From exobiology to cosmobiology at LISA and elsewhere.

Since the emergence of Exobiology, back to the l960ties, this field drastically increased and, although differently named, is today a largely recognized scientific domain of wild interdisciplinarity. It includes not only the search for extraterrestrial living Systems, in particular by direct exploration of planetary bodies and studies of extraterrestrial materials, but also the study on the origins of life on Earth and, in connection to this field, the study of extraterrestrial organic chemistry. The exobiology programmes currently developed at LISA are related to this last aspect. They include the study of prebiotic-like chemistry in the gas and solid phases, based on laboratory simulation experiments, theoretical modeling and future in situ measurements in Titan's atmosphere and in cometary nuclei. A national program of exobiology, coordinated by LISA is under development in France, it covers many of the various aspects of Exobiology, including the study of life in extreme environments, as a reference tool for extraterrestrial life, the study of the primitive environment of the Earth, of the organic chemistry in comets and on Titan, of Mars and Europa and even of extrasolar planets as potential niches for extraterrestrial living systems, associated to the determination of the electromagnetic signatures of life. In parallel to this general program, a proposal for a large simulation chamber to be used as a national facility in particular to simulate the organic chemistry in various planetary environments, and in the interstellar medium, is under preparation. International cooperations linked to these programmes, in particular in the frame of the development of an exobiology facility on the International Space Station, would be of crucial interest.     

Abiogenic synthesis of oligopeptides in the open space

Exobiology is a relatively new field of sciences, which was established in connection with the development of the space technology, expanding the range of biological studies beyond the Earth. The major task of exobiology is the study of processes that give rise to the life, biological evolution, and distribution of living creatures in the universe. The term exobiology was introduced by the Dutch researcher Lederberg (1960). During fifty years of progressive development, it turned into a wide interdisciplinary field of sciences, including a number of disciplines, such as astrophysics, organic and analytical chemistry, geology, geochemistry, and other planet sciences not to mention various biological disciplines. Exobiology has become an inherent part of national and international space programs (Carle et al., 1992; Morrison, 2001).     

Exobiology on Titan

With a dense N₂-CH₄ atmosphere rich in organics, both in gas and aerosol phases, and with the possible presence of hydrocarbons oceans on its surface, Titan, the largest satellite of Saturn, appears as a natural laboratory to study chemical evolution toward complex organic systems, in a planetary environment and over a long time scale. Thanks to many analogies with planet Earth, it provides a unique way to look at the various physical and chemical processes, and their couplings which may have been involved in terrestrial prebiotic chemistry. Indeed, analogies with the Earth have a limit since Titan's temperatures are much lower than on the Earth and since liquid water is totally absent. However, from that aspect, Titan also serves as a reference laboratory worth studying — indirectly — the role of liquid water in exobiology. The Cassini-Huygens mission currently developed by NASA and ESA will send an orbiter around Saturn and Titan and a probe in Titan's atmosphere. This mission which will be launched in 1997 for an expected arrival in 2004, offers a unique opportunity to study in detail extra-terrestrial, not life-controled, organic processes, and consequently it will have significant implications in the fields of exobiology and the origins of life.This paper is dedicated to the memory of Cyril PONNAMPERUMA who largely contributed to the development of the scientific fields of Chemical Evolution and Exobiology.     

Microbial diversity of deep-sea extremophiles--Piezophiles, Hyperthermophiles, and subsurface microorganisms]

