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Life

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https://www.readbyqxmd.com/read/28075387/acknowledgement-to-reviewers-of-life-in-2016
#1
EDITORIAL
Life Editorial Office
The editors of Life would like to express their sincere gratitude to the following reviewers for assessing manuscripts in 2016.
January 10, 2017: Life
https://www.readbyqxmd.com/read/28067845/selection-of-prebiotic-molecules-in-amphiphilic-environments
#2
Christian Mayer, Ulrich Schreiber, María J Dávila
A basic problem in all postulated pathways of prebiotic chemistry is the low concentration which generally is expected for interesting reactants in fluid environments. Even though compounds, like nucleobases, sugars or peptides, principally may form spontaneously under environmental conditions, they will always be rapidly diluted in an aqueous environment. In addition, any such reaction leads to side products which often exceed the desired compound and generally hamper the first steps of a subsequent molecular evolution...
January 7, 2017: Life
https://www.readbyqxmd.com/read/28054992/mobility-of-a-mononucleotide-within-a-lipid-matrix-a-neutron-scattering-study
#3
Loreto Misuraca, Francesca Natali, Laura da Silva, Judith Peters, Bruno Demé, Jacques Ollivier, Tilo Seydel, Valerie Laux-Lesourd, Michael Haertlein, Giuseppe Zaccai, David Deamer, Marie Christine Maurel
An essential question in studies on the origins of life is how nucleic acids were first synthesized and then incorporated into compartments about 4 billion years ago. A recent discovery is that guided polymerization within organizing matrices could promote a non-enzymatic condensation reaction allowing the formation of RNA-like polymers, followed by encapsulation in lipid membranes. Here, we used neutron scattering and deuterium labelling to investigate 5'-adenosine monophosphate (AMP) molecules captured in a multilamellar phospholipid matrix...
January 4, 2017: Life
https://www.readbyqxmd.com/read/28035953/arsenite-as-an-electron-donor-for-anoxygenic-photosynthesis-description-of-three-strains-of-ectothiorhodospira-from-mono-lake-california-and-big-soda-lake-nevada
#4
Shelley Hoeft McCann, Alison Boren, Jaime Hernandez-Maldonado, Brendon Stoneburner, Chad W Saltikov, John F Stolz, Ronald S Oremland
Three novel strains of photosynthetic bacteria from the family Ectothiorhodospiraceae were isolated from soda lakes of the Great Basin Desert, USA by employing arsenite (As(III)) as the sole electron donor in the enrichment/isolation process. Strain PHS-1 was previously isolated from a hot spring in Mono Lake, while strain MLW-1 was obtained from Mono Lake sediment, and strain BSL-9 was isolated from Big Soda Lake. Strains PHS-1, MLW-1, and BSL-9 were all capable of As(III)-dependent growth via anoxygenic photosynthesis and contained homologs of arxA, but displayed different phenotypes...
December 26, 2016: Life
https://www.readbyqxmd.com/read/27918435/piecemeal-buildup-of-the-genetic-code-ribosomes-and-genomes-from-primordial-trna-building-blocks
#5
Derek Caetano-Anollés, Gustavo Caetano-Anollés
The origin of biomolecular machinery likely centered around an ancient and central molecule capable of interacting with emergent macromolecular complexity. tRNA is the oldest and most central nucleic acid molecule of the cell. Its co-evolutionary interactions with aminoacyl-tRNA synthetase protein enzymes define the specificities of the genetic code and those with the ribosome their accurate biosynthetic interpretation. Phylogenetic approaches that focus on molecular structure allow reconstruction of evolutionary timelines that describe the history of RNA and protein structural domains...
December 2, 2016: Life
https://www.readbyqxmd.com/read/27916886/cyanobacteria-as-chassis-for-industrial-biotechnology-progress-and-prospects
#6
REVIEW
Lamya Al-Haj, Yuen Tin Lui, Raeid M M Abed, Mohamed A Gomaa, Saul Purton
Cyanobacteria hold significant potential as industrial biotechnology (IB) platforms for the production of a wide variety of bio-products ranging from biofuels such as hydrogen, alcohols and isoprenoids, to high-value bioactive and recombinant proteins. Underpinning this technology, are the recent advances in cyanobacterial "omics" research, the development of improved genetic engineering tools for key species, and the emerging field of cyanobacterial synthetic biology. These approaches enabled the development of elaborate metabolic engineering programs aimed at creating designer strains tailored for different IB applications...
