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Genome Engineering
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- July 3, 2012
- 06:00 AM
- 262 views
Programmable DNA scissors
by Suzanne Elvidge in Genome Engineering
Researchers at the Lawrence Berkeley National Laboratory have discovered a technique that they describe as ‘programmable DNA scissors’, that could make the editing of genomes more effective. This is based on an RNA structure that can direct a bacterial protein to cleave foreign DNA at specific nucleotide sequences. The research was published in Science.... Read more »
Martin Jinek, Krzysztof Chylinski, Ines Fonfara, Michael Hauer, Jennifer A. Doudna, & Emmanuelle Charpentier. (2012) A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science. DOI: 10.1126/science.1225829
- July 1, 2012
- 12:31 PM
- 388 views
The dolphin’s genome and the evolving brain
by Suzanne Elvidge in Genome Engineering
The closest that many of us get to dolphins is watching Flipper or seeing them perform, but the bottlenose dolphin (Tursiops truncatus) is a highly intelligent mammal, and researchers are looking at the dolphin genome to try to unpack how these animals have evolved such large brains and complex cognitive capacities – the dolphin’s body to brain ratio is similar to that of a human. The results are published in the Proceedings of the Royal Society B.... Read more »
Michael R. McGowen, Lawrence I. Grossman, & Derek E. Wildman. (2012) Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown. Proc. R. Soc. B. DOI: 10.1098/rspb.2012.0869
Darren J. Burgess. (2011) Comparative genomics: Mammalian alignments reveal human functional elements. Nature Reviews Genetics, 12, (December), 806-807. DOI: 10.1038/nrg3112
- June 29, 2012
- 02:44 PM
- 352 views
Mapping the genome of the hunter-gatherer
by Suzanne Elvidge in Genome Engineering
Agriculture, which came from the Middle East, dates back to the Mesolithic period, between the Paleolithic and Neolithic periods, and researchers, led by the Spanish National Research Council, have managed to extract and sequence part of the genome from two surprisingly well-preserved bodies from this period, found at the La Braña-Arintero site, in Valdelugueros in Spain. The research was published in Current Biology.... Read more »
Federico Sánchez-Quinto, Hannes Schroeder, Oscar Ramirez, María C. Ávila-Arcos, Marc Pybus, Iñigo Olalde, Amhed M.V. Velazquez, María Encina Prada Marcos, Julio Manuel Vidal Encinas, Jaume Bertranpetit.... (2012) Genomic Affinities of Two 7,000-Year-Old Iberian Hunter-Gatherers. Current Biology. DOI: 10.1016/j.cub.2012.06.005
- June 21, 2012
- 06:00 AM
- 299 views
The genetics of alcoholism: Is drinking in our genes?
by Suzanne Elvidge in Genome Engineering
Alcohol is something that is part of many of our social lives – it’s technically a sedative hypnotic drug, and it makes us relaxed. However, overusing alcohol is the third leading cause of preventable death in the US, and alcohol dependence does seem to be an inherited trait. As part of the Study of Addiction: Genetics and Environment (SAGE), researchers have found that copy number variations (CNVs; increases or decreases in the number of copies of each gene) can be linked with alcoh........ Read more »
Peng Lin, Sarah M. Hartz, Jen-Chyong Wang, Arpana Agrawal, Tian-Xiao Zhang, Nicholas McKenna, Kathleen Bucholz, Andrew I. Brooks, Jay A. Tischfield, Howard J. Edenberg.... (2012) Copy Number Variations in 6q14.1 and 5q13.2 are Associated with Alcohol Dependence. Copy Number Variations in 6q14.1 and 5q13.2 are Associated with Alcohol Dependence. DOI: 10.1111/j.1530-0277.2012.01758.x
- June 19, 2012
- 06:00 AM
- 288 views
Fragile X mutation leads to fragile health
by Suzanne Elvidge in Genome Engineering
Fragile X syndrome is caused by a genetic mutation in the FMR1 gene on the X chromosome that is the most common form of mental retardation in boys. Researchers at University of Wisconsin-Madison, in research published in the American Journal of Medical Genetics, have found that changes in this gene could be more common than was previously thought.... Read more »
