A. Microfabrication der Mikrofluidikvorrichtung <ol><li> 4-Zoll-Si-Wafer ist mit reaktiven Sauerstoff-Plasma (5 min bei 30W, Harrick Scientific, NY) behandelt. </li><li> Negative Photolack (SU-8 2015 Microchem, MA) ist durch Spin-Coating bei 900 rpm für 1 min auf einem Si-Wafer. </li><li> Der Wafer ist weich gebacken bei 95 ° C für 6 min auf einer Heizplatte und wird mit UV-Licht (200W) für 4 min durch eine Maske Film mit Mikrokanälen ausgesetzt. </li><li> Der Wafer wird post bei 95 ° C gebacken für 6 min und entwickelt mit SU-8 Fotolack-Entwickler. </li><li> Der Fotolack strukturierten Wafer mit Mikrokanälen ist in einer Petri-Schale gelegt. </li><li> Poly (dimethylsiloxan) (PDMS) (Sylgard 184) Formen werden durch Mischen Silikon-Elastomer und Härter (10:1 Verhältnis) hergestellt. </li><li> Die PDMS-Mischung wird auf die Si-Master gegossen und befindet sich auf einem Vakuumexsikkator, um Luftblasen zu entfernen platziert. </li><li> PDMS ist bei 70 ° C für 1 bis 2 Stunden ausgehärtet. </li><li> PDMS Formen werden dann von der Si Master-Form geschält. </li></ol> B. Montieren Sie das Gerät <ol><li> 40 um dicke top Fluidik-Kanäle und 40 um dicken Boden microgrooved Kanäle (25, 50, 75 und 100 μ m breit) sind aus zwei verschiedenen Si Master Formen erhalten. </li><li> Kanal Ein-und Auslass der fluidischen Gerät ausgestanzt werden. </li><li> Fluidic Kanäle und microgroove Kanäle sind irreversibel durch die reaktive Sauerstoff-Plasma (5 min bei 30W, Harrick Scientific, NY) gebunden. </li><li> Extrazellulären Matrix (ECM) (dh Fibronektin) ist in mikrofluidischen Gerät für 1 Stunde im Brutschrank (37 ° C) beschichtet. </li></ol> C. Zellaussaat und Versuchsaufbau <ol><li> NIH-3T3 Maus-Fibroblasten in einer Zellkulturflasche mit Dulbecco modifiziertem Eagle-Medien (DMEM) mit 10% fötalem Rinderserum (FBS) gezüchtet. </li><li> Die Zellen werden trypsiniert und distanziert. </li><li> Dissoziierten Zellen werden in die microgroove Kanäle an der Zelldichte von 3 × 10 6 Zellen / ml (Abbildung 1) geladen. <img src="/files/ftp_upload/old/270_2008_8_24_3/270_Figure-01.png" alt="Abbildung 1" width="191" height="300" /> Abbildung 1 </li><li> 2 mL Medien, 100 mM H 2 O 2 und Apoptose-Assay (20 ul Annexin V und 40 ul Propidiumiodid, Invitrogen, CA) werden in einem Kanal mit Hilfe einer Spritzenpumpe (1 ml / min) infundiert. </li><li> Die Zellen werden in Echtzeit mit einem inversen Mikroskop (Nikon TE 2000) überwacht. </li></ol>

<ol>
	<li>Chung, B. G., Park, J. W., Hu, J. S., Huang, C., Monuki, E. S., Jeon, N. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+hybrid+microfluidic-vacuum+device+for+interfacing+with+conventional+cell+culture+platform.">A hybrid microfluidic-vacuum device for interfacing with conventional cell culture platform.</a> BMC Biotechnol. 7, (2007).</li><li>Khademhosseini, A., Yeh, J., Eng, G., Karp, J., Kaji, H., Borenstein, J., Farokhzad, O. C., Langer, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+docking+inside+microwells+within+reversibly+sealed+microfluidic+channels+for+fabricating+multiphenotype+cell+arrays.">Cell docking inside microwells within reversibly sealed microfluidic channels for fabricating multiphenotype cell arrays.</a> Lab Chip. 5, 1380-1386 (2005).</li><li>Whittemore, E. R., Loo, D. T., Watt, J. A., Cotman, C. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+detailed+analysis+of+hydrogen+peroxide-induced+cell+death+in+primary+neuronal+culture.">A detailed analysis of hydrogen peroxide-induced cell death in primary neuronal culture.</a> Neuroscience. 67, 921-932 (1995).</li></ol>

Die Zellen wurden fixiert und strukturiert innerhalb microgrooved Substrate in einer mikrofluidischen Vorrichtung. Die Apoptose-Prozess von Zellen, die Wasserstoffperoxid in Echtzeit beobachtet und analysiert mit Annexin V und Propidiumiodid. So könnte dieses Mikrofluidiksystem mit microgroove Kanäle nützlich sein für das Hochdurchsatz-Wirkstoffsuche.

