Cell biology

Amazing protein diversity in maize From Eurekalert: Cold Spring Harbor, NY — The genome of the corn plant – or maize, as it’s called almost everywhere except the US – “is a lot more exciting” than scientists have previously believed. So says the lead scientist in a new effort to analyze and annotate the depth of the plant’s genetic resources. “Our new research establishes the amazing diversity of maize, even beyond what we already knew was there,” says Doreen Ware, Ph.D., of the US Department of Agriculture and Cold Spring Harbor Laboratory (CSHL) in New York. “This diversity is fascinating in its own right and at the same time has great import for agriculture.” Maize is one of the world’s Read More ›

From ScienceDaily: Although scientists generally agree that eukaryotes can trace their ancestry to a merger between archaea and bacteria, there’s been considerable disagreement about what the first eukaryote and its immediate ancestors must have looked like. As Thattai and his colleagues Buzz Baum and Gautam Dey of University College London explain in their paper, that uncertainty has stemmed in large part from the lack of known intermediates that bridge the gap in size and complexity between prokaryotic precursors and eukaryotes. As a result, they say, the origin of the first eukaryotic cell has remained “one of the most enduring mysteries in modern biology.” That began to change last year with the discovery of DNA sequences for an organism that no Read More ›

From Globe and Mail: While fertilization is the crucial first step to all human life, it has not been easy for scientists to determine precisely what happens when egg and sperm meet. In addition to the technical challenges, experiments that require human fertilization immediately raise ethical issues. To sidestep these dilemmas, researchers in both groups found ways to separately generate two proteins that are known to be crucial for fertilization and studied their interaction. The teams were then able to deduce the three-dimensional structures of the proteins and show precisely how they fit together, atom to atom. Their complementary findings were published Wednesday in the journal Nature. … One intriguing detail is that the Izumo1 protein, which is long and Read More ›

From BBC: The microbes, called Geobacter metallireducens, were getting their electrons from organic compounds, and passing them onto iron oxides. In other words they were eating waste – including ethanol – and effectively “breathing” iron instead of oxygen. f course, this is not breathing as we would recognise it. For one thing, bacteria do not have lungs. Instead, the bacteria pass their electrons to metal oxides that lie outside the cell. They do this through special hair-like wires that protrude from the cell’s surface. These tiny wires act in much in the same way that copper wire does when it conducts electricity. They have been dubbed “microbial nanowires”. More. We’ve noted this before, here and here. If a life form Read More ›

From ScienceDaily: Researchers are resurrecting ancient bacterial protein complexes to determine how 3.5-billion-year-old cells functioned versus cells of today. Surprisingly, they are not that different. Despite a popular hypothesis that primordial organisms had simple enzyme proteins, evidence suggests that bacteria around 500 million years after life began already had the sophisticated cellular machinery that exists today.” More. See also: See also: Michael Denton on the discontinuity of nature: Denton focuses on the many examples of fundamental features of life forms, like the pentadactyl limb of vertebrates, that are uniform, but serve no adaptive purpose in particular, pointing perhaps to discoverable physical patterns in nature, like the patterns in the chemical elements. and Sometimes Denton sounds like a Darwin who got Read More ›

600 mya. From ScienceDaily: Cells need to ‘know’ where they are in relation to all other cells in order to give rise into the correct cell types and tissues. The so-called ‘organizer’ is responsible for the formation of these body axes. Developmental biologists have shown that the molecular principles of the organizer are much more ancient than previously thought. The same signals were used already in the common ancestor of sea anemones and vertebrates 600 million years ago. … In vertebrate early development, an “organizer” forms in the region of the primitive mouth (the blastopore) of the embryo. This organizer is responsible for guiding axis formation of the organism. Its discovery won Hans Spemann a Nobel Prize in 1935. The Read More ›

From Kirkus Reviews, on science writer Ed Yong’s new book, I contain multitudes: The Microbes Within Us and a Grander View of Life: Prepare to meet some weird animals and weirder microbes, as Yong guides us through the animal kingdom to explain how microbes facilitate digestion, reproduction, and other functions integral to the survival of a species. In humans, microbes have been shown to regulate inflammation, an immune response linked to dozens of chronic conditions. In fact, in the absence of symbiotic microbes, life as we know it would quickly collapse—and yet it was only recently that microbes were understood to be more than disease-carrying bugs and more recently still that scientists have begun to understand their potential medicinal power. Read More ›

