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Cell biology

DNA has a molecular ambulance

From BioTechniques: A molecular motor that transports damaged DNA is also necessary for its repair. Double-strand breaks in DNA are a source of stress and sometimes death for cells. But the breaks can be fixed if they find their way to repair sites within the cell. In yeast, one of the main repair sites resides on the nuclear envelope where a set of proteins, including nuclear pore subcomplex Nup84, serves as a molecular hospital of sorts. The kinesin-14 motor protein complex, a “DNA ambulance,” moves the breaks to repair sites, according to a new study in Nature Communications (1). “To think of motor proteins moving DNA inside cells-it was very surprising,” said corresponding author Karim Mekhail at the University of Read More ›

Origin of complex cells: Can energy create information?

Origin of life researcher Nick Lane, author of The Vital Question asks at The Scientist: Did endosymbiosis-and the innovations in membrane bioenergetics it engendered-make it possible for eukaryotic life to evolve? There’s a black hole at the heart of biology. Why is it that complex eukaryotic cells share so many fundamental traits, from the nucleus to meiotic sex, which are essentially absent from prokaryotes? Most people would be hard pressed to distinguish a human cell from those of a mushroom, a plant, or a zoospore. Yet those cells diverged a billion years ago, and have utterly different ways of life. He argues at The Scientist for membrane bioenergetics: Genes point to an answer, but don’t explain the whole story. All Read More ›

New forms of life found on Earth, none elsewhere?

Really small bacteria. From Quanta Magazine: At Tiny Scales, a Giant Burst on Tree of Life DNA sequencing is at the heart of this current study, though the researchers’ success also owes a debt to more basic technology. The team gathered water samples from a research site on the Colorado River near the town of Rifle, Colo. Before doing any sequencing, they passed the water through a pair of increasingly fine filters — with pores 0.2 and 0.1 microns wide — and then analyzed the cells captured by the filters. At this point they already had undiscovered life on their hands, for the simple reason that scientists had not thought to look on such a tiny scale before. “Most people Read More ›

Life forms found at abyssal depths

Here. The life forms are not abundant, and their metabolisms run at very low levels. Still, they are alive and well, surviving on powdered coal and hydrogen and pumping out methane, the signature molecule leftover by life in extreme environments. They belong to the less commonly known domain of life called Archaea, home also to the extremophiles living in volcanic hot springs and deep sea hydrothermal vents. “They’re kind of just really cool bugs,” Huber said. “They are very successful organisms.” There are still a number of questions left to answer. Have these new microbes changed over the course of time? Have they adapted or branched off into new species? Or have they always been the same critter just barely Read More ›

We are told: One gene may drive leap from single cell to multicellular life

A philosopher used to say, beware the man of one book. Today, we might say, be cautious considering the claims of the scientist of one gene. From New Scientist we hear,: The leap from single-celled life to multicellular creatures is easier than we ever thought. And it seems there’s more than one way it can happen. … At some point after life first emerged, some cells came together to form the first multicellular organism. This happened perhaps as early as 2.1 billion years ago. Others followed – multicellularity is thought to have evolved independently at least 20 times – eventually giving rise to complex life, such as humans. How about making it easier? complex life such as millipedes? But no Read More ›

Bacteria created iron deposits by metabolizing iron?

Researchers: Half of iron atoms in some cores were processed by microbes 2.5 bya/Clark Johnson 2.5 billion years ago? That’s the theory here: These ancient deposits, up to 150 meters deep, were begging for explanation, says Johnson. Scientists thought the iron had entered the ocean from hot, mineral-rich water released at mid-ocean vents that then precipitated to the ocean floor. Now Johnson and Li, who is currently at Nanjing University in China, show that half of the iron in banded iron was metabolized by ancient bacteria living along the continental shelves. More. … Biologists say this process “is really deep in the tree of life, but we’ve had little evidence from the rock record until now,” Johnson says. “These ancient Read More ›

The ocean’s microbiome resembles the human gut’s microbia

From New Scientist: The biome of the ocean resembles that of the human gut We’re a step closer to understanding the microbial community that inhabits the ocean – and it has some striking similarities to the community that lives inside our guts. The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways. … For example, we already knew of about 4350 species of microalgae, 1350 species of protists and 5500 species of tiny animals, based on direct studies of their appearance. But the new genetic evidence suggests that there are probably three to eight times as many distinct species in each group as currently recognised. Shades of issues around claims about Read More ›

“Do Life and Living Forms present a problem for materialism?”

