Sandwalk: Nobel Laureate: Walter Gilbert
The Nobel Prize in Chemistry 1980. "for their contributions concerning the determination of base sequences in nucleic acids" Walter Gilbert (1932 - ) was awarded the Nobel Prize for developing a chemical method of sequencing DNA (with Allan Maxam). The method relied on chemical reactions that cleaved DNA at specific residues. By carrying out partial reactions where only one cleavage occurred in each DNA strand, it was possible to separate the cleavage products on an acrylamide gel and determine the position of each residue by the length of the fragment. The chemical sequencing strategy has [more...]
Date: 2008-12-10 14:35:00
Al Fin: A Hint of Epigenetics
We are learning that the genetic code is only the short, first chapter in a very long book. The non-genetic "code" -- the non-coding DNA and RNA -- has a logic all its own. We are just beginning to decrypt the obscure cipher. The possibilities for the transformation of life as we know it seem just as grandiose as were the hopes of the early promoters of the human genome enterprise. Only this time, we are working at a deeper level of sophistication. How many more levels will we need to descend before we reach the promised land of genetic medicine? ... some 95 or 98 percent of human DNA was [more...]
Date: 2010-10-13 15:07:00
CIENCIASMEDICASNEWS: Researchers report MALAT1 gene regulates pre ...
Researchers report this month that MALAT1, a long non-coding RNA that is implicated in certain cancers, regulates pre-mRNA splicing - a critical step in the earliest stage of protein production. Their study appears in the journal Molecular Cell. Nearly 5 percent of the human genome codes for proteins, and scientists are only beginning to understand the role of the rest of the "non-coding" genome. Among the least studied non-coding genes - which are transcribed from DNA to RNA but generally are not translated into proteins - are the long non-coding RNAs (lncRNAs). Before the human genome was [more...]
Date: 2010-10-01 22:18:00
Dienekes' Anthropology Blog: mtDNA of Yemeni and Ethiopian Jews
The way I see it, only a large-scale study of all global Jewish populations may uncover verified ancient Jewish lineages for both Y-chromosomes and mtDNA. The recent studies on Jews have uncovered several genetic sub-clusters of Jews, and only lineages that occur in 2 or more of these clusters, and preferably geographically separated ones have a strong claim of representing original Jewish lineages. There is a limit on what can be uncovered about the past from the study of living populations. American Journal of Physical Anthropology doi: 10.1002/ajpa.21360 Mitochondrial DNA reveals distinct [more...]
Date: 2010-07-14 18:00:00
IVF News - Sperm linked to ART-related genetic disorders
A process called DNA methylation is critical to imprinting. A team led by Dr Takahiro Arima from Tohoku University examined DNA methylation in 78 six to nine-week-old embryos and fetuses conceived using ART, and 38 conceived without ART. They also examined the father's sperm and DNA. In seven of 17 cases where there was abnormal DNA methylation in the ART sample, identical alterations were present in the father's sperm. The abnormal DNA methylation in the sperm was associated with variations in a gene coding for DNMT3L - a key enzyme in DNA methylation associated with abnormal imprinting and [more...]
Date: 2009-12-07 08:00:00
Evolution News & Views: "Junk" DNA: Darwinism's Last Stand?
In 1980, Francis Crick and Leslie Orgel argued in Nature that "much DNA in higher organisms is little better than junk." The spread of junk DNA in the course of evolution "can be compared to the spread of a not-too-harmful parasite within its host." Since it is unlikely that such DNA has a function, "it would be folly in such cases to hunt obsessively for one." In a companion article, W. Ford Doolittle and Carmen Sapienza similarly argued that many organisms contain "DNAs whose only 'function' is survival within genomes," and that "the search for other explanations may prove, if not [more...]
Date: 2009-06-04 16:00:00
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
All of GTG's Core Non-Coding DNA Patent Claims Upheld in Full by ...
All of GTG's Core Non-Coding DNA Patent Claims Upheld in Full by US Patent and Trademark Office, : Genetic Technologies Limited has received formal notification from the United States Patent and Trademarks Office (USPTO) that it has [more...]
