (EDIs) of SCCPs and MCCPs, with average values of 7.0 × 10² and 4.7 × 10² ng kg^-1 day^-1, respectively, were mostly contributed by cereals, vegetables, and meats. Risk assessment indicated the EDIs of CPs posed no significant risk to residents in South China.

Evaluating age and temporal trends of chlorinated paraffins in pooled serum collected from males in Australia between 2004 and 2015

Chlorinated paraffins (CPs) are high production volume chemicals of which some show resistance to environmental degradation, long-rang transport, bioaccumulation and toxicity potential. Information regarding their presence in humans is limited, including their human bioaccumulation potential. The present study aimed to evaluate CP levels in human serum from Australia in order to better understand their exposure and current pollution status as well as trends associated with age and time between 2004 and 2015. For this, we selected a male sub-group of the Australian population under 60 years old (n = 16 pools, total 1600 serum samples). While long-chain CP (C_18-20) and most short-chain CP (C_10-13, SCCPs) levels were below method detection limits (MDL), medium-chain CPs (C_14-17, MCCPs) were found in most serum samples (detection frequency 94%) as well as CPs with a carbon chain length of nine (detection frequency 76%). The levels of ΣSCCPs and ΣMCCPs ranged from <MDL-140 and <MDL-520 ng/g lipid weight (lw), respectively, with a median value of 97 ng/g lw for SCCPs and 190 ng/g lw for MCCPs. Analysis by age stratification did not identify any trends but an increase of a factor of 2 in MCCPs levels was observed over time (p < 0.05). Plotting the MCCP/SCCP ratio of all available data in humans over time showed also an increasing trend, including for China. The reported levels are relatively low considering the levels reported in environmental media from Australia such which raises the question to what extent CPs accumulate in humans. Future studies on this aspect are required.

Bioaccumulation and biomagnification of short-chain chlorinated paraffins in marine organisms from the Pearl River Estuary, South China

Short-chain chlorinated paraffins (SCCPs) are a series of new persistent organic pollutants, posing a risk of significant adverse effects to biota. Increasing attention has been paid to SCCP pollution in China as large amounts of chlorinated paraffin (CP) products containing SCCPs have been produced and used there. However, knowledge of the bioaccumulation of SCCPs in marine organisms from the Pearl River Estuary (PRE), Southern China, is still scarce. In this study, SCCP concentrations were measured in seawater, sediments, and marine organisms from the PRE. SCCP concentrations ranged from 180 to 460 ng/L in seawater, from 180 to 620 ng/g dry weight (dw) in sediments, and from 870 to 36,000 ng/g lipid weight (lw) in marine biota samples. C_10-11 SCCPs were the predominant homologues in all the samples, with an average abundance of 68% in seawater, 57% in sediments, and 56-77% in marine organisms. However, chlorine patterns of SCCPs in seawater, sediments, and marine organisms were different. Cl_8-10 SCCPs dominated in sediments, whereas Cl_5-7 SCCPs were the predominant SCCP homologues in water and most organism species. The logarithm bioaccumulation factors (BAFs) of SCCPs ranged from 1.6 to 3.0, and increased significantly with the increase of K_ow values for most marine biota species, indicating that K_ow was the major factor controlling the bioaccumulation of SCCPs and that SCCPs with higher lipophilicity were more prone to being bioaccumulated from water. Opposite to that observed for log BAFs, biota-sediment accumulation factors of specific SCCPs (range: 0.01-30) decreased significantly with the increase of K_ow values. The biomagnification factor of total SCCPs for oyster-mangrove crab was 2.40, implying the potential biomagnification of SCCPs for benthos in the PRE.

