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https://www.readbyqxmd.com/read/30423937/noise%C3%A2-seeded-developmental-pattern-formation-in-filamentous-cyanobacteria
#1
REVIEW
Rinat Arbel-Goren, Francesca Di Patti, Duccio Fanelli, Joel Stavans
Under nitrogen-poor conditions, multicellular cyanobacteria such as Anabaena sp. PCC 7120 undergo a process of differentiation, forming nearly regular, developmental patterns of individual nitrogen-fixing cells, called heterocysts, interspersed between intervals of vegetative cells that carry out photosynthesis. Developmental pattern formation is mediated by morphogen species that can act as activators and inhibitors, some of which can diffuse along filaments. We survey the limitations of the classical, deterministic Turing mechanism that has been often invoked to explain pattern formation in these systems, and then, focusing on a simpler system governed by birth-death processes, we illustrate pedagogically a recently proposed paradigm that provides a much more robust description of pattern formation: stochastic Turing patterns...
November 9, 2018: Life
https://www.readbyqxmd.com/read/30404133/exploring-the-emergence-of-rna-nucleosides-and-nucleotides-on-the-early-earth
#2
REVIEW
Annabelle Biscans
Understanding how life began is one of the most fascinating problems to solve. By approaching this enigma from a chemistry perspective, the goal is to define what series of chemical reactions could lead to the synthesis of nucleotides, amino acids, lipids, and other cellular components from simple feedstocks under prebiotically plausible conditions. It is well established that evolution of life involved RNA which plays central roles in both inheritance and catalysis. In this review, we present historically important and recently published articles aimed at understanding the emergence of RNA nucleosides and nucleotides on the early Earth...
November 6, 2018: Life
https://www.readbyqxmd.com/read/30400661/catalytic-protective-properties-of-martian-minerals-and-implications-for-possible-origin-of-life-on-mars
#3
REVIEW
Teresa Fornaro, Andrew Steele, John Robert Brucato
Minerals might have played critical roles for the origin and evolution of possible life forms on Mars. The study of the interactions between the "building blocks of life" and minerals relevant to Mars mineralogy under conditions mimicking the harsh Martian environment may provide key insight into possible prebiotic processes. Therefore, this contribution aims at reviewing the most important investigations carried out so far about the catalytic/protective properties of Martian minerals toward molecular biosignatures under Martian-like conditions...
November 5, 2018: Life
https://www.readbyqxmd.com/read/30400350/exposed-areas-above-sea-level-on-earth-3-5-gyr-ago-implications-for-prebiotic-and-primitive-biotic-chemistry
#4
Jeffrey L Bada, Jun Korenaga
How life began on Earth is still largely shrouded in mystery. One of the central ideas for various origins of life scenarios is Darwin's "warm little pond". In these small bodies of water, simple prebiotic compounds such as amino acids, nucleobases, and so on, were produced from reagents such as hydrogen cyanide and aldehydes/ketones. These simple prebiotic compounds underwent further reactions, producing more complex molecules. The process of chemical evolution would have produced increasingly complex molecules, eventually yielding a molecule with the properties of information storage and replication prone to random mutations, the hallmark of both the origin of life and evolution...
November 4, 2018: Life
https://www.readbyqxmd.com/read/30400226/g-protein-coupled-receptor-protein-synthesis-on-a-lipid-bilayer-using-a-reconstituted-cell-free-protein-synthesis-system
#5
Belay Gessesse, Takashi Nagaike, Koji Nagata, Yoshihiro Shimizu, Takuya Ueda
Membrane proteins are important drug targets which play a pivotal role in various cellular activities. However, unlike cytosolic proteins, most of them are difficult-to-express proteins. In this study, to synthesize and produce sufficient quantities of membrane proteins for functional and structural analysis, we used a bottom-up approach in a reconstituted cell-free synthesis system, the PURE system, supplemented with artificial lipid mimetics or micelles. Membrane proteins were synthesized by the cell-free system and integrated into lipid bilayers co-translationally...
