The authors thank Dr. Yoav Barak from the Chemistry Faculty, Weizmann Institute, for support and advice. This study was supported by the Israel Science Foundation (grant # 913/12), and by the Minerva Foundation with funding from the Federal German Ministry for Education and Research.

<ol>
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The authors have nothing to disclose.

Bu çalışma Filtreler üzerinde toplanan aerosol örneklerinde endotoksin ve DNA hediyesi hem ölçülmesi için çıkarma ve algılama yöntemleri anlatılmaktadır. yöntemler doğru rutinleri gerektiren ve uzun Deneyciler Burada tartışılan birkaç temel ve önemli noktaları yapışır gibi kolayca yapılabilir. endotoksin algılama adım için, lizat çözüm oldukça viskoz ve pipetleme üzerine kabarcıkları üretmek eğiliminde olduğunu unutmayın. Sana kabarcıklar kaldırmak ...

Filtrelerin hava örnekleme atmosferik aerosoller araştırma temel araçtır. 1 örneklenmiş filtreler çeşitli kimyasal, fiziksel ve toplanan çevre parçacıkların biyolojik karakterizasyonları için başlangıç ​​noktasıdır. 2-11 Bu yaklaşımın avantajı çeşitli analizler olabilmesidir aynı numune üzerinde off-line gerçekleştirilir. Araştırmacı tüm farklı analizler verileri etkinleştirir derlenmesi atmosfer bilimleri karmaşık sorunların çözümünde toplanan parçacıkların ve yardımların özelliklerinin iyi bir anlayış elde etmek için. 12,13 Örneğin, deniz ve iç hava örnekleri aynı sırasında alınan süresi Bu çalışma için örnek partikül toksisite ve biyolojik kompozisyon. 14 ile ilgili olarak karşılaştırılabilir, lipopolisakarit (LPS), aynı zamanda endotoksinlerin şekilde bilinmektedir gram-negatif bakteri hücre duvarları, bileşenler, kıyı-ve örneklendiği filtrelerden ekstre edildi bir iç site ve kullanılarak değerlendirildilimulus amebocyte lizat (LAL) testi. Buna paralel olarak, bakteriyel içeriğin bir genomik değerlendirme (toplam bakteri, gram negatif ve siyanobakteri kantitatif) polimeraz zincir reaksiyonu (Q-PCR) kullanılarak aynı numune üzerinde gerçekleştirilmiştir. LAL Test endotoksin içeren bir sulu çözeltiye, at nalı yengeç, Limulus Polyphemus&#39;un gelen amebocytes sulu ekstraktının ilave edildikten sonra oluşan bulanıklık ölçümlerine dayanır. Örnek yüksek endotoksin konsantrasyonu hızlı türbidite geliştirir. 15 Q-PCR analizi, belirli bir DNA fragmanı amplifiye olarak yayılan bir floresan sinyali dayanır. 16 sinyal gerçek zamanlı izleme PCR üslü fazda standart bir eğri ile reaksiyonu ve kalibre, ilk DNA miktar olarak tespit edilebilir. Bu ikisinin kombinasyonu başka bir yerde ayrıntılı olarak, 14 endotoksin ve düzeyleri iyi bir tahmin sağlayabilir, diğerleriyle birlikte analizleriörneklerinde, kaynak bakteri miktarı. Burada sunulan yöntemin amacı, filtreler çıkarılır, biyo-aerosolleri endotoksin ve DNA içeriği son derece doğru ve güvenilir bir analiz sağlamaktır. Aerosol fiziksel ve inorganik kimyasal özellikleri örnekleme yöntemleri ve daha yakın zamanda, yöntemler organik madde bileşeni araştırmak için geliştirilmiştir iyi bilinen iken, 17 aerosollerin biyolojik bileşeni yetersiz araştırma olmuştur. 18 akımı gerekçesi yöntem ayrıntılı olarak, ayıklanması analiz ve havadaki aerosoller biyolojik kısmını tanımlamak için sağlam bir yöntem sunarak bu boşluğu doldurmak için. 14 Burada açıklanan yöntem filtre analizini içeren biyolojik kapalı ve açık aerosol araştırma projelerinde yaygın kullanım alanı bulur bekleniyor. 20-24

