Genomics

Let’s read the Nature abstract: Nature (2019) Article | Published: 15 May 2019 Total synthesis of Escherichia coli with a recoded genome Julius Fredens, Kaihang Wang, Daniel de la Torre, Louise F. H. Funke, Wesley E. Robertson, Yonka Christova, Tiongsun Chia, Wolfgang H. Schmied, Daniel L. Dunkelmann, Václav Beránek, Chayasith Uttamapinant, Andres Gonzalez Llamazares, Thomas S. Elliott & Jason W. Chin AbstractNature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, Read More ›

Researchers studied the thale cress (an Arabadopsis relative) which can have either a single or a double genome. Genome doubling is not good news: “It’s almost always a bad thing to have too much DNA, but we think that sometimes it makes for a ‘hopeful monster’ that just might flourish.” They seem to have found one: “These tough little plants can become little genetic adaptation machines which allows them to invade hostile environments and even thrive where others can’t. In fact, a large proportion of the most invasive plant species in the world are genome doubled, so we hypothesised that there are adaptations that occur as a result of genome duplication that we can focus on and find the genes Read More ›

If so, it’s remarkable outcome for genome mapping: So it has been dawning on us is that there is no prior plan or blueprint for development: Instructions are created on the hoof, far more intelligently than is possible from dumb DNA. That is why today’s molecular biologists are reporting “cognitive resources” in cells; “bio-information intelligence”; “cell intelligence”; “metabolic memory”; and “cell knowledge”—all terms appearing in recent literature.1,2 “Do cells think?” is the title of a 2007 paper in the journal Cellular and Molecular Life Sciences.3 On the other hand the assumed developmental “program” coded in a genotype has never been described. It is such discoveries that are turning our ideas of genetic causation inside out. We have traditionally thought of cell Read More ›

From ScienceDaily: When a building is damaged, a general contractor often oversees various subcontractors — framers, electricians, plumbers and drywall hangers — to ensure repairs are done in the correct order and on time. Similarly, when DNA is damaged, a molecular general contractor oversees a network of genetic subcontractors to ensure that the diverse cellular tasks needed to protect and repair the genome are carried out correctly and on time. Scientists have known for some time that a master gene named SOG1 acts like a general contractor for repair, coordinating with various genetic subcontractors of the plant cell to mount an effective DNA damage response. But, it wasn’t clear which specific genes were among the subcontractors, nor how SOG1 interacted Read More ›

From ScienceDaily: University of Otago researchers have discovered information about a gene that sets primates — great apes and humans — apart from other mammals, through the study of a rare developmental brain disorder. … Dr O’Neill and research collaborators from Max Planck Institute of Psychiatry, Germany, then set forth to test the point that the gene drives aspects of brain development that are unique to primates. Some amazing data was found using a novel approach through studying human “mini-brains” in culture. It is now possible to take a skin cell and transform it using a set of genetic tricks, so that it can be triggered to form a tiny brain-like structure in culture in the lab. Their results showed Read More ›

A computer programmer looks at DNA … and finds it to be “amazing” code. From 2006 through 2017, Dutch entrepreneur and software developer Bert Hubert contributed from time to time to a web page where he listed many of the ways the workings of DNA can be likened to coding decisions by programmers. Some of his thoughts: The human genome is about 3 gigabases long, which boils down to 750 megabytes. Depressingly enough, this is only 2.8 Mozilla browsers. DNA is not like C source but more like byte-compiled code for a virtual machine called ‘the nucleus’. It is very doubtful that there is a source to this byte compilation – what you see is all you get. It is Read More ›

From ScienceDaily: Many wild and cultivated plants arise through the combination of two different species. The genome of these so-called polyploid species often consists of a quadruple set of chromosomes — a double set for each parental species — and thus has about twice as many genes as the original species. About 50 years ago, evolutionary biologists postulated that this process drives evolution, leading to new species. Due to the size and complexity of such genomes, however, proving this theory on a genetic level has been difficult. Arabidopsis kamchatica arose through the natural hybridization of the two parental species A. halleri and A. lyrata between 65,000 and 145,000 years ago. With 450 million base pairs, its genome is somewhat small Read More ›

The world’s simplest animal is trichoplax adhaerens. It is so simple that researchers wisely decided to forego the venerable Biological Species Concept that depends on an animal’s form (tricoplax doesn’t have much of a form) and just use genetics. But when evolutionary biologist Michael Eitel sequenced the genomes of several thousand of them, he was in for a surprise: A quarter of the genes were in the wrong spot or written backward. Instructions for similar proteins were spelled nearly 30 percent differently on average, and in some cases as much as 80 percent. The Hong Kong variety was missing 4 percent of its distant cousin’s genes and had its own share of genes unique to itself. Overall, the Hong Kong Read More ›

Earlier this month, 15 genomes were released. The Vertebrate Genomes Project aims to sequence every extant vertebrate species—there are about 66,000—and to make them of the highest possible value. … “What we thought was a ‘genome’ back [when G10K was launched] really wasn’t suitable for in-depth studies,” G10K cofounder David Haussler, a computational biologist at the University of California, Santa Cruz, tells Science. “I think we’ve reached a turning point.” Jef Akst, “Massive Animal Sequencing Effort Releases First Set of Genomes” at The Scientist Given how much genome mapping has done to debunk straightforward Darwinism, just from the genomes released to date, however complete, one can only guess at what all 66k would do. It was nice to see the Read More ›

Seen from below: Professor Hugenholtz said the scientific community generally agrees that evolutionary relationships are the most natural way to classify organisms, but bacterial taxonomy is riddled with errors, due to historical difficulties. “This is mainly because microbial species have very few distinctive physical features, meaning that there are thousands of historically misclassified species,” he said. “It’s also compounded by the fact that we can’t yet grow the great majority of microorganisms in the laboratory, so have been unaware of them until quite recently.” Dr. Donovan Parks, the lead software developer on the project, is excited about the recent advancement of genome sequencing technology, and how it’s helping reconstruct the bacterial tree of life. … The research team then used Read More ›

And we are not sure which ones they are. From ScienceDaily: Research Centre (CNIO) reveals that up to 20% of genes classified as coding (those that produce the proteins that are the building blocks of all living things) may not be coding after all because they have characteristics that are typical of non-coding or pseudogenes (obsolete coding genes). They don’t mean “junk DNA,” do they? Not this again. The work once again highlights doubts about the number of real genes present in human cells 15 years after the sequencing the human genome. Although the most recent data indicates that the number of genes encoding human proteins could exceed 20,000, Federico Abascal, of the Wellcome Trust Sanger Institute in the United Read More ›