Our blogs and videos choice: dna fragment analysis

Genome-Wide DNA Methylation Maps in Follicular Lymphoma Cells ...

Methodology/Principal Findings We performed methylation-enriched genome-wide bisulfite sequencing of FL cells and normal CD19+ B-cells using 454 sequencing technology. The methylated DNA fragments were enriched with methyl-binding proteins, treated with bisulfite, and sequenced using the Roche-454 GS FLX sequencer. The total number of bases covered in the human genome was 18.2 and 49.3 million including 726,003 and 1.3 million CpGs in FL and CD19+ B-cells, respectively. 11,971 and 7,882 methylated regions of interest (MRIs) were identified respectively. The genome-wide distribution of these [more...]

Date: 2010-09-30 21:12:52

Blog posts (33) | Videos (8)

Factors That Will Affect Sperm Health_26166

It should be noted that when the typical sperm analysis reveals normal count, morphology and motility this does not mean that sperm DNA fragmentation is not manifest. In other words, unless the SDIA test is specifically run, fragmentation issues will not be revealed. This type of case then may be labeled ‘idiopathic’ infertility. It is our opinion based on clinical experience that ideally, both the man and the women should be treated even if there is no apparent male factor evident. The reason for this is that stress has been shown to reduce sperm count. Going through the tortuous trial [more...]

Date: 2010-10-04 08:50:32

Interview with Arun Kumar: Genographic Postdoc, India - Genographica

I have worked with state of the art DNA technologies like Taqman assays, Fragment Analysis and DNA sequencing and have gained a true global experience working with on the Genographic team. Everyday brings a new learning experience! GP: Wait a minute, for those of us that aren't scientists, what is an assay? Arun Kumar: An assay is a way to genotype a specific mutation within DNA. In other words, it is an experiment that helps to identify a specific nucleotide with Y chromosome or mitochondrial DNA. This mutation will define the ancestral or derived state which will help to identify the [more...]

Date: 2010-10-07 19:07:51

Genetic Fingerprinting of Bacillus thuringiensis Isolates by ...

RAPD-PCR mixture was set up that contained 20-50 ng of genomic DNA, 40 pmol of primer, 1 U of Taq polymerase (Bangalore GENEI.), 200 uM (each) deoxynucleoside triphosphate, 10 mM Tris-Cl (pH 8.3), 50 mM KCl, 3 mM MgCl2 and 1% DMSO. Each reaction mixture was overlaid with 25 ul of mineral oil and amplified with a Perkin-Elmer Cetus DNA Thermal Cycler model TC-1 as follows: (i) Initial denaturation, 1 cycle consisting of 5 min at 94oC and (ii) 35 cycles, with 1 cycle consisting of 1 min at 94oC, 2 min at 36oC, and 3 min at 72oC, followed by a final extension step at 72oC for 10 min. RAPD [more...]

Date: 2009-09-25 16:32:00

Expression of Rod-Derived Cone Viability Factor: Dual Role of CRX ...

However, despite the fact that endogenous NXNL2 expression is photoreceptor-specific within the retina, neither of these DNA sequences nor larger upstream regions demonstrated photoreceptor-specific expression. Further analysis showed that a 79 bp NXNL2 positive regulatory sequence (−393 to 315 bp) combined with a 134 bp inactive minimal NXNL1 promoter fragment (−77 to +57 bp) was able to drive photoreceptor-specific expression, suggesting that the minimal NXNL1 fragment contains latent elements that encode cell-type specificity. Finally, based on bioinformatic analysis that suggested the [more...]

Date: 2010-10-08 17:25:00

Upcoming Next-Gen Sequencing Conferences | RNA-Seq Blog

NeXt-GENeration sequencing platforms create sequence reads of DNA fragments for genome variation studies, RNA for transcriptome studies, DNA-protein interactions for epigenetic studies, and chromosomal DNA of  large genome nucleotide variations for copy number studies.  The X-Gen Congress and Expo is uniquely designed to facilitate the cross fertilization of established and emerging genomic technologies, along with exciting applications. In addition, you will learn why data is the driving force that enables genomic discoveries.  Next-Gen Sequencing Congress April 26th – 27th, 2011 [more...]

Date: 2010-09-29 15:13:14

Bio Saga Blog: 5-Day Hands-on Workshop on Molecular Biotechnology ...

Recombinant DNA Technology: Cutting & pasting of DNA molecules (i.e. restriction digestion, ligation, DNA gel eectrophoresis, and gel extraction.) Bioinfo part: Bioinformatics of DNA database / SequenceAnalysis: Pairwise sequence alignment, Multiple sequence alignment, Pattern search.Tools: BLAST, CLUSTALW/X, CLC Bio Main Workbench Genetic Engineering: Transformation and plasmid purification, cloning and sub-cloning, amplification of DNA fragments by polymerase chain reaction (PCR). Bioinfo part: Designing of PCR primers In-silico cloning Searching for homologous and paralogous [more...]

