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Cell biology

From The Scientist: How first and “very, very complex” trees got to be so big 420 million to 359 mya

From Shawna Williams at The Scientist: Ancient fossils reveal how woodless trees got so big: by continuously ripping apart their xylem and knitting it back together. The trees’ woody fibers—namely, xylem, which carries water up the trunk—formed rings in the outer part of the trunk and connected to one another by horizontal strands, says Berry. Soft tissue filled the spaces between the fibrous network. As the trees grew outward, the xylem slowly ripped apart to accommodate the expansion, then knitted itself back together. The cores of the trees were hollow. While the architecture allowed the trees to support their weight as they expanded, they also caused what Stein terms a “structural failure”: the weight bearing down on the tree’s base Read More ›

Long term evolution experiments (LTEE) reveal too much complexity to be “disentangled”

So much for Darwinism. Joshua B. Plotkin writes at Nature: Ecological interactions emerge spontaneously in an experimental study of bacterial populations cultured for 60,000 generations, and sustain rapid evolution by natural selection. (paywall) Yes, that’s the abstract. It’s a model of economy. This is from the article: The authors’ most profound discovery is the spontaneous emergence of ecological interactions that fuel ongoing evolution (Fig. 1). Persistent subgroups have previously been identified in one of Lenski’s populations, but Good et al. reveal that at least 9 of the populations divide into two separate clades (genetic groups). These clades co-exist for tens of thousands of generations, and so must be maintained by some form of interdependence. These emergent ecologies sustain ongoing adaptation Read More ›

Intelligent design and the origin of the visual cycle

From commenter Otangelo Grasso, some thoughts:  The irreducible process of phototransduction, 11 cis retinal synthesis, and the visual cycle, essential for vertebrate vision http://reasonandscience.heavenforum.org/t1638-origin-of-phototransduction-the-visual-cycle-photoreceptors-and-retina#5753 William Bialek: More Perfect Than We Imagined – March 23, 2013 Excerpt: photoreceptor cells that carpet the retinal tissue of the eye and respond to light, are not just good or great or phabulous at their job. They are not merely exceptionally impressive by the standards of biology, with whatever slop and wiggle room the animate category implies. Photoreceptors operate at the outermost boundary allowed by the laws of physics, which means they are as good as they can be, period. Each one is designed to detect and respond to single photons of light — the Read More ›

Microbiology needs more math to help sort out the concept of “species”? Oh but wait…

From Mikhail Tikhonov at The Scientist: More profoundly, microbial ecosystems are a strange world where many familiar concepts start to break down, including “species,” “fitness,” and maybe even “organism.” In our everyday experience, we are rarely in doubt whether a given creature is a fox or a rabbit. Further, it seems very easy to delineate where an “individual” ends, and its “environment” begins. Our ability to do so is often taken for granted, and underlies how we think about both ecology and evolution. Whether these assumptions remain adequate for microbes is, however, increasingly doubtful. … The issue of microbial species being ill-defined is a hot topic in the biological literature. In a recent paper in Physical Review E, I try Read More ›

Could more than 30,000 biomed studies be suspect due to contaminated cells?

Yes. From Peter Dockrill at Science Alert: Of the 451 cell lines known to be compromised, the most famous contaminating source is what’s known as HeLa cells, named after their source, Henrietta Lacks. In 1951, this 31-year-old mother of five from Virginia died from cervical cancer. But during treatment before her death, cells were taken from Lacks’ cervix in a biopsy without her consent. Later, cell biologist George Otto Gey discovered these cells could be kept alive and grow indefinitely in a lab – as such, HeLa cells became the first immortalised cell line, meaning they didn’t eventually die due to cellular senescence. That everlasting quality made them a valuable research specimen that was distributed across the world, ultimately contributing Read More ›

Fatty tissues found in fossil bird from 48 million years ago

From ScienceDaily: As a rule, soft parts do not withstand the ravages of time; hence, the majority of vertebrate fossils consist only of bones. Under these circumstances, a new discovery from the UNESCO World Heritage Site “Messel Pit” near Darmstadt in Germany comes as an even bigger surprise: a 48-million-year old skin gland from a bird, containing lipids of the same age. The oldest lipids ever recorded in a fossil vertebrate were used by the bird to preen its plumage. … “As shown by our detailed chemical analysis, the lipids have kept their original chemical composition, at least in part, over a span of 48 million years. The long-chain hydrocarbon compounds from the fossil remains of the uropygial gland can Read More ›

Physics “tweezers” help study the engine room of the cell

From Matteo Rini at Physics: Life is hectic inside a living cell. To keep a cell functioning, myriad processes such as protein synthesis, power generation, waste disposal, and DNA replication are constantly and simultaneously running. These processes all rely on the precise and coordinated transport of organelles, proteins, and other biomolecules to the places where the cell needs them. George Shubeita, a professor of physics at New York University Abu Dhabi, studies the mechanisms by which tiny molecular motors move these cargoes. He observes the motors with superresolution microscopes and uses optical traps, commonly known as optical tweezers, to engage the motors in a “tug-of-war” game that allows him to measure their strength. In a conversation with Physics, Shubeita explains Read More ›

