Sunday, December 5, 2010

Arsenic-aliens? Arsenated-DNA? or simply Arsenic-Adaptation?

                                                         GFAJ-1 bacteria
Even at the risk of sounding deliriously dreamy, I'd say that the impact of the present discovery is such that humans could well be witnessing the emergence of alternative life-forms on earth.  In fact,  existing (but yet-undiscovered) life-forms could well push us enough to gape at the limits of endurance and stunning adaptations of Life. High-dreaming, Science fiction writers now only have to thank NASA for vindicating their way-off-the-scale 'absurd'-imaginations; which of course now seems inane and possible. What was earlier sci-fi is now routine, what was earlier a 'distant-possibility' is now 'present' and possible.  This report raises the possibility that we could indeed well be staring right in the face of creatures which might not care for Carbon.

In other words, there is a heightened likelihood of life-on-earth that uses elements other than what is normally 'prescribed'. The protagonist of this bizarre scientific-discovery (a bacterium) does exactly that - it substitutes Arsenic (As) for Phosphorus (P) in major bio-molecules to sustain its growth. 
But why the chest-thumps? why the brouhaha? Because, the knowledge of the occurrence of  exchange of major bio-elements raises a brazen possibility which could have profound evolutionary and geochemical significance. In fact, it is the first time in the history of biology that there's been anything found that can swap a major element for another in the basic structure. Ha, SETI just got a shot in the arm!
                                                  Are we talking to 'them' yet?!
Important: please visit the "Critique" section at the end of the post for a more nuanced understanding of some of the pitfalls of the paper, discussed in detail by a trained and practicing microbiologist.

Some background: Life on earth depends largely on six major nutrient elements - Carbon [C], Hydrogen [H], Nitrogen [N], oxygen [O], Sulfur [S], and Phosphorus [P], which make up the bulk of the cellular macromolecules - proteins, lipids and DNA. NO element has ever been shown to replace any of the 6-mentioned elements as core-constituents, efficiently and effectively, Never! This is what makes the discovery very special. It goes on to show just that! 
Having said that, let me also mention that As-loving bacteria have been known for some time, and indeed, a previous study by the same group, also published in 'Science', showed that bacteria  (some species of cyanobacteria and others taken from the same source [Mono-Lake, Calif.]) could effectively photosynthesize by extracting electrons from arsenite by oxidation, in order to help convert CO2 to biomass [source]. Undoubtedly, a rigorous scan of extremophiles in our lava-spewing volcanoes, hot-water springs, oceans etc. might throw up other interesting life forms. Indeed, a recent study in PNAS showed that there were hitherto unknown ultrasmall, nanoscale organisms (500 nm in diameter) residing in extreme conditions in a copper mine sludge that is as acidic as battery acid. They called the organisms ARMAN (archaeal Richmond Mine acidophilic nanoorganisms).

Rationale: 'As' is considered to be a chemical-analog of 'P', as it lies directly below P on the periodic table. There are tremendous physico-chemical similarities between their common salts AsO43- and PO43-, but owing to the relative instability of As-salts which get very easily hydrolyzed, they are not incorporated into biological processes [read metabolism], and are actually poisonous.
The question these guys asked was: Would organisms incorporate AsO43- into their system, if theres just no PO43- around? As it turned out, they actually did! Read on.

The bacterium: Samples of the rod-shaped GFAJ-1 bacteria, belonging to the salt-loving Halomonadaceae family of proteobacteria (identified by 16S rRNA sequence phylogeny), were recovered from the toxic, hypersaline and alkaline waters of Mono Lake, California, where the dissolved arsenic concentrations reached upto 200 μM on average, making it one of the highest natural concentrations of As in the world.
methodology: The investigators used lake sediments as inocula into an aerobic defined artificial medium at pH 9.8 containing 10 mM glucose, vitamins, trace metals but no added PO43- nor any additional complex organic supplements (e.g. yeast extract, peptone) with a regimen of increasing AsO43- additions spanning the range 100 μM to 5mM. Currently this isolate, strain GFAJ-1 is maintained aerobically with 40 mM AsO43-, 10 mM glucose and no added PO43- (+As/-P condition).

Stoichiometry and elemental distribution in the cell: Investigators used radiolabeled [73-AsO4-3-] to obtain more specific information about the intracellular distribution of arsenic. Wolfe-Simon and colleagues learned that about one-tenth of the arsenic absorbed by the bacteria ended up in their nucleic acids, but more than three quarters of the 73-AsO4-3- into the protein fraction, with a small fraction going into lipids.
This meant that the bacteria indeed could use As as a substitute, and was not merely using [and reusing] the scarce P-pool. 
Data produced by mass-spectrometry methods known as ICP-MS and NanoSIMS, showing the distribution of various chemical elements within GFAJ-1 cells, revealed a clear difference between cells grown with As [which were loaded with As] and those grown with P [had very little phosphorus]. In cells grown with phosphorus, the opposite was true. 
To confirm that the As was actually being incorporated into DNA, folks used gel purification of DNA to isolate and concentrate DNA from GFAJ-1 cells.
NanoSIMS measurement of these concentrated DNA extractions showed that arsenic was indeed present in their DNA.
Clinching evidence came from Micro extended X-ray absorption fine structure spectroscopy (µEXAFS) experiments, which showed that As bonded to O and C in the same way P bonds to O.
In other words: GFAJ-1 probably can substitute As for P in its DNA and all the while continue its life happily with children, as if nothing happened!