Biochemist James Shapiro told Suzan Mazur in The Paradigm Shifters: Overthrowing “the Hegemony of the Culture of Darwin,” Genome change is not the result of accidents. If you have accidents and they’re not fixed, the cells die. It’s in the course of fixing damage or responding to damage or responding to other inputs—in the case I studied, it was starvation—that cells turn on the systems they have for restructuring their genomes. So what we have is something different from accidents and mistakes as a source of genetic change. We have what I call “natural genetic engineering.” Cells are acting on their own genomes in a large variety of well-defined non-random ways to bring about change. p. 15 This is consistent Read More ›

Closing our religion coverage for the week (a bit late again), from Biosemiosis at Discourse at BioLogos: It is well known that Biologos has objections to the concept of design in biology (aka ID). I post the following short article as a conversation piece for those who agree with that assessment, or those who question it: … What JCVI has done, and is doing, is experimentally quantifying those requirements in terms of discrete function and numbers of base pairs. And this leads me to a couple of questions for those who profess (against massive physical evidence to the contrary) that this all came into being by naught (or whatever word you’d like to use). Considering the list of functions that Read More ›

From Suzan Mazur’s The Paradigm Shifters: Overthrowing “the Hegemony of the Culture of Darwin”: Scientists remain divided in their assessment of whether origin of life and evolution are linked. One investigator I’ve discussed this with for The Paradigm Shifters, Eugene Koonin, an expert in viruses and microbes, comments: “So, in a sense, you cannot help thinking the origin is a boundary, so there is something distinct in the origin problem from the rest of evolution.” Koonin also thinks paradigm shift is crucial since viruses and microbes, which transfer “genetic” information nonlinearly (non-Darwinian) and are the largest part of the biomass, were left out of the Modern Synthesis. And, says Koonin further, “in nature, any multicellular organism – animal, fungus, or Read More ›

“Directed mutations” means that the cell alters its own genome for its own protection, rather than simply being the recipient of random interventions. Here: APOBEC enzymes are thought to defend human cells against viruses by mutating them so they don’t work any more. Pinto et al. wondered if there might be evidence of APOBEC enzymes acting on human and ape genomes as well. Think of it as a sort of “collateral damage” in the war against viruses. In their survey, they found eight thousand unique clusters of mutations that look like APOBEC mutations in the human genome, as well as the genomes of Neandertal and Denisovans. They found almost a half million that were unique to the entire genus Homo. Read More ›

From ScienceDaily: Earth could contain nearly 1 trillion species, with only one-thousandth of 1 percent now identified, according to a study from biologists. The estimate is based on the intersection of large datasets and universal scaling laws. Scaling laws, like those discovered by the IU scientists, are known to accurately predict species numbers for plant and animal communities. For example, the number of species scales with the area of a landscape. “Until now, we haven’t known whether aspects of biodiversity scale with something as simple as the abundance of organisms,” Locey said. “As it turns out, the relationships are not only simple but powerful, resulting in the estimate of upwards of 1 trillion species.” The study’s results also suggest that Read More ›

Word is, in the “mystery function” fraction of the minimal cell Syn 3.0 genome—149 genes of the 473 essential set do not have any known associated functions, but they are demonstrably needed for Syn 3.0’s viability. That’s nearly a third of the essential hardware. From Geekwire: Because the functions of the genes are unknown, the researchers didn’t know they were needed until they were gone. That shows how far geneticists still have to go in understanding how life works. “We know about two-thirds of essential biology. We’re missing a third,” Venter said. Project leader Clyde Hutchison, a researcher at the J. Craig Venter Institute, said some of the genes appear to play a role in transporting small molecules around the Read More ›

From Washington Post: For 3 billion years, life on Earth was only home to water-dwelling, single-celled organisms like bacteria. But suddenly, multicellular life ballooned, knocking over the first domino in an evolutionary cascade that would one day allow you — yes, you — to exist and think and even read stuff on the Internet. Scientists think that until 500 million years ago, life on Earth fell victim to high-energy blasts from the sun, which at the time contained a lot more of the cell-killing gamma, ultraviolet and x-rays than it does today. The atmosphere then was too thin to fully protect our single-celled ancestors, whose DNA would have been damaged by such powerful rays. That kept them from becoming more Read More ›

From ScienceDaily: Salamanders and fish possess genes that can enable healing of damaged tissue and even regrowth of missing limbs. The key to regeneration lies not only in the genes, but in the DNA sequences that regulate expression of those genes in response to an injury. Researchers have discovered regulatory sequences that they call ’tissue regeneration enhancer elements’ or TREEs, which can turn on genes in injury sites. … Over the last decade, researchers have identified dozens of regeneration genes in organisms like zebrafish, flies, and mice. For example, one molecule called neuregulin 1 can make heart muscle cells proliferate and others called fibroblast growth factors can promote the regeneration of a severed fin. Yet, Poss says, what has not Read More ›