Bioinformatics -- a patenting view

The use of bioinformatics in the biological sciences has brought about a change in the way that biological inventions can be protected by patent laws. Using approaches developed in the fields of computer science and business, patent applicants now seek to protect certain aspects of their inventions, which include software, methods of doing business and uses of information as well as more traditional biotechnological products and processes. These approaches are useful in resolving some of the difficulties now faced in prosecuting patent applications directed to biological inventions that are claimed in more conventional terms.     

The functional role of producer diversity in ecosystems

Over the past several decades, a rapidly expanding field of research known as biodiversity and ecosystem functioning has begun to quantify how the world's biological diversity can, as an independent variable, control ecological processes that are both essential for, and fundamental to, the functioning of ecosystems. Research in this area has often been justified on grounds that (1) loss of biological diversity ranks among the most pronounced changes to the global environment and that (2) reductions in diversity, and corresponding changes in species composition, could alter important services that ecosystems provide to humanity (e.g., food production, pest/disease control, water purification). Here we review over two decades of experiments that have examined how species richness of primary producers influences the suite of ecological processes that are controlled by plants and algae in terrestrial, marine, and freshwater ecosystems. Using formal meta-analyses, we assess the balance of evidence for eight fundamental questions and corresponding hypotheses about the functional role of producer diversity in ecosystems. These include questions about how primary producer diversity influences the efficiency of resource use and biomass production in ecosystems, how primary producer diversity influences the transfer and recycling of biomass to other trophic groups in a food web, and the number of species and spatial /temporal scales at which diversity effects are most apparent. After summarizing the balance of evidence and stating our own confidence in the conclusions, we outline several new questions that must now be addressed if this field is going to evolve into a predictive science that can help conserve and manage ecological processes in ecosystems.     

Photonics for life

Light is strictly connected with life, and its presence is fundamental for any living environment. Thus, many biological mechanisms are related to light interaction or can be evaluated through processes involving energy exchange with photons. Optics has always been a precious tool to evaluate molecular and cellular mechanisms, but the discovery of lasers opened new pathways of interactions of light with biological matter, pushing an impressive development for both therapeutic and diagnostic applications in biomedicine. The use of light in different fields has become so widespread that the word photonics has been utilized to identify all the applications related to processes where the light is involved. The photonics area covers a wide range of wavelengths spanning from soft X-rays to mid-infrared and includes all devices related to photons as light sources, optical fibers and light guides, detectors, and all the related electronic equipment. The recent use of photons in the field of telecommunications has pushed the technology toward low-cost, compact, and efficient devices, making them available for many other applications, including those related to biology and medicine where these requirements are of particular relevance. Moreover, basic sciences such as physics, chemistry, mathematics, and electronics have recognized the interdisciplinary need of biomedical science and are translating the most advanced researches into these fields. The Politecnico school has pioneered many of them,and this article reviews the state of the art of biomedical research at the Politecnico in the field internationally known as biophotonics.     

Bioinformatics for the genomic sciences and towards systems biology. Japanese activities in the post-genome era

The knowledge gleaned from genome sequencing and post-genome analyses is having a very significant impact on a whole range of life sciences and their applications. 'Genome-wide analysis' is a good keyword to represent this tendency. Thanks to innovations in high-throughput measurement technologies and information technologies, genome-wide analysis is becoming available in a broad range of research fields from DNA sequences, gene and protein expressions, protein structures and interactions, to pathways or networks analysis. In fact, the number of research targets has increased by more than two orders in recent years and we should change drastically the attitude to research activities. The scope and speed of research activities are expanding and the field of bioinformatics is playing an important role. In parallel with the data-driven research approach that focuses on speedy handling and analyzing of the huge amount of data, a new approach is gradually gaining power. This is a 'model-driven research' approach, that incorporates biological modeling in its research framework. Computational simulations of biological processes play a pivotal role. By modeling and simulating, this approach aims at predicting and even designing the dynamic behaviors of complex biological systems, which is expected to make rapid progress in life science researches and lead to meaningful applications to various fields such as health care, food supply and improvement of environment. Genomic sciences are now advancing as great frontiers of research and applications in the 21st century.This article starts with surveying the general progress of bioinformatics (Section 1), and describes Japanese activities in bioinformatics (Section 2). In Section 3, I will introduce recent developments in Systems Biology which I think will become more important in the future.     