November 2, 2018: Life
https://www.readbyqxmd.com/read/30384503/toward-experimental-evolution-with-giant-vesicles
#6
REVIEW
Hironori Sugiyama, Taro Toyota
Experimental evolution in chemical models of cells could reveal the fundamental mechanisms of cells today. Various chemical cell models, water-in-oil emulsions, oil-on-water droplets, and vesicles have been constructed in order to conduct research on experimental evolution. In this review, firstly, recent studies with these candidate models are introduced and discussed with regards to the two hierarchical directions of experimental evolution (chemical evolution and evolution of a molecular self-assembly). Secondly, we suggest giant vesicles (GVs), which have diameters larger than 1 µm, as promising chemical cell models for studying experimental evolution...
October 31, 2018: Life
https://www.readbyqxmd.com/read/30373240/the-distinctive-regulation-of-cyanobacterial-glutamine-synthetase
#7
REVIEW
Paul Bolay, M Isabel Muro-Pastor, Francisco J Florencio, Stephan Klähn
Glutamine synthetase (GS) features prominently in bacterial nitrogen assimilation as it catalyzes the entry of bioavailable nitrogen in form of ammonium into cellular metabolism. The classic example, the comprehensively characterized GS of enterobacteria, is subject to exquisite regulation at multiple levels, among them gene expression regulation to control GS abundance, as well as feedback inhibition and covalent modifications to control enzyme activity. Intriguingly, the GS of the ecologically important clade of cyanobacteria features fundamentally different regulatory systems to those of most prokaryotes...
October 27, 2018: Life
https://www.readbyqxmd.com/read/30373229/biosensors-based-in-vivo-quantification-of-2-oxoglutarate-in-cyanobacteria-and-proteobacteria
#8
Hai-Lin Chen, Amel Latifi, Cheng-Cai Zhang, Christophe Sébastien Bernard
2-oxoglutarate (α-ketoglutarate; 2-OG) is an intermediate of the Krebs cycle, and constitutes the carbon skeleton for nitrogen assimilation and the synthesis of a variety of compounds. In addition to being an important metabolite, 2-OG is a signaling molecule with a broad regulatory repertoire in a variety of organisms, including plants, animals, and bacteria. Although challenging, measuring the levels and variations of metabolic signals in vivo is critical to better understand how cells control specific processes...
October 27, 2018: Life
https://www.readbyqxmd.com/read/30366364/ultraviolet-irradiation-on-a-pyrite-surface-improves-triglycine-adsorption
#9
Santos Galvez-Martinez, Eva Mateo-Marti
We characterized the adsorption of triglycine molecules on a pyrite surface under several simulated environmental conditions by X-ray photoemission spectroscopy. The triglycine molecular adsorption on a pyrite surface under vacuum conditions (absence of oxygen) shows the presence of two different states for the amine functional group (NH₂ and NH₃⁺), therefore two chemical species (anionic and zwitterionic). On the other hand, molecular adsorption from a solution discriminates the NH₂ as a unique molecular adsorption form, however, the amount adsorbed in this case is higher than under vacuum conditions...
October 25, 2018: Life
https://www.readbyqxmd.com/read/30360410/appropriate-assignment-of-fossil-calibration-information-minimizes-the-difference-between-phylogenetic-and-pedigree-mutation-rates-in-humans
#10
Renata T Capellão, Elisa M Costa-Paiva, Carlos G Schrago
Studies that measured mutation rates in human populations using pedigrees have reported values that differ significantly from rates estimated from the phylogenetic comparison of humans and chimpanzees. Consequently, exchanges between mutation rate values across different timescales lead to conflicting divergence time estimates. It has been argued that this variation of mutation rate estimates across hominoid evolution is in part caused by incorrect assignment of calibration information to the mean coalescent time among loci, instead of the true genetic isolation (speciation) time between humans and chimpanzees...
October 22, 2018: Life
https://www.readbyqxmd.com/read/30347777/correction-sakurai-h-et-al-how-close-we-are-to-achieving-commercially-viable-large-scale-photobiological-hydrogen-production-by-cyanobacteria-a-review-of-the-biological-aspects-life-2015-5-997%C3%A2-1018
#11
Hidehiro Sakurai, Hajime Masukawa, Masaharu Kitashima, Kazuhito Inoue
In the published article "How close we are to achieving commercially viable large-scale photobiological hydrogen production by cyanobacteria:[...].
