Modularity: a new perspective in biology

Several decades of research in biochemistry and molecular biology have been devoted for studies on isolated enzymes and proteins. Recent high throughput technologies in genomics and proteomics have resulted in avalanche of information about several genes, proteins and enzymes in variety of living systems. Though these efforts have greatly contributed to the detailed understanding of a large number of individual genes and proteins, this explosion of information has simultaneously brought out the limitations of reductionism in understanding complex biological processes. The genes or gene products do not function in isolation in vivo. A delicate and dynamic molecular architecture is required for precision of the chemical reactions associated with "life". In future, a paradigm shift is, therefore, envisaged, in biology leading to exploration of molecular organizations in physical and genomic context, a subtle transition from conventional molecular biology to modular biology. A module can be defined as an organization of macromolecules performing a synchronous function in a given metabolic pathway. In modular biology, the biological processes of interest are explored as complex systems of functionally interacting macromolecules. The present article describes the perceptions of the concept of modularity, in terms of associations among genes and proteins, presenting a link between reductionist approach and system biology.     

Stem cells: a plant biology perspective

A recent meeting at the Juan March Foundation in Madrid, Spain brought together plant biologists to discuss the characteristics of plant stem cells that are unique and those that are shared by stem cells from the animal kingdom.     

High resolution 3D perspective of Plasmodium biology: advancing into a new era

Apicomplexan parasites exhibit a great variety of complex life cycles that require adaptation to different niches of parasitism. They invade different host cells and highjack their biological functions. Plasmodium falciparum, responsible for the deadliest form of human malaria, causes disease while completely remodeling the erythrocytes of its human host through mechanisms that are only partly understood. Recent developments in ultrastructural technologies offer new opportunities to investigate fundamental aspects in the biology of the parasite in a three-dimensional (3D) perspective. Here we bring together recent work on host cell invasion, hemoglobin uptake, protein export and nuclear dynamics. A comprehensive 3D view of the ultrastructural biology of the parasite may shed new light on cellular mechanisms that underlie the pathogenicity of P. falciparum.     

The 18 kDa translocator protein (TSPO): a new perspective in mitochondrial biology

In mammals, mitochondria are central in maintaining normal cell function and dissecting the pathways that govern their physiology and pathology is therefore of utmost importance. For a long time, the science world has acknowledged the Translocator Protein (TSPO), an intriguing molecule that, through its position and association with biological processes, stands as one of the hidden regulatory pathways in mitochondrial homeostasis. Here we aim to review the literature and highlight what links TSPO to mitochondrial homeostasis in order to delineate its contribution in the functioning and malfunctioning of this critical organelle. In detail, we will discuss: 1) TSPO localization and interplay with controlling phenomena of mitochondria (e.g. mPTP); 2) TSPO interaction with the prominent mitochondrial player VDAC; consider evidence on how TSPO relates to 3) mitochondrial energy production; 4) Ca2+ signalling and 5) the generation of Reactive Oxygen Species (ROS) before finally describing 6) its part in apoptotic cell death. In essence, we hope to demonstrate the intimate involvement TSPO has in the regulation of mitochondrial homeostasis and muster attention towards this molecule, which is equally central for both cellular and mitochondrial biology.     

Cell biology from a nuclear perspective

Cell biology from a nuclear perspective, Cells, a Laboratory Manual (1998). D.L. Spector, R.D. Goldman, and L.A. Leinwand (Eds). Cold Spring Harbor, NY: CSHL Press, 2,136 pp. (3 vols.) $255 comb-bound; ISBN 0879695218     