Date: 2010-09-29 05:41:00

Thrombosis Journal | Full text | Effect of PlA1/A2 glycoprotein ...

Genomic DNA was prepared from peripheral lymphocytes by the salt precipitation method . The PlA1/A2 alleles of the GP IIIa gene were identified on the basis of MspI enzyme site restriction analysis after amplification of a 476 base pairs GP IIIa fragment (sens amorce 5'-ATA-AGC-TTA-GCT-ATT-GGG-AAG-TGG-TAG-GGC-CTG-3', antisens amorce 5'-CTT-CTG-ACT-CAA-GTC-CTA-ACG-3'). The GP IIIa gene was amplified using the polymerase chain reaction (PCR) method. Each amplification product was verified on an agarose gel. Amplification results in a 476 base pairs (bp) fragment. Digestion was obtained with [more...]

Date: 2008-01-15 08:00:00

MTHFR A1298C polymorphism and idiopathic male infertility Singh K ...

The enzyme methylenetetrahydrofolate reductase (MTHFR) catalyses the formation of folate intermediates that are vital for DNA synthesis and methylation reactions. C677T and A1298C variants of MTHFR result in reduced plasma folate and increase the susceptibility to various multifactorial disorders. We have already shown that homozygosity for 677 (C ®T) mutation in the MTHFR gene, is a risk factor for idiopathic male infertility in an Indian population. Aim: Recently, we showed that homozygosity for the 677(C;T) mutation in the MTHFR gene is a risk factor for idiopathic male infertility and [more...]

Date: 2010-10-08 20:51:33

(IUCr) Crystallization and preliminary X-ray analysis of human ...

N61-APE1) since its N-terminal region is known to be highly flexible. Here, we report the crystallization and preliminary X-ray analysis of APE1 in the presence of a DNA fragment containing a damaged base. [more...]

Date: 2010-06-24 07:00:00

Restriction Fragment Length Polymorphism

The analysis of a relatively small number (4-6) of highly polymorphic regions or loci within the human genome, commonly referred to as minisatellites or variable number of tandem repeats (VNTRs), is sufficient to generate DNA profiles [more...]

Date: 2010-08-01 06:59:59

Genomewide DNA methylation analysis reveals novel targets for drug ...

We analyzed genomewide methylation in MCL patients with the HELP (HpaII tiny fragment Enrichment by Ligation–mediated PCR) assay and found significant aberrancy in promoter methylation patterns compared with normal NBCs. [more...]

Date: 2010-08-19 16:02:55

Future prospects of enzyme engineering and enzyme technology

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Date: 2010-09-27 03:01:18

Somaclonal Variation | Cultivation Guide

Analysis of biochemical and chromosomal basis of variation Relating the variation to alteration in DNA Why variation occurs Variation may also arise as a result of more suitable changes due to single gene mutation in culture, which have cells apparently showing no karyological changes. Every possible factor that could result in a genetic change has been accounted for as a cause for soma clonal variation. Recessive mutations are not detected in plant regenerated in vitro from any cell or tissue, but expressed in progeny. This shows that variants are the mutants. Single gene mutation [more...]

Date: 2010-10-12 04:09:39

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

TPM: The Philosophers' Magazine | Ideas of the century: Meaning ...

“An artificial novelty is never as effective as a repetition that manages to suggest a fresh truth.” Marcel Proust. Have the last ten years really seen the emergence of fifty – fifty? – interesting new philosophical ideas? I doubt it. Some currently-fashionable ideas, I suspect, will turn out to be less interesting, or less novel, than they now seem; or both. And anyway, too much emphasis on “artificial novelty”, besides obscuring the fact that there is no neat way to individuate ideas, tempts us to forget that significant philosophical advance usually requires weaving together a [more...]

Date: 2010-09-01 08:05:06

Sosilawati murder: Chemistry Department Needs More Time To Analyse DNA

"We expect that the process can be completed in the near future. However, we cannot provide any time frame when we can hand over the results to the police. "The time taken to complete the DNA profiling depends on the amount of samples available," he said told Bernama. Sosilawati, 47, her driver Kamaruddin Shamsuddin, 44, lawyer Ahmad Kamil Abdul Karim, 32, and CIMB Bank officer Noorhisham Mohammad, 38, went missing on Aug 30 after they went to Banting in Selangor over a land deal. Police found out that the four were killed, their bodies burnt and the ashes thrown into rivers near Ladang [more...]

