Biotechnology and Bioengineering

Biotechnology and Bioengineering presents the most up-to-date research on biobased technologies. It is designed to help scientists and researchers deepen their knowledge in this critical knowledge field. This solid resource brings together multidisciplinary research, development, and innovation for a wide study of Biotechnology and Bioengineering

FLOWPATH 2019 – NATIONAL MEETING ON HYDROGEOLOGY

FLOWPATH 2019, the 4th National Meeting on Hydrogeology, was held in Milan from 12th to 14th June 2019. According to the aim of the previous Editions of FLOWPATH, held in Bologna (2012), Viterbo (2014) and Cagliari (2017), the conference is an opportunity for Italian hydrogeologists to exchange ideas and knowledge on different groundwater issues. The objectives of the conference are: – To promote dialogue and exchange of scientific knowledge among young hydrogeologists; – To deepen the theoretical and practical aspects of our understanding on groundwater; – To update all the stakeholders, researchers and professionals on recent challenges in the hydrogeological sciences; – To encourage researchers, professionals and administrators to contribute to the improvement of water resources management

Remediation of Soils and Groundwater Contaminated with Hydrocarbons in Area the Operation of Ecopetrol in Palagua oil field, Columbia.

Import 21/10/2013The soils of the Station 1 in Palagua oil field and bordering property indicated similar characteristics of both, classifying them like sandy, which coincides with the high permeability and rapid infiltration, together with low relative thickness and low retention of moisture. Also both present a capacity of cationic exchange and granular structure. The underground water contains phenols and metals as the Barium, Lead, Arsenic, hexavalent Chromium and Cadmium that they overcome the limit allowed by the Colombian current environment policy in several points of sampling. The bioaugmentation process represent better results for biodegradation of TPH in 83,7% in average, as well as for biodegradation of oil and grease (58,2%) and PAHs (31,7%). Combination of two treatments is more convenient for elimination of hydrocarbons than bioremediation solo. The flushing with surfactant and washing with hydrogen peroxide solution as the pre-treatments, presented similar efficiency for elimination of TPH, oil and grease but elimination of PAHs it is better to handle with peroxide pre-treatment, where can be achieved more than 80%.The results of the modeling of groundwater flow in the zone of interest, indicate a predominant direction northwest - south-west (NW to SW) and a maximum speed of flow 0.37 m/d of groundwater. The direction of displacement of the underground water together with the pen is towards the Marsh Palagua. The calibration of model lives average error -0,007m and absolute error 0,346m. After one month of biostimulation and two weeks flushing with surfactant as pre-treatment in Palagua oil field, was achieved elimination of TPH (56,3%) oil and grease(44,8%) and PAHs (49,2%).Prezenční546 - Institut environmentálního inženýrstvívyhově

Study of Biodegradation and Bioremediation

Despite many years of efforts to reduce the emission of toxic pollutants into the environment, the contamination of air, soils and water by heavy metals and organic xenobiotics is still a serious problem. This has urged many scientists around the world to undertake research that aims to find effective methods of removing pollutants from the environment. Special attention is paid to biological methods, which, thanks to their numerous advantages, meet the expectations of the whole society. As part of the Special Issue “Study of Biodegradation and Bioremediation”, in the MDPI journal Processes, several valuable articles have been published, which together form a picture of the current state of advanced research on the effective fight against environmental pollution. These include papers on the biodegradation of petroleum compounds or synthetic dyes by microorganisms or the enzymes they produce. In addition, the Special Issue includes papers on the bioremediation of dangerous heavy metals such as mercury and copper, and the results make a valuable contribution to our current state of knowledge on this topic. A separate and valuable part of this collection of publications are review articles devoted to the remediation of antineoplastic drugs, as well as the hopes and challenges connected with the application of nanotechnology in bioremediation. We are pleased that so many researchers from different parts of the world have submitted their articles on this topic. We are very grateful to them. We hope that readers of this collection will find many interesting ideas and relevant information that will lead to new solutions in the bioremediation and biodegradation of emerging environmental contaminants. Prof. Ewa Kaczorek Dr. Wojciech Smułe