Now that we revere the DNA molecule as the 'ladder-of-life', and P [phosphate] as the backbone of this fantastic ladder [the basic DNA structure is here]; this study hits at the very-bottom of all dogmas and beliefs, by hinting that there could be alternatives to the elements. It reinforces what SETI-believers and star-wars worshippers have long been ranting about; that life can exist under a much wider range of environments than hitherto believed. GFAJ-1 are proof of life’s amazing ability to adapt to even the most difficult conditions. 
But really, are we looking at Arsenated-DNA yet? Life forms that operate beyond the realms of  the mandatory 6-elements? Maybe [or not]!

Questions that remain:
*Does all the phosphate get replaced by arsenates in the backbone of DNA? Then [by virute of its
  inherent instability], every bond in that chain would hydrolyze in minutes.
*Alternatively, if there is an arsenate-for-Phosphate structure, it has to be seriously stabilized by some as-yet-unknown mechanism. We dont know that yet.
*None of the measurements clearly proves that Arsenate is doing what phosphate normally would, in the DNA [although presently its difficult to come up with an alternative explanation].
*Does GFAJ-1 actively employ its arsenic-incorporating ability in its natural state, in the lake; or is it some very bizarre thing, which happens only under controlled laboratory-conditions.
*And, are there other As-using forms waiting to be discovered? Maybe even forms which have done away with DNA?

*These bacteria might one day help to clean up arsenic-contaminated drinking water 
*Or, clean up and bio-remediation after an oil spill [read the disastrous effects of Oil-spill in an earlier post]. 
*The field of custom-engineering microbes is a hot area of alternative energy. A synthetic organism that works by different chemicals entirely might actually just as important as the new arsenic-eating GFAJ-1 bacterium.
But a point to ponder is that GFeAJ-1 does NOT preferentially use As over P, hence all its usage would have to be limited to P-free environs.

Critique: following links lead to an expert's critique (Dr. Rosemary (Rosie) J. Redfield, a microbiologist at University of British Columbia) of the claims made in the paper, posted in her blog. She's torn the paper apart on issues of microbial-assays, but (admittedly) is not an expert on the biophysical aspects of the paper.

* Here is a very insightful paper [Science, 1987,  Vol. 235, 1173-1178], with valuable references which discuss why Nature chose Phosphates as a fundamental building block [and not Arsenate, Citrate or Silicate].

** A Bacterium That Can Grow by Using Arsenic Instead of Phosphorus [here]
    Felisa Wolfe-Simon1, Jodi Switzer Blum, Thomas R. Kulp, Gwyneth W. Gordon, Shelley E.    
    Hoeft, Jennifer Pett-Ridge, John F. Stolz, Samuel M. Webb, Peter K. Weber, Paul C. W. Davies,  
    Ariel D. Anbar and Ronald S. Oremland.
    Science, DOI: 10.1126/science.1197258, published Online 2 December 2010.

** "Microbe gets toxic response"

** Arsenic-eating microbe may redefine chemistry of life [Nature news, here]

** Arsenic eating bacteria opens new possibilities for alien life [here]

** Arsenic-based bacteria point to new life forms [here]

Monday, November 29, 2010

A cure for Alzheimer's: from Mice to Men?

                                                  Faces of Alzheimer's (Source)
A recent scientific-report is scorching news headlines, for very obvious reasons. This study claims, for the first time, that boosting levels of a single 'master regulator' of brain signaling, (EphB2) one  effectively resolves symptoms of the dreaded Alzheimer's disease (AD), at least for now, in mice. Although achieving similar results in humans might still be a long way off, yet findings  of the study have raised hope of an entirely new approach to tackling this debilitating disease in humans.

