Genomics

Did farming change the human genome? If so, the genome has certainly been a work in rapid progress, and maybe regress too From : Genomic analysis of ancient human remains identifies specific genes that changed during and after the transition in Europe from hunting and gathering to farming about 8,500 years ago. Many of the genes are associated with height, immunity, lactose digestion, light skin pigmentation, blue eye color and celiac disease risk. … “From an archaeological perspective, it’s quite amazing,” said co-senior author Ron Pinhasi, associate professor of archaeology at University College Dublin. “The Neolithic revolution is perhaps the most important transition in human prehistory. We now have proof that people did actually go from Anatolia into Europe and Read More ›

… but well, it’s Friday night … From LiveScience: Call them Franken flatworms. Scientists have created worms with the heads and brains of other species just by manipulating cell communication. The research is an example of how development is controlled by more than genetics alone. The researchers did not alter the flatworms’ DNA in any way, but instead manipulated proteins that control conversations between cells. The heads go back to normal after a few weeks. “These findings raise significant questions about how genes and bioelectric networks interact to build complex body structures,” Levin said. If genes provide a blueprint for an organism’s body, cells are like the construction workers required to turn the plan into a structure — and gap Read More ›

But then this is the same life form that can reassemble from a small piece, and lose all its neurons but live. Re the latter feat, new findings may shed light: From Science Daily: Champion of regeneration, the freshwater polyp Hydra is capable of reforming a complete individual from any fragment of its body. It is even able to remain alive when all its neurons have disappeared. Researcher the University of Geneva (UNIGE), Switzerland, have discovered how: cells of the epithelial type modify their genetic program by overexpressing a series of genes, among which some are involved in diverse nervous functions. … “Epithelial cells do not possess typical neuronal functions. However, Hydra’s loss of neurogenesis induces epithelial cells to modify Read More ›

From The Telegraph: The human genome is littered with sequences left behind from long-ago viral infections but now scientists have found the code is still active Now researchers at Stanford University School of Medicine have found that genetic material from a retrovirus called HERV-H is not only active, but is crucial in allowing a fertilised human egg to grow into an embryo. … “What’s really interesting is that these sequences are found only in primates, raising the possibility that their function may have contributed to unique characteristics that distinguish humans from other animals. Let’s back up and be cautious here. For one thing, many primates are not particularly clever, so we need to be much more specific about why it Read More ›

From ScienceDaily: Scientists have long speculated about the nature of the dark proteome, the area of proteins that are completely unknown, but a recent study by CSIRO has mapped the boundaries of these dark regions, bringing us one step closer to discovering the complete structure and function of all proteins. … As knowledge of three-dimensional protein structures continues to expand, we can identify regions within each protein that are different to any region where structure has been determined experimentally, coined the ‘dark proteome’. “These dark regions are unlike any known structure, so they cannot be predicted,” Dr O’Donoghue said. … The research has yielded some surprising results, including that nearly half of the proteome in eukaryotes is dark and has Read More ›

A half billion years ago. This helps us understand why most of the information in a life form cannot be in its genes. From ScienceDaily: Scientists have analyzed the genomes of two acorn worm species and found that approximately two-thirds of human genes have counterparts in the ancestors of these marine animals. These ancient genes, and their organization within the genome, were already in place in the common ancestor of humans and acorn worms that lived over half a billion years ago. … Around 550 million years ago, a great variety of animals burst onto the world in an event known as the Cambrian explosion. This evolutionary radiation revealed several new animal body plans, and changed life on Earth forever, Read More ›

From xkcd: Try out other “physicist-driven” cartoons here. Follow UD News at Twitter!

