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Search results for: MODEL ORGANISMS
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Mytilidae as model organisms in the marine ecotoxicology of pharmaceuticals - A review
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Analysis of differences in the stability of proteins encoded in mitochondrial DNA of model organisms
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Comparative Analysis of CpG Sites and Islands Distributed in Mitochondrial DNA of Model Organisms
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Experimental and model-based evaluation of the role of denitrifying polyphosphate accumulating organisms at two large scale WWTPs in northern Poland
PublicationW pracy dokonano oceny zdolności denitryfikacyjnych bakterii fosforowych na przykładzie oczyszczalni ścieków ''Wschód'' w Gdańsku i ''Dębogórze'' w Gdyni. W tym celu wykonano serię testów z wykorzystaniem tzw. reaktora ''wsadowego'', które następnie były modelowane za pomocą modelu ASM2d. Badania wykazały, że tylko 32% bakterii fosforowych posiada zdolność do denitryfikacji. Szybkość denitryfikacji związana z aktywnością bakterii...
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Evolution of chemotaxis in single-cell artificial organisms
PublicationThe model of a liquid two-dimensional environment, which is based on physics of diffusion, allows us to simulate the diffusion of morphogenes. Artificial organisms move using a chemotaxis reacting to concentration difference. Organisms are controlled by a gene regulatory network coded in a linear genome and reproduce by division. We made a lot of experiments presenting organisms’ behaviour in various environment conditions. We...
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The influence of electromagnetic pollution on living organisms – historical trends and forecasting changes
PublicationCurrent technologies have become a source of omnipresent electromagnetic pollution from generated electromagnetic fields and resulting electromagnetic radiation. In many cases this pollution is much stronger than any natural sources of electromagnetic fields or radiation. Wireless and radio communication, electric power transmission or devices in daily use such as smartphones, tablets and portable computers every day expose people...
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The Properties, Functions, and Use of Selenium Compounds in Living Organisms
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The properties, functions and use of selenium compounds in living organisms
PublicationSelenium occurs in the environment in inorganic and organic compounds. For many years it was regarded as a toxic element, causing numerous illnesses and diseases. But research in the last 50 years has revealed a "bright side" to this element, especially as a component of selenoproteins, selenium makes a significant contribution to the health of humans and animals. The selenium content in an organism depends on its concentration...
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Evolution of artificial single-cell organisms foraging for resources in a 3-dimensional environment
PublicationForaging for resources is a simple cognitive task that even one-celled biological organisms can ac- complish. We present an Artificial Life system in which artificial unicellular organisms (animats) forage for food in a 3-dimensional simulated liquid environment. The movement of animats is controlled by evolving artificial gene regulatory networks encoded in linear genomes. When an animat consumes enough food, it produces offspring...
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The influence of cold season warming on the mercury pool in coastal benthic organisms
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Mercury in Living Organisms: Sources and Forms of Occurrence, Bioaccumulation, and Determination Methods
PublicationMercury (Hg) is a heavy metal with well-known and broadly tested toxicity. Since Hg pollution and its impacts on human health are of global concern, it has become necessary to develop analytical methodologies that will provide tools to obtain reliable analytical information about the levels of Hg in samples, which very often have a complex matrix composition. This chapter summarizes key information on Hg and its chemical forms,...
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Bioaccumulation of Metals in Tissues of Marine Animals, Part I: the Role and Impact of Heavy Metals on Organisms
PublicationHeavy metals contribute to the anthropogenic contamination of marine ecosystems. Some of them are essential to the life processes of organisms; others are toxic, even at low concentrations. They penetrate organisms via food, respiratory pathways or the skin. The extent to which metals penetrate organisms is measured by the bioconcentration and bioaccumulation factors and also by their transport between organisms at different trophic...