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		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>PDMS</td>
<td>Reagent</td>
<td>K.R. Anderson Co. Inc. </td>
<td>2065622 </td>
<td>Poly(dimethylsiloxane), Dow Corning Sylgard 184 (8.6 lb)</td>
</tr>
<tr>
<td>DMEM</td>
<td>medium</td>
<td>Invitrogen</td>
<td>11965 </td>
<td>Dulbecco&#x2019;s Modified Eagle&#x2019;s Media </td>
</tr>
<tr>
<td>FBS</td>
<td>serum</td>
<td>Invitrogen</td>
<td>10082-147 </td>
<td>Fetal Bovine Serum
</td>
</tr>
<tr>
<td>Hydrogen peroxide</td>
<td>Reagent</td>
<td>Sigma Aldrich</td>
<td> H1009 </td>
<td>&nbsp;</td>
<tr>
<td>Apoptosis assay</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>V13242 </td>
<td>Annexin A, propidium iodide</td>
</tr>
<tr>
<td>Negative photoresist </td>
<td>&nbsp;</td>
<td>Microchem</td>
<td>SU-8 2015</td>
<td>&nbsp;</td>
<tr>
<td>Si wafer </td>
<td>Tool</td>
<td>&nbsp;</td>
<td>&nbsp;</td>
<td>4 inch silicone wafer</td>
</tr>
<tr>
<td>Reactive oxygen plasma </td>
<td>Reagent</td>
<td>Harrick Scientific</td>
<td>&nbsp;</td>
<td>treat wafer 5 min at 30W</td>
</tr>
<tr>
<td>inverted microscope </td>
<td>Tool</td>
<td>Nikon </td>
<td>TE 2000</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>
			<div>
					</div>

a microfluidic device with groove patterns for studying cellular behavior

Wir beschreiben ein Mikrofluidiksystem mit microgrooved Muster für die Untersuchung zellulärer Verhalten. Diese mikrofluidischen Plattform besteht aus einem Oberteil Fluidikkanal und eine untere microgrooved Substrat. Zur Herstellung der microgrooved Kanäle, war ein Top-Poly (dimethylsiloxan) (PDMS) Form mit dem Eindruck der mikrofluidischen Kanälen ausgerichtet und verbunden mit einem microgrooved Substrat. Mit diesem Gerät, Maus-Fibroblasten-Zellen wurden fixiert und strukturiert innerhalb microgrooved Substrate (25, 50, 75 und 100 &amp;mgr; m breit). Um die Apoptose in einer mikrofluidischen Vorrichtung Studie wurde Medium mit Wasserstoffperoxid, Annexin V und Propidiumiodid in die Fluidik-Kanal für 2 Stunden perfundiert. Wir fanden, dass Zellen, die den oxidativen Stress apoptotischen wurde. Diese apoptotischen Zellen wurden durch Annexin V bestätigt, dass an Phosphatidylserin an der äußeren Seite der Plasmamembran während der Apoptose-Prozess gebunden. Mit diesem mikrofluidischen Gerät mit microgrooved Muster wurde die Apoptose-Prozess in Echtzeit beobachtet und analysiert mit Hilfe eines inversen Mikroskops mit einer Inkubationszeit Kammer (37 ° C, 5% CO 2). Daher könnte dieses Mikrofluidiksystem mit microgrooved Substrate eingearbeitet werden für die Untersuchung der zellulären Verhaltens und Durchführung von Hochdurchsatz-Wirkstoffsuche.

Watch this Scientific Journal Video about A Microfluidic Device with Groove Patterns for Studying Cellular Behavior at JoVE.com

A Microfluidic Device with Groove Patterns for Studying Cellular Behavior

Wir beschreiben ein Protokoll für die Herstellung von mikrofluidischen Bauteilen, die Zelle zu erfassen und Kultur ermöglichen können. In diesem Ansatz gemusterten Mikrostrukturen wie Rillen in mikrofluidischen Kanälen werden verwendet, um Scherarmut Regionen, in denen Zellen andocken können erstellen.