Marsha Mailick Seltzer, Mei Wang Baker, Jinkuk Hong, Matthew Maenner, Jan Greenberg, & Daniel Mandel. (2012) Prevalence of CGG expansions of the FMR1 gene in a US population-based sample. American Journal of Medical Genetics Part B: Neuropsychiatric Genetics, 133A(5), 589-597. DOI: 10.1002/ajmg.b.32065
- June 18, 2012
- 06:00 AM
- 283 views
Sequencing the malaria parasite
by Suzanne Elvidge in Genome Engineering
Malaria infects over 200 million people and kills approximately 600,000 people every year, primarily children under the age of five in sub-Saharan Africa. The malaria parasite, Plasmodium falciparum, mutates, which can lead to resistance to existing drugs. Researchers at the Wellcome Trust Sanger Institute have created methods for large-scale analysis of malaria parasite genomes from patient blood samples, allowing them to identify hotspots of malaria parasite evolution and track the rise of mal........ Read more »
Magnus Manske, Olivo Miotto, Susana Campino, Sarah Auburn, Jacob Almagro-Garcia, Gareth Maslen, Jack O’Brien, Abdoulaye Djimde, Ogobara Doumbo, Issaka Zongo.... (2012) Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature. DOI: 10.1038/nature11174
- June 12, 2012
- 02:07 AM
- 369 views
Four new migraine mutations
by Suzanne Elvidge in Genome Engineering
Migraine is disabling and distressing, and for some people it can take days out of their work, study or caring responsibilities – 25 million school or work days are lost for migraine each year. Researchers from the International Headache Genetics Consortium in Europe and Australia have found a group of six genetic variants for migraine without aura, the most common subtype of migraine, affecting about two-thirds of sufferers. The research was published in Nature. ... Read more »
Freilinger, T., Anttila, V., de Vries, B., Malik, R., Kallela, M., Terwindt, G., Pozo-Rosich, P., Winsvold, B., Nyholt, D., van Oosterhout, W.... (2012) Genome-wide association analysis identifies susceptibility loci for migraine without aura. Nature Genetics. DOI: 10.1038/ng.2307
- June 8, 2012
- 04:00 PM
- 341 views
Feeling fidgety? Fruit flies get the gene for restless legs
by Suzanne Elvidge in Genome Engineering
Restless legs syndrome (RLS) is really frustrating – mine sets off in the evenings, when my legs feel heavy and the skin itches and crawls, until I just have to move them. It settles for a moment, and then builds until I just have to move again. It can disturb your sleep and irritate people around you, and it runs in families – mine comes from my dad. A study in PLoS Genetics in July 2011 linked restless legs syndrome with the TOX3 gene, and another study, published in Current Biolog........ Read more »
Freeman, A., Pranski, E., Miller, R., Radmard, S., Bernhard, D., Jinnah, H., Betarbet, R., Rye, D., & Sanyal, S. (2012) Sleep Fragmentation and Motor Restlessness in a Drosophila Model of Restless Legs Syndrome. Current Biology. DOI: 10.1016/j.cub.2012.04.027
Winkelmann, J., Czamara, D., Schormair, B., Knauf, F., Schulte, E., Trenkwalder, C., Dauvilliers, Y., Polo, O., Högl, B., Berger, K.... (2011) Genome-Wide Association Study Identifies Novel Restless Legs Syndrome Susceptibility Loci on 2p14 and 16q12.1. PLoS Genetics, 7(7). DOI: 10.1371/journal.pgen.1002171
- June 7, 2012
- 06:00 AM
- 332 views
Researchers map a baby’s genome
by Suzanne Elvidge in Genome Engineering
It has been possible to sequence the DNA of unborn babies but this has involved invasive tests, taking amniotic fluid or tissue samples. A team of researchers led by the University of Washington have been able to map the baby’s genome by sequencing the cell-free strands of foetal DNA found in the mother-to-be’s bloodstream. This could create a non-invasive technique for prenatal genetic diagnostics.... Read more »
