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Conceptualizing organisms (including ourselves) as dynamic molecular systems rather than discrete...

Sat, 18 May 2013 16:22:21 -0700

Conceptualizing organisms (including ourselves) as dynamic molecular systems rather than discrete objects “containing” some ethereal “life-force” is made difficult by our social conditioning (re: “souls,” etc). People seem to think that scrutiny of living systems, e.g. the reduction of an emotional reaction to its physiological components, somehow threatens the beauty of the system. But I have yet to find anything in biology that loses its beauty just by being examined.

Is This Virtual Worm the First Sign of the Singularity? Alexis...

Sat, 18 May 2013 15:22:00 -0700

Is This Virtual Worm the First Sign of the Singularity?

Alexis C. Madrigal

OpenWorm raises fascinating questions about what we mean when we say something is alive. If and when this project succeeds in modeling [Caenorhabditis elegans] successfully, we’ll be faced with a new and fascinating concept to think with: a virtual organism. Imagine downloading the worm and running it in a virtual petri dish on your computer. What, exactly, will you be looking at? Will you consider it to be alive? What would convince you?

Perhaps creations like the digital C. elegans will start to break down our binary conception of the matter in the world as either living or not living. We’ll discover that we can create systems that exist in-between these two spheres, or that certain aspects of life as we know it are not required to meet our definition of being alive.

“I suspect that we’ll recognize that living systems are far-from-equilibrium molecular systems that are carrying out very specific sophisticated physical patterns and have some ability to sustain themselves over time,” OpenWorm’s organizer Stephen Larson wrote to me. “Thinking about it that way makes me go beyond a black and white notion of ‘alive’ to a more functional perspective — living systems are those which self sustain.”

This article is amazing. Read more!

Photo

Thu, 16 May 2013 16:43:00 -0700

macrodan: Even ants slack off to catch up on gossip.

Thu, 16 May 2013 16:30:11 -0700

macrodan:

Even ants slack off to catch up on gossip.

headlikeanorange: A polar bear and her cub investigate the...

Wed, 15 May 2013 18:19:59 -0700

headlikeanorange:

A polar bear and her cub investigate the remains of a whale. (To the Arctic)

Sampling hair from frozen raccoons in the Slater Museum of...

Tue, 14 May 2013 06:18:53 -0700

Sampling hair from frozen raccoons in the Slater Museum of Natural History

Amadee Ricketts

Tue, 14 May 2013 06:02:10 -0700

Amadee Ricketts

How do newts regrow their limbs? by Michaela Alden Adult...

Sat, 11 May 2013 19:18:00 -0700

How do newts regrow their limbs?

by Michaela Alden

Adult urodeles, including newts and salamanders, have unique healing abilities that allow them to regenerate lost limbs, tails, retinae, intestines, and spinal cords. After a loss of limbs or tail, the urodele’s terminally differentiated dermal tissues (regular skin cells) become “reprogrammed,” first healing into a regenerative epithelium (RE) and then transforming into a blastema, a mass of cells capable of growth and development. Blastemata are normally seen only in embryos and the early stages of development, so the ability of fully differentiated adult urodele tissue to dedifferentiate into blastemata is of great interest to researchers. This area of study has potential applications in limb and organ regeneration of other adult vertebrates, including humans, but it is still unclear how urodeles transition from the initial stages of wound healing to blastema recruitment, and from blastema recruitment to tissue replacement.

It was previously thought that the blastema is composed of truly pluripotent stem cells, but blastemata are now understood to be specific to their tissue of origin, retaining partial differentiation. The replacement of a missing structure is accomplished through the recapitulation of the signaling molecules and pathways used when that structure was originally formed, pathways “remembered” by the cells of the blastema. This means that regeneration is specific to the location of the injury: an amputation at the wrist will result in the formation of a new hand, not an entire arm. The blastema is an autonomous morphogenic entity, meaning that if a wrist blastema is removed and grafted onto another part of the body, it will still produce a hand. The search for regeneration signaling molecules expressed in amputated newt limbs is an area of investigation that contributes to our understanding of the overall process of tissue regeneration.

How do blastemal cells “know” their position on a limb? One of the proteins involved is called Prod1. This protein, attached to the surface of the blastemal cells, helps dedifferentiated cells to “remember” their positional identity and is crucial to regeneration. The amount of Prod1 attached to a cell marks its position along the limb, with proximal cells (near the body) having more Prod1 than the distal cells (at the end of the limb). Prod1 is 69 amino acids long and a member of the three-finger protein (TFP) superfamily, a category including proteins present in many metazoans.

