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Sub-cellular Proteomics

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193028 Year: Pages: 254 DOI: 10.3389/978-2-88919-302-8 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
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Whilst significant advances have been made in whole organismal proteomics approaches, many researchers still rely on combinations of tissue selection and subcellular prefractionation methods to reduce the complexity of protein extracts from plants prior to proteomic analysis. Often this will allow identification of many lower abundance proteins of the target proteome and it may involve the selection of specific organs, cell types or the isolation of specific subcellular components. These subcellular proteomes provide insight into functions following various treatments and also contribute to the wider understanding of the entire organismal proteome by cataloguing a series of sub-proteome contents. The aim of this Research Topic is to bring together knowledge of sub cellular components in different plant species to provide a basis for accelerated research. It aims to provide a mini-review for each proposed section that summarizes the current understanding of a particular proteome, with the anticipation that every 5 - 10 years we can update these definitive publications.

Mass Spectrometry Application in Biology

ISBN: 9783906980898 9783906980904 Year: Pages: 252 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2015-10-22 06:39:08
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Mass spectrometry (MS) has become a vital tool for scientist in exploring how biological systems function and how therapeutic drug intervention (both small molecules and biologics) impact these systems. The application of mass spectrometry has advanced our knowledge in the biological sciences through the study of proteins and peptides in proteomics and as biomarkers, imaging via MALDI MS, and analysis of SNP’s in the genome to allow personalized medical treatment.The aim of this book is to provide a glimpse of some of the many applications of the advancing field of mass spectrometry and its application to complex biological problems. The topics presented here touch on many of the areas listed above will hopefully serve as a catalyst to generate new ideas for the continued innovative application of mass spectrometry to the fields of medicine, biology and beyond.

Current challenges in photosynthesis: From natural to artificial

Authors: --- --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192861 Year: Pages: 102 DOI: 10.3389/978-2-88919-286-1 Language: English
Publisher: Frontiers Media SA
Subject: Physiology --- Botany --- Science (General)
Added to DOAB on : 2015-12-10 11:59:07
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Jules Verne (1828-1905), author of Around the World in Eighty Days (1873) and Journey to the Center of the Earth (1864), wrote in 1875:"I believe that water will one day be used as a fuel, because the hydrogen and oxygen which constitute it, used separately or together, will furnish an inexhaustible source of heat and light. I therefore believe that, when coal (oil) deposits are oxidised, we will heat ourselves by means of water. Water is the fuel of the future". Solar energy is the only renewable energy source that has sufficient capacity for the global energy need; it is the only one that can address the issues of energy crisis and global climate change. A vast amount of solar energy is harvested and stored via photosynthesis in plants, algae, and cyanobacteria since over 3 billion years. Today, it is estimated that photosynthesis produces more than 100 billion tons of dry biomass annually, which would be equivalent to a hundred times the weight of the total human population on our planet at the present time, and equal to a global energy storage rate of about 100 TW. The solar power is the most abundant source of renewable energy, and oxygenic photosynthesis uses this energy to power the planet using the amazing reaction of water splitting. During water splitting, driven ultimately by sunlight, oxygen is released into the atmosphere, and this, along with food production by photosynthesis, supports life on our earth. The other product of water oxidation is “hydrogen” (proton and electron). This ‘hydrogen’ is not normally released into the atmosphere as hydrogen gas but combined with carbon dioxide to make high energy containing organic molecules. When we burn fuels we combine these organic molecules with oxygen. The design of new solar energy systems must adhere to the same principle as that of natural photosynthesis. For us to manipulate it to our benefit, it is imperative that we completely understand the basic processes of natural photosynthesis, and chemical conversion, such as light harvesting, excitation energy transfer, electron transfer, ion transport, and carbon fixation. Equally important, we must exploit application of this knowledge to the development of fully synthetic and/or hybrid devices. Understanding of photosynthetic reactions is not only a satisfying intellectual pursuit, but it is important for improving agricultural yields and for developing new solar technologies. Today, we have considerable knowledge of the working of photosynthesis and its photosystems, including the water oxidation reaction. Recent advances towards the understanding of the structure and the mechanism of the natural photosynthetic systems are being made at the molecular level. To mimic natural photosynthesis, inorganic chemists, organic chemists, electrochemists, material scientists, biochemists, biophysicists, and plant biologists must work together and only then significant progress in harnessing energy via “artificial photosynthesis” will be possible. This Research Topic provides recent advances of our understanding of photosynthesis, gives to our readers recent information on photosynthesis research, and summarizes the characteristics of the natural system from the standpoint of what we could learn from it to produce an efficient artificial system, i.e., from the natural to the artificial. This topic is intended to include exciting breakthroughs, possible limitations, and open questions in the frontiers in photosynthesis research.

