Publications by authors named "Ioannis Anastopoulos"

36 Publications

Enhanced uranium removal from acidic wastewater by phosphonate-functionalized ordered mesoporous silica: Surface chemistry matters the most.

J Hazard Mater 2021 Feb 4;413:125279. Epub 2021 Feb 4.

Department of Chemistry, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus. Electronic address:

The removal of uranium species from aqueous phases using non-hazardous chemicals is still an open challenge, and remediation by adsorption is a prosperous strategy. Among the most crucial concerns regarding the design of an efficient material as adsorbent are, except the cost and the green character, the feasibility to be stable and effective under acidic pH, and to selectively adsorb the desired metal ion (e.g. uranium). Herein, we present a phosphonate functionalized ordered mesoporous silica (OMS-P), prepared by a one-step co-condensation synthesis. The physicochemical features of the material were determined by HR-TEM, XPS, EDX, N sorption, and solid NMR, while the surface zeta potential was also measured. The removal efficiency was evaluated at two different temperatures (20 and 50 °C) in acidic environment to avoid interferences like solid phase formation or carbonate complexation and the adsorption isotherms, including data fitting with Langmuir and Freundlich models and thermodynamic parameters are presented and discussed. The high and homogeneous dispersion of the phosphonate groups within the entire silica's structure led to the greatest reported up-todays capacity (345 mg/g) at pH = 4, which was achieved in less than 10 min. Additionally, OMS-P showed that the co-presence of other polyvalent cation like Eu(III) did not affect the efficiency of adsorption, which occurs via inner-sphere complex formation. The comparison to the non-functionalized silica (OMS) revealed that the key feature towards an efficient, stable, and selective removal of the U(VI) species is the specific surface chemistry rather than the textural and structural features. Based on all the results and spectroscopic validations of surface adsorbed U(VI), the main interactions responsible for the elevated uranium removal were proposed.
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http://dx.doi.org/10.1016/j.jhazmat.2021.125279DOI Listing
February 2021

Enhancing cadmium extraction potential of Brassica napus: Effect of rhizosphere interactions.

J Environ Manage 2021 Apr 3;284:112056. Epub 2021 Feb 3.

College of Resources and Environment, Hunan Agricultural University, Changsha, Hunan, 410128, PR China; Key Laboratory for Rural Ecosystem Health in the Dongting Lake Area of Hunan Province, Changsha, 410128, PR China. Electronic address:

Brassica napus L. (oilseed rape) was grown with daikon and white lupin in a polyvinyl chloride split pot experiment (with no barrier between the compartments or by a nylon mesh barrier (37 μm) to license partial root interaction, or a solid barrier to stop any root interactions) to examine the effect of rhizosphere interaction on the cadmium uptake. The results showed that shoot and root biomasses of oilseed rape were 40.66% and 26.94% less than that of the monocropped treatment (solid barrier) when intercropping with daikon under the rhizosphere complete interaction. However, the intermingling of roots between oilseed rape and white lupin notably enhanced the dry biomass of oilseed rape by 40.23% and decreased with the reduction of root contact. Oilseed rape intercropping with daikon enhanced the shoot Cd concentration of oilseed rape. The shoot Cd concentration (44.8 mg/kg) of oilseed rape when intercropped white lupin under complete rhizosphere interaction were greater than those of other treatments. Additionally, the intermingling of roots played a positive role in the content of citric and malic acids when intercropping with white lupin. In all systems, the BCF values of oilseed rape >5. Therefore, intercropping with white lupin may contribute to higher biomass and increased uptake Cd by oilseed rape. We can toward sustainable positive effects on phytoremediation that based on a better understanding of rhizosphere processes.
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http://dx.doi.org/10.1016/j.jenvman.2021.112056DOI Listing
April 2021

Single-use surgical face masks, as a potential source of microplastics: Do they act as pollutant carriers?

J Mol Liq 2021 Mar 5;326:115247. Epub 2021 Jan 5.

Laboratory of Radioanalytical and Environmental Chemistry, Department of Chemistry, University of Cyprus, P.O. Box 20537, CY-1678 Nicosia, Cyprus.

Millions of people are using face coverings (including single-use surgical face masks) as a result of the COVID-19 pandemic and a large number of used masks, particularly single-use masks enter uncontrolled the environment since most of the users have little information on how to dispose of them safely. This new important waste is a potential source of microplastics, which is found nowadays in many parks, streets, and coastlines. Discarded masks will be finally drained to the ocean polluting the marine environment and threatening marine life. This short communication examines the role of face masks and subsequently mask-derived microplastics as pollutant carriers in environmental compartments (e.g. hydrosphere, biosphere, etc.) by investigating their sorption characteristics regarding dye molecules. In this context, batch-type equilibrium experiments were performed and the effect of different sorption parameters has been explored (i.e. contact time and temperature). The results show that single-use surgical face masks can act as dye carriers (Methylene Blue, Crystal Violet and Malachite Green) in the aquatic environment. In addition, preliminary experiments on the thermal treatment of face masks and the use of the resulting carbonaceous material as efficient adsorbent have been performed, pointing out a possibility for used mask disinfection and recycling.
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http://dx.doi.org/10.1016/j.molliq.2020.115247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7834851PMC
March 2021

Arbuscular mycorrhizal fungi-induced mitigation of heavy metal phytotoxicity in metal contaminated soils: A critical review.

J Hazard Mater 2021 01 14;402:123919. Epub 2020 Sep 14.

