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69-652: MIASE is a registered project of the MIBBI (minimum information for biological and biomedical investigations). The MIASE project was launched in 2007 by Dagmar Köhn and Nicolas Le Novère and first presented on the 12th SBML Forum Meeting in October 2007. Since then, MIASE was discussed on various meetings, not only within the SBML community. MIASE has become a community effort involving people from various standardisation communities as well as developers of simulation tools. In April 2009, MIASE

138-577: A Microarray Experiment (MIAME) describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment and is aimed at facilitating the dissemination of data from microarray experiments. It was published by the FGED Society in 2001 and was the first published minimum information standard for high-throughput experiments in

207-524: A Simulation Experiment ( MIASE ) is an effort to standardize the description of simulation experiments in the field of systems biology. The Standards for Reporting Enzymology Data ( STRENDA ) is an initiative which specifically focuses on the development of guidelines for reporting (describing metadata) enzymology experiments with the aim to improve the quality of enzymology data published in the scientific literature. Electrophysiology Electrophysiology (from Greek ἥλεκτ , ēlektron , "amber" [see

276-538: A distributed phenomenon. Interest in the spatial distribution of bioelectric activity prompted development of molecules capable of emitting light in response to their electrical or chemical environment. Examples are voltage sensitive dyes and fluorescing proteins. After introducing one or more such compounds into tissue via perfusion, injection or gene expression, the 1 or 2-dimensional distribution of electrical activity may be observed and recorded. Intracellular recording involves measuring voltage and/or current across

345-603: A flow cytometry experiment . Criteria for Minimum Information About a Phylogenetic Analysis were described in 2006. The MIRAGE project is supported and coordinated by the Beilstein-Institut to establish guidelines for data handling and processing in glycomics research [1] The Minimal Information Required In the Annotation of Models ( MIRIAM ), is a set of rules for the curation and annotation of quantitative models of biological systems. The Minimum Information About

414-456: A model system like a lipid bilayer is subjected to an externally applied voltage. Studies using these setups have been able to study dynamical phenomena like electroporation of membranes and ion translocation by channels. The benefit of such methods is the high level of detail of the active conduction mechanism, given by the inherently high resolution and data density that atomistic simulation affords. There are significant drawbacks, given by

483-487: A reader to interpret and critically evaluate the processes performed and the conclusions reached, and to support their experimental corroboration. In practice a MINI module comprises a checklist of information that should be provided (for example about the protocols employed) when a data set is described for publication. The full specification of the MINI module can be found here. Minimum Information About an RNAi Experiment (MIARE)

552-423: A reference electrode, usually a silver chloride-coated silver wire in contact with the extracellular fluid around the cell. In general, the smaller the electrode tip, the higher its electrical resistance . So an electrode is a compromise between size (small enough to penetrate a single cell with minimum damage to the cell) and resistance (low enough so that small neuronal signals can be discerned from thermal noise in

621-402: A specific, rapid (1–2 minutes), reproducible, and cost-efficient fashion. The method has also been used for the detection of environmental toxins, such as pesticides and mycotoxins in food, and 2,4,6-trichloroanisole in cork and wine, as well as the determination of very low concentrations of the superoxide anion in clinical samples. A BERA sensor has two parts: A recent advance

690-399: A tip diameter of < 1 micrometre, and a resistance of several megohms. The micropipettes are filled with a solution that has a similar ionic composition to the intracellular fluid of the cell. A chlorided silver wire inserted into the pipette connects the electrolyte electrically to the amplifier and signal processing circuit. The voltage measured by the electrode is compared to the voltage of

759-516: A wide variety of scales from single ion channel proteins to whole tissues. This document is a single module, as part of the Minimum Information about a Neuroscience investigation (MINI) family of reporting guideline documents, produced by community consultation and continually available for public comment. A MINI module represents the minimum information that should be reported about a dataset to facilitate computational access and analysis to allow

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828-414: Is a data reporting guideline which describes the minimum information that should be reported about an RNAi experiment to enable the unambiguous interpretation and reproduction of the results. Advances in genomics and functional genomics have enabled large-scale analyses of gene and protein function by means of high-throughput cell biological analyses. Thereby, cells in culture can be perturbed in vitro and