State of Knowledge of Soil Biodiversity – Status, Challenges and Potentialities, Report 2020

Our well-being and the livelihoods of human societies are highly dependent on biodiversity and the ecosystem services it provides. It is essential that we understand these links and the consequences of biodiversity loss for the various global challenges we currently face, including food insecurity and malnutrition, climate change, poverty and diseases. The Agenda 2030 for Sustainable Development sets out a transformative approach to achieve socio-economic development while conserving the environment. There is increasing attention on the importance of biodiversity for food security and nutrition, especially above-ground biodiversity such as plants and animals. However, less attention is being paid to the biodiversity beneath our feet, soil biodiversity. Yet, the rich diversity of soil organisms drives many processes that produce food, regenerate soil or purify water. In 2002, the Conference of the Parties (COP) to the Convention on Biological Diversity (CBD) decided at its 6th meeting to establish an International Initiative for the Conservation and Sustainable Use of Soil Biodiversity and since then, the Food and Agriculture Organization of the United Nations (FAO) has been facilitating this initiative. In 2012, FAO members established the Global Soil Partnership to promote sustainable soil management and increase attention to this hidden resource. The Status of the World’s Soil Resources (FAO, 2015) concluded that the loss of soil biodiversity is considered one of the main global threats to soils in many regions of the world. The 14th Conference of the Parties invited FAO, in collaboration with other organizations, to consider the preparation of a report on the state of knowledge on soil biodiversity covering its current status, challenges and potentialities. This report is the result of an inclusive process involving 300 scientists from around the world under the auspices of the FAO’s Global Soil Partnership and its Intergovernmental Technical Panel on Soils, the Convention on Biological Diversity, the Global Soil Biodiversity Initiative and the European Commission. The report presents the state of knowledge on soil biodiversity, the threats to it, the solutions that soil biodiversity can provide to problems in different fields, including agriculture, environmental conservation, climate change adaptation and mitigation, nutrition, medicine and pharmaceuticals, remediation of polluted sites, and many others. The report will make a valuable contribution to raising awareness of the importance of soil biodiversity and highlighting its role in finding solutions to today’s global threats; it is a cross-cutting topic at the heart of the alignment of several international policy frameworks, including the Sustainable Development Goals (SDGs) and multilateral environmental agreements. Furthermore, soil biodiversity and the ecosystem services it provides will be critical to the success of the recently declared UN Decade on Ecosystem Restoration (2021-2030) and the upcoming Post- 2020 Global Biodiversity Framework. Soil biodiversity could constitute, if an enabling environment is built, a real nature-based solution to most of the problems humanity is facing today, from the field to the global scale. Therefore efforts to conserve and protect biodiversity should include the vast array of soil organisms that make up more than 25% of the total biodiversity of our planet

State of Knowledge of Soil Biodiversity: Status, Challenges, and Potentialities

This report presents the threats to soil biodiversity and the solutions that soil biodiversity can provide to problems in different fields, including agriculture, environmental conservation, climate change adaptation and mitigation, nutrition, medicine and pharmaceuticals, remediation of polluted sites, and many others. There is increasing attention on the importance of biodiversity for food security and nutrition, especially above-ground biodiversity such as plants and animals. Less attention is being paid to the biodiversity beneath our feet: soil biodiversity. Yet the rich diversity of soil organisms drives many processes that produce food, regenerate soil or purify water. This report is the result of an inclusive process involving more than 300 scientists from around the world under the auspices of FAO's Global Soil Partnership and its Intergovernmental Technical Panel on Soils, the Convention on Biological Diversity, the Global Soil Biodiversity Initiative, and the European Commission

