Sunday, 28 December 2008

The Majesty of Rock

Back in August 1992, McDawg & Co. were doing this:-


Re-reading back the lyrics of this fab "Spinal Tap" number, what a classic. I had to cheat half way through though with a copy of the lyrics.

There's a pulse in the new-born sun;
A beat in the heat of noon;
There's a song as the day grows long,
And a tempo in the tides of the moon.
It's all around us and it's everywhere,
And it's deeper than Royal blue.
And it feels so real you can feel the feeling!

And that's The Majesty Of Rock!
The fantasy of Roll!
The ticking of the clock,
The wailing of the soul!
The prisoner in the dock,
The digger in the hole,
We're in this together...and ever...

In the shade of a jungle glade,
Or the rush of the crushing street,
On the plain, on the foamy main,
You can never escape from the beat.
It's in the mud and it's in your blood
And its conquest is complete.
And all that you can do is just surrender.

To the Majesty of Rock!
The Pageantry of Roll!
The crowing of the cock,
The running of the foal!
The shepherd with his flock,
The miner with his coal,
We're in this together...and ever...

When we die, do we haunt the sky?
Do we lurk in the murk of the seas?
What then? Are we born again?
Just to sit asking questions like these?
I know, for I told me so,
And I'm sure each of you quite agrees:
The more it stays the same, the less it changes!

And that's The Majesty Of Rock!
The Mystery of Roll!
The darning of the sock,
The scoring of the goal!
The farmer takes a wife
The barber takes a pole.
We're in this together...and ever...

Saturday, 27 December 2008

Tuesday, 23 December 2008

New Articles this week in PLoS Biology Volume 6 Issue 12 December 2008‏

Historical and Philosophical Perspectives on Contemporary Biology

Keller EF
Evelyn Fox Keller introduces a new series that aims to promote productive dialogue between laboratory researchers and historians and philosophers of science to address the challenges arising from the rapid pace of biological discovery.


Lessons on Life from SENP2
Sedwick C

Loopy Chromatin Brings Distant DNA to Bear on Silencing Promoter Genes

Hoff M

Gal4 Gets Genes to Loosen Up

Sedwick C


Towards an Integrated Framework for Assessing the Vulnerability of Species to Climate Change

Williams SE, Shoo LP, Isaac JL, Hoffmann AA, Langham G
Climate change is a major threat to global biodiversity. A novel integrated framework to assess vulnerability and prioritize research and management action aims to improve our ability to respond to this emerging crisis.

Historical and Philosophical Perspectives

“It's Ok, We're Not Cousins by Blood”: The Cousin Marriage Controversy in Historical Perspective

Paul DB, Spencer HG
Marriage between first cousins is highly stigmatized in the West and, indeed, is illegal in 31 US states. But is the hostility to such marriage scientifically well-grounded?


The Role of Auxin Transport in Plant Patterning Mechanisms

Smith RS
In plants, many patterning processes involve the phytohormone auxin, and controlling how it moves around plays a critical role in pattern formation.
Research Article: Root System Architecture from Coupling Cell Shape to Auxin Transport

Caenorhabditis elegans Meets Microsporidia: The Nematode Killers from Paris

Hodgkin J, Partridge FA
A newly discovered species of Microsporidia, which are obligate intracellular parasitic fungi, has been found able to infect the intestinal cells of the nematode C. elegans and subvert their cytoskeletal architecture.
Research Article: Microsporidia Are Natural Intracellular Parasites of the Nematode Caenorhabditis elegans

Animal Defenses against Infectious Agents: Is Damage Control More Important Than Pathogen Control
Read AF, Graham AL, Råberg L
The ability of hosts to withstand a given number of pathogens is a critical component of health. Now playing catch-up with plant biologists, animal biologists are starting to formally separate this form of defense from classical resistance.
Research Article: A Signaling Protease Required for Melanization in Drosophila Affects Resistance and Tolerance of Infections

