Toward a Global Public Repository of Community Protocols to Encourage Best Practices in Biomolecular Ocean Observing and Research

Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. It is an especially effective approach for investigating the marine microbiome. To mature marine microbiome research and operations within a global ocean biomolecular observing network (OBON) for the UN Decade of Ocean Science for Sustainable Development and beyond, research groups will need a system to effectively share, discover, and compare “omic” practices and protocols. While numerous informatic tools and standards exist, there is currently no global, publicly-supported platform specifically designed for sharing marine omics [or any omics] protocols across the entire value-chain from initiating a study to the publication and use of its results. Toward that goal, we propose the development of the Minimum Information for an Omic Protocol (MIOP), a community-developed guide of curated, standardized metadata tags and categories that will orient protocols in the value-chain for the facilitated, structured, and user-driven discovery of suitable protocol suites on the Ocean Best Practices System. Users can annotate their protocols with these tags, or use them as search criteria to find appropriate protocols. Implementing such a curated repository is an essential step toward establishing best practices. Sharing protocols and encouraging comparisons through this repository will be the first steps toward designing a decision tree to guide users to community endorsed best practices.

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Dake Chen: unraveling the secrets of ocean–climate interaction

National Science Review ◽

10.1093/nsr/nww100 ◽

2017 ◽

Vol 4 (1) ◽

pp. 136-139 ◽

Cited By ~ 1

Author(s):

Ling Wang

Keyword(s):

Ocean Dynamics ◽

Global Ocean ◽

Practical Applications ◽

Ocean Climate ◽

Ocean Science ◽

National Strategic Plan ◽

Ocean Atmosphere Interaction ◽

Atmosphere Interaction ◽

Academy Of Sciences ◽

Ocean Observing

Abstract The ocean is a complex and mysterious system that attracts scientists around the world to unravel its secrets. Dake Chen, a distinguished physical oceanographer and an academician of the Chinese Academy of Sciences, is one of them. Since the mid-1980s, he has been studying ocean dynamics and ocean–atmosphere interaction, and has made seminal contributions to the understanding and prediction of short-term climate variability, especially the El Niño phenomenon. In a recent interview with NSR, Professor Dake Chen says that China has made significant progress in recent years in ocean research, but, in order to make breakthroughs in the field of oceanography, China needs to further expand the scope of research programs from coastal seas to open oceans, to greatly increase the investment in global ocean-observing systems and to pay more attention to fundamental scientific problems in addition to practical applications. He also calls for a better-defined national strategic plan for ocean science and technology.

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Searching for new therapy options – the microbiome in the spotlight of stroke research

The Biochemist ◽

10.1042/bio03902018 ◽

2017 ◽

Vol 39 (2) ◽

pp. 18-21

Author(s):

Andreas Meisel ◽

Katarzyna Winek

Keyword(s):

Neurological Disorders ◽

Proper Function ◽

Disease States ◽

Stroke Research ◽

Trace Back ◽

Microbiome Research ◽

The Central Nervous System ◽

Basic Ideas ◽

And Function ◽

Insight Into

Commensal microorganisms are indispensable for the proper function of the central nervous system, and alterations in the composition and function of the microbiome are linked to different disease states. In this feature, we provide insight into microbiome research from a neuroscientific perspective and trace back basic ideas concerning the contribution of the microbiome to the pathophysiological processes in stroke – one of the most important neurological disorders.

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Maximizing Benefits From Punctual Ocean Infrastructure: An Ethical Perspective

Frontiers in Marine Science ◽

10.3389/fmars.2021.733822 ◽

2021 ◽

Vol 8 ◽

Author(s):

Frederick Whoriskey ◽

Michele Barbier ◽

Mackenzie Mazur ◽

Tobias Hahn ◽

Jacob Kritzer ◽

...