Alzheimer's diesease: (AD)—also called senile dementia of the Alzheimer type, primary degenerative dementia of the Alzheimer's type, or simply Alzheimer's—is the most common form of dementia. As the disease advances, symptoms include confusion, irritability and aggression, mood swings, language breakdown, long-term memory loss and the general withdrawal of the sufferer as their senses decline. This degenerative disease was first described by the German psychiatrist and neuropathologist Alois Alzheimer, in 1906. 
I dont have recent data, but in 2006 alone, there were 26.6 million sufferers worldwide.  And, AD is predicted to affect 1 in 85 people globally by 2050. The disease course is generally characterised with progressive patterns of cognitive and functional impairments.
Mechanism: AD has been identified as a protein misfolding disease (proteopathy), caused by accumulation of abnormally folded A-beta and tau proteins in the brain. Plaques are made up of small peptides, 39–43 amino acids in length, called beta-amyloid. Beta-amyloid is a fragment from a larger transmembrane protein called amyloid precursor protein (APP). APP is critical to neuron growth, survival and post-injury repair. In AD, APP gets divided into smaller fragments by enzymes through proteolysis. One of these fragments gives rise to fibrils of beta-amyloid, which form clumps that deposit outside neurons in dense formations known as senile/amyloid plaques.
AD is also caused due to abnormal aggregation of the tau protein. Every neuron has a cytoskeleton, an internal support structure partly made up of structures called microtubules. These microtubules act like tracks, guiding nutrients and molecules from the body of the cell to the ends of the axon and back. A protein called tau stabilizes the microtubules when phosphorylated, and is therefore called a microtubule-associated protein. In AD, tau undergoes chemical changes, becoming hyperphosphorylated; it then begins to pair with other threads, creating neurofibrillary tangles and disintegrating the neuron's transport system.

About EphB2 (wiki): Members of the Eph family of receptor tyrosine kinases control many aspects of cellular interactions during development, including axon guidance in neurons. Hence, EphB2 acts both as a receptor and an enzyme in a Neuron. EphB2 also regulates postnatal synaptic function in the mammalian CNS. A number of Eph receptors and their ligands (Ephrins) continue to be expressed following the period of primary CNS innervation.  It is considered rather important for dendritic maturation and critical for synaptic functions. Incidentally, brain levels of EphB2 are decreased in AD.

Outline of the study: Scientists at the Gladstone Institute of Neurological Disease (GIND) in San Francisco used a genetically engineered mouse model of AD, which simulates the disease (AD) and has abnormally low levels of EphB2 in memory centers of the brain. As it turned out during the course of the study, improving EphB2 levels in these mice by gene therapy completely fixed their memory problems.

mice used for the study [hAPP-mice]: Human amyloid precursor protein (hAPP) transgenic mice with high brain levels of amyloid-beta oligomers have reduced hippocampal levels of tyrosine-phosphorylated NMDA receptors (a glutamate receptor, is the predominant molecular device for controlling synaptic plasticity and memory function in neurons) and key components of NMDA-receptor-dependent signalling pathways. Very significantly, Hippocampal-levels of the receptor tyrosine kinase EphB2 are depleted in both AD patients and hAPP mice, which makes it an apt model-system choice.

Crucial Experiments / Observations: Investigators used gene therapy to experimentally alter EphB2 levels in memory centers of mice.
Reducing EphB2 levels using sh-RNA in normal healthy mice disrupted neurotransmission, impaired synaptic plasticity and reduced synaptic strength. Overall, it gave them memory problems similar to those seen in AD. This finding suggests that the reduced EphB2 levels in AD brains directly contribute to the memory problems that characterize the AD-condition.
Having achieved this, the cricitcal question of course now, was to assess whether normalizing EphB2 levels could fix memory problems caused by amyloid proteins.
To determine if increasing EphB2 expression in the dentate gyrus of hAPP mice reverses memory deficits, folks used a lentivirus expressing EphB2 (gene therapy method). Indeed, increasing dentate gyrus EphB2 levels reversed LTP deficits in two independent cohorts of hAPP mice. Dumping EphB2 proteins rescued synaptic functions and ameliorated cognitive (Spatial learning and memory) deficits in hAPP mice.

This study shows that EphB2 depletion contributes to amyloid-b-induced neuronal deficits and cognitive dysfunction. It pointedly shows that EphB2 impairment is necessary and sufficient to elicit impaired Long term Potentiation (LTP) and memory. Importantly, they showed that increasing neuronal EphB2 levels in hAPP mice reversed these deficits.
Of course, this work immediately doesn't provide medical advice, diagnosis or treatment for humans but could certainly pave the way for follow-up studies and eventual possible remedies for scores of human patients.
This study also stirs the already-sizzling debate of whether there could be potential "Master-Genes" in our system. Of course, with a growing acceptance for Network-models of signaling, one has to still work out the various possible targets and nodes (sensitive check points of control, where subsets of the signaling module meet) for a better understanding of the signaling pathway leading to AD.

* Reversing EphB2 depletion rescues cognitive functions in Alzheimer model. Nature, November 2010; DOI: 10.1038/nature09635. Moustapha Cissé, Brian Halabisky, Julie Harris, Nino Devidze, Dena B. Dubal, Binggui Sun, Anna Orr, Gregor Lotz, Daniel H. Kim, Patricia Hamto, Kaitlyn Ho, Gui-Qiu Yu and Lennart Mucke.

* The Receptor Tyrosine Kinase EphB2 Regulates NMDA-Dependent Synaptic Function. Neuron, Vol. 32, 1041–1056, December 20, 2001. Jeffrey T. Henderson, John Georgiou, Zhenping Jia, Jennifer Robertson, Sabine Elowe, John C. Roder,and Tony Pawson.