897-506: Is a novel method developed for high throughput electrophysiology. Instead of positioning a pipette on an adherent cell, cell suspension is pipetted on a chip containing a microstructured aperture. A single cell is then positioned on the hole by suction and a tight connection (Gigaseal) is formed. The planar geometry offers a variety of advantages compared to the classical experiment: With this electrophysiological approach, proteo liposomes , membrane vesicles , or membrane fragments containing

966-415: Is a novel method for determination of various chemical and biological molecules by measuring changes in the membrane potential of cells immobilized in a gel matrix. Apart from the increased stability of the electrode-cell interface, immobilization preserves the viability and physiological functions of the cells. BERA is used primarily in biosensor applications in order to assay analytes that can interact with

1035-548: Is a set of reporting requirements – typically presented as a table or a checklist. Secondly, there is a data format. Information about an experiment needs to be converted into the appropriate data format for it to be submitted to the relevant database. In the case of MIAME , the data format is provided in spreadsheet format (MAGE-TAB). Some of the communities that maintain minimum information standards also provide tools to help experimental researchers to annotate their data. The individual minimum information standards are brought by

1104-422: Is generated by passing 10 nanoamperes of current across 1 MΩ of resistance. The electrometer changes this "high impedance signal" to a "low impedance signal" by using a voltage follower circuit. A voltage follower reads the voltage on the input (caused by a small current through a big resistor ). It then instructs a parallel circuit that has a large current source behind it (the electrical mains) and adjusts

1173-405: Is included within the category of electrodiagnostic testing . The various "ExG" modes are as follows: Optical electrophysiological techniques were created by scientists and engineers to overcome one of the main limitations of classical techniques. Classical techniques allow observation of electrical activity at approximately a single point within a volume of tissue. Classical techniques singularize

1242-427: Is now applied, the small patch of membrane in the electrode tip can be displaced, leaving the electrode sealed to the rest of the cell. This "whole-cell" mode allows very stable intracellular recording. A disadvantage (compared to conventional intracellular recording with sharp electrodes) is that the intracellular fluid of the cell mixes with the solution inside the recording electrode, and so some important components of

1311-403: Is placed next to a cell, and gentle suction is applied through the microelectrode to draw a piece of the cell membrane (the 'patch') into the microelectrode tip; the glass tip forms a high resistance 'seal' with the cell membrane. This configuration is the "cell-attached" mode, and it can be used for studying the activity of the ion channels that are present in the patch of membrane. If more suction

1380-646: Is primarily maintained through the EMBL-EBI Industry program (www.ebi.ac.uk/industry). This specification is being developed by the Genomic Standards Consortium The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) is a standard related to flow cytometry which establishes criteria to record information on experimental overview, samples, instrumentation and data analysis. It promotes consistent annotation of clinical, biological and technical issues surrounding

1449-522: Is since 2008 being harmonized by "Minimum Information about a Biomedical or Biological Investigation" (MIBBI) project. MIAPPE is an open, community driven project to harmonize data from plant phenotyping experiments. MIAPPE comprises both a conceptual checklist of metadata required to adequately describe a plant phenotyping experiment. Published in 2009 these guidelines for the basis of requirements by many journals when submitting QPCR data, sadly they are not adhered to enough. Minimum Information About

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1518-511: Is the development of a technique called molecular identification through membrane engineering (MIME). This technique allows for building cells with defined specificity for virtually any molecule of interest, by embedding thousands of artificial receptors into the cell membrane. While not strictly constituting an experimental measurement, methods have been developed to examine the conductive properties of proteins and biomembranes in silico . These are mainly molecular dynamics simulations in which

1587-418: Is the study of how electrophysiological principles and technologies can be applied to human health. For example, clinical cardiac electrophysiology is the study of the electrical properties which govern heart rhythm and activity. Cardiac electrophysiology can be used to observe and treat disorders such as arrhythmia (irregular heartbeat). For example, a doctor may insert a catheter containing an electrode into