<table border="0" cellpadding="0" cellspacing="0" width="631">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">Filter sampling</td>
			<td style="width:123px;"></td>
			<td style="width:103px;"></td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">HiVol 3000 - High Air Volume Sampler</td>
			<td style="width:123px;">Ecotech</td>
			<td style="width:103px;"></td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Quartz Microfiber Filters</td>
			<td style="width:123px;">Whatman</td>
			<td style="width:103px;">1851-865</td>
			<td style="width:220px;">203mm X 254mm</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">ELF - Laboratory Chamber Furnaces</td>
			<td style="width:123px;">Carbolite</td>
			<td style="width:103px;">ELF 11series</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">Aluminum foil</td>
			<td style="width:123px;">Opal</td>
			<td style="width:103px;"></td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;width:187px;">Name</td>
			<td style="width:123px;">Company</td>
			<td style="width:103px;">Catalog Number</td>
			<td style="width:220px;">Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">Endotoxin</td>
			<td style="width:123px;"></td>
			<td style="width:103px;"></td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Ethanol</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:103px;">16368&#160;</td>
			<td style="width:220px;">Laboratory Reagent, 96%</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Airstream Class II Biological Safety Cabinet AC-4E1</td>
			<td style="width:123px;">ESCO</td>
			<td style="width:103px;">10011712</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Pyrotell -T</td>
			<td style="width:123px;">Associates of Cape Cod, Inc.</td>
			<td style="width:103px;">T0051</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Control Standard Endotoxin</td>
			<td style="width:123px;">Associates of Cape Cod, Inc.</td>
			<td style="width:103px;">E0005-1</td>
			<td style="width:220px;">Escherichia coli&#160;O113:H10, 0.5 &#181;g/vial 1 Pack</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">LAL Reagent Water</td>
			<td style="width:123px;">Associates of Cape Cod, Inc.</td>
			<td style="width:103px;">W0051</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">10 mL sterile syringe with Luer-Lok Tip</td>
			<td style="width:123px;">Becton-Dickinson &#38; Co.</td>
			<td style="width:103px;">309605</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">BD Precisionglide syringe needle</td>
			<td style="width:123px;">Becton-Dickinson &#38; Co.</td>
			<td style="width:103px;">305129</td>
			<td style="width:220px;">Sterile&#160;</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Parafilm-M sealing tape</td>
			<td style="width:123px;">Parafilm</td>
			<td style="width:103px;">P7543</td>
			<td style="width:220px;">Sigma catalog number</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Microtubes</td>
			<td style="width:123px;">Axigen</td>
			<td style="width:103px;">MCT-200-C</td>
			<td style="width:220px;">2ml, pyrogen free</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">1.12 cm diameter Cork Borer</td>
			<td style="width:123px;">Boekel Scientific</td>
			<td style="width:103px;">1601 BD Series - Steel</td>
			<td style="width:220px;">Part of a cork borer set containing borers with various diameters.&#160;</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">50 mm Petri Dish</td>
			<td style="width:123px;">Miniplast Ein-Shemer</td>
			<td style="width:103px;">72050-01</td>
			<td style="width:220px;">Aseptic</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Vortex Genie 2&#160;</td>
			<td style="width:123px;">Scientific Industries, inc.</td>
			<td style="width:103px;">SI-0297</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">Microcentrifuge 5415 D</td>
			<td style="width:123px;">Eppendorf</td>
			<td style="width:103px;">22621408</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="51">
			<td height="51" style="height:51px;width:187px;">TC MicroWell 96 F SI w/lid</td>
			<td style="width:123px;">Nunc</td>
			<td style="width:103px;">167008</td>
			<td style="width:220px;">Flat bottom wells (with lid (individually wrapped)), sterile, pyrogen free</td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;width:187px;">Synergy HT Multi-Detection Microplate Reader</td>
			<td style="width:123px;">Biotek</td>
			<td style="width:103px;">7091000</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="35">
			<td height="35" style="height:35px;width:187px;">Name</td>
			<td style="width:123px;">Company</td>
			<td style="width:103px;">Catalog Number</td>
			<td style="width:220px;">Comments</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">DNA</td>
			<td style="width:123px;"></td>
			<td style="width:103px;"></td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">DNA away</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:103px;">7010</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="51">
			<td height="51" style="height:51px;width:187px;">Standard DNA of the microbial species of interest</td>
			<td style="width:123px;">ATCC or other culture collection</td>
			<td style="width:103px;"></td>
			<td style="width:220px;">Either the appropriate microbial strain for DNA extraction or the extracted DNA</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Neubauer-improved</td>
			<td style="width:123px;">Marienfeld</td>
			<td style="width:103px;">640030</td>
			<td style="width:220px;">hemocytometer</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">TE buffer, Low EDTA</td>
			<td style="width:123px;">Life Technologies</td>
			<td style="width:103px;">12090-015</td>
			<td style="width:220px;">10 mM Tris-HCl (pH 8.0)&#160;0.1 mM EDTA&#160;</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Nuclease-free PCR-grade water&#160;</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:103px;">3315959001</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">PCR primers</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:103px;"></td>
			<td style="width:220px;">Targets the microbial species of interest</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Dual-Labeled Probes</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:103px;"></td>
			<td style="width:220px;">Targets the microbial species of interest</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">Screw cap tubes</td>
			<td style="width:123px;">Axigen</td>
			<td style="width:103px;">ST-200-SS</td>
			<td>2 mL&#160;</td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">PowerSoil DNA extraction kit&#160;</td>
			<td style="width:123px;">Mo Bio Laboratories</td>
			<td style="width:103px;">12888-100</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Glass beads, acid-washed 425-600 Microns</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:103px;">G8772-100G</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Glass beads, acid-washed &#60;106 microns</td>
			<td style="width:123px;">Sigma Aldrich</td>
			<td style="width:103px;">G4649-100G</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;">PowerSoil Solution C1</td>
			<td style="width:123px;">Mo Bio Laboratories</td>
			<td style="width:103px;">12888-100-1</td>
			<td style="width:220px;">Cell lysis buffer , Power soil Kit</td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Magic Touch ice bucket</td>
			<td style="width:123px;">Bel-Art</td>
			<td style="width:103px;">18848-4001</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="20">
			<td height="20" style="height:20px;width:187px;">Mini-Beadbeater-16</td>
			<td style="width:123px;">BioSpec</td>
			<td style="width:103px;">607EUR</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">StepOnePlus Real-Time PCR System</td>
			<td style="width:123px;">Applied Biosystems</td>
			<td style="width:103px;">4376600</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">Fast SYBR Green Master Mix</td>
			<td style="width:123px;">Applied Biosystems</td>
			<td style="width:103px;">4385612</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">TaqMan Gene Expression Master Mix</td>
			<td style="width:123px;">Applied Biosystems</td>
			<td style="width:103px;">4370048</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="51">
			<td height="51" style="height:51px;width:187px;">MicroAmp Fast Optical 96-Well Reaction Plate with Barcode, 0.1 mL</td>
			<td style="width:123px;">Applied Biosystems</td>
			<td style="width:103px;">4346906</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">MicroAmp Splash-Free 96-Well Base</td>
			<td style="width:123px;">Applied Biosystems</td>
			<td style="width:103px;">4312063</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="34">
			<td height="34" style="height:34px;width:187px;">MicroAmp Optical Adhesive Film</td>
			<td style="width:123px;">Applied Biosystems</td>
			<td style="width:103px;">4311971</td>
			<td style="width:220px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:187px;">Centrifuge 5810 R</td>
			<td style="width:123px;">Eppendorf</td>
			<td style="width:103px;">5811 000.010</td>
			<td style="width:220px;">Rotor A-4-62 with MTP buckets&#160;</td>
		</tr>
	</tbody>
</table>

