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Slime molds

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1 Slime molds on Fri Aug 25, 2017 8:40 am

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Slime molds

http://reasonandscience.heavenforum.org/t2602-slime-molds

https://en.wikipedia.org/wiki/Slime_mold
Slime mold or slime mould is an informal name given to several kinds of unrelated eukaryotic organisms that can live freely as single cells, but can aggregate together to form multicellular reproductive structures. Slime molds were formerly classified as fungi but are no longer considered part of that kingdom Although not related to one another, they are still sometimes grouped for convenience within the paraphyletic group referred to as kingdom Protista.

Slime molds play an ecological role similar to that of fungi. Protozoans play important roles in the fertility of soils.

http://creationwiki.org/Slime_mold
Slime molds can refer to several groups of different and controversial classifications. They have certain characteristics similar to those of fungi, plants, and animals. Their reproduction includes the production of spores similar to that of fungi and some plants, but, like animals, slime molds move (although very slowly) and ingest their food. These amazing organisms can be found almost anywhere, and the reproductive or fruiting phase of their life cycle, when the delicately stalked and often beautifully colored sporangia form, is the one most often observed. Another amazing feature possessed by plasmodial slime molds is that they are the largest unicellular organisms. Physarum polycephalum, for example, can grow to a size of 20 cm in diameter, but it is still a single cell. Slime molds may be seen in forests and gardens all over the world and are found wherever decaying organic matter is present, such as on rotting wood and leaves. Generally, slime molds are divided into two groups: plasmodial or true slime molds and cellular slime molds.

Can slime molds think? Computer scientists say maybe
https://uncommondescent.com/mind/can-slime-molds-think-computer-scientists-say-maybe/

How brainless slime molds redefine intelligence
Single-celled amoebae can remember, make decisions and anticipate change, urging scientists to rethink intelligent behavior.
http://www.nature.com/news/how-brainless-slime-molds-redefine-intelligence-1.11811

The ‘fungus’ that ‘walks’
http://creation.com/the-fungus-that-walks

Can Answers to Evolution Be Found in Slime?
http://www.nytimes.com/2011/10/04/science/04slime.html

The Evolution of Aggregative Multicellularity and Cell–Cell Communication in the Dictyostelia
http://www.sciencedirect.com/science/article/pii/S0022283615004532

Slime that can 'think' its way through a maze could turn our idea of intelligence upside down
http://www.dailymail.co.uk/sciencetech/article-2079394/Slime-think-way-maze-turn-idea-intelligence-upside-down.html?ito=feeds-newsxml

The mould shows unlikely signs of intelligence. Colonies of the mould appear to be able to 'organise' themselves so that they take the most direct route through a maze to find food, while at the same time avoiding damage from light. The mould even appears to be able to 'remember' dangers and avoid them. It's a task that would be beyond the capability of many advanced computers and software packages - and a level of 'information processing' that most of us wouldn't believe a single-celled organism would be capable of. Toshiyuki Nakagaki, of Future University Hakodate told AFP, 'Simple creatures can solve certain kinds of difficult puzzles. If you want to spotlight the essence of intelligence, it's easier to use these simple creatures.' The slime moulds are not intelligent as we understand it, but by flexibly responding to stresses such as light, and adapting, they are able to solve navigation problems that would baffle computers. The mould cells appear to operate as a 'network' that can even remember when they experienced stresses and dangers, and adapt. These primitive networks could be the key to building a new generation of biological computers, say researchers.

Smart but dumb: probing the mysteries of brainless intelligence
https://www.newscientist.com/article/mg23531340-700-smart-but-dumb-probing-the-mysteries-of-brainless-intelligence/

SNAILS, jellyfish and starfish have taught us that you don’t need a brain to learn. These seemingly simple creatures are capable learners, despite being completely brainless. Perhaps this is no great surprise. After all, it’s not as if they lack nerve cells. Strictly speaking, it’s neurons that enable learning – theirs are simply spread out, rather than being packed into centralised bundles.

But what if you take away the neurons?

Most life forms on Earth lack neurons, and yet they frequently manage to behave in complex ways. Previously, we have chalked this up to innate responses refined over generations, but it is beginning to look as if some of these humble non-neural organisms can actually learn. While that’s left some scientists scratching their heads, others are busy investigating how this ability could offer new approaches to fighting diseases and designing intelligent machines.

Take a slime mould. It certainly doesn’t look smart. This unusual creature, which is not a plant, animal or fungus, often resembles a glob of lemon curd that has fallen on the floor. Really, this manifestation is just one stage in the slime mould’s life, formed when many single cells, each with their own distinct DNA, mingle and fuse. The resulting yellow blob can grow to a few square metres, and is just one enormous cell containing thousands of nuclei.