Date: 2010-05-10 10:00:02
Junk DNA and Complexity Science: A Sad mix
A quote from an extremely mediocre book, Complexity: A Guided Tour. Like most people coming out of the 'complexity sciences', the author has a mediocre grasp of molecular biology, both current developments, and the history of the field. It's frustrating that these network people keep hyping supposedly new revolutionary discoveries made the past 10 years of the genome era - discoveries, that in fact have been known for decades. For people clearly new to biology, molecular biology before the year 2000 was a big black hole of ignorance. There are several claims that make me angry in this book, [more...]
Date: 2010-05-21 19:56:10
Insights into watermelon genetic diversity
Insights into watermelon genetic diversity by Jeremy on September 29, 2010 There’s no doubt that most of the time when we non-experts think of genetic diversity in DNA terms, we think about alterations in the actual DNA sequence. Change the genetic code and there’s a chance you change the nature of a gene and as a result change the outward appearance, the phenotype, of an organism. There have been lots of studies relating the differences among species to differences in the DNA code of this sort, but far fewer looking at the differences among varieties of a single species. Amnon Levi and [more...]
Date: 2010-09-29 05:55:20
A Japanese Plant Has the World's Biggest Genome
“Effectively, some cells carry massive amounts of 'junk,' or at least non-coding DNA, whereas others have very little,” Lane said. We can't wait for the reaction of the neo-theocrats at the Discovery Institute's creationist public [more...]
Date: 2010-10-09 23:39:18
Top 10 Cutting-Edge Advances in CSI Technology
Investigators itching to retrieve a fingerprint, but hesitant to disturb material that could be subjected to DNA analysis, may soon be able to use a non-contact retrieval technique. 5. Portable Laser How many people can brag that they carry a portable laser to work? Now smaller, lighter, and more powerful than ever, investigators can use this high-tech tool to find more trace evidence and process crime scenes faster, and we all know that time is of the essence in crime fighting. Nothing short of amazing, even a miniscule piece of a nearly-invisible blond hair found using laser [more...]
Date: 2010-10-06 16:59:00
skin cancer mapping | Cancer Blog
Investigators are still analyzing parts DNA from patients who are non-coded, and can still find other mutations, said Dr. Elaine Mardis, co-director of Center Sequencing genome at the University of Washington, and co-lead author of the study. But as she explained: The role of these mutations Non-coding is more difficult to solve because we do not yet fully understand the function of this part of the genome. Another interesting finding in this study was that when they compared the 8 new mutations in the patient with the DNA of tumor samples from 187 AML patients others there were no matches: [more...]
Date: 2010-10-12 17:22:34
Prescribed Reading On Prescriptive Information | Uncommon Descent
While initiatives such as the Origin Of Life Prize have encouraged researchers to find non-super-naturalistic processes that might explain the origins of prescriptive information, no offerings to-date have withstood the test of scientific scrutiny. Indeed all known cases of such information invariably point to the work of a mind. Johnson emphasizes the relevance of probability in his espousal of this inference- the simplest form of life was found to be 10exp80,000 times more likely of having a mindful than a non-mindful source. Johnson repeatedly stresses how the information content of DNA is [more...]
Date: 2010-10-11 16:49:10
The reanimated zombie gene | MetaFilter
This doesn't sound like non-coding DNA stabilizing mRNA, but the number of D4Z4 repeats affecting how often the DUX4 gene gets transcribed. Fewer repeats means more DUX4 transcription. More DUX4 transcription means more DUX4 protein, [more...]
Date: 2010-08-19 20:15:53
French National DNA Database Found Constitutional, with Reservations
The French Constitutional Council recently reviewed the constitutionality of several articles of the Code of Criminal Procedure relating to the National DNA Database. This database was initially created in 1998 and was designed to include only the genetic data of convicted sexual offenders. Its content was further extended to cover other serious offenses and to include suspected offenders by various laws. The Council rejected arguments that the provisions violated principles on the safeguarding of human dignity and the inviolability of the human body, respect for private life, presumption of [more...]
Date: 2010-10-05 08:15:02
The Genetic Code: History, Facts, and Resources About Genetics ...
TheFreeResource.com (TFR): The Genetic Code: History, Facts, and Resources About Genetics (DNA & RNA). Come be a trusted resource for someone today. ... The genetic code was discovered by Francis Crick between 1953 and 1966. He is responsible for deciphering the code that distinguish the difference between living organisms from non-living things. On a basic level, he answered the question, “What is life?” Crick did not perform this work alone however, and others including [more...]