State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Root Biology Center, College of Natural Resources and Environment, South China Agricultural University, Guangzhou, 510642, Guangdong, PR China. Electronic address:

The heavy metal pollution is a worldwide problem and has received a serious concern for the ecosystem and human health. In the last decade, remediation of the agricultural polluted soil has attracted great attention. Phytoremediation is one of the technologies that effectively alleviate heavy metal toxicity, however, this technique is limited to many factors contributing to low plant growth rate and nature of metal toxicities. Arbuscular mycorrhizal fungi (AMF) assisted alleviation of heavy metal phytotoxicity is a cost-effective and environment-friendly strategy. AMF have a symbiotic relationship with the host plant. The bidirectional exchange of resources is a hallmark and also a functional necessity in mycorrhizal symbiosis. During the last few years, a significant progress in both physiological and molecular mechanisms regarding roles of AMF in the alleviation of heavy metals (HMs) toxicities in plants, acquisition of nutrients, and improving plant performance under toxic conditions of HMs has been well studied. This review summarized the current knowledge regarding AMF assisted remediation of heavy metals and some of the strategies used by mycorrhizal fungi to cope with stressful environments. Moreover, this review provides the information of both molecular and physiological responses of mycorrhizal plants as well as AMF to heavy metal stress which could be helpful for exploring new insight into the mechanisms of HMs remediation by utilizing AMF.
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http://dx.doi.org/10.1016/j.jhazmat.2020.123919DOI Listing
January 2021

A nappies management by-product for the treatment of uranium-contaminated waters.

J Hazard Mater 2021 Feb 2;404(Pt A):124147. Epub 2020 Oct 2.

Laboratory of Radioanalytical and Environmental Chemistry, Department of Chemistry, University of Cyprus, P.O. Box 20537, Cy-1678 Nicosia, Cyprus.

The direct disposal of municipal solid waste such as nappies to the environment may create serious pollution problems. Based on the circular economy and waste management concepts, the conversion of nappies and/or their ingredients (such as super absorbent polymer (SAP)) to high added value products is of great importance. In this work, a modified SAP (MSAP) was examined as an adsorbent for treatment of contaminated waters and uranium recovery. Batch experiments and spectroscopic techniques were used to examine the effect of various parameters (pH, contact time, temperature, initial concentration, and ionic strength), and the mechanism of adsorption U(VI) and desorption process. The U(VI) concentration was determined by alpha spectroscopy after addition of U standard tracer solution to account for possible interferences during electrodeposition and alpha particle counting. The maximum adsorption monolayer capacity was found to be 217.4 mg/g at pH 4.0 and at 298 K. The adsorption of U(VI) on MSAP seems to occur mainly via the formation of inner-sphere surface complexes between U(VI) and the carboxylic surface moieties of MSAP. The MSAP could satisfactorily be regenerated with 0.1 M NaCO (>90%) and it also shows a promising applicability to real wastewaters contaminated with U(VI).
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http://dx.doi.org/10.1016/j.jhazmat.2020.124147DOI Listing
February 2021

Experimental and Theoretical Studies of Methyl Orange Uptake by Mn-Rich Synthetic Mica: Insights into Manganese Role in Adsorption and Selectivity.

Nanomaterials (Basel) 2020 Jul 26;10(8). Epub 2020 Jul 26.

Department of Ecosystem Science and Management and Materials Research Institute, 204 Energy and the Environment Laboratory, The Pennsylvania State University, University Park, PA 16802, USA.

Manganese-containing mica (Mn-mica) was synthesized at 200 °C/96 h using Mn-carbonate, Al-nitrate, silicic acid, and high KOH concentration under hydrothermal conditions. Mn-mica was characterized and tested as a new adsorbent for the removal of methyl orange (MO) dye from aqueous solutions. Compared to naturally occurring mica, the Mn-mica with manganese in the octahedral sheet resulted in enhanced MO uptake by four times at pH 3.0 and 25 °C. The pseudo-second order equation for kinetics and Freundlich equation for adsorption isotherm fitted well to the experimental data at all adsorption temperatures (i.e., 25, 40 and 55 °C). The decrease of Langmuir uptake capacity from 107.3 to 92.76 mg·g within the temperature range of 25-55 °C suggested that MO adsorption is an exothermic process. The role of manganese in MO selectivity and the adsorption mechanism was analyzed via the physicochemical parameters of a multilayer adsorption model. The aggregated number of MO ions per Mn-mica active site ( n ) was superior to unity at all temperatures signifying a vertical geometry and a mechanism of multi-interactions. The active sites number () of Mn-mica and the total removed MO layers () slightly changed with temperature. The decrease in the MO adsorption capacities ( = ·) from 190.44 to 140.33 mg·g in the temperature range of 25-55 °C was mainly controlled by the parameter. The results of adsorption energies revealed that MO uptake was an exothermic (i.e., negative Δ values) and a physisorption process (Δ < 40 kJ mol ). Accordingly, the adsorption of MO onto Mn-mica was governed by the number of active sites and the adsorption energy. This study offers insights into the manganese control of the interactions between MO ions and Mn-mica active sites.
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http://dx.doi.org/10.3390/nano10081464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466402PMC
July 2020

Exfoliated Clay Decorated with Magnetic Iron Nanoparticles for Crystal Violet Adsorption: Modeling and Physicochemical Interpretation.

Nanomaterials (Basel) 2020 Jul 24;10(8). Epub 2020 Jul 24.

Faculty of Earth Science, Beni-Suef University, Beni-Suef 62511, Egypt.