International Plant Proteomics Organization (INPPO) World Congress 2014

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450602 Year: Pages: 407 DOI: 10.3389/978-2-88945-060-2 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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The field of proteomics has advanced considerably over the past two decades. The ability to delve deeper into an organism’s proteome, identify an array of post-translational modifications and profile differentially abundant proteins has greatly expanded the utilization of proteomics. Improvements to instrumentation in conjunction with the development of these reproducible workflows have driven the adoption and application of this technology by a wider research community. However, the full potential of proteomics is far from being fully exploited in plant biology and its translational application needs to be further developed. In 2011, a group of plant proteomic researchers established the International Plant Proteomics Organization (INPPO) to advance the utilization of this technology in plants as well as to create a way for plant proteomics researchers to interact, collaborate and exchange ideas. The INPPO conducted its inaugural world congress in mid 2014 at the University of Hamburg (Germany). Plant proteomic researchers from around the world were in attendance and the event marked the maturation of this research community. The Research Topic captures the opinions, ideas and research discussed at the congress and encapsulates the approaches that were being applied in plant proteomics.The field of proteomics has advanced considerably over the past two decades. The ability to delve deeper into an organism’s proteome, identify an array of post-translational modifications and profile differentially abundant proteins has greatly expanded the utilization of proteomics. Improvements to instrumentation in conjunction with the development of these reproducible workflows have driven the adoption and application of this technology by a wider research community. However, the full potential of proteomics is far from being fully exploited in plant biology and its translational application needs to be further developed. In 2011, a group of plant proteomic researchers established the International Plant Proteomics Organization (INPPO) to advance the utilization of this technology in plants as well as to create a way for plant proteomics researchers to interact, collaborate and exchange ideas. The INPPO conducted its inaugural world congress in mid 2014 at the University of Hamburg (Germany). Plant proteomic researchers from around the world were in attendance and the event marked the maturation of this research community. The Research Topic captures the opinions, ideas and research discussed at the congress and encapsulates the approaches that were being applied in plant proteomics.

Linking Optical and Chemical Properties of Dissolved Organic Matter in Natural Waters

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450817 Year: Pages: 242 DOI: 10.3389/978-2-88945-081-7 Language: English
Publisher: Frontiers Media SA
Subject: Chemistry (General) --- Geography --- Oceanography --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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A substantial increase in the number of studies using the optical properties (absorbance and fluorescence) of dissolved organic matter (DOM) as a proxy for its chemical properties in estuaries and the coastal and open ocean has occurred during the last decade. We are making progress on finding the actual chemical compounds or phenomena responsible for DOM’s optical properties. Ultrahigh resolution mass spectrometry, in particular, has made important progress in making the key connections between optics and chemistry. But serious questions remain and the last major special issue on DOM optics and chemistry occurred nearly 10 years ago. Controversies remain from the non-specific optical properties of DOM that are not linked to discrete sources, and sometimes provide conflicting information. The use of optics, which is relatively easier to employ in synoptic and high resolution sampling to determine chemistry, is a critical connection to make and can lead to major advances in our understanding of organic matter cycling in all aquatic ecosystems. The contentions and controversies raised by our poor understanding of the linkages between optics and chemistry of DOM are bottlenecks that need to be addressed and overcome.