November 30, 2016: Life
https://www.readbyqxmd.com/read/27898036/screening-of-a-haloferax-volcanii-transposon-library-reveals-novel-motility-and-adhesion-mutants
#7
Georgio Legerme, Evan Yang, Rianne N Esquivel, Saija Kiljunen, Harri Savilahti, Mechthild Pohlschroder
Archaea, like bacteria, use type IV pili to facilitate surface adhesion. Moreover, archaeal flagella-structures required for motility-share a common ancestry with type IV pili. While the characterization of archaeal homologs of bacterial type IV pilus biosynthesis components has revealed important aspects of flagellum and pilus biosynthesis and the mechanisms regulating motility and adhesion in archaea, many questions remain. Therefore, we screened a Haloferax volcanii transposon insertion library for motility mutants using motility plates and adhesion mutants, using an adapted air-liquid interface assay...
November 26, 2016: Life
https://www.readbyqxmd.com/read/27827919/taming-prebiotic-chemistry-the-role-of-heterogeneous-and-interfacial-catalysis-in-the-emergence-of-a-prebiotic-catalytic-information-polymer-system
#8
REVIEW
Pierre-Alain Monnard
Cellular life is based on interacting polymer networks that serve as catalysts, genetic information and structural molecules. The complexity of the DNA, RNA and protein biochemistry suggests that it must have been preceded by simpler systems. The RNA world hypothesis proposes RNA as the prime candidate for such a primal system. Even though this proposition has gained currency, its investigations have highlighted several challenges with respect to bulk aqueous media: (1) the synthesis of RNA monomers is difficult; (2) efficient pathways for monomer polymerization into functional RNAs and their subsequent, sequence-specific replication remain elusive; and (3) the evolution of the RNA function towards cellular metabolism in isolation is questionable in view of the chemical mixtures expected on the early Earth...
November 4, 2016: Life
https://www.readbyqxmd.com/read/27618105/functional-annotations-of-paralogs-a-blessing-and-a-curse
#9
Rémi Zallot, Katherine J Harrison, Bryan Kolaczkowski, Valérie de Crécy-Lagard
Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines...
September 8, 2016: Life
https://www.readbyqxmd.com/read/27608044/evidence-supporting-the-uptake-and-genomic-incorporation-of-environmental-dna-in-the-ancient-asexual-bdelloid-rotifer-philodina-roseola
#10
Olaf R P Bininda-Emonds, Claus Hinz, Wilko H Ahlrichs
Increasing evidence suggests that bdelloid rotifers regularly undergo horizontal gene transfer, apparently as a surrogate mechanism of genetic exchange in the absence of true sexual reproduction, in part because of their ability to withstand desiccation. We provide empirical support for this latter hypothesis using the bdelloid Philodina roseola, which we demonstrate to readily internalize environmental DNA in contrast to a representative monogonont rotifer (Brachionus rubens), which, like other monogononts, is facultative sexual and cannot withstand desiccation...
September 6, 2016: Life
https://www.readbyqxmd.com/read/27598206/bipyrimidine-signatures-as-a-photoprotective-genome-strategy-in-g-c-rich-halophilic-archaea
#11
Daniel L Jones, Bonnie K Baxter
Halophilic archaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation. DNA repair systems and carotenoids provide UV protection but do not account for the high resistance observed. Herein, we consider genomic signatures as an additional photoprotective strategy. The predominant forms of UV-induced DNA damage are cyclobutane pyrimidine dimers, most notoriously thymine dimers (T^Ts), which form at adjacent Ts. We tested whether the high G + C content seen in halophilic archaea serves a photoprotective function through limiting T nucleotides, and thus T^T lesions...
September 2, 2016: Life
https://www.readbyqxmd.com/read/27571106/the-genetic-code-francis-crick-s-legacy-and-beyond
#12
EDITORIAL
Koji Tamura
Francis Crick (Figure 1) was born on 8 June 1916, in Northampton, England, and passed away on 28 July 2004, in La Jolla, California, USA.[...].
August 25, 2016: Life
https://www.readbyqxmd.com/read/27556494/the-use-of-a-fractional-factorial-design-to-determine-the-factors-that-impact-1-3-propanediol-production-from-glycerol-by-halanaerobium-hydrogeniformans
#13
Shivani Kalia, Jordan Trager, Oliver C Sitton, Melanie R Mormile
In recent years, biodiesel, a substitute for fossil fuels, has led to the excessive production of crude glycerol. The resulting crude glycerol can possess a high concentration of salts and an alkaline pH. Moreover, current crude glycerol purification methods are expensive, rendering this former commodity a waste product. However, Halanaerobium hydrogeniformans, a haloalkaliphilic bacterium, possesses the metabolic capability to convert glycerol into 1,3-propanediol, a valuable commodity compound, without the need for salt dilution or adjusting pH when grown on this waste...
August 20, 2016: Life
https://www.readbyqxmd.com/read/27548228/pressure-as-a-limiting-factor-for-life
#14
Rachael Hazael, Filip Meersman, Fumihisa Ono, Paul F McMillan
Facts concerning the stability and functioning of key biomolecular components suggest that cellular life should no longer be viable above a few thousand atmospheres (200-300 MPa). However, organisms are seen to survive in the laboratory to much higher pressures, extending into the GPa or even tens of GPa ranges. This is causing main questions to be posed concerning the survival mechanisms of simple to complex organisms. Understanding the ultimate pressure survival of organisms is critical for food sterilization and agricultural products conservation technologies...