Einer mikrofluidischen Vorrichtung mit Groove Patterns für ein Studium Cellular Behavior

We describe a microfluidic device with microgrooved patterns for studying cellular behavior.  This microfluidic platform consists of a top fluidic channel ...

a-microfluidic-device-with-groove-patterns-for-studying-cellular

Research

JoVE Journal

Biology

12.3K Aufrufe.  Brigham and Women's Hospital. Wir beschreiben ein Protokoll für die Herstellung von mikrofluidischen Bauteilen, die Zelle zu erfassen und Kultur ermöglichen können. In diesem Ansatz gemusterten Mikrostrukturen wie Rillen in mikrofluidischen Kanälen werden verwendet, um Scherarmut Regionen, in denen Zellen andocken können erstellen.

Serie: A Microfluidic Device with Groove Patterns for Studying Cellular Behavior

Fabrication of a Microfluidic Device for the Compartmentalization of Neuron Soma and Axons

In this video, we demonstrate the technique of soft lithography with polydimethyl siloxane (PDMS) which we use to fabricate a microfluidic device for culturing neurons. Previously, a silicon wafer was patterned with the design for the neuron microfluidic device using SU-8 and photolithography to create a master mold, or what we simply refer to as a "master". Next, we pour the silicon polymer PDMS on top of the master which is then cured by heating the PDMS to 80&deg;C for 1 hour. The PDMS forms a negative mold of the device. The PDMS is then carefully cut and lifted away from the master. Holes are punched where the reservoirs will be and the excess PDMS trimmed away from the device. Nitrogen is used to blow away any excess debris from the device. At this point the devices are now ready for use and can either bonded to corning No. 1 cover glass with a plasma sterilizer/cleaner or can be reversibly bound to the cover glass by simply placing the device on top of the cover glass. The reversible bonding of the device to glass is covered in a separate video and requires first that the device be sterilized either with 70% ethanol or by autoclaving. Plasma treating sterilizes the devices so no further treatment is necessary. It is, however, important, when plasma-treating the devices, to add liquid to the devices within 10 minutes of the plasma treatment while the surfaces are still hydrophilic. Waiting longer than 10 minutes to add liquid to the device makes it difficult for the liquid to enter the device. The neuron devices are typically plasma-bound to cover glass and 0.5 mg/ml poly-L-lysine (PLL) in pH 8.5 borate buffer is immediately added to the device. After a minimum of 3 hours incubating with PLL, the devices are washed with dH2O water a minimum of 3 times with at least 15 minutes between each wash. Next, the water is removed and fresh media is added to the device. At this point the device is ready for use. It is important to remember at this point to never remove all the media from the device. Always leave media in the main channel.

In this video we demonstrate the technique of soft lithography with polydimethyl siloxane (PDMS) which we use to farbricate a microfluidic device for culturing neurons.

Herstellung eines mikrofluidischen Vorrichtung für die Abschottung der Neuron Soma und Axonen

In this video, we demonstrate the technique of soft lithography with polydimethyl siloxane (PDMS) which we use to fabricate a microfluidic device for ...

Forschung

Biologie

A Gradient-generating Microfluidic Device for Cell Biology

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an enabling experimental tool, because it can precisely manipulate fluid flows, enable high-throughput experiments, and generate stable soluble concentration gradients.  Compared to conventional gradient generators, poly(dimethylsiloxane) (PDMS)-based  microfluidic devices can generate stable concentration gradients of growth factors with well-defined profiles.  Here, we developed simple gradient-generating microfluidic devices with three separate inlets.  Three microchannels combined into one microchannel to generate concentration gradients.  The stability and shape of growth factor gradients were confirmed by fluorescein isothyiocyanate (FITC)-dextran with a molecular weight similar to epidermal growth factor (EGF).  Using this microfluidic device, we demonstrated that fibroblasts exposed to concentration gradients of EGF migrated toward higher concentrations.  The directional orientation of cell migration and motility of migrating cells were quantitatively assessed by cell tracking analysis.  Thus, this gradient-generating microfluidic device might be useful for studying and analyzing the behavior of migrating cells.

