The authors of the research presented in this special collection used the first description of the B73 maize genome to probe some of the most intriguing questions in genetics and plant biology. Read about maize centromeres, new insights into transposon types and distribution, the abundance of very short FLcDNAs encoding predicted peptides, and many other "genetic jewels" contained herein.
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This collection focuses on a rapidly evolving field in which the study of both species-specific and ubiquitous aging mechanisms informs the biological process of aging. Yet the field is not without substantial controversy, differing views arise as we come to understand aging across model systems - from bacteria to humans.
Saba Bank is the largest submarine atoll in the Atlantic Ocean, adjacent to the nearby island of Saba, in the Netherlands Antilles. The submerged platform is ~2200 sq km, with a 50 km fringing reef crest. Large vessels traveling to and from an oil terminal on nearby St. Eustatius Island routinely anchor on Saba Bank, damaging benthic habitats. Marine biodiversity research was necessary to help inform any national and international protective measures. This collection of articles represents an international collaboration to characterize the richness, diversity, and habitat affinities of marine taxa on Saba Bank. Multibeam bathymetry, satellite imagery, scuba transects, roving surveys, remotely operated vehicles, and fish traps were used to study the biotic assemblages. This poorly studied region was found to have unusually high biodiversity, including several undescribed species.
This collection presents some of the recent advances in biogeography and taxonomy within deep-sea chemosynthetic environments: patterns, processes, and synthesis resulting from the Census of Marine Life ChEss Program (2002-2010). Over 110 ChEss researchers have studied various elements of the biogeography of species from deep-water hydrothermal vents, cold seeps, and whale falls, to oxygen minimum zones. Through their concerted efforts our knowledge of these extraordinary habitats and their faunal composition has been greatly expanded. An overall synthesis paper by the ChEss Office summarises the program and the collection contributions.
Clinical immunology is the study of diseases caused by disorders of the immune system (failure, aberrant action, and malignant growth of the cellular elements of the system), and also involves diseases where immune reactions play a part in their pathology and clinical features. The Collection has been organized into broad categories in response to the commonly articulated request from our users that we provide more structured and efficient access to papers of interest in the PLOS corpus. The Clinical Immunology Collection includes sections on Allergies & Anaphylaxis, Tumor Immunology, Immunodeficiency and Autoimmune Diseases. More sections will follow.
This collection of papers highlights research performed under the auspices of the Natural Geography in Shore Areas(NaGISA) project, a component of the Census of Marine Life program. NaGISA is a collaborative effort aimed at inventorying and monitoring biodiversity in rocky bottom macroalgal and soft bottom seagrass communities from the high intertidal zone to 20 meters in depth at a global scale. The papers of this collection describe large-scale distribution patterns of assemblages associated with rocky shores around the globe, as well as specific patterns for taxa such as macroalgae, polychaetes, and echinoderms.
The ecological impacts of climate change are broad and diverse, altering species' range limits, plant phenology and growth, carbon and nutrient cycling, as well as biodiversity and extinction risk. Recent PLOS articles have used a variety of experimental and observational approaches to examine these impacts. The broad range of papers within this Collection emphasize not only the multi-faceted impacts of climate change on ecological and human systems, but also the breadth and depth of research on these subjects being reported in PLOS journals.
With exciting new research opportunities comes the much needed consideration of ethical challenges. This Focus Feature, led by Philip E. Bourne, addresses the ethical challenges that accompany the use of big data in biology and medicine. PLOS Computational Biology "Focus Features" are a resource to encourage community engagement and discussion on a focussed topic. A Focus Feature is directed by the editors with a view to shape the debate on a topic of interest to the computational biology community. By consisting of a small number of articles, each Focus Feature may draw on the new and old research in order to further the conversation.
The Genome Network Project/FANTOM3 collection features articles describing findings that redefine the landscape of the mammalian transcriptome by introducing an extensive collection of novel cDNAs and millions of sequenced tags corresponding to 5'- and 3'-ends of mRNAs. The high-resolution cDNA collection and its analysis represent an important world resource for discovery, and demonstrate the value of large-scale transcriptome approaches toward understanding genome function.