해양생태계 내 유기오염물질의 생지화학적 거동 평가 및 제일원리기법에 기반한 생태독성 반응 규명

학위논문(박사) -- 서울대학교대학원 : 자연과학대학 지구환경과학부, 2022. 8. 김종성.해양 환경은 육상 및 해양에서의 인간 활동으로 인해 광범위한 영향을 받는다. 해양 환경 중 조간대는 영양염류 (총질소 및 총인), 탄화수소 (유류 및 다환방향족탄화수소), 알킬페놀류, 스타이렌 올리고머를 포함한 유기 오염물질의 유입으로부터 육지와 바다 사이의 균형을 유지한다. 유기 오염물질의 거동은 물질의 물리화학적 특성에 크게 좌우된다. 더 큰 소수성 및 입자와의 반응성은 유기 오염물질이 퇴적물에 축적되게 만들고 그 결과, 퇴적물에서는 해수보다 몇 배나 더 큰 유기 오염물질의 농도를 유지한다. 해양 저서 퇴적물은 육상기인오염 물질의 최종 종착지이기 때문에 지속적인 해양 환경 생태서비스를 제공받기 위해서는 해양 환경의 유기 오염물 정화 능력과 생태독성 영향을 명확히 평가하는 것이 중요하다. 현재까지 조간대에서의 유기오염물질 정화 능력은 정량적으로 알려지지 않았고 정화 과정에서 발생하는 화학적, 독성학적, 생태학적 반응은 예측하기 어려웠다. 본 연구에서는 조간대 내 퇴적물이 정화되는 과정에서 발생하는 현상들을 실험적 규모 연구, 즉 메조코즘 연구를 통해 퇴적물의 생태위해성 평가법을 사용하여 정량적으로 확인하였다. 이를 위해 화학 분석, 생물 검정 및 저서 군집 구조 분석도 진행하였다. 그리고 인 실리고 연구를 통해 유기 오염물질의 물리화학적 특성을 분석하여 퇴적물의 정화 과정 속에서 발생하는 화학적, 독성학적, 그리고 생태학적 반응 원인을 제시하였다. 첫째로, 갯벌 퇴적물의 자정능을 평가하기 위해 0.2m3 부피의 유리 수조에 퇴적물을 이식하여 총인을 비롯한 고농도의 유기물질이 포함된 해수를 넣어 시간에 따른 변화 특성을 확인하였다. 갯벌 퇴적물은 총인 및 화학적 산소 요구량의 농도를 각각 2일 및 7일 만에 배경 농도 수준으로 제거하였다. 그리고 갯벌 퇴적물에 갈대를 심은 실험 구에서는 특히 용존 무기인을 빠르고 효율적으로 제거하였으며 이는 식생의 존재가 용존 유기 오염물질의 정화를 촉진하는 것을 의미한다. 또한 유기 오염물질의 침전은 생물학적 교란 효과가 작은 환경에서 우세한 것을 확인하였다. 둘째로, 자갈 조간대 내 유기 오염물질이 유입되었을 때를 가정하고 이를 회복하기 위한 물리적, 생물학적 기술들의 현황을 파악하고 효과를 분석하였다. 이를 위해 60일 동안의 메조코즘 연구로 잔류 유류 제거를 위한 물리적, 생물학적 기술, 그리고 자연정화능의 효과 및 영향을 비교하였다. 우선 고온고압 세척 처리는 잔류 유류를 최대 93% 제거하였다. 하지만 이와 같은 물리적 정화는 초기 정화 처리 기간 저서동물 군집에 악영향을 끼쳤다. 영양염, 유화제, 효소 활성제, 그리고 미생물 제제와 같은 생물학적 처리는 최대 66%의 잔류 유류를 제거하였다. ‘자연정화’는 다른 물리적 및 생물학적 기술들의 잔류 유류 제거 효과와 유사한 효율을 보여주었다. 특히 실험 기간은 미생물들의 천이를 확인하였으며 이는 시간에 따른 잔류 유류 성분의 변화 결과로 확인하였다. 자연정화는 다른 기술들만큼 유기 오염물질 제거에 효율적이었으며 특히 저서 군집에 대한 악영향을 최소화하는 특징이 있음을 확인하였다. 셋째로, 갯벌 퇴적물에서 잔류성 독성물질 특이적 정화와 생태독성 영향을 확인하기 위해 오염 퇴적물을 현장 갯벌에 이식하여 60일간 화학적, 독성학적, 그리고 생태학적 반응의 변화를 확인하였다. 그리고 머신 러닝을 통해 정화 과정 동안 오염 퇴적물의 특징을 4가지로 추출하였다. 대형저서동물과 식생이 함께 이식된 오염 퇴적물은 생물 관개 및 식물 정화 효과로 빠르게 회복되었다. 실험 기간은 잔류성 독성물질 내 다환방향족탄화수소, 알킬페놀류, 그리고 스타이렌 올리고머의 모물질들이 빠르게 감소하였는데 생물 관계 및 식물 정화로 인한 미생물의 활동으로 인한 결과임을 확인하였다. 넷째로, 매질 (해수, 퇴적물 및 해양 생물)에 대한 유기 오염물질의 반응성을 예측하기 위해 유기 오염물질의 물리화학적 성질을 분석하였습니다. 제1 원리를 활용한 밀도범함수이론을 통해 유기 오염물질과 매질 사이 반응을 정량적으로 확인할 수 있는 방향성 반응 인자를 고안하였다. 방향성 반응 모델은 유기 오염물질의 구조, 예로 벤젠 고리의 수, 메틸화 및 하이드록실 화와 같은 구조적 변형이 있는 크라이센의 동족체를 대상으로 계산하였고 특히 아릴 탄화수소수용체와의 반응 관계 중심으로 적용하였다. 본 반응 모델의 결과는 크라이센 동족체의 생물검정 결과와 일치하였다. 제1 원리에 기반한 인 실리코 연구는 유기 오염물질의 물리화학적 성질을 계산하였고 기존의 경험적 접근 방식을 보완하여 향후 해양 환경 내 매질 간의 반응성 예측에 활용할 수 있다. 끝으로, 독성 작용에 대한 반응 중심 접근 방법과 함께 16개의 다환방향족 탄화수소들의 생태독성 효과를 예측하기 위해 방향성 반응 모델을 응용하였다. 분자 역학 모델링 분석을 통해 아릴 탄화수소수용체와 다환방향족탄화수소의 결합 가능성을 확률적으로 계산하였고 이를 바탕으로 방향성 반응 모델과 연관시킨 방향성 반응-결합 인자를 고안하였다. 이 인자를 통해 유기 오염물질-수용체 결합을 예측할 수 있었고 나아가 생물검정 결과와 일치하는 것을 확인하였다. 잠재 독성 예측에 있어 방향성 반응-결합 인자는 유기 오염물질의 물리화학적 특성이 생물과의 독성 반응에 주요 요인이 될 수 있음을 요인이 될 수 있음 보여주었다. 향후 인 실리코 방법을 통한 유기 오염물질의 특성 분석은 생물뿐만 아니라 해수 및 퇴적물과 같은 해양 환경과의 반응 예측에 유의미하게 활용될 가능성을 확인하였다. 이상의 연구 결과를 종합해보면, 첫째, 먼저 조간대에 유입된 유기 오염물질의 농도는 초기 단계에서 전반적으로 급격한 감소를 했고, 모물질의 분해가 활발히 진행되었다. 둘째, 유기 오염물질 농도의 감소와 함께 퇴적물의 잠재 독성도 급격히 감소하였고, 유기 오염물질 농도의 감소 속도보다 더 빨랐다. 셋째, 저서 군집은 기하급수적으로 회복되었으며, 영양수준에 따라 각각의 회복 속도에 차이가 있었다. 넷째, 화학적, 독성학적, 생태학적 회복의 차이와 각 영향 관계는 유기 오염물질의 물리화학적 특성 영향에 기인한 것으로 확인되었다. 마지막으로, 본 연구의 방향성 반응 인자는 생물 내 잠재적인 독성을 예측하는 반응-결합 인자로 개발될 수 있으며 생물검정 결과와 상당히 일치한 것을 확인했다. 본 연구에서 활용한 통합적 접근은 해양 환경 내 유기 오염물질의 정화와 생태 독성학적 효과를 이해하는 데 있어 유용하게 사용될 수 있다. 