Inhibitory effect of metals on animal and plant glutathione transferases.

Glutathione transferases (GSTs) represent a widespread enzyme superfamily in eukaryotes and prokaryotes catalyzing different reactions with endogenous and xenobiotic substrates such as organic pollutants. The latter are often found together with metal contamination in the environment. Besides performing of essential functions, GSTs protect cells by conjugation of glutathione with various reactive electrophiles. The interference of toxic metals with this functionality of GSTs may have unpredictable toxicological consequences for the organisms. In this review results from the recent literature are summarized and discussed describing the ability of metals to inhibit intracellular detoxification processes in animals and plants.

Fungi from metal-polluted streams may have high ability to cope with the oxidative stress induced by copper oxide nanoparticles.

Increased commercialization of products based on metal oxide nanoparticles increases the likelihood that these nanoparticles will be released into aquatic environments, thus making relevant the assessment of their potential impacts on aquatic biota. Aquatic fungi are distributed worldwide and play a key role in organic matter turnover in freshwater ecosystems. The present study investigated the impacts of copper oxide spherical nanoparticles (CuO-NPs; <50 nm powder, 5 levels ≤200 mg/L) on cellular targets and antioxidant defenses in 5 fungal isolates collected from metal-polluted or nonpolluted streams. The CuO-NPs induced oxidative stress in aquatic fungi, as evidenced by intracellular accumulation of reactive oxygen species, and led to plasma membrane damage and DNA strand breaks in a concentration-dependent manner. Effects were more pronounced with a longer exposure time (3 d vs 10 d). Under CuO-NP exposure, mycelia of fungi collected from metal-polluted streams showed less oxidative stress and higher activities of superoxide dismutase and glutathione reductase compared with fungi from nonpolluted streams. The latter fungi responded to CuO-NPs with a stronger stimulation of glutathione peroxidase activity. These findings may indicate that fungi isolated from metal-polluted streams had a greater ability to maintain the pool of reduced glutathione than those from nonpolluted streams. Overall, results suggest that populations adapted to metals may develop mechanisms to cope with the oxidative stress induced by metal nanoparticles.

Physiological responses to nanoCuO in fungi from non-polluted and metal-polluted streams.

Nanocopper oxide (nanoCuO) is among the most widely used metal oxide nanoparticles which increases their chance of being released into freshwaters. Fungi are the major microbial decomposers of plant litter in streams. Fungal laccases are multicopper oxidase enzymes that are involved in the degradation of lignin and various xenobiotic compounds. We investigated the effects of nanoCuO (5 levels, ≤ 200 mg L(-1)) on four fungal isolates collected from metal-polluted and non-polluted streams by analyzing biomass production, changes in mycelial morphology, laccase activity, and quantifying copper adsorbed to mycelia, and ionic and nanoparticulate copper in the growth media. The exposure to nanoCuO decreased the biomass produced by all fungi in a concentration- and time-dependent manner. Inhibition of biomass production was stronger in fungi from non-polluted (EC50(10 days) ≤ 31 mg L(-1)) than from metal-polluted streams (EC50(10 days) ≥ 65.2 mg L(-1)). NanoCuO exposure led to cell shrinkage and mycelial degeneration, particularly in fungi collected from non-polluted streams. Adsorption of nanoCuO to fungal mycelia increased with the concentration of nanoCuO in the medium and was higher in fungi from non-polluted streams. Extracellular laccase activity was induced by nanoCuO in two fungal isolates in a concentration-dependent manner, and was highly correlated with adsorbed Cu and/or ionic Cu released by dissolution from nanoCuO. Putative laccase gene fragments were also detected in these fungi. Lack of substantial laccase activity in the other fungal isolates was corroborated by the absence of laccase-like gene fragments.

The major function of a metallothionein from the aquatic fungus Heliscus lugdunensis is cadmium detoxification.