Surfactant-modified exfoliated Fayum clay (CTAB-EC) obtained after chemical treatment with a CTAB/HO solution was further decorated with magnetic FeO nanoparticles (MNP). The final nanocomposite (MNP/CTAB-EC) was characterized by XRD, SEM, FTIR, TEM and its adsorptive capability against a model cationic dye, crystal violet (CV), was evaluated. A comparison of the adsorption performance of the raw clay and its modified counterparts using HO, CTAB, CTAB/HO or MNP indicated that the adsorption capacity of MNP/CTAB-EC was the highest for CV removal at pH 8.0. The pseudo‒second order for the kinetics and Freundlich model for adsorption equilibrium fitted well the CV removal experimental data at all tested temperatures (25, 40 and 55 °C). The enhancement of the Langmuir adsorption capacity from 447.1 to 499.4 mg g with increasing the temperature from 25 to 55 °C revealed an endothermic nature of the removal process. The interactions between CV and MNP/CTAB-EC were interpreted using advanced statistical physics models (ASPM) in order to elucidate the adsorption mechanism. Multilayer model fitted the adsorption process and therefore, the steric and energetic factors that impacted the CV adsorption were also interpreted using this model. The aggregated number of CV molecules per MNP/CTAB-EC active site ( n ) was more than unity at all temperatures, representing thus a vertical adsorption orientation and a multi‒interactions mechanism. It was determined that the increase of CV uptake with temperature was mainly controlled by the increase of the number of active sites (). Calculated adsorption energies (Δ) revealed that CV removal was an endothermic and a physisorption process (Δ < 40 kJ mol ). MNP/CTAB-EC was magnetically separated, regenerated by NaOH, and reused without significant decrease in its adsorption efficiency, supporting a prosperity of its utilization as an effective adsorbent against hazardous dyes from wastewaters.
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http://dx.doi.org/10.3390/nano10081454DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7466639PMC
July 2020

The effect of chemical and organic N inputs on NO emission from rain-fed crops in Eastern Mediterranean.

J Environ Manage 2020 Sep 20;270:110755. Epub 2020 Jun 20.

Department of Agrobiotechnology, Agricultural Research Institute, P.O.Box 22016, Nicosia, 1516, Cyprus. Electronic address:

Nitrogen has a significant contribution to global warming and its reduction in agriculture is expected to reduce NO emissions having however adverse effects on the productivity of agricultural ecosystems. Maintaining systems productivity with alternative N sources i.e manure and composts could be a strategy also to mitigate NO emissions. In this paper, we present the effect of different N sources (organic and chemical) on field NO emissions and how these emissions are associated with soil available N forms (NH and NO) in three different rain-fed crops namely barley, pea and vetch grown in Cyprus for two growing seasons. The daily emissions ranged from -3.11 to 12.3 g N-NO/ha/day, while cumulative emissions ranged from 119 g N-NO/ha to 660 g N-NO/ha depending on crop and nitrogen source type. The emissions showed a seasonal pattern and WFPS has been identified as a critical soil parameter controlling daily NO emissions. The daily NO fluxes in the current study derives mainly from nitrification irrespectively crop type or nitrogen source type. Specific emission factors for each crop cultivated under different N source type were calculated and ranged from 0.03% ± 0.02-0.34% ± 0.09. The application of manure and chemical fertilizers cause similar intensity of NO emissions while compost exhibited the lower emission factors. These findings suggest that composts could be integrated in a nutrient management strategy of rain-fed crops with less NO emissions. The high background emissions found suggest also that other factors than external inputs are associated with NO emissions and further studies including the response of microbial community structure and their contribution and association with NO emissions.
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http://dx.doi.org/10.1016/j.jenvman.2020.110755DOI Listing
September 2020

Editorial: New Research on Soil Degradation and Restoration.

J Environ Manage 2020 Sep 5;269:110851. Epub 2020 Jun 5.

Bahauddin Zakariya University, Pakistan.

The Virtual Special Issue (VSI) "New Research on Soil Degradation and Restoration" was proposed by the Guest-Editors (the authors of this editorial piece) to Journal of Environmental Management taking into account the following aspects: (a) Firstly, soil degradation is a main issue all over the world; (b) Secondly, physical, chemical and biological degradation of soil environments need detailed research, also going deeper in some new aspects poorly covered up to now; and (c) Similarly, new quality research on restoration of degraded soils, dumping sites, different areas affected by mining activities, and so on, would be clearly useful in order to prevent and/or solve critical environmental hazards. As a result, 110 manuscripts were submitted to the VSI by authors from around the world, and near 50 high quality works were finally published. The Guest-Editors of the VSI consider that the papers published will be of great interest for researchers working in this field, as well as for the overall community, as they include aspects clearly relevant at a global level.
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http://dx.doi.org/10.1016/j.jenvman.2020.110851DOI Listing
September 2020

Hydra: A mixture modeling framework for subtyping pediatric cancer cohorts using multimodal gene expression signatures.

PLoS Comput Biol 2020 04 10;16(4):e1007753. Epub 2020 Apr 10.

Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, United States of America.

Precision oncology has primarily relied on coding mutations as biomarkers of response to therapies. While transcriptome analysis can provide valuable information, incorporation into workflows has been difficult. For example, the relative rather than absolute gene expression level needs to be considered, requiring differential expression analysis across samples. However, expression programs related to the cell-of-origin and tumor microenvironment effects confound the search for cancer-specific expression changes. To address these challenges, we developed an unsupervised clustering approach for discovering differential pathway expression within cancer cohorts using gene expression measurements. The hydra approach uses a Dirichlet process mixture model to automatically detect multimodally distributed genes and expression signatures without the need for matched normal tissue. We demonstrate that the hydra approach is more sensitive than widely-used gene set enrichment approaches for detecting multimodal expression signatures. Application of the hydra analysis framework to small blue round cell tumors (including rhabdomyosarcoma, synovial sarcoma, neuroblastoma, Ewing sarcoma, and osteosarcoma) identified expression signatures associated with changes in the tumor microenvironment. The hydra approach also identified an association between ATRX deletions and elevated immune marker expression in high-risk neuroblastoma. Notably, hydra analysis of all small blue round cell tumors revealed similar subtypes, characterized by changes to infiltrating immune and stromal expression signatures.
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http://dx.doi.org/10.1371/journal.pcbi.1007753DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7176284PMC
April 2020

A Novel Nanocomposite of Activated Serpentine Mineral Decorated with Magnetic Nanoparticles for Rapid and Effective Adsorption of Hazardous Cationic Dyes: Kinetics and Equilibrium Studies.

Nanomaterials (Basel) 2020 Apr 5;10(4). Epub 2020 Apr 5.

Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.

