http://www.mdpi.com/journal/life Latest open access articles published in Life at http://www.mdpi.com/journal/life http://www.mdpi.com/2075-1729/3/2/346 Although hypersaline environments pose challenges to life because of the low water content (water activity), many such habitats appear to support eukaryotic microbes. This contribution presents brief reviews of our current knowledge on eukaryotes of water-column haloclines and brines from Deep Hypersaline Anoxic Basins (DHABs) of the Eastern Mediterranean, as well as shallow-water hypersaline microbial mats in solar salterns of Guerrero Negro, Mexico and benthic microbialite communities from Hamelin Pool, Shark Bay, Western Australia. New data on eukaryotic diversity from Shark Bay microbialites indicates eukaryotes are more diverse than previously reported. Although this comparison shows that eukaryotic communities in hypersaline habitats with varying physicochemical characteristics are unique, several groups are commonly found, including diverse alveolates, strameonopiles, and fungi, as well as radiolaria. Many eukaryote sequences (SSU) in both regions also have no close homologues in public databases, suggesting that these environments host unique microbial eukaryote assemblages with the potential to enhance our understanding of the capacity of eukaryotes to adapt to hypersaline conditions. Life 2013-05-22 3 2 Article 10.3390/life3020346 346 362 2075-1729 2013-05-22 doi: 10.3390/life3020346 Virginia Edgcomb Joan Bernhard http://www.mdpi.com/2075-1729/3/2/331 The origin of life on Earth is widely believed to have required the reactions of organic compounds and their self- and/or environmental organization. What those compounds were remains open to debate, as do the environment in and process or processes by which they became organized. Prebiotic chemistry is the systematic organized study of these phenomena. It is difficult to study poorly defined phenomena, and research has focused on producing compounds and structures familiar to contemporary biochemistry, which may or may not have been crucial for the origin of life. Given our ignorance, it may be instructive to explore the extreme regions of known and future investigations of prebiotic chemistry, where reactions fail, that will relate them to or exclude them from plausible environments where they could occur. Come critical parameters which most deserve investigation are discussed. Life 2013-04-29 3 2 Article 10.3390/life3020331 331 345 2075-1729 2013-04-29 doi: 10.3390/life3020331 Henderson Cleaves http://www.mdpi.com/2075-1729/3/2/321 The prebiotic relevance of mineral struvite, MgNH4PO4·6H2O, was studied experimentally as a phosphorylating reagent and, theoretically, to understand the geochemical requirements for its formation. The effectiveness of phosphorylation by the phosphate mineral, monetite, CaHPO4, was also studied to compare to the efficiency of struvite. The experiments focused on the phosphorylation reactions of the minerals with organic compounds, such as nucleosides, glycerol and choline chloride, and heat at 75 °C for about 7–8 days and showed up to 28% phosphorylation of glycerol. In contrast, the compositional requirements for the precipitation of struvite are high ammonium and phosphate concentrations, as well as a little Ca2+ dissolved in the water. Combined, these requirements suggest that it is not likely that struvite was present in excess on the early Earth to carry out phosphorylation reactions. The present study focuses on the thermodynamic aspects of struvite formation, complementing the results given by Orgel and Handschuh (1973), which were based on the kinetic effects. Life 2013-04-29 3 2 Article 10.3390/life3020321 321 330 2075-1729 2013-04-29 doi: 10.3390/life3020321 Maheen Gull Matthew Pasek http://www.mdpi.com/2075-1729/3/2/308 Hot springs have been investigated since the XIX century, but isolation and examination of their thermophilic microbial inhabitants did not start until the 1950s. Many thermophilic microorganisms and their viruses have since been discovered, although the real complexity of thermal communities was envisaged when research based on PCR amplification of the 16S rRNA genes arose. Thereafter, the possibility of cloning and sequencing the total environmental DNA, defined as metagenome, and the study of the genes rescued in the metagenomic libraries and assemblies made it possible to gain a more comprehensive understanding of microbial communities—their diversity, structure, the interactions existing between their components, and the factors shaping the nature of these communities. In the last decade, hot springs have been a source of thermophilic enzymes of industrial interest, encouraging further study of the poorly understood diversity of microbial life in these habitats. Life 2013-04-25 3 2 Review 10.3390/life3020308 308 320 2075-1729 2013-04-25 doi: 10.3390/life3020308 Olalla López-López María Cerdán María González-Siso http://www.mdpi.com/2075-1729/3/2/295 Magnetotactic bacteria (MTB) represent a diverse collection of motile prokaryotes that biomineralize intracellular, membrane-bounded, tens-of-nanometer-sized crystals of a magnetic mineral called magnetosomes. Magnetosome minerals consist of either magnetite (Fe3O4) or greigite (Fe3S4) and cause cells to align along the Earth’s geomagnetic field lines as they swim, a trait called magnetotaxis. MTB are known to mainly inhabit the oxic–anoxic interface (OAI) in water columns or sediments of aquatic habitats and it is currently thought that magnetosomes function as a means of making chemotaxis more efficient in locating and maintaining an optimal position for growth and survival at the OAI. Known cultured and uncultured MTB are phylogenetically associated with the Alpha-, Gamma- and Deltaproteobacteria classes of the phylum Proteobacteria, the Nitrospirae phylum and the candidate division OP3, part of the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. MTB are generally thought to be ubiquitous in aquatic environments as they are cosmopolitan in distribution and have been found in every continent although for years MTB were thought to be restricted to habitats with pH values near neutral and at ambient temperature. Recently, however, moderate thermophilic and alkaliphilic MTB have been described including: an uncultured, moderately thermophilic magnetotactic bacterium present in hot springs in northern Nevada with a probable upper growth limit of about 63 °C; and several strains of obligately alkaliphilic MTB isolated in pure culture from different aquatic habitats in California, including the hypersaline, extremely alkaline Mono Lake, with an optimal growth pH of >9.0. Life 2013-03-26 3 2 Review 10.3390/life3020295 295 307 2075-1729 2013-03-26 doi: 10.3390/life3020295 Dennis Bazylinski Christopher Lefèvre http://www.mdpi.com/2075-1729/3/1/276 Raman spectroscopy is a valuable analytical technique for the identification of biomolecules and minerals in natural samples, which involves little or minimal sample manipulation. In this paper, we evaluate the advantages and disadvantages of this technique applied to the study of extremophiles. Furthermore, we provide a review of the results published, up to the present point in time, of the bio- and geo-strategies adopted by different types of extremophile colonies of