Knowledge of our Planet's biosphere has increased tremendously during the last 10 to 20 years. In the field of Microbiology in particular, scientists have discovered novel "extremophiles", microorganisms capable of living in extreme environments such as highly acidic or alkaline conditions, at high salt concentration, with no oxygen, extreme temperatures (as low as -20 degrees C and as high as 300 degrees C), at high concentrations of heavy metals and in high pressure environments such as the deep-sea. It is apparent that microorganisms can exist in any extreme environment of the Earth, yet already scientists have started to look for life on other planets; the so-called "Exobiology" project. But as yet we have little knowledge of the deep-sea and subsurface biosphere of our own planet. We believe that we should elucidate the Biodiversity of Earth more thoroughly before exploring life on other planets, and these attempts would provide deeper insight into clarifying the existence of extraterrestrial life. We focused on two deep-sea extremophiles in this article; one is "Piezophiles", and another is "Hyperthermophiles". Piezophiles are typical microorganisms adapted to high-pressure and cold temperature environments, and located in deep-sea bottom. Otherwise, hyperthermophiles are living in high temperature environment, and located at around the hydrothermal vent systems in deep-sea. They are not typical deep-sea microorganisms, but they can grow well at high-pressure condition, just like piezophiles. Deming and Baross mentioned that most of the hyperthermophilic archaea isolated from deep-sea hydrothermal vents are able to grow under conditions of high temperature and pressure, and in most cases their optimal pressure for growth was greater than the environmental pressure they were isolated from. It is possible that originally their native environment may have been deeper than the sea floor and that there had to be a deeper biosphere. This implication suggests that the deep-sea hydrothermal vents are the windows to a deep subsurface biosphere. A vast array of chemoautotrophic deep-sea animal communities have been found to exist in cold seep environments, and most of these animals are common with those found in hydrothermal vent environments. Thus, it is possible to consider that the cold seeps are also one of slit windows to a deep subsurface biosphere. We conclude that the deep-sea extremophiles are very closely related into the unseen majority in subsurface biosphere, and the subsurface biosphere probably concerns to consider the "exobiology".     

Extreme environments and exobiology

Ecological research on extreme environments can be applied to exobiological problems such as the question of life on Mars. If life forms (fossil or extant) are found on Mars, their study will help to solve fundamental questions about the nature of life on Earth. Extreme environments that are beyond the range of adaptability of their inhabitants are defined as "absolute extreme". Such environments can serve as terrestrial models for the last stages of life in the history of Mars, when the surface cooled down and atmosphere and water disappeared. The cryptoendolithic microbial community in porous rocks of the Ross Desert in Antarctica and the microbial mats at the bottom of frozen Antarctic lakes are such examples. The microbial communities of Siberian permafrost show that, in frozen but stable communities, long-term survival is possible. In the context of terraforming Mars, selected microorganisms isolated from absolute extreme environments are considered for use in creation of a biological carbon cycle.     

Creating a Cosmic Discipline: The Crystallization and Consolidation of Exobiology, 1957–1973

The new discipline of exobiology formed fromthe intertwining of origin of life researchwith the search for life or its building blockson other planets, from 1957–1973. The fieldwas inherently highly interdisciplinary, yet itcoalesced very quickly and was responsible inits first twenty years for numerous importantcontributions to twentieth century life scienceand planetary sciences such as climatology, thestudy of mass extinctions, etc. NASA played avery important role in catalyzing the rapidconsolidation of exobiology, both throughresearch grants and through sponsored meetingsthat overcame disciplinary boundaries, bringingtogether scientists from diverse backgrounds. The presence of a handful of prominent seniorscientists such as Joshua Lederberg, MelvinCalvin and Norman Horowitz helped gaincredibility for exobiology, in the face ofcriticism and competition from existing lifesciences disciplines. Tensions within theexobiology research community and betweenNASA-funded science and the academic researchcommunity are explored, as are such milestonesof discipline formation as journals andprofessional societies.     

What is an ‘extant’ type specimen? Problems arising from naming mammalian species‐group taxa without preserved types

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Errata corrige

Abstract

Ecological research on extreme environments can be applied to exobiological problems such as the question of life on Mars. If life forms (fossil or extant) are found on Mars, their study will help to solve fundamental questions about the nature of life on Earth. Extreme environments that are beyond the range of adaptability of their inhabitants are defined as “absolute extreme.” Such environments can serve as terrestrial models for the last stages of life in the history of Mars, when the surface cooled down and atmosphere and water disappeared. The cryptoendolithic microbial community in porous rocks of the Ross Desert in Antarctica and the microbial mats at the bottom of frozen Antarctic lakes are such examples. The microbial communities of Siberian permafrost show that, in frozen but stable communities, long-term survival is possible. In the context of terraforming Mars, selected microorganisms isolated from absolute extreme environments are considered for use in creation of a biological carbon cycle.     