air-sampled filter analysis for endotoxins and dna content

Açık aerosol araştırmaları yaygın filtreler örneklenmiş partiküler madde kullanır. Bu prosedür, toplanan partiküllerin değişik karakterizasyonları paralel yapılmasını sağlar. Burada sunulan yöntemin amacı, filtreler çıkarılır, biyo-aerosolleri endotoksin ve DNA içeriği son derece doğru ve güvenilir bir analiz sağlamaktır. örnek filtrelerden Lipopolisakkaridler gibi yüksek moleküler ağırlıklı organik moleküllerin, ekstraksiyonu pirojensiz su bazlı ortam içinde örnek çalkalama içerir. Daha sonra yapılan analiz bir türbidimetrik ölçümü kullanılarak tespit edilebilir bir enzimatik reaksiyona dayanır. örneklenmiş filtreler üzerindeki yüksek organik içeriğin bir sonucu olarak, örneklerden DNA ekstraksiyon ilk topraklar için tasarlanmış ve DNA verimi artırmak için modifiye edilmiş bir ticari bir DNA ekstraksiyon kiti kullanılarak gerçekleştirilir. Algılama ve kantitatif polimeraz zincir Reacti kullanarak belirli mikrobiyal türlerin miktar(Q-PCR) analizi tarif diğer yöntemlerden karşılaştırılmıştır.