A widely distributed mineral, serpentine, obtained from Wadi Ghadir (Eastern Desert in Egypt) was studied as a potential naturally and abundantly available source for the synthesis of an efficient adsorbent for aquatic remediation applications. A novel nanocomposite was synthesized after the exfoliation of the layered structure of serpentine by hydrogen peroxide treatment (serpentine (SP)), followed by decoration with magnetic FeO nanoparticles (MNP). The goal behind the utilization of the latter phase was to increase the environmental remediation capability and to incorporate magnetic properties at the final adsorbent, toward a better separation after the use. The fabricated composite (MNP/SP) was characterized by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), and transmission electron microscopy (TEM). The composite's potential adsorption application toward the removal of two cationic dyes, methylene blue (MB) and malachite green (MG), was investigated. The observed adsorption kinetics was fast, and the highest uptake was observed at pH = 8, with the capacities to reach 162 and 176 mg g for MB and MG, respectively, values significantly higher than various other materials tested against these two cationic dyes. Compared to hydrogen peroxide-treated serpentine, the removal efficiency of the composite was higher by 157 and 127% for MB and MG, respectively. The MB and MG were adsorbed because of the favorable electrostatic interactions between MNP/SP active sites and the cationic dyes. The close value capacities suggest that the difference in chemistry of the two dyes does not affect the interactions, with the later occurring via the dyes' amine functionalities. With increasing ionic strength, the adsorption of the studied basic dyes was slightly decreased, suggesting only partial antagonistic ion effect. The sorbent can be easily regenerated and reused without significant deterioration of its adsorption efficiency, which makes MNP/SP a promising adsorbent for the removal of hazardous pollutants from aquatic environments.
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http://dx.doi.org/10.3390/nano10040684DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7221753PMC
April 2020

Use of nano-/micro-magnetite for abatement of cadmium and lead contamination.

J Environ Manage 2020 Jun 31;264:110477. Epub 2020 Mar 31.

MoA Key Laboratory for Clean Production and Utilization of Renewable Energy, MoST National Center for International Research of BioEnergy Science and Technology, College of Engineering, China Agricultural University, 100083, Beijing, China.

Structural variations of a mineral dictate its adsorption capacity which affects the mobility and toxicity of contaminants in natural and engineered systems. Present batch study evaluates the adsorption of lead (Pb) and cadmium (Cd) onto three magnetites having nanometric (M1-30 nm and M2-60 nm) and micrometric particle sizes (M3-1.5 μm). Obtained data revealed that particle size of tested magnetites strongly affected the extent and kinetics of metal adsorption and desorption. Observed order of adsorption efficiency was M1 > M2 > M3 with optimum monolayer adsorption of 408.14, 331.40, 178.47 mg/g (for Pb) and 228.05, 170.86, 83.49 mg/g (for Cd), respectively. Adsorption data were well fitted to the Freundlich (R = 0.99), Langmuir (R = 0.99) and pseudo-first order models (R = 0.98). Electrostatic attraction and surface precipitation interaction via external mass transfer between bulk liquid-solid interfaces were the potential adsorption pathways. Pb showed higher affinity than Cd in multi-metal system. Desorption efficiency was higher in acidic environment (92%) than in distilled water (44%). Moreover, regenerated magnetite samples retained good adsorption capacity for six cycles. As soils are characterized by large variability of iron minerals, these findings have important implications regarding the transport and immobilization of contaminants particularly in the management of contaminated soils.
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http://dx.doi.org/10.1016/j.jenvman.2020.110477DOI Listing
June 2020

Tailoring Surface Chemistry of Sugar-Derived Ordered Mesoporous Carbons Towards Efficient Removal of Diclofenac From Aquatic Environments.

Materials (Basel) 2020 Apr 1;13(7). Epub 2020 Apr 1.

Department of Theoretical Chemistry, Institute of Chemical Sciences, Faculty of Chemistry, Maria Curie- Skłodowska University in Lublin, 20-031 Lublin, Poland.

Ordered mesoporous carbon (CMK-3), obtained from an abundant natural source, sugar, was thermochemically modified with dicyandiamide and thiourea as well as by classical oxidization with hydrogen peroxide to introduce specific surface groups. Thermochemical modifications resulted in carbon with almost unchanged porosity and altered surface chemistry while porosity of HO-treated carbon was seriously deteriorated. The obtained carbons were tested as sorbents of diclofenac, considered as one of the emerging water contaminants. Changes in porosity and surface chemistry of modified carbons resulted in significant differences with regard to the uptake of diclofenac. Dicyandiamide-modified carbon showed highest uptake of drugs, reaching 241 mg g that is attributed to its developed microporosity as well as surface chemistry composed of basic groups facilitating electrostatic interactions with diclofenac anions. Desorption study showed that diclofenac is strongly bonded, albeit with a different degree depending on the modification of the CMK-carbon. The obtained results were compared with up-to-date literature regarding sorption of diclofenac by carbon-based sorbents.
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http://dx.doi.org/10.3390/ma13071625DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7178346PMC
April 2020

Removal of caffeine, nicotine and amoxicillin from (waste)waters by various adsorbents. A review.

J Environ Manage 2020 May 2;261:110236. Epub 2020 Mar 2.

Dept. Soil Sci. and Agric. Chem., Engineering Polytech. School, Univ. Santiago de Compostela, 27002, Lugo, Spain.

