NBI Knowledgebase

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NBI [1] is short for the Nanomaterial-Biological Interactions Knowledgebase, located at Oregon State University. The knowledgebase serves as a repository for annotated data on nanomaterials characterization (purity, size, shape, charge, composition, functionalization, agglomeration state), synthesis methods, and nanomaterial-biological interactions (beneficial, benign or deleterious) defined at multiple levels of biological organization (molecular, cellular, organismal). Computational and data mining tools are currently being developed and incorporated into the NBI to provide a logical framework to conduct species, route, dose, and scenario extrapolations and identify key data required to predict the biological interactions of nanomaterials.

Oregon State University public university in Corvallis, Oregon, United States

Oregon State University (OSU) is a public research university in Corvallis, Oregon. The university offers more than 200 undergraduate degree programs along with a variety of graduate and doctoral degrees. It is also the largest university in the state, with a total enrollment exceeding 28,000. More than 230,000 students have graduated from OSU since its founding. The Carnegie Foundation designates Oregon State University as a "Community Engagement" university and classifies it as a doctoral university with a status of "Highest research activity".

Nanomaterials materials of which a single unit is sized (in at least one dimension) between 1 to 1000 nanometres (10−9 meter), but usually is 1 to 100 nm

Nanomaterials describe, in principle, materials of which a single unit is sized between 1 to 1000 nanometres but usually is 1 to 100 nm.

Flocculation, in the field of chemistry, is a process in which colloids come out of suspension in the form of floc or flake, either spontaneously or due to the addition of a clarifying agent. The action differs from precipitation in that, prior to flocculation, colloids are merely suspended in a liquid and not actually dissolved in a solution. In the flocculated system, there is no formation of a cake, since all the flocs are in the suspension.

Information currently being gained in the emerging field of nanotechnology is extremely diverse including a multitude of widely varying nanomaterials that are being or will be tested in a broad array of animal systems and in vitro assays. Knowledge of nanomaterial-biological interactions will likely only be arrived at upon inclusion and consideration of the entire body of data produced from global efforts in this research area. Compilation of this data will allow for the definition of nanomaterial structure-activity relationships. Such mathematical representations can be used to predict nanomaterial properties in the absence of empirical data.

Nanotechnology ("nanotech") is manipulation of matter on an atomic, molecular, and supramolecular scale. The earliest, widespread description of nanotechnology referred to the particular technological goal of precisely manipulating atoms and molecules for fabrication of macroscale products, also now referred to as molecular nanotechnology. A more generalized description of nanotechnology was subsequently established by the National Nanotechnology Initiative, which defines nanotechnology as the manipulation of matter with at least one dimension sized from 1 to 100 nanometers. This definition reflects the fact that quantum mechanical effects are important at this quantum-realm scale, and so the definition shifted from a particular technological goal to a research category inclusive of all types of research and technologies that deal with the special properties of matter which occur below the given size threshold. It is therefore common to see the plural form "nanotechnologies" as well as "nanoscale technologies" to refer to the broad range of research and applications whose common trait is size. Because of the variety of potential applications, governments have invested billions of dollars in nanotechnology research. Through 2012, the USA has invested $3.7 billion using its National Nanotechnology Initiative, the European Union has invested $1.2 billion, and Japan has invested $750 million.

<i>In vitro</i> test-tube experiments

In vitro studies are performed with microorganisms, cells, or biological molecules outside their normal biological context. Colloquially called "test-tube experiments", these studies in biology and its subdisciplines are traditionally done in labware such as test tubes, flasks, Petri dishes, and microtiter plates. Studies conducted using components of an organism that have been isolated from their usual biological surroundings permit a more detailed or more convenient analysis than can be done with whole organisms; however, results obtained from in vitro experiments may not fully or accurately predict the effects on a whole organism. In contrast to in vitro experiments, in vivo studies are those conducted in animals, including humans, and whole plants.

Related Research Articles

Bioinformatics Software tools for understanding biological data

Bioinformatics is an interdisciplinary field that develops methods and software tools for understanding biological data. As an interdisciplinary field of science, bioinformatics combines biology, computer science, information engineering, mathematics and statistics to analyze and interpret biological data. Bioinformatics has been used for in silico analyses of biological queries using mathematical and statistical techniques.