Bu &quot;off-line&quot; örneklenmiş filtreleri analizleri kullanılarak atmosferik aerosoller incelemek için yaygındır (Şekil 2). 32 Kimyasal örneklenmiş madde, organik (örneğin protein, hidrokarbon molekülleri, sakkaritler) ve inorganik (örneğin metaller, tuzlar) dahil içeriği analizleri . Biyolojik analizler uygulanabilir ve cansız mikroorganizma içeriği, bir DNA ya da yaklaşımı mikroskobu kullanarak tür tanımlamak, h...

Watch this Scientific Journal Video about Air-sampled Filter Analysis for Endotoxins and DNA Content at JoVE.com

Air-sampled Filter Analysis for Endotoxins and DNA Content

Two complementary analyses of atmospheric biological particles from air sampled filters are described herein: the extraction and detection of endotoxin, and of DNA.

Endotoksin ve DNA İçeriği için Hava örneklenmiş Filtresi Analizi

Outdoor aerosol research commonly uses particulate matter sampled on filters. This procedure enables various characterizations of the collected particles ...

air-sampled-filter-analysis-for-endotoxins-and-dna-content

Research

JoVE Journal

Environment

9.6K Görüntüleme.  Weizmann Institute of Science. Two complementary analyses of atmospheric biological particles from air sampled filters are described herein: the extraction and detection of endotoxin, and of DNA.

Video: Air-sampled Filter Analysis for Endotoxins and DNA Content

Analysis of Fatty Acid Content and Composition in Microalgae

A method to determine the content and composition of total fatty acids present in microalgae is described. Fatty acids are a major constituent of microalgal biomass. These fatty acids can be present in different acyl-lipid classes. Especially the fatty acids present in triacylglycerol (TAG) are of commercial interest, because they can be used for production of transportation fuels, bulk chemicals, nutraceuticals (&omega;-3 fatty acids), and food commodities. To develop commercial applications, reliable analytical methods for quantification of fatty acid content and composition are needed. Microalgae are single cells surrounded by a rigid cell wall. A fatty acid analysis method should provide sufficient cell disruption to liberate all acyl lipids and the extraction procedure used should be able to extract all acyl lipid classes.
With the method presented here all fatty acids present in microalgae can be accurately and reproducibly identified and quantified using small amounts of sample (5 mg) independent of their chain length, degree of unsaturation, or the lipid class they are part of.
This method does not provide information about the relative abundance of different lipid classes, but can be extended to separate lipid classes from each other.
The method is based on a sequence of mechanical cell disruption, solvent based lipid extraction, transesterification of fatty acids to fatty acid methyl esters (FAMEs), and quantification and identification of FAMEs using gas chromatography (GC-FID). A TAG internal standard (tripentadecanoin) is added prior to the analytical procedure to correct for losses during extraction and incomplete transesterification.

A method for the determination of fatty acid content and composition in microalgae based on mechanical cell disruption, solvent based lipid extraction, transesterification, and quantification and identification of fatty acids using gas chromatography is described. A tripentadecanoin internal standard is used to compensate for the possible losses during extraction and incomplete transesterification.

Mikroalglerden yağlı asit içeriği ve bileşimi analizi

A method to determine the content and composition of total fatty acids present in microalgae is described. Fatty acids are a major constituent of ...