microorganisms. We also show the characteristic Raman signatures for the identification of pigments and minerals, which appear in those complex samples. Life 2013-03-13 3 1 Review 10.3390/life3010276 276 294 2075-1729 2013-03-13 doi: 10.3390/life3010276 Susana Jorge-Villar Howell Edwards http://www.mdpi.com/2075-1729/3/1/260 Cell-to-cell communication, or quorum-sensing (QS), systems are employed by bacteria for promoting collective behaviour within a population. An analysis to detect QS signal molecules in 43 species of the Halomonadaceae family revealed that they produced N-acyl homoserine lactones (AHLs), which suggests that the QS system is widespread throughout this group of bacteria. Thin-layer chromatography (TLC) analysis of crude AHL extracts, using Agrobacterium tumefaciens NTL4 (pZLR4) as biosensor strain, resulted in different profiles, which were not related to the various habitats of the species in question. To confirm AHL production in the Halomonadaceae species, PCR and DNA sequencing approaches were used to study the distribution of the luxI-type synthase gene. Phylogenetic analysis using sequence data revealed that 29 of the species studied contained a LuxI homolog. Phylogenetic analysis showed that sequences from Halomonadaceae species grouped together and were distinct from other members of the Gammaproteobacteria and also from species belonging to the Alphaproteobacteria and Betaproteobacteria. Life 2013-03-05 3 1 Article 10.3390/life3010260 260 275 2075-1729 2013-03-05 doi: 10.3390/life3010260 Ali Tahrioui Melanie Schwab Emilia Quesada Inmaculada Llamas http://www.mdpi.com/2075-1729/3/1/244 Halococcus salifodinae BIpT DSM 8989T, an extremely halophilic archaeal isolate from an Austrian salt deposit (Bad Ischl), whose origin was dated to the Permian period, was described in 1994. Subsequently, several strains of the species have been isolated, some from similar but geographically separated salt deposits. Hcc. salifodinae may be regarded as one of the most ancient culturable species which existed already about 250 million years ago. Since its habitat probably did not change during this long period, its properties were presumably not subjected to the needs of mutational adaptation. Hcc. salifodinae and other isolates from ancient deposits would be suitable candidates for testing hypotheses on prokaryotic evolution, such as the molecular clock concept, or the net-like history of genome evolution. A comparison of available taxonomic characteristics from strains of Hcc. salifodinae and other Halococcus species, most of them originating from surface waters, is presented. The cell wall polymer of Hcc. salifodinae was examined and found to be a heteropolysaccharide, similar to that of Hcc. morrhuae. Polyhydroxyalkanoate granules were present in Hcc. salifodinae, suggesting a possible lateral gene transfer before Permian times. Life 2013-02-28 3 1 Article 10.3390/life3010244 244 259 2075-1729 2013-02-28 doi: 10.3390/life3010244 Andrea Legat Ewald Denner Marion Dornmayr-Pfaffenhuemer Peter Pfeiffer Burkhard Knopf Harald Claus Claudia Gruber Helmut König Gerhard Wanner Helga Stan-Lotter http://www.mdpi.com/2075-1729/3/1/234 The capability of osmoadaptation is a prerequisite of organisms that live in an environment with changing salinities. Halobacillus halophilus is a moderately halophilic bacterium that grows between 0.4 and 3 M NaCl by accumulating both chloride and compatible solutes as osmolytes. Chloride is absolutely essential for growth and, moreover, was shown to modulate gene expression and activity of enzymes involved in osmoadaptation. The synthesis of different compatible solutes is strictly salinity- and growth phase-dependent. This unique hybrid strategy of H. halophilus will be reviewed here taking into account the recently published genome sequence. Based on identified genes we will speculate about possible scenarios of the synthesis of compatible solutes and the uptake of potassium ion which would complete our knowledge of the fine-tuned osmoregulation and intracellular osmolyte balance in H. halophilus. Life 2013-02-27 3 1 Review 10.3390/life3010234 234 243 2075-1729 2013-02-27 doi: 10.3390/life3010234 Inga Hänelt Volker Müller http://www.mdpi.com/2075-1729/3/1/211 Existence of life in extreme environments has been known for a long time, and their habitants have been investigated by different scientific disciplines for decades. However, reports of multidisciplinary research are uncommon. In this paper, we report an interdisciplinary three-day field campaign conducted in the framework of the Coordination Action for Research Activities on Life in Extreme Environments (CAREX) FP7EU program, with participation of experts in the fields of life and earth sciences. In situ experiments and sampling were performed in a 20 m long hot springs system of different temperature (57 °C to 100 °C) and pH (2 to 4). Abiotic factors were measured to study their influence on the diversity. The CO2 and H2S concentration varied at different sampling locations in the system, but the SO2 remained the same. Four biofilms, mainly composed by four different algae and phototrophic protists, showed differences in photosynthetic activity. Varying temperature of the sampling location affects chlorophyll fluorescence, not only in the microbial mats, but plants (Juncus), indicating selective adaptation to the environmental conditions. Quantitative polymerase chain reaction (PCR), DNA microarray and denaturing gradient gel electrophoresis (DGGE)-based analysis in laboratory showed the presence of a diverse microbial population. Even a short duration (30 h) deployment of a micro colonizer in this hot spring system led to colonization of microorganisms based on ribosomal intergenic spacer (RISA) analysis. Polyphasic analysis of this hot spring system was possible due to the involvement of multidisciplinary approaches. Life 2013-02-25 3 1 Article 10.3390/life3010211 211 233 2075-1729 2013-02-25 doi: 10.3390/life3010211 Viggó Marteinsson Parag Vaishampayan Jana Kviderova Francesca Mapelli Mauro Medori Carlo Calfapietra Angeles Aguilera Domenica Hamisch Eyjólfur Reynisson Sveinn Magnússon Ramona Marasco Sara Borin Abigail Calzada Virginia Souza-Egipsy Elena González-Toril Ricardo Amils Josef Elster Robert Hänsch http://www.mdpi.com/2075-1729/3/1/189 A nine year study was carried out on the evolution of macroscopic “acid streamer” growths in acidic, metal-rich mine water from the point of construction of a new channel to drain an abandoned underground copper mine. The new channel became rapidly colonized by acidophilic bacteria: two species of autotrophic iron-oxidizers (Acidithiobacillus ferrivorans and “Ferrovum myxofaciens”) and a heterotrophic iron-oxidizer (a novel genus/species with the proposed name “Acidithrix ferrooxidans”). The same bacteria dominated the acid streamer communities for the entire nine year period, with the autotrophic species accounting for ~80% of the micro-organisms in the streamer growths (as determined by terminal restriction enzyme fragment length polymorphism (T-RFLP) analysis). Biodiversity of the acid streamers became somewhat greater in time, and included species of heterotrophic acidophiles that reduce ferric iron (Acidiphilium, Acidobacterium, Acidocella and gammaproteobacterium WJ2) and other autotrophic iron-oxidizers (Acidithiobacillus ferrooxidans and Leptospirillum ferrooxidans). The diversity of archaea in the acid streamers was far more limited; relatively few clones were obtained, all of which were very distantly related to known species of euryarchaeotes. Some differences were apparent between the acid streamer community and planktonic-phase bacteria. This study has provided unique insights into the evolution of an extremophilic microbial community, and identified several novel species of acidophilic prokaryotes. Life 2013-02-07 3 1 Article 10.3390/life3010189 189 210 2075-1729 2013-02-07 doi: 10.3390/life3010189 Catherine Kay Owen Rowe Laura Rocchetti Kris Coupland Kevin Hallberg D. Johnson http://www.mdpi.com/2075-1729/3/1/181 The extremely halophilic archaeon Natrialba aegyptiaca secretes the L-homo type of poly-g-glutamate (PGA) as an extremolyte. We examined the enzymes involved in glutamate metabolism and verified the presence of L-glutamate dehydrogenases, L-aspartate aminotransferase, and L-glutamate synthase. However, neither glutamate racemase nor D-amino acid aminotransferase activity was detected, suggesting the absence of sources of D-glutamate. In contrast, D-glutamate-rich PGA producers mostly possess such intracellular sources of D-glutamate. The results of our present study indicate that the D-glutamate-anabolic enzyme “glutamate racemase” is pivotal in the biosynthesis of PGA. Life 2013-02-06 3 1 Communication 10.3390/life3010181 181 188 2075-1729 2013-02-06 doi: 10.3390/life3010181 Makoto Ashiuchi Takashi Yamamoto Tohru Kamei http://www.mdpi.com/2075-1729/3/1/161 Extreme habitats are often characterized by reduced predation pressures, thus representing refuges for the inhabiting species. The present study was designed to investigate predator avoidance of extremophile populations of Poecilia mexicana and P. sulphuraria that either live in hydrogen sulfide-rich (sulfidic) springs or cave habitats, both of which are known to have impoverished piscine predator regimes. Focal fishes that inhabited sulfidic springs showed slightly weaker avoidance reactions when presented with several naturally occurring predatory cichlids, but strongest differences to populations from non-sulfidic habitats were found in a decreased shoaling tendency with non-predatory swordtail (Xiphophorus hellerii) females. When comparing avoidance reactions between P. mexicana from a sulfidic cave (Cueva del Azufre) and the adjacent sulfidic surface creek (El Azufre), we found only slight differences in predator avoidance, but surface fish reacted much more strongly to the non-predatory cichlid Vieja bifasciata. Our third experiment was designed to disentangle learned from innate effects of predator recognition. We compared laboratory-reared (i.e., predator-naïve) and wild-caught (i.e., predator-experienced) individuals of P. mexicana from a non-sulfidic river and found no differences in their reaction towards the presented predators. Overall, our results indicate (1) that predator avoidance is still functional in extremophile Poecilia spp. and (2) that predator recognition and avoidance reactions have a strong genetic basis. Life 2013-02-06 3 1 Article 10.3390/life3010161 161 180 2075-1729 2013-02-06 doi: 10.3390/life3010161 David Bierbach Matthias Schulte Nina Herrmann Claudia Zimmer Lenin Arias-Rodriguez Jeane Indy Rüdiger Riesch Martin Plath http://www.mdpi.com/2075-1729/3/1/149 Arginine-binding protein from the extremophile Thermotoga maritima is a 27.7 kDa protein possessing the typical two-domain structure of the periplasmic binding proteins family. The protein is characterized by a very high specificity and affinity to bind to arginine, also at high temperatures. Due to its features, this protein could be taken into account as a potential candidate for the design of a biosensor for arginine. It is important to investigate the stability of proteins when they are used for biotechnological applications. In this article, we review the structural and functional features of an arginine-binding protein from the extremophile Thermotoga maritima with a particular eye on its potential biotechnological applications. Life 2013-02-05 3 1 Review 10.3390/life3010149 149 160 2075-1729 2013-02-05 doi: 10.3390/life3010149 Alessio Ausili Maria Staiano Jonathan Dattelbaum Antonio Varriale Alessandro Capo Sabato D'Auria http://www.mdpi.com/2075-1729/3/1/131 Microbial communication, particularly that of quorum sensing, plays an important role in regulating gene expression in a range of organisms. Although this phenomenon has been well studied in relation to, for example, virulence gene regulation, the focus of this article is to review our understanding of the role of microbial communication in extreme environments. Cell signaling regulates many important microbial processes and may play a pivotal role in driving microbial functional diversity and ultimately ecosystem function in extreme environments. Several recent studies have characterized cell signaling in modern analogs to early Earth communities (microbial mats), and characterization of cell signaling systems in these communities may provide unique insights in understanding the microbial interactions involved in function and survival in extreme environments. Cell signaling is a fundamental process that may have co-evolved with communities and environmental conditions on the early Earth. Without cell signaling, evolutionary pressures may have even resulted in the extinction rather than evolution of certain microbial groups. One of the biggest challenges in extremophile biology is understanding how and why some microbial functional groups are located where logically they would not be expected to survive, and tightly regulated communication may be key. Finally, quorum sensing has been recently identified for the first time in archaea, and thus communication at multiple levels (potentially even inter-domain) may be fundamental in extreme environments. Life 2013-01-29 3 1 Review 10.3390/life3010131 131 148 2075-1729 2013-01-29 doi: 10.3390/life3010131 Kate Montgomery James Charlesworth Rebecca LeBard Pieter Visscher Brendan Burns http://www.mdpi.com/2075-1729/3/1/118 Viruses that infect the third domain of life, Archaea, are a newly emerging field of interest. To date, all characterized archaeal viruses infect archaea that thrive in extreme conditions, such as halophilic, hyperthermophilic, and methanogenic environments. Viruses in general, especially those replicating in extreme environments, contain highly mosaic genomes with open reading frames (ORFs) whose sequences are often dissimilar to all other known ORFs. It has been estimated that approximately 85% of virally encoded ORFs do not match known sequences in the nucleic acid databases, and this percentage is even higher for archaeal viruses (typically 90%–100%). This statistic suggests that either virus genomes represent a larger segment of sequence space and/or that viruses encode genes of novel fold and/or function. Because the overall three-dimensional fold of a protein evolves more slowly than its sequence, efforts have been geared toward structural characterization of proteins encoded by archaeal viruses in order to gain insight into their potential functions. In this short review, we provide multiple examples where structural characterization of archaeal