Illness behavior of housewives in a rural area in Japan: A health diary study

A health diary study was conducted to examine the incidence and nature of health problems and illness behavior among rural residents in Japan. Attention was paid in particular to the utilization of folk medicine or alternative practitioners in the context of illness behavior. One hundred and sixty-one health problems were recorded over a 4-week diary period by 28 housewives aged 35–64 years. Headache, tiredness and gastrointestinal problems were among the most common problems. Emotional/psychological problems, the most frequently recorded problems in the health diary studies conducted in the United States or England, were recorded by only 3 participants. Only 6 problems (3.7 percent) resulted in consulting a doctor. Three women utilized an acupuncturist, shinkyshi, during the diary period. Self-care, such as resting by lying down, using home remedies and self-medication including household drugs, Toyama kusuri and folk medicine, was practiced for 101 problems (62.7 percent). Folk medicine or alternative practitioners played important roles in the health seeking process. The health diary method was shown to be suitable not only to Western communities but also in a rural Japanese context.     

On the definition, nomenclature and classification of water channel proteins (aquaporins and relatives)

A water channel protein (WCP) or a water channel can be defined as a transmembrane protein that has a specific three-dimensional structure with a pore that provides a pathway for water permeation across biological membranes. The pore is formed by two highly conserved regions in the amino acid sequence, called NPA boxes (or motifs) with three amino acid residues (asparagine-proline-alanine, NPA) and several surrounding amino acids. The NPA boxes have been called the "signature" sequence of WCPs. WCPs are a family of proteins belonging to the Membrane Intrinsic Proteins (MIPs) superfamily. In addition, in the MIP superfamily (with more than 1000 members) there are also proteins with no channel activity. The WCP family include three subfamilies: aquaporins, aquaglyceroporins and S-aquaporins. (1) The aquaporins (AQPs) are water selective or specific water channels, also named by various authors as "orthodox", "ordinary", "conventional", "classical", "pure", "normal", or "sensu strictu" aquaporins); (2) The aquaglyceroporins are permeable to water, but also to other small uncharged molecules, in particular glycerol; this family includes the glycerol facilitators, abbreviated as GlpFs, from glycerol permease facilitators. The "signature" sequence for aquaglyceroporins is the aspartic acid residue (D) in the second NPA box. (3) The third subfamily of WCPs have little conserved amino acid sequences around the NPA boxes, unclassifiable to the first two subfamilies. I recommend to use always for this subfamily the name S-aquaporins. They are also named "superaquaporins", "aquaporins with unusual (or deviated) NPA boxes", "subcellular aquaporins", or "sip-like aquaporins". I also recommend to use always the spelling aquaporin (not aquaporine), and, for various AQPs, the abbreviation AQP followed immediately by the number, (e.g. AQP1), with no space or - which might create confusions with "minus".     

CHEMICAL EVOLUTION ON TITAN: COMPARISONS TO THE PREBIOTIC EARTH

Models for the origin of Titan's atmosphere, the processing of the atmosphere and surface and its exobiological role are reviewed. Titan has gained widespread acceptance in the origin of life field as a model for the types of evolutionary processes that could have occurred on prebiotic Earth. Both Titan and Earth possess significant atmospheres ( 1 atm) composed mainly of molecular nitrogen with smaller amounts of more reactive species. Both of these atmospheres are processed primarily by solar ultraviolet light with high energy particles interactions contributing to a lesser extent. The products of these reactions condense or are dissolved in other atmospheric species (aerosols/clouds) and fall to the surface. There these products may have been further processed on Titan and the primitive Earth by impacting comets and meteorites. While the low temperatures on Titan ( 72–180 K) preclude the presence of permanent liquid water on the surface, it has been suggested that tectonic activity or impacts by meteors and comets could produce liquid water pools on the surface for thousands of years. Hydrolysis and oligomerization reactions in these pools might form chemicals of prebiological significance. Other direct comparisons between the conditions on present day Titan and those proposed for prebiotic Earth are also presented.     

When does a clone deserve a name? A perspective on bacterial species based on population genetics.