Keyword(s):

Best Practices ◽

Ethical Dilemma ◽

Research Community ◽

Ethical Perspective ◽

Original Intent ◽

Transient Nature ◽

Ocean Science ◽

Ocean Observing ◽

Ocean Observing Systems ◽

Observing Systems

Ethics are becoming a component of best practices in ocean science and observing systems, with the research community facing a duty to society to maximize the efficient use and benefits that stem from investments in ocean science/monitoring. Sustained ocean observing systems on issues of global importance are coordinated, internationally sanctioned and making the most out of the resources accorded to them and consequently fulfilling their duty to society. However, globally huge investments are made annually in establishing infrastructure for shorter-term, punctual studies that address targeted as opposed to broad science needs. More could be done to maximize the benefits and impacts of these punctual efforts. Given punctual infrastructure’s small and frequently transient nature, connections to enable sharing will probably be done locally, and both potential additional users and owners of the infrastructure will need to be energetic, receptive and flexible. The accommodation of new uses will have to be balanced against any costs of these additional activities, which could pose an ethical dilemma in themselves if they compromise the infrastructure’s ability to meet its original intent. However, such adaptive infrastructures may be the most efficient way to provide the resources needed to identify and monitor emerging or new ocean stressors.

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Bio-GO-SHIP: The Time Is Right to Establish Global Repeat Sections of Ocean Biology

Frontiers in Marine Science ◽

10.3389/fmars.2021.767443 ◽

2022 ◽

Vol 8 ◽

Author(s):

Sophie Clayton ◽

Harriet Alexander ◽

Jason R. Graff ◽

Nicole J. Poulton ◽

Luke R. Thompson ◽

...

Keyword(s):

Optical Sensors ◽

Large Scale ◽

New Technologies ◽

Chemical Properties ◽

Trophic Levels ◽

Global Ocean ◽

Technological Advances ◽

And Function ◽

Physical And Chemical ◽

Ocean Observing

In this article, we present Bio-GO-SHIP, a new ocean observing program that will incorporate sustained and consistent global biological ocean observations into the Global Ocean Ship-based Hydrographic Investigations Program (GO-SHIP). The goal of Bio-GO-SHIP is to produce systematic and consistent biological observations during global ocean repeat hydrographic surveys, with a particular focus on the planktonic ecosystem. Ocean plankton are an essential component of the earth climate system, form the base of the oceanic food web and thereby play an important role in influencing food security and contributing to the Blue Economy. Despite its importance, ocean biology is largely under-sampled in time and space compared to physical and chemical properties. This lack of information hampers our ability to understand the role of plankton in regulating biogeochemical processes and fueling higher trophic levels, now and in future ocean conditions. Traditionally, many of the methods used to quantify biological and ecosystem essential ocean variables (EOVs), measures that provide valuable information on the ecosystem, have been expensive and labor- and time-intensive, limiting their large-scale deployment. In the last two decades, new technologies have been developed and matured, making it possible to greatly expand our biological ocean observing capacity. These technologies, including cell imaging, bio-optical sensors and 'omic tools, can be combined to provide overlapping measurements of key biological and ecosystem EOVs. New developments in data management and open sharing can facilitate meaningful synthesis and integration with concurrent physical and chemical data. Here we outline how Bio-GO-SHIP leverages these technological advances to greatly expand our knowledge and understanding of the constituents and function of the global ocean plankton ecosystem.

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Technological Trends and Significance of the Essential Ocean Variables by the Indian Moored Observatories: Relevance to UN Decade of Ocean Sciences

Marine Technology Society Journal ◽

10.4031/mtsj.55.3.8 ◽

2021 ◽

Vol 55 (3) ◽

pp. 34-49

Author(s):

Ramasamy Venkatesan ◽

Manickavasagam Arul Muthiah ◽

Narayanaswamy Vedachalam ◽

Gopal Vengatesan ◽

Krishnamoorthy Ramesh ◽

...

Keyword(s):