Date: 2010-07-20 19:06:49
CIENCIASMEDICASNEWS: New Functions For New Genes, Non-coding RNAs ...
DNA regions have been known for many years to confer both negative and positive regulation of protein synthesis. "The fact that RNA is much easier to manipulate than DNA could mean that this discovery has a vast therapeutic potential" explains Ørom. The work has been led by Ramin Shiekhattar, group leader at the Centre for Genomic Regulation (CRG) in Barcelona and now at the Wistar Institute and co-authored by Cedric Notredame and Roderic Guigo from the Bioinformatics and Genomics Programme at the Centre for Genomic Regulation (CRG). Shiekhattar and collaborators have seen a new role for a [more...]
Date: 2010-10-08 13:03:00
Genetic Technologies Ltd.?s Non-coding DNA Patent Upheld on ...
s (GTG's) patent for non-coding DNA technologies. U.S. Patent No. 5,612,179 titled "Intron sequence analysis method for detection of adjacent locus alleles as haplotypes" claims a method for facilitating the detection of specific gene variations. The third party initiated ex parte re-examination Control No. 90/010,318, was filed on October, 15, 2008 requesting that each of claims 26-32 be found invalid in view of a new reference, which was not previously cited in the prosecution of the '179 patent; namely a printed publication titled "Comparison of Multiple HLA-A Alleles at the [more...]
Date: 2010-07-13 16:50:00
Evolution News & Views: Intelligent Design and the Death of the ...
For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how "non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development." Design encourages scientists to look for function where evolution discourages it. (William Dembski, "Intelligent Science and Design," First Things, Vol. 86:21-27 (October 1998))In 2002, Dr. Richard Sternberg surveyed the literature and found extensive evidence for function of certain types of junk-DNA and argued that "neo-Darwinian 'narratives' have been the primary obstacle to elucidating [more...]
Date: 2007-06-15 23:03:39
Evolution News & Views: Does Darrel Falk's Junk DNA Argument for ...
Dr. Falk appears to be too hasty in his assumption that pseudogenes have "no function" and thereby show evidence for common ancestry. The bottom line is that the "junk" or "gibberish" DNA paradigm is being consistently overturned as time goes on, and we now know that the vast majority of our DNA has function. As one news article said when reporting on the results of the ENCODE project in 2007: The findings, from a project involving hundreds of scientists in 11 countries and detailed in 29 papers being published today, confirm growing suspicions that the stretches of 'junk DNA' flanking [more...]
Date: 2010-03-23 19:00:45
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
Facebook Friday, Oct. 8, 2010
Look for links to news and reviews for eco-conscious products such as jute toys, coupon codes for a variety of dog products, and recent sales on products ranging from doggie DNA kits to the Marley movie! Doggies and Stuff The fan page for DoggiesandStuff.com features links to many reviews and giveaways for dog lovers. This site gives 50 percent of all income earned from affiliates and advertising to local non-profit pet charities and pet welfare organizations! My Pet Savings On the fan page for My Pet Savings, look for coupons and special offers for pet lovers, everything from freebies (right [more...]
Date: 2010-10-08 17:52:48
Creation: Darwinian Evolutionary Frauds Pt. III
In short, the claim is that between 97% and 99 % percent of human DNA (depending upon which evolutionary biologist you asked) is “junk” DNA, that is that it is noncoding DNA and does not code for any proteins. Until the late 1990s, it was thought to serve no purpose whatsoever. Darwinists claim that it was just, therefore, leftover vestigial garbage collected along the evolutionary road traveled throughout the ages. Just junk, refuse, garbage, waste, that might have once served a purpose but is now just leftover “vestigial” evolutionary errata. Naturally, this notion is being proved [more...]
Date: 2010-06-27 09:30:58
Old Dog Reveals New Tricks | Focus
Senior author Pier Paolo Pandolfi, the George C. Reisman professor of medicine at HMS and Beth Israel Deaconess Medical Center, and his colleagues have found that a stretch of human DNA—formerly called junk because it does not code for protein—indirectly regulates a critical tumor suppressor protein, called PTEN. This molecule, which controls the cycle of cell division, preventing the cell from multiplying too rapidly, is one of the most commonly lost tumor suppressors in human cancer. Researchers in the Pandolfi lab had previously shown that even a 20 percent reduction in the levels of [more...]
