Epigenetics Papers: A Genomic Sequencing Protocol that Yields a ...
Genomic sequencing protocols, which have been developed to ascertain the methylation status of selected regions within genes, utilize the Maxam and Gilbert chemical cleavage reactions [. ... To address these problems, we have developed a genomic sequencing method that provides positive identification and localization of 5-methylcytosine in genomic DNA. The method is based on sodium bisulfite-mediated conversion of cytosine to uracil in single-stranded DNA, followed by PCR [more...]
Date: 2007-03-13 21:09:00
PhD Scholarship for Molecular Ecology and Ecological Epigenetics ...
A (partial) 454 based transcriptome sequence is available, and more than 10.000 SNPs, hundreds of EST-SSRs, and routine protocols for DNA methylation study are available for this species. Recently, an ecological epigenetics line has been started up, which aims to investigate in what way DNA methylation could be important for rapid adaptation to rapidly changing environmental conditions. A central theme in all lines is how inbreeding affects gene expression, and how inbreeding might disrupt epigenetic regulation mechanisms. The institute is well equipped, has a very modern molecular lab, and [more...]
Date: 2010-10-12 12:30:00
PLoS ONE: Whole-Genome Sequencing and Assembly with High ...
In this paper we describe SHRAP (SHort Read Assembly Protocol), a sequencing protocol and assembly methodology designed to assemble a complex mammalian genome with high fidelity using short reads from such technologies. ...... (1990) Automated DNA sequencing of the human HPRT locus. Genomics 6: 593–608. Find this article online; Roach JC, Boysen C, Wang K, Hood L (1995) Pairwise end sequencing: a unified approach to genomic mapping and sequencing. Genomics 26: 345–353. [more...]
Date: 2007-05-30 00:00:00
Improving Molecular Detection of Fungal DNA in Formalin-Fixed ...
assays, followed by sequencing of the DNA fragments ob- tained. The protocols were assessed for time spent in perform- ing the procedure, quality of DNA detection, and efficiency of fungal-DNA detection. MATERIALS AND METHODS [more...]
Date: 2010-08-27 20:37:26
CIENCIASMEDICASNEWS: Recurrent Granulibacter bethesdensis ...
DNA was isolated from human tissue by using the Maxwell 16 Tissue DNA Purification Kit (Promega, Madison, WI, USA) according to the manufacturer’s protocol. DNA concentrations were measured by using a UV spectrophotometer (NanoDrop, Wilmington, DE, USA). The 16S rRNA and methanol dehydrogenase subunit 1 (GeneID YP_744165.1) genes of G. bethesdensis were analyzed by using a PCR and primer sequences 16S-forward: 5'-TCGGGTGGGCACTCTAAAGG-3', 16S-reverse: 5'-GCATCACTGCCTAGCTTCCC-3', MDH-forward: 5'-CCGCAATACGGTCAATTCG-3', and MDH-reverse: 5'-GCCGATCTTCCAGGTTTCTTC-3'. Each reaction mixture [more...]
Date: 2010-09-02 23:42:00
To obtain these structures, a new, efficient solid-phase synthesis protocol was developed as well. To determine the binding affinity and selectivity of these compounds among all possible 4-base pair sequences of DNA, a high throughput (HT), fluorescence intercalator displacement (FID) assay was employed. The FID results indicate that these compounds are good DNA minor groove binders as predicted (more than 50% fluorescence decrease at 10 μM for A/T only sequences); the amidine group improves the binding affinity and selectivity compared to amino acid-benzimidazole conjugates without an [more...]
Date: 2010-08-25 22:40:17
Scientist Solutions - The Sanger DNA Sequencing Method
Would you like to save this topic, event, protocol or job so you can find it again easily? Just click the "Save to My Lab Drawer" link and the item will be saved in the My Lab Drawer section of your bench space. Available to members only. Please log in or register for your free account [more...]
Date: 2009-02-04 18:51:55
iGEM UT-Tokyo（東大）実験ノート - 9/2 purification of DNA by ...