Epigenetic and phenotypic variability in populations of Schistosoma mansoni– a possible kick‐off for adaptive host/parasite evolution

Epigenetics, the science of heritable but modifiable information, is now a well‐accepted component of many research fields. Nevertheless, epigenetics has not yet found broad appreciation in one of the most exciting fields of biology: the comprehension of evolution. This is surprising, since the reason for the existence of this alternative information‐transmitting system lies certainly in the evolutionary advantage it provides. Theoretical considerations support a model in which epigenetic mechanisms allow for increasing phenotypic variability and permit populations to explore the adaptive landscape without modifications of the genotype. The data presented here support the view that modulating the epigenotype of the human bloodfluke Schistosoma mansoni by treatment of larvae with histone deacetylase inhibitor leads indeed to an increase of phenotypic variability. It is therefore conceivable that environmentally induced changes in the epigenotype release new phenotypes on which selection can act and that this process is the first step in adaptive evolution.     

Horseradish peroxidase: a modern view of a classic enzyme

Horseradish peroxidase is an important heme-containing enzyme that has been studied for more than a century. In recent years new information has become available on the three-dimensional structure of the enzyme and its catalytic intermediates, mechanisms of catalysis and the function of specific amino acid residues. Site-directed mutagenesis and directed evolution techniques are now used routinely to investigate the structure and function of horseradish peroxidase and offer the opportunity to develop engineered enzymes for practical applications in natural product and fine chemicals synthesis, medical diagnostics and bioremediation. A combination of horseradish peroxidase and indole-3-acetic acid or its derivatives is currently being evaluated as an agent for use in targeted cancer therapies. Physiological roles traditionally associated with the enzyme that include indole-3-acetic acid metabolism, cross-linking of biological polymers and lignification are becoming better understood at the molecular level, but the involvement of specific horseradish peroxidase isoenzymes in these processes is not yet clearly defined. Progress in this area should result from the identification of the entire peroxidase gene family of Arabidopsis thaliana, which has now been completed.     

Bioorganic chemistry: Institutes,journals, publications,a short scientific metric analysis <Emphasis Type="Italic">on the 50th anniversary of the Institute of Natural Compound Chemistry,Institute of Bioorganic Chemistry</Emphasis>

An attempt to illustrate the development of bioorganic chemistry in Russia and all over the world has been made. The development of a new field of science was accompanied by the emergence of specialized journals, organizations, departments and institutions for research in this field. A brief report about the four most important world journals on bioorganic chemistry is represented. The analysis of publications of world scientific institutions, having the word “bioorganic” in their title since 1972 to the middle of 2008, has been made with the help of information from Web Science. The publication distribution among countries, institutions, languages, journals, and the list of the most productive authors clearly demonstrate the leading role of the USSR and Russia and of the Institute of Natural Compound Chemistry, Institute of Bioorganic Chemistry, in the creation and development of this field of science in the world. The publication distribution among the areas of knowledge displays a close connection between bioorganic chemistry and a number of the other fields of science, first of all, biochemistry and molecular biology, and also organic chemistry.     

The definitions of information and meaning two possible boundaries between physics and biology.

The standard approach to the definition of the physical quantities has not produced satisfactory results with the concepts of information and meaning. In the case of information we have at least two unrelated definitions, while in the case of meaning we have no definition at all. Here it is shown that both information and meaning can be defined by operative procedures, but it is also pointed out that we need to recognize them as a new type of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because are not subjective features. Here it is proposed to call them nominable entities, i.e., entities which can be specified only by naming their components in their natural order. If the genetic code is not a linguistic metaphor but a reality, we must conclude that information and meaning are real natural entities, and now we must also conclude that they are not equivalent to the quantities and qualities of our present theoretical framework. This gives us two options. One is to extend the definition of physics and say that the list of its fundamental entities must include information and meaning. The other is to say that physics is the science of quantities only, and in this case information and meaning become the exclusive province of biology. The boundary between physics and biology, in short, is a matter of convention, but the existence of information and meaning is not. We can decide to study them in the framework of an extended physics or in a purely biological framework, but we cannot avoid studying them for what they are, i.e., as fundamental components of the fabric of Nature.     

Pressure mounts on policy restrictions

Following the Democratic primaries, the build-up to the US presidential election has begun and there is a growing call for changes to the science agenda.     

Strong Inference: rationale or inspiration?

John Platt's article "Strong Inference" (1964) suggested a general and effective method of scientific investigation. It describes a disciplined strategy of falsification of multiple, clearly formulated hypotheses that is used more regularly in some scientific fields than in others. Platt urged that strong inference be more widely and more systematically applied, particularly in slower-moving fields of science. The article has influenced integrative biological fields since its publication, ranging from ecology to psychology, and has had a substantial following in some of the social sciences. It has also evoked severe criticism for its idealization of certain fields as exemplars and for its imperfections in historiography and philosophy of science. I argue here that the article was more an inspirational tract than the development of a formal scientific methodology. Although both Platt's critics and his adherents appeared to take the article far too seriously, its influence has transcended its limitations.     