앞으로 우리나라 해양 생태계 서비스의 가치를 재고하고 해안을 체계적으로 관리하기 위해서는 위와 같은 다학제적 접근이 지속해서 필요하다.The marine environment is subject to a broad range of adverse impacts from anthropogenic activities. Among the marine environment, an intertidal zone maintains a balance as a buffer between the land and the sea from the introduction of organic pollutants, including nutrients (total nitrogen, TN; total phosphorus, TP), hydrocarbons (oil and polycyclic aromatic hydrocarbons, PAHs), alkylphenols (APs+APEOs), and styrene oligomers (SOs). The fate of organic pollutants in the marine environment is highly dependent on their physicochemical properties. Due to their hydrophobicity and particle reactivity, many organic pollutants have concentrations in sediments that are several orders of magnitude greater than those in the surrounding water. As a result, sediments are frequently regarded as the final destination for pollutants in the environment. Thus, it is crucial to estimate the restoration capacity and ecotoxicological effect of organic pollutants in the marine environment to maintain environmental services. Until this study, the restoration ability of organic pollutants in the intertidal zone was not quantitatively known, and the chemical, toxicological and ecological reactions occurring during the restoration process were not predicted. In this study, the ecological processes occurring in sediments being purified were identified quantitatively using an enhanced integrated sediment quality triad (SQT) approach with an enclosed experimental scale study (mesocosm). Additionally, using an in silico study, by examining the physico-chemical properties of organic pollutants, the causes of the restoration and ecotoxicity were analyzed. For evaluating the specific recovery of the benthic community health from the organic pollutants, instrumental analysis, bioassays, and investigation of the benthic community structure were also implemented. The mudflat sediments significantly removed waterborne organic pollutants to background levels in ~2 and 6–7 days for TP and COD (chemical oxygen demand), respectively. This rapid removal of organic matters by natural sediments could be attributed to the microbe community degrading the corresponding pollutants. The temporal trend and removal efficacy for COD and TP were found to be similar between the bare tidal flat and salt marsh. Meantime, it was noteworthy that the salt marsh removed waterborne DIP much more quickly and efficiently, implying a high affinity of the halophyte on dissolved forms of organic matters. Of note, sedimentary organic sink prevailed in a defaunated condition under the lesser bioturbation effect. Physical and biological remediation techniques were compared to natural attenuation for the removal of residual oil using a 60-day mesocosm experiment with SQT. First, physical treatment of hot water + high pressure flushing maximally removed residual oils (max=93%), showing the greatest recovery among the SQT variables (mean=72%). Physical cleanup generally involved adverse effects such as depression of the microphytobenthic community during the initial period. Next, biological treatments, such as fertilizer, emulsifier, enzyme, and augmentation of the microbes, all facilitated the removal of oil (max=66%) enhancing the ecological recovery. Natural attenuation with “no treatment” showed a comparable recovery to the other remediations (max=54%). During the experimental periods, the dynamics of the benthic community