1656-433: The etymology of "electron" ]; φύσις , physis , "nature, origin"; and -λογία , -logia ) is the branch of physiology that studies the electrical properties of biological cells and tissues. It involves measurements of voltage changes or electric current or manipulations on a wide variety of scales from single ion channel proteins to whole organs like the heart . In neuroscience , it includes measurements of

1725-645: The immobilized cells by changing the cell membrane potential. In this way, when a positive sample is added to the sensor, a characteristic, "signature-like" change in electrical potential occurs. BERA is the core technology behind the recently launched pan-European FOODSCAN project, about pesticide and food risk assessment in Europe. BERA has been used for the detection of human viruses ( hepatitis B and C viruses and herpes viruses), veterinary disease agents ( foot and mouth disease virus, prions , and blue tongue virus ), and plant viruses (tobacco and cucumber viruses) in

1794-757: The Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info) and describes the Minimum Information about a Molecular Interaction experiment. The Minimum Information About a Protein Affinity Reagent has been developed and maintained by the Molecular Interaction worktrack of the HUPO-PSI (www.psidev.info)in conjunction with the HUPO Antibody Initiative and a European consortium of binder producers and seeks to encourage users to improve their description of binding reagents, such as antibodies, used in

1863-539: The Nobel Prize in Physiology or Medicine for their contribution to understanding the mechanisms underlying the generation of action potentials in neurons. Their experiments involved intracellular recordings from the giant axon of Atlantic squid ( Loligo pealei ), and were among the first applications of the "voltage clamp" technique. Today, most microelectrodes used for intracellular recording are glass micropipettes, with

1932-407: The action potentials that are recorded intracellularly, but the signals are very much smaller (typically about 1 mV). Most recordings of the activity of single neurons in anesthetized and conscious animals are made in this way. Recordings of single neurons in living animals have provided important insights into how the brain processes information. For example, David Hubel and Torsten Wiesel recorded

2001-479: The activity of several nearby cells simultaneously, termed multi-unit recording . As electrode size increases, the resolving power decreases. Larger electrodes are sensitive only to the net activity of many cells, termed local field potentials . Still larger electrodes, such as uninsulated needles and surface electrodes used by clinical and surgical neurophysiologists, are sensitive only to certain types of synchronous activity within populations of cells numbering in

2070-604: The activity of single neurons in the primary visual cortex of the anesthetized cat, and showed how single neurons in this area respond to very specific features of a visual stimulus. Hubel and Wiesel were awarded the Nobel Prize in Physiology or Medicine in 1981. To prepare the brain for such electrode insertion, delicate slicing devices like the compresstome vibratome, leica vibratome, microtome are often employed. These instruments aid in obtaining precise, thin brain sections necessary for electrode placement, enabling neuroscientists to target specific brain regions for recording. If

2139-509: The biological processes addressed and understand biological principles. We propose the Minimum Information About a Cellular Assay (MIACA) for reporting a cellular assay, and CA-OM, the modular cellular assay object model, to facilitate exchange of data and accompanying information, and to compare and integrate data that originate from different, albeit complementary approaches, and to elucidate higher order principles. Documents describing MIACA are available and provide further information as well as

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2208-456: The brain's major immune cells, microglia , which must be taken into consideration when using this model. The voltage clamp technique allows an experimenter to "clamp" the cell potential at a chosen value. This makes it possible to measure how much ionic current crosses a cell's membrane at any given voltage. This is important because many of the ion channels in the membrane of a neuron are voltage-gated ion channels , which open only when

2277-429: The channel or transporter of interest are adsorbed to a lipid monolayer painted over a functionalized electrode. This electrode consists of a glass support, a chromium layer, a gold layer, and an octadecyl mercaptane monolayer. Because the painted membrane is supported by the electrode, it is called a solid-supported membrane. Mechanical perturbations, which usually destroy a biological lipid membrane, do not influence

2346-435: The checklist of terms that should be reported. The Minimum Information About a Proteomic Experiment documents describe information which should be given along with a proteomic experiment. The parent document describes the processes and principles underpinning the development of a series of domain specific documents which now cover all aspects of a MS-based proteomics workflow. This document has been developed and maintained by