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Environmental transformation and nano-toxicity of engineered nano-particles (ENPs) in aquatic and terrestrial organisms
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Principles and applications of Ligation Mediated PCR methods for DNA-based typing of microbial organisms
PublicationA significant number of DNA-based techniques has been introduced into the field of microorganisms’ characterization and taxonomy. These genomic fingerprinting methods were developed to detect DNA sequence polymorphisms by using general principles, such as restriction endonuclease analysis, molecular hybridization, and PCR amplification. In recent years, some alternative techniques based on ligation of oligonucleotide adapters before...
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Synthesis of Novel Phosphonic‐Type Activity‐Based Probes for Neutrophil Serine Proteases and Their Application in Spleen Lysates of Different Organisms
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Toxicity of ionic liquid cations and anions towards activated sewage sludge organisms from different sources – Consequences for biodegradation testing and wastewater treatment plant operation
PublicationIonic liquids (ILs) have attracted great interest in academia and industry during the last decade. So far, several ILs have been used in technological processes, from small scale to industrial applications, which makes it more and more likely that they will be released into the environment. Researches have been actively studying the environmental and toxicological bevaviour of ILs, but their influence on the activated sewage sludge...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublicationRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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Modeling nitrous oxide production by a denitrifying-enhancedbiologically phosphorus removing (EBPR) activated sludge in thepresence of different carbon sources and electron acceptors
PublicationIn this study, the IWA Activated Sludge Model No. 2d (ASM2d) was expanded to identify the most important mechanisms leading to the anoxic nitrous oxide (N2O) production in the combined nitrogen (N) and phosphorus (P) removal activated sludge systems. The new model adopted a three-stage denitrification concept and was evaluated against the measured data from one/two-phase batch experiments carried out with activated sludge withdrawn...
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Trophic Transfer of Mercury in a Temperate Marine Food Web, Southern Baltic Sea
PublicationMercury (Hg) is considered to be one of the most dangerous global environmental pollutants. The toxicity and bioavailabilityof Hg depend on its chemical form, and the greatest hazard is posed by the organomercurial compounds. Hg is introduced into the human body primarily through the consumption of fish and seafood. Despite numerous studies on Hg in marine organisms, there is still a gap in the knowledge on Hg uptake and...
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Modeling N2O behavior during denitrification with different carbon sources and electron acceptors
PublicationA mathematical model was developed for identification of the most important mechanism leading to nitrous oxide (N2O) accumulation in denitrifying activated sludge systems. The activated sludge model No. 2d (ASM2d) was extended to include intermediate three steps of the denitrification process. The formation and accumulation of nitric oxide (NO) was assumed to be very low in the performed laboratory experiments. These experiments...
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Modeling the Effect of External Carbon Source Addition under Different Electron Acceptor Conditions in Biological Nutrient Removal Activated Sludge Systems
Publicationhe aim of this study was to expand the International Water Association Activated Sludge Model No. 2d (ASM2d) to predict the aerobic/anoxic behavior of polyphosphate accumulating organisms (PAOs) and “ordinary” heterotrophs in the presence of different external carbon sources and electron acceptors. The following new aspects were considered: (1) a new type of the readily biodegradable substrate, not available for the anaerobic activity...
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The metabolic activity of denitrifying microorganisms accumulating polyphosphate in response to addition of fusel oil
PublicationThe effect of distillery waste product (fusel oil) as an alternative external organic carbon source (EOCS) was investigated in terms of the metabolic properties of denitrifying polyphosphate accumulating organisms (DPAOs). Samples of the non-acclimated biomass were collected from a local full-scale wastewater treatment plant employing A2/O type bioreactors. The acclimated biomass was obtained after cultivation (with fusel oil added)...
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Migration of container terminals as their natural process of evolution: Case study of Gdańsk and Gdynia ports
PublicationThe paper proposes a theoretical model of container terminals and container port development, based on the life cycle theory, threshold theory and catastrophe theory, and in references to Kuznets' swings (interpreted as waves of infrastructural investments), and Kondratiev long economic waves. The aim of this model is to explain the development process of a container terminal and a port within one technological generation, as...