Biotechnology and the birth of a third culture

Biotechnology represents such an important challenge for present day culture that one can speak of a biotechnological revolution in many other scientific fields as well, such as biology, clinical medicine, pharmacology, and genetic engineering. It also significantly affects political and economic choices to such a degree that they call for a new kind of attention from jurisprudence which has to regulate an ever changing world. Many important queries arise particularly at a bioethical level, issues that will also affect future generations. Scientific progress has unexpectedly widened the biological knowledge of human kind. Thanks to the contribution of continuously more refined and advanced technology, it has nurtured the hope of solving all problems and of overcoming all limits. The scientist's intellectual curiosity, encompassing these new resources, is spurred on by the desire for knowledge and understanding. However sometimes he loses sight of the repercussions and of the possible uses his achievements may have. Only a profound personal education, integrated with the scientist's technical and scientific expertise, will allow science to knock down some barriers, advancing constantly but without losing respect for man's dignity. However the separation between scientific and ethical expertise can only raise new barriers and create limits to the freedom of science which will appear just restrictive, while a kind of medieval obscurantism will be opposed to ethical rigour.     

Model selection in ecology and evolution

Recently, researchers in several areas of ecology and evolution have begun to change the way in which they analyze data and make biological inferences. Rather than the traditional null hypothesis testing approach, they have adopted an approach called model selection, in which several competing hypotheses are simultaneously confronted with data. Model selection can be used to identify a single best model, thus lending support to one particular hypothesis, or it can be used to make inferences based on weighted support from a complete set of competing models. Model selection is widely accepted and well developed in certain fields, most notably in molecular systematics and mark-recapture analysis. However, it is now gaining support in several other areas, from molecular evolution to landscape ecology. Here, we outline the steps of model selection and highlight several ways that it is now being implemented. By adopting this approach, researchers in ecology and evolution will find a valuable alternative to traditional null hypothesis testing, especially when more than one hypothesis is plausible.     

Functional continuum of regulatory peptides (RPs): vector model of RP-effects representation

During the past decades, bioactive (regulatory) peptides have been identified as the major players in the regulation of many important biological processes. Dozens of peptides have found their application as pharmaceutical agents, which further stimulated research in this field making it one of the most rapidly developing areas on the edge of biological science and medicine. However, the fast accumulation of enormous amounts of experimental data has revealed a great difficulty in their analysis and demanded the development of a systematic approach for generalization of the obtained information. We propose a new computer-based algorithm for studying biological activities of regulatory peptides and their groups based on their representation as vectors in n -dimensional functional space. Our method allows the rapid analysis of databases containing thousands of polyfunctional regulatory peptides with overlapping spectra of physiological activity. The described method permits to perform several types of correlations which, when applied to the large databases, could reveal new important information about the system of regulatory peptides. It can select the groups of peptides with similar physiological role (peptide constellations) and search for the optimal peptide combinations with predetermined spectrum of effects and minimal side effects for their further pharmacological application. It can also reveal the role of regulatory peptides in induction of chain physiological reactions.     

The 'aerial plankton' and atmospheric convergence

Airborne migration is one of the most common adaptations for surviving and exploiting habitat variability. One weather feature that airborne migrants sometimes encounter, convergence, has the potential to concentrate populations in localities where climatic conditions have made a habitat temporarily favourable. Studies of migratory insects have now begun to establish which of several forms of atmospheric convergence are most likely to affect population processes.     

《生物资源学》教材与课程建设初探

生物资源与水资源、土地资源、矿产资源、能源资源和气候资源等都是人类赖以生存与发展的最为重要的物质基础,其中生物资源主要包括生物遗传资源、生物质资源和生物信息资源三大类型。生物资源学是现代生命科学、资源科学和工程科学等相关领域交叉和衍生出的新兴学科,已在国内外部分高校作为新专业进行开设。《生物资源学导论》是在高等教育出版社和中国生物工程学会生物资源专委会的倡议与指导下完成的国内首部生物资源系列教材,在出版后的两年多时间内,已在国内部分高等院校的课程建设中得到使用。本文简要地综述了《生物资源学导论》教材的二次开发与利用和新形态教材的建设与应用,以及《生物资源学》课程建设的基本情况,以期为我国生物资源学学科教育事业的发展尽绵薄之力。