A spring from a former copper shale mine in the area of Mansfelder Land, Germany, shows extremely high transition metal ion concentrations, i.e. 40mM Zn(II), 208µM Cu(II), 61µM As(V), and 25µM Cd(II). This makes it a challenging habitat for living organisms as they have to cope with metal ion concentrations that by far exceed the values usually observed in spring water. One of the surviving species found is the aquatic fungus Heliscus lugdunensis (teleomorph: Nectria lugdunensis). Investigation of its redox related heavy metal tolerance revealed the presence of small thiol containing compounds as well as a small metallothionein, Neclu_MT1 (MT1_NECLU: P84865). While Cd(II)-induction of metallothioneins is observed in many species, the fact that exclusively Cd(II), but not Zn(II), Cu(I), As(III) or oxidative stress can induce Neclu_MT1 protein synthesis is unparalleled. To complement the physiological studies performed in the fungus H. lugdunensis, the Cd(II) and Zn(II) binding characteristics of the recombinantly expressed protein were spectroscopically analysed in vitro aiming to demonstrate the observed Cd(II) specificity also on the protein level. Stoichiometric analyses of the recombinant protein in combination with photospectrometric metal ion titrations and (113)Cd-NMR experiments reveal that metal ion binding capacities and consequently the structures formed at physiological Neclu_MT1 concentrations differ from each other. Concluding, we describe the first solely Cd(II)-inducible metallothionein, Neclu_MT1, from H. lugdunensis, featuring a difference in the structure of the Cd(II)versus the Zn(II) metalated protein in a physiologically relevant concentration range.

Identification of phytochelatins in the cadmium-stressed conjugating green alga Micrasterias denticulata.

Aquatic environments like peat bogs are affected by anthropogenic metal input into the environment. These ecosystems are inhabited by unicellular green algae of the class Zygnematophyceae. In this study the desmid Micrasterias denticulata was stressed with 600 nM Cd, 10 µM Cr and 300 nM Cu for 3 weeks. GSH levels were measured with HPLC and did not differ between the different treatments or the control. According to the metallo-thiolomics concept, mass spectrometry was used as a method for unambiguous thiol peptide identification. PC2, PC3 and PC4 were clearly identified in the Cd stressed sample with UPLC-MS by their MS spectrum and molecular masses. PC2 and PC3 were determined to be the main thiol compounds, while PC4 was only abundant in traces in Micrasterias. In addition, the identity of PC2 and PC3 was confirmed by MS/MS. No PCs were detected in the Cu stressed algae sample. However, in the Cr stressed sample traces of PC2 were indicated by a peak in UPLC-MS at the retention time of the PC2 standard, but the intensity was too low to acquire reliable MS and MS/MS spectra. In this study PCs have been detected for the first time in a green alga of the division Streptophyta, a close relative to higher plants.

The relevance of compartmentation for cysteine synthesis in phototrophic organisms.

In the vascular plant Arabidopsis thaliana, synthesis of cysteine and its precursors O-acetylserine and sulfide is distributed between the cytosol, chloroplasts, and mitochondria. This compartmentation contributes to regulation of cysteine synthesis. In contrast to Arabidopsis, cysteine synthesis is exclusively restricted to chloroplasts in the unicellular green alga Chlamydomonas reinhardtii. Thus, the question arises, whether specification of compartmentation was driven by multicellularity and specified organs and tissues. The moss Physcomitrella patens colonizes land but is still characterized by a simple morphology compared to vascular plants. It was therefore used as model organism to study evolution of compartmented cysteine synthesis. The presence of O-acetylserine(thiol)lyase (OAS-TL) proteins, which catalyze the final step of cysteine synthesis, in different compartments was applied as criterion. Purification and characterization of native OAS-TL proteins demonstrated the presence of five OAS-TL protein species encoded by two genes in Physcomitrella. At least one of the gene products is dual targeted to plastids and cytosol, as shown by combination of GFP fusion localization studies, purification of chloroplasts, and identification of N termini from native proteins. The bulk of OAS-TL protein is targeted to plastids, whereas there is no evidence for a mitochondrial OAS-TL isoform and only a minor part of OAS-TL protein is localized in the cytosol. This demonstrates that subcellular diversification of cysteine synthesis is already initialized in Physcomitrella but appears to gain relevance later during evolution of vascular plants.

Fungi in freshwaters: ecology, physiology and biochemical potential.

