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https://read.qxmd.com/read/30781413/making-molecules-with-clay-layered-double-hydroxides-pentopyranose-nucleic-acids-and-the-origin-of-life
#1
Harold S Bernhardt
A mixture of sugar diphosphates is produced in reactions between small aldehyde phosphates catalysed by layered double hydroxide (LDH) clays under plausibly prebiotic conditions. A subset of these, pentose diphosphates, constitute the backbone subunits of nucleic acids capable of base pairing, which is not the case for the other products of these LDH-catalysed reactions. Not only that, but to date no other polymer found capable of base pairing-and therefore information transfer-has a backbone for which its monomer subunits have a plausible prebiotic synthesis, including the ribose-5-phosphate backbone subunit of RNA...
February 15, 2019: Life
https://read.qxmd.com/read/30744207/single-frame-multiple-frame-and-framing-motifs-in-genes
#2
Christian J Michel
We study the distribution of new classes of motifs in genes, a research field that has not been investigated to date. A single-frame motif SF has no trinucleotide in reading frame (frame 0) that occurs in a shifted frame (frame 1 or 2), e.g., the dicodon AAACAA is SF as the trinucleotides AAA and CAA do not occur in a shifted frame. A motif which is not single-frame SF is multiple-frame MF. Several classes of MF motifs are defined and analysed. The distributions of single-frame SF motifs (associated with an unambiguous trinucleotide decoding in the two 5'⁻3' and 3'⁻5' directions) and 5' unambiguous motifs 5'U (associated with an unambiguous trinucleotide decoding in the 5'⁻3' direction only) are analysed without and with constraints...
February 10, 2019: Life
https://read.qxmd.com/read/30717360/low-digit-and-high-digit-polymers-in-the-origin-of-life
#3
Peter Strazewski
Extant life uses two kinds of linear biopolymers that mutually control their own production, as well as the cellular metabolism and the production and homeostatic maintenance of other biopolymers. Nucleic acids are linear polymers composed of a relatively low structural variety of monomeric residues, and thus a low diversity per accessed volume. Proteins are more compact linear polymers that dispose of a huge compositional diversity even at the monomeric level, and thus bear a much higher catalytic potential...
February 2, 2019: Life
https://read.qxmd.com/read/30717250/microfluidic-reactors-for-carbon-fixation-under-ambient-pressure-alkaline-hydrothermal-vent-conditions
#4
Victor Sojo, Aya Ohno, Shawn E McGlynn, Yoichi M A Yamada, Ryuhei Nakamura
The alkaline-hydrothermal-vent theory for the origin of life predicts the spontaneous reduction of CO₂, dissolved in acidic ocean waters, with H₂ from the alkaline vent effluent. This reaction would be catalyzed by Fe(Ni)S clusters precipitated at the interface, which effectively separate the two fluids into an electrochemical cell. Using microfluidic reactors, we set out to test this concept. We produced thin, long Fe(Ni)S precipitates of less than 10 µm thickness. Mixing simplified analogs of the acidic-ocean and alkaline-vent fluids, we then tested for the reduction of CO₂...
February 1, 2019: Life
https://read.qxmd.com/read/30696090/synthetic-mutualism-and-the-intervention-dilemma
#5
REVIEW
Jai A Denton, Chaitanya S Gokhale
Ecosystems are complex networks of interacting individuals co-evolving with their environment. As such, changes to an interaction can influence the whole ecosystem. However, to predict the outcome of these changes, considerable understanding of processes driving the system is required. Synthetic biology provides powerful tools to aid this understanding, but these developments also allow us to change specific interactions. Of particular interest is the ecological importance of mutualism, a subset of cooperative interactions...
January 28, 2019: Life
https://read.qxmd.com/read/30691149/dynamical-task-switching-in-cellular-computers
#6
Angel Goñi-Moreno, Fernando de la Cruz, Alfonso Rodríguez-Patón, Martyn Amos
We present a scheme for implementing a version of task switching in engineered bacteria, based on the manipulation of plasmid copy numbers. Our method allows for the embedding of multiple computations in a cellular population, whilst minimising resource usage inefficiency. We describe the results of computational simulations of our model, and discuss the potential for future work in this area.
January 26, 2019: Life
https://read.qxmd.com/read/30691012/heterocyst-thylakoid-bioenergetics
#7
REVIEW
Ann Magnuson
Heterocysts are specialized cells that differentiate in the filaments of heterocystous cyanobacteria. Their role is to maintain a microoxic environment for the nitrogenase enzyme during diazotrophic growth. The lack of photosynthetic water oxidation in the heterocyst puts special constraints on the energetics for nitrogen fixation, and the electron transport pathways of heterocyst thylakoids are slightly different from those in vegetative cells. During recent years, there has been a growing interest in utilizing heterocysts as cell factories for the production of fuels and other chemical commodities...