We describe a protocol for the microfabrication of the gradient-generating microfluidic device that can generate spatial and temporal gradients in well-defined microenvironment. In this approach, the gradient-generating microfluidic device can be used to study directed cell migration, embryogenesis, wound healing, and cancer metastasis.

Ein Gradient-Erzeugung Mikrofluidikvorrichtung für Zellbiologie

 The fabrication and operation of a gradient-generating microfluidic device for studying cellular behavior is described.  A microfluidic platform is an ...

Preparing E18 Cortical Rat Neurons for Compartmentalization in a Microfluidic Device

In this video, we demonstrate the preparation of E18 cortical rat neurons. E18 cortical rat neurons are obtained from E18 fetal rat cortex previously dissected and prepared. The E18 cortex is, upon dissection, immediately dissociated into individual neurons. It is possible to store E18 cortex in Hibernate E buffer containing B27 at 4&deg;C for up to a week before the dissociation is performed. However, there will be a drop in cell viability. Typically we obtain our E18 Cortex fresh. It is transported to the lab in ice cold Calcium free Magnesium free dissection buffer (CMFM). Upon arrival, trypsin is added to the cortex to a final concentration of 0.125%. The cortex is then incubated at 37&deg;C for 8 minutes. DMEM containing 10% FBS is added to the cortex to stop the reaction. The cortex is then centrifuged at 2500 rpm for 2 minutes. The supernatant is removed and 2 ml of Neural Basal Media (NBM) containing 2% B27 (vol/vol) and 0.25% Glutamax (vol/vol) is added to the cortex which is then re-suspended by pipetting up and down. Next, the cortex is triturated with previously fire polished glass pipettes, each with a successive smaller opening. After triturating, the cortex is once again centrifuged at 2500 rpm for 2 minutes. The supernatant is then removed and the cortex pellet re-suspended with 2 ml of NBM containing B27 and Glutamax. The cell suspension is then passed through a 40 um nylon cell strainer. Next the cells are counted. The neurons are now ready for loading into the neuron microfluidic device.

In this video we demonstrate the preparation of E18 Cortical Rat Neurons.

Vorbereitung E18 Kortikale Rattenneuronen für Kompartimentierung in einer mikrofluidischen Vorrichtung

In this video, we demonstrate the preparation of E18 cortical rat neurons. E18 cortical rat neurons are obtained from E18 fetal rat cortex previously ...

Cell Capture Using a Microfluidic Device

Zell-Capture mit einer mikrofluidischen Vorrichtung

Assessing Neural Stem Cell Motility Using an Agarose Gel-based Microfluidic Device

While microfluidic technology is reaching a new level of maturity for macromolecular assays, cell-based assays are still at an infant stage1. This is largely due to the difficulty with which one can create a cell-compatible and steady microenvironment using conventional microfabrication techniques and materials. We address this problem via the introduction of a novel microfabrication material, agarose gel, as the base material for the microfluidic device. Agarose gel is highly malleable, and permeable to gas and nutrients necessary for cell survival, and thus an ideal material for cell-based assays. We have shown previously that agarose gel based devices have been successful in studying bacterial and neutrophil cell migration2. In this report, three parallel microfluidic channels are patterned in an agarose gel membrane of about 1mm thickness. Constant flows with media/buffer are maintained in the two side channels using a peristaltic pump. Cells are maintained in the center channel for observation. Since the nutrients and chemicals in the side channels are constantly diffusing from the side to center channel, the chemical environment of the center channel is easily controlled via the flow along the side channels. Using this device, we demonstrate that the movement of neural stem cells can be monitored optically with ease under various chemical conditions, and the experimental results show that the over expression of epidermal growth factor receptors (EGFR) enhances the motility of neural stem cells. Motility of neural stem cells is an important biomarker for assessing cells aggressiveness, thus tumorigenic factor3. Deciphering the mechanism underlying NSC motility will yield insight into both disorders of neural development and into brain cancer stem cell invasion.

We demonstrate that the over expression of epidermal growth factor receptors (EGFR) enhances the motility of neural stem cells(NSCs) using a novel agarose gel based microfluidic device. This technology can be readily adaptable to other mammalian cell systems where cell sources are scarce, such as human neural stem cells, and the turn around time is critical.

Die Beurteilung Neural Stem Cell Motilität Mit einem Agarosegel-basierte Mikrofluidikvorrichtung

While microfluidic technology is reaching a new level of maturity for macromolecular assays, cell-based assays are still at an infant stage1. This is ...