Quantitative structure–activity relationship models are regression or classification models used in the chemical and biological sciences and engineering. Like other regression models, QSAR regression models relate a set of "predictor" variables (X) to the potency of the response variable (Y), while classification QSAR models relate the predictor variables to a categorical value of the response variable.

The National Bridge Inventory (NBI) is a database, compiled by the Federal Highway Administration, with information on all bridges and tunnels in the United States that have roads passing above or below. This is similar to the grade crossing identifier number database compiled by the Federal Railroad Administration which identifies all railroad crossings. This bridge information includes the design of the bridge and the dimensions of the usable portion. The data is often used to analyze bridges and judge their conditions. The inventory is developed with the purpose of having a unified database for bridges to ensure the safety of the traveling public as required by the Federal-Aid Highway Act of 1968. It includes identification information, bridge types and specifications, operational conditions, bridge data including geometric data and functional description, and inspection data. Any bridge more than 20 feet long used for vehicular traffic is included.

Protein–protein interaction

Protein–protein interactions (PPIs) are the physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by electrostatic forces including the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context.

The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets. As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug data with comprehensive drug target information. DrugBank uses a fair bit of content from Wikipedia. Wikipedia also often links to Drugbank.

MPEG-4 Audio Lossless Coding, also known as MPEG-4 ALS, is an extension to the MPEG-4 Part 3 audio standard to allow lossless audio compression. The extension was finalized in December 2005 and published as ISO/IEC 14496-3:2005/Amd 2:2006 in 2006. The latest description of MPEG-4 ALS was published as subpart 11 of the MPEG-4 Audio standard in August 2009.

Reactome is a free online database of biological pathways. There are several Reactomes that concentrate on specific organisms, the largest of these is focused on human biology, the following description concentrates on the human Reactome. It is authored by expert biologists, in collaboration with Reactome editorial staff who are all PhD level biologists. Content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the source data available in a computationally accessible format.

Nonparametric regression

Nonparametric regression is a category of regression analysis in which the predictor does not take a predetermined form but is constructed according to information derived from the data. Nonparametric regression requires larger sample sizes than regression based on parametric models because the data must supply the model structure as well as the model estimates.

The impact of nanotechnology extends from its medical, ethical, mental, legal and environmental applications, to fields such as engineering, biology, chemistry, computing, materials science, and communications.

Nanotoxicology is the study of the toxicity of nanomaterials. Because of quantum size effects and large surface area to volume ratio, nanomaterials have unique properties compared with their larger counterparts that affect their toxicity. Of the possible hazards, inhalation exposure appears to present the most concern, with animal studies showing pulmonary effects such as inflammation, fibrosis, and carcinogenicity for some nanomaterials. Skin contact and ingestion exposure are also a concern.

The following outline is provided as an overview of and topical guide to nanotechnology:

Green nanotechnology refers to the use of nanotechnology to enhance the environmental sustainability of processes producing negative externalities. It also refers to the use of the products of nanotechnology to enhance sustainability. It includes making green nano-products and using nano-products in support of sustainability.

Because of the ongoing controversy on the implications of nanotechnology, there is significant debate concerning whether nanotechnology or nanotechnology-based products merit special government regulation. This mainly relates to when to assess new substances prior to their release into the market, community and environment.

Pollution from nanomaterials

Nanopollution is a generic name for waste generated by nanodevices or during the nanomaterials manufacturing process. Ecotoxicological impacts of nanoparticles and the potential for bioaccumulation in plants and microorganisms is a subject of current research, as nanoparticles are considered to present novel environmental impacts. Of the US$710 million spent in 2002 by the U.S. government on nanotechnology research, $500,000 was spent on environmental impact assessments.

Amanda Susan Barnard is an Australian theoretical physicist working in predicting the real world behavior of nanoparticles using analytical models and supercomputer simulations. Barnard is a pioneer in the thermodynamic cartography of nanomaterials, creating nanoscale phase diagrams relevant to different environmental conditions, and relating these to structure/property maps. Her current research involves developing and applying statistical methods and machine/deep learning in nanoscience and nanotechnology, and materials and molecular informatics. In 2014 she became the first person in the southern hemisphere, and the first woman, to win the Feynman Prize in Nanotechnology, which she won for her work on diamond nanoparticles.

The 'German Network for Bioinformatics Infrastructure – de.NBI' is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data.

References

  1. "NBI Knowledgebase Website". 12uroninja. 18 August 2010. Retrieved 18 August 2010.