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https://www.readbyqxmd.com/read/29997353/metagenomic-analysis-of-microbial-community-compositions-and-cold-responsive-stress-genes-in-selected-antarctic-lacustrine-and-soil-ecosystems
#1
Hyunmin Koo, Joseph A Hakim, Casey D Morrow, Michael R Crowley, Dale T Andersen, Asim K Bej
This study describes microbial community compositions, and various cold-responsive stress genes, encompassing cold-induced proteins (CIPs) and cold-associated general stress-responsive proteins (CASPs) in selected Antarctic lake water, sediment, and soil metagenomes. Overall, Proteobacteria and Bacteroidetes were the major taxa in all metagenomes. Prochlorococcus and Thiomicrospira were highly abundant in waters, while Myxococcus , Anaeromyxobacter , Haliangium, and Gloeobacter were dominant in the soil and lake sediment metagenomes...
July 11, 2018: Life
https://www.readbyqxmd.com/read/29997327/the-nitrogen-heterocycle-content-of-meteorites-and-their-significance-for-the-origin-of-life
#2
REVIEW
Zita Martins
Carbonaceous chondrites are very primitive meteorites that are rich in carbon. They contain many soluble organic compounds, including nitrogen heterocycles. These play a crucial role in present-day living organisms as they are components of the genetic material and of the co-factors of enzymes. This review outlines the nitrogen heterocycle content of carbonaceous meteorites. The potential mechanisms of formation of these molecules are also described. Measurements of the compound-specific carbon and hydrogen isotopic compositions are mentioned as a way of establishing the origin of the nitrogen heterocycles detected in meteorites...
July 11, 2018: Life
https://www.readbyqxmd.com/read/29973501/bioremediation-of-landfill-leachate-with-fungi-autochthonous-vs-allochthonous-strains
#3
Federica Spina, Valeria Tigini, Alice Romagnolo, Giovanna Cristina Varese
Autochthonous fungi from contaminated wastewater are potential successful agents bioremediation thanks to their adaptation to pollutant toxicity and to competition with other microorganisms present in wastewater treatment plant. Biological treatment by means of selected fungal strains could be a potential tool to integrate the leachate depuration process, thanks to their fungal extracellular enzymes with non-selective catalytical activity. In the present work, the treatability of two real samples (a crude landfill leachate and the effluent coming from a traditional wastewater treatment plant) was investigated in decolorization experiments with fungal biomasses...
July 4, 2018: Life
https://www.readbyqxmd.com/read/30004454/the-abc-transporter-components-hgdb-and-hgdc-are-important-for-glycolipid-layer-composition-and-function-of-heterocysts-in-anabaena-sp-pcc-7120
#4
Dmitry Shvarev, Carolina N Nishi, Lars Wörmer, Iris Maldener
Anabaena sp. PCC 7120 is a filamentous cyanobacterium able to fix atmospheric nitrogen in semi-regularly spaced heterocysts. For correct heterocyst function, a special cell envelope consisting of a glycolipid layer and a polysaccharide layer is essential. We investigated the role of the genes hgdB and hgdC , encoding domains of a putative ABC transporter, in heterocyst maturation. We investigated the subcellular localization of the fusion protein HgdC-GFP and followed the differential expression of the hgdB and hgdC genes during heterocyst maturation...
July 2, 2018: Life
https://www.readbyqxmd.com/read/29933597/bioinformatic-workflows-for-generating-complete-plastid-genome-sequences-an-example-from-cabomba-cabombaceae-in-the-context-of-the-phylogenomic-analysis-of-the-water-lily-clade
#5
Michael Gruenstaeudl, Nico Gerschler, Thomas Borsch
The sequencing and comparison of plastid genomes are becoming a standard method in plant genomics, and many researchers are using this approach to infer plant phylogenetic relationships. Due to the widespread availability of next-generation sequencing, plastid genome sequences are being generated at breakneck pace. This trend towards massive sequencing of plastid genomes highlights the need for standardized bioinformatic workflows. In particular, documentation and dissemination of the details of genome assembly, annotation, alignment and phylogenetic tree inference are needed, as these processes are highly sensitive to the choice of software and the precise settings used...
