the biofixer

"The actual achievements of biology are explanations in terms of mechanisms founded on physics and chemistry, which is not the same thing as explanations in terms of physics and chemistry." My Primary Blog

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In many bat colonies, almost all the females birth their babirs at the same time.

Photo credit: Steven Bourne

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Cautionary note! Count data should not be analysed by log-transforming it, but instead models based on Poisson and negative binomial distributions should be used.

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Red-tailed Green Ratsnake - Gonyosoma oxycephalum (Boie, 1827) This is a diurnal, arboreal snake that occurs in primary forest, but appears to prefer edge habitats, secondary growth, plantations and rural gardens. As the name suggests, the snake has a green body with a red tail but is usually brown. It also has a dark line horizontally across its eye. It has smaller, smooth scales on its back that is usually bright green or light green and may have black net-like pattern.

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A Trachops cirrhosus (Fringe lipped bat) in pursuit of an unwary prey. Male tungara frogs (Engystomops pustulosus) have evolved a distinctive vocalization that function for specific signalling to female tungara frogs; this adaptation helps them find mates. Unluckily for the frog, the frog eating bat - Trachops cirrhosus make use of such mating signal to find its tasty meal. (Photo credit: Merlin Tuttle. Bat Conservation International.)

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"The Undertaking of a Lifetime Mate : the Case of a Monogynous Cannibalistic Spider" In contrast to the stereotype of male eagerness to mate with multiple females, monogynous males in various species actively limit themselves to mating with a single female in their lifetime. As monogyny eliminates the usual trade-off between investment in the current mating versus investment in future matings, it allows for the evolution of strikingly counter-intuitive male traits. Using a state-dependent dynamic game model based on the biology of the cannibalistic spider Argiope bruennichi, it was confirmed that conditional monogyny can evolve under broad conditions, including an even sex ratio. It was predicted that males should make a terminal investment when mating with large, virgin females, especially if population density is low and the encounter occurs late in the season. Read more: http://onlinelibrary.wiley.com/doi/10.1002/ece3.372/fullCollapse this post

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What makes you move? The Myosin Paradigm and the Power Stroke

          The movement of your eyes as you  scan your friends' posts at the moment, the clicks of your fingers as you choose relevant links that suit your interest or even the perplex of your Zygomaticus major and minor along with the rest of muscles involve in smiling as you saw your crush dear photo flashing across the screen - there must be something that drive such motions. What powers your every move  at daily occasion from walking, writing, eating or even the subtle laugh is primed by the simple yet efficacious molecule. Commendably, whatever your situation at this instance, all of the varied movements you are making right now are powered by this molecule named Myosin.  Whether voluntarily or involuntarily, it’s the Myosin that sets you on the Go! 

So whats with Myosin then? Myosin is a molecule-sized muscle that uses chemical energy to perform a deliberate motion. Myosin captures a molecule of ATP, the molecule used to transfer energy in cells, and breaks it, using the energy to perform a "power stroke."  Myosin is composed of several protein chains: two large "heavy" chains (color red) and four small "light" chains (colors orange and yellow). Each myosin performs only a tiny molecular motion. But by working together, the tiny individual power stroke of each myosin is summed to provide macroscopic power in our familiar world.

Myosin requires huge amounts of ATP when muscles are exerted. Say for instance your in the mood for a run. When you start running, the supply of ATP in your muscles lasts only about a second. Then, the muscle cells shift to phosphocreatine, a backup source of energy, which can be converted quickly into about 10 seconds worth of ATP. Then, if you are still running full tilt, your muscles start using glycogen, a molecule that stores glucose. This lasts for a minute or two, building up toxic acids as the sugar is used up. Then, the sprint is over and you have pushed your muscles to the limit. If, however, you slow down and pace yourself, your muscles can perform much longer. The blood vessels will dilate and your heart rate will increase, bringing twenty times as much blood through the muscles. Your muscle cells can then use this extra oxygen to produce far more ATP from the sugar in glycogen. Instead of collapsing after a short sprint, you now have the resources for a mountain hike or a marathon.

So where does the mighty Myosin takes into play?. We do know that ATP is the energy currency of the cell. ATP contains a key phosphate-phosphate bond that is difficult to create and is used to power many processes inside cells. You might be surprised to find, however, that breakage of this phosphate-phosphate bond is not directly responsible for the power stroke in myosin. Instead, it is release of the phosphate left over after ATP is cleaved that powers the stroke. Think of myosin like an arm that can flex towards you or push away. The cleavage of ATP is used in a priming step. When ATP is cleaved, myosin adopts a bent, flexed form. This prepares myosin for the power stroke. The flexed myosin then grabs the actin filament ( and release of phosphate snaps it into the straight "rigor" form. This power stroke pushes the myosin molecule along the actin filament. When finished, the remaining ADP is replaced by a new ATP, the myosin lets go of the actin filament. Then, it is ready for the next stroke. As this process goes on and on, you are abled to do movements just like your extraocular muscles do move your eyes as you read this post.

              photo Credit: David Goodsell

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Transcription Factor in Glioma Cells Regulated by Novel Genes

Scientists discovered a cellular pathway in the deadly brain cancer malignant glioma, a pathway essential to the cancer's ability to grow--and a potential target for therapy that would stop the cancer's ability to thrive. 