The History of Marine Animal Populations (HMAP) is a global research initiative to study the past ocean life and human interaction with the sea, and is part of the global Census of Marine Life. About 100 researchers have developed an interdisciplinary research program using historical and environmental archives to analyze marine population data before and after human impacts on the ocean became significant. The overall goal is to enhance knowledge and understanding of how the diversity, distribution and abundance of marine life in the world's oceans has changed over the long term. The HMAP Collection draws together representative examples of the results of this initiative.
Immunobiology is the study of the components that make up the body's immune system, how these arise during embryogenesis and function together, and how they evolve in different organisms in response to pathogens and the environment encountered. This collection collates some of the best and most recent immunobiology articles published at PLOS, featuring papers that examine cellular and molecular immunology, evolutionary immunology, animal models of the human immune system and ontogeny of the immune system. The biology featured in this collection serves to complement the studies in the Clinical Immunology Collection that highlight immune-related challenges faced by individuals and the health care profession.
In this collection of newly published research articles, Ruth Nussinov (Editor-in-Chief) and Amarda Shehu (George Mason University, USA) highlight some of the latest advancements in computational treatments of macromolecules focusing upon recent computational methods investigating various aspects of the relationship between macromolecular structure, dynamics, and function. Through this the editors hope to convey and celebrate the tremendous progress that computational structural biology has made over the last two decades.
This collection presents research in the field of Marine Barcoding under the auspices of MarBOL: a joint effort of the Consortium for the Barcode of Life and the Census of Marine Life to enhance our capacity to identify marine life by utilizing DNA barcoding. DNA barcoding uses a short DNA sequence from a standardized and agreed-upon position in the genome as a molecular diagnostic for species-level identification. The MarBOL collection highlights the variety of applications of DNA barcodes. Primarily they are very useful tools to accelerate species-level analysis of biodiversity and to facilitate conservation efforts. Barcodes have been used for identification of prey in gut contents, detection of invasive species, forensics, reveal cryptic species, and discover new species. Recent advances in sequencing technology allow the use of barcodes for rapid and increasingly automated biodiversity assessment.
The Census of Marine Life on Seamounts (CenSeam) was a 5 year research program carried out under the umbrella of the Census of Marine Life. Its principal goal was to create an international network of scientists to address key research questions about seamounts. This collection brings together the latest seamount research, enabling a wide variety of scientific results to be linked.
The Marine Megafauna Collection presents research focused on the biology, ecology and conservation of the most captivating creatures in the ocean. These articles represent a broad survey of fascinating organisms and systems, and provide a core set of reading materials for marine science educators seeking to increase the engagement of students in class using compelling examples.
The ability to live for long periods in the absence of normal gravity requires comprehensive understanding of structural and functional changes that occur in the bodies of humans and other mammals. The Italian Space Agency contracted a spaceflight payload (Mice Drawer System) for mice research on the International Space Station, including wild type and transgenic strains. These studies examined changes that occurred in the flight animals in a wide range of physiological systems, such as muscle, bone, organs and glands, blood, brain (and behavior), and neurosensory, and collectively offer an integrative view of the mammal's physiological response to ?G.
Neuroscience is the scientific study of the nervous system and is an interdisciplinary biological science that extends across multiple fields including chemistry, computer science, engineering, linguistics, mathematics, medicine, philosophy, physics, and psychology. Neuroscience involves various approaches to the study of the molecular, cellular, computational, systems, and cognitive aspects of the nervous system, using techniques from molecular and cellular studies of individual nerve cells to neuroimaging of complex human behaviors.
The J. Craig Venter Institute's Global Ocean Sampling Expedition revealed an enormous amount of previously unexplored diversity in the world's oceans. In addition to the research articles, this collection includes commentary and analysis highlighting the achievements and challenges of this work.
The Open Source movement revolutionized the way computer systems were developed and how companies made their businesses. Its philosophy requires that all source code should be freely shared, so that as many people as possible can use, change, learn, and improve upon it. In recent years the increasing availability and low costs of electronic components, processors and 3D printers meant that an open model of development has taken root also in the world of hardware, including the development of scientific lab equipment. The implications for research can hardly be overstated: Open Labware designs are almost always cheaper than closed source ones, allow for distributed development and, critically, customization by the end user, the lab scientist. PLOS welcomes submissions in this field.
