An overview of in situ remediation for groundwater co-contaminated with heavy metals and petroleum hydrocarbons

Groundwater is an important component of water resources. Mixed pollutants comprising heavy metals (HMs) and petroleum hydrocarbons (PHs) from industrial activities can contaminate groundwater through such processes as rainfall infiltration, runoff and discharge, which pose direct threats to human health through the food chain or drinking water. In situ remediation of contaminated groundwater is an important way to improve the quality of a water environment, develop water resources and ensure the safety of drinking water. Bioremediation and permeable reactive barriers (PRBs) were discussed in this paper as they were effective and affordable for in situ remediation of complex contaminated groundwater. In addition, media types, technology combinations and factors for the PRBs were highlighted. Finally, insights and outlooks were presented for in situ remediation technologies for complex groundwater contaminated with HMs and PHs. The selection of an in situ remediation technology should be site specific. The remediation of complex contaminated groundwater can be approached from various perspectives, including the development of economical materials, the production of slow-release and encapsulated materials, and a combination of multiple technologies. This review is expected to provide technical guidance and assistance for in situ remediation of complex contaminated groundwater.

An evaluation framework for quantifying vegetation loss and recovery in response to meteorological drought based on SPEI and NDVI

Drought affects vegetation growth to a large extent. Understanding the dynamic changes of vegetation during drought is of great significance for agricultural and ecological management and climate change adaptation. The relations between vegetation and drought have been widely investigated, but how vegetation loss and restoration in response to drought remains unclear. Using the standardized precipitation evapotranspiration index (SPEI) and the normalized difference vegetation index (NDVI) data, this study developed an evaluation framework for exploring the responses of vegetation loss and recovery to meteorological drought, and applied it to the humid subtropical Pearl River basin (PRB) in southern China for estimating the loss and recovery of three vegetation types (forest, grassland, cropland) during drought using the observed NDVI changes. Results indicate that vegetation is more sensitive to drought in high-elevation areas (lag time < 3 months) than that in low-elevation areas (lag time > 8 months). Vegetation loss (especially in cropland) is found to be more sensitive to drought duration than drought severity and peak. No obvious linear relationship between drought intensity and the extent of vegetation loss is found. Regardless of the intensity, drought can cause the largest probability of mild loss of vegetation, followed by moderate loss, and the least probability of severe loss. Large spatial variability in the probability of vegetation loss and recovery time is found over the study domain, with a higher probability (up to 50 %) of drought-induced vegetation loss and a longer recovery time (>7 months) mostly in the high-elevation areas. Further analysis suggests that forest shows higher but cropland shows lower drought resistance than other vegetation types, and grassland requires a shorter recovery time (4.2-month) after loss than forest (5.1-month) and cropland (4.8-month).

Significance of temperature as a key driver in ZVI PRB applications for PCE degradation

We report on the potential of elevated groundwater temperatures and zero-valent iron permeable reactive barriers (ZVI PRBs), for example, through a combination with underground thermal energy storage (UTES), to achieve enhanced remediation of chlorinated hydrocarbon (CHC) contaminated groundwater. Building on earlier findings concerning deionized solutions, we created a database for mineralized groundwater based on temperature dependence of tetrachloroethylene (PCE) degradation using two popular ZVIs (i.e., Gotthart-Maier cast iron [GM] and ISPAT sponge iron [IS]) in column experiments at 25 °C-70 °C to establish a temperature-dependent ZVI PRB dimensioning approach. Scenario analysis revealed that a heated ZVI PRB system in a moderate temperature range up to 40 °C showed the greatest efficiency, with potential material savings of ~55% to 75%, compared to 10 °C, considering manageability and longevity. With a 25 °C-70 °C temperature increase, rate coefficients of PCE degradation increased from 0.4 ± 0.0 h-1 to 2.9 ± 2.2 h-1 (GM) and 0.1 ± 0.1 h-1 to 1.8 ± 0.0 h-1 (IS), while TCE rate coefficients increased from 0.6 ± 0.1 h-1 to 5.1 ± 3.9 h-1 at GM. Activation energies for PCE degradation yielded 32 kJ mol-1 (GM) and 56 kJ mol-1 (IS). Temperature-dependent anaerobic iron corrosion was key in regulating mineral precipitation and passivation of the iron surface as well as porosity reduction due to gas production.