Bioaccessibility of short chain chlorinated paraffins in meat and seafood

Bioaccessibility of short chain chlorinated paraffins (SCCPs), which is important for estimation of dietary exposure, has not been evaluated in previous studies. In the present study, we determined the bioaccessibility of SCCPs in meat (pork, beef and chicken) and seafood (fish, clams, and prawns) using the colon-extended physiologically based extraction test as an in vitro model. The bioaccessibility percentages (BAs) ranged from 33% to 84% in the fed state and from 41% to 63% in the unfed state. The BAs observed in the fed state were lower than in the unfed state in most samples, except for pork sample, which had the highest lipid content. This could be attributed to the effects caused by dietary components added in the fed state. The effects of lipid and protein in samples on bioaccessibility were investigated. In food with a high lipid content, like pork in this study, lipid was the main factor controlling SCCP bioaccessibility. In the other five foods, which had low-medium lipid contents, BA in the unfed state was positively correlated with lipid content (p < 0.05) and negatively correlated with the protein-to-lipid content ratio (p < 0.05). No significant relationships between lipid and protein content and BA were found in the fed state. As to SCCP congener groups, a positive relationship between the BAs of SCCP congener groups and their octanol-water partition coefficients (log K_ow) was found in pork sample in the fed state (p < 0.05). The BAs obtained in samples from fish, prawn, clam, and pork in the unfed state and that obtained in clam sample in the fed state were negatively correlated with log K_ow (p < 0.05). We calculated more accurate estimated dietary intakes of SCCPs using our SCCP bioaccessibility data. These results will contribute to more reliable dietary risk assessments of SCCPs.

Validation of a HRGC-ECNI/LRMS method to monitor short-chain chlorinated paraffins in human plasma

Short-chain chlorinated paraffins (SCCPs) are produced in high volume and have the high potential to pose a threat to human health. However, little information is available for SCCP contamination in human blood/plasma/serum, mainly due to the difficulty of sample preparation and quantitative analysis. A method using high resolution gas chromatography coupled with electron capture negative ionization low resolution mass spectrometry (HRGC-ECNI/LRMS) was developed and validated to measure SCCPs in human plasma. The pretreatment process included protein denaturation and lipid elimination, liquid-liquid extraction with a mixture of n-hexane/dichloromethane (1:1, V/V), and cleanup on a multi-layer silica column. The blank controls, including procedural blank, vacuum blood collection tube blank, and instrumental blank, were the most pivotal points for the reliable analysis of SCCPs. The average value of procedural blanks was 9.0ng/g; and the method detection limit (MDL), calculated as the sum of the average procedural blank value and 3 times of the standard deviation of the procedural blanks, was 12.6ng/g plasma. The validated method was applied to measure the concentrations of the total SCCPs (∑SCCPs) in 50 plasma samples from a general population. The measured plasma concentrations of ∑SCCPs ranged from <MDL to 203ng/g wet weight (ww), with an average value of 32.0ng/g ww. The relative abundance profiles of SCCPs in plasma samples were dominated by C₁₀- and C₁₁-CP congener groups centered on Cl_6-7. The developed method can be used for the comprehensive and large-scale investigation of SCCP levels in human plasma.

Isolation and characterization of biosurfactant producing and oil degrading Bacillus subtilis MG495086 from formation water of Assam oil reservoir and its suitability for enhanced oil recovery

The strains isolated from the formation water were characterized and screened considering their crude oil degradation capability and biosurfactant production ability. The growth kinetics study of isolated Bacillus subtilis MG495086 was carried out by varying growth parameters i.e. carbon source, temperature, pH and salinity. The biosurfactant production was optimized adopting RSM-CCD considering carbon source (1-5%), pH (3-11) and temperature (25-65 °C) as matrix parameters. The optimum biosurfactant production (6.3 ± 0.1 g/L) and the minimum surface tension 29.85 mN/m were obtained after 96 h of incubation under optimal conditions i.e. 3.8% (v/v) of light-paraffin oil as sole carbon source at 62.4 °C and pH 7.7 with the maximum oil degradation capability of 91.3 ± 5%. Critical micelle concentration value of crude biosurfactant was found to be 40 mg/L with high emulsification activity of 72.45 ± 0.85%. The produced biosurfactant was identified as lipopeptide (Surfactin) and characterized using various analytical techniques to establish its suitability for microbial enhanced oil recovery.

Bioaccumulation of organic pollutants in Indo-Pacific humpback dolphin: A review on current knowledge and future prospects