* Gene Therapy Prevents Memory Problems in Mice With Alzheimer's Disease [Source]

* An Alzheimer's cure? Boosting levels of a 'master regulator' of brain signaling could resolve symptoms [Source]

Monday, November 22, 2010

Rethinking Genomic Structures

                                                  Oikopleura dioica (source)

In a fascinating find, investigators described the genomic sequence of a tiny, transparent, mucus-covered marine animal, as the "alien-genome". Reason? It simply shatters a lot of our etched-in-stone scientific notions about eukaryotic genome architecture.
The genome of Oikopleura dioica breaks all the organizational rules previously thought to be critical for animal genomes - turning on its head a long held scientific-belief, that common architectural features of genomes observed across all animal kingdoms, are maintained by natural selection. 
This  study goes on to show that genome arrangement could actually be rather plastic!
The belief: Decades of arduous scientific work has shown that there exists a remarkable similarity in genome organization between species as distant and diverse as humans and sea sponges. These common multiple genomic features includes the order of genes, intron-exon organization, transposon diversity and developmental gene repertoire. This enormous amount of data somehow (mis)-led many of us to infer that a designated, non-flexible animal genome architecture is necessary to preserve form and function and is actively maintained by natural selection.
As it turns out, the genome of this tunicate, Oikopleura shatters this long-held belief!
About the animal: Tunicates are viewed as the closest living relatives of vertebrates, were probably simplified from more complex chordate ancestors.
Larvacean tunicates represent the second most abundant component of marine zooplankton and filter small particles by their gelatinous house which it secretes from a terminally differentiated oikplastic epithelium. Oikopleura dioica is the most cosmopolitan larvacean, has a very short life cycle (4 days at 20°C) and can be reared in the laboratory for hundreds of generations. Unique among tunicates, it has separate sexes. In fact, Oikopleura dioica is a favorite model-system for genetic, genomic and embryological studies.
The effort: Over 50 collaborating researchers at the Sars International Centre for Marine Molecular Biology at the University of Bergen in Norway, together with colleagues at Genoscope, a national sequencing center in France, sequenced and analyzed the Oikopleura genome, with high coverage shotgun reads (14X) using males.
At only 70 million base pairs (Mb), it turned out to be the smallest known animal genome. Remarkably, with 18,020 predicted genes, almost as much as a human's, but tucked into a DNA sequence 40 times shorter, makes the Oikopleura genome unusually compact. Although, two exceptions to global compaction are particularly interesting, as they may illustrate where excessive reduction could be harmful. First, a small population of Oikopleura developmentally regulated transcription factor genes have relatively large introns and intergenic spaces, and second, genes on the Y chromosome (since sex is genetically defined in Oikopleura), all expressed in the testis during spermatogenesis, have giant introns.
Moreover, while animals from sea anemones to primates have conserved the physical location of certain genes near each other, Oikopleura's genes appeared to have been randomly located, almost shuffled. Yet, Oikopleura has many of the same essential phenotypic features as other tunicates with traditional genome architecture.
Another significant peculiarity was the locations of introns - another structural feature conserved across several phyla - was gone, yet newer introns (5 to 6) had emerged all over the genome, sharing sequence-similarity to neighbours. This perhaps adds another dimension to the old scientific debate - where do introns originate?
Additionally, the Oikopleura genome leacked genes involved in immunity. In fact, many conserved immunity genes failed detection, supporting a minimized immune system consistent with the short Oikopleura life history.
Reason: Experts suggest that Oikopleura, is a rapidly evolving animal, with constant mutations in its nuclear and mitochondrial genomes. This speedy evolution is likely due to the fact that the animal spends most its life just below the ocean surface, bombarded by UV rays and other mutagens. Evolution of this rate, might have resulted this distinctively different genomic-architecture, unparalled in the animal kingdom. 
Overall, this work suggests that multiple genome organization features, have dramatically changed in the Oikopleura lineage. And despite an unprecedented genome revolution, the Oikopleura lineage preserved essential morphological features, even maintaining the chordate body plan to the adult stage.
It also throws up interesting questions..
-How does Oikopleura deal with this immense radiation induced DNA-damage? Does it have a unique DNA-recombination-repair mechanism?
-Fundamentally, why do larger animals (like us) need larger genomes?

* Plasticity of Animal Genome Architecture Unmasked by Rapid Evolution of a Pelagic Tunicate.
  Science, published online 18 November 2010, doi:10.1126/science.1194167.
* Thomson group, working on Oikopleura.

Tuesday, October 12, 2010

Tumbled-Thinkers of the world - Unite [and Rejoice]!

                                                      the "tumbled-thinker"

It's that time of the year, when the air's chilly and festive, the Hot-n'-Serious Nobels' have just left us dreamy-eyed, soaked in sweat and a wide anticipatory grin lies plastered across our's time for some serious-fun and serious-thought...its time to celebrate the intelligently-whacky Ig-Nobel-awards.

