LIFE MUSIC: THE SONIFICATION OF PROTEINS

(From left to right: 3D molecular structure of enzymes Alcohol-Dehydrogenase, Trioso-Phosphate Isomerase, Lysozyme C )

A few years ago, artist John Dunn and biologist Mary Anne Clark collaborated on the sonification of protein data to produce the audio CD "Life Music." “When we began the protein music project, we wanted to convey both something about primary aminoacid sequence and something about the folding patterns of proteins. Our goal was to create an audio CD album that would stand on its own as art music, and at the same time offer empirical proof of the esthetic patterning of nature’s deep structure”.

In the following article, authors describe the process by which this collaboration merges scientific knowledge and artistic expression to produce soundscapes from these basic building blocks of life, that may be encountered as esthetic experiences, as scientific inquiry, or both. The rationale for both artistic use of the science and scientific use of the art is described from the separate viewpoints of artist and scientist.

Life Music: The Sonification of Proteins by John Dunn and Mary Anne Clark
http://lea.mit.edu/isast/articles/lifemusic.html


Protein Music Samples (Pieces from the Life Music CD).

In each piece below, pitch is determined by aminoacid identity. The structural features of the protein are emphasized by choosing instrumentation according to protein folding pattern, with different instruments representing regions of alpha-helix, beta-strands and turns. In some pieces, different instruments may identify functional domains of the protein.

Enjoy!

1. Alcohol Dehydrogenase Listen! http://whozoo.org/mac/Music/adh.ra
2. Triose Phosphate Isomerase Listen! http://whozoo.org/mac/Music/tpi2x.ra

Learn more about protein music by reading Protein Primer: A Musical Introduction to Protein Structure and visiting the Website http://whozoo.org/mac/Music/index.htm

THE IBIOCAT’S BOOK CORNER: “ENZYME BIOCATALYSIS: PRINCIPLES AND APPLICATIONS”

Enzyme Biocatalysis
Principles and Applications
Edited by: Andrés Illanes
Publisher: SPNL (8 July 2008 - Dordrecht, Netherlands)
Imprint: Springer
Format: Hardback, 408 pp

Audience
Researchers and students in biochemistry, biotechnology, genetic engineering; an excellent book for those working in the field of enzyme technology
Professional and scholarly

Book Description
The book is intended to provide a sound basis for enzyme reactor design based on kinetic principles, and give an updated vision of the potentials and limitations of enzyme biocatalysis, especially with respect to recent applications in processes of organic synthesis. The book is structured in the form of a textbook that goes from basic principles of enzyme structure and function to reactor design for homogeneous systems with soluble enzymes, and heterogeneous systems with insolubilized enzymes. It contains an introductory chapter that gives an updated overview of enzyme technology, a chapter on enzyme production focused on large-scale operations, two chapters devoted to homogeneous and heterogeneous enzyme kinetics and a chapter on enzyme reactor design and operation based on enzyme kinetics principles, mass transfer limitations and enzyme inactivation. The book is complemented with case studies of biocatalytic processes of industrial relevance or potential, written by experts in those fields. Applications of proteases, acylases, lipases, aldolases and dehydrogenases in reactions of organic synthesis, and peroxidases in the degradation of recalcitrant organic compounds, are used as selected examples to illustrate the realities and potentials of enzymes as process catalysts.

Table of Contents
Introduction (Andrés Illanes)2. Enzyme Production (Andrés Illanes) 3. Homogeneous Enzyme Kinetics (Andres Illanes, Claudia Altamirano, Lorena Wilson) 4. Heterogeneous Enzyme Kinetics (Andres Illanes, Roberto Fernández-Lafuente, José Manuel Guisán, Lorena Wilson) 5. Enzyme Reactors (Andrés Illanes, Claudia Altamirano) 6. Study Cases of Enzymatic Processes6.1. Proteases as catalysts for peptide synthesis (Sonia Barberis, Fanny Guzmán, Josep López-Santín) 6.2. Synthesis of ß-lactam antibiotics with penicillin acylases (Andrés Illanes, Lorena Wilson) 6.3. Chimioselective esterification of wood sterols with lipases (Gregorio Alvaro, Andrés Illanes) 6.4. Oxidoreductases as powerful biocatalysts for green chemistry José Manuel Guisán, Roberto Fernández-Lafuente, Lorena Wilson, César Mateo) 6.5. Use of aldolases for asymmetric synthesis (Josep López-Santín, Gregorio Alvaro, Pere Clapés) 6.6. Application of enzymatic reactors for the degradation of highly and poorly soluble recalcitrant compounds (Juan M. Lema et al.)