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Modeling external carbon addition in combined N-P activated sludge systems with an extension of the IWA Activated Sludge Models
PublicationThe aim of this study was to expand the IWA Activated Sludge Model No. 2d (ASM2d) to account for a newly defined readily biodegradable substrate that can be consumed by polyphosphate accumulating organisms (PAOs) under anoxic and aerobic conditions, but not under anaerobic conditions. The model change was to add a new substrate component and process terms for its use by PAOs and other heterotrophic bacteria under anoxic and aerobic...
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Modeling external carbon addition in combined N-P activated sludge systems with an extension of the IWA Activated Sludge Models
PublicationThe aim of this study was to expand the IWA Activated Sludge Model No. 2d (ASM2d) to account for a newly defined readily biodegradable substrate that can be consumed by polyphosphate accumulating organisms (PAOs) under anoxic and aerobic conditions, but not under anaerobic conditions. The model change was to add a new substrate component and process terms for its use by PAOs and other heterotrophic bacteria under anoxic and aerobic...
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Phytoplankton in the Kashubian Lakes – microscopic photo archive
Open Research DataPhytoplankton is a group of microscopic plant organisms passively floating in water. The organisms included in the phytoplankton of lakes include the following main taxonomic groups: cyanobacteria (Cyanobacteria), green algae (Chlorophyta), dinoflagellates (Dinophyta), diatoms (Bacillariophyceae), cryptophytes (Cryptophyta), chrysophytes (Chrysophyceae)...
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Solar light driven degradation of textile dye contaminants for wastewater treatment – studies of novel polycationic selenide photocatalyst and process optimization by response surface methodology desirability factor
PublicationThe unplanned anthropogenic activities and raced industrial revolution detrimentally causes serious threat to terrestrial and aquatic life. A high discharge of wastewater from industries using dyes affects living organisms and the environment. This paper presents studies on polycationic selenides (PCS) synthesized by hydrothermal methods for photocatalytic degradation of dyes. The synthesized PCS were confirmed by various characterization...
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Assessing ecotoxicity and the endocrine potential of selected phthalates, BADGE and BFDGE derivatives in relation to environmentally detectable levels
PublicationThere is no doubt that the subject area of plasticmaterials (e.g., production of epoxy resins or polyesters) is inherently connected to issues concerning bisphenol A (BPA) and its analogues. Unfortunately, much less attention has been given to other compounds, which are also used for the production of these materials. Bisphenol A diglycidyl ether (BADGE) is a synthetic industrial compound obtained by a condensation reaction between...
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Binary Mixtures of Selected Bisphenols in the Environment: Their Toxicity in Relationship to Individual Constituents
PublicationBisphenol A (BPA) is one of the most popular and commonly used plasticizer in the industry. Over the past decade, new chemicals that belong to the bisphenol group have increasingly been used in industrial applications as alternatives to BPA. Nevertheless, information on the combined effects of bisphenol (BP) analogues is insufficient. Therefore, our current study aimed to find the biological response modulations induced by the...
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Seagrass vegetation and meiofauna enhance the bacterial abundance in the Baltic Sea sediments (Puck Bay)
PublicationThis study presents the first report on bacterial communities in the sediments of eelgrass (Zostera marina) meadows in the shallow southern Baltic Sea (Puck Bay). Total bacterial cell numbers (TBNs) and bacteria biomass (BBM) assessed with the use of epifluorescence microscope and Norland’s formula were compared between bare and vegetated sediments at two localities and in two sampling summer months. Significantly higher TBNs and...
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The particle method for simulation of self-organization phenomena
PublicationThe aim of the work was to design, implement, and use, in a number of experiments, an abstract software environment (an artificial world)suitable for modelling systems consisting of many moving and interactingobjects distributed in space. The environment, named DigiHive, is directed towards modeling of complex systems manifested by processes of self-organization, self-reproduction and self modifications. The environment is mainly...