Research on freshwater fungi has concentrated on their role in plant litter decomposition in streams. Higher fungi dominate over bacteria in terms of biomass, production and enzymatic substrate degradation. Microscopy-based studies suggest the prevalence of aquatic hyphomycetes, characterized by tetraradiate or sigmoid spores. Molecular studies have consistently demonstrated the presence of other fungal groups, whose contributions to decomposition are largely unknown. Molecular methods will allow quantification of these and other microorganisms. The ability of aquatic hyphomycetes to withstand or mitigate anthropogenic stresses is becoming increasingly important. Metal avoidance and tolerance in freshwater fungi implicate a sophisticated network of mechanisms involving external and intracellular detoxification. Examining adaptive responses under metal stress will unravel the dynamics of biochemical processes and their ecological consequences. Freshwater fungi can metabolize organic xenobiotics. For many such compounds, terrestrial fungal activity is characterized by cometabolic biotransformations involving initial attack by intracellular and extracellular oxidative enzymes, further metabolization of the primary oxidation products via conjugate formation and a considerable versatility as to the range of metabolized pollutants. The same capabilities occur in freshwater fungi. This suggests a largely ignored role of these organisms in attenuating pollutant loads in freshwaters and their potential use in environmental biotechnology.

Quantification of phytochelatins in Chlamydomonas reinhardtii using ferrocene-based derivatization.

A method for the identification and quantification of canonic and isoforms of phytochelatins (PCs) from Chlamydomonas reinhardtii was developed. After disulfide reduction with tris(2-carboxyethyl)phosphine (TCEP) PCs were derivatized with ferrocenecarboxylic acid (2-maleimidoyl)ethylamide (FMEA) in order to avoid oxidation of the free thiol functions during analysis. Liquid chromatography (LC) coupled to electrospray mass spectrometry (ESI-MS) and inductively coupled plasma-mass spectrometry (ICP-MS) was used for rapid and quantitative analysis of the precolumn derivatized PCs. PC(2-4), CysGSH, CysPC(2-4), CysPC(2)desGly, CysPC(2)Glu and CysPC(2)Ala were determined in the algal samples depending on the exposure of the cells to cadmium ions.

Chiral separation of the ß2-sympathomimetic fenoterol by HPLC and capillary zone electrophoresis for pharmacokinetic studies.

The development of methods for the separation of the enantiomers of fenoterol by chiral HPLC and capillary zone electrophoresis (CZE) is described. For the HPLC separation precolumn fluorescence derivatization with naphthyl isocyanate was applied. The resulting urea derivatives were resolved on a cellulose tris(3,5-dimethylphenylcarbamate)-coated silica gel column employing a column switching procedure. Detection was carried out fluorimetrically with a detection limit in the low ng/mL range. The method was adapted to the determination of fenoterol enantiomers in rat heart perfusates using liquid-liquid extraction. As an alternative a CE method was used for the direct separation of fenoterol enantiomers comparing different cyclodextrin derivatives as chiral selectors.

Regulation of sulfate assimilation in Physcomitrella patens: mosses are different!

Sulfur is an essential nutrient, taken up as sulfate from soil, reduced and incorporated into bioorganic compounds in plant cells. The pathway of sulfate assimilation is highly regulated in a demand-driven manner in seed plants. To test the evolutionary conservation of the regulatory mechanisms, we analyzed regulation of the pathway in the model for basal plants, the moss Physcomitrella patens. While in Arabidopsis the key enzyme of sulfate assimilation, adenosine 5'-phosphosulfate reductase (APR), is feedback repressed by thiols and induced by reduced levels of glutathione, in P. patens such regulation does not occur. The control of the pathway was not moved to other components as these conditions affected neither mRNA accumulation of other genes of sulfate assimilation nor sulfate uptake. Other treatments known to regulate APR, O-acetylserine, cadmium and sulfur deficiency affected APR transcript levels, but not enzyme activity. It appears that the sulfate assimilation pathway in P. patens is much more robust than in seed plants. Thus, the regulatory networks controlling the pathway have probably evolved only later in the evolution of the seed plants after separation of the bryophytes.

Analytical approach for characterization of cadmium-induced thiol peptides--a case study using Chlamydomonas reinhardtii.