August 17, 2016: Life
https://www.readbyqxmd.com/read/27529283/a-self-assembled-aggregate-composed-of-a-fatty-acid-membrane-and-the-building-blocks-of-biological-polymers-provides-a-first-step-in-the-emergence-of-protocells
#15
REVIEW
Roy A Black, Matthew C Blosser
We propose that the first step in the origin of cellular life on Earth was the self-assembly of fatty acids with the building blocks of RNA and protein, resulting in a stable aggregate. This scheme provides explanations for the selection and concentration of the prebiotic components of cells; the stabilization and growth of early membranes; the catalysis of biopolymer synthesis; and the co-localization of membranes, RNA and protein. In this article, we review the evidence and rationale for the formation of the proposed aggregate: (i) the well-established phenomenon of self-assembly of fatty acids to form vesicles; (ii) our published evidence that nucleobases and sugars bind to and stabilize such vesicles; and (iii) the reasons why amino acids likely do so as well...
August 11, 2016: Life
https://www.readbyqxmd.com/read/27509525/ultra-large-gene-families-a-matter-of-adaptation-or-genomic-parasites
#16
Philipp H Schiffer, Jan Gravemeyer, Martina Rauscher, Thomas Wiehe
Gene duplication is an important mechanism of molecular evolution. It offers a fast track to modification, diversification, redundancy or rescue of gene function. However, duplication may also be neutral or (slightly) deleterious, and often ends in pseudo-geneisation. Here, we investigate the phylogenetic distribution of ultra large gene families on long and short evolutionary time scales. In particular, we focus on a family of NACHT-domain and leucine-rich-repeat-containing (NLR)-genes, which we previously found in large numbers to occupy one chromosome arm of the zebrafish genome...
August 8, 2016: Life
https://www.readbyqxmd.com/read/27527219/aglm-and-vng1048g-two-haloarchaeal-udp-glucose-dehydrogenases-show-different-salt-related-behaviors
#17
Lina Kandiba, Jerry Eichler
Haloferax volcanii AglM and Halobacterium salinarum VNG1048G are UDP-glucose dehydrogenases involved in N-glycosylation in each species. Despite sharing >60% sequence identity and the ability of VNG1048G to functionally replace AglM in vivo, these proteins behaved differently as salinity changed. Whereas AglM was active in 2-4 M NaCl, VNG1048G lost much of its activity when salinity dropped below 3 M NaCl. To understand the molecular basis of this phenomenon, each protein was examined by size exclusion chromatrography in 2 M NaCl...
August 3, 2016: Life
https://www.readbyqxmd.com/read/27527218/gene-family-extension-measures-and-correlations
#18
Gon Carmi, Alexander Bolshoy
The existence of multiple copies of genes is a well-known phenomenon. A gene family is a set of sufficiently similar genes, formed by gene duplication. In earlier works conducted on a limited number of completely sequenced and annotated genomes it was found that size of gene family and size of genome are positively correlated. Additionally, it was found that several atypical microbes deviated from the observed general trend. In this study, we reexamined these associations on a larger dataset consisting of 1484 prokaryotic genomes and using several ranking approaches...
August 3, 2016: Life
https://www.readbyqxmd.com/read/27490571/a-hypothesis-life-initiated-from-two-genes-as-deduced-from-the-rna-world-hypothesis-and-the-characteristics-of-life-like-systems
#19
Kunio Kawamura
RNA played a central role in the emergence of the first life-like system on primitive Earth since RNA molecules contain both genetic information and catalytic activity. However, there are several drawbacks regarding the RNA world hypothesis. Here, I briefly discuss the feasibility of the RNA world hypothesis to deduce the RNA functions that are essential for forming a life-like system. At the same time, I have conducted a conceptual analysis of the characteristics of biosystems as a useful approach to deduce a realistic life-like system in relation to the definition of life...
August 2, 2016: Life
https://www.readbyqxmd.com/read/27472365/dry-wet-cycling-and-the-thermodynamics-and-kinetics-of-prebiotic-polymer-synthesis
#20
David S Ross, David Deamer
The endoergic nature of protein and nucleic acid assembly in aqueous media presents two questions that are fundamental to the understanding of life's origins: (i) how did the polymers arise in an aqueous prebiotic world; and (ii) once formed in some manner, how were they sufficiently persistent to engage in further chemistry. We propose here a quantitative resolution of these issues that evolved from recent accounts in which RNA-like polymers were produced in evaporation/rehydration cycles. The equilibrium Nm + Nn ↔ Nm+n + H₂O is endoergic by about 3...
July 26, 2016: Life
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