Çevre

Use of Chironomidae (Diptera) Surface-Floating Pupal Exuviae as a Rapid Bioassessment Protocol for Water Bodies

Rapid bioassessment protocols using benthic macroinvertebrate assemblages have been successfully used to assess human impacts on water quality. Unfortunately, traditional benthic larval sampling methods, such as the dip-net, can be time-consuming and expensive. An alternative protocol involves collection of Chironomidae surface-floating pupal exuviae (SFPE). Chironomidae is a species-rich family of flies (Diptera) whose immature stages typically occur in aquatic habitats. Adult chironomids emerge from the water, leaving their pupal skins, or exuviae, floating on the water&#8217;s surface. Exuviae often accumulate along banks or behind obstructions by action of the wind or water current, where they can be collected to assess chironomid diversity and richness. Chironomids can be used as important biological indicators, since some species are more tolerant to pollution than others. Therefore, the relative abundance and species composition of collected SFPE reflect changes in water quality. Here, methods associated with field collection, laboratory processing, slide mounting, and identification of chironomid SFPE are described in detail. Advantages of the SFPE method include minimal disturbance at a sampling area, efficient and economical sample collection and laboratory processing, ease of identification, applicability in nearly all aquatic environments, and a potentially more sensitive measure of ecosystem stress. Limitations include the inability to determine larval microhabitat use and inability to identify pupal exuviae to species if they have not been associated with adult males.

Use of Chironomidae Diptera Surface-Floating Pupal Exuviae as a Rapid Bioassessment Protocol for Water Bodies

Rapid bioassessment protocols using benthic macroinvertebrates are often used to monitor and assess water quality. An efficient protocol involves collections of Chironomidae surface-floating pupal exuviae (SFPE). Here, techniques for field collection, laboratory processing, slide mounting, and identification of Chironomidae SFPE are described.

Chironomidae (Diptera) kullanılması Yüzey Yüzer Su Organları bir Rapid Bioassessment Protokolü Pupa Exuviae

Rapid bioassessment protocols using benthic macroinvertebrate assemblages have been successfully used to assess human impacts on water quality. ...

Modification and Application of a Leaf Blower-vac for Field Sampling of Arthropods

Rice fields host a large diversity of arthropods, but investigating their population dynamics and interactions is challenging. Here we describe the modification and application of a leaf blower-vac for suction sampling of arthropod populations in rice. When used in combination with an enclosure, application of this sampling device provides absolute estimates of the populations of arthropods as numbers per standardized sampling area. The sampling efficiency depends critically on the sampling duration. In a mature rice crop, a two-minute sampling in an enclosure of 0.13 m2 yields more than 90% of the arthropod population. The device also allows sampling of arthropods dwelling on the water surface or the soil in rice paddies, but it is not suitable for sampling fast flying insects, such as predatory Odonata or larger hymenopterous parasitoids. The modified blower-vac is simple to construct, and cheaper and easier to handle than traditional suction sampling devices, such as D-vac. The low cost makes the modified blower-vac also accessible to researchers in developing countries.

Assessment of arthropod abundance in crops is critical for investigating population dynamics and species interactions. Here we describe the modification and application of a leaf blower-vac for suction sampling of arthropods in rice.

Modifikasyon ve Arthropodların Saha Örnekleme için bir Yaprak Blower-vac Uygulama

Rice fields host a large diversity of arthropods, but investigating their population dynamics and interactions is challenging. Here we describe the ...

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing. The main portions of this protocol consists of 1) filtration of water samples (water volumes &#8804;4 L or &gt;4 L); (2) extraction of DNA on the filter using a roller shaker placed in a preheated incubator; and (3) purification of DNA using a commercial kit. With the use of this and previously-used protocols, we perform metabarcoding analysis of eDNA taken from a huge aquarium tank (7,500 m3) with known species composition, and show the number of detected species per library from the two protocols as the representative results. This protocol has been developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

We describe a protocol for filtration of water samples with a filter cartridge and extraction of environmental DNA (eDNA) without having to cut open the housing to remove the filter. This protocol is developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

Filtrasyon Su Örnekleri ve Çevre DNA Ekstraksiyon için bir Filtre Kartuşu Kullanımı

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies ...

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of scientific publications address microplastic pollution of the sea surface. The protocol below describes the methodology for sampling, sample preparation, separation and chemical identification of microplastic particles. A manta net fixed on an &#187;A frame&#171; attached to the side of the vessel was used for sampling. Microplastic particles caught in the cod end of the net were separated from samples by visual identification and use of stereomicroscopes. Particles were analyzed for their size using an image analysis program and for their chemical structure using ATR-FTIR and micro FTIR spectroscopy. The described protocol is in line with recommendations for microplastics monitoring published by the Marine Strategy Framework Directive (MSFD) Technical Subgroup on Marine Litter. This written protocol with video guide will support the work of researchers that deal with microplastics monitoring all over the world.