viral proteins has indeed provided significant functional and evolutionary insight. Life 2013-01-24 3 1 Review 10.3390/life3010118 118 130 2075-1729 2013-01-24 doi: 10.3390/life3010118 Nikki Dellas C. Lawrence Mark Young http://www.mdpi.com/2075-1729/3/1/86 Organisms representing diverse subgroupings of the Domain Archaea are known to possess unusual surface structures. These can include ones unique to Archaea such as cannulae and hami as well as archaella (archaeal flagella) and various types of pili that superficially resemble their namesakes in Bacteria, although with significant differences. Major advances have occurred particularly in the study of archaella and pili using model organisms with recently developed advanced genetic tools. There is common use of a type IV pili-model of assembly for several archaeal surface structures including archaella, certain pili and sugar binding structures termed bindosomes. In addition, there are widespread posttranslational modifications of archaellins and pilins with N-linked glycans, with some containing novel sugars. Archaeal surface structures are involved in such diverse functions as swimming, attachment to surfaces, cell to cell contact resulting in genetic transfer, biofilm formation, and possible intercellular communication. Sometimes functions are co-dependent on other surface structures. These structures and the regulation of their assembly are important features that allow various Archaea, including thermoacidophilic, hyperthermophilic, halophilic, and anaerobic ones, to survive and thrive in the extreme environments that are commonly inhabited by members of this domain. Life 2013-01-24 3 1 Review 10.3390/life3010086 86 117 2075-1729 2013-01-24 doi: 10.3390/life3010086 Ken Jarrell Yan Ding Divya Nair Sarah Siu http://www.mdpi.com/2075-1729/3/1/52 Caldicellulosiruptor saccharolyticus is one of the most thermophilic cellulolytic organisms known to date. This Gram-positive anaerobic bacterium ferments a broad spectrum of mono-, di- and polysaccharides to mainly acetate, CO2 and hydrogen. With hydrogen yields approaching the theoretical limit for dark fermentation of 4 mol hydrogen per mol hexose, this organism has proven itself to be an excellent candidate for biological hydrogen production. This review provides an overview of the research on C. saccharolyticus with respect to the hydrolytic capability, sugar metabolism, hydrogen formation, mechanisms involved in hydrogen inhibition, and the regulation of the redox and carbon metabolism. Analysis of currently available fermentation data reveal decreased hydrogen yields under non-ideal cultivation conditions, which are mainly associated with the accumulation of hydrogen in the liquid phase. Thermodynamic considerations concerning the reactions involved in hydrogen formation are discussed with respect to the dissolved hydrogen concentration. Novel cultivation data demonstrate the sensitivity of C. saccharolyticus to increased hydrogen levels regarding substrate load and nitrogen limitation. In addition, special attention is given to the rhamnose metabolism, which represents an unusual type of redox balancing. Finally, several approaches are suggested to improve biohydrogen production by C. saccharolyticus. Life 2013-01-17 3 1 Review 10.3390/life3010052 52 85 2075-1729 2013-01-17 doi: 10.3390/life3010052 Abraham Bielen Marcel Verhaart John van der Oost Servé Kengen http://www.mdpi.com/2075-1729/3/1/38 Hydrolases constitute a class of enzymes widely distributed in nature from bacteria to higher eukaryotes. The halotolerance of many enzymes derived from halophilic bacteria can be exploited wherever enzymatic transformations are required to function under physical and chemical conditions, such as in the presence of organic solvents and extremes in temperature and salt content. In recent years, different screening programs have been performed in saline habitats in order to isolate and characterize novel enzymatic activities with different properties to those of conventional enzymes. Several halophilic hydrolases have been described, including amylases, lipases and proteases, and then used for biotechnological applications. Moreover, the discovery of biopolymer-degrading enzymes offers a new solution for the treatment of oilfield waste, where high temperature and salinity are typically found, while providing valuable information about heterotrophic processes in saline environments. In this work, we describe the results obtained in different screening programs specially focused on the diversity of halophiles showing hydrolytic activities in saline and hypersaline habitats, including the description of enzymes with special biochemical properties. The intracellular lipolytic enzyme LipBL, produced by the moderately halophilic bacterium Marinobacter lipolyticus, showed advantages over other lipases, being an enzyme active over a wide range of pH values and temperatures. The immobilized LipBL derivatives obtained and tested in regio- and enantioselective reactions, showed an excellent behavior in the production of free polyunsaturated fatty acids (PUFAs). On the other hand, the extremely halophilic bacterium, Salicola marasensis sp. IC10 showing lipase and protease activities, was studied for its ability to produce promising enzymes in terms of its resistance to temperature and salinity. Life 2013-01-10 3 1 Review 10.3390/life3010038 38 51 2075-1729 2013-01-10 doi: 10.3390/life3010038 María de Lourdes Moreno Dolores Pérez María García Encarnación Mellado http://www.mdpi.com/2075-1729/3/1/21 The presence of microbialite structures in a freshwater, dimictic mid-latitudelake and their establishment after the last ice age about 10,000 years ago is puzzling.Freshwater calcite microbialites at Pavilion Lake, British Columbia, Canada, consist of acomplex community of microorganisms that collectively form large, ordered structuredaggregates. This distinctive assemblage of freshwater calcite microbialites was studied through standard microbial methods, morphological observations, phospholipid fatty acid(PLFA) analysis, DNA sequencing and the identification of quorum sensing molecules.Our results suggest that the microbialites may represent a transitional form from theexclusively prokaryotic colonial precursors of stromatolites to the multicellular organismicaggregates that give rise to coral reefs. Life 2012-12-27 3 1 Article 10.3390/life3010021 21 37 2075-1729 2012-12-27 doi: 10.3390/life3010021 Dirk Schulze-Makuch Darlene Lim Bernard Laval Carol Turse Marina António Olivia Chan Stephen Pointing Allyson Brady Donnie Reid Louis Irwin http://www.mdpi.com/2075-1729/3/1/1 A few extremely halophilic Archaea (Halobacterium salinarum, Haloquadratum walsbyi, Haloferax mediterranei, Halorubrum vacuolatum, Halogeometricum borinquense, Haloplanus spp.) possess gas vesicles that bestow buoyancy on the cells. Gas vesicles are also produced by the anaerobic endospore-forming halophilic Bacteria Sporohalobacter lortetii and Orenia sivashensis. We have extensive information on the properties of gas vesicles in Hbt. salinarum and Hfx. mediterranei and the regulation of their formation. Different functions were suggested for gas vesicle synthesis: buoying cells towards oxygen-rich surface layers in hypersaline water bodies to prevent oxygen limitation, reaching higher light