       A genome-wide RNAi screening tool was used to identify a dozen genes that affect the function of a crucial protein necessary for glioma cells to grow. In addition, the key pathway appears in laboratory cultures and mouse models to be susceptible to two cancer drugs already in use for other types of cancer.       A hallmark of cancer is uncontrolled cell growth, often caused by over-expression of genes that help cells survive, or under-expression of those genes that induce normal cell death. Genes that are expressed highly in cancer cells and are essential for their survival are attractive targets for drug therapy.

      Recent research revealed the essential cellular survival pathway, CREB3L2-ATF5-MCL1, in malignant glioma. The team identified novel genes that regulate the expression of a transcription factor called ATF5 (activating transcription factor 5) in malignant glioma cells. 

      ATF5 is linked to many cellular function including cell cycle progression, metabolite homeostasis cellular differentiation and apoptosis. ATF5 is a member of basic-region leucine zipper (bZIP) proteins family which binds the cAMP response element (CRE) consensus sequence: 5'GTGACGT(C/A)(G/A). This sequence is present in many viral and cellular promoters. ATF within or between subgroups can form homo- or hetero-dimer through the bZIP domain and the dimer can then bind to the DNA through the basic-motif and function as a transcription factor. Recently, another novel ATF5 consensus DNA binding sequence (CYTCTYCCTTW) was found in C6 glioma and MCF7 using a cyclic amplification and selection of targets.       The discovery of at least one previously unknown genetic pathway that appears to regulate this key transcription factor, and the subsequent determination that the cancer drugs sorafenib and temozolomide inhibit glioma growth, indicate new possibilities for potential therapeutics.

     (Source: Biotechdaily )

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Biology is a science of three dimensions. The first is the study of each species across all levels of biological organization, molecule to cell to organism to population to ecosystem. The second dimension is the diversity of all species in the biosphere. The third dimension is the history of each species in turn, comprising both its genetic evolution and the environmental change that drove the evolution. Biology, by growing in all three dimensions, is progressing toward unification and will continue to do so.

Edward O. Wilson. In ''Systematics and the Future of Biology'', Systematics and the Origin of Species: on Ernst Mayr's 100th anniversary.

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The Denouement of Lonesomeness! : A Glimpse into the Close Knit Association between Snail's Memory and its state of Social Confinement.

"Memory is perhaps a person's most distinctive characteristic. We often begin to have memories by simply exposing ourselves into the outer space of life - the environment. Like any other living creature, a snail (Lymnaea stagnalis) doesn't just live but also learn. However, under external factors and isolation, changes on their cognitive ability may be possible involving their behavior as well."

           Basically, snail breathe using its skin as it directly absorbs air when exposed to high oxygen condition. However, it shifts to aerial respiration by means of opening its lung for the air to pass via pneumostome and this mechanism was further investigated by Sarah Dalesman and Ken Lukowiak in their experiment. Three social conditions plus stressors were also involved to further realize its effect when the snails were isolated.

           As a result, snails that have been trained and maintained in groups under low calcium condition showed learning. Additionally, presence of a predator Kairomones greatly enhanced the snail's capability on forming long-term memory (LTM) and learning as well as when exposed to social groups. But, the twist is, inability to form LTM occured when the snail has been added with predator kairomones under the presence of low calcium because LTM formation has been blocked. This indicates that snails have their optimum levels as to how long they can be able to cope up with stressors as explained by Yerkes-Dodson Law.

           Reproductive ability showed no significant effects in terms of low calcium condition. Studies shows that it is probably upon on the isolation in which cognitive function may be altered and that data inconsistencies may be due to other environmental variables in which the snails can become adaptive and adjusted enabling their behavioral mechanism to change.

           The study implies that loneliness of snails aren't good enough for them and that high level of stressors could either increase the snail's performance to process memory or too much enough making them unable to go on with their cognitive skill. The environment to which they are laid as influenced their over-all mechanism. "Environmental manipulation of socially isolated animals will further elucidate context-specific effects on cognition as found here' so says Dalesman and Lukowiak.

Author: Nice E. Tambora. BS Biology.

Reference: Dalesman, S. and Lukowiak, K. Social snails : the effect of social isolation on cognition is dependent on environmental context. J.Exp.Biol.214,4179-4185.?