...following words (and the story thereon), are from the Ig-nobel site on Improbable-research
Why We Do It

Our goal is to make people laugh, then make them think. We also hope to spur people's curiosity, and to raise the question: How do you decide what's important and what's not, and what's real and what's not — in science and everywhere else?
"The most exciting phrase to hear in science, the one that heralds new discoveries, is not 'Eureka!' but, 'That's funny..." —Isaac Asimov
"Once you eliminate the impossible, whatever remains, no matter how improbable, must be the truth." —Sherlock Holmes

The 2010 Ig Nobel Prize Winners
The 2010 Ig Nobel Prizes were awarded on Thursday night, September 30, at the 20th First Annual Ig Nobel Prize Ceremony, at Harvard's Sanders Theatre.

ENGINEERING PRIZE: Karina Acevedo-Whitehouse and Agnes Rocha-Gosselin of the Zoological Society of London, UK, and Diane Gendron of Instituto Politecnico Nacional, Baja California Sur, Mexico, for perfecting a method to collect whale snot, using a remote-control helicopter.
REFERENCE: "A Novel Non-Invasive Tool for Disease Surveillance of Free-Ranging Whales and Its Relevance to Conservation Programs," Karina Acevedo-Whitehouse, Agnes Rocha-Gosselin and Diane Gendron, Animal Conservation, vol. 13, no. 2, April 2010, pp. 217-25.

MEDICINE PRIZE: Simon Rietveld of the University of Amsterdam, The Netherlands, and Ilja van Beest of Tilburg University, The Netherlands, for discovering that symptoms of asthma can be treated with a roller-coaster ride.
REFERENCE: "Rollercoaster Asthma: When Positive Emotional Stress Interferes with Dyspnea Perception," Simon Rietveld and Ilja van Beest, Behaviour Research and Therapy, vol. 45, 2006, pp. 977–87.

TRANSPORTATION PLANNING PRIZE: Toshiyuki Nakagaki, Atsushi Tero, Seiji Takagi, Tetsu Saigusa, Kentaro Ito, Kenji Yumiki, Ryo Kobayashi of Japan, and Dan Bebber, Mark Fricker of the UK, for using slime mold to determine the optimal routes for railroad tracks.
REFERENCE: "Rules for Biologically Inspired Adaptive Network Design," Atsushi Tero, Seiji Takagi, Tetsu Saigusa, Kentaro Ito, Dan P. Bebber, Mark D. Fricker, Kenji Yumiki, Ryo Kobayashi, Toshiyuki Nakagaki, Science, Vol. 327. no. 5964, January 22, 2010, pp. 439-42.
[NOTE: THE FOLLOWING ARE CO-WINNERS BOTH THIS YEAR AND IN 2008 when they were awarded an Ig Nobel Prize for demonstrating that slime molds can solve puzzles: Toshiyuki Nakagaki, Ryo Kobayashi, Atsushi Tero]

PHYSICS PRIZE: Lianne Parkin, Sheila Williams, and Patricia Priest of the University of Otago, New Zealand, for demonstrating that, on icy footpaths in wintertime, people slip and fall less often if they wear socks on the outside of their shoes.
REFERENCE: "Preventing Winter Falls: A Randomised Controlled Trial of a Novel Intervention," Lianne Parkin, Sheila Williams, and Patricia Priest, New Zealand Medical Journal. vol. 122, no, 1298, July 3, 2009, pp. 31-8.

PEACE PRIZE: Richard Stephens, John Atkins, and Andrew Kingston of Keele University, UK, for confirming the widely held belief that swearing relieves pain.
REFERENCE: "Swearing as a Response to Pain," Richard Stephens, John Atkins, and Andrew Kingston, Neuroreport, vol. 20 , no. 12, 2009, pp. 1056-60.

PUBLIC HEALTH PRIZE: Manuel Barbeito, Charles Mathews, and Larry Taylor of the Industrial Health and Safety Office, Fort Detrick, Maryland, USA, for determining by experiment that microbes cling to bearded scientists.
REFERENCE: "Microbiological Laboratory Hazard of Bearded Men," Manuel S. Barbeito, Charles T. Mathews, and Larry A. Taylor, Applied Microbiology, vol. 15, no. 4, July 1967, pp. 899–906.

ECONOMICS PRIZE: The executives and directors of Goldman Sachs, AIG, Lehman Brothers, Bear Stearns, Merrill Lynch, and Magnetar for creating and promoting new ways to invest money — ways that maximize financial gain and minimize financial risk for the world economy, or for a portion thereof.

CHEMISTRY PRIZE: Eric Adams of MIT, Scott Socolofsky of Texas A&M University, Stephen Masutani of the University of Hawaii, and BP [British Petroleum], for disproving the old belief that oil and water don't mix.
REFERENCE: "Review of Deep Oil Spill Modeling Activity Supported by the Deep Spill JIP and Offshore Operator’s Committee. Final Report," Eric Adams and Scott Socolofsky, 2005.