intensities for the light-driven proton pump bacteriorhodopsin, positioning the cells optimally for light absorption, light shielding, reducing the cytoplasmic volume leading to a higher surface-area-to-volume ratio (for the Archaea) and dispersal of endospores (for the anaerobic spore-forming Bacteria). Except for Hqr. walsbyi which abounds in saltern crystallizer brines, gas-vacuolate halophiles are not among the dominant life forms in hypersaline environments. There only has been little research on gas vesicles in natural communities of halophilic microorganisms, and the few existing studies failed to provide clear evidence for their possible function. This paper summarizes the current status of the different theories why gas vesicles may provide a selective advantage to some halophilic microorganisms. Life 2012-12-27 3 1 Review 10.3390/life3010001 1 20 2075-1729 2012-12-27 doi: 10.3390/life3010001 Aharon Oren http://www.mdpi.com/2075-1729/2/4/377 Quantum mechanics has an important role in photosynthesis, magnetoreception, and evolution. There were many attempts in an effort to explain the structure of genetic code and transfer of information from DNA to protein by using the concepts of quantum mechanics. The existing biological quantum channel models are not sufficiently general to incorporate all relevant contributions responsible for imperfect protein synthesis. Moreover, the problem of determination of quantum biological channel capacity is still an open problem. To solve these problems, we construct the operator-sum representation of biological channel based on codon basekets (basis vectors), and determine the quantum channel model suitable for study of the quantum biological channel capacity and beyond. The transcription process, DNA point mutations, insertions, deletions, and translation are interpreted as the quantum noise processes. The various types of quantum errors are classified into several broad categories: (i) storage errors that occur in DNA itself as it represents an imperfect storage of genetic information, (ii) replication errors introduced during DNA replication process, (iii) transcription errors introduced during DNA to mRNA transcription, and (iv) translation errors introduced during the translation process. By using this model, we determine the biological quantum channel capacity and compare it against corresponding classical biological channel capacity. We demonstrate that the quantum biological channel capacity is higher than the classical one, for a coherent quantum channel model, suggesting that quantum effects have an important role in biological systems. The proposed model is of crucial importance towards future study of quantum DNA error correction, developing quantum mechanical model of aging, developing the quantum mechanical models for tumors/cancer, and study of intracellular dynamics in general. Life 2012-12-10 2 4 Article 10.3390/life2040377 377 391 2075-1729 2012-12-10 doi: 10.3390/life2040377 Ivan Djordjevic http://www.mdpi.com/2075-1729/2/4/364 Today, one of the major challenges in biophysics is to disclose the molecular mechanisms underlying biological processes. In such a frame, the understanding of the survival strategies in extreme conditions received a lot of attention both from the scientific and applicative points of view. Since nature provides precious suggestions to be applied for improving the quality of life, extremophiles are considered as useful model-systems. The main goal of this review is to present an overview of some systems, with a particular emphasis on trehalose playing a key role in several extremophile organisms. The attention is focused on the relation among the structural and dynamic properties of biomolecules and bioprotective mechanisms, as investigated by complementary spectroscopic techniques at low- and high-temperature values. Life 2012-12-07 2 4 Article 10.3390/life2040364 364 376 2075-1729 2012-12-07 doi: 10.3390/life2040364 Salvatore Magazù Federica Migliardo Miguel Gonzalez Claudia Mondelli Stewart Parker Beata Vertessy http://www.mdpi.com/2075-1729/2/4/323 In memoriam Jeffrey S. Wicken (1942–2002)—the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken’s legacy. (i) Connecting life’s origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic ‘charging’ of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called ‘microspheres’ is more realistic as a kinetic transition model of primal biogenesis than ‘hypercycle replication’ theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic ‘microspheres’. On the ‘continuist vs. miraculist’ schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic ‘continuist’ views and agenda. Life 2012-11-13 2 4 Essay 10.3390/life2040323 323 363 2075-1729 2012-11-13 doi: 10.3390/life2040323 Richard Egel http://www.mdpi.com/2075-1729/2/4/313 We describe the initial realization of behavior in the biosphere, which we term behavioral chemistry. If molecules are complex enough to attain a stochastic element to their structural conformation in such as a way as to radically affect their function in a biological (evolvable) setting, then they have the capacity to behave. This circumstance is described here as behavioral chemistry, unique in its definition from the colloquial chemical behavior.  This transition between chemical behavior and behavioral chemistry need be explicit when discussing the root cause of behavior, which itself lies squarely at the origins of life and is the foundation of choice.  RNA polymers of sufficient length meet the criteria for behavioral chemistry and therefore are capable of making a choice. Life 2012-11-07 2 4 Article 10.3390/life2040313 313 322 2075-1729 2012-11-07 doi: 10.3390/life2040313 Brian Larson R. Jensen Niles Lehman http://www.mdpi.com/2075-1729/2/4/286 At all levels of Life, systems evolve on the 'scales of equilibria'. At the level of bacteria, the individual cell must favor one of two opposing strategies and either take risks to grow or avoid risks to survive. It has been proposed in the Dualism hypothesis that the growth and survival strategies depend on non-equilibrium and equilibrium hyperstructures, respectively. It has been further proposed that the cell cycle itself is the way cells manage to balance the ratios of these types of hyperstructure so as to achieve the compromise solution of living on the two scales. Here, we attempt to re-interpret a major event, the initiation of chromosome replication in Escherichia coli, in the light of scales of equilibria. This entails thinking in terms of hyperstructures as responsible for intensity sensing and quantity sensing and how this sensing might help explain the role of the DnaA protein in initiation of replication. We outline experiments and an automaton approach to the cell cycle that should test and refine the scales concept. Life 2012-10-29 2 4 Article 10.3390/life2040286 286 312 2075-1729 2012-10-29 doi: 10.3390/life2040286 Vic Norris Patrick Amar http://www.mdpi.com/2075-1729/2/4/274 The evolution of life on earth has been a long process that began nearly 3,5 x 109 years ago. In their initial moments, evolution was mainly influenced by anaerobic environments; with the rise of O2 and the corresponding change in bioavailability of metal ions, new mechanisms of survival were created. Here we review the relationships between ancient