In the wake of the sequencing of the human genome in the early 2000s, genome pioneers and social scientists alike called for an end to the use of race as a variable in genetic research. Unfortunately, by some measures, the use of race as a biological category has increased in the postgenomic age. Although inconsistent definition and use has been a chief problem with the race concept, it has historically been used as a taxonomic categorization based on common hereditary traits (such as skin color) to elucidate the relationship between our ancestry and our genes. We believe the use of biological concepts of race in human genetic research—so disputed and so mired in confusion—is problematic at best and harmful at worst. It is time for biologists to find a better way. - An editorial in Science exploring the conundrum facing genomic researchers where race is both fundamentally flawed as a scientific model and violently dangerous but still the only consistent lens through which study participants understand the information they have about their own connection to human diversity [more inside]
Bacterial diseases cause millions of deaths every year. Most of these bacteria were benign at some point in their evolutionary past, and we don’t always understand what turned them into disease-causing pathogens. In a new study, researchers have tracked down when this switch happened in one flesh-eating bacteria. They think the knowledge might help predict future epidemics. [more inside]
Mosses Make Two Different Plants From the Same Genome, and a Single Gene Can Make the Difference
One of the most astonishing secrets in biology is this: every plant you see makes two different plants from the same genome. And, scientists recently reported, a single gene from an ancient, powerful lineage can make the difference.
What we currently call breast cancer should be thought of as 10 completely separate diseases, according to an international study which has been described as a "landmark". The categories could improve treatment by tailoring drugs for a patient's exact type of breast cancer and help predict survival more accurately. The study in Nature analysed breast cancers from 2,000 women [Abstract] . It will take at least three years for the findings to be used in hospitals. [more inside]
Provirophages and transpovirons as the diverse mobilome of giant viruses
Abstract: A distinct class of infectious agents, the virophages1 that infect giant viruses of the Mimiviridae family, has been recently described. Here we report the simultaneous discovery of a giant virus of Acanthamoeba polyphaga (Lentille virus) that contains an integrated genome2 of a virophage (Sputnik 2), and a member of a previously unknown class of mobile genetic elements3, the transpovirons4. The transpovirons are linear DNA elements of ∼7 kb [kilobases]5 that encompass six to eight protein-coding genes, two of which are homologous6 to virophage genes. Fluorescence7 in situ hybridization8 showed that the free form of the transpoviron replicates within the giant virus factory and accumulates in high copy numbers inside giant virus particles, Sputnik 2 particles, and amoeba cytoplasm. Analysis of deep-sequencing data showed that the virophage and the transpoviron can integrate9 in nearly any place in the chromosome of the giant virus host and that, although less frequently, the transpoviron can also be linked to the virophage chromosome. In addition, integrated fragments of transpoviron DNA were detected in several giant virus and Sputnik genomes. Analysis of 19 Mimivirus strains revealed three distinct transpovirons associated with three subgroups of Mimiviruses. The virophage, the transpoviron, and the previously identified self-splicing introns10 and inteins11 constitute the complex, interconnected mobilome12 of the giant viruses and are likely to substantially contribute to interviral gene transfer.[Full Text PDF] and two explanations in English [more inside]
Omes have a long history and describe general interactions of biological information objects in various omes. But not all omes are real omes. Some have a problem with omes as neologisms.
Invasive amniocentesis and chorionic villi sampling (CVS) tests are commonly used to determine the chromosomal, structural and genetic abnormalities in fetuses. But could they eventually become obsolete? A Chinese study has found that a complete copy of the fetal genome exists in the mother's blood, suggesting many prenatal diagnoses could potentially be performed noninvasively. [more inside]
Neandertals are the closest ancestral relatives to modern humans. Today, Nature published a special report on the Neandertal genome, for which a draft sequencing of three billion nucleotides has been completed. This high-throughput sequencing project shows how the genetic relationship between Neandertals and modern Europeans and Asians suggests localized interbreeding between the two species roughly 40-80,000 years ago, complicating the common "out-of-Africa" story of how modern humans originated. Additional research extends this low-coverage, first-pass sequencing with a microarray approach that uncovers specific differences between the human and Neandertal genomes.
Followup to this post: A US District Court has ruled that Myriad Genetic's patents on breast cancer genes BRCA1 and BRCA2, which allow them to hold exclusive rights to a widely used genetic test for inherited breast and ovarian cancer susceptibility, are invalid. Genomics Law Report analyzes the ruling in two posts. The decision is likely to be challenged in a legal appeal — but if upheld, it could have huge implications for the biotechnology industry. [more inside]
We may soon be able to clone Neanderthals. But should we? An essay from Archaeology Magazine examines the ethical, scientific and legal ramifications. (Via Heather Pringle's Time Machine blog, where essay author Zach Zorich posted a reply and elicited a response.) [more inside]
On behalf of medical organizations, universities, & individual patients, pathologists and genetics researchers, the ACLU has filed a lawsuit against Utah-based Myriad Genetics and the US Patent and Trademark Office. Myriad holds the US patents to the BRCA1 and BRCA2 genes, associated with hereditary causes of breast and ovarian cancers. Their patents guarantee the company the right to prevent anyone else from testing or studying those genes, which the ACLU says is unconstitutional and inhibits researchers from finding treatments and cures. [more inside]
A more efficient microbe genome. A more efficient sorting algorithm. A more efficient keyboard layout.
"We are becoming the masters of our own DNA. But does that give us the right to decide that my children should never have been born?" John Sundman is a science fiction novelist and the father of two children with severe medical conditions. In this two-part article he shares his experiences and thoughts on bioethics, the Human Genome Project and whether genetics research is paving the way for a resurgent eugenics movement.
DNA used to ascertain race of unidentified serial killer. Florida company DNAPrint Genomics claims their test can identify the race (ie, African, Caucasian, East Asian or American Indian) of a person from their DNA. CEO Tony Frudakis says that "of over 2,200 blind samples tested, the test is yet to get one wrong."
Genome liberation. "Life science researchers -- even those who work in academic settings -- are finding that corporations are just as eager to patent the tools as they are the data, and in many cases, universities are bending over backward to let the private sector have its way. As a result, a growing number of bioinformatics researchers are beginning to look to the free-software and open-source software movements for inspiration in their quest for bio freedom."
"There are only a few hundred genes that we have in the human genome that are not in the mouse genome,"
"There are only a few hundred genes that we have in the human genome that are not in the mouse genome," says Craig Venter, chief scientific officer at Celera Genomics. Information on the human genome released today reveals that there are far fewer genes than first thought - humans only have double the amount that worms and flies do. [more inside...]
The Missyplicity Project seeks to clone a dog for the first time in history - a specific dog named Missy. Missy is a beloved pet, getting on in years, whose wealthy owners wish to reproduce her. See also Genetic Savings and Clone
A beta version of the source code for humans is now available for download.
Not that I'd have any idea what to do with this. Anyone up for a 740mb download?
Not that I'd have any idea what to do with this. Anyone up for a 740mb download?