Molecular population-genetic analysis has revealed that for several human diseases, including tuberculosis, plague and shigellosis, the generally accepted taxonomic status of the organisms involved does not fit the usually accepted genus or species criteria. This raises the question of what species concept to apply to bacteria. We suggest that the species definition in bacteria should be based on analysis of sequence variation in housekeeping genes, and also that the "clone" be given official status in bacterial nomenclature. This will allow demotion of the species or genus status of several traditionally recognized human pathogens, but retention of current names of anomalous species and genera as clone names.     

The terrestrial bioluminescent animals of Japan

Light production by organisms, or bioluminescence, has fascinated not only scientists but also ordinary people all over the world, and it has been especially so in Japan. Here we review the biological information available to date for all luminous terrestrial animals known from Japan, particularly focusing on their diversity and systematics, their biology and ecology in Japan, and putative function and biochemistry of their luminescence. In total 58 luminous terrestrial animals have been described from Japan, which consist of 50 fireflies (Coleoptera: Lampyridae), one glowworm beetle (Coleoptera: Phengodidae), two fungus gnats (Diptera: Keroplatidae), one springtail (Collembola), one millipede (Diplopoda), one centipede (Chilopoda) and two earthworms (Oligochaeta). For all except some firefly species, the DNA "barcode" sequences of a cytochrome oxidase subunit I region are provided. We also introduce how intricately the seasonal appearance and glimmering of luminous insects, in particular those of fireflies, have been interwoven into the culture, art, literature and mentality of Japanese people.     

Efficient docking of peptides to proteins without prior knowledge of the binding site

Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein-protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different protein/ligand complexes for which the structure was known, without prior knowledge of the binding site. More specifically, we look at factors influencing the accuracy of the final structure, such as the number of torsional degrees of freedom in the ligand. We conclude that the Autodock program package is able to select the correct complexes based on the energy without prior knowledge of the binding site. We named this application blind docking, as the docking algorithm is not able to "see" the binding site but can still find it. The success of blind docking represents an important finding in the era of structural genomics.     

Where is the origin of the Japanese gamecocks?

The tradition of cockfighting is widespread throughout the world. There is no doubt that the gamecock has evolved together with the human culture of cockfighting for a long time. In Japan, there is a group of gamecocks called "Shamo" that are used specifically for cockfighting. However, the process of the geographic distribution of cockfighting and the influx route of gamecocks into Japan are totally unclear. The molecular evolutionary study of gamecocks is obviously useful to gain profound insight into the understanding of not only the evolutionary origin of "Shamo" but also the distribution process of cockfighting as a culture. In this study, we collected blood samples of gamecocks from 11 different prefectures in Japan. Then, a phylogenetic tree was constructed using a total of 42 mtDNAs (D-loop, 1100 bp) sequenced. It showed that Japanese Shamo was clearly separated into two different groups: One group contains the samples from the island of Okinawa and the other group is composed of the samples mainly from Kyushu and Honshu of Japan. It suggests that Japanese Shamo must have been brought to Japan from two different origins. Our examination of historical records showed that the results of the phylogenetic analysis is consistent with the view that Japanese Shamo was originated from Southeast Asia and the mainland China independently, but was geographically a bit mixed afterwards.     

Abiotic formation of bioorganic compounds in space--preliminary experiments on ground and future exobiology experiments in space.

Simulation experiments on ground have shown that "amino acid precursors", which give amino acids after acid-hydrolysis, can be formed when an ice mixture simulating ice mantles of interstellar dust particles (lSDs) is irradiated with high energy particles or UV light. It is strongly suggested that such bioorganic compounds were delivered by comets for the first biosphere on the Earth. It is of great interest to confirm this hypothesis in actual space conditions, such as in an exposed facility of JEM. Fundamental designs for such exobiology experiments in earth orbit (EEEO) will be discussed.     

Photobiology in space: an experiment on Spacelab I

The joint European/US Spacelab Mission I, scheduled for October 1983 for a 9 day lasting Earth-orbiting flight, provides a laboratory system for various disciplines of science, including exobiology. On the pallet, in the experiment ES 029 "Microorganisms and Biomolecules in Space Hard Environment" 316 dry samples of Bacillus subtilis spores will be exposed to space vacuum and/or selected wavelenghs of solar UV radiation. After recovery action spectra of inactivation, mutation induction, reparability and photochemical damage in DNA and protein will be determined. The results will contribute to the understanding of the mechanism of the increased UV sensitivity of bacterial spores in vacuo and to a better assessment of the chance of survival of resistant life forms in space and of interplanetary transfer of life.     