Indo-Pacific humpback dolphin (Sousa chinensis) are chronically exposed to organic pollutants since they inhabit shallow coastal waters that are often impacted by anthropogenic activities. The aim of this review was to evaluate existing knowledge on the occurrence of organic pollutants in Indo-Pacific humpback dolphins, identify knowledge gaps, and offer recommendations for future research directions. We discussed the trends in the bioaccumulation of organic pollutants in Indo-Pacific humpback dolphins focusing on sources, physicochemical properties, and usage patterns. Furthermore, we examined factors that influence bioaccumulation such as gender, age, dietary intake and tissue-specific distribution. Studies on bioaccumulation in Indo-Pacific humpback dolphin remain scarce, despite high concentrations above 13,000 ng/g lw we previously detected for PFOS, ∑PBDE and chlorinated paraffins. The maximum concentration of organochlorines detected was 157,000 ng/g wt. Furthermore, variations in bioaccumulation were shown to be caused by factors such as usage patterns and physicochemical properties of the pollutant. However, restrictions in sampling inhibit investigations on exposure pathway and toxicity of organic pollutants in Indo-Pacific humpback dolphin. We proposed the use of biopsy sampling, predictive bioaccumulation and toxicity modeling, and monitoring other emerging contaminants such as microplastics and pharmaceuticals for future health risk assessment on this critically endangered marine mammal species.

Comparison of chlordecone and NDL-PCB decontamination dynamics in growing male kids after cessation of oral exposure: Is there a potential to decrease the body levels of these pollutants by dietary supplementation of activated carbon or paraffin oil?

Sixteen weaned male Alpine kids (Capra hircus) were subjected to a 21-day oral daily exposure of 0.05 mg kg^-1 BW. d^-1 of chlordecone (CLD) and 0.30 μg kg^-1 BW. d^-1 of each non-dioxin-like polychlorinated biphenyls (NDL-PCBs, congeners 28, 52, 101, 138, 153 and 180). Four kids, identified as the CONTA group, were slaughtered at the end of the exposure, while the remaining animals (n = 12) were fed with specific diets for an additional 21-day decontamination period before slaughtering. Kids from the DECONTA (n = 4) group were fed a control diet, while those from the AC10% and PO8% group received pellets supplemented with 10% activated carbon (AC) and 8% paraffin oil (PO), respectively. CLD and NDL-PCB levels in blood, liver, peri-renal fat and muscles from different groups were analysed to compare the decontamination dynamics of the pollutants and to determine the efficiency of AC and PO to decrease the body levels of pollutants. After the decontamination period, the CLD levels considerably decreased (more than 60%) in blood, liver, muscles and fat. Concerning NDL-PCBs, the decontamination process was much lower. Overall, CLD appeared to be less retained in kids' organism compared with NDL-PCBs, and the decontamination dynamics of these pollutants appeared to be different because of their specific physicochemical properties and lipophilicity. Furthermore, the dietary supplementation with AC or PO did not significantly affect the decontamination dynamics.

Methanogenic Paraffin Biodegradation: Alkylsuccinate Synthase Gene Quantification and Dicarboxylic Acid Production

Paraffinic n-alkanes (>C17) that are solid at ambient temperature comprise a large fraction of many crude oils. The comparatively low water solubility and reactivity of these long-chain alkanes can lead to their persistence in the environment following fuel spills and pose serious problems for crude oil recovery operations by clogging oil production wells. However, the degradation of waxy paraffins under the anoxic conditions characterizing contaminated groundwater environments and deep subsurface energy reservoirs is poorly understood. Here, we assessed the ability of a methanogenic culture enriched from freshwater fuel-contaminated aquifer sediments to biodegrade the model paraffin n-octacosane (C28H58). Compared with that in controls, the consumption of n-octacosane was coupled to methane production, demonstrating its biodegradation under these conditions. Smithella was postulated to be an important C28H58 degrader in the culture on the basis of its high relative abundance as determined by 16S rRNA gene sequencing. An identified assA gene (known to encode the α subunit of alkylsuccinate synthase) aligned most closely with those from other Smithella organisms. Quantitative PCR (qPCR) and reverse transcription qPCR assays for assA demonstrated significant increases in the abundance and expression of this gene in C28H58-degrading cultures compared with that in controls, suggesting n-octacosane activation by fumarate addition. A metabolite analysis revealed the presence of several long-chain α,ω-dicarboxylic acids only in the C28H58-degrading cultures, a novel observation providing clues as to how methanogenic consortia access waxy hydrocarbons. The results of this study broaden our understanding of how waxy paraffins can be biodegraded in anoxic environments with an application toward bioremediation and improved oil recovery.IMPORTANCE Understanding the methanogenic biodegradation of different classes of hydrocarbons has important applications for effective fuel-contaminated site remediation and for improved recovery from oil reservoirs. Previous studies have clearly demonstrated that short-chain alkanes (C17) that comprise many fuel mixtures. Using an enrichment culture derived from a freshwater fuel-contaminated site, we demonstrate that the model waxy alkane n-octacosane can be biodegraded under methanogenic conditions by a presumed Smithella phylotype. Compared with that of controls, we show an increased abundance and expression of the assA gene, which is known to be important for anaerobic n-alkane metabolism. Metabolite analyses revealed the presence of a range of α,ω-dicarboxylic acids found only in n-octacosane-degrading cultures, a novel finding that lends insight as to how anaerobic communities may access waxes as growth substrates in anoxic environments.