were presented. Artificial remediation techniques showed a better efficacy as indicated by the SQT parameters (mean=47%). Natural restoration was also often as efficient as most active restoration alternatives and was cost-effective while minimizing the impacts on benthic communities. Contaminated sediments were transplanted into the site tidal flats to confirm the PTS specific restoration in the tidal flat and their ecotoxicological effects. A 60-day in situ mesocosm study was implemented to quantify the restoration capacity using the SQT. Contaminated sediments recovered rapidly through bio-irrigation and phytoremediation (max. recovery: 71.2%). Machine learning classified the sedimentary qualities of the natural restoration process into four groups. During the 60-day sediment recovery period the benthic community changed through four stages. The reduction of parent compounds of PTSs (high molecular weight PAHs, STs, and APEOs) progressed primarily through bio-irrigation and phytoremediation. The results show that the presence of macrofauna and macrophytes in the tidal flat can promote the degradation of parent compounds with a rapid reduction of toxicity. The influence of the dipole-driven orientation and the resulting directional configuration of the organic pollutants on the predicted reactivity to the media (seawater, sediment, and marine organisms) were investigated. Using physico-chemical properties calculated by ab initio density functional theory, directional reactivity factors (DRF) were devised as the main indicators of reactivity, linking the interaction between the organic pollutants and the media. The directional reactive model was applied to predict the variation of the aryl hydrocarbon receptor (AhR)-mediated toxic potencies among homologues of chrysene with structural modifications such as the number of constituent benzene rings, methylation, and hydroxylation. The results of this study explain why the toxic responses of the parent and metabolites of the organic pollutants were different. Moreover, the results of the predictive models were consistent with the empirical potencies determined by the use of the H4IIE-luc transactivation bioassay. An experiment-free approach based on first principles would provide an analytical framework for estimating the molecular reactivity in silico and complements conventional empirical approaches for studying molecular initiating events in adverse outcome pathways. Because the advanced DRF model was calculated for the interaction between organic pollutants and media, quantitatively calculations for the dynamical mechanism were used for applying the potential toxicity prediction model. Using molecular dynamics (MD) analysis, given the possibility of AhR-organic pollutants binding (conjugated state), it was confirmed that the directional reactive binding factor (DRBF) could be a mechanistic predictive index linking molecular ligand-receptor binding to in vitro toxicity. The DR model accurately estimated the toxic potency of a set of 16 similar PAHs, as confirmed by the H4IIE-luc bioassay. The first application of DRF to the prediction of potential toxicity implies that the physico-chemical properties of organic pollutants can be a major driving factor in the reaction with a medium, and the in silico method will provide important basic data for predicting the restoration