A preliminary approach based on numerical simulation modelling and evaluation of permeable reactive barrier for aquifer remediation susceptible to selenium contaminant

In this study, numerical groundwater modelling software (GMS) was applied for a 2D transient state predictive (flow and contaminant fate and transport) conceptual model for heavy metal (Selenium in this research) contaminated groundwater, Imamzadeh-Jafar Aquifer, Kohgiluyeh and Boyer-Ahmad Province, Iran. The performances of permeable reactive barrier (PRB) in pollutant removal in the contaminated aquifers were studied by helping the MODFLOW-MT3DMS model. The spatiotemporal distribution of Selenium (Se) contaminant over the aquifer was illustrated using the calibrated flow and contaminant model. According to the findings, the downward movement of Se has resulted in an unsafe and undesirable water quality status in the Imamzadeh-Jafar aquifer, which is supported by field data. The sensitivity analysis of PRB layouts, geometric features, and reactant material characteristics was conducted in groundwater remediation. The numerical model results illustrated that the PRB thickness, ranging from 10 to 500 m, manifested the drop in Se concentration approximately from 40 to 46%. The results shed light on the hydraulic conductivity variations of reactant materials have effects less than 0.5% in Se removals. Furthermore, the decay rate variations in the ranges from 0.0001 to 0.01 d^-1 could result in Se removal from 5 to 100%. According to studies, if the contaminant sources are prevented, in a) installation of PRB and b) not installation of PRB scenarios, the Imamzadeh-Jafar aquifer remediation will take 6 months and 84 months, respectively.

Nickel Isotope Fractionation As an Indicator of Ni Sulfide Precipitation Associated with Microbially Mediated Sulfate Reduction

Microbially mediated sulfate reduction is a promising cost-effective and sustainable process utilized in permeable reactive barriers (PRB) and constructed wetlands to treat mine wastewater. Laboratory batch experiments were performed to evaluate nickel (Ni) isotope fractionation associated with precipitation of Ni-sulfides in the presence of the sulfate-reducing bacterium (SRB) Desulfovibrio desulfuricans^T (DSM-642). Precipitates were collected anaerobically and characterized by synchrotron powder X-ray diffraction (PXRD), scanning electron microscopy combined with energy-dispersive X-ray spectroscopy (SEM-EDS), and transmission electron microscopy (TEM). Solid-phase analyses showed that the precipitates associated with bacteria attached to the serum bottle walls were characterized by enhanced size and crystallinity. Lighter Ni isotopes were preferentially concentrated in the solid phase, whereas the solution was enriched in heavier Ni isotopes compared to the input solution. This fractionation pattern was consistent with closed-system equilibrium isotope fractionation, yielding a fractionation factor of Δ⁶⁰Ni_solid-aq = -1.99‰. The Ni isotope fractionation measured in this study indicates multiple Ni reaction mechanisms occurring in the complex SRB-Ni system. The results from this study offer insights into Ni isotope fractionation during interaction with SRB and provide a foundation for the characterization and development of Ni stable isotopes as tracers in environmental applications.

