Life | September 2015 - Browse Articles

1819 KiB

Open AccessArticle

The Effects of Temperature and Growth Phase on the Lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii

by Sara Munk Jensen, Vinnie Lund Neesgaard, Sandra Landbo Nedergaard Skjoldbjerg, Martin Brandl, Christer S. Ejsing and Alexander H. Treusch

Life 2015, 5(3), 1539-1566; https://doi.org/10.3390/life5031539 - 25 Aug 2015

Cited by 30 | Viewed by 6475

Abstract

The functionality of the plasma membrane is essential for all organisms. Adaption to high growth temperatures imposes challenges and Bacteria, Eukarya, and Archaea have developed several mechanisms to cope with these. Hyperthermophilic archaea have earlier been shown to synthesize tetraether membrane lipids with an increased number of cyclopentane moieties at higher growth temperatures. Here we used shotgun lipidomics to study this effect as well as the influence of growth phase on the lipidomes of Sulfolobus islandicus and Sulfolobus tokodaii for the first time. Both species were cultivated at three different temperatures, with samples withdrawn during lag, exponential, and stationary phases. Three abundant tetraether lipid classes and one diether lipid class were monitored. Beside the expected increase in the number of cyclopentane moieties with higher temperature in both archaea, we observed previously unreported changes in the average cyclization of the membrane lipids throughout growth. The average number of cyclopentane moieties showed a significant dip in exponential phase, an observation that might help to resolve the currently debated biosynthesis pathway of tetraether lipids. Full article

(This article belongs to the Special Issue Archaea: Evolution, Physiology, and Molecular Biology)

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916 KiB

Open AccessArticle

Markov Chain-Like Quantum Biological Modeling of Mutations, Aging, and Evolution

by Ivan B. Djordjevic

Life 2015, 5(3), 1518-1538; https://doi.org/10.3390/life5031518 - 24 Aug 2015

Cited by 3 | Viewed by 6810

Abstract

Recent evidence suggests that quantum mechanics is relevant in photosynthesis, magnetoreception, enzymatic catalytic reactions, olfactory reception, photoreception, genetics, electron-transfer in proteins, and evolution; to mention few. In our recent paper published in Life, we have derived the operator-sum representation of a biological channel based on codon basekets, and determined the quantum channel model suitable for study of the quantum biological channel capacity. However, this model is essentially memoryless and it is not able to properly model the propagation of mutation errors in time, the process of aging, and evolution of genetic information through generations. To solve for these problems, we propose novel quantum mechanical models to accurately describe the process of creation spontaneous, induced, and adaptive mutations and their propagation in time. Different biological channel models with memory, proposed in this paper, include: (i) Markovian classical model, (ii) Markovian-like quantum model, and (iii) hybrid quantum-classical model. We then apply these models in a study of aging and evolution of quantum biological channel capacity through generations. We also discuss key differences of these models with respect to a multilevel symmetric channel-based Markovian model and a Kimura model-based Markovian process. These models are quite general and applicable to many open problems in biology, not only biological channel capacity, which is the main focus of the paper. We will show that the famous quantum Master equation approach, commonly used to describe different biological processes, is just the first-order approximation of the proposed quantum Markov chain-like model, when the observation interval tends to zero. One of the important implications of this model is that the aging phenotype becomes determined by different underlying transition probabilities in both programmed and random (damage) Markov chain-like models of aging, which are mutually coupled. Full article

(This article belongs to the Section Hypotheses in the Life Sciences)

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769 KiB

Open AccessReview

Fitness Landscapes of Functional RNAs

by Ádám Kun and Eörs Szathmáry

Life 2015, 5(3), 1497-1517; https://doi.org/10.3390/life5031497 - 21 Aug 2015

Cited by 10 | Viewed by 7808

Abstract

The notion of fitness landscapes, a map between genotype and fitness, was proposed more than 80 years ago. For most of this time data was only available for a few alleles, and thus we had only a restricted view of the whole fitness landscape. Recently, advances in genetics and molecular biology allow a more detailed view of them. Here we review experimental and theoretical studies of fitness landscapes of functional RNAs, especially aptamers and ribozymes. We find that RNA structures can be divided into critical structures, connecting structures, neutral structures and forbidden structures. Such characterisation, coupled with theoretical sequence-to-structure predictions, allows us to construct the whole fitness landscape. Fitness landscapes then can be used to study evolution, and in our case the development of the RNA world. Full article

(This article belongs to the Special Issue The Origins and Early Evolution of RNA)

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601 KiB

Open AccessReview

Halophilic Archaea: Life with Desiccation, Radiation and Oligotrophy over Geological Times

by Helga Stan-Lotter and Sergiu Fendrihan

Life 2015, 5(3), 1487-1496; https://doi.org/10.3390/life5031487 - 28 Jul 2015

Cited by 58 | Viewed by 12669

Abstract

Halophilic archaebacteria (Haloarchaea) can survive extreme desiccation, starvation and radiation, sometimes apparently for millions of years. Several of the strategies that are involved appear specific for Haloarchaea (for example, the formation of halomucin, survival in fluid inclusions of halite), and some are known from other prokaryotes (dwarfing of cells, reduction of ATP). Several newly-discovered haloarchaeal strategies that were inferred to possibly promote long-term survival—halomucin, polyploidy, usage of DNA as a phosphate storage polymer, production of spherical dormant stages—remain to be characterized in detail. More information on potential strategies is desirable, since evidence for the presence of halite on Mars and on several moons in the solar system increased interest in halophiles with respect to the search for extraterrestrial life. This review deals in particular with novel findings and hypotheses on haloarchaeal long-term survival. Full article

(This article belongs to the Special Issue The Physico-Chemical Limits of Life)

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682 KiB

Open AccessHypothesis

The Physical, Chemical and Physiological Limits of Life

by Dirk Schulze-Makuch, Alexander Schulze-Makuch and Joop M. Houtkooper

Life 2015, 5(3), 1472-1486; https://doi.org/10.3390/life5031472 - 17 Jul 2015

Cited by 11 | Viewed by 23388

Abstract

Life on Earth displays an incredible diversity in form and function, which allows it to survive not only physical extremes, but also periods of time when it is exposed to non-habitable conditions. Extreme physiological adaptations to bridge non-habitable conditions include various dormant states, such as spores or tuns. Here, we advance the hypothesis that if the environmental conditions are different on some other planetary body, a deviating biochemistry would evolve with types of adaptations that would manifest themselves with different physical and chemical limits of life. In this paper, we discuss two specific examples: putative life on a Mars-type planet with a hydrogen peroxide-water solvent and putative life on a Titan-type planetary body with liquid hydrocarbons as a solvent. Both examples would have the result of extending the habitable envelope of life in the universe. Full article

(This article belongs to the Special Issue The Physico-Chemical Limits of Life)

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Life, Volume 5, Issue 3 (September 2015) – 5 articles , Pages 1472-1566

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