Январь 2006 г.

Российская наука и мир (по материалам зарубежной электронной прессы)

CONTENTS / ОГЛАВЛЕНИЕ


• Russia masters high techs
• Effective testing for Helicobacter pylori bacteria
• Biocad Announces New Treatment for Oncological Diseases
• Making Proteins To Fight Cancer
• Computer Synthesis Of Chimeric Proteins
• Small Particles Bring Great Benefit
• Beam therapy in 3D format
• Russia Will Rebuild Nuclear Industrial Complex
• Cadence sur le point d'aider le secteur électronique russe

Если долгое время основным инструментом биохимика был хроматограф или установка для электрофореза, то теперь существует специальное программное обеспечение, позволяющее имитировать биохимические процессы и поведение сложных молекул. С помощью подобного оборудования ученые из НИИ биомедицинской химии им. В.Н.Ореховича РАМН и Университета Вандербилт (США) исследовали ферменты семейства цитохромов Р 450.

Not long ago, the biochemist's main tool was a chromatograph or an electrophoresis plant, but now specialists in bio-informatics use special software to simulate biochemical processes and the behaviour of complex molecules.
This approach was used to research factitious proteins of the cytochrome P450 family by researchers from the V.N. Orekhovich Research Institute of Biomedical Chemistry, Russian Academy of Medical Sciences, guided by A.V. Lisitsa, Ph.D. (Biology), and their colleagues from Vanderbilt University (USA) guided by Doctor Larisa Podust. The project has been sponsored by Rosnauka and the CRDF foundation.
Proteins of this family play an important role in the organism: they are responsible for oxidation of xenobiotics - alien chemical compounds harmful to cells. Oxidation assists in removing xenobiotics from the organism, providing for cells' purification from chemical skimming. The primary importance of cytochromes P450 resulted in the fact that these proteins are found practically in all existing organisms - in bacteria, plants, fungi and animals. Preserving general function universality, cytochromes P450 show great diversity in their structural organization.
The main aim is to consider various structural elements of real existing proteins as a peculiar meccano, out of which factitious chimeric proteins can be assembled to combine components of several different structures. It is assumed that chimeric proteins will be able to perform a pre-programmed biological function. Why is that needed? - The answer is simple: factitious cytochrome P450-based proteins may be used by biotechnologists for complicated chemical synthesis leading to creation of drug prototypes, agricultural chemistry preparations and many others. The main question facing the researchers is as follows - what are the rules to "play" the meccano consisting of protein elements?
"About three years ago, we set up a hypothesis that the leading role of cytochromes P450 in the structural organization and in their interaction with chemical substances is played by motives, i.e., a certain spatial configuration of individual protein fragments, typical folds and spirals of this long molecule," says A.V. Lisitsa. "It is them that we are going to identify at the first stage of the work. Then, with the help of a PC, we shall replace some motives by others, and a three-dimensional structures calculation will allow to select such chimeric proteins, which will take the necessary spatial configuration and will be responsible for definite functions, but will not remain a senseless chain of molecules after the synthesis. And then, the neurocomputer will begin its work."
The "neurocomputer" is used in bio-informatics to denote the simplified representation of the brain in the form of a virtual neurons network. Such a network is capable of accumulating information and learning. The network (by the example of experimentally known reactions of the entire spectrum of substances with cytochromes P450) learns to recognise correct interaction types. Then the network will evaluate with what substances the factitious protein built from elements of natural structures will interact. The work will be considered successful if the researchers succeed to prove that the developed method allows to forecast correctly the artificial proteins' functions.
"Contemporary genetic engineering methods allow to produce rather easily a transgene (recombinant) organism that will synthesize computer-designed chimeric proteins," says A.V. Lisitsa. "The preparations required for that will be produced and delivered to us by the US colleagues, and we shall clone microorganisms in Russia, purify the protein produced by it and check their activity with the help of the US reagents. If everything goes on successfully, factitious protein preparations will be sent to Vanderbilt University, where they will be crystallized, and then the structure for assessment of computor simulators accuracy will be investigated. One of Russian students will be involved in these experiments, he/she will go to the USA to acquire protein crystallography skills. The statistical model developed in the course of the research may be used for rational construction of other proteins with new or improved properties."

