Nucleic Acids Extraction From Formalin Fixed And Paraffin Embedded Tissues

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Nucleic Acids Extraction from Formalin-Fixed and Paraffin-Embedded Tissues

Author : Gisele R. Gouveia
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (115 download)

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Book Synopsis Nucleic Acids Extraction from Formalin-Fixed and Paraffin-Embedded Tissues by : Gisele R. Gouveia

Download or read book Nucleic Acids Extraction from Formalin-Fixed and Paraffin-Embedded Tissues written by Gisele R. Gouveia and published by . This book was released on 2016 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Formalin-fixed paraffin-embedded (FFPE) tissues are an important sample source for retrospective studies. Despite its ability to preserve proteins and cell morphology, formalin hinders molecular biology tests since it fragments and chemically modifies nucleic acids, especially RNA. Although several studies describe techniques that allow extracting nucleic acids from FFPE tissues, so far there is no consensus in the literature about the best protocol to be used in this type of material. Thus, the current chapter aims to describe the factors affecting the FFPE tissue nucleic acid extracting process, compare the available protocols and to describe the modifications developed by our group in some protocols. Such modifications enable nucleic acids obtainment in satisfactory quantity and quality for molecular biology studies.

Nucleic Acids

Author : Marcelo Larramendy
Publisher : BoD – Books on Demand
ISBN 13 : 9535122649
Total Pages : 222 pages
Book Rating : 4.5/5 (351 download)

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Book Synopsis Nucleic Acids by : Marcelo Larramendy

Download or read book Nucleic Acids written by Marcelo Larramendy and published by BoD – Books on Demand. This book was released on 2016-03-16 with total page 222 pages. Available in PDF, EPUB and Kindle. Book excerpt: This edited book, "Nucleic Acids - From Basic Aspects to Laboratory Tools", contains a series of chapters that highlight the development and status of the various aspects of the nucleic acids related to DNA chemistry and biology and the molecular application of these small DNA molecules and related synthetic analogues within biological systems. Furthermore, it is hoped that the information in the present book will be of value to those directly engaged in the handling and use of nucleic acids, and that this book will continue to meet the expectations and needs of all who are interested in the different fascinating aspects of molecular biology.

Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collections

Author : National Research Council
Publisher : National Academies Press
ISBN 13 : 0309180821
Total Pages : 64 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collections by : National Research Council

Download or read book Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collections written by National Research Council and published by National Academies Press. This book was released on 2006-09-26 with total page 64 pages. Available in PDF, EPUB and Kindle. Book excerpt: Museums catalogue our knowledge of the Earth's biodiversity, and their collections represent many decades of work by experts. Access to DNA sequence information in archival specimens would greatly extend knowledge of the genetic relationships within our biosphere. However, molecular genetic analysis of museum specimens has been slowed by the usual practice of fixation and storage of samples in formalin. Formalin is an environmental toxin and induces genetic and chromosomal alterations to the samples. Few of the many attempts to obtain and sequence DNA from formalin-fixed specimens stored in aqueous formalin or ethanol have been successful. All of the protocols are slow, difficult, and often expensive, and few produce DNA fragments longer than 500 base pairs. Path to Effective Recovering of DNA from Formalin-Fixed Biological Samples in Natural History Collections examines past attempts on DNA recovery from formalin-preserved biological specimens and discusses the research needed to advance the development of similar but more efficient and cost-effective protocols.

Handbook of Nucleic Acid Purification

Author : Dongyou Liu
Publisher : CRC Press
ISBN 13 : 1420070975
Total Pages : 572 pages
Book Rating : 4.4/5 (2 download)

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Book Synopsis Handbook of Nucleic Acid Purification by : Dongyou Liu

Download or read book Handbook of Nucleic Acid Purification written by Dongyou Liu and published by CRC Press. This book was released on 2009-01-14 with total page 572 pages. Available in PDF, EPUB and Kindle. Book excerpt: An Indispensable Roadmap for Nucleic Acid Preparation Although Friedrich Miescher described the first isolation of nucleic acid in 1869, it was not until 1953 that James Watson and Francis Crick successfully deciphered the structural basis of DNA duplex. Needless to say, in the years since, enormous advances have been made in the study of nucleic a