2415-407: The collective activity of many cells. Usually, a field potential is generated by the simultaneous activation of many neurons by synaptic transmission . The diagram to the right shows hippocampal synaptic field potentials. At the right, the lower trace shows a negative wave that corresponds to a current sink caused by positive charges entering cells through postsynaptic glutamate receptors , while

2484-546: The communities of cross-disciplinary specialists focused on the problematic of the specific method used in experimental biology. The standards then provide specifications what information about the experiments ( metadata ) is crucial and important to be reported together with the resultant data to make it comprehensive. The need for this standardization is largely driven by the development of high-throughput experimental methods that provide tremendous amounts of data. The development of minimum information standards of different methods

2553-460: The electrical activity of neurons , and, in particular, action potential activity. Recordings of large-scale electric signals from the nervous system , such as electroencephalography , may also be referred to as electrophysiological recordings. They are useful for electrodiagnosis and monitoring . Electrophysiology is the branch of physiology that pertains broadly to the flow of ions ( ion current ) in biological tissues and, in particular, to

2622-512: The electrical recording techniques that enable the measurement of this flow. Classical electrophysiology techniques involve placing electrodes into various preparations of biological tissue. The principal types of electrodes are: The principal preparations include: Neuronal electrophysiology is the study of electrical properties of biological cells and tissues within the nervous system. With neuronal electrophysiology doctors and specialists can determine how neuronal disorders happen, by looking at

2691-439: The electrode tip is slightly larger, then the electrode might record the activity generated by several neurons. This type of recording is often called "multi-unit recording", and is often used in conscious animals to record changes in the activity in a discrete brain area during normal activity. Recordings from one or more such electrodes that are closely spaced can be used to identify the number of cells around it as well as which of

2760-467: The electrode tip). Maintaining healthy brain slices is pivotal for successful electrophysiological recordings. The preparation of these slices is commonly achieved with tools such as the Compresstome vibratome, ensuring optimal conditions for accurate and reliable recordings. Nevertheless, even with the highest standards of tissue handling, slice preparation induces rapid and robust phenotype changes of

2829-473: The electrodes depending on the polarity of the dye. An electrode introduced into the brain of a living animal will detect electrical activity that is generated by the neurons adjacent to the electrode tip. If the electrode is a microelectrode, with a tip size of about 1 micrometre, the electrode will usually detect the activity of at most one neuron. Recording in this way is in general called "single-unit" recording. The action potentials recorded are very much like

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2898-408: The experiment must be provided. All information necessary to obtain the desired numerical results must be provided. Minimum Information Standards Minimum information standard s are sets of guidelines and formats for reporting data derived by specific high-throughput methods. Their purpose is to ensure the data generated by these methods can be easily verified, analysed and interpreted by

2967-525: The heart to record the heart muscle's electrical activity. Another example of clinical electrophysiology is clinical neurophysiology . In this medical specialty, doctors measure the electrical properties of the brain , spinal cord , and nerves . Scientists such as Duchenne de Boulogne (1806–1875) and Nathaniel A. Buchwald (1924–2006) are considered to have greatly advanced the field of neurophysiology , enabling its clinical applications. Minimum Information (MI) standards or reporting guidelines specify

3036-436: The individual's brain activity. Activity such as which portions of the brain light up during any situations encountered. If an electrode is small enough (micrometers) in diameter, then the electrophysiologist may choose to insert the tip into a single cell. Such a configuration allows direct observation and intracellular recording of the intracellular electrical activity of a single cell. However, this invasive setup reduces

3105-434: The induced effects recorded and analyzed. Perturbations can be triggered in several ways, for instance with molecules (siRNAs, expression constructs, small chemical compounds, ligands for receptors, etc.), through environmental stresses (such as temperature shift, serum starvation, oxygen deprivation, etc.), or combinations thereof. The cellular responses to such perturbations are analyzed in order to identify molecular events in

3174-412: The intracellular fluid can be diluted. A variant of this technique, the "perforated patch" technique, tries to minimize these problems. Instead of applying suction to displace the membrane patch from the electrode tip, it is also possible to make small holes on the patch with pore-forming agents so that large molecules such as proteins can stay inside the cell and ions can pass through the holes freely. Also