Химики Московского государственного университета имени М.В.Ломоносова и Техасского университета сборки и технического обслуживания повысили эффективность синтеза фармацевтических веществ. Концепция нанореактора, которую они использовали, позволит сделать химические и фармацевтические технологии более простыми и экологически безопасными.

Chemistry teams from two universities - Lomonosov Moscow State University and Texas A&M University (USA) have improved the efficacy of pharmaceutical substance synthesis by simplifying the process. The Russian team is guided by Academician Irina Beletskaya, and the US team by Professor David Edward Bergbreiter. These two teams play on the same side because the nanoreactor concept they are using will in the long run allow to simplify in many respects chemical and pharmaceutical technology and, most importantly, to make it cleaner from the ecological point of view. The research has been sponsored by the CRDF foundation and the Federal Agency for Science and Innovation (Rosnauka).
Synthesis of biologically active molecules, such as pharmaceutical drugs, is connected with a number of complications. It is easy on paper to "assemble" chains of various atoms into required structures, but in nature, enzymes - natural catalysts - help to synthesize these substances. The synthesis can not be performed without catalysts in the laboratory and, accordingly, in the industry.
In live systems, catalysts are a natural part of these systems, which have been perfected over millions of years of evolution, to the minutest detail. However in the human body, even the best of known catalysts, such as platinum metals and palladium suffer from at least two drawbacks.
Firstly, these processes involve unsafe organic matters - dissolvents and ligands, i.e., complexing agents for catalyst metals - which are rather toxic. Secondly, separation of the product from metal is a complicated task. It is difficult to wash their traces from the drug, in the drug they are not only unneeded, but also harmful. Also, it is impossible to collect all of palladium when washing.
To solve these problems, i.e. to create such palladium nanoparticles, which would allow to synthesize necessary substances easily and quickly and would not get into the final product, will be permitted by the approach being developed by chemists under the guidance of Irina Beletskaya and David Bergbreiter. As a result of this, stable palladium particles of the size of only several nanometers may be synthesized directly in the polymeric matrix. The process will be going in the smallest pores of this matrix - tiny, extremely active particles of palladium will be formed, which in turn, will help to get reaction products from inters.
Groups of ligands (included in the polymer composition in advance) will help to retain the catalyst inside the matrix. These are "suspended", as chemists put it, in the main chain of the polymer, where they will strongly retain metal in the matrix from which it is impossible to wash out.
It is certainly an enormous effort to develop the required polymer and to synthesize such polymers in order to choose the best ones. Rather diverse requirements need to be considered, such as the stability of palladium nanoparticles, their activity, ease of regeneration, accessibility for reagents, and freedom of movement of inters and reaction products.
On top of that, the researchers plan to investigate another approach using polymeric micellas. Palladium nanoparticles are formed in the nucleus of polymeric micellas and the target product is found at the border of phase division between the nucleus and the so-called corona of micellas. In this case, it consists of long and flexible "tails" of polyethylene oxide, which are, in contrast to the nuclei of polystyrene micellas, well-soluble in water. Constructing these micellas allows the team to carry out the reaction in water, without organic solvents, in strict compliance with the requirements of the so-called "green" (safe) chemistry. However, the researchers have polymers available that are capable to form micellas in an nonaqueous environment.
In any case, all these polymeric systems, both micellas and nanoporomeric cross-linked ones, i.e. three-dimensional polymers, will be easy to separate from the solution of obtained drug together with the harmful ligand being part of the polymer and reliably connected to it.
"The main goal of our project is to develop new efficient catalysts, which can be reused, says Academician Irina Beletskaya. With the help of these catalysts we shall be able to receive drugs not contaminated by phosphines or traces of metals, this would significantly simplify drugs' extraction and purification and minimize organic solvent application. In the long run, our project would solve a diversity of problems connected with the synthesis of biologically important compounds from simple parent substances."

Совершенно безопасных способов бороться со злокачественными опухолями пока нет. В конечном итоге все средства, убивающие опухоль, в той или иной степени вредят и здоровым клеткам. Часто наиболее эффективный и наименее вредный для пациента вариант - это так называемая оптимальная лучевая терапия, в ходе которой необходимую для лечения опухоли дозу облучения получит сама опухоль, а остальные ткани и органы получают минимальную дозу.
Ученые из МИФИ и Института прикладной математики им. М.В.Келдыша РАН при поддержке Международного научно-технического центра разрабатывают алгоритмы и программы, которые помогут онкологам вычислить оптимальную дозу облучения всего за несколько минут.