Date: 2010-09-20 22:10:00


GENOMIC CHARACTRIZATION OF AEROMONAS HYDROPHILA ISOLATES USING RAPD-PCR TECHNIQUE by Mitali Dhiman and S. S. Mishra Central Inland Fisheries Resear Aeromonas hydrophila are  involved in various disease problems in humans and aquatic  animals and are known to be  phenotypically, serologically and genetically quite diverse. Development and use of a sensitive and specific  diagnostic test is warranted for detection and characterization of this pathogen.In the present study,  Fish  and water samples from river Hooghly were streaked onto Aeromonas selective growth medium (Rimler-shotts [more...]

Date: 2010-10-08 20:08:05

Free molecular biology software for Macs | Bioinformatics Blog

Posted on the October 12th, 2010 under Free mac software by bioinformatics-blog 1. Serial Cloner Serial Cloner is fantastic all-in-one workbench; import and manipulate sequences, construct plasmid and restriction site maps, determine %GC and fragment TM, extract and ligate fragments, perform virtual PCR… and lots more, all in one window using a very intuitive graphical interface. 2. 4Peaks 4Peaks is an extremely user friendly DNA sequence chromatogram viewer and editor from the extremely talented guys at Mekentosj. It’s miles better than any of it’s clunky counterparts… try it, [more...]

Date: 2010-10-12 11:08:47

Information About Non Paternity And Non Maternity

All the same, requirements for consent and counselling for DNA testing are unique from each country's laws and policies. DNA testing would be the most state-of-the-art and precise technique to figure out both non-paternity and non-maternity. In figuring out if the presumed parents are genuine biological ones or in determining actual biological mother or father-child bond, subjects undergo parental screening. This sort of practice uses the genetic fingerprinting (or DNA profiling), that is a approach to recognize identity by means of DNA profiles. A paternity test serves as an inherited proof [more...]

Date: 2010-10-09 18:01:01

EveryDay Science » Blog Archive » New roles for new genes ...

Thanks to new technological advances in genomic sequencing , we know that much of the DNA genome is transcribed into RNA but only a small portion of this RNA (transcriptome ) contains sequences that encode for the synthesis of proteins. Thus, although long RNA fragments are non-coding transcriptome most mammals, their cellular functions are still unknown. Scientists have already described the role of small RNAs in gene regulation but we still know very little about the long fragments . The long noncoding RNAs are RNA fragments longer than 100 nucleotides. The authors of this paper have shown [more...]

Date: 2010-10-01 14:35:23

Atrial Natriuretic Peptide Frameshift Mutation in Familial Atrial ...

Atrial Natriuretic Peptide Frameshift Mutation in Familial Atrial Fibrillation Denice M. Hodgson-Zingman, M.D., Margaret L. Karst, B.A., Leonid V. Zingman, M.D., Denise M. Heublein, C.L.T., Dawood Darbar, M.D., Kathleen J. Herron, B.A., Jeffrey D. Ballew, M.S., Mariza de Andrade, Ph.D., John C. Burnett, Jr., M.D., and Timothy M. Olson, M.D.N Engl J Med 2008; 359:158-165July 10, 2008Abstract Atrial fibrillation is a common arrhythmia that is hereditary in a small subgroup of patients. In a family with 11 clinically affected members, we mapped an atrial fibrillation locus to chromosome 1p36-p35 [more...]

Date: 2008-07-09 20:55:26

csirhrdg.res.in | CSIR UGC NET 2011 Life Science Syllabus 2011 ...

Analysis of RNA, DNA and proteins by one and two dimensional gel electrophoresis, Isoelectric focusing gels. Molecular cloning of DNA or RNA fragments in bacterial and eukaryotic systems. Expression of recombinant proteins using bacterial, animal and plant vectors. Isolation of specific nucleic acid sequences Generation of genomic and cDNA libraries in plasmid, phage, cosmid, BAC and YAC vectors. In vitro mutagenesis and deletion techniques, gene knock out in bacterial and eukaryotic organisms. Protein sequencing methods, detection of post translation modification of proteins. DNA [more...]

Date: 2008-06-21 07:00:00

Hisar Practical Training Course Recombinant DNA Techniques ...


Date: 2010-10-05 04:07:03

PLoS ONE: Analysis of Short Tandem Repeats by Parallel DNA Threading

Abstract TopThe majority of studies employing short tandem repeats (STRs) require investigation of several of these genetic markers. As such, we demonstrate the feasibility of the trinucleotide threading (TnT) approach for scalable analysis of STRs. The TnT method represents a parallel amplification alternative that addresses the obstacles associated with multiplex PCR. In this study, analysis of the STR fragments was performed with capillary gel electrophoresis; however, it should be possible to combine our approach with the massive 454 sequencing platform to considerably increase the [more...]

Date: 2009-11-13 08:00:00

PLoS ONE: Evidence of Authentic DNA from Danish Viking Age ...