Sustainable Development ◽

Large Scale ◽

The United States ◽

Global Scale ◽

Global Ocean ◽

Comprehensive Overview ◽

Essential Information ◽

Ocean Science ◽

Observation Network ◽

Ocean Observing

Abstract The ocean plays a key role in regulating the climate as well as supporting diverse ecosystems. Technology is the key for the sustained and precise in-situ spatio-temporal measurements of the physical, biological, biogeochemical, and near-atmospheric meteorological parameters essential for carrying out effective assessments of the status, variability, and change in the ocean ecosystems and for creating policies at the right time. The United Nations Decade of Ocean Science for Sustainable Development 2021‐2030 provides a timeframe to build a comprehensive, sustainable, and data-based informed decision-making global ocean observing system. This demands global-scale investigations, trans-disciplinary science, and mechanisms to integrate and distribute data that otherwise would appear to be disparate. The essential ocean variables (EOVs) conceptualized by the Global Ocean Observing System (GOOS) of UNESCO's Intergovernmental Oceanographic Commission guide observation of the ocean. In order to achieve the goal of UN Decade envisaged and to have an Earth System approach under the World Meteorological Organization reforms, it is imperative to address globally and nationally relevant indicators and assessments, which require increased sharing of data and analytical methods, sustained long-term and large-scale observations, and resources dedicated to these tasks. Technology for observing the ocean is important, which is not addressed in detail in the recent past. In this paper we provide a comprehensive overview of Sensor versus Essential Ocean Variable from our experience in sustained 25 years of moored ocean observation network and collaborating with institutions and experts in the United States and GOOS. An attempt has been made to furnish an overview for any group or nation to start or sustain an observation network using EOVs with guiding principles of Findable, Accessible, Interoperable, Reusable data that is targeted to deliver essential information needed for sustainable development and protecting ocean health.

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Coastal Ocean Observing and Modeling Systems in Brazil: Initiatives and Future Perspectives

Frontiers in Marine Science ◽

10.3389/fmars.2021.681619 ◽

2021 ◽

Vol 8 ◽

Author(s):

Guilherme Franz ◽

Carlos A. E. Garcia ◽

Janini Pereira ◽

Luiz Paulo de Freitas Assad ◽

Marcelo Rollnic ◽

...

Keyword(s):

National Level ◽

Coastal Ocean ◽

Global Ocean ◽

Marine Biodiversity ◽

Amazon Forest ◽

Integrated Network ◽

Ocean Science ◽

Modeling Systems ◽

Spatial Coverage ◽

Ocean Observing

Coastal ocean observing and modeling systems (coastal observatories), connected with regional and global ocean systems, improve the quality of information and forecasts for effective management of safe and sustainable maritime activities. The public availability of systematic and long-term information of the ocean is an engine for the Blue Economy, boosting economic growth, employment, and innovation. An overview of some Brazilian initiatives is presented in this paper, involving universities, private companies, federal and state agencies, covering institutions from south to north of Brazil. Although these initiatives focus mainly on ocean physics, integrated efforts can extend the scope to include biogeochemistry and marine biodiversity, helping to address interdisciplinary problems. Existing initiatives can be connected, and new ones fostered, to fill in the gaps of temporal and spatial coverage of ocean monitoring in the vast oceanic area under Brazilian jurisdiction (nationally referred to as the Blue Amazon, in reference to the similar richness of the Amazon Forest). The alignment among national and regional initiatives, as well as with international programs, can be promoted if coordinated by a national-level organization, maximizing the return of public investment and socioeconomic benefits. In light of international examples, possible future institutional arrangements are discussed, leveraging from existing national public policies and international cooperation that Brazil is taking part. The United Nations Decade of Ocean Science for Sustainable Development is a timely opportunity to encourage an institutional arrangement to support and articulate an integrated network of coastal observatories in Brazil.

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Boundary Ocean Observation Network for the Global South

Marine Technology Society Journal ◽

10.4031/mtsj.55.3.30 ◽

2021 ◽

Vol 55 (3) ◽

pp. 80-81

Author(s):

Christopher E Ordoñez ◽

John A. Barth ◽

Moninya Roughan

Keyword(s):

Prediction Models ◽

Global Environmental Change ◽

Global South ◽

Global Ocean ◽

Data Sets ◽

Ocean Climate ◽

Ocean Science ◽

Observation Network ◽

Ocean Observing

Abstract The UN Decade of Ocean Science for Sustainable Development should establish a Boundary Ocean Observing Network (BOON) for the Global South (GS). The BOON is part of the OceanGlider Program, which is part of the Global Ocean Observing System (GOOS). The BOON is a network of established timeseries transects collecting long-term data sets. Timeseries are critical for making immediate operational decisions and for identifying long-term trends of anthropogenic global environmental change. The network has proven important enough to continue observations and expand them. Due to resource and expertise limitations, expanded locations are in similar locations. The UN should build on this success and establish a BOON for the Global South. The same benefits will be garnered by countries and regions that have been missing out. Increased observation coverage will benefit humanity, improving understanding of the Ocean-Climate System, e.g. leading to improved climate prediction models. The UN will facilitate activities to realize a BOON for the Global South including: coordinating local scientists, partnering scientific and technical experts with local scientists, identifying new affordable and easy-to-operate technologies, channeling funds for initial and ongoing costs, and building a framework to continue the BOON-GS long after the Ocean Science Decade.