MANAGEMENT PRIZE: Alessandro Pluchino, Andrea Rapisarda, and Cesare Garofalo of the University of Catania, Italy, for demonstrating mathematically that organizations would become more efficient if they promoted people at random.
REFERENCE: “The Peter Principle Revisited: A Computational Study,” Alessandro Pluchino, Andrea Rapisarda, and Cesare Garofalo, Physica A, vol. 389, no. 3, February 2010, pp. 467-72.

BIOLOGY PRIZE: Libiao Zhang, Min Tan, Guangjian Zhu, Jianping Ye, Tiyu Hong, Shanyi Zhou, and Shuyi Zhang of China, and Gareth Jones of the University of Bristol, UK, for scientifically documenting fellatio in fruit bats.
REFERENCE: "Fellatio by Fruit Bats Prolongs Copulation Time," Min Tan, Gareth Jones, Guangjian Zhu, Jianping Ye, Tiyu Hong, Shanyi Zhou, Shuyi Zhang and Libiao Zhang, PLoS ONE, vol. 4, no. 10, e7595.


Thursday, August 26, 2010

* c u r i o s i t a s *: Science of Symbiosis in the Solar-Salamander.

Science of Symbiosis in the Solar-Salamander.

                                                      spotted salamander (source)

Be forewarned!...Another long-held scientific-dogma could be in the pipeline for complete annihilation! gulp further, and faster...[sorry for sounding like the eager foreword of a naive novella]...but this story IS as seductive as it can get...

For long, scientists heve believed, with good reason though, that the vertebrate system owing to it's highly specialized and robust adaptive-immune system rejects anything that is not 'self'. It translates into the following - It is impossible for a symbiont to live and propagate 'inside' a healthy vertebrate body, without retaliation from the host's immune system! Period!

         (A) Individual eggs within a salamander egg-mass, with tiny green alga Oophila, which provides the greenish appearance.

..Not any more, says Ryan Kerney of Dalhousie University in Halifax, Nova Scotia, Canada (Ryan is here). And the basis for this new-found boom in Ryan's voice comes from his close observations of a clutch of spotted-salamander (Ambystoma maculatum) eggs, which are green in appearance. He watched and watched and noticed something really extraordinary in those otherwise mundane and oft-studied eggs.

He realized for the first time, that the salamander eggs have a intracellular-guest - the single-celled alga, Oophila amblystomatis! Actually, these alga are generally called "salamander algae", and are a species of single-celled alga. The Latin specific name actually translates into "loves salamander eggs". And, it is these alga which give the characterisitc emerald-green colour to the salamander embryos as well as the jelly capsule that encases them.

Interestingly, it had been earlier known that the algae enjoy a symbiotic relationship with the spotted salamander, which lays its eggs in bodies of water. However, the symbiosis was thought to occur between the salamander embryo and algae living 'outside' it — a relationship hinging on the embryo producing nitrogen-rich waste that is useful to algae, and the algae reciprocating with increasing the oxygen content of the water in the immediate vicinity of the respiring embryos...but this new observation totally destroys the paradigm of symbiosis without far so good....

 (B) Detail of a single image. Head and gills of the dark, developing embryo are visible and the tiny green dots are the endosymbiont algae (source for A and B). 
Ryan goes on to suggest, that the green alga could be directly providing the products of photosynthesis — oxygen and carbohydrate — to the salamander cells that encapsulate them, thus making them energy-sufficient! This is indirectly-evidenced by Transmission Electron Microscopy (TEM) images which show several mitochrondria (which are the 'powerhouses' of animal cells, converting oxygen and a metabolic product of glucose into ATP, a molecule that cells use to store chemical energy) bordering the algal symbiont in the salamander cells. So salamander mitochondria gathered around an algal cell might be there to take advantage of the oxygen and carbohydrate generated by photosynthesis in that particular cell.

An earlier study by Lynda Goff, a molecular marine biologist and a host-parasite-interaction specialist, at the UC, Santa Cruz, who worked on this pair of organisms about 30 years ago, had successfully demonstrated, among other things, that embryos lacking algae in their surrounding jelly are slow to hatch also saw a logarithmic increase in algal cells as the embryo developed, and in those that did contain algae, the community was not static.

The question however remains as to how are the algal-cells present in the embryos evade self-destruction? Ryan says the it could be that either the salamander cells have turned their internal immune system off, or the algae have somehow bypassed it.

Another interesting question could be to probe the mode of entry of the algae inside the embryos?
A naturally happening likely moment is when the embryos' nervous systems begin to form. A time-lapse video made by Roger Hangarter at Indiana University in Bloomington reveals a fluorescent green flash next to each embryo at that point in its development. The flare is a bloom of algae, which is probably drawn to a release of nitrogen-rich waste from the embryo. Ryan postulates that if waste is released, then there must also be a way in — and the large number of algae in the bloom increases the chances that some will make it in...fair logic!

One of Ryan's most curious discoveries is of the presence of algae in the oviducts of adult female spotted salamanders, where the embryo-encompassing jelly sacs form — a finding that points to the possibility that symbiotic algae could be passed from mother to the offspring's jelly sacs during reproduction. Therefore is this a maternal-gift? This in turn raises another possibility - that whether algae could be getting into the germ [sex] cells.  That would really challenge the dogma [of vertebrate cells disposing of foreign biological material].