The mucopolysaccharidoses: Inborn errors of glycosaminoglycan catabolism

Summary The mucopolysaccharidoses are genetic disorders of glycosaminoglycan metabolism. Patients with these diseases accumulate within the lysosomes of most tissues excessive amounts of dermatan and/or heparan sulfates, or of keratan sulfate. The clinical consequences of such glycosaminoglycan storage range from skeletal abnormalities to cardiovascular problems, and to motor and mental retardation.In all mucopolysaccharidoses, except Morquio disease, an excessive accumulation of sulfate-labeled glycosaminoglycans has been demonstrated in fibroblasts cultured from the patient's skin. It was subsequently shown that this was due to the deficiency of specific proteins which were named corrective factors, because their addition to the culture medium effected a normalization of the impaired glycosaminoglycan catabolism in the respective mucopolysaccharidosis fibroblasts. The investigation of the function of the corrective factors, and other studies, led to the identification of the enzymatic defect in each of the mucopolysaccharidoses.Seven lysosomal enzyme deficiencies are now recognized among this group of disorders. A classification of the diseases, according to the mutant gene products, reveals that there is considerable phenotypic variation not only between diseases, but also within several disease types. With the availability of the appropriate enzyme assays, the previous difficulties in diagnosing these disorders have now been overcome. Methods are also available for the prenatal diagnosis, and the detection of heterozygous individuals, in most of the mucopolysaccharidoses.Although correction of the metabolic defect through enzyme replacement has been achieved in tissue culture, many problems remain to be solved before such therapy may become applicable in the patients themselves.     

Patterns of hobo elements and their effects in natural populations of Drosophila melanogaster in Japan

We studied the dynamics of hobo elements of Drosophila melanogaster in Japan with the goal of better understanding the invasion and evolution of transposons in natural populations. One hundred and twenty-six isofemale lines and 11 older stocks were tested for the presence and genetic phenotype of hobo elements. The oldest H strain, containing complete and deleted hobo elements, is Hikone-H (1957), but Hikone-R (1952) has no hobo-homologous sequences. The findings suggest that the hobo element invaded Japanese populations in the mid-1950s, at about the same time as the P element invasion in Japan. This chronology is consistent with the hypothesis of a recent worldwide hobo element invasion into D. melanogaster in the mid-1950s. In recently collected populations, H degrees strains (low hobo activity and high repression potency) are predominant, whereas H+ strains (high hobo activity and high repression potency) are predominant in the Sakishima Islands, the most southwestern islands of the Japanese archipelago. H' strains (high hobo activity and low repression potency) were first found in limited island populations. Japanese populations have not only full-size hobo elements and 1.5 kb Th elements but also characteristic deletion derivatives (1.6 and 1.8 kb XhoI fragments) that we have named Jh elements. These results are consistent with transgenic experiments with complete hobo elements, in which populations evolved to H+ or H degrees via H', and in which 1.8 kb fragments appeared. We conclude that hobo elements invaded the central region of Japan, spread to the far islands, and that the invasion is currently at an intermediate, nonequilibrium stage.     

Europa as an Abode of Life

Life as we know it on Earth depends on liquid water, a suite of `biogenic' elements (most famously carbon) and a useful source of free energy. Here we review Europa's suitability for life from the perspective of these three requirements. It is likely, though not yet certain, that Europa harbors a subsurface ocean of liquid water whose volume is about twice that of Earth's oceans. Little is known about Europa's inventory of carbon, nitrogen, and other biogenic elements, but lower bounds on these can be placed by considering the role of cometary delivery over Europa's history. Sources of free energy are challenging for a world covered with an ice layer kilometers thick, but it is possible that hydrothermal activity and/or organics and oxidants provided by the action of radiation chemistry at Europa's surface and subsequent mixing into Europa's ocean could provide the electron donors and acceptors needed to power a Europan ecosystem. It is not premature to draw lessons from the search for life on Mars with the Viking spacecraft for planning exobiological missions to Europa.