Development of matrix solid-phase dispersion method for the extraction of short-chain chlorinated paraffins in human placenta

Chlorinated paraffins (SCCPs) are widely used worldwide, and they can be released into the environment during their production, transport, usage and disposal, which pose potential risks for human health. In this work, an efficient, reliable and rapid pretreatment method based on matrix solid-phase dispersion (MSPD) was developed for the analysis of short-chain CPs (SCCPs) in human placenta by gas chromatograph-electron capture negative ion low-resolution mass spectrometry (GC-ECNI-LRMS) and gas chromatography-quadrupole time-of-flight mass spectrometry (GC-QTOF-HRMS). The MSPD-relevant parameters including dispersing sorbent, sample-to-sorbent mass ratio, and elution solvent were optimized using the orthogonal test. Silica gel was found to be the optimal dispersing sorbent among the selected matrices. Under the optimal conditions, 44% acidic silica gel can be used as the co-sorbent to remove lipid and eluted by the mixture of hexane and dichloromethane (7:3, V/V). The spiked recoveries of the optimized method were 77.4% and 91.4% for analyzing SCCPs in human placenta by GC-ECNI-LRMS and GC-QTOF-HRMS, and the corresponding relative standard deviations were 10.2% and 5.6%, respectively. The method detection limit for the total SCCPs was 36.8ng/g (dry weight, dw) and 19.2ng/g (dw) as measured by GC-ECNI-LRMS and GC-QTOF-HRMS, respectively. The concentrations of SCCPs in four human placentas were in the range of <method detection limit (MDL) to 782ng/g (dw), which is also the first description of SCCPs detected in placentas.

Endosulfan, Short-Chain Chlorinated Paraffins (SCCPs) and Octachlorostyrene in Wildlife from Greenland: Levels, Trends and Methodological Challenges

Besides globally banned "legacy" persistent organic pollutants, other compounds might be present in Arctic wildlife, for which regulation was introduced recently (the insecticide endosulfan), is considered (short-chain chlorinated paraffins, SCCPs) or does not exist (octachlorostyrene, OCS, a byproduct of manufacturing and combustion processes involving chlorine). The purpose of this study was to analyze the time trend of endosulfan (1986-2012) in ringed seals and to address the levels of SCCPs and OCS in wildlife species from Greenland (black guillemot, glaucous gull, ringed seal, polar bear), while taking a critical standpoint to analytical methods typically applied. The metabolite endosulfan sulfate was the only endosulfan compound consistently above detection limits, with a median concentration of 0.23 ng/g lipid weight (lw) and a significant annual decrease of -5.6%. The low-resolution mass spectrometry (LRMS) method appeared accurate and sufficiently precise; however, the gel permeation chromatography had to balance lipid removal and analyte loss. SCCPs and OCS were present in all samples. OCS median concentrations were between 2.8 (ringed seal blubber) and 29 (glaucous gull liver) ng/g lw, determined by a straightforward dual column electron capture detection method. SCCPs were analyzed by LRMS, following removal of potential interferences, and had median concentrations of several 100 ng/g wet weight. While the method showed good precision and recovery rates as well as acceptable accuracy in control samples, the Greenland samples had high concentrations in an Arctic context, possibly indicating limited selectivity of the LRMS method.

