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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
#1
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
https://www.readbyqxmd.com/read/30241312/controlled-construction-of-stable-network-structure-composed-of-honeycomb-shaped-microhydrogels
#2
Masayuki Hayakawa, Satoshi Umeyama, Ken H Nagai, Hiroaki Onoe, Masahiro Takinoue
Recently, the construction of models for multicellular systems such as tissues has been attracting great interest. These model systems are expected to reproduce a cell communication network and provide insight into complicated functions in living systems./Such network structures have mainly been modelled using a droplet and a vesicle. However, in the droplet and vesicle network, there are difficulties attributed to structural instabilities due to external stimuli and perturbations. Thus, the fabrication of a network composed of a stable component such as hydrogel is desired...
September 20, 2018: Life
https://www.readbyqxmd.com/read/30200614/biodiversity-and-abundance-of-cultured-microfungi-from-the-permanently-ice-covered-lake-fryxell-antarctica
#3
Laurie Connell, Benjamin Segee, Regina Redman, Russell J Rodriguez, Hubert Staudigel
In this work, we explore the biodiversity of culturable microfungi from the water column of a permanently ice-covered lake in Taylor Valley, Antarctica from austral field seasons in 2003, 2008 and 2010, as well as from glacial stream input (2010). The results revealed that there was a sharp decline in total culturable fungal abundance between 9 and 11 m lake depth with a concurrent shift in diversity. A total of 29 species were identified from all three water sources with near even distribution between Ascomycota and Basidomycota (15 and 14 respectively)...
September 6, 2018: Life
https://www.readbyqxmd.com/read/30150578/monosaccharides-and-their-derivatives-in-carbonaceous-meteorites-a-scenario-for-their-synthesis-and-onset-of-enantiomeric-excesses
#4
REVIEW
George Cooper, Andro C Rios, Michel Nuevo
Carbonaceous meteorites provide the best glimpse into the solar system's earliest physical and chemical processes. These ancient objects, ~4.56 billion years old, contain evidence of phenomena ranging from solar system formation to the synthesis of organic compounds by aqueous and (likely) low-temperature photolytic reactions. Collectively, chemical reactions resulted in an insoluble kerogen-like carbon phase and a complex mixture of discrete soluble compounds including amino acids, nucleobases, and monosaccharide (or "sugar") derivatives...
August 27, 2018: Life
https://www.readbyqxmd.com/read/30150570/green-rust-the-simple-organizing-seed-of-all-life
#5
REVIEW
Michael J Russell
Korenaga and coworkers presented evidence to suggest that the Earth's mantle was dry and water filled the ocean to twice its present volume 4.3 billion years ago. Carbon dioxide was constantly exhaled during the mafic to ultramafic volcanic activity associated with magmatic plumes that produced the thick, dense, and relatively stable oceanic crust. In that setting, two distinct and major types of sub-marine hydrothermal vents were active: ~400 °C acidic springs, whose effluents bore vast quantities of iron into the ocean, and ~120 °C, highly alkaline, and reduced vents exhaling from the cooler, serpentinizing crust some distance from the heads of the plumes...
August 27, 2018: Life
https://www.readbyqxmd.com/read/30149508/the-ser-thr-kinase-pknh-is-essential-for-maintaining-heterocyst-pattern-in-the-cyanobacterium-anabaena-sp-strain-pcc-7120
#6
Shun-Ichi Fukushima, Shigeki Ehira
In the filamentous cyanobacterium Anabaena sp. strain, PCC 7120, heterocysts (which are nitrogen-fixing cells) are formed in the absence of combined nitrogen in the medium. Heterocysts are separated from one another by 10 to 15 vegetative cells along the filaments, which consist of a few hundred of cells. hetR is necessary for heterocyst differentiation; and patS and hetN , expressed in heterocysts, play important roles in heterocyst pattern formation by laterally inhibiting the expression of hetR in adjacent cells...
August 24, 2018: Life
https://www.readbyqxmd.com/read/30126201/population-dynamics-of-autocatalytic-sets-in-a-compartmentalized-spatial-world
#7
Wim Hordijk, Jonathan Naylor, Natalio Krasnogor, Harold Fellermann
Autocatalytic sets are self-sustaining and collectively catalytic chemical reaction networks which are believed to have played an important role in the origin of life. Simulation studies have shown that autocatalytic sets are, in principle, evolvable if multiple autocatalytic subsets can exist in different combinations within compartments, i.e., so-called protocells . However, these previous studies have so far not explicitly modeled the emergence and dynamics of autocatalytic sets in populations of compartments in a spatial environment...
August 18, 2018: Life
https://www.readbyqxmd.com/read/30081459/jarosite-and-alunite-in-ancient-terrestrial-sedimentary-rocks-reinterpreting-martian-depositional-and-diagenetic-environmental-conditions
#8
Sally L Potter-McIntyre, Thomas M McCollom
Members of the alunite group are precipitated at low pH (<1 to ~4) in oxidizing environments, are unstable in circumneutral conditions, and are widespread on Mars. At Mollies Nipple in Kane County, Utah, USA, jarosite and alunite are abundant as diagenetic cements in Jurassic sandstones. This research characterizes the jarosite and alunite cements with the goal of determining their origin, and tests the hypothesis that jarosite and alunite may be more stable than the current understanding indicates is possible...
August 3, 2018: Life
https://www.readbyqxmd.com/read/30041476/global-molecular-diversity-of-the-halotolerant-fungus-hortaea-werneckii
#9
Alessia Marchetta, Bert Gerrits van den Ende, Abdullah M S Al-Hatmi, Ferry Hagen, Polona Zalar, Montarop Sudhadham, Nina Gunde-Cimerman, Clara Urzì, Sybren de Hoog, Filomena De Leo
A global set of clinical and environmental strains of the halotolerant black yeast-like fungus Hortaea werneckii are analyzed by multilocus sequencing and AFLP, and physiological parameters are determined. Partial translation elongation factor 1-α proves to be suitable for typing because of the presence/absence of introns and also the presence of several SNPs. Local clonal expansion could be established by a combination of molecular methods, while the population from the Mediterranean Sea water also responds differently to combined temperature and salt stress...
July 23, 2018: Life
https://www.readbyqxmd.com/read/30011950/roof-inhabiting-cousins-of-rock-inhabiting-fungi-novel-melanized-microcolonial-fungal-species-from-photocatalytically-reactive-subaerial-surfaces
#10
Constantino Ruibal, Laura Selbmann, Serap Avci, Pedro M Martin-Sanchez, Anna A Gorbushina
Subaerial biofilms (SAB) are an important factor in weathering, biofouling, and biodeterioration of bare rocks, building materials, and solar panel surfaces. The realm of SAB is continually widened by modern materials, and the settlers on these exposed solid surfaces always include melanized, stress-tolerant microcolonial ascomycetes. After their first discovery on desert rock surfaces, these melanized chaetothyrialean and dothidealean ascomycetes have been found on Mediterranean monuments after biocidal treatments, Antarctic rocks and solar panels...
July 15, 2018: Life
https://www.readbyqxmd.com/read/29997353/metagenomic-analysis-of-microbial-community-compositions-and-cold-responsive-stress-genes-in-selected-antarctic-lacustrine-and-soil-ecosystems
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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&mdash;and also new built&mdash;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
#19
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
#20
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
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