Algorithms and programs being developed by scientists from the Moscow Physics Engineering Institute and the Keldysh Institute of Applied Mathematics RAS with the support of the International Science and Technology Centre will help oncologists to accurately and rapidly calculate an optimal dose of radiation. Then, they will be able to determine the direction and intensity of radioactive flows so as to have maximum harmful effect on the tumour with minimum irradiation of healthy tissue, and all within a few minutes.
Unfortunately humans are not yet aware of totally safe means to fight malignant tumours. In the final analysis all resources that kill a tumour cause varying degrees of harm to healthy cells; they destroy the tissues of the heart, kidneys, testicles and so on. Sometimes the most effective kind of therapy and, strange though it may seem, the least harmful to the patient, is the so-called optimal beam therapy, in the course of which the dose required to treat the tumour is received by the tumour itself, while the patient's remaining organs and tissues receive a minimum dose load.
Naturally the developers of the beam therapy apparatus are doing their utmost to optimize where possible the dose distribution and, to do this, to increase the accuracy of its calculation. In an ideal situation a beam is required which would hit the tumour directly and which would rapidly weaken beyond its outer limits. But is it possible to calculate in advance the parameters of the beam in such a way so as to pre-plan the radiation dose throughout its path in the patient's organism? Our body after all is not an ideal homogeneous environment; knowing the laws of interaction of it with one or another form of radiation, it would be easy to calculate the dose in each point of the organism during the course of the irradiation. Skin, bone, muscle: as such all tissue types interact with radiation in their own way, not to mention the fact that the human body surface itself is nothing if not irregular.
It is clear that only a computer is able to resolve such a non-uniform task as the planning of remote beam therapy. In principle methods already exist in other applied fields to calculate the spread of radiation effects and the algorithms and programs required to solve other tasks. Under their direct application to resolve tasks in radiation therapy planning, they ensure high precision but are so difficult to implement that it would take one PC not minutes but tens of hours to solve such a task. It is understood that such terms are unacceptable for the purposes of practical medicine.
So, what are the project authors proposing? The fact is that they have considerable and very successful experience behind them in solving similar problems for calculations related to nuclear reactors and the protection of nuclear installations. To reduce the calculation time with three-dimensional systems, they were able to divide the total time and, accordingly, the calculation time between several computers, having taught the computers to exchange information between themselves. In other words they developed programs to transfer to multiprocessor technologies and to parallelize calculations.
It is this experience that the authors propose to use in order to facilitate the calculation of parameters of radiation beams that are required for optimal irradiation of a specific point in the patient's body.
"To compute the radiation dose a patient will receive in the course of a procedure, in each point in their body, we have developed a principally new computational algorithm, based on a combination of Monte-Carlo methods and a discrete ordinates method," explains Project Manager Alexander Kryanev. "This set up differs from all those before, not only in a reduction in the time required to model the trajectory of radiating particles, but also in that it uses a new class for estimating the radiation dose. The essence of the set up is fairly complicated, although the result is understood by all: it has been possible to reduce calculation time by orders of magnitude. And as the new algorithm, by way of its features, can almost completely parallelize calculations, all calculations of the doses in the radiation volume can be performed in just a few minutes."
As a result the authors hope to develop a remote beam therapy complex to rapidly and accurately plan optimal irradiation on computers with parallel architecture. Then the authors intend to test their complex in a clinic of the Russian Federation Oncology Centre. In their turn oncologists and patients hope that the researchers will have the requisite conditions in place to create such a complex. There is no doubt that the scientists are equipped with the knowledge and experience required.

Россия планирует восстановить весь атомный комплекс бывшего СССР. Элементы этого комплекса находятся на территории России, Украины и Казахстана. Глава Росатома Сергей Кириенко считает, что выгоднее собрать комплекс заново, чем достраивать отдельные его части.