From ScienceDaily: A new study from Sweden’s Karolinska Institutet shows that the ‘grammar’ of the human genetic code is more complex than that of even the most intricately constructed spoken languages in the world. The findings, published in the journal Nature, explain why the human genome is so difficult to decipher — and contribute to the further understanding of how genetic differences affect the risk of developing diseases on an individual level. Under the supervision of Professor Jussi Taipale, researchers at Karolinska Institutet have previously identified most of the DNA words recognised by individual transcription factors. However, much like in a natural human language, the DNA words can be joined to form compound words that are read by multiple transcription Read More ›

Discussed as a design but believed, by dogma, not to be a design. From the Atlantic: Genomes are so regularly represented as strings of letters-As, Gs, Cs, and Ts-that it’s easy to forget that they aren’t just abstract collections of data. They exist in three dimensions. They are made of molecules. They are physical objects that take up space-a lot of space. Consider that the human genome is longer than the average human. It consists of around two meters of DNA, which must somehow fit into cells, whose nuclei are about 200,000 times narrower. So it folds. And it folds in such a way that any given stretch can be easily unfolded, so the genes within it can be read Read More ›

Phys.Org has a new summary about a new finding regarding heterochromatin repair in the nucleus which involves the nuclear membrane. In their discussion, they make some interesting points: Previously, the nuclear membrane was thought to be mostly just a protective bubble around the nuclear material, with pores acting as channels to transport molecules in and out. But in a study published on October 26 in Nature Cell Biology, a research team led by Irene Chiolo documents how broken strands of a portion of DNA known as heterochromatin are dragged to the nuclear membrane for repair. The reason why we don’t experience thousands of cancers every day in our body is because we have incredibly efficient molecular mechanisms that repair the Read More ›

From ScienceDaily: Ancient wild ox genome reveals complex cow ancestry The ancestry of domesticated cattle proves more complex than previously thought, reports a paper published in the open access journal Genome Biology. … The team of researchers discovered clear evidence of breeding between wild British aurochs and early domesticated cattle. David MacHugh, senior author on the study from the School of Agriculture and Food Science at University College Dublin, said: “Our results show the ancestors of modern British and Irish breeds share more genetic similarities with this ancient specimen than other European cattle. This suggests that early British farmers may have restocked their domesticated herds with wild aurochs.” More. Rob Sheldon writes, What is being done in this paper is Read More ›

While shopping at the gene counter, we learned from The Scientist : Published genomes are chock-full of contamination. But as awareness of the problem grows, so do methods to help combat it. When Supratim Mukherjee noticed the same bacteriophage sequence popping up again and again in hundreds of microbial genomes from a database he was analyzing, he got excited. Mukherjee, a bioinformatician at Lawrence Berkeley National Laboratory, was comparing the metabolic pathways of the microbes, and he began to wonder what the nearly ubiquitous sequence was. “I thought we must have discovered something novel,” he recalls. “This entire bacteriophage genome was intact in all these diverse microbes.” But when Mukherjee looked up the bacteriophage sequence, he learned that it was Read More ›

From obit: Inherent in the idea of gene regulatory networks was the concept that genome sequences that provided information about how genes should be expressed would be as important as the genome sequences that coded for the proteins themselves. Although non-protein-coding DNA was long considered to be “junk,” Davidson recognized that the key regulatory code resided in this genetic material. In 2006, Davidson co-led a group of 240 researchers from more than 70 institutions that sequenced the purple sea urchin’s genome. In 2008, a consortium of institutions led by Davidson’s lab characterized the 23,000 genes of that genome. In parallel, the Davidson group systematically created a comprehensive functional testing strategy to detect all of the control connections between the genes Read More ›

Rockefeller University researchers

found that part of a DNA repair protein known as 53BP1 fits over the phosphorylated part of H2AX “like a glove,” says Kleiner. This interaction helps bring 53BP1 to the site of DNA damage, where it mediates the repair of double-stranded breaks in DNA by encouraging the repair machinery to glue the two ends back together.

New findings shed light on fundamental process of DNA repair

What are the prospects of a DNA self replicating entity surviving with rapid cumulative DNA mutations until it assembles the DNA repair mechanism – by random stochastic processes? Read More ›

Wasn’t suppose to happen in the old days, right? But it turns out to be surprisingly common. From ScienceDaily: The common baker’s yeast (Saccharomyces cerevisiae) is used to make bread, wine and beer, and is the laboratory workhorse for a substantial proportion of research into molecular and cell biology. It was also the first non-bacterial living thing to have its genome sequenced, back in 1996. However, when the sequence of that genome emerged it appeared that the scientists were seeing double – the organism seemed to have two very different versions of many of its genes. How could this have happened? Researchers from the Centre for Genomic Regulation (CRG) Barcelona, Spain, writing in the Open Access journal PLOS Biology in Read More ›