Phytochelatins (PC) were described earlier to play a role in metal detoxification in Chlamydomonas reinhardtii but were not clearly identified. The focus of this case study was to identify PC synthesized by C. reinhardtii exposed to Cd. Only low intracellular concentrations of cadmium (85 nmol g(-1) fresh weight) were sufficient to cause significant changes in thiol peptide pools. Thus, results showed a progressive decline of the glutathione content, accompanied by an induction of phytochelatins. Not only canonic phytochelatins but for the first time also the iso-phytochelatins CysPC(n) and PC(2)Ala were identified in this unicellular green alga using electrospray ionization quadrupole time-of-flight tandem mass spectrometry. Additionally, CysPC(n)desGly, PC(n)desGly, CysPC(n)Glu, and PC(2)Glu were found throughout MS analysis. Also, low abundant PCs could be detected due to the high sample preconcentration combined with little sample amounts (0.3 microL min(-1)) necessary for electrospray. Identified PCs had a maximum number of 5 gamma-glutamyl cysteine (gamma-GluCys) units. Thiol peptides of higher molecular masses suggesting PC(n) with n > 5 could be identified as intermolecular oxidation products of smaller PCs. Thiols may easily be oxidized. Therefore, PCs were reduced prior to MS analysis. Dithiothreitol and tris(2-carboxyethyl) phosphine were compared concerning their reduction effort.

Fungi in a heavy metal precipitating stream in the Mansfeld mining district, Germany.

Fungal growth on alder leaves was studied in two heavy metal polluted streams in central Germany. The aim of the study was to examine previously observed differences in leaf decomposition rates, heavy metal precipitation and fungal involvement in these processes at the microscopic level. Ergosterol analyses indicated that neither habitat was optimal for fungi, but leaves exposed at the less polluted site (H8) decomposed rapidly and were colonized externally and internally by fungi and other microorganisms. Leaves exposed at the more polluted site (H4) decomposed very slowly and fungal colonization was restricted to external surfaces. An amorphous organic layer, deposited within 24 h of exposure, quickly became covered with a pale blue-green crystalline deposit (zincowoodwardite) with significant amounts of Al, S, Cu and Zn, determined by energy dispersive X-ray spectroscopy (EDS). Scanning electron microscopy (SEM) analysis of the precipitate revealed a branching arrangement of the precipitated particles caused by the presence of fungal hyphae growing on the surface. Hyphae that were not disturbed by handling were usually completely encased in the precipitate, but hyphae did not contain EDS-detectable amounts of precipitate metals. Elemental analysis using inductively coupled plasma (ICP) atomic emission spectrometry and ICP mass spectrometry revealed continuing accumulation of Zn, Cu and several other metals/metalloids on and in leaves. The formation of metal precipitates on various artificial substrates at site H4 was much reduced compared to leaves, which we attribute to the absence of fungal colonization on the artificial substrates. We could not determine whether fungi accelerate the precipitation of heavy metals at site H4, but mycelial growth on leaves continues to create new surfaces and therefore thicker layers of precipitate on leaves compared to artificial substrates.

Interaction of heavy metals with the sulphur metabolism in angiosperms from an ecological point of view.

The metabolism of sulphur in angiosperms is reviewed under the aspect of exposure to ecologically relevant concentrations of sulphur, heavy metals and metalloids. Because of the inconsistent use of the term 'metal tolerance', in this review the degree of tolerance to arsenic and heavy metals is divided into three categories: hypotolerance, basal tolerance and hypertolerance. The composition of nutrient solutions applied to physiological experiments let see that the well-known interactions of calcium, sulphate and zinc supply with uptake of heavy metals, especially cadmium are insufficiently considered. Expression of genes involved in reductive sulphate assimilation pathway and enzyme activities are stimulated by cadmium and partially by copper, but nearly not by other heavy metals. The synthesis of the sulphur-rich compounds glucosinolates, metallothioneins and phytochelatins is affected in a metal-specific way. Phytochelatin levels are low in all metal(loid)-hypertolerant plant species growing in the natural environment on metal(loid)-enriched soils. If laboratory experiments mimic the natural environments, especially high Zn/Cd ratios and good sulphur supply, and chemical analyses are extended to more mineral elements than the single metal(loid) under investigation, a better understanding of the impact of metal(loid)s on the sulphur metabolism can be achieved.

Stress response in two strains of the aquatic hyphomycete Heliscus lugdunensis after exposure to cadmium and copper ions.