Moscow, Jan 13 (Prensa Latina) Russia plans to rebuild the atomic industrial complex of the former Soviet Union in conjunction with Ukraine and Kazakhstan, Sergey Kirivenko, chief of the Russian Nuclear Energy Agency, said in this capital on Thursday.
The territories of Russia, Ukraine and Kazakhstan have resources that make up a whole complex that has to be rebuilt, pointed out Kirivenko.
The scientist said that it is more rational to use the already existing components, adding that it would be more beneficial to join efforts to complete the complex rather than act separately.
The director of Russia"s nuclear program explained that the nucleus of that industry in the territory of the Community of Independent States is in the Russian Federation, but some elements are outside the country.
Kazakhstan produces uranium, while Ukraine makes turbines, said the expert, who was quoted by RIA Novosti.
Russian President Vladimir Putin discussed the issue this week in Astana, Kazakhstan, where he met with his Ukrainian counterpart, Victor Yuschenko, and Kazak leader Nursultan Nazarbayev.
We are interested in fostering cooperation in the use of nuclear energy with peaceful ends, said the Russian president during his meeting with Nazarbayev.
The first electronuclear plant in history was designed and built by Soviet experts in Dubna, Russia, in 1954.
The plant was based on the chain reaction of nuclei of uranium divided by bombarded neutrons.
Scientists from the extinct Soviet Union also designed the first reactor of controlled thermonuclear fusion, which was named with the Russian word Tokomak, which is the foundation for the current project ITER.

Компания Cadence Design Systems, занимающаяся созданием систем автоматизированного проектирования, и Московский институт электронной техники (МИЭТ) объявили о начале новой программы "Содействие развитию российской инновационной системы в области микроэлектроники" (Inspire the Russian Innovation System - IRIS). Цель программы - поддержка инновационных проектов в области микроэлектроники, а также помощь в интеграции российских микроэлектронных компаний в мировую индустрию. В рамках этой программы Cadence стала ключевым поставщиком технологий для нового специализированного Центра проектирования МИЭТ.

MANHASSET, New York - Le Miet (Moscow Institute of Electronic Technology) a choisi Cadence Design Systems en tant que fournisseur exclusif de technologies de conception afin d'aider le Miet à développer le secteur électronique russe et fournir aux jeunes entreprises locales un meilleur accès à l'industrie.
Cadence (San Jose) devrait prendre la tête d'un projet russe appelé "Inspire the Russian Innovation System" ("Inspirez le système d'innovation russe"), connu également sous le nom d'Iris. Ce projet devrait relancer une large gamme de technologie Cadence, notamment le modèle de service VCAD (Virtual Integrated CAD, CAD intégré virtuel) et les kits Cadence.
Le Miet a choisi le modèle de service VCAD de Cadence afin de permettre aux concepteurs d'accéder à un large éventail de ressources et d'expertise de Cadence, donnant ainsi un coup de fouet aux relations de Cadence avec les principaux partenaires de la chaîne de conception.
"Cadence possède le meilleur des outils et des services de conception capables de nous aider à développer le marché russe des composants et des conceptions électroniques et de soutenir le développement des nos jeunes centres", affirme le professeur Y.A. Chaplygin, membre correspondant de l'Académie russe des sciences. "Le modèle VCAD de Cadence non seulement nous donne accès à la pointe de la technologie mais nous permet également de former et de qualifier des concepteurs mais aussi de soutenir la communauté avec une expertise en marketing et en gestion. L'accès aux partenaires mondiaux participant au marché russe est également très important pour nous".
"La Russie possede un potentiel énorme basé sur sa communauté d'ingénieurs jeunes, talentueux et particulièrement bien formés sur le plan scientifique", explique Wolf-Ekkehard Matzke, membre de Cadence Design Systems. "Le concept Iris constitue une excellente manière de renforcer l'écosystème requis pour libérer ce potentiel. Nous sommes très impatients de prendre part au projet Iris".
Cadence travaille avec le Miet depuis trois ans environ, depuis l'ouverture, au sein du prestigieux institut, d'un centre de formation sur la conception en septembre 2002. Cadence rejoint d'autres sociétés de haute technologie qui ont des affaires en Russie, notamment Intel, Sun, Samsung, Motorola, Texas Instruments, Synopsys et Mentor Graphics.
En janvier dernier, le Président russe Vladimir Putin a appelé à la mise en place de zones économiques de haute technologique afin de relancer le secteur informatique et électronique. A cet instant, il a été rapporté que la Russie investirait 650 millions de dollars dans le secteur informatique au cours des cinq prochaines années.

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