January 25, 2019: Life
https://read.qxmd.com/read/30682803/origin-of-life-s-building-blocks-in-carbon-and-nitrogen-rich-surface-hydrothermal-vents
#8
Paul B Rimmer, Oliver Shorttle
There are two dominant and contrasting classes of origin of life scenarios: those predicting that life emerged in submarine hydrothermal systems, where chemical disequilibrium can provide an energy source for nascent life; and those predicting that life emerged within subaerial environments, where UV catalysis of reactions may occur to form the building blocks of life. Here, we describe a prebiotically plausible environment that draws on the strengths of both scenarios: surface hydrothermal vents. We show how key feedstock molecules for prebiotic chemistry can be produced in abundance in shallow and surficial hydrothermal systems...
January 24, 2019: Life
https://read.qxmd.com/read/30678368/the-beginning-of-systems-chemistry
#9
REVIEW
Peter Strazewski
Systems Chemistry has its roots in the research on the autocatalytic self-replication of biological macromolecules, first of all of synthetic deoxyribonucleic acids. A personal tour through the early works of the founder of Systems Chemistry, and of his first followers, recalls what's most important in this new era of chemistry: the growth and evolution of compartmented macromolecular populations, when provided with "food" and "fuel" and disposed of "waste".
January 24, 2019: Life
https://read.qxmd.com/read/30658501/role-of-mineral-surfaces-in-prebiotic-chemical-evolution-in-silico-quantum-mechanical-studies
#10
REVIEW
Albert Rimola, Mariona Sodupe, Piero Ugliengo
There is a consensus that the interaction of organic molecules with the surfaces of naturally-occurring minerals might have played a crucial role in chemical evolution and complexification in a prebiotic era. The hurdle of an overly diluted primordial soup occurring in the free ocean may have been overcome by the adsorption and concentration of relevant molecules on the surface of abundant minerals at the sea shore. Specific organic⁻mineral interactions could, at the same time, organize adsorbed molecules in well-defined orientations and activate them toward chemical reactions, bringing to an increase in chemical complexity...
January 17, 2019: Life
https://read.qxmd.com/read/30650642/thermodynamics-of-duplication-thresholds-in-synthetic-protocell-systems
#11
Bernat Corominas-Murtra
Understanding the thermodynamics of the duplication process is a fundamental step towards a comprehensive physical theory of biological systems. However, the immense complexity of real cells obscures the fundamental tensions between energy gradients and entropic contributions that underlie duplication. The study of synthetic, feasible systems reproducing part of the key ingredients of living entities but overcoming major sources of biological complexity is of great relevance to deepen the comprehension of the fundamental thermodynamic processes underlying life and its prevalence...
January 15, 2019: Life
https://read.qxmd.com/read/30634485/unevolved-de-novo-proteins-have-innate-tendencies-to-bind-transition-metals
#12
Michael S Wang, Kenric J Hoegler, Michael H Hecht
Life as we know it would not exist without the ability of protein sequences to bind metal ions. Transition metals, in particular, play essential roles in a wide range of structural and catalytic functions. The ubiquitous occurrence of metalloproteins in all organisms leads one to ask whether metal binding is an evolved trait that occurred only rarely in ancestral sequences, or alternatively, whether it is an innate property of amino acid sequences, occurring frequently in unevolved sequence space. To address this question, we studied 52 proteins from a combinatorial library of novel sequences designed to fold into 4-helix bundles...
January 9, 2019: Life
https://read.qxmd.com/read/30621107/real-world-synthetic-biology-is-it-founded-on-an-engineering-approach-and-should-it-be
#13
Jamie A Davies
Authors often assert that a key feature of 21st-century synthetic biology is its use of an 'engineering approach'; design using predictive models, modular architecture, construction using well-characterized standard parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey of synthetic biology projects that have reached, or are near to, commercial application outside laboratories shows that they showed very few of these attributes...
January 7, 2019: Life
https://read.qxmd.com/read/30621097/the-hidden-charm-of-life
#14
Manuel Porcar
Synthetic biology is an engineering view on biotechnology, which has revolutionized genetic engineering. The field has seen a constant development of metaphors that tend to highlight the similarities of cells with machines. I argue here that living organisms, particularly bacterial cells, are not machine-like, engineerable entities, but, instead, factory-like complex systems shaped by evolution. A change of the comparative paradigm in synthetic biology from machines to factories, from hardware to software, and from informatics to economy is discussed...
January 7, 2019: Life
https://read.qxmd.com/read/30609847/metatranscriptomic-analysis-of-the-bacterial-symbiont-dactylopiibacterium-carminicum-from-the-carmine-cochineal-dactylopius-coccus-hemiptera-coccoidea-dactylopiidae
#15
Rafael Bustamante-Brito, Arturo Vera-Ponce de León, Mónica Rosenblueth, Julio César Martínez-Romero, Esperanza Martínez-Romero
The scale insect Dactylopius coccus produces high amounts of carminic acid, which has historically been used as a pigment by pre-Hispanic American cultures. Nowadays carmine is found in food, cosmetics, and textiles. Metagenomic approaches revealed that Dactylopius spp. cochineals contain two Wolbachia strains, a betaproteobacterium named Candidatus Dactylopiibacterium carminicum and Spiroplasma , in addition to different fungi. We describe here a transcriptomic analysis indicating that Dactylopiibacterium is metabolically active inside the insect host, and estimate that there are over twice as many Dactylopiibacterium cells in the hemolymph than in the gut, with even fewer in the ovary...