Research and application of arsenic-contaminated groundwater remediation by manganese ore permeable reactive barrier

Arsenic pollution in the water environment is one of the important environmental problems at present. High arsenic groundwater and its resulting local arsenic poisoning have caused a great threat to human life and health. The permeable reactive barrier (PRB) is an underground in-situ remediation technology, which has the advantages of high efficiency, low energy consumption, long aging, low operating and maintenance costs. By studying the arsenic removal effects of different materials, this paper selected natural manganese ore, manganese ore granulation, loaded manganese ore and mixed manganese ore as fillers for PRB. And it conducted a simulated experiment to study the feasibility of actual PRB engineering to repair arsenic-containing groundwater. The experiment proves that the removal rate of arsenic by four manganese ore materials exceeds 90%. After examining the geographical location and hydrogeological conditions of the PRB project, the Dengjiatang area of Chenzhou City, Hunan Province was selected as the construction area. Studies show that after the completion of PRB, the arsenic content of the effluent at each monitoring point is below 10 μg/L. It indicates that all four fillers achieve the purpose of removing arsenic, and can be applied to the project according to actual needs. Finally, the safety evaluation of the PRB project was carried out. And FeCl₃·6H₂O was selected as the base curing material and cement was as the process auxiliary stabilizer to solidify the arsenic-containing waste residue. The arsenic concentration in the leaching solution of the arsenic slag after curing is only 1 μg/L.

Characterization of Nuclear Progesterone Receptor Isoforms in the Term Equine Placenta

In equine parturition, the role of progestins along with the nuclear progesterone receptor (nPR) signaling pathway in the placenta is not completely clarified. The progestins play an integral role in maintaining myometrial quiescence during the late stage of pregnancy via acting on nPR isoforms (PRA and PRB; PRB is more active than PRA). The current study aimed to determine the PRA and PRB expressions in the term equine placenta at the gene and protein levels. Six term equine placentas were used in this study. Reverse transcription polymerase chain reaction (RT-PCR) was used to quantify the mRNA expression for PRA and PRB. The protein expression was detected using the Western Blot technique. The results revealed that the mRNA and protein expressions for PRA were significantly higher (P < 0.0001) in the term equine placental tissue compared to the mRNA and protein expressions of PRB. These results demonstrated that nPRs are detectable in the term placenta of mares and PRA is the dominant isoform expressed. The present findings raised the possibility that the PRA plays an important role in the parturition process and expulsion of the placenta in mares.

Application of enhanced electrokinetic approach to remediate Cr-contaminated soil: Effect of chelating agents and permeable reactive barrier

Enhanced electrokinetic (EK) technique was employed to remediate Cr-contaminated soil using a permeable reactive barrier (PRB) and chelating agents. Synthesized nanomagnetic Fe₃O₄ was used as a reactive material in PRB. Moreover, EDTA and citric acid (CA) were used as chelating agents. Sequential extraction method (SEM) was employed to determine Cr-elimination mechanism during the EK process. The results revealed that EDTA (78% Cr removal) was more effective than CA (54% Cr removal) in eliminating Cr from the contaminated soil during the EK process. The application of PRB in combination with EDTA was able to reduce the Cr removal rate to 70 and 66% by locating PRB in the middle section and near the anode/cathode reservoir, respectively. The use of PRB coupled with EDTA near the anode and cathode led to a more uniform Cr removal from the soil during the EK process. The highest energy consumption was 0.12 KWh during the EK remediation using PRB. Traditional EK remediation could only remove exchangeable and carbonate fractions of Cr. The use of chelating agents led to a significant (more than 90%) increase in Cr removal from the following fractions: exchangeable phase, carbonate phase, and bond to Fe-Mn oxides. In addition to electromigration (EM) mechanism, electroosmotic flow (EOF) played an important role in Cr removal during the EK process, especially when coupled with PRB.

Ligand-activated progesterone receptor B activates transcription factor EB to promote autophagy in human breast cancer cells