Date: 2010-07-30 18:43:53
Free Online Guides: New class of objects encoded within the genome ...
In the October 1 issue of the journal Cell researchers at The Wistar Institute shed new light on the genetic unknown with the discovery of the ability of long non-coding RNA (ncRNA) to promote gene expression. The researchers believe these long ncRNA molecules may represent so-called gene enhancer elements -- short regions of DNA that can increase gene transcription. While scientists have known about gene enhancers for decades, there has been no consensus about how these enhancers work.See Also:Health & MedicineGenesHuman BiologyGene TherapyPlants & [more...]
Date: 2010-10-09 23:01:00
#The Search for Meaning in Noncoding DNA - Clark2001.pdf by ...
Fullpath : /bergman/Papers/Clark2001.pdf Publisher : bioinf.manchester.ac.uk Found at Saturday, 7 Aug 2010 17:24:28 PM View online via : GoogleZohoPdfEscape Further searches : bergman papers clark2001 pdf search meaning noncoding dna Search by domain name: site:manchester.ac.uk Search by filename: file:clark2001 Short link: http://findpdf.us/d/414326 ARIZONA STATE LAND DEPARTMENTOct 13, 2010land.state.az.usbrokerInfoAll.pdfARIZONA STATE LAND DEPARTMENT. CLIENT/BROKER INFORMATION and ELIGIBILITY REQUIREMENTS ... of a sale or long-term commercial lease of state trust land at public [more...]
Date: 2010-08-07 17:24:28
Sequencing and Analysis of Approximately 40 000 Soybean cDNA ...
9Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan 10Department of Applied Biological Sciences, Faculty of Agriculture, Saga University, Honjo 840-8502, Saga, Japan 11National Agricultural Research Center for Hokkaido Region, 1 Hitsujigaoka, Sapporo, Hokkaido 062-8555, Japan 12Experimental Farm, Kyoto University, Takatsuki, Osaka 569-0096, Japan 13Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan 14Division of BioResource, Frontier Science Research Center, University of Miyazaki, Miyazaki 889-2192, Japan 15Laboratory of [more...]
Date: 2010-09-04 19:42:59
How Do We Protect Fathers' Rights After Late, Negative DNA Tests ...
Carnell Smith of Georgia founded U.S. Citizens Against Paternity Fraud in 2001 after his own struggle. When his daughter turned 11, Smith had a paternity test as part of a child support modification case. Years before, he had believed his ex-girlfriend when she told him she was pregnant with his child. He was wrong. Smith's organization has succeeded in getting laws passed in Georgia and Ohio to address the situation. The idea is that a man who steps up to care for a child based on a mistake should never be punished for doing so. The current law encourages fathers to protect themselves by [more...]
Date: 2010-06-28 21:05:53
Science Centric | News | Wistar researchers discover new class of ...
— McDonald's recalls Shrek glasses due to potential cadmium risk — The U.S. Consumer Product Safety Commission (CPSC) just announced a recall of 'Shrek Forever After 3D' Collectable Drinking… — Hogchoker - the new Internet star — A small flatfish living along the coast of North America is the new Internet star. Currently the hotness for this particular… — Cancer deaths are projected to double by 2030 — Cancer deaths are projected to double in the next two decades. A report issued by the International Agency for Research on… More Boiling point… — Fossils of earliest [more...]
Date: 2010-10-07 17:00:00
Evolution News & Views: When "Junk DNA" Isn't Junk: Farewell to a ...
In the Darwinist repertoire, a standard response to evidence of design in the genome is to point to the existence of "junk DNA." What is it doing there, if purposeful design really is detectable in the history of life's development? Of course this assumes that the "junk" really is junk. That assumption has been cast increasingly into doubt. New research just out in the journal Nature Genetics finds evidence that genetic elements previously thought of as rubbish are anything but that. The research describes tiny strands of RNA, previously thought to be junk, that now turn out to play a role in [more...]
Date: 2009-04-28 16:20:29
Responding to Merlin Part III – Merlin's Delineation Between ...
In bacteria, this is often done by increasing transcription rates using a mutagenic DNA polymerase. In your immune system this is done, at least in part, by a deaminase attaching to the antibody gene to cause mutations. This deaminase is targeted by a non-coding DNA element, which points it not only to the correct gene, but the correct *part* of the correct gene. It would make no sense to mutate the part of the antibody which attaches to the cell, but only the part which attaches to the antigen. And, in fact, that is precisely the part that gets mutated. The region which attaches to the [more...]