Researchers: Novel mechanism protects mitochondrial DNA

From Eurekalert: Researchers at the University of Eastern Finland have discovered a novel mechanism safeguarding mitochondrial DNA. The study, published in PNAS earlier this week, was carried out in close collaboration with research groups from CBMSO in Madrid, Spain, and Umeå University in Sweden. A central part of the protective mechanism is an unusual enzyme, PrimPol, which can re-initiate mitochondrial DNA replication after damage. Besides nuclear genomic DNA, mitochondria also contain their own small genomes, mitochondrial DNA (mtDNA), which encodes for thirteen essential parts of the cellular respiration machinery. mtDNA is especially vulnerable to oxidative damage as it is located close to the free radical producing mitochondrial electron transport chain. Cells protect their mitochondria by repairing mtDNA as well as constantly Read More ›

And now, the internet of cells

From Monya Baker at Nature: Yukiko Yamashita thought she knew the fruit-fly testis inside out. But when she carried out a set of experiments on the organ five years ago, it ended up leaving her flummoxed. Her group had been studying how fruit flies maintain their sperm supply and had engineered certain cells involved in the process to produce specific sets of proteins. But instead of showing up in the engineered cells, some proteins seemed to have teleported to a different group of cells entirely. … But Richard Cheney, a cell biologist at the University of North Carolina in Chapel Hill, is not ready to start revising the textbooks. Cheney has followed the field and at one point collaborated with Read More ›

An information theory approach to homeostasis

From Cell: A prevailing view among physiologists is that homeostasis evolves to protect organisms from damaging variation in physiological factors. Here, we propose that homeostasis also evolves to minimize noise in physiological channels. Fluctuations in physiological factors constitute inescapable noise that corrupts the transfer of information through physiological systems. We apply information theory to homeostasis to develop two related ideas. First, homeostatic regulation creates quiet physiological backgrounds for the transmission of all kinds of physiological information. Second, the performance of any homeostatic system influences information processing in other homeostatic systems. This dependence implies that multiple homeostatic systems, embedded within individual organisms, should show strongly nonadditive effects. Paper. (public access) – H. Arthur Woods, J. Keaton Wilson, An information hypothesis for Read More ›

Transcription Factors Play “Football”

This just in from PhysOrg: We had no idea that we would discover that transcription factors operated in this clustered way. The textbooks all suggested that single molecules were used to switch genes on and off, not these crazy nano footballs that we observed.” The team believe the clustering process is due to an ingenious strategy of the cell to allow transcription factors to reach their target genes as quickly as possible. Professor Leake said: “We found out that the size of these nano footballs is a remarkably close match to the gaps between DNA when it is scrunched up inside a cell. As the DNA inside a nucleus is really squeezed in, you get little gaps between separate strands Read More ›

Darwinism vs science: Even flu bugs are complex

Further to why flu vaccines so often fail, from Jon Cohen at Science, on efforts to find out wy the flu vaccine is so “lackluster”(10% to 60& protection): They’re questioning what was once received wisdom: that the vaccine fails when manufacturers, working months ahead of flu season, incorrectly guess which strains will end up spreading. And they’re learning instead that the vaccine may falter even when the right strains were used to make it, perhaps because of how it is produced or quirks of individual immune systems. “It’s much more complicated than we thought,” Osterholm says. “I know less about influenza today than I did 10 years ago.” … Danuta Skowronski, an epidemiologist at the BC Centre for Disease Control Read More ›

Researcher: Genome not an unstructured strand but “a highly structured and meaningful design”

From Mario Aguilera at U San Diego News: Intricate human physiological features such as the immune system require exquisite formation and timing to develop properly. Genetic elements must be activated at just the right moment, across vast distances of genomic space. “Promoter” areas, locations where genes begin to be expressed, must be paired precisely with “enhancer” clusters, where cells mature to a targeted function. Faraway promoters must be brought in proximity with their enhancer counterparts, but how do they come together? When these elements are not in sync, diseases such as leukemia and lymphoma can result. How does this work? Biologists at the University of California San Diego believe they have the answer. Calling it the “big bang” of immune Read More ›

Microprotein helps cells decide on best path to repair genes and avoid cancer

From the Salk Institute: Is it better to do a task quickly and make mistakes, or to do it slowly but perfectly? When it comes to deciding how to fix breaks in DNA, cells face the same choice between two major repair pathways. The decision matters, because the wrong choice could cause even more DNA damage and lead to cancer. Salk Institute scientists found that a tiny protein called CYREN helps cells choose the right pathway at the right time, clarifying a longstanding mystery about DNA repair and offering researchers a powerful tool that could guide better treatments for cancer. The work appears in Nature on September 20, 2017.More. And it all just happens, you understand without any intelligence underlying Read More ›