Cryptobiosis: a new theoretical perspective

The tardigrade is a microscopic creature that under environmental stress conditions undergoes cryptobiosis [Feofilova, E.P., 2003. Deceleration of vital activity as a universal biochemical mechanism ensuring adaptation of microorganisms to stress factors: A review. Appl. Biochem. Microbiol. 39, 1-18; Nelson, D.R., 2002. Current status of the tardigrada: Evolution and ecology. Integrative Comp. Biol. 42, 652-659]-a temporary metabolic depression-which is considered to be a third state between life and death [Clegg, J.S., 2001. Cryptobiosis-a peculiar state of biological organization. Comp. Biochem. Physiol. Part B 128, 613-624]. In contrast with death, cryptobiosis is a reversible state, and as soon as environmental conditions change, the tardigrade "returns to life." Cryptobiosis in general, and among the tardigrade in particular, is a phenomenon poorly understood [Guppy, M., 2004. The biochemistry of metabolic depression: a history of perceptions. Comp. Biochem. Physiol. Part B 139, 435-442; Schill, R.O., et al., 2004. Stress gene (hsp70) sequences and quantitative expression in Milensium tardigradum (Tardigrade) during active and cryptobiotic stages. J. Exp. Biol. 207, 1607-1613; Watanabe, M., et al., 2002. Mechanisn allowing an insect to survive complete dehydration and extreme temperatures. J. Exp. Biol. 205, 2799-2802; Wright, J.C., 2001. Cryptobiosis 300 years on from van Leuwenhoek: what have we learned about tardigrades? Zool. Anz. 240, 563-582]. Moreover, the ability of the tardigrade to bootstrap itself and to return to life seems paradoxical like the legendary Baron von Munchausen who pulled himself out of the swamp by grabbing his own hair. Two theoretical obstacles prevent us from advancing our knowledge of cryptobiosis. First, we lack appropriate theoretical understanding of reversible processes of biological computation in living systems. Second, we lack appropriate theoretical understanding of bootstrapping in living systems. In this short opinion article, I would like to present the idea that although cryptobiosis is obscure from a certain point of view, it makes sense within a scientific perspective suggesting that "organization becomes cause in the matter" [Strohman, R.C., 2000. Organization becomes cause in the matter. Nat. Biotechnol. 18, 575-576]. I present Bateson's idea that organisms have a "recursive hierarchical" form of organization [Neuman, Y., 2004. Meaning making in the immune system. Perspect. Biol. Med. 48, 320-327; Neuman, Y., in press. A theory of meaning. Inform. Sci.] and suggest that this form of organization allows bootstrapping through reversible process of computation as discussed by theoretical physicists [Bennett, C.H., 1982. The thermodynamics of computation-a review. Int. J. Theoret. Phys. 1, 905-940; Landauer and Bennett, 1985].     

Fasciola hepatica virulence-associated cysteine peptidases: a systems biology perspective

Fasciola hepatica is a food-borne parasite of animals and humans. It secretes a large family of cysteine peptidases, termed cathepsins, that are important virulence factors. Here, we discuss how advances in molecular technologies have helped to probe the function of liver fluke cathepsins, and consider how evolving systems/molecular biology approaches can continue to inform our understanding of these important parasite enzymes.     

Feeding biology of a habitat-forming antipatharian in the Azores Archipelago

Coral Reefs - Benthic suspension feeders have developed a variety of feeding strategies and food availability has often proven to be a key factor explaining their occurrence and distribution. The...     

生物学的新军——合成生物学

合成生物学是一个新兴而极具研究前景的领域．旨在通过将多种天然或人工设计的生物学元件进行合理组合,创造出重构的或非天然的生物系统。综述了合成生物学这一新兴学科的核心理念、研究内容以及与相关学科的联系,详细介绍了J．CraigVenter研究小组所合成的“人造生命”,并展望了合成生物学广阔的发展前景和所面临的问题。     

Personality disorder: a new global perspective

Personality disorder is now being accepted as an important condition in mainstream psychiatry across the world. Although it often remains unrecognized in ordinary practice, research studies have shown it is common, creates considerable morbidity, is associated with high costs to services and to society, and interferes, usually negatively, with progress in the treatment of other mental disorders. We now have evidence that personality disorder, as currently classified, affects around 6% of the world population, and the differences between countries show no consistent variation. We are also getting increasing evidence that some treatments, mainly psychological, are of value in this group of disorders. What is now needed is a new classification that is of greater value to clinicians, and the WPA Section on Personality Disorders is currently undertaking this task.     

Porotic hyperostosis: a new perspective.

Porotic hyperostosis is a paleopathologic condition that has intrigued researchers for over a century and a half. It is now generally accepted that anemia, most probably an iron deficiency anemia, is the etiologic factor responsible for lesion production. Although there can be a number of factors involved in the development of iron deficiency anemia, a dietary explanation has often been invoked to explain the occurrence of porotic hyperostosis in past human skeletal populations. In fact, porotic hyperostosis has been referred to as a "nutritional" stress indicator. Traditionally those groups with a higher incidence of porotic hyperostosis have been considered to be less successful in adapting to their environment or more nutritionally disadvantaged than other groups. A new perspective is emerging that is challenging previous views of the role of iron in health and disease, thus having profound implications for the understanding of porotic hyperostosis. There is a new appreciation of the adaptability and flexibility of iron metabolism; as a result it has become apparent that diet plays a very minor role in the development of iron deficiency anemia. It is now understood that, rather than being detrimental, hypoferremia (deficiency of iron in the blood) is actually an adaptation to disease and microorganism invasion. When faced with chronic and/or heavy pathogen loads individuals become hypoferremic as part of their defense against these pathogens, thus increasing their susceptibility to iron deficiency anemia. Within the context of this new perspective porotic hyperostosis is seen not as a nutritional stress indicator, but as a indication that a population is attempting to adapt to the pathogen load in its environment.     