June 21, 2018: Life
https://www.readbyqxmd.com/read/29925796/chemomimesis-and-molecular-darwinism-in-action-from-abiotic-generation-of-nucleobases-to-nucleosides-and-rna
#6
REVIEW
Raffaele Saladino, Judit E Šponer, Jiří Šponer, Giovanna Costanzo, Samanta Pino, Ernesto Di Mauro
Molecular Darwinian evolution is an intrinsic property of reacting pools of molecules resulting in the adaptation of the system to changing conditions. It has no a priori aim. From the point of view of the origin of life, Darwinian selection behavior, when spontaneously emerging in the ensembles of molecules composing prebiotic pools, initiates subsequent evolution of increasingly complex and innovative chemical information. On the conservation side, it is a posteriori observed that numerous biological processes are based on prebiotically promptly made compounds, as proposed by the concept of Chemomimesis...
June 20, 2018: Life
https://www.readbyqxmd.com/read/29921763/integrity-of-the-dna-and-cellular-ultrastructure-of-cryptoendolithic-fungi-in-space-or-mars-conditions-a-1-5-year-study-at-the-international-space-station
#7
Silvano Onofri, Laura Selbmann, Claudia Pacelli, Jean Pierre de Vera, Gerda Horneck, John E Hallsworth, Laura Zucconi
The black fungi Cryomyces antarcticus and Cryomyces minteri are highly melanized and are resilient to cold, ultra-violet, ionizing radiation and other extreme conditions. These microorganisms were isolated from cryptoendolithic microbial communities in the McMurdo Dry Valleys (Antarctica) and studied in Low Earth Orbit (LEO), using the EXPOSE-E facility on the International Space Station (ISS). Previously, it was demonstrated that C. antarcticus and C. minteri survive the hostile conditions of space (vacuum, temperature fluctuations, and the full spectrum of extraterrestrial solar electromagnetic radiation), as well as Mars conditions that were simulated in space for a 1...
June 19, 2018: Life
https://www.readbyqxmd.com/read/29903995/big-sound-and-extreme-fungi-xerophilic-halotolerant-aspergilli-and-penicillia-with-low-optimal-temperature-as-invaders-of-historic-pipe-organs
#8
Katja Sterflinger, Christian Voitl, Ksenija Lopandic, Guadalupe Piñar, Hakim Tafer
Recent investigations have shown that xerophilic fungi may pose a biodeterioration risk by threatening objects of cultural heritage including many types of materials, including wood, paint layers, organic glues or leather and even metal. Historic—and also new built—pipe organs combine all those materials. In this study, halotolerant aspergilli and penicillia with low optimal temperatures were shown to be the most frequent invaders of pipe organs. The fungi form white mycelia on the organic components of the organs with a clear preference for the bolus paint of the wooden pipes, the leather-made hinges of the stop actions and all parts fixed by organic glue...
June 14, 2018: Life
https://www.readbyqxmd.com/read/29882802/homochirality-through-photon-induced-denaturing-of-rna-dna-at-the-origin-of-life
#9
Karo Michaelian
Since a racemic mixture of chiral nucleotides frustrates the enzymeless extension of RNA and DNA, the origin of homochirality must be intimately connected with the origin of life. Homochirality theories have elected to presume abiotic mechanisms for prebiotic enantiomer enrichment and post amplification, but none, so far, has been generally accepted. Here I present a novel hypothesis for the procurement of homochirality from an asymmetry in right- over left-circularly polarized photon-induced denaturing of RNA and DNA at the Archean ocean surface as temperatures descended below that of RNA and DNA melting...
June 6, 2018: Life
https://www.readbyqxmd.com/read/29874797/phylotar-an-automated-pipeline-for-retrieving-orthologous-dna-sequences-from-genbank-in-r
#10
Dominic J Bennett, Hannes Hettling, Daniele Silvestro, Alexander Zizka, Christine D Bacon, Søren Faurby, Rutger A Vos, Alexandre Antonelli
The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabeling encountered when searching for suitable sequences for phylogenetic analysis. These issues include, among others, the incorrect identification of sequenced species, non-standardized and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users...