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An animal that never olds : a unique case of Paedomorphic Axolotl (Ambystoma mexicanum)

Almost everyone wishes to be forever young. Scientist had exerted a great deal of effort in finding the so called "the secret of youth" assorting in modelling of molecules that may retain youthfulness up to the very widely held stem cell research. As humans are engaged with this quandary, an amphibian in a name of axolotl are of free from distress with such predicaments - hence they had the secret of youth, but the drawback is, they are deprived of the refinement of maturity. Fair enough so I say.!

        Paedomorphosis is the retention of ancestral juvenile characters by adult stages of descendants. Paedomorphosis has occurred when reproduction is seen in what was ancestrally a juvenile morphological stage. This can be the result of neoteny or progenesis.

       In neoteny, the physiological (or somatic) development of an animal or organism is slowed or delayed while in Progenesis, it involves the retention of ancestral juvenile characters by adult stages of descendants due to an acceleration of the sexual maturation and thus is often regarded as a fast evolutionary process.

Paedomorphosis may have two important evolutionary effects:

• It may stop recapitulation that occurs during the development of the organism.

• It may be important in the origin of higher taxa. The first component of the argument is empirical. For many large groups of animals, the adults appear to resemble an early developmental stage of a possible ancestor.

        The axolotl  is a famous example of paedomorphosis, retaining in maturity the feathery gills that related species lose in infancy. In fact, it becomes sexually mature in this state. This adaptation, known as neoteny, is often viewed as a backward step in evolution because it prevents the axolotl from living on land, and as a result, it can't colonize new habitats. Axolotls are also famous for their fabulous regeneration ability. This regeneration occurs via the formation of a "bud" at the end of the damaged appendage, followed by growth of the new foot. Entire limbs can be regenerated and even portions of the brain and spine. How cool!..

(Photo credit: Axolotl.org)?

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The Creative Role of Natural Selection

         The genetic changes by which species adapt to their environment are the underlying structure of evolutionary progress. However, genetic opportunities at any time are limited. The reason for this is that the cost of evolution to a population is probably high, especially if many gene changes are being selected simultaneously. It is therefore, hardly surprising to find that many species become extinct because of changing environment to which they are unable to respond effectively. These evolutionary limitations extend also to the direction toward which a species is capable of evolving. The genetic endowment of a species produced by its past evolutionary history thus closes off certain evolutionary pathways and opens other which appear to be unique and “creative”. In such sense, the creativity one may observe in evolution is restrictive; that is guided by all of its many prior historical interactions.

        The creativity of evolution, however, does not mean “purposefulness” in the human sense. Except for artificial selection, there are no observable agents either within or without the organism that are consciously capable of directing evolution toward any particular stage. According to the modern view, evolutionary creativity is primarily caused by the important role played by natural selection as it acts upon genetic variability and thereby exposes a species too further selection for the same or closely connected environment.

         These considerations lead to the following important distinction. If we were artificially to partition the causation of evolution into two forces, selection and mutation, the argument that mutation alone is insufficient to produce most of the observed complex biological structures would be quite true. Without the creativity of selection, millions of possible structures may be produced at random, but it is hardly likely that any of them will show the remarkably precise functional relationships of organs such as vertebrate eyes or the human brain. It is primarily because of the guiding role of selection in choosing only those mutations that increase vision functionality in animals fore say and intelligence in humans that structures such as the eyes and brain have evolved. In other words, the random process of mutation produces the variation which natural selection then molds into structures which could not have arisen all at once by themselves. Ads aptly phrased by Fischer, “Natural Selection is a mechanism for generating an exceedingly high degree of improbability”.

         Restriction of future genetic change because of natural selection, however, does not mean that each type of organism must evolve a unique set of structures, different from those evolved in all other evolutionary lines. Many different organisms have similar phenotypic adaptations which have evolved separately, such as eyes bearing retinal pigments, lenses and focusing devices. In such instances, called “parallelism” or “convergence’, different genes in different organisms act to produce the same phenotypic result. Thus, on the one hand, they bear many similar features because they have faced many similar adaptive problems.

           Reference:

Fischer, R.A. The Genetical Theory of natural Selection.

Strickberger, M.W. 1976. Genetics.

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The Use of Fluorescent Powedered Pigments as a Tracking Technique for Snakes

Fluorescent powder tracking provides an exact record of movement and is therefore useful in discovering how an animal moves through its environment. Using fluorescent powder is also noninvasive, inexpensive, and can be performed successfully with little training. However, application of fluorescent powder on body surfaces is an underused method for obtaining data on  reptiles.