Formalin-Fixed Paraffin-Embedded Tissues

Author : Fahd Al-Mulla
Publisher : Humana Press
ISBN 13 : 9781493961719
Total Pages : 312 pages
Book Rating : 4.9/5 (617 download)

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Book Synopsis Formalin-Fixed Paraffin-Embedded Tissues by : Fahd Al-Mulla

Download or read book Formalin-Fixed Paraffin-Embedded Tissues written by Fahd Al-Mulla and published by Humana Press. This book was released on 2016-08-23 with total page 312 pages. Available in PDF, EPUB and Kindle. Book excerpt: Presenting an area of research that intersects with and integrates diverse disciplines, including genomics, epigenetics, proteomics, and cellular biology, among others, Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols collects contributions from expert researchers in order to provide practical guidelines to this complex study. Compiled in order to provide researchers with up-to-date methodological information pertaining to the utilization of genomic, transcriptomic, and proteomic data in diagnosis, prognosis, and tailored therapy, the ultimate aim of this volume is to decipher diseases at a molecular level. Divided into multiple convenient chapters, this detailed book covers various techniques to construct and utilize tissue arrays, it also provides detailed protocols in immunohistochemistry, immunofluorescence, fluorescent and chromogenic in situ hybridization, and ultimately introduces protocols for FFPET microdissection and nucleic acids extraction for their utilization in advanced techniques such as microarray CGH, DNA methylation and pyrosequencing. The volume also discusses FFPET research from an ethical standpoint and concludes with a chapter on novel tissue fixative. Written in the highly successful Methods in Molecular BiologyTM series format, chapters contain introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and accessible, Formalin-Fixed Paraffin-Embedded Tissues: Methods and Protocols serves as a practical guide for scientists of all backgrounds and aims to convey the appropriate sense of fascination associated with this vital field of research.

Guidelines for Molecular Analysis in Archive Tissues

Author : Giorgio Stanta
Publisher : Springer Science & Business Media
ISBN 13 : 3642178901
Total Pages : 301 pages
Book Rating : 4.6/5 (421 download)

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Book Synopsis Guidelines for Molecular Analysis in Archive Tissues by : Giorgio Stanta

Download or read book Guidelines for Molecular Analysis in Archive Tissues written by Giorgio Stanta and published by Springer Science & Business Media. This book was released on 2011-06-06 with total page 301 pages. Available in PDF, EPUB and Kindle. Book excerpt: A huge amount of fixed and paraffin-embedded tissue is stored in every hospital. This is very precious material that can be used for translational research and for diagnostics. The molecular methods employed for analysis of these tissues are similar to the usual molecular biology and proteomics methods, but reliable results can be obtained only if specific steps are followed with great care. This book provides detailed and precise guidelines for molecular analysis of archive tissues and will serve as an invaluable aid for researchers and pathologists involved in translational research and diagnostics. Clear notes and explanations are included to simplify use of the protocols for the less experienced. The authors are a group of acknowledged experts who have developed the described methods and validated them within the European project "Archive Tissues: Improving Molecular Medicine Research and Clinical Practice - IMPACTS", which has involved 21 leading institutions in 11 countries.

General Methods in Biomarker Research and their Applications

Author : Victor R. Preedy
Publisher : Springer
ISBN 13 : 9789400776951
Total Pages : 0 pages
Book Rating : 4.7/5 (769 download)

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Book Synopsis General Methods in Biomarker Research and their Applications by : Victor R. Preedy

Download or read book General Methods in Biomarker Research and their Applications written by Victor R. Preedy and published by Springer. This book was released on 2015-08-14 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: In the past decade there has been a major sea change in the way disease is diagnosed and investigated due to the advent of high throughput technologies, such as microarrays, lab on a chip, proteomics, genomics, lipomics, metabolomics etc. These advances have enabled the discovery of new and novel markers of disease relating to autoimmune disorders, cancers, endocrine diseases, genetic disorders, sensory damage, intestinal diseases etc. In many instances these developments have gone hand in hand with the discovery of biomarkers elucidated via traditional or conventional methods, such as histopathology or clinical biochemistry. Together with microprocessor-based data analysis, advanced statistics and bioinformatics these markers have been used to identify individuals with active disease or pathology as well as those who are refractory or have distinguishing pathologies. New analytical methods that have been used to identify markers of disease and is suggested that there may be as many as 40 different platforms. Unfortunately techniques and methods have not been readily transferable to other disease states and sometimes diagnosis still relies on single analytes rather than a cohort of markers. There is thus a demand for a comprehensive and focused evidenced-based text and scientific literature that addresses these issues. Hence the formulation of Biomarkers in Disease. The series covers a wide number of areas including for example, nutrition, cancer, endocrinology, cardiology, addictions, immunology, birth defects, genetics and so on. The chapters are written by national or international experts and specialists.