In nature, a slime mould relies on chemical receptors on its surface to sense substances in its path as it creeps along the forest floor. If it gets a whiff of something attractive, like food, it will rapidly pulsate, pushing itself closer to the source.

Slime mold uses an externalized spatial “memory” to navigate in complex environments
http://sci-hub.cc/10.1073/pnas.1215037109
Spatial memory enhances an organism’s navigational ability. Memory typically resides within the brain, but what if an organism has no brain? We show that the brainless slime mold Physarum polycephalum constructs a form of spatial memory by avoiding areas it has previously explored. This mechanism allows the slime mold to solve the U-shaped trap problem—a classic test of autonomous navigational ability commonly used in robotics—requiring the slime mold to reach a chemoattractive goal behind a U-shaped barrier. Drawn into the trap, the organism must rely on other methods than gradient-following to escape and reach the goal. Our data show that spatial memory enhances the organism’s ability to navigate in complex environments. We provide a unique demonstration of a spatial memory system in a nonneuronal organism, supporting the theory that an externalized spatial memory may be the functional precursor to the internal memory of higher organisms.

Genetics: Sex and the social slime mold
http://sci-hub.cc/10.1126/science.1197423
The social amoeba Dictyostelium discoideum has three different sexes — members of one sex, or 'mating type', can fuse with either of the other two to form giant, dormant cysts.

Slime mold motility



Aggregation 1

i) cAMP wave propagation and chemotaxis

In Dictyostelium, aggregation occurs by chemotaxis to periodic cyclic AMP (cAMP) signals released from the aggregation centre  that propagate as waves. Cyclic AMP or cyclic adenosine monophosphate is a cyclic molecule derived from ATP (adenosine  trisphosphate). Cells move chemotactically towards increasing cAMP concentrations leading to aggregation streams and  multicellular aggregates.

1.        The cAMP is detected by a high affinity receptor, cAR1
2.        Which upon binding cAMP couples to a hetero-trimeric G protein
3.        Which liberates the bg complex
4.        Which attracts the cytosolic cAMP regulator (CRAC) to the membrane
5.        which then activates adenylyl (adenyl or adenylate) cyclise
6.        leading to cAMP synthesis
7.        cAMP is secreted and binds to the receptor again – autocatlytic feedback
8.        Binding of cAMP to the receptor leads to desensitisation
9.        cAMP is degraded extracellularly by phosphodiesterases, resensitising the receptor.

The results are periodic oscillations of cAMP. Cells undergoing chemotaxis are elongated. The waves may appear as expanding  spirals or concentric ring waves (as predicted by mathematical models using reaction-diffusion equations). Accumulation of cells  speeds up wave propagation. This locally distorts the wave front leading to the formation of bifurcating aggregation streams – that is  branching streams of migrating cells that converge on a central position. Eventually a mound of cells develops in the centre where  the cells accumulate.

Migrating cells thus secrete cAMP, which is sensed by other migrating cells by binding to the cAR1 receptor (expressed during early  development) which are thus stimulated to synthesise and secrete more cAMP to relay the signal to other cells. This sets-up  periodic pulses or waves of cAMP, peeking in the nM range of concentrations, radiating away from the aggregation centre to which  the cells are converging. (Such a centre will be set-up once several cells move close together). The binding of cAMP to the receptor  stimulates both adenylyl cyclase and guanylyl cyclase. Adenylyl cyclase is not essential for chemotaxis but is essential for  aggregation. Guanylyl cyclase is essential for chemotaxis. There are a number of cAR receptors (cAR1 to cAR4) but cAR1 is the  high-affinity receptor active early on.

Adenylyl cyclase is a membrane protein with 12 membrane spanning helices and several regions extending below the membrane  into the cytosol, inclusing a catalytic site where ATP binds and is converted into cAMP. Adenylyl cyclase is regulated by G proteins,  both stimulatory (Gs) and inhibitory (Gi). Guanylyl cyclase manufactures cyclic gunaine monophosphate, cGMP.

ii) Signals in mounds

Strain specific patterns of periodic cAMP signals occur within the mound. Some mounds are organised by single concentric ring  pacemakers, several concentric ring pacemakers, or 1,2,3,5 or multi-armed spirals. These patterns may interchange. Initially the  waves propagate fast at low frequency; later frequency increases while speed decreases. All these patterns eventually produce a  tip, which protrudes from the top of the mound. Differences and changes in wave patterns may result from alterations in the speed  of cAMP production and sensitivity to cAMP (e.g. a switch from cAR1 to the less sensitive cAR2 and cAR3 receptors).