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Convolutional Neural Networks for C. Elegans Muscle Age Classification Using Only Self-Learned Features
PublicationNematodes Caenorhabditis elegans (C. elegans) have been used as model organisms in a wide variety of biological studies, especially those intended to obtain a better understanding of aging and age-associated diseases. This paper focuses on automating the analysis of C. elegans imagery to classify the muscle age of nematodes based on the known and well established IICBU dataset. Unlike many modern classification methods, the proposed...
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Lead In drinking water: Adsorption method and role of zeolitic imidazolate frameworks for its remediation: A review
PublicationDue to various characteristics properties lead(II) metal is utilized in many applications like lead ion batteries, water pipes, ammunition and paints. For this reason, concentration of lead(II) ions in water is increasing days by days which is alarming for water pollution. Water pollution is a major problem worldwide which affects biosphere badly, and causes continuous reduction of accessible sources of fresh water and ground water, available...
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The lethal effect of hydrotechnical concrete on freshwater Bivalvia
PublicationMost hydrotechnical buildings under construction demand the concrete mixture to be set directly under water. The main reason for such a procedure is to limit the washing away of the the concrete binding mixture and to increase the efficiency of organisation of work so as to ensure continuity in concreting. The impact on the aquatic environment of recent developments in concrete technology and the use of new components has not yet...
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Analizy ilości i jakości odpływu wód deszczowych i roztopowych z kontrolowanej zlewni zurbanizowanej
PublicationIstotnym problemem Gdańska staje się bezpieczeństwo ekologiczne związane ze spływami miejskimi odprowadzanymi bezpośrednio do wód powierzchniowych, często akwenów użyteczności publicznej. W latach 2011÷2013, Katedra Hydrotechniki Wydziału Inżynierii Lądowej i Środowiska Politechniki Gdańskiej, we współpracy z Wojewódzkim Funduszem Ochrony Środowiska i Gospodarki Wodnej w Gdańsku oraz Gdańskimi Melioracjami, podjęła się wdrożenia...
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Ichtiofauna seasonal changes in Redłowo area
Open Research DataSallow water areas of the Baltic Sea are very important feeding, spawning, and nursery grounds for many fish species. The dataset includes data from fish mass analysis and detailed analysis. The mass analysis includes total abundance and a total weight of fish species caught during sampling. Detailed analysis includes individual fish total length, weight,...
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Analyzing sets of phylogenetic trees using metrics
PublicationThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationships between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations among organisms and geographical areas. In this paper, we describe a general method for comparing phylogenetictrees...
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Revision of Biological Methods for Determination of EDC Presence and Their Endocrine Potential
PublicationEndocrine-disrupting compounds (EDC) are chemicals responsible for disturbances in the hormonal balance of organisms. This group of chemicals includes both egzogenic and endogenic substances or their mixtures that impact functioning of natural hormones in organisms. In the available literature one can find information on the application of chromatographic and related techniques in the analysis of environmental samples for detection,...
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Bioassays as one of the Green Chemistry tools for assessing environmental quality: A review
PublicationFor centuries, mankind has contributed to irreversible environmental changes, but due to the modern science of recent decades, scientists are able to assess the scale of this impact. The introduction of laws and standards to ensure environmental cleanliness requires comprehensive environmental monitoring, which should also meet the requirements of Green Chemistry. The broad spectrum of Green Chemistry principle applications should...
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The use of bioassays in the analysis of environmental samples
PublicationToxicological tests are increasingly used as effective tool to complement the information obtained during the environmental monitoring. Moreover bioassays provide basic knowledge about the health effects of exposure to harmful factors associated with the environment. Toxicity tests might be a source of information about the content of pollutants in the sample, and the possibility of their interactions. They can be considered as...