Kitzman, J., Snyder, M., Ventura, M., Lewis, A., Qiu, R., Simmons, L., Gammill, H., Rubens, C., Santillan, D., Murray, J.... (2012) Noninvasive Whole-Genome Sequencing of a Human Fetus. Science Translational Medicine, 4(137), 137-137. DOI: 10.1126/scitranslmed.3004323
- May 30, 2012
- 06:00 AM
- 339 views
Sperm gene could lead to the male pill
by Suzanne Elvidge in Genome Engineering
Researchers have pinpointed a gene that is essential for sperm development, and this could lead to a new form of contraceptive that doesn’t depend on hormones, which can cause side effects. The research was published in PLoS Genetics.... Read more »
Smith, L., Milne, L., Nelson, N., Eddie, S., Brown, P., Atanassova, N., O'Bryan, M., O'Donnell, L., Rhodes, D., Wells, S.... (2012) KATNAL1 Regulation of Sertoli Cell Microtubule Dynamics Is Essential for Spermiogenesis and Male Fertility. PLoS Genetics, 8(5). DOI: 10.1371/journal.pgen.1002697
- May 24, 2012
- 06:00 AM
- 424 views
Making rewritable DNA
by Suzanne Elvidge in Genome Engineering
DNA is designed to store genetic information, but it’s not intended to be rewritable, which is what’s needed for using it to store other information. Researchers at the Stanford School of Medicine have created a technique that allows them to repeatedly encode, store and erase digital data within the DNA of living cells. The study was published in PNAS.... Read more »
Bonnet, J., Subsoontorn, P., & Endy, D. (2012) Rewritable digital data storage in live cells via engineered control of recombination directionality. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1202344109
- May 19, 2012
- 08:33 AM
- 447 views
Mapping the sense of smell
by Suzanne Elvidge in Genome Engineering
Our sense of smell comes from the control of around 300 olfactory receptor genes, allowing each sensory neuron to detect a small number of different components of smell, or odorants. Researchers at RIKEN have mapped the odorant receptors in mice, finding the promoter sequences that control the genes. The research was published in Genome Research.... Read more »
Plessy, C., Pascarella, G., Bertin, N., Akalin, A., Carrieri, C., Vassalli, A., Lazarevic, D., Severin, J., Vlachouli, C., Simone, R.... (2011) Promoter architecture of mouse olfactory receptor genes. Genome Research, 22(3), 486-497. DOI: 10.1101/gr.126201.111
Plessy, C., Bertin, N., Takahashi, H., Simone, R., Salimullah, M., Lassmann, T., Vitezic, M., Severin, J., Olivarius, S., Lazarevic, D.... (2010) Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nature Methods, 7(7), 528-534. DOI: 10.1038/nmeth.1470
Shiraki, T. (2003) Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proceedings of the National Academy of Sciences, 100(26), 15776-15781. DOI: 10.1073/pnas.2136655100
- May 17, 2012
- 05:00 PM
- 382 views
Four bases in RNA? Think again…
by Suzanne Elvidge in Genome Engineering
Back in school, I was taught that DNA was made up of four bases – A (adenine), T (thymine), C (cytosine) and G (guanine), but research has shown that this isn’t quite that simple – since then, researchers have found a fifth, a fake fifth, sixth, seventh and eighth bases, as well as creating a bacterial genome that uses an artificial base, 5-chlorouracil. Now it seems that messenger RNA (mRNA) also has surprises with a modification to one of its bases that could affect how genes........ Read more »
Meyer, K., Saletore, Y., Zumbo, P., Elemento, O., Mason, C., & Jaffrey, S. (2012) Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons. Cell. DOI: 10.1016/j.cell.2012.05.003
Lister, R., & Ecker, J. (2009) Finding the fifth base: Genome-wide sequencing of cytosine methylation. Genome Research, 19(6), 959-966. DOI: 10.1101/gr.083451.108
Ratel, D., Ravanat, J., Berger, F., & Wion, D. (2006) N6-methyladenine: the other methylated base of DNA. BioEssays, 28(3), 309-315. DOI: 10.1002/bies.20342
Ito, S., Shen, L., Dai, Q., Wu, S., Collins, L., Swenberg, J., He, C., & Zhang, Y. (2011) Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine. Science, 333(6047), 1300-1303. DOI: 10.1126/science.1210597
- May 15, 2012
- 05:00 PM
- 354 views
Is your well-being down to your genes?