3243-402: The life of the cell and causes a leak of substances across the cell membrane. Intracellular activity may also be observed using a specially formed (hollow) glass pipette containing an electrolyte. In this technique, the microscopic pipette tip is pressed against the cell membrane, to which it tightly adheres by an interaction between glass and lipids of the cell membrane. The electrolyte within

3312-439: The life sciences. MIAME contains a number of extensions to cover specific biological domains, including MIAME-env, MIAME-nut and MIAME-tox, covering environmental genomics, nutritional genomics and toxogenomics, respectively. Electrophysiology is a technology used to study the electrical properties of biological cells and tissues. Electrophysiology typically involves the measurements of voltage change or electric current flow on

3381-496: The life-time of an SSM. The capacitive electrode (composed of the SSM and the absorbed vesicles) is so mechanically stable that solutions may be rapidly exchanged at its surface. This property allows the application of rapid substrate/ligand concentration jumps to investigate the electrogenic activity of the protein of interest, measured via capacitive coupling between the vesicles and the electrode. The bioelectric recognition assay (BERA)

3450-406: The membrane of a cell. To make an intracellular recording, the tip of a fine (sharp) microelectrode must be inserted inside the cell, so that the membrane potential can be measured. Typically, the resting membrane potential of a healthy cell will be -60 to -80 mV, and during an action potential the membrane potential might reach +40 mV. In 1963, Alan Lloyd Hodgkin and Andrew Fielding Huxley won

3519-420: The membrane voltage is within a certain range. Voltage clamp measurements of current are made possible by the near-simultaneous digital subtraction of transient capacitive currents that pass as the recording electrode and cell membrane are charged to alter the cell's potential. The current clamp technique records the membrane potential by injecting current into a cell through the recording electrode. Unlike in

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3588-444: The micropipette electrode is reduced by filling with 2-4M KCl, rather than a salt concentration which mimics the intracellular ionic concentrations as used in patch clamping. Often the tip of the electrode is filled with various kinds of dyes like Lucifer yellow to fill the cells recorded from, for later confirmation of their morphology under a microscope. The dyes are injected by applying a positive or negative, DC or pulsed voltage to

3657-503: The millions. Other classical electrophysiological techniques include single channel recording and amperometry . Electrophysiological recording in general is sometimes called electrography (from electro- + -graphy , "electrical recording"), with the record thus produced being an electrogram. However, the word electrography has other senses (including electrophotography ), and the specific types of electrophysiological recording are usually called by specific names, constructed on

3726-430: The minimum amount of meta data (information) and data required to meet a specific aim or aims in a clinical study. The "Minimum Information about a Neuroscience investigation" (MINI) family of reporting guideline documents aims to provide a consistent set of guidelines in order to report an electrophysiology experiment. In practice a MINI module comprises a checklist of information that should be provided (for example about

3795-475: The patch may be left intact ( patch recording ). The electrophysiologist may choose not to insert the tip into a single cell. Instead, the electrode tip may be left in continuity with the extracellular space. If the tip is small enough, such a configuration may allow indirect observation and recording of action potentials from a single cell, termed single-unit recording . Depending on the preparation and precise placement, an extracellular configuration may pick up

3864-456: The patch of membrane can be pulled away from the rest of the cell. This approach enables the membrane properties of the patch to be analyzed pharmacologically. Patch-clamp may also be combined with RNA sequencing in a technique known as patch-seq by extracting the cellular contents following recording in order to characterize the electrophysiological properties relationship to gene expression and cell-type. In situations where one wants to record

3933-429: The pattern of electro- + [body part combining form ] + -graphy (abbreviation ExG). Relatedly, the word electrogram (not being needed for those other senses ) often carries the specific meaning of intracardiac electrogram, which is like an electrocardiogram but with some invasive leads (inside the heart) rather than only noninvasive leads (on the skin). Electrophysiological recording for clinical diagnostic purposes

4002-458: The pipette may be brought into fluid continuity with the cytoplasm by delivering a pulse of negative pressure to the pipette in order to rupture the small patch of membrane encircled by the pipette rim ( whole-cell recording ). Alternatively, ionic continuity may be established by "perforating" the patch by allowing exogenous pore-forming agents within the electrolyte to insert themselves into the membrane patch ( perforated patch recording ). Finally,