Autophagy is an evolutionary conserved, self-eating process that targets cellular constituents for lysosomal degradation. Transcription factor EB (TFEB) is a master regulator of autophagy by inducing the expression of genes involved in autophagic and lysosomal degradation. In breast cancer, ligand-activated progesterone receptor has been reported to influence cancer development by manipulating the autophagy pathway. However, understanding of the mechanism that underlies this autophagic response remains limited. Herein, we report that prolonged treatment with progestin R5020 upregulates autophagy in MCF-7 human breast cancer cells via a novel interplay between progesterone receptor B (PRB) and TFEB. R5020 upregulates TFEB gene expression and protein levels in a PRB-dependent manner. Additionally, R5020 enhances the co-recruitment of PRB and TFEB to each other to facilitate TFEB nuclear localization. Once in the nucleus, TFEB induces the expression of autophagy and lysosomal genes to potentiate autophagy. Together, our findings highlight a novel functional connection between ligand-activated PRB and TFEB to modulate autophagy in MCF-7 breast cancer cells. As breast cancer development is controlled by autophagy, the progestin-PRB-TFEB transduction pathway warrants future attention as a potential therapeutic target in cancer therapy.

Pervious concrete reactive barrier containing nano-silica for nitrate removal from contaminated water

In this research, the effectiveness of using pervious concrete as a reactive barrier to decrease the concentration of nitrates in polluted water was investigated. Parameters of concrete mix design including water to cement ratio (W/C), aggregate to cement ratio (A/C), the amount of nano-silica (NS), and fine aggregates (FA) were studied based on Taguchi method. Properties of concrete such as compressive strength, density, permeability, and porosity, as well as pH measurement and the column method were carried out to assess the nitrate removal capacity of pervious concrete. Also, SEM-EDX, XRD, and FTIR were used to analyze the results. It was found that the optimum mix design in terms of nitrate removal corresponded to the mix with W/C = 0.26, A/C = 5, NS = 6%, and FA = 20%. Based on the results, it can be said that adding NS (up to 6%) and FA (up to 20%) to pervious concrete had the best influence on nitrate removal and compressive strength. Addition of NS increased the nitrate removal capacity due to increase in surface positive charges and provision of new surface functional groups.

Effect and mechanism analysis of MnO2 on permeable reactive barrier (PRB) system for the removal of tetracycline

Effect of manganese dioxide (MnO₂) on tetracycline (TC) removal/degradation in zero-valent iron (ZVI) based permeable reactive barrier (PRB) system was investigated. To analyze the role of MnO₂, three different PRB columns packed with ZVI, ZVI and a layer of MnO₂, and MnO₂ were set up to investigate the removal effect and reaction mechanism of ZVI coupling with MnO₂ on TC removal, respectively. The results show that the removal efficiencies of three PRB columns are 65%, 85%, and 50%, respectively. MnO₂ could accelerate the transformation of Fe²⁺ into Fe³⁺ and combine with Fe³⁺ to degrade TC in different reaction sites in the ZVI-MnO₂ PRB system. Hydroxyl radicals (·OH) were produced in this process, which contributed to about 58.3% for the TC degradation. The UV-Vis spectrum demonstrated that A ring of TC was the main reaction site for interaction with Fe³⁺ and the BCD rings were crucial for interactions with MnO₂. On the basis of intermediates identified by LC-ESI-MS, the ring structure of TC was opened, and low-molecular-weight compounds were produced in ZVI-MnO₂ PRB system.

Remediation of persistent organic pollutant-contaminated soil using biosurfactant-enhanced electrokinetics coupled with a zero-valent iron/activated carbon permeable reactive barrier

Zero-valent iron/activated carbon (Fe/C) particles can degrade persistent organic pollutants via micro-electrolysis and therefore, they may be used to develop materials for permeable reactive barriers (PRBs). In this study, surfactant-enhanced electrokinetics (EK) was coupled with a Fe/C-PRB to treat phenanthrene (PHE) and 2,4,6-trichlorophenol (TCP) co-contaminated clay soil. An environment-friendly biosurfactant, rhamnolipid, was selected as the solubility-enhancing agent. Five bench-scale tests were conducted to investigate the performance of EK-PRB on PHE and TCP removal from soil as well as the impact of pH and rhamnolipid concentration. The results show that both PHE and TCP, driven by electro-osmotic flow (EOF), moved toward the cathode and reacted with the Fe/C-PRB. Catholyte acidification and rhamnolipid concentration increase improved the removal efficiencies of PHE and TCP. The highest removal efficiency of PHE in soil column was five times the efficiency of the control group on which only EK was applied (49.89 versus 9.40%). The highest removal efficiency of TCP in soil column was 4.5 times the efficiency of the control group (64.60 versus 14.30%). Desorption and mobility of PHE and TCP improved with the increase of rhamnolipid concentration when this exceeded the critical micelle concentration. This study indicates that the combination of EK and a Fe/C-PRB is efficient and promising for removing persistent organic pollutants (POPs) from contaminated soil with the enhancement of rhamnolipid.

