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Organic Ligands in Marine Trace Metal Biogeochemistry

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453764 Year: Pages: 303 DOI: 10.3389/978-2-88945-376-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Oceanography
Added to DOAB on : 2018-11-16 17:17:57
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This research topic highlights the most recent accomplishments of a Scientific Committee on Oceanic Research (SCOR) Working Group, SCOR WG 139: Organic Ligands - A Key Control on Trace Metal Biogeochemistry in the Ocean.

Quantitative Biology: Dynamics of Living Systems

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452132 Year: Pages: 136 DOI: 10.3389/978-2-88945-213-2 Language: English
Publisher: Frontiers Media SA
Subject: Biology --- Neurology --- Physiology --- Science (General)
Added to DOAB on : 2017-10-13 14:57:01
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With the emergence of Systems Biology, there is a greater realization that the whole behavior of a living system may not be simply described as the sum of its elements. To represent a living system using mathematical principles, practical quantities with units are required. Quantities are not only the bridge between mathematical description and biological observations; they often stand as essential elements similar to genome information in genetics. This important realization has greatly rejuvenated research in the area of Quantitative Biology. Because of the increased need for precise quantification, a new era of technological development has opened. For example, spatio-temporal high-resolution imaging enables us to track single molecule behavior in vivo. Clever artificial control of experimental conditions and molecular structures has expanded the variety of quantities that can be directly measured. In addition, improved computational power and novel algorithms for analyzing theoretical models have made it possible to investigate complex biological phenomena. This research topic is organized on two aspects of technological advances which are the backbone of Quantitative Biology: (i) visualization of biomolecules, their dynamics and function, and (ii) generic technologies of model optimization and numeric integration. We have also included articles highlighting the need for new quantitative approaches to solve some of the long-standing cell biology questions. In the first section on visualizing biomolecules, four cutting-edge techniques are presented. Ichimura et al. provide a review of quantum dots including their basic characteristics and their applications (for example, single particle tracking). Horisawa discusses a quick and stable labeling technique using click chemistry with distinct advantages compared to fluorescent protein tags. The relatively small physical size, stability of covalent bond and simple metabolic labeling procedures in living cells provides this type of technology a potential to allow long-term imaging with least interference to protein function. Obien et al. review strategies to control microelectrodes for detecting neuronal activity and discuss techniques for higher resolution and quality of recordings using monolithic integration with on-chip circuitry. Finally, the original research article by Amariei et al. describes the oscillatory behavior of metabolites in bacteria. They describe a new method to visualize the periodic dynamics of metabolites in large scale cultures populations. These four articles contribute to the development of quantitative methods visualizing diverse targets: proteins, electrical signals and metabolites. In the second section of the topic, we have included articles on the development of computational tools to fully harness the potential of quantitative measurements through either calculation based on specific model or validation of the model itself. Kimura et al. introduce optimization procedures to search for parameters in a quantitative model that can reproduce experimental data. They present four examples: transcriptional regulation, bacterial chemotaxis, morphogenesis of tissues and organs, and cell cycle regulation. The original research article by Sumiyoshi et al. presents a general methodology to accelerate stochastic simulation efforts. They introduce a method to achieve 130 times faster computation of stochastic models by applying GPGPU. The strength of such accelerated numerical calculation are sometimes underestimated in biology; faster simulation enables multiple runs and in turn improved accuracy of numerical calculation which may change the final conclusion of modeling study. This also highlights the need to carefully assess simulation results and estimations using computational tools.

Radiation-induced and oxidative DNA damages

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196609 Year: Pages: 93 DOI: 10.3389/978-2-88919-660-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Chemistry (General)
Added to DOAB on : 2016-08-16 10:34:25
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DNA stores and passes the genetic information of almost all living organisms. Its molecular structure and their intramolecular interactions are particularly suitable to maximize stability against oxidative stress and UV-light absorption. Yet the protection and repair strategies are still error-prone: DNA lesions are produced, including the most complex and highly mutagenic ones. An important threat to DNA stability comes from photosensitization, i.e. from the dramatic multiplication of radiation-induced defects mediated by the presence of organic or organometallic dyes compared to the direct exposure to UVA radiation. Moreover, the photo-induced production of singlet oxygen generates an extremely high oxidative stress on DNA that, in vivo, normally results in extended cellular apoptosis. Elucidating the processes leading to DNA damages, from the production of a simple radical entity to deleterious lesions, as well as the opportunities of repair by devoted enzymes, is a cornerstone towards the development of more efficient protection strategies. Sensitization and selective production of DNA lesions can also be exploited to induce the selective apoptosis of cancer cells upon exposition to radiation or to oxidative stress, for instance in the field of photodynamic therapy. The importance and relevance of the field is witnessed by the impressive amount of high-level papers dealing with this complex subject, and notably tackling the structural elucidation of DNA and DNA-drug adducts, the mechanisms of formation of DNA lesions (including the precise detection of the final lesion products), as well as the influence of the lesions on the DNA stability and dynamics and the consequences on the ease of repair. Due to the complexity of the field lying at the frontiers between chemistry, physics and biology, multidisciplinary strategies allying modeling and experience are needed. This topic aims at giving an extended overview of the current research in the domain, with fundamental contribution from the leading groups in the field of DNA reactivity, structural characterization, photo-chemistry and photo-physics, as well as repair mechanism. It will therefore be a fundamental guide for scientists wanting to address the field of DNA lesion and repair, but also more generally for researchers working in rational drug design or in the development of biomarkers and medical imaging techniques.