October 19, 2018: Life
https://www.readbyqxmd.com/read/30347745/the-reaction-of-aminonitriles-with-aminothiols-a-way-to-thiol-containing-peptides-and-nitrogen-heterocycles-in-the-primitive-earth-ocean
#12
Ibrahim Shalayel, Seydou Coulibaly, Kieu Dung Ly, Anne Milet, Yannick Vallée
The Strecker reaction of aldehydes with ammonia and hydrogen cyanide first leads to α-aminonitriles, which are then hydrolyzed to α-amino acids. However, before reacting with water, these aminonitriles can be trapped by aminothiols, such as cysteine or homocysteine, to give 5- or 6-membered ring heterocycles, which in turn are hydrolyzed to dipeptides. We propose that this two-step process enabled the formation of thiol-containing dipeptides in the primitive ocean. These small peptides are able to promote the formation of other peptide bonds and of heterocyclic molecules...
October 19, 2018: Life
https://www.readbyqxmd.com/read/30308967/chemical-diversity-of-metal-sulfide-minerals-and-its-implications-for-the-origin-of-life
#13
REVIEW
Yamei Li, Norio Kitadai, Ryuhei Nakamura
Prebiotic organic synthesis catalyzed by Earth-abundant metal sulfides is a key process for understanding the evolution of biochemistry from inorganic molecules, yet the catalytic functions of sulfides have remained poorly explored in the context of the origin of life. Past studies on prebiotic chemistry have mostly focused on a few types of metal sulfide catalysts, such as FeS or NiS, which form limited types of products with inferior activity and selectivity. To explore the potential of metal sulfides on catalyzing prebiotic chemical reactions, here, the chemical diversity (variations in chemical composition and phase structure) of 304 natural metal sulfide minerals in a mineralogy database was surveyed...
October 10, 2018: Life
https://www.readbyqxmd.com/read/30301223/testing-new-concepts-for-crop-cultivation-in-space-effects-of-rooting-volume-and-nitrogen-availability
#14
Silje A Wolff, Carolina F Palma, Leo Marcelis, Ann-Iren Kittang Jost, Sander H van Delden
Long term human missions to the Moon and Mars, rely on life support systems for food production and regeneration of resources. In the EU H2020 TIME SCALE-project, an advanced life support system concept was developed to facilitate plant research and technology demonstration under different gravity conditions. Ground experiments assessed irrigation systems and effects of rooting- and nutrient solution volume. The maximal allowed volume for existing International Space Station research facilities (3.4 L) was able to support cultivation of two lettuce heads for at least 24 days...
October 6, 2018: Life
https://www.readbyqxmd.com/read/30279401/possible-emergence-of-sequence-specific-rna-aminoacylation-via-peptide-intermediary-to-initiate-darwinian-evolution-and-code-through-origin-of-life
#15
Dimiter Kunnev, Anastas Gospodinov
One of the most intriguing questions in biological science is how life originated on Earth. A large number of hypotheses have been proposed to explain it, each putting an emphasis on different events leading to functional translation and self-sustained system. Here, we propose a set of interactions that could have taken place in the prebiotic environment. According to our hypothesis, hybridization-induced proximity of short aminoacylated RNAs led to the synthesis of peptides of random sequence. We postulate that among these emerged a type of peptide(s) capable of stimulating the interaction between specific RNAs and specific amino acids, which we call "bridge peptide" (BP)...