Dechlorination and chlorine rearrangement of 1,2,5,5,6,9,10-heptachlorodecane mediated by the whole pumpkin seedlings

Short chain chlorinated paraffins (SCCPs) are ubiquitously present as persistent organic pollutants in the environment. However, little information on the interaction of SCCPs with plants is currently available. In this work, young pumpkin plants (Cucurbita maxima × C. Moschata) were hydroponically exposed to the congener of chlorinated decane, 1,2,5,5,6,9,10-heptachlorodecane (1,2,5,5,6,9,10-HepCD), to investigate the uptake, translocation and transformation of chlorinated decanes in the intact plants. It was found that parent HepCD was taken up by the pumpkin roots, translocated from root to shoots, and phytovolatilized from pumpkin plants to air via the plant transpiration flux. Our data suggested that dechlorination of 1,2,5,5,6,9,10-HepCD to lower chlorinated decanes and rearrangement of chlorine atoms in the molecule were all mediated by the whole pumpkin seedlings. Chlorinated decanes were found in the shoots and roots of blank controls, indicating that chlorinated decanes in the air could be absorbed by leaves and translocated from shoots to roots. Lower chlorinated congeners (C₁₀H₁₇Cl₅) tended to detain in air compared to higher chlorinated congeners (C₁₀H₁₆Cl₆ and other C₁₀H₁₅Cl₇). Potential transformation pathway and behavior of 1,2,5,5,6,9,10-HepCD in pumpkin were proposed based on these experiments.

Short-chain chlorinated paraffins in marine organisms from the Pearl River Estuary in South China: Residue levels and interspecies differences

There is limited information available on the bioaccumulation of short-chain chlorinated paraffins (SCCPs), a complicated group of persistent organic pollutants (POPs) candidates listed in the Stockholm Convention, in estuarine ecosystem. This study analyzed SCCPs in marine organisms (five fish and six invertebrates) from the Pearl River Estuary in South China. The concentrations of total SCCPs ranged from 210 to 21,000 ng · g(-1) lipid weight, with relatively higher levels in benthic invertebrates (shrimp, crabs and bivalves) than in non-benthic species (pelagic and mesopelagic fish and squid). SCCPs were biomagnified from prey fish (tapertail anchovy, Coilia mystus) to predator fish (Bombay duck, Harpadon nehereus), and the biomagnification factors (BMFs) of SCCP congeners ranged from 1.1 (C10H16Cl6) to 3.4 (C13H18Cl10). Species-specific homologue group patterns were also observed, with significantly lower proportions of C10 congeners in the shrimp, bivalves and Bombay duck than in the other species.

Short-chain chlorinated paraffins in terrestrial bird species inhabiting an e-waste recycling site in South China

Short-chain chlorinated paraffins (SCCPs) are under review by the Stockholm Convention on Persistent Organic Pollutants. Currently, limited data are available about SCCPs in terrestrial organisms. In the present study, SCCP concentration in the muscles of seven terrestrial bird species (n = 38) inhabiting an e-waste recycling area in South China was determined. This concentration varied from 620 to 17,000 ng/g lipid. Resident birds accumulated significantly higher SCCP concentrations than migratory birds (p < 0.01). Trophic magnification was observed for migratory bird species but not for resident, which was attributed to high heterogeneity of SCCP in e-waste area. Two different homologue group patterns were observed in avian samples. The first pattern was found in five bird species dominated by C10 and C11 congeners, while the second was found in the remains, which show rather equal abundance of homologue groups. This may be caused by two sources of SCCPs (local and e-waste) in the study area.

Bioaccumulation and trophic transfer of short chain chlorinated paraffins in a marine food web from Liaodong Bay, North China

Short chain chlorinated paraffins (SCCPs) are under the evaluation for inclusion into the Stockholm Convention on persistent organic pollutants. However, information on their bioconcentration and biomagnification in marine ecosystems is unavailable, limiting the evaluation of their ecological risks. In this study, seawater, sediment, zooplankton, invertebrates, and fishes collected from Liaodong Bay, Bohai Sea, North China were analyzed to investigate the residual level, congener group profile, bioaccumulation, and trophic transfer of SCCPs in a marine food web. The total concentrations of SCCPs ranged from 4.1 to 13.1 ng L(-1) in seawater, 65 to 541 ng g(-1) (dw) in sediment, and 86 to 4400 ng g(-1) (ww) in organisms. Correspondence analysis indicated the relative enrichment of C10Cl5 and C11Cl5 formula groups in most aquatic organisms. Both the logarithm bioaccumulation factors (log BAFs: 4.1-6.7) and biota-sediment accumulation factors (BSAFs: 0.1-7.3) of individual congeners implied the bioaccumulation of SCCPs. The trophic magnification factor (TMF) of ∑SCCPs was determined to be 2.38 in the zooplankton-shrimp-fish food web, indicating biomagnification potential of SCCPs in the marine ecosystem. The TMF values of individual congener groups significantly correlated with their log KOW values.