Detection of Viral RNA From Paraffin-Embedded Tissues After Prolonged Formalin Fixation

Author :
Publisher :
ISBN 13 :
Total Pages : 5 pages
Book Rating : 4.:/5 (574 download)

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Book Synopsis Detection of Viral RNA From Paraffin-Embedded Tissues After Prolonged Formalin Fixation by :

Download or read book Detection of Viral RNA From Paraffin-Embedded Tissues After Prolonged Formalin Fixation written by and published by . This book was released on 2009 with total page 5 pages. Available in PDF, EPUB and Kindle. Book excerpt: Isolating amplifiable RNA from formalin-fixed, paraffin-embedded (FFPE) tissues is more difficult than isolating DNA because the potential for RNA degradation by RNases, chemical modification of the RNA by addition of methylol groups ( -CH2OH), and cross-linking of nucleic acids and proteins during the fixation process. In our laboratories, these difficulties are increased when extended fixation times of 3 to 4 weeks are required for tissues infected with BSL-3 or -4 agents. Four commercially available kits with different nucleic acid isolation chemistries were evaluated for their ability to isolate RNA from FFPE West Nile virus-infected tissues. The quality of the extracted RNA was determined by using a fluorogenic 5' nuclease TaqManTM) PCR assay. A modification of the Paraffin Block RNA Isolation Kit that included an overnight proteinase K digestion was necessary to obtain amplifiable RNA from tissues formalin-fixed for 21 days. Extracting TaqManTM amplifiable RNA from Marburg- and Ebola virus-infected tissues, formalin-fixed for at least 30 days, further tested the modified extraction method. This improved extraction procedure for obtaining amplifiable RNA combined with the more sensitive and specific fluorogenic probe-based PCR assays will now permit retrospective and prospective studies on FFPE tissues infected with BSL-3 and -4 pathogens.

Nucleic Acids

Author : Botho Bowien
Publisher : American Scientific Publishers
ISBN 13 :
Total Pages : 208 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Nucleic Acids by : Botho Bowien

Download or read book Nucleic Acids written by Botho Bowien and published by American Scientific Publishers. This book was released on 2003 with total page 208 pages. Available in PDF, EPUB and Kindle. Book excerpt: Although it's stated only on the back cover, this book seems to initiate a new series (from this new publisher) titled "Genome Science and Nucleic Acids." Ten review chapters address the stabilization of nucleic acids prior to isolation; isolation of genomic DNA, and of plasmid DNA; purification of plasmid DNA, and of viral nucleic acids; isolation of RNA; DNA cleanup from gels, PCR, sequencing, and others; nucleic acids of pathogens from biological samples for real-time PCR analysis; extraction of DNA from paraffin embedded bone marrow trephine biopsies; and DNA and forensic applications. Nineteen of the 20 contributors to the present work are based in Germany (one is in the UK); their work was brought together by editors Bowien (microbiology and genetics, U. of Gottingen) and Durre (microbiology and biotechnology, U. of Ulm). Annotation (c)2003 Book News, Inc., Portland, OR (booknews.com).