Biochemical responses to cadmium (Cd2+) and copper (Cu2+) exposure were compared in two strains of the aquatic hyphomycete (AQH) Heliscus lugdunensis. One strain (H4-2-4) had been isolated from a heavy metal polluted site, the other (H8-2-1) from a moderately polluted habitat. Conidia of the two strains differed in shape and size. Intracellular accumulation of Cd2+ and Cu2+ was lower in H4-2-4 than in H8-2-1. Both strains synthesized significantly more glutathione (GSH), cysteine (Cys) and gamma-glutamylcysteine (gamma-EC) in the presence of 25 and 50 microM Cd2+, but quantities and rates of synthesis were different. In H4-2-4, exposure to 50 microM Cd2+ increased GSH levels to 262% of the control; in H8-2-1 it increased to 156%. Mycelia of the two strains were analysed for peroxidase, dehydroascorbate reductase, glutathione reductase and glucose-6-phosphate dehydrogenase. With Cd2+ exposure, peroxidase activity increased in both strains. Cu2+ stress increased dehydroascorbate reductase activity in H4-2-4 but not in H8-2-1. Dehydroascorbate reductase and glucose-6-phosphate dehydrogenase activities progressively declined in the presence of Cd2+, indicating a correlation with Cd2+ accumulation in both strains. Cd2+ and Cu2+ exposure decreased glutathione reductase activity.

Sulphate assimilation under Cd2+ stress in Physcomitrella patens--combined transcript, enzyme and metabolite profiling.

Cd(2+) causes disturbance of metabolic pathways through severe damage on several levels. Here we present a comprehensive study of Cd(2+)-mediated effects on transcript, enzyme and metabolite levels in a plant without phytochelatin (PC). The moss Physcomitrella patens (Hedw.) B.S.G. was stressed with up to 10 microm Cd(2+) to investigate the regulation of gene transcription and activities of enzymes involved in the assimilatory sulphate reduction pathway and in glutathione biosynthesis. Real-time PCR, specific enzyme assays as well as thiol peptide profiling techniques were applied. Upon supplementation of 10 microm Cd(2+), the moss showed a more than fourfold increase in expression of genes encoding ATP sulphurylase (ATPS), adenosylphosphosulphate reductase, phosphoradenosylphosphorsulphate reductase, sulphite reductase (SiR) and gamma-glutamyl cysteine synthetase (gamma-ECS). Likewise, elevated enzyme activities of gamma-ECS and glutathione synthetase were observed. Contrarily, activity of O-acetylserine (thiol) lyase (OAS-TL), responsible for biosynthesis of cysteine, was diminished. At the metabolite level, nearly doubling of intracellular cysteine and glutathione content was noted, while the moss did not produce any detectable amounts of PCs. These results suggest a Cd(2+)-induced activation of the assimilatory sulphate reduction pathway as well as of glutathione biosynthesis on different levels of regulation.

Species-specific Cd-stress response in the white rot basidiomycetes Abortiporus biennis and Cerrena unicolor.

The effect of cadmium (Cd) on fungal growth, Cd bioaccumulation and biosorption, and on the formation of potential heavy metal response indicators such as thiols, oxalate, and laccase was investigated in the white rot fungi Cerrena unicolor andAbortiporus biennis. Only the highest Cd concentration employed (200 microM) inhibited growth of C. unicolor, whereas already lower Cd concentrations caused decreasing mycelia dry weights in A. biennis. Cd biosorption onto the mycelial surface was the predominant Cd sequestration mechanism in C. unicolor. Surface-bound and bioaccumulated Cd concentrations were essentially in the same range in A. biennis, leading to considerably higher intracellular Cd concentrations in A. biennis than in C. unicolor. Oxalate and laccase were produced by both of the fungal strains and their extracellular levels were elevated upon Cd exposure. Oxalate concentrations and laccase titres were considerably higher in C. unicolor than in A. biennis. Both fungi responded to increasing Cd concentrations by increasing intracellular amounts of thiol compounds (cysteine, gamma-glutamylcysteine, glutathione in both its reduced and oxidized form) but Cd application increased the amounts of thiols to a higher extend in A. biennis. Taken together, these species-specific responses towards Cd suggest that C. unicolor possesses a more efficient system than A. biennis to keep intracellular Cd concentrations low.

Biotransformation of 1-naphthol by a strictly aquatic fungus.