Congener-specific distribution and bioaccumulation of short-chain chlorinated paraffins in sediments and bivalves of the Bohai Sea, China

Short-chain chlorinated paraffins (SCCPs) are a new type of persistent organic pollutants that are of great environmental concern because of their wide distribution. In this study, surface sediments and bivalve samples were collected from the coastal area of the Bohai Sea in China. Total SCCP (ΣSCCP) concentrations in surface sediments and bivalves ranged from 97.4 ng g(-1) dry weight (dw) to 1756.7 ng g(-1) dw and 476.4-3269.5 ng g(-1) dw, respectively. C10-CPs and C11-CPs were the predominant homologue groups in all sediments and bivalves. Specific congener composition analysis and correspondence analysis indicated that the local SCCP source mainly came from CP-42 and CP-52 products, and riverine input had an important function. The biota-sediment accumulation factors of ΣSCCPs for bivalves ranged from 1.08 to 1.61, and a significant correlation indicated that the SCCP congener with higher chlorination degree was more likely to be accumulated in bivalves.

Using quantitative structural property relationships, chemical fate models, and the chemical partitioning space to investigate the potential for long range transport and bioaccumulation of complex halogenated chemical mixtures

Some substances are mixtures of very large number of constituents which vary widely in their properties, and thus also in terms of their environmental fate and the hazard that they may pose to humans and the environment. Examples of such substances include industrial chemicals such as the chlorinated paraffins, technical pesticides such as toxaphene, and unintended combustion side products, such as mixed halogenated dibenzo-p-dioxins and dibenzofurans. Here we describe a simple graphical superposition method that could precede a more detailed hazard assessment for such substances. First, partitioning and degradation properties for each individual constituent of a mixture are estimated with high-throughput quantitative structure-property relationships. Placed in a chemical partitioning space, i.e. a coordinate system defined by two partitioning coefficients, the mixtures appear as 'clouds'. When model-derived hazard assessment metrics, such as the potential for bioaccumulation and long range transport, are superimposed on these clouds, the resulting maps identify the constituents with the highest value for a particular parameter and thus potentially the greatest hazard. The maps also indicate transparently how the potential for long range transport and bioaccumulation is dependent on structural attributes, such as chain length, and the degree and type of halogenation. In contrast to previous approaches, in which the mixture is represented by a single set of properties or those of a few selected constituents, the whole range of environmental fate behaviors displayed by the constituents of a mixture are being considered. The approach is illustrated with three sets of chemical substances.

Data analysis considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues

The Whole Genome Sampling Analysis (WGSA) assay in combination with Affymetrix GeneChip Mapping Arrays is used for copy number analysis of high-quality DNA samples (i.e., samples that have been collected from blood, fresh or frozen tissue, or cell lines). Formalin-fixed, paraffin-embedded (FFPE) samples, however, represent the most prevalent form of archived clinical samples, but they provide additional challenges for molecular assays. FFPE processing usually results in the degradation of FFPE DNA and in the contamination and chemical modification of these DNA samples. In this article, we describe the steps needed to obtain reliable copy number predictions from degraded and contaminated FFPE samples.

High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues

We describe protocols to acquire high-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissues for the use in array comparative genome hybridization (CGH). Formalin fixation combined with paraffin embedding is routine procedure for solid malignancies in the diagnostic practice of the pathologist. As a consequence, large archives of FFPE tissues are available in pathology institutes across the globe. This archival material is for many research questions an invaluable resource, with long-term clinical follow-up and survival data available. FFPE is, thus, highly attractive for large genomics studies, including experiments requiring samples for test/learning and validation. Most larger array CGH studies have, therefore, made use of FFPE material and show that CNAs have tumor- and tissue-specific traits (Chin et al. Cancer Cell 10: 529-541, 2006; Fridlyand et al. BMC Cancer 6: 96, 2006; Weiss et al. Oncogene 22: 1872-1879, 2003; Jong et al. Oncogene 26: 1499-1506, 2007). The protocols described are tailored to array CGH of FFPE solid malignancies: from sectioning FFPE blocks to specific cynosures for pathological revisions of sections, DNA isolation, quality testing, and amplification. The protocols are technical in character and elaborate up to the labeling of isolated DNA while further processes and interpretation and data analysis are beyond the scope.