In 2009, Garza-Garcia et al. investigated some of the properties of Prod1 in the Eastern Newt, Notophthalmus viridescens. They were searching for orthologs, which are genes in different species that originated from a single gene of a common ancestor. The first step was to resolve the structure of Prod1, which involved both visualization of the protein by heteronuclear magnetic resonance (NMR) spectroscopy and a molecular dynamics-based computer simulation based on Prod1’s amino acid sequence. The structure of Prod1 was compared to known structures of other TFPs. The researchers then paired this structure-based approach with sequence-based phylogenetic analysis, using alignment software to compare the DNA sequence coding for Prod1 with the DNA sequence of other TFPs. Their analysis showed that Prod1 is not similar to other known proteins in structure or in sequence. These results suggest that proteins like Prod1 are specific to urodeles.

Nerves are required in regeneration and are thought to play a major role, possibly even initiating the entire process. In a study published in 2007, Kumar et al. searched for molecules that interact with Prod1 and identified a candidate ligand, dubbed the newt Anterior Gradient or “nAG” protein, that is secreted by nerves. To do this, they used a yeast two-hybrid screening assay, a technique commonly used to check for protein-protein interactions. In this technique, two factors required for transcription initiation are separately attached to “bait” and “prey” proteins of interest. Successful transcription indicates that the two proteins have interacted.

When denervated (separated from the nerve), the regenerative epithelium (RE) does not contain nAG, showing that it is supplied to the RE by nerve axons. Specifically, nAG is secreted by Schwann cells, the principle type of glial cell (support neuron). After identifying nAG as a Prod1 ligand, Kumar et al. used nAG-specific antibodies to investigate when and where nAG is expressed in the process of regeneration. They found that nAG is expressed after amputation in the nerve and, later, in the RE of the regenerating structure.

Urodele tissue regeneration will continue to be a major area of research in developmental biology because it is an unusual case of differentiated tissues being able to revert to a somewhat undifferentiated state and recapitulate their original growth. Perhaps the most interesting question raised by this research is not why adult urodeles can regenerate, but why other adult vertebrates cannot. One direction for research could involve the introduction of molecular signals like Prod1 and nAG to non-urodele embryonic tissues. With Prod1 proteins expressed since the beginning of development, perhaps it would be possible for fully differentiated adult non-urodele cells to retain the memory of their positional identity. If Prod1 and nAG could not be expressed for some reason in other vertebrates, a search for orthologs of nAG could help researchers design a pathway similar to the Prod1-nAG system.

Sources (click through to read more!)

Garza-Garcia, A, R Harris, D Esposito, PB Gates, and PC Driscoll. 2009. Solution structure and phylogenetics of Prod1, a member of the three-finger protein superfamily implicated in salamander limb regeneration. PLoS ONE 4: e7123.

Kumar, A, JW Godwin, PB Gates, AA Garza-Garcia, JP Brockes. 2007. Molecular basis for the nerve dependence of limb regeneration in an adult vertebrate. Science 318: 772-777.

rhamphotheca: Granulated Sea Star (Choriaster...

Sat, 11 May 2013 16:42:30 -0700

rhamphotheca:

Granulated Sea Star (Choriaster granulatus)

Choriaster granulatus is a large seastar, and is easily identified by its five distinctive large, short, thick conical arms. It is usually pale pink in colour, has small, brown papillae in clusters located in the central part of its body. This species grows to a maximum radius of approximately 27 cm.

It lives in shallow waters, of the Indo-Pacific, at depths of up to 40 m, and is found on rubble slopes, coral reefs,in the reef front, back reef, the external reef, and frequently in locations with rubble and detritus.

This starfish feeds on algae, detritus, and dead animals. One of its predators is the sea snail Triton’s trumpet (Charonia tritonis). It also eats various small invertebrates and coral polyps…

(read more: Wikipedia)

(photos: T - Sam Chow: M - Bernard DuPont; B - Richard Ling)

lauren-tregenza: There was an ice storm in my area a few weeks...

Mon, 06 May 2013 21:57:31 -0700

lauren-tregenza:

There was an ice storm in my area a few weeks ago. Everything was coated in ice! It was amazing but also no so amazing since the power was out for 30 hours. The weight of the ice brought down many older trees… which sometimes took down power-lines with them. A little apocalyptic, but beautiful!

LT.

thatscienceguy: A White Blood Cell chasing and consuming a...