Experimenter Kariyazono, Nakatake, Zen Abstract purification of location sequence(digested by X & P on 9/2) by electrophoresis & extraction of bands from the gel Protocols 1.separating of DNAs through electrophoresis ←direction sample1 sample2 sample3 sample4 nothing(for 3 lanes) sample3′ sample4′ sample1′ 2.Extraction of DNAs Result;consentration of DNA sample1 5.3ng/ul sample2 7.8ng/ul sample3 6.9ng/ul sample4 7.3ng/ul sample1′ 7.8ng/ul sample3′ 5.8ng/ul sample4′ 6.8ng/ul flpe(PCR②) 3.6ng/ul stored in the [more...]
Date: 2010-09-02 04:27:41
(IUCr) Preliminary crystallographic study of the Streptococcus ...
The DNA fragment was cloned into pMCSG7 by ligation-independent cloning according to a published protocol (Stols et al., 2002 [Stols, L., Gu, M., Dieckman, L., ). After verification by DNA sequencing, the resulting plasmid pSrtAS82-Q238 was ..... We are grateful to the staff of the NE-CAT (24-ID) and SER-CAT (22-ID) beamlines of the Advanced Photon Source, Illinois, Chicago for their help with data collection. This work was supported by funding from NIH (SVLN). [more...]
Date: 2010-08-28 07:00:00
Oligonucleotide Synthesis: Methods and Applications (Methods in ...
Among the protocol highlights are a novel two-step process that yields a high purity, less costly, DNA, the synthesis of phosphorothioates using new sulfur transfer agents, the synthesis of LNA, peptide conjugation methods to improve cellular delivery and cell-specific targeting, and triple helix formation. The applications include using molecular beacons to monitor the PCR amplification process, nuclease footprinting to study the sequence-selective binding of small molecules of DNA, nucleic acid libraries, and the use of small interference RNA (siRNA) as an inhibitor of gene [more...]
Date: 2004-07-30 07:00:00
"Polymerase Chain Reaction (PCR)" Biology Animation Library ...
"Polymerase Chain Reaction (PCR)" Biology Animation Library :: Dolan DNA Learning Center: "Polymerase Chain Reaction Polymerase chain reaction (PCR) enables researchers to produce millions of copies of a specific DNA sequence in approximately two hours. This automated process bypasses the need to use bacteria for amplifying DNA. This animation is featured in our 'Spotlight Collection' on Polymerase Chain Reaction, along with video interviews with Kary Mullis, a 3D molecular animation of PCR, and several laboratory [more...]
Date: 2010-08-23 17:54:00
AIR™ DNA Sample Prep Kits Now Available for Illumina-Compatible ...
Bioo Scientific has expanded its line of kits for next generation sequencing sample preparation with the introduction of the AIR Genomic and AIR Paired-End DNA Sequencing Kits, designed for use with the llumina GAII and HiSeq 2000 sequencers. These kits offer flexible, cost-effective, single day sample preparation protocols. It has become obvious that the use of the same preparatory methods to identify and quantify rare sequences and perform large scale comparative evolutionary studies is not ideal and that there are clear advantages for particular applications over others. Bioo [more...]
Date: 2010-10-05 18:12:01
Thrombosis Journal | Full text | Expression of sterol regulatory ...
DNA was extracted from frozen cardiac muscle samples. The SCAP 2386A>G genotyping was based on PCR amplification, restriction enzyme analysis and DNA electrophoresis. The DNA samples were amplified by PCR, using the primers 5'-TTGTGCTGCGCGGCCACCTCA-3' and 5'-AGGAGGAAAGGGCAGCCGCAC-3'. PCR was performed in a volume of 50 μl. Cycle conditions were 94°C for 4 min, then 28 cycles of 94°C for 1 min, 64°C for 1 min and 72°C for 1 min, with a final extension step of 5 min at 72°C in a PTC-225 thermal cycler (MJ research, Massachusetts, USA). 10% DMSO was included in PCR reaction. The [more...]
Date: 2009-02-18 08:00:00
Variants of PCR (1)
The bacteriophage T4 DNA polymerase was also tested shortly after the first reports of PCR. It has a higher fidelity of replication than the Klenow fragment. Since it is also destroyed by heat, it has seen little use since the development of thermostable polymerases. The DNA polymerase from Thermus aquaticus (or Taq), was the first thermostable polymerase used in PCR, and is still the one most commonly used. The enzyme can be isolated from its 'native' bacterial source, or from a cloned gene expressed in E. coli. The Stoffel fragment is produced from a truncated gene for Taq polymerase, [more...]