The protocol below describes the methodology for: microplastics sampling on the sea surface, separation of microplastic and chemical identification of particles. This protocol is in line with the recommendations for microplastics monitoring published by the MSFD Technical Subgroup on Marine Litter.

Deniz Yüzey ve Numune Analizi Microplastics Örnekleme Protokolü

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of ...

Extraction of Organochlorine Pesticides from Plastic Pellets and Plastic Type Analysis

Plastic resin pellets, categorized as microplastics (&#8804;5 mm in diameter), are small granules that can be unintentionally released to the environment during manufacturing and transport. Because of their environmental persistence, they are widely distributed in the oceans and on beaches all over the world. They can act as a vector of potentially toxic organic compounds (e.g., polychlorinated biphenyls) and might consequently negatively affect marine organisms. Their possible impacts along the food chain are not yet well understood. In order to assess the hazards associated with the occurrence of plastic pellets in the marine environment, it is necessary to develop methodologies that allow for rapid determination of associated organic contaminant levels. The present protocol describes the different steps required for sampling resin pellets, analyzing adsorbed organochlorine pesticides (OCPs) and identifying the plastic type. The focus is on the extraction of OCPs from plastic pellets by means of a pressurized fluid extractor (PFE) and on the polymer chemical analysis applying Fourier Transform-InfraRed (FT-IR) spectroscopy. The developed methodology focuses on 11 OCPs and related compounds, including dichlorodiphenyltrichloroethane (DDT) and its two main metabolites, lindane and two production isomers, as well as the two biologically active isomers of technical endosulfan. This protocol constitutes a simple and rapid alternative to existing methodology for evaluating the concentration of organic contaminants adsorbed on plastic pieces.

Microplastics act as vector of potentially toxic organic contaminants with unpredictable effects. This protocol describes an alternative methodology for assessing the levels of organochlorine pesticides adsorbed on plastic pellets and identifying the polymer chemical structure. The focus is on pressurized fluid extraction and attenuated total reflectance Fourier transform infrared spectroscopy.

Plastik Peletlerden Organochlorine Pestisitlerin Çıkarılması ve Plastik Tipi Analizi

Plastic resin pellets, categorized as microplastics (&#8804;5 mm in diameter), are small granules that can be unintentionally released to the environment ...

Nanopore DNA Sequencing for Metagenomic Soil Analysis

This article describes the steps for construction of a DNA library from soil, preparation and use of the nanopore flow cell, and analysis of the DNA sequences identified using computer software. Nanopore DNA sequencing is a flexible technique that allows for rapid microbial genome sequencing to identify bacterial and viral species, to characterize bacterial strains, and to detect genetic mutations that confer resistance to antibiotics. The advantages of nanopore sequencing (NS) for life sciences include its low complexity, reduced cost, and rapid real-time sequencing of purified genomic DNA, PCR amplicons, cDNA samples, or RNA. NS is an example of "strand sequencing" which involves sequencing DNA by guiding a single stranded DNA molecule through a nanopore that is inserted into a synthetic polymer membrane. The membrane has an electrical current applied across it, so as the individual bases pass through the nanopore the electrical current is disrupted to varying degrees by the four nucleotide bases. The identification of each nucleotide occurs by detecting the characteristic modulation of the electrical current by the different bases as they pass through the nanopore. The NS system consists of a handheld, USB powered portable device and a disposable flow cell that contains a nanopore array. The portable device plugs into a standard laptop computer that reads and records the DNA sequence using computer software.

Nanopore technology for sequencing biomolecules has wide applications in the life sciences, including identification of pathogens, food safety monitoring, genomic analysis, metagenomic environmental monitoring, and characterization of bacterial antibiotic resistance. In this article, the procedure for metagenomic soil DNA sequencing for species identification using the nanopore sequencing technology is demonstrated.

Nanopore DNA sıralama Metagenomic toprak analizleri için

This article describes the steps for construction of a DNA library from soil, preparation and use of the nanopore flow cell, and analysis of the DNA ...