Now, is this smacking of Epigenetics? Inheritance that is modulated not by DNA,  and in this specific case, not even by intracellular molecular factors, but at an organismal level? Big Question.

The salamander happens to be an interesting animal - most of its cells retain a degree of pluripotency. That is, the animal has the capability to regrow its lost limbs when it loses them (remember the common Gecko which lets off its tail when threatened and usually regrows it)...does this mean that such animals have different modes of 'self' and 'non-self'-recognition?

The answer probably is very easy.....we have absolutely No-Idea at this point! 

Food for Thought? Yes. Yes.


* Green Eggs and Jam: Adaptations That Help Spotted Salamanders Reproduce (here).

* Green eggs power solar salamanders (here).

* Salamander's egg surprise (here)

* A solar salamander (here)
* Henrey Orr (1888). Note on the development of amphibians, chiefly concerning the central nervous system; with additional observations on the hypophysis, mouth, and the appendages and skeleton of the head Quarterly Journal of Microscopical Science
* Gilbert, P. (1944). The Alga-Egg Relationship in Ambystoma Maculatum, A Case of Symbiosis Ecology, 25 (3)

Friday, August 13, 2010

Mysterious cell component Nucleolinus (re)-discovered!

                       DIC image of Nucleolinus within the surf-calm, spisula (right) oocyte.                    

Surprise, Surprise! In the ripe age of satellite imagery and femto-scale probes, when folks are busy tweezing protein surfaces, these guys have (re)-discovered a cell-organelle. Perhaps, it's akin to the discovery of a new continent in the age of the terrace-pervading 'google-earth'.

Folks from the Marine Biological Laboratory's (MBL) Josephine Bay Paul Center, at the University of Illinois present their discoveries regarding the "Nucleolinus" in a paper in the Proceedings of the National Academy of Sciences (PNAS).
Although the nucleolinus, a cellular structure observed in the nucleus of many cells, including invertebrate egg cells and some mammalian cells, was discovered (and forgotten) more than 150 years ago, and other scientists had proposed its involvement in cell division, difficulties in visualizing the nucleolinus inside most cells had kept further studies at bay.
The scientists went on to develop a ribo-probe - NLi-1 for the RNA molecule present exclusively in the nucleolinus compartment in the oocytes of the surf clam, Spisula solidissima (the unfortunate clam is a valued delicacy in some cultures!). This breakthrough development of a marker for the elusive organelle would now serve the purpose of a beacon, and make future studies into its relevance and consequence in cells easier.
Other in situ observations in the oocytes revealed that the nucleolinus (and NLI-1) were inseparably associated with the developing spindle and centrosomes, and therefore could be related to cell-division.
Laser microsurgery that targeted the nucleolinus resulted in failed meiotic cell division in parthenogenetically activated oocytes and failed mitosis in fertilized oocytes, hence acribing a definitive role to the Nucleolinus in cell-division.

This investigation could clarify recent studies indicating an important role for the nucleolus in cell division. Possibly it was the shy Nucleolinus, all the way!

Curiously, the paper's bibliography cites references from as further back as 1857! (We, Indians were busy fighting the 1st war of independence against imperialist marauders then...)..
* Alliegro, M.A., Henry, J.J., Alliegro, M.C. Rediscovery of the Nucleolinus, a Dynamic RNA-Rich Organelle Associated with the Nucleolus, Spindle, and Centrosomes. Proceedings of the National Academy of Sciences, 2010; DOI: 10.1073/pnas.1008469107
*Alliegro MC, Alliegro MA, Palazzo RE (2006) Centrosome-associated RNA in surf clam
oocytes. Proc Natl Acad Sci USA 103:9034–9038.

* Scientists Confirm Role for Mysterious Cell Component -- The Nucleolinus.

Monday, July 26, 2010

investigating the Science of Death in Living Colour.

Pictured is an optical micrograph of cells 24 hours after initiation of apoptosis. The image combines coherent anti-Stokes Raman scattering (CARS) microscopy and two-photon excited fluorescence (TPEF) to show spatial distributions of major biomolecules such as proteins (red), RNA (green), DNA (blue) and lipids (grey) during apoptosis. Here, proteins abandon the nucleolus, accumulating in a highly irregular distribution in the nucleoplasm, and genomic DNA condenses and partially segregates from the proteins. (from the cover page of PNAS, July 20.)