Microinjection Techniques for Studying Mitosis in the Drosophila melanogaster Syncytial Embryo

This protocol describes the use of the Drosophila melanogaster syncytial embryo for studying mitosis1. Drosophila has useful genetics with a sequenced genome, and it can be easily maintained and manipulated. Many mitotic mutants exist, and transgenic flies expressing functional fluorescently (e.g. GFP) - tagged mitotic proteins have been and are being generated. Targeted gene expression is possible using the GAL4/UAS system2. 

The Drosophila early embryo carries out multiple mitoses very rapidly (cell cycle duration, &asymp;10 min). It is well suited for imaging mitosis, because during cycles 10-13, nuclei divide rapidly and synchronously without intervening cytokinesis at the surface of the embryo in a single monolayer just underneath the cortex. These rapidly dividing nuclei probably use the same mitotic machinery as other cells, but they are optimized for speed; the checkpoint is generally believed to not be stringent, allowing the study of mitotic proteins whose absence would cause cell cycle arrest in cells with a strong checkpoint. Embryos expressing GFP labeled proteins or microinjected with fluorescently labeled proteins can be easily imaged to follow live dynamics (Fig. 1). In addition, embryos can be microinjected with function-blocking antibodies or inhibitors of specific proteins to study the effect of the loss or perturbation of their function3. These reagents can diffuse throughout the embryo, reaching many spindles to produce a gradient of concentration of inhibitor, which in turn results in a gradient of defects comparable to an allelic series of mutants. Ideally, if the target protein is fluorescently labeled, the gradient of inhibition can be directly visualized4. It is assumed that the strongest phenotype is comparable to the null phenotype, although it is hard to formally exclude the possibility that the antibodies may have dominant effects in rare instances, so rigorous controls and cautious interpretation must be applied. Further away from the injection site, protein function is only partially lost allowing other functions of the target protein to become evident.

Microinjection Techniques for Studying Mitosis in the Drosophila melanogaster Syncytial Embryo

This protocol describes the use of microinjection and high resolution imaging in the Drosophila melanogaster syncytial embryo to study mitosis.

Mikroinjektion Techniken zur Untersuchung Mitose in der Drosophila melanogaster Syncytial Embryo

This protocol describes the use of the Drosophila melanogaster syncytial embryo  for studying mitosis1.  Drosophila has useful genetics with a sequenced ...

A Multi-Parametric Islet Perifusion System within a Microfluidic Perifusion Device

A microfluidic islet perifusion device was developed for the assessment of dynamic insulin secretion of multiple islets and simultaneous fluorescence imaging of calcium influx and mitochondrial potential changes. The device consists of three layers: first layer contains an array of microscale wells (500 &mu;m diameter and 150 &mu;m depth) that help to immobilize the islets while exposed to flow and maximize the exposed surface area of the islets; the second layer contains a circular perifusion chamber (3 mm deep, 7 mm diameter); and the third layer contains an inlet-mixing channel that fans out before injection into the perifusion chamber (2 mm in width, 19 mm in length, and 500 &mu;m in height) for optimizing the mixing efficiency prior to entering the perifusion chamber. The creation of various glucose gradients including a linear, bell shape, and square shapes also can be created in the microfluidic perifusion network and is demonstrated.

A microfluidic islet perifusion device was developed for the assessment of dynamic insulin secretion of multiple islets and simultaneous fluorescence imaging of calcium influx and mitochondrial potential changes.

Ein Multi-Parametric Islet Perifusion System innerhalb eines mikrofluidischen Perifusion Geräte

A microfluidic islet perifusion device was developed for the assessment of dynamic insulin secretion of multiple islets and simultaneous fluorescence ...

Window on a Microworld: Simple Microfluidic Systems for Studying Microbial Transport in Porous Media