Research Articles

Mutualistic Interactions Drive Ecological Niche Convergence in a Diverse Butterfly Community
Elias M, Gompert Z, Jiggins C, Willmott K
Müllerian mimicry, a classic mutualism, is associated with microhabitat convergence in tropical butterflies, outweighing both common ancestry and competition. Positive interactions may thus be more important in community assembly than commonly assumed.
Author Summary

The Worldwide Variation in Avian Clutch Size across Species and Space

Jetz W, Sekercioglu CH, Böhning-Gaese K
Why do some bird species lay only one egg in their nest, and others ten? An analysis combining comparative and macroecological approaches across more than half of all bird species explains the global variation in this trait with high confidence.
Author Summary

High Functional Diversity in Mycobacterium tuberculosis Driven by Genetic Drift and Human Demography
Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, et al.
DNA sequence analysis of a global collection of M. tuberculosis strains reveals high functional diversity, severely reduced selective constraint, and global spread through both ancient and recent human migrations.
Author Summary

Timing Precision in Population Coding of Natural Scenes in the Early Visual System
Desbordes G, Jin J, Weng C, Lesica NA, Stanley GB, et al.
Early neural representation of visual scenes occurs with a temporal precision on the order of 10 ms, which is precise enough to strongly drive downstream neurons in the visual pathway. Unlike individual neurons, the neural population code is largely insensitive to pronounced changes in visual contrast.
Author Summary

Identifying Neural Drivers with Functional MRI: An Electrophysiological Validation
David O, Guillemain I, Saillet S, Reyt S, Deransart C, et al.
Neural long-range interactions can be distinguished from hemodynamic confounds in functional magnetic resonance imaging using new data analysis techniques that will allow experimental validation of models of brain function.
Author Summary

PKMζ Maintains Spatial, Instrumental, and Classically Conditioned Long-Term Memories

Serrano P, Friedman EL, Kenney J, Taubenfeld SM, Zimmerman JM, et al.
The persistent activity of a brain enzyme, PKMζ, stores specific associations, both unpleasant and rewarding, for places, events, and actions, and is thus a general mechanism for memory storage.
Author Summary

The Maternally Expressed WRKY Transcription Factor TTG2 Controls Lethality in Interploidy Crosses of Arabidopsis
Dilkes BP, Spielman M, Weizbauer R, Watson B, Burkart-Waco D, et al.
Hybrid lethality in crosses between diploids and tetraploids, plants with whole genome duplication, is determined by an epidermal regulator expressed in the maternal tissue that envelops the seed.
Author Summary

Root System Architecture from Coupling Cell Shape to Auxin Transport

Laskowski M, Grieneisen VA, Hofhuis H, Hove CAt, Hogeweg P, et al.
Experimental data and computer modeling show that lateral root positioning can be controlled by the physical stimulus of root curvature, which triggers self-organizing alterations in auxin transport.
Author Summary
Primer: The Role of Auxin Transport in Plant Patterning Mechanisms

Microsporidia Are Natural Intracellular Parasites of the Nematode Caenorhabditis elegans
Troemel ER, Félix MA, Whiteman NK, Barrière A, Ausubel FM
A newly identified intracellular pathogen of wild-caught Caenorhabditis elegans represents a new microsporidian species that will provide a model to study this class of pathogen in humans.
Author Summary
Primer: Caenorhabditis elegans Meets Microsporidia: The Nematode Killers from Paris

The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster
Teixeira L, Ferreira A, Ashburner M
Wolbachia are one of the most widespread intracellular bacteria. In Drosophila melanogaster, the presence of Wolbachia increases resistance to infection by RNA viruses.
Author Summary

A Signaling Protease Required for Melanization in Drosophila Affects Resistance and Tolerance of Infections
Ayres JS, Schneider DS
It isn't easy to predict how mutations will affect a host's immune response. Mutations that affect the interaction of a fly with one pathogen can increase or decrease resistance or tolerance to other pathogens.
Author Summary
Primer: Animal Defenses against Infectious Agents: Is Damage Control More Important Than Pathogen Control?