For more information please visit:
http://www.books-express.co.uk/book/9781402083600/Enzyme-Biocatalysis.html

22 APRILE 2009 - AUGURI A RITA LEVI MONTALCINI, CENTO ANNI DI SCIENZA E COSCIENZA

«Il fattore più importante dell' esistenza umana, diceva Einstein, è la creazione di un fine. E' necessario un grande sforzo interiore, da parte delle comunità di persone libere, per liberarsi dell'eredità di istinti antisociali e distruttivi. L'uso delle capacità intellettuali, basate su principi morali, dà contenuto e significato alla vita».

«La conoscenza è per definizione un bene - forse il bene primario dell' uomo - perché senza di essa non possono esistere le altre libertà fondamentali alle quali ci si appella di continuo. Gli scienziati non detengono il monopolio della saggezza. La soluzione dei problemi che affliggono l'intero genere umano, fino a porne in pericolo la sopravvivenza, spetta in pari misura a filosofi, uomini di religione, educatori e appartenenti ad altre discipline».

«Oltre agli immensi contributi che la scienza e la tecnologia possono oggi apportare, per una migliore condizione di vita in tutte le regioni a vantaggio dei suoi abitanti, deve essere preso in considerazione quello che di gran lunga è il più importante: la promozione di un'amicizia basata su scambi di conoscenze e contatti reciproci. Soltanto così si può pervenire al superamento di differenze derivate da ostilità e intolleranze etniche. La scienza permette un linguaggio senza ambiguità e comprensibile nelle nazioni più diverse».

Rita Levi Montalcini

(Tratto dall’intervista rilasciata a Barbara Palombelli: Rita Levi Montalcini: «Io, agnostica difendo la vita e i principi morali», Corriere della Sera (27 novembre 2006), pagina 23

Libri di Rita Levi Montalcini

Cronologia di una scoperta Levi-Montalcini Rita, 2009, Baldini Castoldi Dalai

L'asso nella manica a brandelli Levi-Montalcini Rita, 2008, Baldini Castoldi Dalai

La clessidra della vita di Rita Levi-Montalcini Tripodi Giuseppina; Levi-Montalcini Rita, 2008, Baldini Castoldi Dalai

Ritmi d'arte Levi-Montalcini Rita, 2008, Serra Tarantola

Senz'olio contro vento Levi-Montalcini Rita, 2008, Baldini Castoldi Dalai

Le tue antenate. Donne pioniere nella società e nella scienza dall'antichità ai giorni nostri Levi-Montalcini Rita; Tripodi Giuseppina; Ferri Giuliano, 2008, Gallucci

Rita Levi Montalcini racconta la scuola ai ragazzi Levi-Montalcini Rita; Tripodi Giuseppina, 2007, Fabbri

Tempo di mutamenti-Tempo di azione-Tempo di revisione Levi-Montalcini Rita; Tripodi Giuseppina, 2007, Baldini Castoldi Dalai

I nuovi magellani nell'er@ digitale Levi-Montalcini Rita; Tripodi Giuseppina, 2006, Rizzoli

Tempo di revisione Levi-Montalcini Rita; Tripodi Giuseppina, 2006, Baldini Castoldi Dalai

Abbi il coraggio di conoscere Levi-Montalcini Rita, 2005, BUR Biblioteca Univ. Rizzoli

Eva era africana -Levi-Montalcini Rita, 2005, Gallucci

Tempo di azione Levi-Montalcini Rita, 2004, Baldini Castoldi Dalai

Tempo di mutamenti Levi-Montalcini Rita, 2002, Baldini Castoldi Dalai

La galassia mente Levi-Montalcini Rita, 2001, Baldini Castoldi Dalai

Un universo inquieto. Vita e opere di Paola Levi Montalcini Levi-Montalcini Rita, 2001, Baldini Castoldi Dalai

Cantico di una vita Levi-Montalcini Rita, 2000, Cortina Raffaello

IBIOCAT SCIENCE&ART- INTRODUCING PHILIP SCHOFIELD, ART-SCIENTIST

Dr. Philip Schofield is a Conjoint Professor in the School of Fine Art at the University of Newcastle. Prior to that he was an Associate Professor in Biochemistry at the University of N.S.W.