Treatment of decabromodiphenyl ether (BDE209) contaminated soil by solubilizer-enhanced electrokinetics coupled with ZVI-PRB

Decabromodiphenyl ether (BDE209) is a typical soil contaminant released from e-waste recycling sites (EWRSs). Electrokinetics (EK) has been considered as an excellent treatment technology with a promising potential to effectively remove organic pollutants in soil. In this study, the treatment of BDE209-polluted soil by EK was explored. All the EK experiments were conducted under a constant voltage gradient (2 V cm^-1) for 14 days. Deionized water (DI water), hydroxypropyl-β-cyclodextrin (HPCD), sodium dodecyl sulfate (SDS), and humic acid (HA) were applied as the processing fluid. The experimental results showed that all the solubilizers could effectively promote the mobility and transport of BDE209 in the soil via the electro-osmotic flow (EOF) or electromigration. The removal efficiencies achieved in S1 section were 24, 22, and 26% using HPCD, SDS, and HA as the processing fluid. However, the removal of BDE209 for the entire soil cell was not achieved until zero valence iron (ZVI) was inserted at the center of soil column as a permeable reactive barrier (PRB) or (ZVI-PRB), which enhanced the degradation of BDE209. As ZVI-PRB was installed in EK5 and EK6 experiments, the corresponding average removal efficiencies increased to 16 and 13%, respectively. Additionally, the degradation products of BDE209 analyzed by GC-MS suggested that debromination of BDE209 was the main potential degradation mechanism in the EK treatment in the presence of ZVI-PRB.

Concentration effects on biotic and abiotic processes in the removal of 1,1,2-trichloroethane and vinyl chloride using carbon-amended ZVI

A permeable reactive barrier, consisting of both zero valent iron (ZVI) and a biodegradable organic carbon, was evaluated for the remediation of 1,1,2-trichloroethane (1,1,2-TCA) contaminated groundwater. During an 888 day laboratory column study, degradation rates initially stabilized with a degradation half-life of 4.4±0.4 days. Based on the accumulation of vinyl chloride (VC) and limited production of 1,1-dichloroethene (1,1-DCE) and 1,2-dichloroethane (1,2-DCA), the dominant degradation pathway was likely abiotic dichloroelimination to form VC. Degradation of VC was not observed based on the accumulation of VC and limited ethene production. After a step reduction in the influent concentration of 1,1,2-TCA from 170±20 mg L(-1) to 39±11 mg L(-1), the degradation half-life decreased 5-fold to 0.83±0.17 days. The isotopic enrichment factor of 1,1,2-TCA also changed after the step reduction from -14.6±0.7‰ to -0.72±0.12‰, suggesting a possible change in the degradation mechanism from abiotic reductive degradation to biodegradation. Microbiological data suggested a co-culture of Desulfitobacterium and Dehalococcoides was responsible for the biodegradation of 1,1,2-TCA to ethene.