October 2, 2018: Life
https://www.readbyqxmd.com/read/30257439/efficient-arrangement-of-the-replication-fork-trap-for-in-vitro-propagation-of-monomeric-circular-dna-in-the-chromosome-replication-cycle-reaction
#16
Tomonori Hasebe, Kouhei Narita, Shiomi Hidaka, Masayuki Su'etsugu
Propagation of genetic information is a fundamental prerequisite for living cells. We recently developed the replication cycle reaction (RCR), an in vitro reaction for circular DNA propagation, by reconstitution of the replication cycle of the Escherichia coli chromosome. In RCR, two replication forks proceed bidirectionally from the replication origin, oriC , and meet at a region opposite oriC , yielding two copies of circular DNA. Although RCR essentially propagates supercoiled monomers, concatemer byproducts are also produced due to inefficient termination of the replication fork progression...
September 25, 2018: Life
https://www.readbyqxmd.com/read/30249032/formamide-adsorption-at-the-amorphous-silica-surface-a-combined-experimental-and-computational-approach
#17
Matteo Signorile, Clara Salvini, Lorenzo Zamirri, Francesca Bonino, Gianmario Martra, Mariona Sodupe, Piero Ugliengo
Mineral surfaces have been demonstrated to play a central role in prebiotic reactions, which are understood to be at the basis of the origin of life. Among the various molecules proposed as precursors for these reactions, one of the most interesting is formamide. Formamide has been shown to be a pluripotent molecule, generating a wide distribution of relevant prebiotic products. In particular, the outcomes of its reactivity are strongly related to the presence of mineral phases acting as catalysts toward specific reaction pathways...
September 23, 2018: Life
https://www.readbyqxmd.com/read/30249016/serpentinization-connecting-geochemistry-ancient-metabolism-and-industrial-hydrogenation
#18
REVIEW
Martina Preiner, Joana C Xavier, Filipa L Sousa, Verena Zimorski, Anna Neubeck, Susan Q Lang, H Chris Greenwell, Karl Kleinermanns, Harun Tüysüz, Tom M McCollom, Nils G Holm, William F Martin
Rock⁻water⁻carbon interactions germane to serpentinization in hydrothermal vents have occurred for over 4 billion years, ever since there was liquid water on Earth. Serpentinization converts iron(II) containing minerals and water to magnetite (Fe₃O₄) plus H₂. The hydrogen can generate native metals such as awaruite (Ni₃Fe), a common serpentinization product. Awaruite catalyzes the synthesis of methane from H₂ and CO₂ under hydrothermal conditions. Native iron and nickel catalyze the synthesis of formate, methanol, acetate, and pyruvate-intermediates of the acetyl-CoA pathway, the most ancient pathway of CO₂ fixation...
September 22, 2018: Life
https://www.readbyqxmd.com/read/30248960/dissecting-the-repertoire-of-dna-binding-transcription-factors-of-the-archaeon-pyrococcus-furiosus-dsm-3638
#19
Antonia Denis, Mario Alberto Martínez-Núñez, Silvia Tenorio-Salgado, Ernesto Perez-Rueda
In recent years, there has been a large increase in the amount of experimental evidence for diverse archaeal organisms, and these findings allow for a comprehensive analysis of archaeal genetic organization. However, studies about regulatory mechanisms in this cellular domain are still limited. In this context, we identified a repertoire of 86 DNA-binding transcription factors (TFs) in the archaeon Pyrococcus furiosus DSM 3638, that are clustered into 32 evolutionary families. In structural terms, 45% of these proteins are composed of one structural domain, 41% have two domains, and 14% have three structural domains...
September 21, 2018: Life
https://www.readbyqxmd.com/read/30241342/geochemistry-and-the-origin-of-life-from-extraterrestrial-processes-chemical-evolution-on-earth-fossilized-life-s-records-to-natures-of-the-extant-life
#20
REVIEW
Satoru Nakashima, Yoko Kebukawa, Norio Kitadai, Motoko Igisu, Natsuki Matsuoka
In 2001, the first author (S.N.) led the publication of a book entitled "Geochemistry and the origin of life" in collaboration with Dr. Andre Brack aiming to figure out geo- and astro-chemical processes essential for the emergence of life. Since then, a great number of research progress has been achieved in the relevant topics from our group and others, ranging from the extraterrestrial inputs of life's building blocks, the chemical evolution on Earth with the aid of mineral catalysts, to the fossilized records of ancient microorganisms...
September 20, 2018: Life
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