Since he is both an artist and a scientist he is in an unique position to facilitate the interfacing of art and science. He is committed to bridging the perceived gap between art and science. He is also currently a member of the ArtsHealth Research and Practice Centre at the University of Newcastle.

The principal theme of his art practice is the fusing of art and science, and the bridging of the "two cultures". By virtue of his experience in science and in medical research, he is uniquely placed to initiate and consolidate such syncretism.

In practice, he uses the printouts from a variety of imaging devices used in biology and medicine, such as DNA scans, and combines these with personal fragments such as photographs and documents.These juxtapositions produce new forms of biography and autobiography, and allow new expressions of singularity and selfhood. They also provide new forms by which to visualise and decode contemporary biology and medicine.

In his recent works he fuses fragments of photographs of personal lives with various imaging systems of contemporary biology and medicine. This fusion produces new perspectives of persona and self, and generates new forms of expression of biography and autobiography. It also provides new perspectives by which to visualise and interpret aspects of modern biology and medical science.

ART + SCIENCE bridges the perceived gap between art and science/medicine by interfacing elements of the visual arts with elements of current biological research methods in molecular biology and medicine.The works incorporate strands of contemporary genetic research with fragments related to individuals or to historical figures in the fields of biology and medicine.

The fusion of fragments of personal photographs or documentation or constructs of historical items with the output of imaging systems of modern biology and medicine generates new perspectives of biography and of contemporary biological and medical science.

Life is...

The mechanistic Cartesian view is that life is a complex algorithm of definable chemical reactions and physicochemical events.The alternative view is that life is much more than an intricate clockwork mechanism. It is also the psyche, and the id and the ego and the super ego, and the spirit.Philosophy may debate the nature of life, but inevitably and inexorably life's experiences are etched and smudged and overlaid on the psyche and on the body. The body is the palimpsest of life (Philip Schofield).

Learn more about Dr. Philip Schofield’s art by visiting his official Website: http://www.philipschofield.net/

GREEN QUOTE FOR TODAY April 19, 2009

“There is, it would seem, in the dimensional scale of the world a kind of delicate meeting place between imagination and knowledge, a point, arrived at by diminishing large things and enlarging small ones, that is intrinsically artistic."

Vladimir Nabokov (1899-1977), from Speak, Memory

(Please note that this image of the brainstem of a Brainbow mouse, by Jean Livet of Harvard University, awarded 1st prize in the 2007 Olympus Bioscapes International Digital Imaging Competition).

ECOSEARCH.COM: IL MOTORE DI RICERCA ECOLOGICO

Che cos'è Ecosearch?

Utilizzando la tecnologia di Yahoo, Ecosearch aiuta a riforestare l'Amazzonia e a preservare le risorse naturali di acqua dolce, così come altri ecosistemi minacciati.

Impiegando Ecosearch come motore di ricerca, si aiuta l'associazione no-profit Aquaverde (ONG) e la Fondazione Canaria per la riforestazione (FORESTA).

Come funziona?

Ogni ricerca realizzata con Ecosearch contribuisce simbolicamente a riforestare una foglia.

Per ogni 10.000 ricerche/foglie, Ecosearch dona il denaro necessario per piantare un albero nell'Amazzonia.