4071-411: The potential inside the cell membrane with minimal effect on the ionic constitution of the intracellular fluid a sharp electrode can be used. These micropipettes (electrodes) are again like those for patch clamp pulled from glass capillaries, but the pore is much smaller so that there is very little ion exchange between the intracellular fluid and the electrolyte in the pipette. The electrical resistance of

4140-426: The process of protein identification. The Minimum Information About a Bioactive Entity was produced by representatives from both large pharma and academia who are looking to improve the description of usually small molecules which bind to, and potentially modulate the activity of, specific targets in a living organism. This document encompasses drug-like molecules as well as herbicides, pesticides and food additives. It

4209-542: The recording electrode in a process known as "scanning". Because certain brain chemicals lose or gain electrons at characteristic voltages, individual species can be identified. Amperometry has been used for studying exocytosis in the nervous and endocrine systems. Many monoamine neurotransmitters ; e.g., norepinephrine (noradrenalin), dopamine , and serotonin (5-HT) are oxidizable. The method can also be used with cells that do not secrete oxidizable neurotransmitters by "loading" them with 5-HT or dopamine. Planar patch clamp

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4278-496: The resistance of that parallel circuit to give the same output voltage, but across a lower resistance. This technique was developed by Erwin Neher and Bert Sakmann who received the Nobel Prize in 1991. Conventional intracellular recording involves impaling a cell with a fine electrode; patch-clamp recording takes a different approach. A patch-clamp microelectrode is a micropipette with a relatively large tip diameter. The microelectrode

4347-485: The spikes come from which cell. This process is called spike sorting and is suitable in areas where there are identified types of cells with well defined spike characteristics. If the electrode tip is bigger still, in general the activity of individual neurons cannot be distinguished but the electrode will still be able to record a field potential generated by the activity of many cells. Extracellular field potentials are local current sinks or sources that are generated by

4416-472: The uncertainty of the legitimacy of the model and the computational cost of modeling systems that are large enough and over sufficient timescales to be considered reproducing the macroscopic properties of the systems themselves. While atomistic simulations may access timescales close to, or into the microsecond domain, this is still several orders of magnitude lower than even the resolution of experimental methods such as patch-clamping. Clinical electrophysiology

4485-415: The upper trace shows a positive wave that is generated by the current that leaves the cell (at the cell body) to complete the circuit. For more information, see local field potential . Amperometry uses a carbon electrode to record changes in the chemical composition of the oxidized components of a biological solution. Oxidation and reduction is accomplished by changing the voltage at the active surface of

4554-502: The voltage changes recorded from the cell. The "amplifier" is actually an electrometer , sometimes referred to as a "unity gain amplifier"; its main purpose is to reduce the electrical load on the small signals (in the mV range) produced by cells so that they can be accurately recorded by low- impedance electronics. The amplifier increases the current behind the signal while decreasing the resistance over which that current passes. Consider this example based on Ohm's law: A voltage of 10 mV

4623-569: The voltage clamp mode, where the membrane potential is held at a level determined by the experimenter, in "current clamp" mode the membrane potential is free to vary, and the amplifier records whatever voltage the cell generates on its own or as a result of stimulation. This technique is used to study how a cell responds when electric current enters a cell; this is important for instance for understanding how neurons respond to neurotransmitters that act by opening membrane ion channels . Most current-clamp amplifiers provide little or no amplification of

4692-490: The wider scientific community . Ultimately, they facilitate the transfer of data from journal articles (unstructured data) into databases (structured data) in a form that enables data to be mined across multiple data sets. Minimal information standards are available for a vast variety of experiment types including microarray ( MIAME ), RNAseq ( MINSEQE ), metabolomics (MSI) and proteomics ( MIAPE ). Minimum information standards typically have two parts. Firstly, there

4761-422: Was part of the " CellML , SBGN , SBO , BioPAX , and MIASE Super-Workshop 2009 ". The MIASE Guidelines are composed of the following parts: Information about the models to use, information about the simulation steps, and Information about the output: All models used in the experiment must be identified, accessible, and fully described. A precise description of the simulation steps and other procedures used by

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