Prestalk (pst) and prespore (psp) cells relay the signal. Prestalk cells originally form at random positions within the mound. Prestalk  cells turnover cAMP faster and have the low affinity cAR2 receptor, allowing them to relay the cAMP signal at high amplitude. The  result is an accumulation of prestalk cells in the tip, which thus becomes the sole signal-generating centre. Prespore cells express  cAR3. During this transition, localised groups of cells may form other centres, but ultimately only the centre in the tip survives.  Periodic microinjection of cAMP into mounds counteracts the endogenous signal and disrupts mound formation. The details are  more complex, with prestalk type A (pstA) cells accumulating in the tip and prestalk type B (pstB) cells accumulating in the base of  the mound, both these types form initially at random positions in the mound. Type pstA cells express ecmA markers, pstB cells  express ecmB. EcmA and EcmB are extracellular matrix proteins.

iii) Cell movement in mounds

Cell movement is directed antiparallel to the direction of wave propagation. The different patterns of cell migration are strain  specific. In spirals, cell movement is counter-rotational and cell movement is several times faster than in concentric ring patterns,  where cells may be periodically stationary.

In strain AX3, the cell speed is 10 micrometres/min during aggregation, 50 micrometres/min during mound formation. Cell velocity 
increases slightly when cells enter the aggregation streams. At the aggregation centre, movement slows down and becomes  temporarily disordered. Cell movement then suddenly increases in speed and becomes highly ordered and strongly rotational.  Movement slows again at the time of tip formation. Regulation of these processes could be due to changes in cAMP receptor  expression, changes in the cytoskeleton, cell adhesion and cell-matrix interactions?

iv) Tip formation

The amoebae differentiate into two principal cell types: prestalk (pst) and prespore (psp) cells. The prestalk cells differentiate and  sort out to form the tip on the top of the mound (pstA cells at the very tip, followed by pstO cells). The mound extends into the air  and contracts at the base. Cell movement in the tip appears to be always rotational. The period suddenly increases from 2 minutes  to 4 minutes (switch from cAR1 to cAR2?). Tip formation is cAMP dependent. Low affinity receptors may allow prestalk cells to  further respond to cAMP gradients when prespore cells are adapted. Prestalk cells also move faster and are less adhesive, which  may favour migration to the centre of the cell mass.

v) Arrest in mound stage

Evidence indicates that movement up to the top of the mound requires a high motive force involving both actin and myosin. Mutants  with actin and myosin defects are unable to pass the mound stage and culminate. Prestalk cells undergo rotational migration while  the cells at the base of the mound undergo periodic upward movement. The tip contracts and the mound elongates to form a  standing slug or grex. The grex eventually becomes unstable and topples over. In Acytostelium leptosomum several grexes usually  form from a single aggregation centre.


Differentiation and Morphogenesis in Dictyostelium: Cell Adhesion

The life cycle of dictyostelium

Another type of multicellular organization derived from unicellular organisms is found in Dictyostelium discoideum.* The life cycle of this fascinating organism is illustrated below



In its asexual cycle, solitary haploid amoebae (called myxamoebae or "social amoebae" to distinguish them from amoeba species that always remain solitary) live on decaying logs, eating bacteria and reproducing by binary fission. When they have exhausted their food supply, tens of thousands of these myxamoebae join together to form moving streams of cells that converge at a central point. Here they pile atop one another to produce a conical mound called a tight aggregate. Subsequently, a tip arises at the top of this mound, and the tight aggregate bends over to produce the migrating slug (with the tip at the front). The slug (often given the more dignified title of pseudoplasmodium or grex) is usually 2 4 mm long and is encased in a slimy sheath. The grex begins to migrate (if the environment is dark and moist) with its anterior tip slightly raised. When it reaches an illuminated area, migration ceases, and the grex differentiates into a fruiting body composed of spore cells and a stalk. The anterior cells, representing 15 20% of the entire cellular population, form the tubed stalk. This process begins as some of the central anterior cells, the prestalk cells, begin secreting an extracellular coat and extending a tube through the grex. As the prestalk cells differentiate, they form vacuoles and enlarge, lifting up the mass of prespore cells that had made up the posterior four-fifths of the grex (Jermyn and Williams 1991). The stalk cells die, but the prespore cells, elevated above the stalk, become spore cells. These spore cells disperse, each one becoming a new myxamoeba. In addition to this asexual cycle, there is a possibility for sex in Dictyostelium. Two myxamoebae can fuse to create a giant cell, which digests all the other cells of the aggregate. When it has eaten all its neighbors, it encysts itself in a thick wall and undergoes meiotic and mitotic divisions; eventually, new myxamoebae are liberated. Dictyostelium has been a wonderful experimental organism for developmental biologists because initially identical cells are differentiated into one of two alternative cell types, spore and stalk. It is also an organism wherein individual cells come together to form a cohesive structure composed of differentiated cell types, akin to tissue formation in more complex organisms. The aggregation of thousands of myxamoebae into a single organism is an incredible feat of organization that invites experimentation to answer questions about the mechanisms involved.