1 ricerca = 1 foglia 10.000 foglie = 1 albero

Inoltre Ecosearch partecipa ad una collaborazione che mira al rimboscamento di 1200 alberi nell'arcipelago Canario, nel giro di un anno.

http://www.ecosearch.com/

THE BOOK CORNER - “MULTI-SCALE QUANTUM MODELS FOR BIOCATALYSIS: MODERN TECHNIQUES AND APPLICATIONS"

Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications

Series: Challenges and Advances in Computational Chemistry and Physics , Vol. 7
York, Darrin M.; Lee, Tai-Sung (Eds.)
Publisher: Springer
2009, Approx. 600 p., Hardcover
ISBN: 978-1-4020-9955-7


About this book
Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications explores various molecular modelling techniques and their applications in providing an understanding of the detailed mechanisms at play during biocatalysis in enzyme and ribozyme systems. These areas are reviewed by an international team of experts in theoretical, computational chemistry, and biophysics.
This book has three sections that group together different aspects of multi-scale quantum simulations. The first section consists of four chapters that describe strategies for multi-scale quantum models and present an overview of the current state-of-the-art molecular modelling methodologies most relevant to handling these complex systems with quantum mechanics and molecular simulation. With five chapters, the second section mainly focuses on the current efforts to improve the accuracy of quantum calculations using simplified empirical model forms. The last section consists of five chapters focused on the applications of important biological systems using multi-scale quantum models. This book presents detailed reviews concerning the development of various techniques, including ab initio molecular dynamics, density functional theory, combined QM/MM methods, solvation models, force field methods, and free-energy estimation techniques, as well as successful applications of multi-scale methods in the biocatalysis systems including several protein enzymes and ribozymes.
Multi-scale Quantum Models for Biocatalysis: Modern Techniques and Applications is an excellent source of information for research professionals involved in computational chemistry and physics, material science, nanotechnology, rational drug design and molecular biology. It is also likely to be of interest to graduate and undergraduate students exposed to these research areas.
Written for:
Researchers and students in computational chemistry and physics, materials science, nanotechnology, rational drug design and molecular biology.
Keywords: Biocatalysis; Free Energy Methods; Linear Scaling Techniques; Path Integrals; Polarizable Force Fields; QM/MM methods; Solvent Boundries ; abinitio MD

For more information please visit: http://www.springer.com/chemistry/book/978-1-4020-9955-7

Art and Science Converge: The Periodic Table Printmaking Project

Ninety-seven printmakers of all experience levels, have joined together to produce 118 prints in any medium: woodcut, linocut, monotype, etching, lithograph, silkscreen, or any combination. The end result is a periodic table of elements intended to promote both science and the arts.

You can view the full table in its glory here: Web Table of Elements


The Periodic Table Printmaking Project at a glance:

• 97 printmakers


• 7 countries - Australia, Canada, England, Italy, Japan, Scotland, United States


• 29 states & Puerto Rico from the US are represented - Arkansas, California, Colorado, Connecticut, Delaware, Georgia, Hawaii, Illinois, Indiana, Kentucky, Maryland, Massachusetts, Michigan, Minnesota, Missouri, Montana, New Hampshire, New Jersey, New York, North Carolina, North Dakota, Ohio, Oregon, Pennsylvania, Puerto Rico, South Carolina, Texas, Virginia, Washington, and Wisconsin.
  
  For more information please visit the Periodic Table Printmaking Project website.

DEDICATO ALLE VITTIME DEL TERREMOTO IN ABRUZZO

A Coffin - is a small Domain,
[ J943 (1864) / F890 (1864)]

A Coffin - is a small Domain,

Yet able to contain

A Citizen of Paradise

In it's diminished Plane -

A Grave - is a restricted Breadth -

Yet ampler than the Sun -

And all the Seas He populates -

And Lands He looks upon

To Him who on it's small Repose

Bestows a single Friend -

Circumference without Relief -

Or Estimate - or End

Emily Dickinson


Una Bara - è un esiguo Dominio,
[ J943 (1864) / F890 (1864)]

Una Bara - è un esiguo Dominio,

Eppure capace di contenere

Un Cittadino del Paradiso

Nella sua ridotta Superficie -

Una Tomba - è una ristretta Estensione -

Eppure più ampia del Sole -

E di tutti i Mari che Egli popola -

E delle Terre a cui guarda

A Colui che in quell'esiguo Riposo

Colloca l'unico Amico -

Circonferenza senza Sollievo -

O Previsione - o Fine.

Emily Dickinson
(Traduzione italiana di Giuseppe Ierolli)

HAPPY EASTER EVERYONE!

JUNGLE TOWN