An essay contest from the Royal Institute of Philosophy and Cambridge University Press Entrants could win £2,500, publication in Philosophy, and a half hour of fame. No, but seriously, they could contribute to an increasingly significant discussion. Old style vitalism, attributing an internal animating substance or force to living things gave way to the idea that life may yet be a property over and above physical and chemical ones. Subsequent to that it was widely thought that life is an organisational or functional feature of bodies instantiated by their physical properties. With ongoing debates about analogous issues relating to mind (especially consciousness and intentionality) still running, and renewed interest in anti-reductionist interpretations of emergence and of teleological description and explanation Read More ›

A new ocean mystery: Bacterium allegedly doesn’t make sense

Life forms always make sense. Some theories do not. From Phys.org: By sequencing multiple Trichodesmium genomes—and using a wide variety of samples to ensure that there was no error—researchers found that only about 63 percent of the bacteria’s genome is expressed as protein. That’s an incredibly low amount for a bacterium and unheard of for a free-living oligotroph. (lives under very poor conditions, in this case it thrives massively in barren stretches of the ocean) “The unique evolutionary path reflected in this genome contradicts nearly all accounts of free-living microbial genome architectures to date,” said lead author Nathan Walworth, a Ph.D. candidate at USC. “Different evolutionary paths are foundational to all arenas of biology, including biotechnology, so it is important Read More ›

New Yorker Magazine considers the sponge

Here: A sponge essentially carves organs out of negative space, using its layers and jelly to delineate a complex network of channels and pores, which transport nutrients and waste much like a human kidney or bloodstream. This Spartan anatomy is so efficient that a single sponge can filter up to a thousand times its body volume of water in one day. Off the coast of Canada, reefs of glass sponges (so named for their silicate skeletons) can clean more than five hundred vertical feet of overlying water. And, if they take in dirt or toxins, sponges can clear themselves out with a languorous sneeze. … Even some professional biologists disregard sponges as lowly, primitive proto-animals, sitting at the bottom of Read More ›

Telomeres don’t just protect the ends of chromosomes

They modulate gene expressions over cells’ lifetimes. From The Scientist : Not only do telomeres protect the ends of chromosomes, they also modulate gene expression over cells’ lifetimes. … New work led by Jerry W. Shay and Woodring Wright of the University of Texas Southwestern Medical Center in Dallas demonstrates that telomeres are more than just buffer zones. The team found that as chromosomes fold within the nucleus, telomeres come into contact with faraway genes and alter their expression. As telomeres shorten, which happens with aging, chromosome looping and gene-expression patterns change. “I’m delighted with this evidence that the [telomere] sequence may actually be doing some regulation and that the decrease of the sequence in some cells may drastically affect Read More ›

Detailed pictures of smallest life forms

Really small: The snapshots may not look like much, but they’re revealing a lot about lifeforms at this extremely miniscule size. For one thing, their metabolisms are so minimal that they likely depend on resources from other bacteria to stay alive. While there’s still a lot that remains a mystery (it’s not certain what half of the genes do), this up-close imagery could eventually fill in a lot of blanks in biology — it’s clear that there’s a world of unusual organisms that have gone largely unnoticed. Engadget Note: If they depend on other bacteria for resources, they probably aren’t going to help much with origin of life studies. They might well be devolved from more metabolically endowed free-living organisms. Read More ›

Cell duplication, biocybernetics in action

John von Neumann, in his mid-1950s ground breaking studies about the mathematical theory of self-reproducing automata, argued that self-replication basically involves: — import of materials; — symbolic description/instructions; — memory; — constructor; — controller. He developed his theory before the discovery of DNA and the cellular machinery based on information processing. Here I will deal a little with the relations and similarities between such cybernetic theory and the biological process of cellular duplication. First, we must keep in mind that the biological cell is a natural living thing, a true whole, something characterized by a far higher degree of integration and unity compared to any artificial automaton. This is the reason why in cell division (and in general all what Read More ›