Collection and Extraction of Occupational Air Samples for Analysis of Fungal DNA

Traditional methods of identifying fungal exposures in occupational environments, such as culture and microscopy-based approaches, have several limitations that have resulted in the exclusion of many species. Advances in the field over the last two decades have led occupational health researchers to turn to molecular-based approaches for identifying fungal hazards. These methods have resulted in the detection of many species within indoor and occupational environments that have not been detected using traditional methods. This protocol details an approach for determining fungal diversity within air samples through genomic DNA extraction, amplification, sequencing, and taxonomic identification of fungal internal transcribed spacer (ITS) regions. ITS sequencing results in the detection of many fungal species that are either not detected or difficult to identify to species level using culture or microscopy. While these methods do not provide quantitative measures of fungal burden, they offer a new approach to hazard identification and can be used to determine overall species richness and diversity within an occupational environment.

Determining the fungal diversity within an environment is a method utilized in occupational health studies to identify health hazards. This protocol describes DNA extraction from occupational air samples for amplification and sequencing of fungal ITS regions. This approach detects many fungal species that can be overlooked by traditional assessment methods.

Toplama ve mesleki hava örnekleri çıkarma mantar DNA analizi için

Traditional methods of identifying fungal exposures in occupational environments, such as culture and microscopy-based approaches, have several ...

Quantifying Plant Soluble Protein and Digestible Carbohydrate Content, Using Corn (Zea mays) As an Exemplar

Elemental data are commonly used to infer plant quality as a resource to herbivores. However, the ubiquity of carbon in biomolecules, the presence of nitrogen-containing plant defensive compounds, and variation in species-specific correlations between nitrogen and plant protein content all limit the accuracy of these inferences. Additionally, research focused on plant and/or herbivore physiology require a level of accuracy that is not achieved using generalized correlations. The methods presented here offer researchers a clear and rapid protocol for directly measuring plant soluble proteins and digestible carbohydrates, the two plant macronutrients most closely tied to animal physiological performance. The protocols combine well characterized colorimetric assays with optimized plant-specific digestion steps to provide precise and reproducible results. Our analyses of different sweet corn tissues show that these assays have the sensitivity to detect variation in plant soluble protein and digestible carbohydrate content across multiple spatial scales. These include between-plant differences across growing regions and plant species or varieties, as well as within-plant differences in tissue type and even positional differences within the same tissue. Combining soluble protein and digestible carbohydrate content with elemental data also has the potential to provide new opportunities in plant biology to connect plant mineral nutrition with plant physiological processes. These analyses also help generate the soluble protein and digestible carbohydrate data needed to study nutritional ecology, plant-herbivore interactions and food-web dynamics, which will in turn enhance physiology and ecological research.

Quantifying Plant Soluble Protein and Digestible Carbohydrate Content, Using Corn Zea mays As an Exemplar

The protocols described herein provide a clear and approachable methodology for measuring soluble protein and digestible (non-structural) carbohydrate content in plant tissues. The ability to quantify these two plant macronutrients has significant implications for advancing the fields of plant physiology, nutritional ecology, plant-herbivore interactions and food-web ecology.

Bitki çözünür Protein ve sindirilebilir karbonhidrat içeriği, Mısır (Zea mays) kullanarak bir suret olarak miktarının

Elemental data are commonly used to infer plant quality as a resource to herbivores. However, the ubiquity of carbon in biomolecules, the presence of ...

Combining Eye-tracking Data with an Analysis of Video Content from Free-viewing a Video of a Walk in an Urban Park Environment

As individuals increasingly live in cities, methods to study their everyday movements and the data that can be collected becomes important and valuable. Eye-tracking informatics are known to connect to a range of feelings, health conditions, mental states and actions. But because vision is the result of constant eye-movements, teasing out what is important from what is noise is complex and data intensive. Furthermore, a significant challenge is controlling for what people look at compared to what is presented to them.
The following presents a methodology for combining and analyzing eye-tracking on a video of a natural and complex scene with a machine learning technique for analyzing the content of the video. In the protocol we focus on analyzing data from filmed videos, how a video can be best used to record participants&#39; eye-tracking data, and importantly how the content of the video can be analyzed and combined with the eye-tracking data. We present a brief summary of the results and a discussion of the potential of the method for further studies in complex environments.

The objective of the protocol is to detail how to collect video data for use in the laboratory; how to record eye-tracking data of participants looking at the data and how to efficiently analyze the content of the videos that they were looking at using a machine learning technique.

Göz izleme verilerini ücretsiz video Içeriğinin analiziyle birleştirme-kentsel park ortamında bir yürüyüşe video görüntüleme

As individuals increasingly live in cities, methods to study their everyday movements and the data that can be collected becomes important and valuable. ...