January 3, 2019: Life
https://read.qxmd.com/read/30587790/is-research-on-synthetic-cells-moving-to-the-next-level
#16
Pasquale Stano
"Synthetic cells" research focuses on the construction of cell-like models by using solute-filled artificial microcompartments with a biomimetic structure. In recent years this bottom-up synthetic biology area has considerably progressed, and the field is currently experiencing a rapid expansion. Here we summarize some technical and theoretical aspects of synthetic cells based on gene expression and other enzymatic reactions inside liposomes, and comment on the most recent trends. Such a tour will be an occasion for asking whether times are ripe for a sort of qualitative jump toward novel SC prototypes: is research on "synthetic cells" moving to a next level?...
December 26, 2018: Life
https://read.qxmd.com/read/30583535/genomic-signals-of-adaptation-towards-mutualism-and-sociality-in-two-ambrosia-beetle-complexes
#17
Jazmín Blaz, Josué Barrera-Redondo, Mirna Vázquez-Rosas-Landa, Anahí Canedo-Téxon, Eneas Aguirre von Wobeser, Daniel Carrillo, Richard Stouthamer, Akif Eskalen, Emanuel Villafán, Alexandro Alonso-Sánchez, Araceli Lamelas, Luis Arturo Ibarra-Juarez, Claudia Anahí Pérez-Torres, Enrique Ibarra-Laclette
Mutualistic symbiosis and eusociality have developed through gradual evolutionary processes at different times in specific lineages. Like some species of termites and ants, ambrosia beetles have independently evolved a mutualistic nutritional symbiosis with fungi, which has been associated with the evolution of complex social behaviors in some members of this group. We sequenced the transcriptomes of two ambrosia complexes ( Euwallacea sp. near fornicatus ⁻ Fusarium euwallaceae and Xyleborus glabratus⁻Raffaelea lauricola ) to find evolutionary signatures associated with mutualism and behavior evolution...
December 22, 2018: Life
https://read.qxmd.com/read/30577420/cyanobacterial-septal-junctions-properties-and-regulation
#18
REVIEW
Enrique Flores, Mercedes Nieves-Morión, Conrad W Mullineaux
Heterocyst-forming cyanobacteria are multicellular organisms that grow as chains of cells (filaments or trichomes) in which the cells exchange regulators and nutrients. In this article, we review the morphological, physiological and genetic data that have led to our current understanding of intercellular communication in these organisms. Intercellular molecular exchange appears to take place by simple diffusion through proteinaceous structures, known as septal junctions, which connect the adjacent cells in the filament and traverse the septal peptidoglycan through perforations known as nanopores...
December 20, 2018: Life
https://read.qxmd.com/read/30562935/the-paleomineralogy-of-the-hadean-eon-revisited
#19
REVIEW
Shaunna M Morrison, Simone E Runyon, Robert M Hazen
A preliminary list of plausible near-surface minerals present during Earth's Hadean Eon (>4.0 Ga) should be expanded to include: (1) phases that might have formed by precipitation of organic crystals prior to the rise of predation by cellular life; (2) minerals associated with large bolide impacts, especially through the generation of hydrothermal systems in circumferential fracture zones; and (3) local formation of minerals with relatively oxidized transition metals through abiological redox processes, such as photo-oxidation...
December 17, 2018: Life
https://read.qxmd.com/read/30551580/impact-of-rearing-conditions-on-the-ambrosia-beetle-s-microbiome
#20
Luis Arturo Ibarra-Juarez, Damaris Desgarennes, Mirna Vázquez-Rosas-Landa, Emanuel Villafan, Alexandro Alonso-Sánchez, Ofelia Ferrera-Rodríguez, Andrés Moya, Daniel Carrillo, Luisa Cruz, Gloria Carrión, Abel López-Buenfil, Clemente García-Avila, Enrique Ibarra-Laclette, Araceli Lamelas
Ambrosia beetles, along with termites and leafcutter ants, are the only fungus-farming lineages within the tree of life. Bacteria harbored by ambrosia beetles may play an essential role in the nutritional symbiotic interactions with their associated fungi; however, little is known about the impact of rearing conditions on the microbiota of ambrosia beetles. We have used culture-independent methods to explore the effect of rearing conditions on the microbiome associated with Xyleborus affinis , Xyleborus bispinatus , and Xyleborus volvulus , evaluating different media in laboratory-controlled conditions and comparing wild and laboratory conditions...
December 13, 2018: Life
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