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Evolution analysis

Jing Jin, Megan K Moore, William K Wilson, Seiichi P T Matsuda
The Brassica rapa oxidosqualene cyclase Bra032185 makes 60% astertarone A (1) and 20 minor triterpenes (0.1-11%). Mechanistic analysis indicates the absence of an enol intermediate to generate the 4 S epimer of 1, unless workup involves saponification. Bra032185 and its closest Arabidopsis thaliana homologue diverged markedly in product profiles over a short evolutionary distance, while developing opposite C18 configurations. Active-site residue comparison of Bra032185 with friedelin and shionone synthases suggests convergent evolution to 3-ketotriterpenes...
March 20, 2018: Organic Letters
Maziar Derakhshandeh, Brandy K Pilapil, Ben Workman, Milana Trifkovic, Steven L Bryant
Emulsions are widely used in industrial applications, including in food sciences, cosmetics, and enhanced oil recovery. For these industries, an in depth understanding of the stability and rheological properties of emulsions under both static and dynamic conditions is vital to their successful application. Presented here is a thorough assessment of a model nanoparticle (NP) stabilized dodecane-in-water emulsion as a route to improved understanding of the relationship between NP properties, microstructure and droplet-droplet interactions on the stability and rheological properties of emulsions...
March 20, 2018: Soft Matter
Alina Dima, Ciprian Jurcut, Anca Manolache, Daniel Vasile Balaban, Alina Popp, Mariana Jinga
BACKGROUND AND AIMS: Celiac disease (CD) presents with a wide spectrum of extra-digestive symptoms, including hemorrhagic manifestations. The aim of this review was to conduct an extensive analysis of the hemorrhagic events reported in adult CD patients. METHODS: Case report and review of the literature. Pubmed (MEDLINE) database search from January 1970 onwards was performed using the medical subject headings [MeSH] terms "celiac disease" AND "blood coagulation disorders", "hemorrhage", "hematoma", "hematuria", "hemoptysis", "epistaxis", "hemosiderosis"...
March 2018: Journal of Gastrointestinal and Liver Diseases: JGLD
Apuã C M Paquola, Huma Asif, Carlos Alberto de Bragança Pereira, Bruno César Feltes, Diego Bonatto, Wanessa Cristina Lima, Carlos Frederico Martins Menck
Horizontal gene transfer (HGT) has a major impact on the evolution of prokaryotic genomes, as it allows genes evolved in different contexts to be combined in a single genome, greatly enhancing the ways evolving organisms can explore the gene content space and adapt to the environment. A systematic analysis of HGT in a large number of genomes is of key importance in understanding the impact of HGT in the evolution of prokaryotes. We developed a method for the detection of genes that potentially originated by HGT based on the comparison of BLAST scores between homologous genes to 16S rRNA-based phylogenetic distances between the involved organisms...
March 19, 2018: Journal of Molecular Evolution
Hyun Jik Kim, Young Hun Seo, Sujin An, Ara Jo, Ick Chan Kwon, Sehoon Kim
Rationale: Hydrogen peroxide (H2 O2 ) provides an important mechanism for resisting infectious pathogens within the respiratory tract, and accordingly, the in situ analysis of H2 O2 generation in real time provides a valuable tool for assessing immune response. Methods: In this study, we applied a chemiluminescent nanoparticle-based real-time imaging approach to noninvasive evaluation of the Duox2-mediated H2 O2 generation after viral infection, and assessed its usefulness for analytical purposes in mouse nasal mucosa...
2018: Theranostics
Qi Wang, Qian Wang, Yan-Le Zhou, Shuang Shan, Huan-Huan Cui, Yong Xiao, Kun Dong, Adel Khashaveh, Liang Sun, Yong-Jun Zhang
The phytophagous mirid bugs of Apolygus lucorum, Lygus pratensis as well as three Adelphocoris spp., including Adelphocoris lineolatus, A. suturalis , and A. fasciaticollis are major pests of multiple agricultural crops in China, which have distinct geographical distribution and occurrence ranges. Like many insect species, these bugs heavily rely on olfactory cues to search preferred host plants, thereby investigation on functional co-evolution and divergence of olfactory genes seems to be necessary and is of great interest...