and ecotoxicity of organic pollutants in the future. To summarize the above study results, first, the concentration of organic pollutants introduced into the intertidal zone showed a rapid decrease in the initial stage overall, and the decomposition of the parent material proceeded actively. Second, with the decrease of the concentration of the organic pollutants, the potential toxicity of the sediment also decreased rapidly, and the rate of decrease was faster than the decrease of the concentration of the organic pollutants. Third, the benthic cluster recovered exponentially, and there was a difference in each recovery rate according to the trophic level. Fourth, it was confirmed that the differences in chemical, toxicological, and ecological recovery were affected by the physicochemical properties of the organic pollutants. Finally, the DRF in this study could be developed into a DRBF predicting the potential toxicity and corresponded to the results of the in vitro bioassay. An integrated approach for understanding the restoration capacity and ecotoxicological effects of organic pollutants in this study can be useful for interpreting the chemical, toxicological, and ecological responses. In the future, to systematically manage coastal waters with severe contamination of benthic sediments, continuous development of ecological risk assessment techniques is required. In the future, to reconsider the value of ecosystem services in the intertidal zone of Korea and systematically manage coasts, the above interdisciplinary approach is continuously needed.CHAPTER. 1. Introduction 1 1.1. Backgrounds 2 1.2. Objectives 15 CHAPTER. 2. Natural Restoration Capacity of Tidal Flats for Organic Matters and Nutrients: A Mesocosm Study 18 2.1. Introduction 19 2.2. Materials and Methods 21 2.2.1. Study design and development of mesocosm system 21 2.2.2. Sampling and data analyses 22 2.3. Results and Discussion 28 2.3.1. Natural restoration under waterborne organic matters and nutrients in tidal flat 28 2.3.2. Comparison of restoration capacity between bare and vegetated sediment 31 2.3.3. Restoration capacity in Bongam tidal flat, Masan Bay 38 2.3.4. Comparison to other mesocosm studies for restoration capacity of tidal flats 40 2.4. Conclusions 44 CHAPTER. 3. Best Available Technique for the Recovery of Marine Benthic Communities in a Gravel Shore after the Oil Spill: a Mesocosm-based Sediment Triad Assessment 45 3.1. Introduction 46 3.2. Materials and Methods 48 3.2.1. Sample preparations 48 3.2.2. Mesocosm experimental setting 49 3.2.3. Instrumental analysis of residual TPH and UCM in gravel 57 3.2.4. Zebrafish (Danio rerio) embryo test 57 3.2.5. Vibrio fischeri (V. fischeri) biossay 58 3.2.6. H4llE-luciferase transactiviation bioassay 58 3.2.7. Identification of MPB individual 58 3.2.8. Bacterial metagenomic analysis 59 3.2.9. Measurements of benthic primary production 59 3.2.10. Multi-attribute utility theory (MAUT) analysis for selection of the best available technique for remediation of oil 60 3.2.11. Statistical analysis 60 3.3. Results and Discussion 62 3.3.1. Physical and biological remediations 62 3.3.2. Dynamics in bacterial communities 78 3.3.3. Effectiveness of remediation techniques 85 3.3.4. Best available remediation techniques 86 3.4. Conclusions 95 CHAPTER. 