The Communication Factor EDF and the Toxin–Antitoxin Module mazEF Determine the Mode of Action of Antibiotics
Kolodkin-Gal I, Sat B, Keshet A, Kulka HE
The mode of action of certain antibiotics is revealed in a study using different strains of E. coliM, which implicates mazEF-mediated cell death and the formation of reactive oxygen species.
Author Summary

Twist-2 Controls Myeloid Lineage Development and Function

Sharabi AB, Aldrich M, Sosic D, Olson EN, Friedman AD, et al.
The transcription factor Twist-2 is a new regulator that inhibits the proliferation and differentiation of granulocyte macrophage progenitors. Twist-2 also inhibits proinflammatory cytokine production, while stimulating IL-10 by myeloid cells.
Author Summary

SUMO-Specific Protease 2 Is Essential for Modulating p53-Mdm2 in Development of Trophoblast Stem Cell Niches and Lineages
Chiu SY, Asai N, Costantini F, Hsu W
Targeted disruption of SUMO-specific protease 2 in mice reveals that SUMO modulation of the p53/Mdm2 pathway is pivotal for G/S transition of mitosis and endoreduplication during trophoblast development.
Author Summary
Synopsis: Lessons on Life from SENP2

Nutrient-Regulated Antisense and Intragenic RNAs Modulate a Signal Transduction Pathway in Yeast
Nishizawa M, Komai T, Katou Y, Shirahige K, Ito T, et al.
During nutritional adaptation, transcriptional activation in yeast produces noncoding RNAs that allow the formation of a positive-feedback regulatory loop.
Author Summary

Modeling a Snap-Action, Variable-Delay Switch Controlling Extrinsic Cell Death
Albeck JG, Burke JM, Spencer SL, Lauffenburger DA, Sorger PK
A combination of single-cell experiments and mathematical modeling reveals the mechanisms underlying all-or-none caspase activation during receptor-induced apoptosis.
Author Summary

Senescence-Associated Secretory Phenotypes Reveal Cell-Nonautonomous Functions of Oncogenic RAS and the p53 Tumor Suppressor
Coppé JP, Patil CK, Rodier F, Sun Y, Muñoz DP, et al.
By controlling how damaged cells modify their surrounding tissue environment, a tumor suppressor gene can restrain, and an oncogene can promote, the development of cancer.
Author Summary

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits
Heinzen EL, Ge D, Cronin KD, Maia JM, Shianna KV, et al.
We investigated tissue-specific genetic control of gene expression and alternative splicing in primary human cells, and we describe here the implications for understanding how genetic variation influences human disease.
Author Summary

Epigenomic Consequences of Immortalized Plant Cell Suspension Culture

Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, et al.
Immortalized plant cells undergo epigenomic changes, reminiscent of immortalized animal cell lines and cancer cells, accompanied by shifts in small RNA classes, implicating a role for the RNAi machinery in regulating the epigenome.
Author Summary

BEAF Regulates Cell-Cycle Genes through the Controlled Deposition of H3K9 Methylation Marks into Its Conserved Dual-Core Binding Sites
Emberly E, Blattes R, Schuettengruber B, Hennion M, Jiang N, et al.
Chromatin Dual-Cores define new potent nucleosome-associated cis-regulatory elements that regulate the accessibility of promoters of genes controlling chromosome organization/segregation and the cell cycle.
Author Summary

PcG Proteins, DNA Methylation, and Gene Repression by Chromatin Looping

Tiwari VK, McGarvey KM, Licchesi JD, Ohm JE, Herman JG, et al.
Chromatin regions enriched for Polycomb group proteins physically interact in a series of loops around a single gene in mammalian cells. This higher order structure maintains a poised, low transcription state in embryonic cancer cells and, with addition of DNA methylation, a completely repressed transcription in adult cancer cells.
Author Summary
Synopsis: Loopy Chromatin Brings Distant DNA to Bear on Silencing Promoter Genes