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Structure and function of neural networks in the retina

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102213 ◽

1988 ◽

Vol 46 ◽

pp. 26-27

Author(s):

Peter Sterling

Keyword(s):

Ganglion Cells ◽

Three Dimensional ◽

Structure And Function ◽

Synaptic Connections ◽

Visual Axis ◽

One Dimensional ◽

Cat Retina ◽

Ultrathin Sections ◽

And Function ◽

Insight Into

The synaptic connections in cat retina that link photoreceptors to ganglion cells have been analyzed quantitatively. Our approach has been to prepare serial, ultrathin sections and photograph en montage at low magnification (˜2000X) in the electron microscope. Six series, 100-300 sections long, have been prepared over the last decade. They derive from different cats but always from the same region of retina, about one degree from the center of the visual axis. The material has been analyzed by reconstructing adjacent neurons in each array and then identifying systematically the synaptic connections between arrays. Most reconstructions were done manually by tracing the outlines of processes in successive sections onto acetate sheets aligned on a cartoonist's jig. The tracings were then digitized, stacked by computer, and printed with the hidden lines removed. The results have provided rather than the usual one-dimensional account of pathways, a three-dimensional account of circuits. From this has emerged insight into the functional architecture.

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The Developing Relationship Among Cognition, Amplification, and Aural Rehabilitation

Perspectives of the ASHA Special Interest Groups ◽

10.1044/persp1.sig6.46 ◽

2016 ◽

Vol 1 (6) ◽

pp. 47-54 ◽

Cited By ~ 1

Author(s):

Jeffrey J. DiGiovanni ◽

Travis L. Riffle

Keyword(s):

Working Memory ◽

Best Practices ◽

Cognitive Abilities ◽

Hearing Aid ◽

Hearing Aid Fitting ◽

Aural Rehabilitation ◽

Basic Concepts ◽

And Function

The search for best practices in hearing aid fittings and aural rehabilitation has generally used the audiogram and function stemming from peripheral sensitivity. In recent years, however, we have learned that individuals respond differently to various hearing aid and aural rehabilitation techniques based on cognitive abilities. In this paper, we review basic concepts of working memory and the literature driving our knowledge in newer concepts of hearing aid fitting and aural rehabilitation.

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Computational Approaches to Predict the Non-canonical DNAs

Current Bioinformatics ◽

10.2174/1574893614666190126143438 ◽

2019 ◽

Vol 14 (6) ◽

pp. 470-479 ◽

Cited By ~ 3

Author(s):

Nazia Parveen ◽

Amen Shamim ◽

Seunghee Cho ◽

Kyeong Kyu Kim

Keyword(s):

Computational Methods ◽

Genetic Instability ◽

Computational Prediction ◽

Structure And Function ◽

Sequence Motifs ◽

Computational Approaches ◽

Functional Roles ◽

And Function ◽

Genetic Events ◽

Insight Into

Background: Although most nucleotides in the genome form canonical double-stranded B-DNA, many repeated sequences transiently present as non-canonical conformations (non-B DNA) such as triplexes, quadruplexes, Z-DNA, cruciforms, and slipped/hairpins. Those noncanonical DNAs (ncDNAs) are not only associated with many genetic events such as replication, transcription, and recombination, but are also related to the genetic instability that results in the predisposition to disease. Due to the crucial roles of ncDNAs in cellular and genetic functions, various computational methods have been implemented to predict sequence motifs that generate ncDNA. Objective: Here, we review strategies for the identification of ncDNA motifs across the whole genome, which is necessary for further understanding and investigation of the structure and function of ncDNAs. Conclusion: There is a great demand for computational prediction of non-canonical DNAs that play key functional roles in gene expression and genome biology. In this study, we review the currently available computational methods for predicting the non-canonical DNAs in the genome. Current studies not only provide an insight into the computational methods for predicting the secondary structures of DNA but also increase our understanding of the roles of non-canonical DNA in the genome.

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