Date: 2010-09-08 04:41:08
New Class of Objects Encoded Within the Genome: Non-Coding RNA ...
The idea that molecules of RNA can have a DNA-regulating effect is well established. More than 1,000 so-called microRNAs are known to science, for example, and their effect on silencing genes has been well described. According to Shiekhattar, he assumed that long ncRNAs would also silence genes, not promote their activation. To his surprise, the researchers found that depleting a cell of ncRNAs actually decreased the degree of overall gene expression of neighboring genes, revealing a role for ncRNAs in potentiating gene expression. In fact, when Shiekhattar and his colleagues depleted adult [more...]
Date: 2010-10-07 01:31:09
Coralville's IDT Partners with Marshall University
The Marshall Institute for Interdisciplinary Research (MIIR) has announced it has entered into an applied research and product development partnership with leading biotechnology company Integrated DNA Technologies (IDT). According to the terms of the agreement, scientists at MIIR will be developing optimized biomolecular analyses or “assays” to be used by IDT for the detection and quantification of ribonucleic acid (RNA). The goal of the co-development project is to significantly improve the specificity of IDT’s current assay methods without substantially increasing the cost. IDT’s [more...]
Date: 2010-05-21 20:59:12
The effect of DNA signals on nucleosome formation, chromatin ...
Much of the human genome is non-coding and it seems likely that at least some of the non-coding DNA is functionally important. However, only little is known about the possible function of the bulk of the human genome. Since essentially all the nuclear DNA is packaged into chromatin, it is likely that functional effects of non-coding DNA are mediated by the chromatin structure. By making use of human genomic sequence information now available, we showed that a specific set of periodic DNA motifs (period-10 VWG/CWB) encoded in genomic DNA is predicted to influence human chromosome function. The [more...]
Date: 2010-08-25 23:15:17
Pleiotropy: Some more junk DNA shown to have function
It shows a function for some "junk DNA" - DNA that does not serve any function for the developing organisms - namely in coding for micropeptides (very short proteins), which have now been shown to have a regulatory function in Drosophila. The first lines of the abstract readsA substantial proportion of eukaryotic transcripts are considered to be noncoding RNAs because they contain only short open reading frames (sORFs). Recent findings suggest, however, that some sORFs encode small bioactive peptides. Here, we show that peptides of 11 to 32 amino acids encoded by the polished rice (pri) sORF [more...]
Date: 2010-07-19 07:00:00
The ID Report - Prescribed Reading On Prescriptive Information
Shannon information, which provides a mathematical measure of improbability without regard to functionality does not help us in the description of life since the digital code of DNA is rich in what Johnson terms 'functional prescriptive information'. While initiatives such as the Origin Of Life Prize have encouraged researchers to find non-super-naturalistic processes that might explain the origins of prescriptive information, no offerings to-date have withstood the test of scientific scrutiny. Indeed all known cases of such information invariably point to the work of a mind. Johnson [more...]
Date: 2010-10-13 17:04:50
Genome Size, Code Bloat, And Proof-by-analogy
For a process of inter-lineage sorting to affect genome size more generally, large amounts of non-coding DNA would have to be insufficiently detrimental in the short term to be removed by organism-level selection, and would have to improve lineage survival and/or enhance speciation rates, such that over time one would observe a world dominated by lineages with huge genomes. In principle, this would be compatible with the conclusions of the model under discussion, at least in broad outline. In practice, however, this is undone by evidence that lineages with exorbitant genomes are restricted to [more...]
Date: 2008-01-17 10:58:47
Evolution News & Views: Time Aping over Human-Chimp Genetic ...
Darwinists often cite similarities in non-coding DNA as evidence of chimp-human common ancestry. Yet the Time article explains that non-coding DNA has function--perhaps holding the functions responsible for the differences between humans and chimps: Those molecular switches lie in the noncoding regions of the genome--once known dismissively as junk DNA but lately rechristened the dark matter of the genome. ... "But it may be the dark matter that governs a lot of what we actually see." Though the article still asserts much of the genome is junk, Richard Sternberg and James A. Shapiro wrote [more...]
Date: 2006-10-04 18:02:26