Cell adhesion molecules in dictyostelium

How do individual cells stick together to form a cohesive organism? This problem is the same one that embryonic cells face, and the solution that evolved in the protists is the same one used by embryos: developmentally regulated cell adhesion molecules

While growing mitotically on bacteria, Dictyostelium cells do not adhere to one another. However, once cell division stops, the cells become increasingly adhesive, reaching a plateau of maximum cohesiveness around 8 hours after starvation. The initial cell-cell adhesion is mediated by a 24,000-Da (24-kDa) glycoprotein that is absent in myxamoebae but appears shortly after division ceases (Knecht et al. 1987; Loomis 1988). This protein is synthesized from newly transcribed mRNA and becomes localized in the cell membranes of the myxamoebae. If myxamoebae are treated with antibodies that bind to and mask this protein, they will not stick to one another, and all subsequent development ceases.

Once this initial aggregation has occurred, it is stabilized by a second cell adhesion molecule. This 80-kDa glycoprotein is also synthesized during the aggregation phase. If it is defective or absent in the cells, small slugs will form, and their fruiting bodies will be only about one-third the normal size. Thus, the second cell adhesion system seems to be needed for retaining a large enough number of cells to form large fruiting bodies (Müller and Gerisch 1978; Loomis 1988). In addition, a third cell adhesion system is activated late in development, while the slug is migrating. This protein appears to be important in the movement of the prestalk cells to the apex of the mound (Ginger et al. 1998). Thus, Dictyostelium has evolved three developmentally regulated systems of cell-cell adhesion that are necessary for the morphogenesis of individual cells into a coherent organism. As we will see , metazoan cells also use cell adhesion molecules to form the tissues and organs of the embryo.

Dictyostelium is a "part-time multicellular organism" that does not form many cell types (Kay et al. 1989), and the more complex multicellular organisms do not form by the aggregation of formerly independent cells. Nevertheless, many of the principles of development demonstrated by this "simple" organism also appear in embryos of more complex phyla (see Loomis and Insall 1999). The ability of individual cells to sense a chemical gradient (as in the myxamoeba's response to cAMP) is very important for cell migration and morphogenesis during animal development. Moreover, the role of cell surface proteins in cell cohesiveness is seen throughout the animal kingdom, and differentiation-inducing molecules are beginning to be isolated in metazoan organisms.

Differentiation in dictyostelium

Differentiation into stalk cell or spore cell reflects another major phenomenon of embryogenesis: the cell's selection of a developmental pathway. Cells often select a particular developmental fate when alternatives are available. A particular cell in a vertebrate embryo, for instance, can become either an epidermal skin cell or a neuron. In Dictyostelium, we see a simple dichotomous decision, because only two cell types are possible. How is it that a given cell becomes a stalk cell or a spore cell? Although the details are not fully known, a cell's fate appears to be regulated by certain diffusible molecules. The two major candidates are differentiationinducing factor (DIF) and cAMP. DIF appears to be necessary for stalk cell differentiation. This factor, like the sex-inducing factor of Volvox, is effective at very low concentrations (10-10M); and, like the Volvox protein, it appears to induce differentiation into a particular type of cell. When added to isolated myxamoebae or even to prespore (posterior) cells, it causes them to form stalk cells. The synthesis of this low molecular weight lipid is genetically regulated, for there are mutant strains of Dictyostelium that form only spore precursors and no stalk cells. When DIF is added to these mutant cultures, stalk cells are able to differentiate (Kay and Jermyn 1983; Morris et al. 1987), and new prestalk-specific mRNAs are seen in the cell cytoplasm (Williams et al. 1987). While the mechanisms by which DIF induces 20% of the grex cells to become stalk tissue are still controversial (see Early et al. 1995), DIF may act by releasing calcium ions from intracellular compartments within the cell (Shaulsky and Loomis 1995).

Although DIF stimulates myxamoebae to become prestalk cells, the differentiation of prespore cells is most likely controlled by the continuing pulses of cAMP. High concentrations of cAMP initiate the expression of presporespecific mRNAs in aggregated myxamoebae. Moreover, when slugs are placed in a medium containing an enzyme that destroys extracellular cAMP, the prespore cells lose their differentiated characteristics (Figure 2.20; Schaap and van Driel 1985; Wang et al. 1988a,b).

1. http://cronodon.com/BioTech/Dictyostelium.html



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2 Re: Slime molds on Fri Aug 25, 2017 9:02 am

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