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+{
+  "titles": [
+    "2008 - Gene Expression Profiling.pdf",
+    "2017 - Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug.pdf",
+    "2008 - Gene Expression Profiling.pdf",
+    "2016 - Sequence Capture and Phylogenetic Utility.pdf",
+    "2008 - Gene Expression Profiling.pdf",
+    "2008 - Gene Expression Profiling.pdf",
+    "2016 - Sequence Capture and Phylogenetic Utility.pdf",
+    "2016 - Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes.pdf",
+    "2016 - Sequence Capture and Phylogenetic Utility.pdf",
+    "2004 - Linking nutrition to genomics.pdf"
+  ],
+  "extraction_id": [
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+  "contexts": [
+    "by shearing. A flow diagram summarizing the extraction of DNA is given in  Fig. 1.2. The above-described procedure is suitable for total cellular DNA.  If the DNA from a specific organelle or viral particle is needed, it is best to  isolate the organelle or virus before extracting its DNA, because the recovery  of a particular type of DNA from a mixture is usually rather difficult. Where  a high degree of purity is required, DNA may be subjected to density gradient",
+    "2017 Nature America, Inc., part of Springer Nature. All rights reserved. nature medicine doi:10.1038/nm.434564. Salonen, A. et al.  Comparative analysis of fecal DNA extraction methods with  phylogenetic microarray: effective recovery of bacterial and archaeal DNA using  mechanical cell lysis. J. Microbiol. Methods  81, 127134 (2010). 65. Murphy, N.R. & Hellwig, R.J. Improved nucleic acid organic extraction through use  of a unique gel barrier material. Biotechniques  21, 934936, 938939 (1996).",
+    "is the suitable preparation of the DNA template with a high level of purity  and free from contaminating DNA (14). Different procedures are used for  DNA extraction with specific protocol for mammals, plants, fungi, bacteria,  protozoan, helminthes, insects, and others. In specific cases, such as insects,  contamination can be reduced by hypochlorite treatment before extraction  to avoid contact with foreign DNA (15). DNA preparation includes the",
+    "this method is well suited for larger scale investigations of museum insect phylogenomics. We did extract DNA from relatively large insects, where one leg yields more tissue than is availablefrom crushing the entire body of most ants, for example. Thus, it remains now to be tested whether sufficient input DNA can also be obtained from smaller dried insect specimens. None-",
+    "usually requires that it be isolated and purified to a certain degree. DNA is  usually recovered from cells by methods that include cell rupture but that  prevent the DNA from fragmenting by mechanical shearing. This is gener- ally undertaken in the presence of EDTA, which chelates the magnesium ions  needed as cofactors for enzymes that degrade DNA, termed DNase. Ideally,  cell walls, if present, should be digested enzymatically (e.g., lysozyme in the",
+    "DNA and then using a gene probe representing a protein or enzyme from  one of the organisms. In this way, it is possible to search for related genes in  different species. This technique is generally termed Zoo blotting. A similar  process of nucleic acid blotting can be used to transfer RNA separated by gel  electrophoresis onto membranes similar to that used in Southern blotting. This  process, termed Northern blotting , allows the identification of specific mRNA",
+    "6. Staats M, Erkens RH, van de Vossenberg B, Wieringa JJ, Kraaijeveld K, Stielow B, et al. Genomic trea- sure troves: complete genome sequencing of herbarium and insect museum specimens. PLOS ONE. 2013; 8:e69189. doi: 10.1371/journal.pone.0069189 PMID: 23922691 7. Burrell AS, Disotell TR, Bergey CM. The use of museum specimens with high-throughput DNA sequencers. J Hum Evol. 2015; 79:35 44. doi: 10.1016/j.jhevol.2014.10.015 PMID: 25532801",
+    "were extracted from unthawed, frozen faecal subsamples (150 mg) after pretreatment of the weighed subsamples with 1.5 ml RNAlater ICE (LifeTechnologies) overnight.The faeces-RNAlater ICE mixture was homogenized by bead-beating, as previously described 53. Differential centrifugation and extraction using the All-In-One kit (Norgen Biotek) to recover DNA and proteins were carried out as previously described53. DNA fractions were supplemented with DNA extracted from 200 mg",
+    "DNA was then extracted destructively by grinding the frozen tissue with a sterile pestle, using aDNeasy Blood and TissueKit (Qiagen, Valencia, CA, USA) and following the manufacturer s protocol, except the DNA was eluted in 130 L ddH 2O instead of the supplied buffer. We ran 10L of each extract for 60 min at 100 volt on 1.5% agarose SB (sodium borate) gels, to estimate size of the genomic DNA. From a pool of 60 successful extractions (12 extractions produced no quantifiable DNA), we",
+    "Extracting biological information"
+  ],
+  "answer": "To extract DNA from flora or fauna, one can follow these general steps:  1. **Cell Rupture**: The cells need to be ruptured to release the DNA. This can be done using mechanical methods such as grinding the tissue with a sterile pestle [9] or using bead-beating for homogenization [8]. Enzymatic digestion of cell walls, if present, can also be used (e.g., lysozyme) [5].  2. **Preventing DNA Degradation**: During the extraction process, it is crucial to prevent DNA from fragmenting. This can be achieved by using EDTA, which chelates magnesium ions necessary for DNase enzymes that degrade DNA [5].  3. **Purification**: The DNA needs to be purified to remove contaminants. This can involve differential centrifugation and using specific kits designed for DNA extraction, such as the All-In-One kit [8] or the DNeasy Blood and Tissue Kit [9].  4. **Specific Protocols for Different Organisms**: Different organisms may require specific protocols. For example, insects may need hypochlorite treatment before extraction to reduce contamination [3].  5. **High Purity Requirements**: If a high degree of purity is required, DNA can be subjected to density gradient centrifugation [1].  By following these steps, one can effectively extract DNA from various types of flora and fauna.",
+  "question": "How would one extract the DNA, from say, flora or fauna?"
+}
+\ No newline at end of file