Microbial growth and transport in porous media have important implications for the quality of groundwater and surface water, the recycling of nutrients in the environment, as well as directly for the transmission of pathogens to drinking water supplies. Natural porous media is composed of an intricate physical topology, varied surface chemistries, dynamic gradients of nutrients and electron acceptors, and a patchy distribution of microbes. These features vary substantially over a length scale of microns, making the results of macro-scale investigations of microbial transport difficult to interpret, and the validation of mechanistic models challenging. Here we demonstrate how simple microfluidic devices can be used to visualize microbial interactions with micro-structured habitats, to identify key processes influencing the observed phenomena, and to systematically validate predictive models. Simple, easy-to-use flow cells were constructed out of the transparent, biocompatible and oxygen-permeable material poly(dimethyl siloxane). Standard methods of photolithography were used to make micro-structured masters, and replica molding was used to cast micro-structured flow cells from the masters. The physical design of the flow cell chamber is adaptable to the experimental requirements: microchannels can vary from simple linear connections to complex topologies with feature sizes as small as 2 &mu;m. Our modular EcoChip flow cell array features dozens of identical chambers and flow control by a gravity-driven flow module. We demonstrate that through use of EcoChip devices, physical structures and pressure heads can be held constant or varied systematically while the influence of surface chemistry, fluid properties, or the characteristics of the microbial population is investigated. Through transport experiments using a non-pathogenic, green fluorescent protein-expressing Vibrio bacterial strain, we illustrate the importance of habitat structure, flow conditions, and inoculums size on fundamental transport phenomena, and with real-time particle-scale observations, demonstrate that microfluidics offer a compelling view of a hidden world.

Microfluidic devices can be used to visualize complex natural processes in real time and at the appropriate physical scales. We have developed a simple microfluidic device that mimics key features of natural porous media for studying growth and transport of bacteria in the subsurface.

Fenster an einem Microworld: Einfache mikrofluidische Systeme für Studium Mikrobielle Transport in porösen Medien

Microbial growth and transport in porous media have important implications for the quality of groundwater and surface water, the recycling of nutrients in ...

A Microfluidic Device for Quantifying Bacterial Chemotaxis in Stable Concentration Gradients

Chemotaxis allows bacteria to approach sources of attractant chemicals or to avoid sources of repellent chemicals. Bacteria constantly monitor the concentration of specific chemoeffectors by comparing the current concentration to the concentration detected a few seconds earlier. This comparison determines the net direction of movement. Although multiple, competing gradients often coexist in nature, conventional approaches for investigating bacterial chemotaxis are suboptimal for quantifying migration in response to concentration gradients of attractants and repellents. Here, we describe the development of a microfluidic chemotaxis model for presenting precise and stable concentration gradients of chemoeffectors to bacteria and quantitatively investigating their response to the applied gradient. The device is versatile in that concentration gradients of any desired absolute concentration and gradient strength can be easily generated by diffusive mixing. The device is demonstrated using the response of Escherichia coli RP437 to gradients of amino acids and nickel ions.

This protocol describes the development of a microfluidic device for investigating bacterial chemotaxis in stable concentration gradients of chemoeffectors.

Einer mikrofluidischen Vorrichtung zur Quantifizierung von bakteriellen Chemotaxis in Stable Konzentrationsgradienten

Chemotaxis allows bacteria to approach sources of attractant chemicals or to avoid sources of repellent chemicals. Bacteria constantly monitor the ...

Genomic MRI - a Public Resource for Studying Sequence Patterns within Genomic DNA

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in their nucleotide composition and consist of a complex mosaic of sequence patterns. These patterns include so-called Mid-Range Inhomogeneity (MRI) regions -- sequences 30-10000 nucleotides in length that are enriched by a particular base or combination of bases (e.g. (G+T)-rich, purine-rich, etc.). MRI regions are associated with unusual (non-B-form) DNA structures that are often involved in regulation of gene expression, recombination, and other genetic processes (Fedorova &amp; Fedorov 2010). The existence of a strong fixation bias within MRI regions against mutations that tend to reduce their sequence inhomogeneity additionally supports the functionality and importance of these genomic sequences (Prakash et al. 2009).
Here we demonstrate a freely available Internet resource -- the Genomic MRI program package -- designed for computational analysis of genomic sequences in order to find and characterize various MRI patterns within them (Bechtel et al. 2008). This package also allows generation of randomized sequences with various properties and level of correspondence to the natural input DNA sequences. The main goal of this resource is to facilitate examination of vast regions of non-coding DNA that are still scarcely investigated and await thorough exploration and recognition.

We present a public computational web site for the analysis of genomic sequences. It detects DNA sequence patterns with various non-random nucleotide compositions. This resource also generates randomized sequences with diverse levels of complexity.

Genomic MRI - eine öffentliche Ressource für ein Studium Sequence Patterns in genomischer DNA

Non-coding genomic regions in complex eukaryotes, including intergenic areas, introns, and untranslated segments of exons, are profoundly non-random in ...