Date: 2008-09-11 03:56:00
University of California - UC Newsroom | State order alters DNA ...
In July, incoming students received a packet of information about the DNA testing program, a saliva kit, an anonymous bar code to attach to the sample, and a consent form authorizing the campus to test for three gene variants that would reveal aspects of how an individual metabolizes milk, alcohol and vitamin B9 (folic acid). The campus has scheduled a series of lectures, panel discussions and class sessions - which will go on as planned - around the subject of genetic testing. "Of the three million genetic differences that distinguish any two people, we are testing only three common [more...]
Date: 2010-08-12 16:00:00
Quick & Reliable DNA Purification and Sequencing…
BioCel DNA Purification and Sequencing Royston, UK -- An applications bulletin is available from Agilent Automation Solutions that describes an automated system that provides for quick and reliable DNA purification and sequencing. The demand for quick and reliable DNA sample preparation for sequencing has risen dramatically during recent years. The long and complex pipetting protocols needed for DNA preparation have been a challenge for many lab automation systems. Agilent Automation Solutions met this challenge by designing a BioCel system based around the Agilent Vertical Pipetting [more...]
Date: 2010-08-14 14:00:00
JoVE: Electroeluting DNA Fragments (Video Protocol)
Purified DNA fragments are used for different purposes in Molecular Biology and they can be prepared by several procedures. Most of them require a previous electrophoresis of the DNA fragments in order to separate the band of interest. Then, this band is excised out from an agarose or acrylamide gel and purified by using either: binding and elution from glass or silica particles, DEAE-cellulose membranes, "crush and soak method", electroelution or very often expensive commercial purification kits. Thus, selecting a method will depend mostly of what is available in the laboratory. The [more...]
Date: 2010-09-05 22:00:00
ISPUB - Identification Of Lipase – Producing Psychrophilic Yeast ...
Lambda HindIII was used as DNA marker. After the electrophoresis, gel was stained with ethidium bromide and documented by the Gel Doc 2000 (Bio-Rad). Purification of PCR product was done by using QiAquick Gel Extraction Kit. Then, the purified PCR product obtained was sequenced and submitted for BLAST (Basic Local Alignment Search Tools) at NCBI (National Center for Biotechnological Information). Lipase assay by titrationActivity of lipase was assayed by titration using oil emulsion (polyvinyl alcohol: olive oil; 3:1) as substrate (Arima et al., 1972). The assay medium consists of 5ml oil [more...]
Date: 2010-08-25 00:51:13
MyJournals.org - 'Screening of the DNA mismatch repair genes MLH1 ...
Screening of the DNA mismatch repair genes MLH1, MSH2 and MSH6 in a Greek cohort of Lynch syndrome suspected families (BMC Cancer) Background: Germline mutations in the DNA mismatch repair genes predispose to Lynch syndrome, thus conferring a high relative risk of colorectal and endometrial cancer. The MLH1, MSH2 and MSH6 mutational spectrum reported so far involves minor alterations scattered throughout their coding regions as well as large genomic rearrangements. Therefore, a combination of complete sequencing and a specialized technique for the detection of genomic rearrangements should be [more...]
Date: 2010-10-11 16:25:57
Virology Journal | Full text | 3'-coterminal subgenomic RNAs and ...
© 2010 Jarugula et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. AbstractBackground The family Closteroviridae comprises genera with monopartite genomes, Closterovirus and Ampelovirus, and with bipartite and tripartite genomes, Crinivirus. By contrast to closteroviruses in the genera Closterovirus and Crinivirus, much less is known [more...]
Date: 2010-08-03 00:00:00
Research Associate (San Diego) | PCR Jobs
"How To Answer Any Question An Interviewer Could Possibly Throw At You! ... " Click Here! Purpose of the Position:Â Responsible for research and/or development of molecular diagnostic test kits, reagents and procedures in a team environment.Â Performs experiments independently after receiving general direction from supervisor. Makes detailed observations, analyzes data and interprets results.Â Prepares technical reports, summaries, protocols and quantitative analyses.Â Maintains and develops skills in molecular biology and company technology through reading of internal reports [more...]