Efficacy of a Multimolecular Extraction from Formalin-fixed Paraffin-embedded Tissue

Author : Nancy Cummings
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (128 download)

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Book Synopsis Efficacy of a Multimolecular Extraction from Formalin-fixed Paraffin-embedded Tissue by : Nancy Cummings

Download or read book Efficacy of a Multimolecular Extraction from Formalin-fixed Paraffin-embedded Tissue written by Nancy Cummings and published by . This book was released on 2021 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: As the genetic basis and gene expression components are being discovered for an increasing number of diseases and disorders there is a rising interest in using multiomic approaches to better understand these conditions. The large tissue banks of formalin fixed (FF) and formalin-fixed paraffin-embedded (FFPE) tissues present a unique opportunity to study rare conditions and difficult to sample organs such as brains. Current molecular studies on FFPE look at single molecule extractions, which provide only a partial picture of disease mechanisms. This study compared the efficacy of TRIzol®, a tri-molecule extraction method, to that of the traditional single molecule methods for DNA and RNA extraction in frozen, FF, and FFPE brain tissue using animal models. Optimization of this would allow for DNA and RNA to be obtained from the same sample providing a more accurate and comprehensive picture of the mechanism of disease or disorder. The quantity and purity of the DNA and RNA extracted from frozen, FF, and FFPE brain samples (aged for 3 years) were determined by spectrophotometry. Quality was determined by real-time PCR (qPCR) and reverse transcriptase qPCR (RT-qPCR) using beta-2-microglobulin (98bp) and glyceraldehyde 3-phosphate dehydrogenase (227bp) targets. Our study found no significant difference in efficacy between TRIzol® and the traditional methods employed in the literature, indicating that TRIzol® is comparable to the currently used, single molecule extractions when applied to FF and FFPE brain tissue. This finding requires further investigation with a larger set of samples, but if supported may help maximize the amount of information obtained from rare samples as multiple data sets would be obtained from a single sample. Unexpectedly, this study also observed a higher rate of success in extracting high quality RNA compared to DNA regardless of extraction method. Due to the low number of samples, the statistical significance of this observation could not be established however we feel that it warrants further investigation.

Antigen Retrieval Techniques

Author : Shan-Rong Shi
Publisher : Eaton Publishing Company/Biotechniques Books
ISBN 13 :
Total Pages : 388 pages
Book Rating : 4.3/5 (91 download)

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Book Synopsis Antigen Retrieval Techniques by : Shan-Rong Shi

Download or read book Antigen Retrieval Techniques written by Shan-Rong Shi and published by Eaton Publishing Company/Biotechniques Books. This book was released on 2000 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt:

PCR Protocols

Author : John M. S. Bartlett
Publisher : Springer Science & Business Media
ISBN 13 : 1592593844
Total Pages : 1083 pages
Book Rating : 4.5/5 (925 download)

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Book Synopsis PCR Protocols by : John M. S. Bartlett

Download or read book PCR Protocols written by John M. S. Bartlett and published by Springer Science & Business Media. This book was released on 2008-02-03 with total page 1083 pages. Available in PDF, EPUB and Kindle. Book excerpt: In this new edition, the editors have thoroughly updated and dramatically expanded the number of protocols to take advantage of the newest technologies used in all branches of research and clinical medicine today. These proven methods include real time PCR, SNP analysis, nested PCR, direct PCR, and long range PCR. Among the highlights are chapters on genome profiling by SAGE, differential display and chip technologies, the amplification of whole genome DNA by random degenerate oligonucleotide PCR, and the refinement of PCR methods for the analysis of fragmented DNA from fixed tissues. Each fully tested protocol is described in step-by-step detail by an established expert in the field and includes a background introduction outlining the principle behind the technique, equipment and reagent lists, tips on trouble shooting and avoiding known pitfalls, and, where needed, a discussion of the interpretation and use of results.

Nucleic Acid Extraction and Detection Across Two-dimensional Tissue Samples

Author : Michael Daniel Armani
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (722 download)

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Book Synopsis Nucleic Acid Extraction and Detection Across Two-dimensional Tissue Samples by : Michael Daniel Armani

Download or read book Nucleic Acid Extraction and Detection Across Two-dimensional Tissue Samples written by Michael Daniel Armani and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt:

Bioinformatics Methods and Protocols

Author : Stephen Misener
Publisher : Springer Science & Business Media
ISBN 13 : 1592591922
Total Pages : 495 pages
Book Rating : 4.5/5 (925 download)

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Book Synopsis Bioinformatics Methods and Protocols by : Stephen Misener