The Chemistry of Imaging Probes

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889455980 Year: Pages: 129 DOI: 10.3389/978-2-88945-598-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Chemistry (General)
Added to DOAB on : 2019-01-23 14:53:43
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Over the past decades, the field of molecular imaging has been rapidly growing involving multiple disciplines such as medicine, biology, chemistry, pharmacology and biomedical engineering. Any molecular imaging procedure requires an imaging probe that is an agent used to visualize, characterize and quantify biological processes in living systems. Such a probe typically consists of an agent that usually produces signal for imaging purpose, a targeting moiety, and a linker connecting the targeting moiety and the signaling agent.Many challenging problems of molecular imaging can be addressed by exploiting the great possibilities offered by modern synthetic organic and coordination chemistry and the powerful procedures provided by conjugation chemistry. Thus, chemistry plays a decisive role in the development of this cutting-edge methodology.Currently, the diagnostic imaging modalities include Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Ultrasound (US), Nuclear Imaging (PET, SPECT), Optical Imaging (OI) and Photoacoustic Imaging (PAI). Each of these imaging modalities has its own advantages and disadvantages, and therefore, a multimodal approach combining two techniques is often adopted to generate complementary anatomical and functional information of the disease. The basis for designing imaging probes for a given application is dictated by the chosen imaging modality, which in turn is dependent upon the concentration and localization profile (vascular, extracellular matrix, cell membrane, intracellular, near or at the cell nucleus) of the target molecule. The development of high-affinity ligands and their conjugation to the targeting vector is also one of the key steps for pursuing efficient molecular imaging probes. Other excellent reviews, text and monographs describe the principles of biomedical imaging, focusing on molecular biology or on the physics behind the techniques. This Research Topic aims to show how chemistry can offer molecular imaging the opportunity to express all its potential.

Quantum Mechanical/Molecular Mechanical Approaches for the Investigation of Chemical Systems - Recent Developments and Advanced Applications

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889456260 Year: Pages: 188 DOI: 10.3389/978-2-88945-626-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Chemistry (General)
Added to DOAB on : 2019-01-23 14:53:43
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The QM/MM method, short for quantum mechanical/molecular mechanical, is a highly versatile approach for the study of chemical phenomena, combining the accuracy of quantum chemistry to describe the region of interest with the efficiency of molecular mechanical potentials to represent the remaining part of the system. Originally conceived in the 1970s by the influential work of the the Nobel laureates Martin Karplus, Michael Levitt and Arieh Warshel, QM/MM techniques have evolved into one of the most accurate and general approaches to investigate the properties of chemical systems via computational methods. Whereas the first applications have been focused on studies of organic and biomolecular systems, a large variety of QM/MM implementations have been developed over the last decades, extending the range of applicability to address research questions relevant for both solution and solid-state chemistry as well. Despite approaching their 50th anniversary in 2022, the formulation of improved QM/MM methods is still an active field of research, with the aim to (i) extend the applicability to address an even broader range of research questions in chemistry and related disciplines, and (ii) further push the accuracy achieved in the QM/MM description beyond that of established formulations. While being a highly successful approach on its own, the combination of the QM/MM strategy with other established theoretical techniques greatly extends the capabilities of the computational approaches. For instance the integration of a suitable QM/MM technique into the highly successful Monte-Carlo and molecular dynamics simulation protocols enables the description of the chemical systems on the basis of an ensemble that is in part constructed on a quantum-mechanical basis. This eBook presents the contributions of a recent Research Topic published in Frontiers in Chemistry, that highlight novel approaches as well as advanced applications of QM/MM method to a broad variety of targets. In total 2 review articles and 10 original research contributions from 48 authors are presented, covering 12 different countries on four continents. The range of research questions addressed by the individual contributions provide a lucid overview on the versatility of the QM/MM method, and demonstrate the general applicability and accuracy that can be achieved for different problems in chemical sciences. Together with the development of improved algorithms to enhance the capabilities of quantum chemical methods and the continuous advancement in the capacities of computational resources, it can be expected that the impact of QM/MM methods in chemical sciences will be further increased already in the near future.

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