The fast growth in the anthropogenic activities, that involve a wide use of pharmaceuticals, has led to the appearance of new toxic and hazardous chemical compounds, called "emerging pollutants", which could cause unpredictable consequences to the ecosystems. The current review is focused on emerging pollutants occurring in food or air and include caffeine and nicotine, as well as on pharmaceuticals, in particular amoxicillin, and the concerns caused by its wide usage for medical purposes. This review, for the first time, analyzes and discusses the potential risks and implications of caffeine, nicotine and amoxicillin as emerging environmental pollutants, a field that remains underrepresented to date. Both caffeine and nicotine belong to life style compounds, while pharmaceutical amoxicillin is one of the very popular β-lactam antibiotics used to take care of human and animal infections. The review covers the toxic effect caused by caffeine, nicotine and amoxicillin on humans and animals and describes some of the main adsorbents utilized for their removal (e.g., grape stalk, tea waste, wheat grains, bentonite, activated carbon, acid and base modified grape slurry wastes, graphene oxides, modified graphene oxides, zeolites, etc.). The isotherm and kinetic models for the analysis of caffeine, nicotine and amoxicillin adsorption by different adsorbents are presented. The impact of pH, temperature, adsorbent dosage and thermodynamic studies were deeply analyzed. The review also discusses the mechanism of adsorption for the above-mentioned emerging pollutants, which includes π-π interaction, cation-π bonding, electron-donor and electron-acceptor forces, van der Waals forces, electrostatic interactions, etc. The present review has a potential value for chemists, ecologists, toxicologists, environmental engineers, and other professionals that are involved in environmental protection.
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http://dx.doi.org/10.1016/j.jenvman.2020.110236DOI Listing
May 2020

Using Transcriptional Signatures to Find Cancer Drivers with LURE.

Pac Symp Biocomput 2020 ;25:343-354

Dept. of Biomolecular Engineering and UC Santa Cruz Genomics Institute, University Of California, Santa Cruz, Santa Cruz, CA 95064, USA.

Cancer genome projects have produced multidimensional datasets on thousands of samples. Yet, depending on the tumor type, 5-50% of samples have no known driving event. We introduce a semi-supervised method called Learning UnRealized Events (LURE) that uses a progressive label learning framework and minimum spanning analysis to predict cancer drivers based on their altered samples sharing a gene expression signature with the samples of a known event. We demonstrate the utility of the method on the TCGA Pan-Cancer Atlas dataset for which it produced a high-confidence result relating 59 new connections to 18 known mutation events including alterations in the same gene, family, and pathway. We give examples of predicted drivers involved in TP53, telomere maintenance, and MAPK/RTK signaling pathways. LURE identifies connections between genes with no known prior relationship, some of which may offer clues for targeting specific forms of cancer. Code and Supplemental Material are available on the LURE website: https://sysbiowiki.soe.ucsc.edu/lure.
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6924983PMC
January 2020

Use of chicken feather and eggshell to synthesize a novel magnetized activated carbon for sorption of heavy metal ions.

Bioresour Technol 2020 Feb 20;297:122452. Epub 2019 Nov 20.

Department of Environmental health Engineering, Faculty of Health, Sabzevar University of Medical Sciences, Sabzevar, Iran; Department of Engineering, Kashmar Branch, Islamic Azad University, PO Box 161, Kashmar, Iran. Electronic address:

Keeping environment and sustainability concept in view with preparation of new sorbents, two waste by-products from the poultry industry, i.e. feather and eggshell, were used for synthesis of a new magnetic activated carbon for sorption of heavy metal ions. Using response surface methodology based central composite design (RSM-CCD) technique, chicken feather and acid-digested eggshell were used as precursor and activation material, respectively, for the synthesis of the herein studied activated carbon (eggshell activated chicken feather carbon; ESCFC). The prepared activated carbon was magnetized for easy separation from water media, and iron oxide magnetized ESCFC (IOM-ESCFC) was comprehensively examined for removing some heavy metallic ions (Pb, Cd, Cu, Zn, and Ni) from water. The maximum mono-layer sorption capacities and the highness of sorption speed, along with thermodynamic studies, demonstrated that IOM-ESCFC can be regarded as a potential adsorbent against heavy metal ions from waters and wastewaters.
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http://dx.doi.org/10.1016/j.biortech.2019.122452DOI Listing
February 2020

Synthesis and characterization of a novel FeO-loaded oxidized biochar from pine needles and its application for uranium removal. Kinetic, thermodynamic, and mechanistic analysis.

J Environ Manage 2019 Dec 16;252:109677. Epub 2019 Oct 16.

Department of Chemistry, University of Cyprus, P.O. Box 20537, Cy-1678, Nicosia, Cyprus.

This work investigates the fabrication of magnetic biochar (pncm) and FeO-loaded oxidized biochar (pncom) obtained from pine needles for uranium removal. Adsorbent properties were characterized by scanning electron microscopy with energy dispersive X-ray spectroscopy (SEM-EDX), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared spectroscopy (FTIR) techniques. Using batch-type experiments the effect of the uranium concentration, solution pH, contact time, temperature and ionic strength on the uranium adsorption was investigated. The results showed better adsorptive properties for pncom, particularly in the acidic pH range. The experimental adsorption data were found to be well fitted with the Langmuir isotherm and the pseudo-second order kinetic model. For pncom, the maximum adsorption capacity obtained applying the Langmuir isotherm model was found to amount 2.6 mol/kg at pH 6 and 25 °C. Spectroscopic data indicated that the U(VI) adsorption was associated with the formation of inner-sphere complexes. Regeneration and reusability studies were performed with 0.1 M NaCO. After four cycles, the % relative adsorption and the desorption for pncom decreased from 99.5% to 87.2% and 99.6%-62.6%, respectively. The present results show that magnetization of oxidized pine needle biochar improves significantly the adsorption characteristics regarding the uranium removal from aqueous solutions.
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http://dx.doi.org/10.1016/j.jenvman.2019.109677DOI Listing
December 2019

Valorization of agricultural wastes could improve soil fertility and mitigate soil direct NO emissions.

J Environ Manage 2019 Nov 6;250:109389. Epub 2019 Sep 6.