atmospheric conditions, metal ion bioavailability and adaptation of metals homeostasis during early evolution. A general picture linking geochemistry, biochemistry and homeostasis is supported by the reviewed literature and is further illustrated in this report using simple database searches. Life 2012-10-29 2 4 Article 10.3390/life2040274 274 285 2075-1729 2012-10-29 doi: 10.3390/life2040274 Rolando P. Hong Enriquez Trang N. Do http://www.mdpi.com/2075-1729/2/3/255 Both Venus and Mars have captured the human imagination during the twentieth century as possible abodes of life. Venus had long enchanted humans—all the more so after astronomers realized it was shrouded in a mysterious cloak of clouds permanently hiding the surface from view. It was also the closest planet to Earth, with nearly the same size and surface gravity. These attributes brought myriad speculations about the nature of Venus, its climate, and the possibility of life existing there in some form. Mars also harbored interest as a place where life had or might still exist. Seasonal changes on Mars were interpreted as due to the possible spread and retreat of ice caps and lichen-like vegetation. A core element of this belief rested with the climatology of these two planets, as observed by astronomers, but these ideas were significantly altered, if not dashed during the space age. Missions to Venus and Mars revealed strikingly different worlds. The high temperatures and pressures found on Venus supported a “runaway greenhouse theory,” and Mars harbored an apparently lifeless landscape similar to the surface of the Moon. While hopes for Venus as an abode of life ended, the search for evidence of past life on Mars, possibly microbial, remains a central theme in space exploration. This survey explores the evolution of thinking about the climates of Venus and Mars as life-support systems, in comparison to Earth. Life 2012-09-19 2 3 Article 10.3390/life2030255 255 273 2075-1729 2012-09-19 doi: 10.3390/life2030255 Roger D. Launius http://www.mdpi.com/2075-1729/2/3/243 In this analysis natural systems are posed to subsystemize in a manner facilitating both structured information/energy sharing and an entropy maximization process projecting a three-dimensional, spatial, outcome. Numerical simulations were first carried out to determine whether n × n input-output matrices could, once entropy-maximized, project a three-dimensional Euclidean metric. Only 4 × 4 matrices could; a small proportion passed the test. Larger proportions passed when grouped random patterns on and within two- and three-dimensional forms were tested. Topographical patterns within 31 stream basin systems in the state of Kentucky, USA, were then similarly investigated, anticipating that the spatial configuration of elevations within each basin would provide evidence of evolutionary control when interpreted as internal group relations. Twenty-eight of thirty-one of the systems pass the test unambiguously, with the remaining three approaching or reaching passage when sampling density is increased. Two measures of subsystem-level redundancies are also introduced; these show: (1) surprisingly, minimized internal redundancy levels at the four subsystems level of analysis of the stream systems (as opposed to the five or six, in contrast with the simulations), and (2) much lower average levels than those obtained in the simulations at the same dimensions, both suggesting a preferred evolutionary path under real world conditions. Life 2012-08-31 2 3 Concept Paper 10.3390/life2030243 243 254 2075-1729 2012-08-31 doi: 10.3390/life2030243 Charles H. Smith Megan Derr http://www.mdpi.com/2075-1729/2/3/229 The habitat of metal respiring acidothermophilic lithoautotrophs is perhaps the most oxidizing environment yet identified. Geothermal heat, sulfuric acid and transition metals contribute both individually and synergistically under aerobic conditions to create this niche. Sulfuric acid and metals originating from sulfidic ores catalyze oxidative reactions attacking microbial cell surfaces including lipids, proteins and glycosyl groups. Sulfuric acid also promotes hydrocarbon dehydration contributing to the formation of black “burnt” carbon. Oxidative reactions leading to abstraction of electrons is further impacted by heat through an increase in the proportion of reactant molecules with sufficient energy to react. Collectively these factors and particularly those related to metals must be overcome by thermoacidophilic lithoautotrophs in order for them to survive and proliferate. The necessary mechanisms to achieve this goal are largely unknown however mechanistics insights have been gained through genomic studies. This review focuses on the specific role of metals in this extreme environment with an emphasis on resistance mechanisms in Archaea. Life 2012-08-23 2 3 Review 10.3390/life2030229 229 242 2075-1729 2012-08-23 doi: 10.3390/life2030229 Yukari Maezato Paul Blum http://www.mdpi.com/2075-1729/2/2/215 The invariance principle of enzyme enantioselectivity must be absolute because it is absolutely essential to the homochiral biological world. Most enzymes are strictly enantioselective, and tryptophanase is one of the enzymes with extreme absolute enantioselectivity for L-tryptophan. Contrary to conventional knowledge about the principle, tryptophanase becomes flexible to catalyze D-tryptophan in the presence of diammonium hydrogenphosphate. Since D-amino acids are ordinarily inert or function as inhibitors even though they are bound to the active site, the inhibition behavior of D-tryptophan and several inhibitors involved in this process was examined in terms of kinetics to explain the reason for this flexible enantioselectivity in the presence of diammonium hydrogenphosphate. Diammonium hydrogenphosphate gave tryptophanase a small conformational change so that D-tryptophan could work as a substrate. As opposed to other D-amino acids, D-tryptophan is a very bulky amino acid with a benzene ring in its heterocyclic moiety, and so we suggest that this structural feature makes the catalysis of D-tryptophan degradation possible, consequently leading to the flexible enantioselectivity. The present results not only help to understand the mechanism of enzyme enantioselectivity, but also shed light on the origin of homochirality. Life 2012-05-30 2 2 Article 10.3390/life2020215 215 228 2075-1729 2012-05-30 doi: 10.3390/life2020215 Akihiko Shimada Haruka Ozaki http://www.mdpi.com/2075-1729/2/1/213 Life (ISSN 2075-1729, http://www.mdpi.com/journal/life/) is a new journal that deals with new and sometime difficult interdisciplinary matters. Consequently, the journal will occasionally be presented with submitted articles that are controversial and/or outside conventional scientific views. Some papers recently accepted for publication in Life have attracted significant attention. Moreover, members of the Editorial Board have objected to these papers; some have resigned, and others have questioned the scientific validity of the contributions. In response I want to first state some basic facts regarding all publications in this journal. All papers are peer-reviewed, although it is often difficult to obtain expert reviewers for some of the interdisciplinary topics covered by this journal. I feel obliged to stress that although we will