microfluidic 장치의 A.의 Microfabrication <ol><li> 4 인치 웨이퍼는시 반응 산소 플라즈마 (30W, Harrick 과학에서 5 분, NY)로 처리됩니다. </li><li> 부정적인 포토 레지스트 (SU - 8 2015, Microchem, MA)는시 웨이퍼 1 분 900 rpm으로 스핀 - 코팅입니다. </li><li> 웨이퍼는 부드럽 95에서 구운 ° C가 열판에 6 분 및 microchannels를 포함하는 마스크 필름을 통해 4 분에 대한 자외선 (200W)에 노출됩니다. </li><li> 웨이퍼 95에서 구운 게시물 ° C 6 분 및 SU - 8 포토 레지스트 개발를 사용하여 개발된 것입니다. 것입니다 </li><li> microchannels를 포함하는 포토 레지스트 패턴 웨이퍼는 페트리 접시에 - 배치됩니다. </li><li> 폴리 (dimethylsiloxane) (PDMS) (Sylgard 184) 금형은 혼합 실리콘 엘라스토머 및 치료 에이전트 (10시 1분 비율)에 의해 가공됩니다. </li><li> PDMS 혼합물은시 마스터 몰드에 붓고하고 거품을 제거하는 진공 건조기에 배치됩니다. </li><li> PDMS는 1 ~ 2 시간 동안 70 ° C에서 치료됩니다. </li><li> PDMS 금형은 다음시 마스터 금형으로부터 떨어져 벗겨 수 있습니다. </li></ol> B.이 장치를 조립 <ol><li> 40 μm의 두께가 상단 유체 채널 및 40 μm의 두께 하단 microgrooved 채널 (25, 50, 75, 100 μ m 폭) 두 개의 서로 다른시 마스터 금형으로부터 얻을 수 있습니다. </li><li> 유체 장치의 채널 입구와 출구는 펀치입니다. </li><li> 유체 채널과 마이크로 그루브 채널 irreversibly 반응 산소 플라즈마 (30W, Harrick 과학에서 5 분, NY)에 의해 결합됩니다. </li><li> 세포외 매트릭스 (ECM) (즉, fibronectin)는 인큐베이터에서 1 시간 (37 ° C)에 대한 microfluidic 장치 내부에 코팅됩니다. </li></ol> C. 셀 시딩 및 실험 설정 <ol><li> NIH - 3T3 섬유아 세포는 마우스 10% 태아 소 혈청 (FBS)이 포함된 Dulbecco의 수정된 이글의 미디어 (DMEM)을 사용하여 조직 배양 플라스크에 양식 있습니다. </li><li> 세포가 trypsinized 및 dissociated 있습니다. </li><li> Dissociated 세포는 3 셀 밀도 × 10 6 세포 / ML (그림 1)에서 마이크로 그루브 채널로로드됩니다. <img src="/files/ftp_upload/old/270_2008_8_24_3/270_Figure-01.png" alt="그림 1" width="191" height="300" /> 그림 1 </li><li> 2 ML 미디어, 100 MM H 2 O 2, apoptosis 분석 (20 μL Annexin V 40 μL propidium의 요오드화물, Invitrogen, CA)를 주사기 펌프 (1 μl / 분)을 사용하여 채널에 들어갈 수 있습니다. </li><li> 세포는 거꾸로 현미경 (니콘 TE 2000)를 사용하여 모니터링 실시간 있습니다. </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>

전지 microfluidic 장치에서 고정 및 microgrooved 기판 내에 패턴했다. 과산화수소에 노출 세포의 apoptosis 과정이 실시간으로 관찰 및 Annexin V 및 propidium 요오드화물의를 사용하여 분석되었다. 따라서, 마이크로 그루브 채널을 포함하는이 microfluidic 장치는 높은 처리량 약물 검사에 유용 수 있습니다.

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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

우리는 세포 행위를 연구에 대한 microgrooved 패턴과 microfluidic 장치를 설명합니다. 이 microfluidic 플랫폼은 최고의 유체 채널 및 하단 microgrooved 기판으로 구성되어 있습니다. microgrooved 채널을 조작하려면, microfluidic 채널의 인상을 포함하는 최고의 폴리 (dimethylsiloxane) (PDMS) 몰드는 정렬과 microgrooved 기판에 접착했습니다. , 마우스 fibroblast 세포가 (25, 50, 75, 100 μm의 폭) 고정 및 microgrooved 기판 내에 패턴했다이 장치를 사용합니다. microfluidic 장치에서 apoptosis를 공부하려면, 과산화수소, Annexin V 및 propidium 요오드화물의를 포함하는 미디어는 2 시간 동안 유체 채널로 perfused되었습니다. 우리는 산화 스트레스에 노출된 세포가 apoptotic 된 것으로 나타났습니다. 이러한 apoptotic 세포는 apoptosis 과정에서 플라즈마 막의 바깥쪽 전단지에 phosphatidylserine로 바운드되는 Annexin V에 의해 확인되었다. microgrooved 패턴이 microfluidic 장치를 사용하여 apoptosis의 과정은 실시간으로 관찰 및 배양 챔버 (37 ° C, 5 % CO 2)를 포함 거꾸로 현미경을 사용하여 분석되었다. 따라서, microgrooved 기판과 통합이 microfluidic 장치는 세포 행동을 공부하고 높은 처리량 약물 검사를 수행하는 데 유용 수 있습니다.

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

우리는 세포 캡처 및 문화를 활성화할 수 있습니다 microfluidic 장치의 제조를위한 프로토콜을 설명합니다. 이 방법에서는 이러한 microfluidic 채널 내에서 홈과 같은 패턴 microstructures는 셀 수있는 부두 내에서 낮은 전단 응력 영역을 작성하는 데 사용됩니다.

세포 행동 유학을위한 그루브 패턴 Microfluidic 장치

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 조회수.  Brigham and Women's Hospital. 우리는 세포 캡처 및 문화를 활성화할 수 있습니다 microfluidic 장치의 제조를위한 프로토콜을 설명합니다. 이 방법에서는 이러한 microfluidic 채널 내에서 홈과 같은 패턴 microstructures는 셀 수있는 부두 내에서 낮은 전단 응력 영역을 작성하는 데 사용됩니다.

비디오: 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.

신경 소마와 Axons의 Compartmentalization위한 Microfluidic 장치의 제작

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

연구

생물학

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.

세포 생물학을위한 그라디언트 생성 Microfluidic 장치

 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.

Microfluidic 장치에서 Compartmentalization에 대한 E18 두피 랫 뉴런 준비

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

Microfluidic 장치를 사용하여 셀 캡처

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.

아가로 오스 겔 기반 Microfluidic 장치를 사용 신경 줄기 세포의 운동성 평가

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.

의 유사 분열 유학을위한 Microinjection 기법 Drosophila melanogaster Syncytial 엠브료

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.

Microfluidic Perifusion 장치 내에서 멀티 파라메 트릭 아일릿 Perifusion 시스템

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.

다공성 매체에서 미생물 교통 유학에 대한 간단한 Microfluidic 시스템 : 미생물의 창

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.

안정적인 농도 기울기에 박테리아 Chemotaxis을 Quantifying위한 Microfluidic 장치

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.

게놈 MRI - 게놈 DNA 시퀀스 내의 패턴을 학습에 대한 공개 자료

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