Linea Melchior1, Toomas Kivisild2, Niels Lynnerup3, Jørgen Dissing1*1 Research Laboratory, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark, 2 Leverhulme Center for Human Evolutionary Studies, The Henry Wellcome Building, University of Cambridge, Cambridge, United Kingdom, 3 Laboratory of Biological Anthropology, Institute of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark Abstract Top Background Given the relative abundance of modern human DNA and the inherent impossibility for incontestable proof of authenticity, results obtained on ancient [more...]

Date: 2008-05-28 07:00:00

FinchTalk: From Reads to Data Sets, Why Next Gen is not like ...

The first widely-used sequencing systems were based on the “Sanger” method. DNA was synthesized in the presence of chain terminating radioactive dideoxy-nucleotides (1). Mixtures of DNA fragments were separated by size using gel electrophoresis and the bases were identified and entered into a computer through manual techniques. Automated DNA sequencing instruments arrived later. These instruments made DNA sequencing thousands of times more efficient by detecting fluorescently labeled fragments and sending the information directly to a computer (2). For the first time, it became possible [more...]

Date: 2009-01-06 19:16:00

Methylation Test May Aid Colon Cancer Diagnosis (CME/CE) | Discuss ...

To develop a more sensitive test for DNA methylation, investigators employed a form of technology known as BEAMing (beads, emulsion, amplification, and magnetics). They performed PCR amplification of individual DNA fragments covalently linked to magnetic beads suspended in water-based nanoparticles immersed in oil droplets. The beads contained a DNA sequence specific for exon 1 of the vimentin gene, which is hypermethylated in colon cancer. Following PCR amplification, the beads were hybridized by means of fluorescent probes specific to the state of methylation and then sorted and analyzed by [more...]

Date: 2010-10-09 11:00:27

Bioinformatics and its applications

Shotgun sequence techniques are also used for sequence analysis of numerous fragments of DNA. Special software is used to see the overlapping of fragments and their assembly. Prediction of Protein Structure:- It is easy to determine the primary structure of proteins in the form of amino acids which are present on the DNA molecule but it is difficult to determine the secondary, tertiary or quaternary structures of proteins. For this purpose either the method of crystallography is used or tools of bioinformatics can also be used to determine the complex protein structures. Genome [more...]

Date: 2010-09-24 07:00:00

Analysis of the relationships between oxidative stress, DNA damage ...

ROC analysis indicated that the frequency distribution of 8OHdG and DNA fragmentation data were significantly different between patients and donors (P < 0.001), permitting the development of thresholds that would allow the accurate diagnosis of DNA damage in the male germ line. CONCLUSION The aetiology of DNA damage in spermatozoa involves a cascade of changes that progress from the induction of oxidative stress and oxidized DNA base adduct formation to DNA fragmentation and cell death. Preparation of spermatozoa on discontinuous density gradients aggravates the problem by stimulating the [more...]

Date: 2010-08-17 07:56:38

Technology Review: A Portable DNA Detector

A new portable DNA analyzer performs real-time analysis of blood samples left at the scene of a crime. Researchers at the University of California, Berkeley, developed the device, which packs microfluidics, electronics, optics, and chemical detection technology into a single briefcase-sized unit. "While previous groups have developed lab-on-a-chip systems, none of them have succeeded in making a completely portable, robust system that can be used at a scene," says team leader Richard Mathies. On-site CSI: After a blood sample is collected from the scene of a crime, this briefcase-sized [more...]

Date: 2008-09-24 04:00:00

How Fingerprinting Helps In DNA Paternity Testing

This form of fingerprinting method is also known as DNA profiling. Using this technique, the individuals are identified on the basis of their unique DNA profiles. This DNA profiling is done by analyzing the VNTR sequences. It stands for variable number tandem repeats. This sequence is found to be different in individuals except in twins. As per the facts mentioned above, the DNA samples of the child will exhibit the similar VNTR loci as that of their parents. This fingerprinting helps in identifying that whether the known father of a child is genuinely his biological dad. In fact, it is [more...]

Date: 2010-08-09 11:41:10

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Complete DNA Sequencing & Synthesis Services,DNA Sequencing Analysis System. Custom DNA Synthesis Get the synthetic advantage. Guaranteed Expression available. AltaVista found 823,000 results . DNA/RNA- Synthesizer – DNA/RNA-Synthesizer DNA/RNA Synthesizers. Oligo-Purifiers. Laboratories. Partners. Company  We are the future of DNA/RNA synthesis. K&A Laborgeraete. Impressum | Druckversion. DNA / RNA Oligonucleotide Synthesizer: MerMade Whether your DNA or RNA synthesizer requirements are a few custom oligos a week or several thousand a day we have a MerMade that will fit your [more...]

Date: 2010-07-11 06:58:31

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