Proteomics of Microbial Human Pathogens

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450886 Year: Pages: 152 DOI: 10.3389/978-2-88945-088-6 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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According to the World Health Organization (WHO), in 2012 infectious diseases and related conditions account for more than 70% of premature deaths across 22 African countries and estimated 450 000 people worldwide developed multi-drug resistant tuberculosis. This alarming situation, of great public health concern, calls for the urgent development of novel and efficient responding strategies. The employment of important research platforms, such as genomics and proteomics, has contributed significant insight into the mechanisms underlying microbial infection and microbe-host interaction. In this Frontiers Research Topic, we aim to produce a timely and pertinent discussion regarding the current status of “Proteomics of microbial Human pathogens” and the role of proteomics in combating the challenges posed by microbial infection and indeed acquired anti-microbial resistance. As the field of proteomics progressed from 2-DE gel based approaches to modern LC-MS/MS based workflows, remarkable advances have been reported in terms of data quantity and quality. Given the immediate and enormous advantages that high resolution and accurate mass spectrometers have brought to the field, proteomics has now evolved into a robust platform capable of generating large amounts of comprehensive data comparable to that reported previously in genomics studies. For example, detection of the complete yeast proteome has been reported and other small proteomes, such as those of bacteria, are within reach. Mass spectrometry-based proteomics has become an essential tool for biologists and biochemists, and is now considered by many as an essential component of modern structural biology. Additionally, the introduction of high-resolution mass spectrometers has driven the development of various different strategies aimed at accurate quantification of absolute and relative amount of protein(s) of interest. Emerging targeted mass spectrometry methodologies such as; Selected Reaction Monitoring (SRM), Parallel Reaction Monitoring (PRM) and SWATH, are perhaps the latest breakthrough within the proteomics community. Indeed, through a label free approach, targeted mass spectrometry offers an unequalled capability to characterize and quantify a specific set of proteins reproducibility, in any biological sample. Usefully, Aebersold and colleagues have recently generated and validated a number of assays to quantify 97% of the 4,012 annotated Mycobacterium tuberculosis (Mtb) proteins by SRM. As such, the Mtb Proteome library represents a valuable experimental resource that will undoubtedly bring new insight to the complex life cycle of Mtb. Finally, as reviewed recently in Frontiers Research Topic, mass spectrometry-based proteomics has had a tremendous impact on our current understanding of post translational modification (PTM) in bacteria including the key role of PTMs during interaction of pathogenic bacteria and host interactions. We believe that our understanding of microbial Human pathogens has benefited enormously from both 2-DE gel and modern LC-MS/MS based proteomics. It is our wish to produce an integrated discussion surrounding this topic to highlight the existing synergy between these research fields. We envisage this Research Topic as a window to expert opinions and perspectives on the realistic practicalities of proteomics as an important tool to address healthcare problems caused by microbial pathogens.

Glycan Diversity in Fungi, Bacteria and Sea Organisms

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199426 Year: Pages: 85 DOI: 10.3389/978-2-88919-942-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Internal medicine
Added to DOAB on : 2016-01-19 14:05:46
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The cell surface of fungi, bacteria and sea organisms is highly glycosylated. These glycans are oligo- or polysaccharide molecules that can be secreted or attached to protein or lipids forming glycoconjugates. They present extraordinary structural diversity that could explain their involvement in many fundamental cellular processes, including growth, differentiation and morphogenesis. Considerable advances have been made on the structural elucidation of these glycans. Their primary structures were determined based on a combination of mass spectrometry and NMR spectroscopy techniques. The combination of these sensitive and powerful techniques has allowed us to increase our structural knowledge of a wide variety of glycans expressed by different fungi, bacteria and sea organisms.