by Suzanne Elvidge in Genome Engineering
While traits like well-being and success are never going to be down to a single gene, and while they will always involve hard work, environment and simple luck as well, recent research from the University of Edinburgh has suggested that there is an influence from the genes too, and that it is stronger than previously thought.... Read more »
Archontaki, D., Lewis, G., & Bates, T. (2012) Genetic influences on psychological well-being: A nationally representative twin study. Journal of Personality. DOI: 10.1111/j.1467-6494.2012.00787.x
- May 14, 2012
- 06:00 AM
- 356 views
Gene therapy for hearing loss
by Suzanne Elvidge in Genome Engineering
Hearing loss can be caused by advancing years, or by head injuries or loud noises, all of which lead to loss of the sensory hair cells. A new gene therapy could have potential to replace the damaged hair cells, but isn’t likely to be the answer by itself. The study was published in the Journal of Neuroscience.... Read more »
Kelly MC, Chang Q, Pan A, Lin X, & Chen P. (2012) Atoh1 directs the formation of sensory mosaics and induces cell proliferation in the postnatal Mammalian cochlea in vivo. The Journal of neuroscience : the official journal of the Society for Neuroscience, 32(19), 6699-710. PMID: 22573692
- May 7, 2012
- 04:16 AM
- 632 views
Genes and body clocks
by Suzanne Elvidge in Genome Engineering
The ‘body clock’ or circadian rhythms controls things like alertness, sleep patterns, appetite and hormones, and travelling across time zones or working nights can disturb it. Researchers from the University of Sydney and from the Salk Institute have worked on how the genes behind this are controlled and their research was published in Nature.... Read more »
Cho, H., Zhao, X., Hatori, M., Yu, R., Barish, G., Lam, M., Chong, L., DiTacchio, L., Atkins, A., Glass, C.... (2012) Regulation of circadian behaviour and metabolism by REV-ERB-α and REV-ERB-β. Nature, 485(7396), 123-127. DOI: 10.1038/nature11048
- May 4, 2012
- 12:33 PM
- 475 views
Blond gene in Melanesia: Fair hair is not just from Europe
by Suzanne Elvidge in Genome Engineering
Naturally blond hair is found almost entirely in Northern Europe and Oceania – but is it from the same gene? In the Solomon Islands, 5-10% of the population is blond and research led by Stanford University School of Medicine has shown that the mutation leading to blond hair arose separately here. The research was published in Science.... Read more »
Kenny, E., Timpson, N., Sikora, M., Yee, M., Moreno-Estrada, A., Eng, C., Huntsman, S., Burchard, E., Stoneking, M., Bustamante, C.... (2012) Melanesian Blond Hair Is Caused by an Amino Acid Change in TYRP1. Science, 336(6081), 554-554. DOI: 10.1126/science.1217849
- May 3, 2012
- 05:34 PM
- 473 views
Repairing broken DNA
by Suzanne Elvidge in Genome Engineering
DNA gets broken, and this could give rise to cancer. However, the broken end of the DNA is able to use a similar sequence for repair, and researchers at the Kavli Institute of Nanoscience at Delft University of Technology have found out how this works, in a paper published in Molecular Cell.... Read more »
De Vlaminck, I., van Loenhout, M., Zweifel, L., den Blanken, J., Hooning, K., Hage, S., Kerssemakers, J., & Dekker, C. (2012) Mechanism of Homology Recognition in DNA Recombination from Dual-Molecule Experiments. Molecular Cell. DOI: 10.1016/j.molcel.2012.03.029
- April 22, 2012
- 04:00 PM
- 595 views
Synthetic genetic material, XNA, can replicate and evolve
by Suzanne Elvidge in Genome Engineering
Following on from the creation of a cell based on a synthetic genome and the synthetic mouse mitochondrial genome in 2010, and proteins based on ‘unnatural’ DNA sequences and the poem inserted as a synthetic gene into a bacterium in 2011, the next step towards synthetic life is the creation of a synthetic genetic polymer, XNA, that is capable of heredity and evolution.... Read more »
Pinheiro, V., Taylor, A., Cozens, C., Abramov, M., Renders, M., Zhang, S., Chaput, J., Wengel, J., Peak-Chew, S., McLaughlin, S.... (2012) Synthetic Genetic Polymers Capable of Heredity and Evolution. Science, 336(6079), 341-344. DOI: 10.1126/science.1217622
Schoning, K. (2000) Chemical Etiology of Nucleic Acid Structure: The alpha -Threofuranosyl-(3'rightarrow 2') Oligonucleotide System. Science, 290(5495), 1347-1351. DOI: 10.1126/science.290.5495.1347
Yu, H., Zhang, S., & Chaput, J. (2012) Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor. Nature Chemistry, 4(3), 183-187. DOI: 10.1038/nchem.1241
- April 22, 2012
- 06:00 AM
- 446 views
DNA data: Polar bears evolved 600,000 years ago
by Suzanne Elvidge in Genome Engineering
According to an analysis of the nuclear DNA of polar bears, brown bears and black bears published in Science, polar bears evolved around 600,000 years ago, making them five times older than previously thought. This extra time explains how they have managed to adapt so well to the conditions of the arctic.... Read more »
Hailer, F., Kutschera, V., Hallstrom, B., Klassert, D., Fain, S., Leonard, J., Arnason, U., & Janke, A. (2012) Nuclear Genomic Sequences Reveal that Polar Bears Are an Old and Distinct Bear Lineage. Science, 336(6079), 344-347. DOI: 10.1126/science.1216424
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