strive to guarantee the scientific standard of the papers published in this journal, all the responsibility for the ideas contained in the published articles rests entirely on their authors. Discussions on previously published articles are welcome and I hope that, by fostering discussion and by keeping an open-minded attitude towards new ideas, the journal will spur progress in this little explored, difficult and very exciting area of knowledge. [...] Life 2012-02-03 2 1 Editorial 10.3390/life2010213 213 214 2075-1729 2012-02-03 doi: 10.3390/life2010213 Shu-Kun Lin http://www.mdpi.com/2075-1729/2/1/170 This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution—leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other. Life 2012-01-23 2 1 Essay 10.3390/life2010170 170 212 2075-1729 2012-01-23 doi: 10.3390/life2010170 Richard Egel http://www.mdpi.com/2075-1729/2/1/165 The on-going whole genome sequencing and whole cell assays of metabolites and proteins imply that complex systems could ultimately be mastered by perfecting knowledge into great detail. However, courses of nature are inherently intractable because flows of energy and their driving forces depend on each other. Thus no data will suffice to predict precisely the outcomes of e.g., engineering experiments. All path-dependent processes, most notably evolution in its entirety, display this capricious character of nature. Life 2012-01-11 2 1 Communication 10.3390/life2010165 165 169 2075-1729 2012-01-11 doi: 10.3390/life2010165 Jaana Keto Arto Annila http://www.mdpi.com/2075-1729/2/1/135 The paper develops the Life Origination Hydrate Hypothesis (LOH-hypothesis), according to which living-matter simplest elements (LMSEs, which are N-bases, riboses, nucleosides, nucleotides), DNA- and RNA-like molecules, amino-acids, and proto-cells repeatedly originated on the basis of thermodynamically controlled, natural, and inevitable processes governed by universal physical and chemical laws from CH4, niters, and phosphates under the Earth's surface or seabed within the crystal cavities of the honeycomb methane-hydrate structure at low temperatures; the chemical processes passed slowly through all successive chemical steps in the direction that is determined by a gradual decrease in the Gibbs free energy of reacting systems. The hypothesis formulation method is based on the thermodynamic directedness of natural movement and consists ofan attempt to mentally backtrack on the progression of nature and thus reveal principal milestones alongits route. The changes in Gibbs free energy are estimated for different steps of the living-matter origination process; special attention is paid to the processes of proto-cell formation. Just the occurrence of the gas-hydrate periodic honeycomb matrix filled with LMSEs almost completely in its final state accounts for size limitation in the DNA functional groups and the nonrandom location of N-bases in the DNA chains. The slowness of the low-temperature chemical transformations and their “thermodynamic front” guide the gross process of living matter origination and its successive steps. It is shown that the hypothesis is thermodynamically justified and testable and that many observed natural phenomena count in its favor. Life 2012-01-04 2 1 Article 10.3390/life2010135 135 164 2075-1729 2012-01-04 doi: 10.3390/life2010135 Victor Ostrovskii Elena Kadyshevich http://www.mdpi.com/2075-1729/2/1/106 Is life physicochemically unique? No. Is life unique? Yes. Life manifests innumerable formalisms that cannot be generated or explained by physicodynamics alone. Life pursues thousands of biofunctional goals, not the least of which is staying alive. Neither physicodynamics, nor evolution, pursue goals. Life is largely directed by linear digital programming and by the Prescriptive Information (PI) instantiated particularly into physicodynamically indeterminate nucleotide sequencing. Epigenomic controls only compound the sophistication of these formalisms. Life employs representationalism through the use of symbol systems. Life manifests autonomy, homeostasis far from equilibrium in the harshest of environments, positive and negative feedback mechanisms, prevention and correction of its own errors, and organization of its components into Sustained Functional Systems (SFS). Chance and necessity—heat agitation and the cause-and-effect determinism of nature’s orderliness—cannot spawn formalisms such as mathematics, language, symbol systems, coding, decoding, logic, organization (not to be confused with mere self-ordering), integration of circuits, computational success, and the pursuit of functionality. All of these characteristics of life are formal, not physical. Life 2011-12-30 2 1 Review 10.3390/life2010106 106 134 2075-1729 2011-12-30 doi: 10.3390/life2010106 David L. Abel http://www.mdpi.com/2075-1729/2/1/1 Life is an inordinately complex unsolved puzzle. Despite significant theoretical progress, experimental anomalies, paradoxes, and enigmas have revealed paradigmatic limitations. Thus, the advancement of scientific understanding requires new models that resolve fundamental problems. Here, I present a theoretical framework that economically fits evidence accumulated from examinations of life. This theory is based upon a straightforward and non-mathematical core model and proposes unique yet empirically consistent explanations for major phenomena including, but not limited to, quantum gravity, phase transitions of water, why living systems are predominantly CHNOPS (carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur), homochirality of sugars and amino acids, homeoviscous adaptation, triplet code, and DNA mutations. The theoretical framework unifies the macrocosmic and microcosmic realms, validates predicted laws of nature, and solves the puzzle of the origin and evolution of cellular life in the universe. Life 2011-12-23 2 1 Article 10.3390/life2010001 1 105 2075-1729 2011-12-23 doi: 10.3390/life2010001 Erik D. Andrulis http://www.mdpi.com/2075-1729/1/1/34 I discuss briefly the history of the origin of life field, focusing on the “Miller” era of prebiotic synthesis, through the “Orgel” era seeking enzyme free template replication of single stranded RNA or similar polynucleotides, to the RNA world era with one of its foci on a ribozyme with the capacity to act as a polymerase able to copy itself. I give the history of the independent invention in 1971 by T. Ganti, M. Eigen and myself of three alternative theories of the origin of molecular replication: the Chemotron, the Hypercycle, and Collectively Autocatalytic Sets, CAS, respectively. To date, only collectively autocatalytic DNA, RNA, and peptide sets have achieved molecular reproduction of polymers. Theoretical work and experimental work on CAS both support their plausibility as models of openly evolvable protocells, if housed in dividing compartments such as dividing liposomes. My own further hypothesis beyond that of CAS in themselves, of their formation as a phase transition in complex chemical reaction systems of substrates, reactions and products, where the molecules in the system are candidates to catalyze the very same reactions, now firmly established as theorems, awaits experimental proof using combinatorial chemistry to make libraries of stochastic DNA, RNA and/or polypeptides, or other classes