June 5, 2018: Life
https://www.readbyqxmd.com/read/29865244/sun-exposure-shapes-functional-grouping-of-fungi-in-cryptoendolithic-antarctic-communities
#11
Claudia Coleine, Laura Zucconi, Silvano Onofri, Nuttapon Pombubpa, Jason E Stajich, Laura Selbmann
Antarctic cryptoendolithic microbial communities dominate ice-free areas of continental Antarctica, among the harshest environments on Earth. The endolithic lifestyle is a remarkable adaptation to the exceptional environmental extremes of this area, which is considered the closest terrestrial example to conditions on Mars. Recent efforts have attempted to elucidate composition of these extremely adapted communities, but the functionality of these microbes have remained unexplored. We have tested for interactions between measured environmental characteristics, fungal community membership, and inferred functional classification of the fungi present and found altitude and sun exposure were primary factors...
June 2, 2018: Life
https://www.readbyqxmd.com/read/29857564/data-driven-astrochemistry-one-step-further-within-the-origin-of-life-puzzle
#12
REVIEW
Alexander Ruf, Louis L S d'Hendecourt, Philippe Schmitt-Kopplin
Astrochemistry, meteoritics and chemical analytics represent a manifold scientific field, including various disciplines. In this review, clarifications on astrochemistry, comet chemistry, laboratory astrophysics and meteoritic research with respect to organic and metalorganic chemistry will be given. The seemingly large number of observed astrochemical molecules necessarily requires explanations on molecular complexity and chemical evolution, which will be discussed. Special emphasis should be placed on data-driven analytical methods including ultrahigh-resolving instruments and their interplay with quantum chemical computations...
June 1, 2018: Life
https://www.readbyqxmd.com/read/29843462/testing-the-domino-theory-of-gene-loss-in-buchnera-aphidicola-the-relevance-of-epistatic-interactions
#13
David J Martínez-Cano, Gil Bor, Andrés Moya, Luis Delaye
The domino theory of gene loss states that when some particular gene loses its function and cripples a cellular function, selection will relax in all functionally related genes, which may allow for the non-functionalization and loss of these genes. Here we study the role of epistasis in determining the pattern of gene losses in a set of genes participating in cell envelope biogenesis in the endosymbiotic bacteria Buchnera aphidicola . We provide statistical evidence indicating pairs of genes in B . aphidicola showing correlated gene loss tend to have orthologs in Escherichia coli known to have alleviating epistasis...
May 29, 2018: Life
https://www.readbyqxmd.com/read/29795023/molecular-evolution-in-a-peptide-vesicle-system
#14
Christian Mayer, Ulrich Schreiber, María J Dávila, Oliver J Schmitz, Amela Bronja, Martin Meyer, Julia Klein, Sven W Meckelmann
Based on a new model of a possible origin of life, we propose an efficient and stable system undergoing structural reproduction, self-optimization, and molecular evolution. This system is being formed under realistic conditions by the interaction of two cyclic processes, one of which offers vesicles as the structural environment, with the other supplying peptides from a variety of amino acids as versatile building blocks. We demonstrate that structures growing in a combination of both cycles have the potential to support their own existence, to undergo chemical and structural evolution, and to develop unpredicted functional properties...
May 24, 2018: Life
https://www.readbyqxmd.com/read/29789469/fungal-diversity-in-lichens-from-extremotolerance-to-interactions-with-algae
#15
REVIEW
Lucia Muggia, Martin Grube
Lichen symbioses develop long-living thallus structures even in the harshest environments on Earth. These structures are also habitats for many other microscopic organisms, including other fungi, which vary in their specificity and interaction with the whole symbiotic system. This contribution reviews the recent progress regarding the understanding of the lichen-inhabiting fungi that are achieved by multiphasic approaches (culturing, microscopy, and sequencing). The lichen mycobiome comprises a more or less specific pool of species that can develop symptoms on their hosts, a generalist environmental pool, and a pool of transient species...