The aquatic hyphomycete Heliscus lugdunensis belongs to a group of exclusively aquatic mitosporic fungi with an only scarcely explored potential to oxidatively attack xenobiotic compounds, and was used to study the biotransformation of the environmental pollutant metabolite 1-naphthol. H. lugdunensis metabolized approximately 74% of 1-naphthol within 5 days. The identification and quantification of degradation products using gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, and high performance liquid chromatography revealed that approximately 12% of the parent compound was converted into 1-naphthylsulfate, 3% was transformed into 1-methoxy-naphthalene, and less than 1% was converted into 1,4-naphthoquinone. A further metabolite, most likely 4-hydroxy-1-naphthylsulfate, was also detected. In contrast to sulfate conjugate metabolites, no glucuronide and glucoside conjugates of 1-naphthol were found, and neither UDP-glucuronyltransferase nor UDP-glucosyltransferase present in H. lugdunensis showed activity towards 1-naphthol. These results support a role of fungi adapted to aquatic environments in affecting the environmental fate of pollutants in aquatic ecosystems.

Cadmium induces a novel metallothionein and phytochelatin 2 in an aquatic fungus.

Cadmium stress response was measured at the thiol peptide level in an aquatic hyphomycete (Heliscus lugdunensis). In liquid culture, 0.1 mM cadmium increased the glutathione (GSH) content and induced the synthesis of additional thiol peptides. HPLC, electrospray ionization mass spectrometry, and Edman degradation confirmed that a novel small metallothionein as well as phytochelatin (PC2) were synthesized. The metallothionein has a high homology to family 8 metallothioneins (http://www.expasy.ch/cgi-bin/lists?metallo.txt). The bonding of at least two cadmium ions to the metallothionein was demonstrated by mass spectrometry (MALDI MS). This is the first time that simultaneous induction of metallothionein and phytochelatin accompanied by an increase in GSH level has been shown in a fungus under cadmium stress, indicating a potential function of these complexing agents for in vivo heavy metal detoxification. The method presented here should be applicable as biomarker tool.

Cadmium and zinc response of the fungi Heliscus lugdunensis and Verticillium cf. alboatrum isolated from highly polluted water.

The aquatic hyphomycete Heliscus lugdunensis and the terrestrial fungus Verticillium cf. alboatrum, both isolated from a highly polluted surface water, were investigated for their tolerance against Cd and Zn. Hl-H4 showed a 50% growth inhibition at 0.1 mM Cd, whereas at 0.7 mM Cd the growth of Va-H4 was only reduced by 30%. The fungi also showed a remarkable difference in their Zn-tolerance. The growth of Va-H4 was not inhibited at 1 mM Zn, whereas for Hl-H4 no growth occurred above 0.3 mM Zn. The biosorption and accumulation capacities for Cd or Zn of both fungi differed between the fungal species. In a 0.1 mM Cd-medium Hl-H4 biosorbed 15-fold and accumulated 39-fold more Cd than Va-H4. Exposure to 0.3 mM Zn resulted in a 13-fold higher biosorption and 11-fold higher accumulation for Hl-H4 than Va-H4. As glutathione (GSH) is known to be involved in the phytochelatin synthesis and other stress related processes we investigated its synthesis. Both fungi increased their synthesis of GSH in response to Cd. For Hl-H4 a concentration of 0.0125 mM Cd, corresponding to an intracellular Cd content of 2.1 nmol Cd mg(-1) dw, increased the GSH content, whereas Va-H4 only responded with a higher production of GSH at 1 mM Cd and a concomitant intracellular Cd content of 22.5 nmol Cd mg(-1) dw. An increased GSH synthesis under Zn-stress was only detectable for Va-H4 (20 mM).

Quantification of metallothionein-like proteins in the mussel Mytilus galloprovincialis using RP-HPLC fluorescence detection.

A HPLC-fluorescence method, using the fluorophore SBD-F (ammonium-7-fluorobenz-2-oxa-1,3-diazole-4-sulfonate), was adapted for the quantification of metallothioneins and their isoforms from the Moroccan mussel Mytilus galloprovincialis. The method was first optimized using a rabbit liver metallothionein. The effects of EDTA, tris(2-carboxyethyl)phosphine, and SBD-F on the labeling efficiency were studied. The optimized method was then applied to evaluate the amount of metallothionein in the mussels either exposed to cadmium in the laboratory or collected from the Casablanca coast, Morocco. The concentrations of metallothioneins measured in the field samples describe the degree of contamination of the sites and are reflected by distinct isoform patterns.