This collection represents those articles published in PLOS ONE on the general topic of Paleontology (the study of fossils and of life forms that existed in past geological periods). The discipline is very broad, overlapping with both biology and geology, and the findings reported in these articles span several geological eras and further our understanding of organisms from multiple phyla. We welcome submissions in this field.
The Prokaryotic Genome Collection aims to present and highlight a number of important articles that describe whole genome sequence and/or comparative genomics of important prokaryotic organisms. We believe that this collection will be able to facilitate understanding of the biology and lifestyle of the underlying organisms not only through the content of the Research Articles, but also from the external information sources which are linked to from the original articles. Editorial oversight and coordination of the peer-review for most of the articles was provided by Niyaz Ahmed,PLOS ONE Section Editor for Genomics and Microbiology.
As the world's population continues to expand, and as water resources come under increasing pressure and pathogens that cause devastating crop losses continue to spread, there is a pressing need for plant research to contribute solutions to improving food security in a sustainable and safe way. Plant translational research has a vital role to play in meeting these challenges, and given the importance of research in this field, PLOS believes that such work should be published in open access journals, ensuring that it reaches the widest possible audience without any barriers to access. The technical advances highlighted in this collection exemplify how basic research discoveries are being translated into methods to develop and improve, both agriculturally and environmentally, important crop traits. Produced with the support of The Bill & Melinda Gates Foundation.
Over the past few decades, numerous initiatives have sought to engage members of the public in decisions concerning life sciences research and biotechnologies as early as possible in their development based on the belief that such participation advances the public interest. The motivations for seeking public input vary considerably, however, with consequences for what public engagement initiatives can achieve and who benefits. This series aims to investigate, through specific case studies, whether, and under what conditions, it is possible to engage the public in scientific issues in meaningful ways in decision-making about the innovation pathways of biosciences.
Sauropod dinosaurs were the largest terrestrial animals to roam the Earth, exceeding all other land-dwelling vertebrates in both mean and maximal body size. While convergently evolving many features seen in large terrestrial mammals, such as upright, columnar limbs and barrel-shaped trunks, sauropods evolved some unique features, such as the extremely long neck and diminutive head they are famous for. The unique gigantism of sauropod dinosaurs has long been recognized as an important issue in the evolution of vertebrates, raising questions as to why no other land-based lineage has ever reached this size, how these dinosaurs functioned as living animals and how they were able to maintain stable populations over distinct geological time periods. This collection discusses major efforts by evolutionary biologists and paleontologists to understand their evolutionary success and uniquely gigantic body size.
This collection of articles represents some of the research highlights from the Structural Genomics Consortium (SGC). The SGC is an international public-private partnership that determines three dimensional structures of medically important proteins from both human and human parasites and places this information into the public domain, free from restrictions on use. The articles describe the structure and further characterisation of the proteins in an easily accessible way. All articles in this collection can be read on-line as interactive documents, where relevant features described in the text can be visualised as 3D molecular scenes.
Synthetic Biology is an emerging, trans-disciplinary field at the intersection between many engineering and scientific disciplines such as biology, chemical engineering, chemistry, electrical engineering, or computer science. The Collection has been organized into broad categories focused on DNA synthesis and assembly techniques, the development of libraries for biological parts, the use of synthetic biology in protein engineering applications, work focussing on synthetic life and multicellular systems, gene editing, and the engineering of gene regulatory networks and metabolic pathways. Finally, we include sections that describe enabling technologies such as software and modeling, along with new methods and instrumentation.
This collection has been created by the editors of the World Register of Marine Species (WoRMS), an open-access online database which holds information on all marine species, and some of their freshwater and terrestrial relatives. The WoRMS database contains species names, synonyms, sources and a range of other information, as described in the overview. The collection complements the database by synthesising current knowledge and understanding about a variety of taxa. Papers can cover any taxonomic level, from a genus to phylum, and any number of species. The scope of individual papers may vary because of the peculiarities of the taxon, available information, and interests of the authors. However, they generally contain information on the history, anatomy and diagnostic features, ecology, biogeography, physiology, and economic importance.