Forty Years of Heel Prick Screening in the Netherlands

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ISBN: 9783038421894 9783038421900 Year: Pages: 114 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2016-06-01 16:35:30
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This book aims to provide an overview of developments in the heel prick screening programme in the Netherlands in which similarities with the situation elsewhere in the world, where relevant, will be mentioned. In the Netherlands, the preparations for the national screening programme started in 1964. The formal launch of the programme was on September 1, 1974. In 2014, therefore this programme had existed 40 years. The book is structured as follows. Chapter 1 describes how the programme began with one disease and over the years has continued to expand to currently covering 19 disorders. Chapter 2 focuses on the organisation of the screening programme and the agencies that have been involved over the years. Chapter 3 is intended to provide a global view of the programme in its current form. Chapter 4 describes how neonatal screening programmes elsewhere in the world developed and outline their main differences with the Dutch programme. Finally, Chapter 5 contains the summary and conclusions. This chosen structure leads to some aspects being mentioned more than once. The book is intended for a broad audience that is interested in policy making on heel prick screening; hence, scientific depth is limited. Where possible and useful, references to the scientific literature have been included but completeness has not been pursued. The main sources were the archives of the National Steering Committees for Phenylketonuria and Congenital Hypothyroidism (LBCs), supplemented with interviews with the persons listed in Annex 1 and, if available, their personal archives. This is a translation of the book “Veertig Jaar Hielprikscreening in Nederland”, that was published by Prelum Publishers, Houten, the Netherlands with ISBN 978-90-8562-133-1 © 2014 Prelum, Houten; RIVM, Bilthoven; Vumc, Amsterdam.

Mineralogy of Quartz and Silica Minerals

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ISBN: 9783038973485 9783038973492 Year: Pages: 274 DOI: 10.3390/books978-3-03897-349-2 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Chemistry (General) --- Geology --- Earth Sciences --- Environmental Sciences
Added to DOAB on : 2018-11-20 11:34:22
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The present book reports recent contributions from research in the field of quartz and other silica minerals. The various forms of silica (SiO2) represent important constituents of the Earth crust and play a central role in the composition of geological materials. In particular, quartz is widely used as a raw material in numerous industrial sectors. The knowledge of the formation and specific properties of SiO2 rocks and minerals is indispensable for the understanding and reconstruction of geological processes, as well as for specific technical applications.The works presented in this book are contributed by leading scientists and deal with aspects of the formation and processing of SiO2 raw materials, the analysis of high-purity quartz, and the specifics and varieties (e.g., quartz, amethyst, opal, agate) of SiO2 modifications. The presentations cover the main interrelations between theoretical, analytical, and industrial studies and provide information concerning recent developments in the research on SiO2 materials.

Antioxidants and Second Messengers of Free Radicals

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ISBN: 9783038975335 / 9783038975342 Year: Pages: 194 DOI: 10.3390/books978-3-03897-534-2 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology --- Medicine (General) --- Chemistry (General)
Added to DOAB on : 2019-01-17 09:35:49
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The history of science can teach modern men that our understanding of life is to a great extent based on the accuracy of the analytical methods that we use and, on our readiness to oppose dogmatic opinions, which are based on outdated methods and black/white approaches to the major questions raised by mankind in the past. The recent decades have brought a lot of new insights into the fundamentals of the active principles of reactive oxygen species that are necessary for living cells, but which also cause dangerous pathophysiological processes. Accordingly, although they were previously considered to be the most undesired toxic compounds generated as the final products of the oxidative degradation of lipids, reactive aldehydes are now considered to play important roles both in health and in major diseases. Represented mostly by 4-hydroxynonenal (HNE), a substance discovered only fifty years ago, reactive aldehydes are the focus of research not only because of their toxicity but also because of their positive effects regulating the most important metabolic processes such as growth of living cells or the death of cells. Better understanding the interactions between reactive aldehydes and natural or synthetic antioxidant substances might eventually help us to better monitor, prevent and control modern diseases, thus building pillars for the development of the modern, multidisciplinary life sciences and integrative medicine of the 21st century.

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