Activator Control of Nucleosome Occupancy in Activation and Repression of Transcription
Bryant GO, Prabhu V, Floer M, Wang X, Spagna D, et al.
A new nucleosome-occupancy technique reveals how the transcriptional activator Gal4 determines chromatin structure as genes are activated and repressed.
Author Summary
Synopsis: Gal4 Gets Genes to Loosen Up


Correction: Fish Invasions in the World's River Systems: When Natural Processes Are Blurred by Human Activities

Leprieur F, Beauchard O, Blanchet S, Oberdorff T, Brosse S

Correction: Survival of Migrating Salmon Smolts in Large Rivers With and Without Dams

Welch DW, Rechisky EL, Melnychuk MC, Porter AD, Walters CJ, et al.

All journal content, except where otherwise noted, is licensed under a Creative Commons Attribution License.

Sunday, 21 December 2008

Where in the world is my nearest Institutional Repository?

"This site is a mashup of data from ROAR and OpenDOAR overlayed onto Google maps. You can read about the development of the maps on the repository map mashup blog".

McDawg has known about Repository 66 for about 18 months now but hadn't blogged anything until now. This was overdue.

Muchos Kudos to Stuart Lewis @ Aberystwyth University in Wales for maintaining the Repository 66 website/Maps and blog.

See the "About The Maps" page for more details about Repository 66.

As of 18th Dec 2008, "There are 11,351,618 items held in the 1177 repositories on this map".

Consider this. From the Rep66 blog in May 2008, there were 8.7 million items collectively. As such, in the space of only 7 months, I make that an increase of 2.5 million !!

Also of interest is the Stuart Lewis’ Blog - RSS.

Institutional Repository wiki

Regardless of where you choose to publish your work, PLEASE archive a copy for the world to see.

Friday, 19 December 2008

Saturday, 13 December 2008

Volatile Anaesthetics - Where Next?

Have been meaning to "blog" something about this about a year before I started blogging.

This research area is out of my radar objectively, but not subjectively.

In Feb 2007, the Journal of Neuroscience published:- "The Inhalation Anesthetic Isoflurane Induces a Vicious Cycle of Apoptosis and Amyloid ß-Protein Accumulation" by Xie et al


Full Text

Also worth a mention is the work of Prof. (of Anesthesia) Rod Eckenhoff & colleagues at the Department of Anesthesiology and Critical Care, University of Pennsylvania School of Medicine, Philadelphia

Thanks to PubMed Central (PMC), here is a link to 13 peer reviewed and published articles of Eckenhoff's work.

Whilst not OA yet, the following are of interest:-

1) Brain and behavior changes in 12-month-old Tg2576 and nontransgenic mice exposed to anesthetics
2)Inhaled anesthetics elicit region-specific changes in protein expression in mammalian brain


Most recently, Xie et al has had published "The common inhalation anesthetic isoflurane induces caspase activation and increases amyloid beta-protein level in vivo"

Where we appear to be now is "These findings indicate that inhaled anesthetics influence cognition and amyloidogenesis, but that the mechanistic relationship remains unclear."

Conclusions: Inhaled anesthetics enhance oligomerization
and cytotoxicity of Alzheimer disease-associated peptides. In
addition to the possibility of a general mechanism for anesthetic
neurotoxicity, these results call for further evaluation of
the interaction between neurodegenerative disorders, dementia,
and inhalational anesthesia.

WIKI Section

There are lots of other anaesthetics that could be used other than isoflurane. Sevoflurane and Desflurane are volatiles available now. Xenon is being trialled. Intravenous anaesthetics include propofol which is now off-patent and getting cheaper.

Thursday, 11 December 2008