Arguably, the most celebrated phenomenon studied by biologists, the science of programmed cell-death or Apoptosis, is essential to normal development, healthy immune system function, cancer prevention and a plethora of other functions. The pace of investigation in this already deadly field would now surely hotten up with the monitoring of Real-Time Dynamics of apoptotic cells in Living Color.
New science featured on the cover of the current issue of PNAS, University at Buffalo (UB) scientists have developed a biophotonic imaging approach capable of monitoring in real-time, the transformations that cellular macromolecules undergo during programmed cell death.
To develop the know-how of efficiently capturing transient and high-resolution cellular images of the phenomenon, an interdisciplinary UB team of biologists, chemists and physicists, led by Paras N. Prasad, executive director of the UB Institute for Lasers, Photonics and Biophotonics, utilized an advanced biophotonic approach that combines three techniques: a nonlinear, optical imaging system CARS (Coherent anti-Stokes Raman scattering), TPEF (two-photon excited fluorescence), which images living tissue and cells at deep penetration and Fluorescence Recovery after Photobleaching (FRAP), to measure dynamics of proteins.
This approach allows one to to monitor in a single scan, four different types of images, characterizing the distribution of proteins, DNA, RNA and lipids, the 4 major macromolecules, in the cell. The resulting composite image integrates in one picture the information on all four types of biomolecules, with each type of molecule represented by a different color: proteins in red, RNA in green, DNA in blue and lipids in grey, as shown on the PNAS cover. This kind of Multiplex imaging provided new information on the rate at which proteins diffuse through the cell nucleus, the UB scientists say.
Researchers noted that before apoptosis was induced, the distribution of proteins in the cell was relatively uniform, but once apoptosis develops, nuclear structures disintegrate, the proteins become irregularly distributed and their diffusion rate slows down.
This ability of dynamic mapping of molecular transformations could potentially help realize the promise of customized molecular medicine, in which chemotherapy, for example, can be precisely targeted to cellular changes exhibited by individual patients. It can also be a valuable drug development tool for screening new compounds. With the increased understanding of cellular events at the molecular level, where one can clearly visualise the changing dynamics of DNA, RNA and lipids during the cell's disintegration, one could specifically use it for monitoring how specific cancer drugs affect individual cells.
The advancement in Biophotonic-tools to effectively investigate, and perhaps use it for predictive and therapeutic purposes has opened up the field of customized bio-medicine. Moreover, this could be employed towards the study of new fundamental cellular investigations and structural reorganization throughout the mitotic cell cycle.

* Biophotonic probing of macromolecular transformations during apoptosis.  
   Proceedings of the National Academy of Sciences, 2010; 107 (29)
* Wikipedia for basic information on Apoptosis, (Bio)-Photonics, Cancer, Immune regulations etc.

Wednesday, July 21, 2010

scary thing is...can get away with Temper-Issues in some cultures, not in some others!

Anger is “an emotional state that varies in intensity from mild irritation to intense fury and rage,” according to Charles Spielberger, PhD, a psychologist who specializes in the study of anger. Like other emotions, it is accompanied by physiological and biological changes; when you get angry, your heart rate and blood pressure go up, as do the levels of adrenaline, and noradrenaline.
Getting angry might help you get your way if you're negotiating with European Americans, but watch out – in negotiations with East Asians, getting angry may actually hurt your cause. That's the conclusion of a new study on how people from different ethnic groups react to anger in their negotiations.
Most scientific research on negotiations, done on western populations have shown that anger is a good strategy – it gets you larger concessions than other emotions, like happiness, or no emotions. Recent work done by Hajo Adam, of INSEAD in France, who coauthored with William Maddux of INSEAD and Aiwa Shirako of the University of California - Berkeley, noticed differences in emotions in people working from different ethnicities. They noticed that sometimes people get angry, and react differently to a given situation. He thought this differential-response to a particular emotion could be due to intercultural differences.
The experiment used volunteers at the University of California - Berkeley. Half were Americans of European ethnicity and half were Asian or Asian American.
Each student took part in a negotiation on a computer and were told that they were negotiating with another human participant, when actually they were negotiating with a computer program. The student was supposed to be selling an electronic gadget, and making deals on sale-issues like warranty period and price. In some negotiations, the computer said it was angry about the negotiation; in others, it did not mention emotion.
European Americans made larger concessions to an angry opponent than to a non-emotional opponent. Asians and Asian Americans, however, made smaller concessions if their opponent was angry rather than non-emotional.
A subsequent experiment suggested that this may happen because of cultural norms about whether it's appropriate to get mad. 
This experiment started with telling the participants whether or not expressing anger was acceptable during the study. Asians and Asian Americans made greater concessions to an angry opponent if they were told that expressing anger was acceptable. European Americans were less likely to make concessions if they were told that anger was unacceptable.
When anger expressions are perceived as inappropriate, "People tend to react negatively. They no longer want to concede," says Adam. "They may even want to shut down and potentially penalize the counterpart for acting inappropriately." "I think what's important is that one person expressing emotions really affects another person's feelings, thoughts, and behavior," says Adam. "And these
reactions to emotional displays can critically depend on a person's cultural background." 
Do different genders follow the same ethnic-vulnerability pattern? We don't know yet.

* Association for Psychological Science, 2010, July 20. Getting angry can help negotiations in some cultures, hurt it in others.  
* ScienceDaily 
* Image-
* Research review on anger in psychotherapy. Journal of Clinical Psychology, 1999, Volume 55 Issue 3, Pages 353 - 363