Microbial and mineral evolution in zero valent iron-based permeable reactive barriers during long-term operations

Impacts of subsurface biogeochemical processes over time have always been a concern for the long-term performance of zero valent iron (Fe(0))-based permeable reactive barriers (PRBs). To evaluate the biogeochemical impacts, laboratory experiments were performed using flow-through glass columns for 210 days at controlled temperature (20 °C). Two different particle sizes of Fe(0) were used in the columns, and to simulate indigenous microbial activity, extra carbon source was provided in the two columns (biotic columns) and the remaining two columns were kept abiotic using gamma radiations. Heavy metals (Zn, As) were removed efficiently in all the columns, and no exhaustion of treatment capability or clogging was observed during our experimental duration. Newly formed Fe mineral phases and precipitates were characterized using X-ray diffraction (XRD), scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX), and micro-XRF techniques in solid phase at the end of the experiment. In addition, 16S rRNA gene extraction was used for microbial community identification in biotic columns. During the incubation, microbial population shifted in favor of Desulfosporosinus species (sulfate-reducing bacteria) from initial dominance of Acidithiobacillus ferrooxidans in sediments. Dominant mineral phases detected in biotic columns were mackinawite (FeS) and sulfate green rust, while in abiotic columns, magnetite/maghemite phases were more prevalent.

A permeable reactive barrier (PRB) media sequence for the remediation of heavy metal and hydrocarbon contaminated water: A field assessment at Casey Station, Antarctica

A field trial was conducted at Casey Station, Antarctica to assess the suitability of a permeable reactive barrier (PRB) media sequence for the remediation of sites containing both hydrocarbon and heavy metal contamination. An existing PRB was modified to assess a sequence consisting of three sections: (i) Nutrient release/hydrocarbon sorption using ZeoPro™ and granular activated carbon; (ii) Phosphorus and heavy metal capture by granular iron and sand; (iii) Nutrient and excess iron capture by zeolite. The media sequence achieved a greater phosphorus removal capacity than previous Antarctic PRB configurations installed on site. Phosphorus concentrations were reduced during flow through the iron/sand section and iron concentrations were reduced within the zeolite section. However, non-ideal flow was detected during a tracer test and supported by analysis of media and liquid samples from the second summer of operation. Results indicate that the PRB media sequence trialled might be appropriate for other locations, especially less environmentally challenging contaminated sites.

The specific reactive surface area of granular zero-valent iron in metal contaminant removal: Column experiments and modelling

A series of dynamic-flow kinetic experiments were conducted to assess the removal rates of aqueous Cu(2+) and Zn(2+) ions by zero-valent iron (ZVI), a promising material for inclusion in cold-climate remediation applications. The influence of experimental parameters on contaminant removal rates, including aqueous flow rate, operating temperature, and the concentrations of ZVI, salt and dissolved oxygen, was investigated. A mass transport model has been developed that accounts (i) aqueous-phase dispersion processes, (ii) film diffusion of contaminant ions to the reactive ZVI surface and (iii) the reactive removal mechanism itself. Regression to the experimental data indicated that when oxygen is present in the solution feed Cu(2+) and Zn(2+) removal processes were limited by film diffusion. In de-aerated solutions film diffusion still controls Cu(2+) removal but a first-order surface reaction provides a better model for Zn(2+) kinetics. Using air as the equilibrium feed gas, the reactive proportion of the total surface area for contaminant removal was calculated to be 97% and 64% of the active spherically-assumed geometric area associated with ZVI media for Cu(2+) and Zn(2+), respectively. Relative to a gas absorption area, determined in previous studies, the reactive proportion is less than 0.41% of the unreacted ZVI total surface area. These findings suggest that only part of the iron oxyhydroxide surface is reacting during ZVI based metal contaminant removal.

Degassing, gas retention and release in Fe(0) permeable reactive barriers

Corrosion of Fe(0) has been successfully utilized for the reductive treatment of multiple contaminants. Under anaerobic conditions, concurrent corrosion leads to the generation of hydrogen and its liberation as a gas. Gas bubbles are mobile or trapped within the irregular pore structure leading to a reduction of the water filled pore volume and thus decreased residence time and permeability (gas clogging). With regard to the contaminant transport to the reactive site, the estimation of surface properties of the reactive material indicated that individual gas bubbles only occupied minor contact areas of the reactive surface. Quantification of gas entrapment by both gravimetrical and tracer investigations revealed that development of preferential flow paths was not significant. A novel continuous gravimetrical method was implemented to record variations in gas entrapment and gas bubble releases from the reactive filling. Variation of grain size fractions revealed that the pore geometry had a significant impact on gas release. Large pores led to the release of comparably large gas amounts while smaller volumes were released from finer pores with a higher frequency. Relevant processes are explained with a simplified pictorial sequence that incorporates relevant mechanisms.