Feeding and reproduction of Calanus finmarchicus during non-bloom conditions in the Irminger Sea

Simultaneous ingestion and egg production experiments were conductedwith female Calanus finmarchicus in April/May and July/August2002 in the Irminger Sea. Experimental animals were providedwith natural microplankton food assemblages and incubated underin situ conditions for 24 h. The quantity of food consumed wassignificantly related to the concentration of prey cells, withtotal daily ingestion rates ranging from 0.6 to 8.1 µgof carbon female^–1 day^–1, corresponding to carbon-specificrates of 0.6–4.7% day^–1. Egg production rates (EPRs)remained relatively low (0.3–11 eggs female^–1 day^–1)during both periods of investigation and were not influencedby food availability. The data were used to construct energeticbudgets in which the microplankton carbon ingested, includingciliates, was compared with the carbon utilized for egg productionand respiration. These budgets showed that ingestion alone couldnot provide the necessary carbon to sustain the observed demandsfor growth and metabolism. Although ciliates constituted >80%of the total material ingested at times, they were not sufficientto provide the metabolic shortfall. Indeed, the females weretypically lacking 5 µg of carbon each day, 5% of theircarbon biomass. Our study results highlight the possible importanceof internal reserves in sustaining reproduction in C. finmarchicusduring periods of food scarcity.     

Dynamics of coexisting Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus populations in a high-Arctic fjord

We studied the population dynamics of Calanus finmarchicus, Calanus glacialis and Calanus hyperboreus in Billefjorden, Svalbard (78°40N). All three species reproduced in the fjord with different timing. The maximum abundance of Calanus spp. copepodite stages peaked on the 11th of July (29,000 ind m^–2). C. glacialis was the dominant species accounting for 60–80% of the total Calanus abundance. C. finmarchicus appear to thrive in the fjord despite the low temperatures (–1.86°C to 5°C) and accounted for 20–30% of the total population. C. hyperboreus contributed less to the total abundance (5–20%). A 1-year life cycle is suggested for C. finmarchicus and C. hyperboreus in the fjord, C. glacialis has a 1- to 2-year life cycle. Highest mortality rates were observed for copepodite stage CV in C. finmarchicus and C. glacialis (0.09 and 0.075 d^–1, respectively) and for females in C. hyperboreus (0.149 d^–1). Mortality of copepodite stages was substantially lower in C. glacialis than in the other species. This is particularly obvious in the early and numerous copepodite stages (CI + CII) during the period of recruitment to these stages. This suggests that differences in secondary production in Arctic pelagic ecosystems are controlled partly by population loss rates.     

Toward a systems biology perspective on enzyme evolution

Large superfamilies of enzymes derived from a common progenitor have emerged by duplication and divergence of genes encoding metabolic enzymes. Division of the functions of early generalist enzymes enhanced catalytic power and control over metabolic fluxes. Later, novel enzymes evolved from inefficient secondary activities in specialized enzymes. Enzymes operate in the context of complex metabolic and regulatory networks. The potential for evolution of a new enzyme depends upon the collection of enzymes in a microbe, the topology of the metabolic network, the environmental conditions, and the net effect of trade-offs between the original and novel activities of the enzyme.     

Conservation metagenomics: a new branch of conservation biology

Multifaceted approaches are required to monitor wildlife populations and improve conservation efforts. In the last decade,increasing evidence suggests that metagenomic analysis offers valuable perspectives and tools for identifying microbial communities and functions. It has become clear that gut microbiome plays a critical role in health, nutrition, and physiology of wildlife, including numerous endangered animals in the wild and in captivity. In this review, we first introduce the human microbiome and metagenomics, highlighting the importance of microbiome for host fitness. Then, for the first time, we propose the concept of conservation metagenomics, an emerging subdiscipline of conservation biology, which aims to understand the roles of the microbiota in evolution and conservation of endangered animals. We define what conservation metagenomics is along with current approaches, main scientific issues and significant implications in the study of host evolution, physiology,nutrition, ecology and conservation. We also discuss future research directions of conservation metagenomics. Although there is still a long way to go, conservation metagenomics has already shown a significant potential for improving the conservation and management of wildlife.