of molecules to test the hypothesis that molecular polymer reproduction has emerged as a true phase transition in complex chemical reaction systems. I remark that my colleague Marc Ballivet of the University of Geneva and I, may have issued the first publications discussing what became combinatorial chemistry, in published issued patents in 1987, 1989 and later, in this field. Life 2011-11-18 1 1 Article 10.3390/life1010034 34 48 2075-1729 2011-11-18 doi: 10.3390/life1010034 Stuart A. Kauffman http://www.mdpi.com/2075-1729/1/1/19 On Earth, marine anaerobic methane oxidation (AOM) can be driven by the microbial reduction of sulfate, iron, and manganese. Here, we have further characterized marine sediment incubations to determine if the mineral dependent methane oxidation involves similar microorganisms to those found for sulfate-dependent methane oxidation. Through FISH and FISH-SIMS analyses using 13C and 15N labeled substrates, we find that the most active cells during manganese dependent AOM are primarily mixed and mixed-cluster aggregates of archaea and bacteria. Overall, our control experiment using sulfate showed two active bacterial clusters, two active shell aggregates, one active mixed aggregate, and an active archaeal sarcina, the last of which appeared to take up methane in the absence of a closely-associated bacterial partner. A single example of a shell aggregate appeared to be active in the manganese incubation, along with three mixed aggregates and an archaeal sarcina. These results suggest that the microorganisms (e.g., ANME-2) found active in the manganese-dependent incubations are likely capable of sulfate-dependent AOM. Similar metabolic flexibility for Martian methanotrophs would mean that the same microbial groups could inhabit a diverse set of Martian mineralogical crustal environments. The recently discovered seasonal Martian plumes of methane outgassing could be coupled to the reduction of abundant surface sulfates and extensive metal oxides, providing a feasible metabolism for present and past Mars. In an optimistic scenario Martian methanotrophy consumes much of the periodic methane released supporting on the order of 10,000 microbial cells per cm2 of Martian surface. Alternatively, most of the methane released each year could be oxidized through an abiotic process requiring biological methane oxidation to be more limited. If under this scenario, 1% of this methane flux were oxidized by biology in surface soils or in subsurface aquifers (prior to release), a total of about 1020 microbial cells could be supported through methanotrophy with the cells concentrated in regions of methane release. Life 2011-11-18 1 1 Article 10.3390/life1010019 19 33 2075-1729 2011-11-18 doi: 10.3390/life1010019 Christopher H. House Emily J. Beal Victoria J. Orphan http://www.mdpi.com/2075-1729/1/1/9 There are several ways that our species might try to send a message to another species separated from us by space and/or time. Synthetic biology might be used to write an epitaph to our species, or simply “Kilroy was here”, in the genome of a bacterium via the patterns of either (1) the codons to exploit Life's non-equilibrium character or (2) the bases themselves to exploit Life's quasi-equilibrium character. We suggest here how DNA movies might be designed using such patterns. We also suggest that a search for mechanisms to create and preserve such patterns might lead to a better understanding of modern cells. Finally, we argue that the cutting-edge microbiology and synthetic biology needed for the Kilroy project would put origin-of-life studies in the vanguard of research. Life 2011-10-20 1 1 Article 10.3390/life1010009 9 18 2075-1729 2011-10-20 doi: 10.3390/life1010009 Victor Norris Yohann Grondin http://www.mdpi.com/2075-1729/1/1/7 Indeed, even if we know that many individual components are necessary for life to exist, we do not yet know what makes life emerge. One goal of this journal Life is to juxtapose articles with multidisciplinary approaches and perhaps to answer in the near future this question of the emergence of life. Different subjects and themes will be developed, starting of course with the multiple definitions of life and continuing with others such as: life diversity and universality; characteristics of living systems; thermodynamics with energy and entropy; kinetics and catalysis; water in its different physical states; circulation of sap and blood and its origin; the first blood pump and first heart; the first exchange of nutrients between cells, sap and blood; essential molecules of living systems; chirality; molecular asymmetry and its origin; formation of enantiomer excess and amplification; microscopic observations on a micrometer and sub-micrometer scales, at molecular and atomic levels; the first molecules at the origin of genetic information, viroids, circular RNA; regions of space or the area inside membranes and cells capable of initiating and maintaining life; phenomena at the origin of the emergence of life; molecules studied in the traditional field of chemistry and in the recent field of nanoscience governed by new laws; interaction between the individual molecules and components of living systems; interaction between living systems and the environment; transfer of information through generations; continuation of life from one generation to the next; prebiotic chemistry and prebiotic signatures on Earth, on Mars, on other planets; biosignatures of the first forms of life; fossils and pseudofossils dating 3.5 Ga ago and more recent ones; experimental fossilization; pluricellular eukaryotes dating 2.1 Ga ago; sudden increase in oxygen in the atmosphere around 2.0 to 2.5 Ga ago and its relation to geology; shell symmetry; aging with transformation of molecules, of their symmetry, their interactions, their exchanges. [...] Life 2011-09-29 1 1 Editorial 10.3390/life1010007 7 8 2075-1729 2011-09-29 doi: 10.3390/life1010007 Marie-Paule Bassez http://www.mdpi.com/2075-1729/1/1/3 Progress in the science of complexity, from the Big Bang to the coming of humankind, from chemistry and biology to geosciences and medicine, and from materials engineering to energy sciences, is leading to a shift of paradigm in the physical sciences. The focus is on the understanding of the non-equilibrium process in fine tuned systems. Quantum complex materials such as high temperature superconductors and living matter are both non-equilibrium and fine tuned systems. These topics have been subbjects of scientific discussion in the Rome Symposium on the “Quantum Physics of Living Matter”. Life 2011-09-29 1 1 Meeting Report 10.3390/life1010003 3 6 2075-1729 2011-09-29 doi: 10.3390/life1010003 Nicola Poccia Antonio Bianconi http://www.mdpi.com/2075-1729/1/1/1 Our publishing company MDPI (Multidisciplinary Digital Publishing Institute) planned to launch this journal Life (ISSN 2075-1729) since June 2009. Life science as a topic covers a very broad area. We decided to focus the scope of this new journal on the origin of life and the evolution of biosystems such as molecular evolution. Of course any fundamental theoretical topics and experimental discoveries in biology, biochemistry and biophysics will be welcomed also. [...] Life 2011-08-23 1 1 Editorial 10.3390/life1010001 1 2 2075-1729 2011-08-23 doi: 10.3390/life1010001 Shu-Kun Lin