May 22, 2018: Life
https://www.readbyqxmd.com/read/29757224/insights-into-abiotically-generated-amino-acid-enantiomeric-excesses-found-in-meteorites
#16
REVIEW
Aaron S Burton, Eve L Berger
Biology exhibits homochirality, in that only one of two possible molecular configurations (called enantiomers) is used in both proteins and nucleic acids. The origin of this phenomenon is currently unknown, as nearly all known abiotic mechanisms for generating these compounds result in equal (racemic) mixtures of both enantiomers. However, analyses of primitive meteorites have revealed that a number of amino acids of extraterrestrial origin are present in enantiomeric excess, suggesting that there was an abiotic route to synthesize amino acids in a non-racemic manner...
May 12, 2018: Life
https://www.readbyqxmd.com/read/29757217/caveats-to-exogenous-organic-delivery-from-ablation-dilution-and-thermal-degradation
#17
Chris Mehta, Anthony Perez, Glenn Thompson, Matthew A Pasek
A hypothesis in prebiotic chemistry argues that organics were delivered to the early Earth in abundance by meteoritic sources. This study tests that hypothesis by measuring how the transfer of organic matter to the surface of Earth is affected by energy-dissipation processes such as ablation and airbursts. Exogenous delivery has been relied upon as a source of primordial material, but it must stand to reason that other avenues (i.e., hydrothermal vents, electric discharge) played a bigger role in the formation of life as we know it on Earth if exogenous material was unable to deliver significant quantities of organics...
May 12, 2018: Life
https://www.readbyqxmd.com/read/29751593/comet-pond-ii-synergistic-intersection-of-concentrated-extraterrestrial-materials-and-planetary-environments-to-form-procreative-darwinian-ponds
#18
Benton C Clark, Vera M Kolb
In the “comet pond” model, a rare combination of circumstances enables the entry and landing of pristine organic material onto a planetary surface with the creation of a pond by a soft impact and melting of entrained ices. Formation of the constituents of the comet in the cold interstellar medium and our circumstellar disk results in multiple constituents at disequilibrium which undergo rapid chemical reactions in the warmer, liquid environment. The planetary surface also provides minerals and atmospheric gases which chemically interact with the pond’s organic- and trace-element-rich constituents...
May 11, 2018: Life
https://www.readbyqxmd.com/read/29748464/amphiphilic-compounds-assemble-into-membranous-vesicles-in-hydrothermal-hot-spring-water-but-not-in-seawater
#19
Daniel Milshteyn, Bruce Damer, Jeff Havig, David Deamer
There is a general assumption that amphiphilic compounds, such as fatty acids, readily form membranous vesicles when dispersed in aqueous phases. However, from earlier studies, it is known that vesicle stability depends strongly on pH, temperature, chain length, ionic concentration and the presence or absence of divalent cations. To test how robust simple amphiphilic compounds are in terms of their ability to assemble into stable vesicles, we chose to study 10- and 12-carbon monocarboxylic acids and a mixture of the latter with its monoglyceride...
May 10, 2018: Life
https://www.readbyqxmd.com/read/29738443/mineral-surface-templated-self-assembling-systems-case-studies-from-nanoscience-and-surface-science-towards-origins-of-life-research
#20
REVIEW
Richard J Gillams, Tony Z Jia
An increasing body of evidence relates the wide range of benefits mineral surfaces offer for the development of early living systems, including adsorption of small molecules from the aqueous phase, formation of monomeric subunits and their subsequent polymerization, and supramolecular assembly of biopolymers and other biomolecules. Each of these processes was likely a necessary stage in the emergence of life on Earth. Here, we compile evidence that templating and enhancement of prebiotically-relevant self-assembling systems by mineral surfaces offers a route to increased structural, functional, and/or chemical complexity...
May 8, 2018: Life
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