4. Determining characteristics of Sediment Quality with Machine Learning to Evaluate the Natural Restoration of Persistent Toxic Substances in Contaminated Tidal Flat Sediments 96 4.1. Introduction 97 4.2. Materials and Methods 100 4.2.1. Sample preparation and In situ mesocosm experimental setting 100 4.2.2. Persistent toxic substances analysis (PAHs, APs, and SOs) 104 4.2.3. H4llE-luciferase transactivation bioassay 105 4.2.4. Bacterial metagenomic analysis 105 4.2.5. Identification of diatom individual 106 4.2.6. Identification of meiofauna individual 106 4.2.7. Measurements of benthic primary production 106 4.2.8. Self-Organizing Map (SOM) 107 4.2.9. K-means clustering via principal component analysis (PCA) 109 4.2.10. Statistical analysis 109 4.3. Results and Discussion 110 4.3.1. Chemical, toxicological, and biological responses in natural restoration process of tidal flat 110 4.3.2. Time series clustering in evaluating the recovery of each treatment with the self-organizing map (SOM) using machine learning 118 4.3.3. Effect of macrofauna (C. sinensis and M. japonicus) and salt marsh (P. australis) on the change of benthic community using K-means clustering: PCA 121 4.3.4. Correlation between composition of PTSs and bacterial community in each treatment groups 125 4.3.5. Evaluation to natural restoration of contaminated sediments & effect of bio-irrigation and phytoremediation in tidal flat by sediment quality triad approach (SQT) 130 4.4. Conclusions 132 CHAPTER. 5. Influence of Ligand’s Directional Configuration, Chrysenes as Model Compounds, on the Binding Activity with Ahr Receptor 133 5.1. Introduction 134 5.2. Materials and Methods 138 5.2.1. Selection of Model Chemicals 138 5.2.2. Density Functional Theory Calculations 140 5.2.3. C 1s NEXAFS Spectroscopy 140 5.2.4. H4llE-luc transactivation bioassay for evaluating AhR-mediated potencies and calculation of EC50 of homologues of chrysene 141 5.2.5. In silico analysis: quantitative structure-activity relationship (QSAR) and molecular docking model 144 5.3. Results and Discussion 145 5.3.1. Directional Reactive Modeling 145 5.3.2. DRF as an indicator of ligand-binding reactivity 147 5.3.3. AhR-mediated toxic potency of chrysene homologues 158 5.3.4. Comparison of predicted potencies: DR model vs. current in silico models 162 5.4. Conclusions 167 CHAPTER. 6. Comprehension of Bio-Physical Communication for Predicting Potential Toxicity of 16 Polycyclic Aromatic Hydrocarbons 169 6.1. Introduction 170 6.2. Materials and Methods 175 6.2.1. Selection of Model Chemicals 175 6.2.2. Density Functional Theory Calculations 175 6.2.3. Molecular dynamics for calculating the probability of binding in ligand:AhR 176 6.2.4. Aryl hydrocarbon receptor homology modeling 177 6.2.5. H4llE bioassay and calculation in median effective concentration 177 6.2.6. In silico toxicity prediction analysis 178 6.3. Results and Discussion 179 6.3.1. A comprehensive driving force of ligand to receptor calculated from DR model based on first principles 179 6.3.2. Probability of 16 PAHs binding to AhR and determination of potential toxicity for 16 PAHs 188 6.3.3. Experimental and predicted potential toxicity of 16 PAHs using in vitro and in silico testing 195 6.4. Conclusions 201 CHAPTER. 7. Conclusions 202 7.1. Summary 203 7.2. Environmental implications and Limitations 208 7.3. Future Research Directions 211 BIBLIOGRAPHY 213 ABSTRACT (IN KOREAN) 236박