Detection of gene expression in mouse embryos and tissue sections

Analysis of gene expression patterns is central to the study of embryonic development. This chapter details methods for detecting gene expression in whole mouse embryos and in tissue sections. The most commonly used methods available in mouse are described and include mRNA in situ hybridization, immunohistochemistry, and detection of enzymatic and fluorescent protein reporters.

The role of frozen section in surgical staging of low risk endometrial cancer

BACKGROUND

The role of frozen section (FS) in intraoperative decision making for surgical staging of endometrial cancer is controversial. Objective of this study is to assess the agreement rate between the FS and paraffin section (PS); and the potential impact of the role of FS in the intra-operative decision making for the complete surgical staging in low risk endometrial cancer.

METHODS

This is a retrospective analysis of patients diagnosed with intra-operative FS stage I, grade I or II endometrial cancer from 1995-2004. FS results were compared with final pathology results with regard to tumor grade, depth of myometrial invasion, cervical involvement, lymphovascular invasion, and lymph node involvement. Agreement statistic with kappa was calculated using SPSS statistical software. Categorical variables were tested using chi-square test with p value of ≤0.05 being statistically significant.

RESULTS

Of the 457 patients with endometrial cancer, 146 were evaluated by intra-operative FS and met inclusion criteria. FS results were in disagreement with permanent section in 35% for the grade (kappa 0.58, p = 0.003), 28% for depth of myometrial invasion (kappa 0.61, p<0.0001), 13% for cervical involvement (kappa 0.78, p = 0.002), and 32% for lymphovascular invasion (kappa 0.6, p = 0.01). Permanent pathology upstaged 31.9% & 23.2% of FS stage IA, & IB specimen respectively. Lymph node dissection was done in 56.8%. Lymph node metastasis was identified in 8.4%. Use of intraoperative FS would have resulted in suboptimal surgical treatment in 13% stage IA and 6.6% of stage IB patients respectively by foregoing lymphadenectomy.

CONCLUSION

A significant number of patients with low risk endometrial cancer by FS were upstaged and upgraded on final pathology. Before placing absolute reliance on intraoperative FS to undertake complete surgical staging, the inherent limitation of the same in predicting final stage and grade highlighted by our data need to be carefully considered.

[Resistance of the petroleum-oxidizing microorganism Dietzia sp. to hyperosmotic shock in reconstituted biofilms]

A number of halotolerant and halophilic bacterial strains were isolated from the Romashkinskoe oil field (Tatarstan) stratal waters having a salinity of up to 100 g/l. The isolation of pure cultures involved biofilm reconstitution on M9 medium with paraffins. The associations obtained were dispersed and reinoculated onto solid media that contained either peptone and yeast extract (PY) or paraffins. It was shown that such associations included both oil-oxidizing bacteria and accompanying chemoheterotrophic bacteria incapable of oil oxidation. The pure cultures that were isolated were used for creating binary biofilms. In these biofilms, interactions between halophilic and nonhalophilic bacteria under hypo- and hyperosmotic shocks were investigated. We conducted a detailed study of a biofilm obtained from an oil-oxidizing halotolerant species (with an upper growth limit of 10-12% NaCl) identified as Dietzia sp. and an extremely halophilic gram-negative bacterium (growing within the 5-20% NaCl concentration range) of the genus Chromohalobacter that did not oxidize paraffins. If these microorganisms were grown in a mixed suspension (planktonic) culture that was not supplemented with an additional amount of NaCl, no viable cells of the halophilic microorganism were detected after reinoculation. In contrast, only halophilic cells were detected at a NaCl concentration of 15%. Thus, no mutual protective influence of the microorganisms manifested itself in suspension culture, either under hypo- or under hyperosmotic shock. Neither could the halophile cells be detected after reinoculating a biofilm obtained on a peptone medium without addition of NaCl. However, biofilms produced at a NaCl concentration of 15% contained approximately equal numbers of cells of the halophilic and halotolerant organisms. Thus, the halophile in biofilms sustaining a hyperosmotic shock exerts a protective influence on the halotolerant microorganism. Preliminary data suggest that this effect is due to release by the halophile of osmoprotective substances (ectoine and glutamate), which are taken up by the halotolerant species. Such substances are diluted by a large medium volume in suspension cultures, whereas, in biofilms, their diffusion into the medium is apparently hampered by their interaction with the intercellular polymer matrix.