Agricultural Research Institute, Department of Agrobiotechnology, Cyprus. Electronic address:

The emerging need for sustainable management of the increasing quantities of urban and industrial organic wastes creates opportunities for the development of alternative strategies for the improvement of degraded soils. The current study was performed to examine the effects of agricultural wastes application on soil bacterial community as well as CO and NO direct gas emissions. Untreated soils were compared with soils, which received the same amount of N (100 μg/g soil) in the form of ammonium nitrate and organic agricultural waste. In particular, soils were incubated with three different organic agricultural wastes, orange (OP), mandarin (MP) and banana peels (BP) and ammonium nitrate (F) after adjusting soil water at 70% of its holding capacity. In the current study, soil chemical characteristics, quantitative PCR of denitrifiers (nirK, nirS, nosZI and nosZII) and16s rRNA amplicon sequencing were assessed to examine the links between the soil microbial communities and short-term soil direct NO emissions when treated with agricultural wastes. The highest soil direct NO emissions were recorded in soils received ammonium nitrate while soils received agricultural wastes exhibited substantially lower soil direct NO emissions. On the contrary, agricultural wastes stimulated CO accumulation as well as the growth of copiotrophic bacterial groups like Proteobacteria and Firmicutes. Interestingly, direct soil NO emissions were decoupled from the density of denitrifier community while agricultural wastes caused a substantial reduction of the relative abundance of bacterial taxa associated with NO emissions in the soil. This study proves evidence that agricultural wastes could be integrated in a waste management strategy, which inter alia includes their direct use in agricultural ecosystems resulting in reduced NO emissions.
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http://dx.doi.org/10.1016/j.jenvman.2019.109389DOI Listing
November 2019

The effects of different soil nutrient management schemes in nitrogen cycling.

J Environ Manage 2019 Aug 13;243:168-176. Epub 2019 May 13.

Department of Agrobiotechnology, Agricultural Research Institute, P.O.Box 22016, Nicosia, 1516, Cyprus.

It is imperative for sustainable agriculture to explore practices and inputs creating low NO emission capacity without reducing the productivity of the agricultural system. To evaluate different nutrient management schemes, a microcosm study was conducted to assess the direct NO emission from soil. Four different treatments were used to provide a preliminary assessment of NO emissions, as well as the concentrations of nitrates (NO) and ammonium (NH) produced in soil: compost (derived from green plant residues), chickpea residues (green manure) in two different N concentrations (2.6% and 5.5%, respectively) and ammonium nitrate (fertilizer). The soil was thoroughly mixed with the organic amendments and ammonium nitrate and incubated for 31 days. The emissions of NO were higher in green manure with high-N content, as a source of nitrogen in the soil, and were similar to the emissions measured from the chemically fertilized soil. In particular, chickpea residues, with high-N content, exhibited cumulative NO emissions, equal to 266.17 μg N/m, whereas in fertilized soil the emissions were 267.10 μg N/m. On the contrary, the incorporation of chickpea plant residues with low-N content can be an efficient way to minimize the NO emissions at 21.63 μg N/m. The emissions of NO when compost was applied, remained relatively low, equal to 5.47 μg N/m, and in comparison to soil without any treatment. Overall, a positive association between NH, NO in soil and NO emissions were observed. However, this response was treatment depended, and the significant positive correlation between NH and NO emissions were noticed in soils treated with ammonium nitrate, chickpea residues with low N content, as well as untreated controls. On the contrary, the positive correlation observed between NO and NO emissions in soils receiving compost and high N chickpea residues, suggest that the different treatments are differentially affecting the processes that are contributing to NO emissions in agricultural soils. These findings, emphasize that the different nutrient management schemes are differentially affecting the main process contributing to NO emissions in agricultural soils.
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http://dx.doi.org/10.1016/j.jenvman.2019.04.115DOI Listing
August 2019

A novel route for preparation of chemically activated carbon from pistachio wood for highly efficient Pb(II) sorption.

J Environ Manage 2019 Apr 31;236:34-44. Epub 2019 Jan 31.

Department of Environmental Health Engineering, Faculty of Health, Sabzevar University of Medical Sciences, Sabzevar, Iran; Department of Engineering, Kashmar Branch, Islamic Azad University, PO Box 161, Kashmar, Iran. Electronic address:

Pistachio wood-derived activated carbon prepared by a two-stage process (PWAC-2), conducting two consecutive chemical activation processes with NHNO and NaOH, respectively. The results showed that explosive characteristic of NHNO can primarily be employed to produce a char, with a large surface area and a highly-ordered pore structure, which can be subjected to a second activation process with NaOH to prepare a more suitable activated carbon, with a highly porous structure and useful functional groups, for removal of lead ions from aqueous media. An L Taguchi experimental design was used by varying impregnation ratio, activation time and temperature in both pre- and post-activation stages, and the results showed that, in both stages, a small activating agent/precursor and a proportional low activation time suffice for preparation of an advantageous activated carbon for Pb(II) adsorption. A comprehensive study was performed on the equilibrium, kinetic and thermodynamic aspects of Pb(II) adsorption by the new activated carbon. The results exhibited that, having had a high lead adsorption capacity (190.2 mg g), a high adsorption rapidness, and thermodynamic favorability, PWAC-2 is a beneficial alternative for utilization in full-scale plants of lead removal from waters and wastewaters.
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http://dx.doi.org/10.1016/j.jenvman.2019.01.087DOI Listing
April 2019

CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing.

Genome Biol 2018 11 26;19(1):202. Epub 2018 Nov 26.

Department of Statistics, The Wharton School, University of Pennsylvania, Philadelphia, PA, 19104, USA.

High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods but suffers from biases and artifacts that lead to false discoveries and low sensitivity. We describe CODEX2, as a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples. We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent. CODEX2 outperforms existing methods and, in particular, significantly improves sensitivity for common CNVs.
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http://dx.doi.org/10.1186/s13059-018-1578-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260772PMC
November 2018

Performance of aquatic weed - Waste Myriophyllum spicatum immobilized in alginate beads for the removal of Pb(II).

J Environ Manage 2019 Feb 21;232:97-109. Epub 2018 Nov 21.

Institute for Technology of Nuclear and Other Mineral Raw Materials, 86 Franchet d'Esperey St., Belgrade, Serbia.