Download or read book Bioinformatics Methods and Protocols written by Stephen Misener and published by Springer Science & Business Media. This book was released on 2008-02-02 with total page 495 pages. Available in PDF, EPUB and Kindle. Book excerpt: Computers have become an essential component of modern biology. They help to manage the vast and increasing amount of biological data and continue to play an integral role in the discovery of new biological relationships. This in silico approach to biology has helped to reshape the modern biological sciences. With the biological revolution now among us, it is imperative that each scientist develop and hone today’s bioinformatics skills, if only at a rudimentary level. Bioinformatics Methods and Protocols was conceived as part of the Methods in Molecular Biology series to meet this challenge and to provide the experienced user with useful tips and an up-to-date overview of current developments. It builds upon the foundation that was provided in the two-volume set published in 1994 entitled Computer Analysis of Sequence Data. We divided Bioinformatics Methods and Protocols into five parts, including a thorough survey of the basic sequence analysis software packages that are available at most institutions, as well as the design and implemen- tion of an essential introductory Bioinformatics course. In addition, we included sections describing specialized noncommercial software, databases, and other resources available as part of the World Wide Web and a stimul- ing discussion of some of the computational challenges biologists now face and likely future solutions.

Epigenetics Protocols

Author : Trygve O. Tollefsbol
Publisher : Humana Press
ISBN 13 : 9781588293367
Total Pages : 304 pages
Book Rating : 4.2/5 (933 download)

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Book Synopsis Epigenetics Protocols by : Trygve O. Tollefsbol

Download or read book Epigenetics Protocols written by Trygve O. Tollefsbol and published by Humana Press. This book was released on 2004-07-23 with total page 304 pages. Available in PDF, EPUB and Kindle. Book excerpt: The field of epigenetics has grown exponentially in the past decade, and a steady flow of exciting discoveries in this area has served to move it to the forefront of molecular biology. Although epigenetics may previously have been considered a peripheral science, recent advances have shown considerable progress in unraveling the many mysteries of nontraditional genetic processes. Given the fast pace of epigenetic discoveries and the groundbreaking nature of these developments, a thorough treatment of the methods in the area seems timely and appropriate and is the goal of Epigenetics Protocols. The scope of epigenetics is vast, and an exhaustive analysis of all of the techniques employed by investigators would be unrealistic. However, this TM volume of Methods in Molecular Biology covers three main areas that should be of greatest interest to epigenetics investigators: (1) techniques related to analysis of chromatin remodeling, such as histone acetylation and methylation; (2) methods in newly developed and especially promising areas of epigenetics such as telomere position effects, quantitative epigenetics, and ADP ribosylation; and (3) an updated analysis of techniques involving DNA methylation and its role in the modification, as well as the maintenance, of chromatin structure.

Ancient DNA

Author : Beth Alison Shapiro
Publisher :
ISBN 13 : 9781617795169
Total Pages : 247 pages
Book Rating : 4.7/5 (951 download)

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Book Synopsis Ancient DNA by : Beth Alison Shapiro

Download or read book Ancient DNA written by Beth Alison Shapiro and published by . This book was released on 2012-01-01 with total page 247 pages. Available in PDF, EPUB and Kindle. Book excerpt: Ancient DNA presents an overview of the many of the protocols commonly used to study ancient DNA. These include laboratory instructions, extraction protocols, laboratory techniques, and suggestions for appropriate analytical approaches to make sense of the sequences obtained.

Molecular Cytopathology

Author : Bin Yang
Publisher : Springer
ISBN 13 : 331930741X
Total Pages : 297 pages
Book Rating : 4.3/5 (193 download)

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Book Synopsis Molecular Cytopathology by : Bin Yang

Download or read book Molecular Cytopathology written by Bin Yang and published by Springer. This book was released on 2016-08-12 with total page 297 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book reviews the current applications of molecular tools in cytopathology and provides a concise handbook for those who provide care in this era of personalized medicine. Specifically, the text provides a comprehensive and concise review of the emerging molecular tests available clinically in different subspecialities of diagnostic pathology. It reviews the current data of molecular testing already applied in cytopathology, discusses some of the biomarkers with potential utility in cytopathology in the near future and reviews the technical challenges in applying and validating molecular tools in liquid-based cytologic materials. Molecular Cytopathology will serve as a valuable resource for cytopathologists, cytotechnologists, pathology trainees, and clinicians with an interest in molecular applications in cytopathology.