                   Benjamen Furman and colleagues describe a new technique for tracking snakes that is an alternative to radio-transmitters and thread trails. They coated the bodies of three species of garter snakes (Thamnophis) in fluorescent powder, then followed and marked the trails with a UV light at night. The use of a UV light allowed them to see very detailed paths left by the snakes.

         The effectiveness of fluorescent powder tracking may vary among and within groups of reptiles based on morphological characteristics. For instance they found out  that smaller garter snakes left shorter tracks than larger garter snakes, presumably because their smaller body surfaces collected less powder that dissipated over shorter distances. Habitat can also affect tracking success. Movement through grassy and herbaceous vegetation, such as used by garter snakes, tends to leave the best powder trails. Daily weather should also be taken into account as rain can reduce the visibility of the trails greatly. Of their tracked snakes, 10% ended up in tunnels or burrows, thus the use of fluorescent powder tracking may prove useful in finding hibernacula sites. Fluorescent powder tracking is proving to be an effective technique for tracking amphibians and reptiles, and was recommend its use for tracking snakes as part of ecological studies.

               . (Source: Furman et al., 2011. The Use of Fluorescent Powedered Pigments as a Tracking Technique for Snakes. Herpetological Conservation and Biology 6(3):473−478.)

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     Toxin for Self Protection : the case of Deadly Cholera Protein

Bacteria pull no punches when they fight to protect themselves. Some bacteria build toxins so powerful that a single molecule can kill an entire cell. This is far more effective than chemical poisons like cyanide or arsenic. Chemical poisons attack important molecules one by one, so many, many molecules of cyanide are needed to kill a cell. Bacterial toxins use two strategies to make their toxins far more deadly than this.

        The first strategy used to build super-deadly toxins is to use a targeting mechanism to deliver the toxin directly to the unlucky cell. Cholera toxin, ( shown as ribbon model on the second photo ), has a ring of five identical protein chains, colored blue here, which binds to carbohydrates on the surface of cells. This delivers the toxic part of the molecule, colored red, to the cell, where it can wreak its havoc.         The second deadly strategy is to use a toxic enzyme instead of a chemical poison. Enzymes are designed to perform their reactions over and over again, hopping from target to target and making their chemical changes. Thus, one enzyme can modify a whole cell full of molecules. Cholera uses this strategy once it gets inside cells. The toxic portion hops from molecule to molecule, disabling each one in turn, until the entire cell is killed.

         The catalytic portion of cholera toxin performs a single function: it seeks out the G proteins used for cellular signaling and attaches an ADP molecule to them (for more on G-proteins. This converts the G-protein into a permanently active state, so it sends a never-ending signal. This confuses the cell, and among other things, it begins to transport lots of water and sodium outwards. This floods the intestine, leading to life-threatening dehydration.

         "The two-part strategy employed by cholera toxin is highly effective, so much so that it is used by many different organisms that seek to protect themselves."

(Photo Credit: Prtotein Data Bank.)

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Egg-eating snakes are highly specialized species that lack teeth altogether. Instead, they have bony protrusions on the inside of their spine that break down egg shells after they've been eaten.

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Stem Cell Differentiation Regulated by Enzymes That Modify Histone Ubiquitinylation Patterns

Molecular biologists have identified two enzymes in embryonic stem cells (ESCs) that regulate differentiation into mature cell types by modifying the structure of chromatin histones in the ESC nucleus.

        ESCs maintain high genomic plasticity, which is essential for their capacity to enter diverse differentiation pathways. Posttranscriptional modifications of chromatin histones play a pivotal role in maintaining this plasticity. Current research  reported that the E3 ligase RNF20 catalyzes monoubiquitylation of histone H2B on lysine 120 (H2Bub1). In contrast, the deubiquitinase USP44 is a negative regulator of H2B ubiquitylation and is downregulated during ESC differentiation, which contributes to an increase in H2Bub1. Thus, optimal ESC differentiation requires dynamic changes in H2B ubiquitylation patterns, which must occur in a timely and well-coordinated manner.

       Ubiquitination is an enzymatic, protein posttranslational modification (PTM) process in which the carboxylic acid of the terminal glycine from the di-glycine motif in the activated ubiquitin forms an amide bond to the epsilon amine of the lysine in the modified protein.         Ubiquitin is a small protein that exists in all eukaryotic cells. It performs myriad functions through conjugation to a large range of target proteins. A variety of different modifications can occur. The ubiquitin protein itself consists of 76 amino acids and has a molecular mass of about 8.5 kDa. Key features include its C-terminal tail and the seven lysine residues. It is highly conserved among eukaryotic species with human and yeast ubiquitin sharing 96% sequence identity.

      Results presented in such research help to explain the significance of molecular defects identified in a number of cancers, for example, the abnormally low levels of RNF20 in certain breast and prostate cancers and the excess of USP44 in certain leukemias.

        (Source: Biotech Daily. 2012)