A new biosorbent - alginate encapsulated with Myriophyllum spicatum - MsA was investigated for lead ions removal. This biosorbent was characterized by scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FT-IR), zeta potential, X ray Diffraction (XRD) and size distribution analysis. FT-IR analysis demonstrated that the lead ions sequestration mechanism included ion exchange and lead complexation with the carboxyl, carbonyl and hydroxyl groups in MsA. In order to better understand the mechanisms of the binding of Pb(II) on immobilized M. spicatum beads, 3 reaction and one diffusion based kinetic models were applied on kinetic data removal lead ions on three materials: M. spicatum, Ca-alginate and MsA. Myriophyllum spicatum encapsulated with alginate - MsA have higher adsorption capacity than M. spicatum. Among examined six isotherms Redlich-Peterson and the Langmuir isotherm model exhibited the best fit to the experimental data, with capacities ranging from 230 to 268.7 mg/g. Among the various tested desorption agents, nitric acid has proven to be the best. The obtained results suggest that the immobilized M. spicatum biosorbent holds great potential for lead wastewater treatment applications.
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http://dx.doi.org/10.1016/j.jenvman.2018.10.075DOI Listing
February 2019

Aloe vera waste biomass-based adsorbents for the removal of aquatic pollutants: A review.

J Environ Manage 2018 Dec 7;227:354-364. Epub 2018 Sep 7.

Laboratory of Biochemical Engineering & Environmental Technology (LBEET), Department of Chemical Engineering, University of Patras, 26504, Patras, Greece. Electronic address:

Aloe vera has been cultivated for many centuries for its beneficial properties, finding application in a wide range of medical and health products. Nowadays, the research has also focused on an alternative use of Aloe vera which is related to environmental applications such as clean water technology/wastewater treatment process. In recent years, biosorption has been shown to be a cost-effective and efficient alternative method for removing various pollutants from wastewater and water. This work provides a comprehensive review on using Aloe vera waste biomass-based sorbents, as well as modified counterparts, for the removal of heavy metals, dyes and other pollutants from aqueous media. The discussed biosorbents have been grouped in five categories based on the treatment of the Aloe vera leaves. Adsorption mechanisms, in addition to the significant factors influencing sorption capability like physical and chemical properties of the adsorbent, initial concentration, initial pH and temperature of the solution, dosage and contact time, have been discussed in detail. Furthermore, the applied equilibrium and kinetic models have been also summarized. The history, taxonomy, botany, and applications of Aloe vera are also presented in brief.
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http://dx.doi.org/10.1016/j.jenvman.2018.08.064DOI Listing
December 2018

Efficient mercury removal from wastewater by pistachio wood wastes-derived activated carbon prepared by chemical activation using a novel activating agent.

J Environ Manage 2018 Oct 17;223:1001-1009. Epub 2018 Jul 17.

Environment Health Engineering Department & Social Determinants of Health Research Centre, Gonabad University of Medical Sciences, Gonabad, Iran; Department of Engineering, Kashmar Branch, Islamic Azad University, PO Box 161, Kashmar, Iran. Electronic address:

Ammonium nitrate (NHNO) with explosive characteristics at high temperatures was used as a novel activating reagent to prepare a surface-engineered activated carbon derived from pistachio wood wastes (PWAC). PWAC was characterized and compared with commercial activated carbon (CAC) by textural and morphological properties, surface chemistry, crystal structure, and surface elemental composition. The results indicated that the optimal conditions of PWAC preparation to obtain the highest mercury adsorption capacity were pyrolysis temperature (800 °C), pyrolysis time (2 h), and impregnation ratio (5%). PWAC was of highly regular-shaped and well-developed pores and possessed a large surface area (1448 m/g) and high total pore volume (0.901 cm/g). The batch experiments indicated that the adsorption process of Hg(II) was strongly dependent on the solution pH and reached fast equilibrium at approximately 30 min. PWAC (202 mg/g) exhibited a significantly higher maximum adsorption capacity than commercial activated carbon (66.5 mg/g). Adsorbent-adsorbate dispersion interaction plays a major role in the adsorption mechanism, compared to the minor role played by pore filling and reduction mechanism. Overall, ammonium nitrate can be considered a newer activating reagent to prepare promising and low-cost PWAC for effectively Hg(II) removal from water media.
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http://dx.doi.org/10.1016/j.jenvman.2018.06.077DOI Listing
October 2018

The use of olive tree pruning waste compost to sequestrate methylene blue dye from aqueous solution.

Int J Phytoremediation 2018 Jul;20(8):831-838

a Laboratory of Soils and Agricultural Chemistry , Department of Natural Resources Management and Agricultural Engineering, Agricultural University of Athens , Athens , Greece.

Considering that quality water supplies are diminishing and climate disorder affects water cycle, wastewaters should be decontaminated for reuse either by the same establishment or in agriculture for the growth of industrial plants. In that context, much research work has been focused on the development of low cost biosorbents. In this study, the effect of composting on the adsorption capacity of olive tree pruning waste (OTPW) biomass for methylene blue (MB) removal from aqueous solutions was examined. Composting procedure may improve the sorption properties of the raw organic materials, is economical and easy to apply. MB adsorption on both OTPW and composted olive tree pruning waste (COTPW) biomasses was found to be fast. The maximum monolayer adsorption capacity obtained from Langmuir isotherm was estimated to be 129.87 and 250.00 mg/g for OTPW and COTPW, respectively, indicating that composting procedure greatly improved the adsorptive properties of OTPW. The raise of temperature from 25°C to 60°C decreased the efficiency of OTPW for MB removal whereas the adsorption capacity of COTPW was not affected at high temperatures. Moreover, COTPW showed constant adsorption over the 2-8 solution pH range.
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http://dx.doi.org/10.1080/15226514.2018.1438353DOI Listing
July 2018

Adsorption property of Br-PADAP-impregnated multiwall carbon nanotubes towards uranium and its performance in the selective separation and determination of uranium in different environmental samples.