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Speciation of heavy metal compounds in samples of biota from marine ecosystems
PublicationIt has become increasingly evident that the toxicity, mobility, bioavailability and bioaccumulation of metals are dependent on the particular physico-chemical form in which the element occurs in the environment. Special attention is paid to metals, which are essential for the proper functioning of organisms if present in appropriate amounts but are toxic if in excess (i.e. Se, Cr, Zn), and also to non-essential elements (i.e. Hg,...
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Activated Sludge Process Development
PublicationThis paper summarizes the most significant steps in the activated sludge process development and recognizes key contributors. Recognition of the roles of oxygen and living organisms was the first step (1882-1914). Ardern and Lockett (1914) named the accumulated olids "activated sludge". The process was rapidly accepted and applied in the period 1914-1930. The most dramatic changes in the activated sludge process understanding and...
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Occurrence of Surface Active Agents in the Environment
PublicationDue to the specific structure of surfactants molecules they are applied in different areas of human activity (industry, household). After using and discharging from wastewater treatment plants as effluent stream, surface active agents (SAAs) are emitted to various elements of the environment (atmosphere, waters, and solid phases), where they can undergo numerous physic-chemical processes (e.g., sorption, degradation) and freely...
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Influence of selected additives and admixtures on underwater concrete and the environment
PublicationThe intensive civilization development has an influence on searching for new possibilities connected with extension of city agglomerations, both the areas of flat building and the industrial areas. One of the most interesting solution is to use water reservoirs, rivers and sea areas. The extension of buildings has an influence on building materials, especially hydrotechnical, which means development of production of hydrotechnical...
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Bioaccumulation of metals in tissues of marine animals, Part II - metal concentrations in animal tissues
PublicationThe bioaccumulation of metals in an animal depends on a multitude of factors: biotic ones, like its body dimensions and mass, age, sex, diet, metabolism and position in the trophic web, as well as abiotic ones such as the distribution of metals in its environment, the salinity, temperature and pH of the water, habitat type, interactions with other metals. But it is diet that has the greatest influence on the accumulation of metals...
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Occurrences, sources, and transport of organochlorine pesticides in the aquatic environment of Antarctica
PublicationWe review information on the concentration levels of organochlorine pesticides in the abiotic aquatic environment (in seawater, sea ice, surface freshwater, snow, firn, and glacial ice) and the organisms inhabiting those, in Antarctica. Particular attention is given to the environmental fate of these pollutants, which modifies their impact on the organisms living in the Antarctic. OCPs have been delivered to the Antarctic environment...
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Analyzing sets of phylogenetic trees obtained from bayesian MCMC process using topology metrics
PublicationThe reconstruction of evolutionary trees is one of the primary objectives in phylogenetics. Such a tree represents historical evolutionary relationship between different species or organisms. Tree comparisons are used for multiple purposes, from unveiling the history of species to deciphering evolutionary associations amongorganisms and geographical areas.In the paper, we describe a general method for comparing hylogenetic trees....
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Polychlorinated Biphenyls (PCBs) and Polycyclic Aromatic Hydrocarbons (PAHs): Sediments and Water Analysis
PublicationUnfavorable side effects of different forms of anthropogenic activities can be found anywhere in the world. One of the basic characteristics of pollutants entering marine and ocean waters is their spread and movement in the global ocean. A portion of the substances entering the marine environment is rapidly degraded by chemical processes occurring in the air, sediments, and water, thereby losing their toxic properties. The biggest...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNA insequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination. Although there are differences in amino...
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Characterization of single-stranded DNA-binding proteins from the psychrophilic bacteria
PublicationSingle-stranded DNA-binding proteins (SSBs) are indispensable elements in the cells of all living organisms. SSB proteins interact with ssDNAinsequence in an independent manner, preventing them from forming secondary structures and from degradation by nucleases. In this way, SSB-binding proteins participate in all processes involving ssDNA, such as replication, repair and recombination.Although there are differences in amino acid...