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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.

imaging --- data visualization --- fluorescence chemistry --- quantum dot --- model optimization --- numerical integration --- GPGPU --- molecular crowding --- cell division

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Biological membranes protect cells and organelles from the surrounding environment, but serve also as organising platforms for physiological processes such as cell signalling. The hydrophobic core of membranes is composed of lipids and proteins influencing each other. Local membrane composition and properties define its molecular organisation and, in this way, regulate the function of all associated molecules. Therefore, studying interactions of components, biophysical properties and overall membrane dynamics provides essential information on its function in the context of cell activities. Such knowledge can contribute to biomedical fields such as pharmacology, immunology, neurobiology and many others. The goal of the Research Topic entitled ‘Molecular organisation of membranes: where biology meets biophysics’ was to provide a comprehensive platform for publishing articles, reviews and opinions focused on membrane organisation and the forces behind its heterogeneous and dynamic structure. We collected 11 works which cover topics as diverse as general membrane organisation models, membrane trafficking and signalling regulation, biogenesis of caveolae, protein-lipid interactions and the importance of membrane-associated tetraspanins networks. The prevalent theme was the existence of membrane nanodomains. To this point, new emerging technologies are presented which own the power to bring a novel insight on how membrane nanodomains are formed and maintained and what is their function. We believe that the collection of works in this Research Topic brings forward some important questions which will stimulate further research in this difficult but exciting field.

Cell Membrane --- Nanodomains --- Tetraspanins --- Caveolae --- Membrane properties --- Membrane trafficking --- fluorescence microscopy --- Superresolution microscopy

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Recombinant viruses expressing reporter fluorescent or bioluminescent proteins are an excellent option to evaluate the dynamics of viral infection progression in both cultured cells and/or validated animal models of viral infection. Reporter proteins are valid surrogates for direct detection of infected cells in vitro and in vivo, without the use of secondary methodologies to identify infected cells. By eliminating the need of secondary labeling, tractable replicating-competent, reporter-expressing viruses provide an ideal approach to monitor viral infections in real time, representing a significant advance in the study of the biology of viruses, to evaluate vaccination approaches, and to identify new therapeutics against viral infections using high-throughput screening settings. In this Special Issue “Replication-Competent Reporter-Expressing Viruses” we review replication-competent, reporter-expressing viruses belonging to different families, methods of characterization, and applications to facilitate the study of in vitro and in vivo viral infections. We also seek to discuss disadvantages and limitations associated with these reporter-expressing viruses. Finally, we provide rational future perspectives and additional avenues for the development, characterization, and applications of recombinant, reporter-expressing, competent viruses.

Recombinant viruses, plasmid-based reverse genetics, virus rescue approaches, reporter genes, fluorescence, luminescence, replicating-competent reporter-expressing viruses

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The cryosphere is very sensitive to climate change, and glaciers represent one of the most important archives of atmospheric composition and its variability. From the Himalaya to the European Alps, the longest mid-latitude mountain chain in the world, lie thousands of glaciers that have collected atmospheric compounds over the last millennia. China and Italy are located at the opposite terminals of this long mountain chain, comprising strategic positions for understanding climate evolution and providing important information for the modeling of future climates. The results presented are highlights of some of the most recent advances in cryospheric studies, especially on the topic of mineral dust and aerosols in the atmosphere. They evidence the complexity of the chemical–physical processes involving solid compounds occurring in glacier, snow, and permafrost environments, covering different aspects such as spatial and temporal trends, as well as the impact of mineral and nonmineral particles. Results also show that recent advances in measurement techniques and source apportionment may be powerful and sophisticated tools to provide novel, high-quality scientific information.

Arctic --- Arctic rapid warming --- global warming hiatus --- global warming slowdown --- particulate matter --- simultaneous measurements --- mineral elements --- compositional data analysis --- ultra-dilution --- droplets --- water --- evaporation --- X-ray fluorescence --- cryoconite --- POPs --- microbiology --- long-range transport --- cryosphere --- contaminants --- bacteria --- atmospheric mineral dust --- ice core --- Antarctica --- paleoclimate --- synchrotron radiation --- X-ray absorption near edge spectroscopy --- X-ray fluorescence --- iron geochemistry --- synchrotron radiation --- X-ray fluorescence spectroscopy --- X-ray absorption fine structure spectroscopy --- trace elements --- cryospheric sciences --- snow --- ice --- dust --- TXRF --- polycapillary optics --- low concentration elemental analysis --- mineral dust --- XANES --- paleoclimatology --- ice cores --- southern hemisphere --- Laohugou glacier --- snow --- insoluble dust --- iron speciation --- XANES and LCF --- XAS spectroscopy --- synchrotron radiation --- environment --- synchrotron radiation --- ice core, atmospheric mineral dust --- X-ray absorption spectroscopy

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The characterization of peptides and proteins is central to understanding their function and expression in biological matrices. Moreover, these macromolecules are important biomarkers of many human diseases. In recent years, the performance of separation techniques based on electromigration have significantly increased. The development of microdevices has reduced sample consumption and waste production while high-sensitivity detectors, such as mass spectrometry (MS) or laser-induced fluorescence (LIF), have significantly improved with regards to separation efficiency and detection limits. All of these advancements have led to appreciably enlarged fields of application. Nowadays, a multitude of studies using separation techniques based on electromigration to study proteins and peptides from numerous real matrices are available in the literature. This Special Issue covers the most recent knowledge and advances in the study of peptides and proteins using several electrophoresis techniques, as well as the characterization of relevant proteins and peptides in application areas such as clinical studies, functional foods, and toxicology.

Naja ashei --- venom composition --- 2-D electrophoresis --- proteomics --- myrosinase --- thioglucosidase --- sulfatase --- on-gel detection --- desulfo-sinigrin --- LC-ESI-MS --- seed proteomics --- seed phosphoproteomics --- seed glycoproteomics --- seed quality traits --- seed molecular breeding --- rhIL-12 --- purity --- SDS-PAGE --- SEC-HPLC --- fragment --- non-covalent binding --- carbon dots --- capillary electrophoresis --- transferrin --- metalloproteins --- fluorescence --- CE-LIF --- immunoassay --- enzyme assay --- chip-based CE-LIF assay