Ecotoxicol Environ Saf 2018 Apr 19;150:136-143. Epub 2017 Dec 19.

Sustainable Management of Natural Resources and Environment Research Group, Faculty of Environment and Labour Safety, Ton Duc Thang University, Ho Chi Minh City, Vietnam. Electronic address:

A newer efficient U(VI) ion adsorbent was synthesized by impregnating Br-PADAP [2-(5-Bromo-2-pyridylazo)-5-(diethylamino)phenol] onto multiwall carbon nanotubes (MWCNTs). The effects of various operation conditions on uranium adsorption (i.e., pH contact time, temperature, and initial uranium concentration) were systematically evaluated using batch experiments. The results indicated that the uranium adsorption on modified MWNCTs (5.571 × 10g/mg × min) reached faster equilibrium than that on pristine MWNCTs (4.832 × 10g/mg × min), reflecting the involvement of appropriate functional groups of Br-PADAP on the chelating ion-exchange mechanism of U(VI) adsorption. Modified MWNCTs (83.4mg/g) exhibited significantly higher maximum Langmuir adsorption capacity than pristine MWNCTs (15.1mg/g). Approximately 99% of uranium adsorbed onto modified MWNCTs can be desorbed by 2.5mL of 1M HNO solution. Therefore, Br-PADAP-modified MWNCTs can server as a promising adsorbent for efficient uranium adsorption applications in water treatment. Subsequently, the proposed solid-phase extraction (using a mini-column packed with Br-PADAP/MWCNT) was successfully utilized for analysing trace uranium levels by the ICP-AES method in different environmental samples with a pre-concentration factor of 300-fold. The coexistence of other ions demonstrated an insignificant interference on the separative pre-concentration of uranium. the detection limit was recognized as 0.14μg/L, and the relative standard deviation was approximately 3.3% (n = 7).
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http://dx.doi.org/10.1016/j.ecoenv.2017.12.039DOI Listing
April 2018

A Comprehensive Patient-Derived Xenograft Collection Representing the Heterogeneity of Melanoma.

Cell Rep 2017 Nov;21(7):1953-1967

Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104, USA. Electronic address:

Therapy of advanced melanoma is changing dramatically. Following mutational and biological subclassification of this heterogeneous cancer, several targeted and immune therapies were approved and increased survival significantly. To facilitate further advancements through pre-clinical in vivo modeling, we have established 459 patient-derived xenografts (PDX) and live tissue samples from 384 patients representing the full spectrum of clinical, therapeutic, mutational, and biological heterogeneity of melanoma. PDX have been characterized using targeted sequencing and protein arrays and are clinically annotated. This exhaustive live tissue resource includes PDX from 57 samples resistant to targeted therapy, 61 samples from responders and non-responders to immune checkpoint blockade, and 31 samples from brain metastasis. Uveal, mucosal, and acral subtypes are represented as well. We show examples of pre-clinical trials that highlight how the PDX collection can be used to develop and optimize precision therapies, biomarkers of response, and the targeting of rare genetic subgroups.
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http://dx.doi.org/10.1016/j.celrep.2017.10.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5726788PMC
November 2017

Genetic and Genomic Characterization of 462 Melanoma Patient-Derived Xenografts, Tumor Biopsies, and Cell Lines.

Cell Rep 2017 Nov;21(7):1936-1952

Department of Medicine, Division of Translational Medicine and Human Genetics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA; Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. Electronic address:

Tumor-sequencing studies have revealed the widespread genetic diversity of melanoma. Sequencing of 108 genes previously implicated in melanomagenesis was performed on 462 patient-derived xenografts (PDXs), cell lines, and tumors to identify mutational and copy number aberrations. Samples came from 371 unique individuals: 263 were naive to treatment, and 108 were previously treated with targeted therapy (34), immunotherapy (54), or both (20). Models of all previously reported major melanoma subtypes (BRAF, NRAS, NF1, KIT, and WT/WT/WT) were identified. Multiple minor melanoma subtypes were also recapitulated, including melanomas with multiple activating mutations in the MAPK-signaling pathway and chromatin-remodeling gene mutations. These well-characterized melanoma PDXs and cell lines can be used not only as reagents for a large array of biological studies but also as pre-clinical models to facilitate drug development.
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http://dx.doi.org/10.1016/j.celrep.2017.10.052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5709812PMC
November 2017

BRCA locus-specific loss of heterozygosity in germline BRCA1 and BRCA2 carriers.

Nat Commun 2017 08 22;8(1):319. Epub 2017 Aug 22.

Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, USA.

Complete loss of BRCA1 or BRCA2 function is associated with sensitivity to DNA damaging agents. However, not all BRCA1 and BRCA2 germline mutation-associated tumors respond. Herein we report analyses of 160 BRCA1 and BRCA2 germline mutation-associated breast and ovarian tumors. Retention of the normal BRCA1 or BRCA2 allele (absence of locus-specific loss of heterozygosity (LOH)) is observed in 7% of BRCA1 ovarian, 16% of BRCA2 ovarian, 10% of BRCA1 breast, and 46% of BRCA2 breast tumors. These tumors have equivalent homologous recombination deficiency scores to sporadic tumors, significantly lower than scores in tumors with locus-specific LOH (ovarian, P = 0.0004; breast P < 0.0001, two-tailed Student's t-test). Absence of locus-specific LOH is associated with decreased overall survival in ovarian cancer patients treated with platinum chemotherapy (P = 0.01, log-rank test). Locus-specific LOH may be a clinically useful biomarker to predict primary resistance to DNA damaging agents in patients with germline BRCA1 and BRCA2 mutations.Most tumours associated with germline BRCA1/BRCA2 loss of function mutations respond to DNA damaging agents, however, some do not. Herein, the authors identify that a subset of breast/ovarian tumors retain a normal allele, which is associated with decreased overall survival after DNA damage-inducing platinum chemotherapy.
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http://dx.doi.org/10.1038/s41467-017-00388-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567274PMC
August 2017