Date: 2010-10-01 19:07:24
Familial Cancer Associated with a Polymorphism in ARLTS1 — NEJM
George Adrian Calin, M.D., Ph.D., Francesco Trapasso, M.D., Ph.D., Masayoshi Shimizu, B.S., Calin Dan Dumitru, M.D., Ph.D., Sai Yendamuri, M.D., Andrew K. Godwin, Ph.D., Manuela Ferracin, Ph.D., Guido Bernardi, Ph.D., Devjani Chatterjee, Ph.D., Gustavo Baldassarre, M.D., Shashi Rattan, B.S., Hansjuerg Alder, Ph.D., Hideaki Mabuchi, M.D., Takeshi Shiraishi, M.D., Lise Lotte Hansen, Ph.D., Jens Overgaard, M.D., D.M.Sc., Vlad Herlea, M.D., Francesca Romana Mauro, M.D., Guillaume Dighiero, M.D., Benjamin Movsas, M.D., Laura Rassenti, Ph.D., Thomas Kipps, M.D., Ph.D., Raffaele Baffa, M.D., Ph.D., [more...]
Date: 2009-06-01 21:13:36
DNA Science: A First Course, Second Edition
It contains a fully upÂ–toÂ–date collection of 12 rigorously tested and reliable lab experiments in molecular biology, developed at the internationally renowned Dolan DNA Learning Center of Cold Spring Harbor Laboratory, which culminate in the construction and cloning of a recombinant DNA molecule. Proven through more than 10 yearsÂ’ of teaching at research and nonresearch colleges and universities, junior colleges, community colleges, and advanced biology programs in high school, this book has been successfully integrated into introductory biology, general biology, genetics, [more...]
Date: 2010-05-13 09:15:50
DSN normalisation clean up - SEQanswers
Invalid Thread specified. If you followed a valid link, please notify the [more...]
Date: 2010-10-07 12:22:24
Quick and reliable DNA purification and sequencing
Keep up with the latest research, events and funding news. Add the observer, dissemination and funding widget to your website or blog The demand for quick and reliable DNA sample preparation for sequencing has risen dramatically during recent years. The long and complex pipetting protocols needed for DNA preparation have been a challenge for many lab automation systems. Agilent Automation Solutions met this challenge by designing a BioCel system based around the Agilent Vertical Pipetting Station, a high-speed precision pipettor. With its versatile shelf configuration options, the [more...]
Date: 2010-07-28 13:03:49
Engineering Mini project: DNA COMPUTERS
After seven days of intensive laboratory work, Adleman's test-tube contained the answer to the problem, subsequently visible as a series of dark bands on a DNA sequencing gel. On the face of it, it might hardly seem worth the bother, especially as Adleman already knew the answer before he started the experiment. But this was much more than a curious laboratory stunt. During the initial 'linking-up' stage of the process, Adleman's test-tube computer effectively performed an astonishing 10^14 calculations. And it did so with the consumption of only a tiny amount of energy, and in a tiny [more...]
Date: 2010-10-12 10:10:00
genomic DNA PCR protocols and methods
Research news, bioproducts, protocols, reagents, forums genomic DNA PCR > Can someone forward me a general protocol for doing PCR using genomic > DNA as the template? I seem to recall needing about 100 ng of DNA, but > I forget stuff like how much Taq to use, concentration of dNTP's, and > concentration of primers. General protocol for PCR Each person uses a slightly different ratio of reagents. For DNA amplicons up to 500 bp, use 25 uL reaction volumes as follows: On ice add to thin-walled pcr tubes 0.125 uL Taq polymerase (1.25 U, Gibco) 2.5 uL of 10 x PCR buffer minus Mg [more...]
Date: 2004-12-27 00:00:00
Next Generation Sequencing » Tweaking the 454 sequencing protocol ...
In the new issue of Biotechniques, a paper by Maricic and Pääbo (login may be required) describes how a change to the standard 454 sequencing protocol can dramatically increase the size of the library of DNA that goes into the actual sequencing reaction. The trick used is to replace the last step in the library preparation where single stranded DNA is released from streptavidin beads. The original 454 protocol employes NaOH denaturation for this step, but the researchers found that this procedure results in a loss of over 99% of the DNA. However, When they replaced the NaOH denaturation [more...]
Date: 2009-01-07 20:04:53