Sun, 05 May 2013 01:11:18 -0700

thatscienceguy:

A White Blood Cell chasing and consuming a Bacterial Organism through a process called Phagocytosis.

steepravine: Late Night Special: Magic Heart Beetle I had the...

Thu, 02 May 2013 23:38:36 -0700

steepravine:

Late Night Special: Magic Heart Beetle

I had the best afternoon ever. I went for a run over to my friend’s house in 80 degree sunny weather (never happens in SF!) and found this magical beetle on the way.

I want to write a science fiction book about a society where magic beetles with hearts on their backs are the key to immortality. You have to go find one in the wild once a year - find one and you are immortal for the next year, don’t find one and you are mortal and take your chances. But if you kill a magic heart beetle or take it out of its home you die immediately.

(Fort Mason. San Francisco, California - 5/2013)

Photo

Mon, 29 Apr 2013 19:51:00 -0700

Everything you see is temporary and that doesn’t make it any less beautiful! You don’t...

Mon, 29 Apr 2013 16:14:09 -0700

Everything you see is temporary and that doesn’t make it any less beautiful!

You don’t have to ignore or avoid death in order to appreciate life!

rhamphotheca: Female frog Boophis bottae (family Mantellidae),...

Tue, 23 Apr 2013 20:37:13 -0700

rhamphotheca:

Female frog Boophis bottae (family Mantellidae), eggs are shining through; picture taken close to Ambatolahy, Ranomafana National Park, Madagascar.

(photo: Axel Strauß)

malformalady: The Leafy Spurge Hawk-moth (Hyles euphorbiae)...

Sun, 21 Apr 2013 19:22:31 -0700

malformalady:

The Leafy Spurge Hawk-moth (Hyles euphorbiae) larvae. Older larvae have a distinctive red, black, yellow, and white color pattern. Mature larvae may approach 10 cm in length; when disturbed, they regurgitate a slimy green liquid.

Photo credit: Ignazio Corda

astrodidact: Artwork of a blue supergiant star compared to the...

Sun, 21 Apr 2013 00:29:21 -0700

astrodidact:

Artwork of a blue supergiant star compared to the Sun. This is to scale, in case you felt terribly self-important today.

Image credit: NASA’s Goddard Space Flight Center/S. Wiessinger

astronomy-to-zoology: Strauch’s Spotted Newt (Neurergus...

Sat, 20 Apr 2013 09:44:58 -0700

astronomy-to-zoology:

Strauch’s Spotted Newt (Neurergus strauchii)

Also known as the Anatolian Newt, strauch’s spotted newt is a species of salamander found only in Anatolian plateau in Turkey. Like most salamanders the Anatolian newt is commonly found in small streams and rivers where it preys nocturnally on annelids, insect larvae and small arthropods. During the mating season male Strauch’s spotted newts perform an elaborate mating display, which involves tail-fanning and other movements, to secure a mate.

Phylogeny

Animalia-Chordata-Amphibia-Caudata-Salamandridae-Neurergus-strauchii

Image Source(s)

Photo

Sat, 20 Apr 2013 08:23:33 -0700

sciencesoup: The Eastern Newt The Eastern Newt (Notophthalmus...

Thu, 18 Apr 2013 18:25:37 -0700

sciencesoup:

The Eastern Newt

The Eastern Newt (Notophthalmus viridescens), a member of the family Salamandridae, lives in deciduous and coniferous forests throughout the eastern United States and adjacent parts of Canada. They have a unique life cycle: They begin life in an aquatic larval stage, develop into the familiar terrestrial form known as a “red eft,” then return to the water as adults. The red eft stage, shown in the top picture, lasts for 2-7 years and makes up about half of the life span. During this time, the newt is nocturnal and may be found wandering through leaf litter on a rainy night snacking on small invertebrates. (In fact, they are thought to play an important role controlling the populations of small insects like mosquitoes.) When they develop into adults and resume life underwater, they lose the bright reddish-orange coloration and turn yellow/olive, though their bright red spots remain. Although the number of Eastern Newts has declined due to habitat degradation, they are still so abundant in their range that they are not considered to be threatened. Although they don’t seem to mind being picked up, it’s best to keep handling to a minimum and wash your hands afterward because—as bright coloration often indicates—they secrete toxins from their skin when threatened. This is a defense mechanism that makes them unpalatable to predators like birds, mammals, and fish.

(Sources: 1, 2. Image Credit: 1, 2)

Guest Post written by Michaela Alden (skeptic-tank.tumblr.com)

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