Coexisting hybrid malignancy in a solitary sporadic solid benign renal mass: implications for treating patients following renal biopsy

PURPOSE

Concern regarding coexisting malignant pathology in benign renal tumors deters renal biopsy and questions its validity. We examined the rates of coexisting malignant and high grade pathology in resected benign solid solitary renal tumors.

MATERIALS AND METHODS

Using our prospectively maintained database we identified 1,829 patients with a solitary solid renal tumor who underwent surgical resection between 1994 and 2012. Lesions containing elements of renal oncocytoma, angiomyolipoma or another benign pathology formed the basis for this analysis. Patients with an oncocytic malignancy without classic oncocytoma and those with known hereditary syndromes were excluded from study.

RESULTS

We identified 147 patients with pathologically proven elements of renal oncocytoma (96), angiomyolipoma (44) or another solid benign pathology (7). Median tumor size was 3.0 cm (IQR 2.2-4.5). As quantified by the R.E.N.A.L. (radius, exophytic/endophytic, nearness to collecting system or sinus, anterior/posterior and location relative to polar lines) nephrometry score, tumor anatomical complexity was low in 28% of cases, moderate in 56% and high in 16%. Only 4 patients (2.7%) were documented as having hybrid malignant pathology, all involving chromophobe renal cell carcinoma in the setting of renal oncocytoma. At a median followup of 44 months (IQR 33-55) no patient with a hybrid tumor experienced regional or metastatic progression.

CONCLUSIONS

In our cohort of patients with a solitary, sporadic, solid benign renal mass fewer than 3% of tumors showed coexisting hybrid malignancy. Importantly, no patient harbored coexisting high grade pathology. These data suggest that uncertainty regarding hybrid malignant pathology coexisting with benign pathological components should not deter renal biopsy, especially in the elderly and comorbid populations.

The effect of multiple primer-template mismatches on quantitative PCR accuracy and development of a multi-primer set assay for accurate quantification of pcrA gene sequence variants

Quantitative PCR (qPCR) is a critical tool for quantifying the abundance of specific organisms and the level or expression of target genes in medically and environmentally relevant systems. However, often the power of this tool has been limited because primer-template mismatches, due to sequence variations of targeted genes, can lead to inaccuracies in measured gene quantities, detection failures, and spurious conclusions. Currently available primer design guidelines for qPCR were developed for pure culture applications, and available primer design strategies for mixed cultures were developed for detection rather than accurate quantification. Furthermore, past studies examining the impact of mismatches have focused only on single mismatches while instances of multiple mismatches are common. There are currently no appropriate solutions to overcome the challenges posed by sequence variations. Here, we report results that provide a comprehensive, quantitative understanding of the impact of multiple primer-template mismatches on qPCR accuracy and demonstrate a multi-primer set approach to accurately quantify a model gene pcrA (encoding perchlorate reductase) that has substantial sequence variation. Results showed that for multiple mismatches (up to 3 mismatches) in primer regions where mismatches were previously considered tolerable (middle and 5' end), quantification accuracies could be as low as ~0.1%. Furthermore, tests were run using a published pcrA primer set with mixtures of genomic DNA from strains known to harbor the target gene, and for some mixtures quantification accuracy was as low as ~0.8% or was non-detect. To overcome these limitations, a multiple primer set assay including minimal degeneracies was developed for pcrA genes. This assay resulted in nearly 100% accurate detection for all mixed microbial communities tested. The multi-primer set approach demonstrated herein can be broadly applied to other genes with known sequences.