2018: Frontiers in Physiology
Rainer Kurmayer, Guntram Christiansen, Andreas Holzinger, Eugen Rott
In order to understand Chamaesiphon spp. evolution and ecological diversification, we investigated the phylogenetic differentiation of three morphospecies from field samples by means of single colony genetics. Individual colonies of three different morphospecies ( C. starmachii, C. polonicus, C. geitleri, ) were isolated from lotic gravel streams and their 16S rDNA nucleotide variability was analyzed. For a number of individual colonies, microscopical and ultrastructural analysis was also performed. A phylogenetic tree of all major lineages of the phylum of Cyanobacteria assigned all Chamaesiphon genotypes (1149-1176 bp) most closely with the family of Gomontiellaceae of the order Oscillatoriales...
April 2018: Hydrobiologia
Melanie Tramontano, Sergej Andrejev, Mihaela Pruteanu, Martina Klünemann, Michael Kuhn, Marco Galardini, Paula Jouhten, Aleksej Zelezniak, Georg Zeller, Peer Bork, Athanasios Typas, Kiran Raosaheb Patil
Bacterial metabolism plays a fundamental role in gut microbiota ecology and host-microbiome interactions. Yet the metabolic capabilities of most gut bacteria have remained unknown. Here we report growth characteristics of 96 phylogenetically diverse gut bacterial strains across 4 rich and 15 defined media. The vast majority of strains (76) grow in at least one defined medium, enabling accurate assessment of their biosynthetic capabilities. These do not necessarily match phylogenetic similarity, thus indicating a complex evolution of nutritional preferences...
March 19, 2018: Nature Microbiology
Achal Rastogi, Uma Maheswari, Richard G Dorrell, Fabio Rocha Jimenez Vieira, Florian Maumus, Adam Kustka, James McCarthy, Andy E Allen, Paul Kersey, Chris Bowler, Leila Tirichine
Diatoms are one of the most successful and ecologically important groups of eukaryotic phytoplankton in the modern ocean. Deciphering their genomes is a key step towards better understanding of their biological innovations, evolutionary origins, and ecological underpinnings. Here, we have used 90 RNA-Seq datasets from different growth conditions combined with published expressed sequence tags and protein sequences from multiple taxa to explore the genome of the model diatom Phaeodactylum tricornutum, and introduce 1,489 novel genes...
March 19, 2018: Scientific Reports
Caroline L Furness, Marcela B Mansur, Victoria J Weston, Luca Ermini, Frederik W van Delft, Sarah Jenkinson, Rosemary Gale, Christine J Harrison, Maria S Pombo-de-Oliveira, Marta Sanchez-Martin, Adolfo A Ferrando, Pamela Kearns, Ian Titley, Anthony M Ford, Nicola E Potter, Mel Greaves
Single-cell genetics were used to interrogate clonal complexity and the sequence of mutational events in STIL-TAL1+ T-ALL. Single-cell multicolour FISH was used to demonstrate that the earliest detectable leukaemia subclone contained the STIL-TAL1 fusion and copy number loss of 9p21.3 (CDKN2A/CDKN2B locus), with other copy number alterations including loss of PTEN occurring as secondary subclonal events. In three cases, multiplex qPCR and phylogenetic analysis were used to produce branching evolutionary trees recapitulating the snapshot history of T-ALL evolution in this leukaemia subtype, which confirmed that mutations in key T-ALL drivers, including NOTCH1 and PTEN, were subclonal and reiterative in distinct subclones...
March 20, 2018: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
Soham Sengupta, Rachel Nechushtai, Patricia A Jennings, Jose' N Onuchic, Pamela A Padilla, Rajeev K Azad, Ron Mittler
The iron-sulfur (2Fe-2S) binding motif CDGSH appears in many important plant and animal proteins that regulate iron and reactive oxygen metabolism. In human it is found in CISD1-3 proteins involved in diabetes, obesity, cancer, aging, cardiovascular disease and neurodegeneration. Despite the important biological role of the CDGSH domain, its origin, evolution and diversification, are largely unknown. Here, we report that: (1) the CDGSH domain appeared early in evolution, perhaps linked to the heavy use of iron-sulfur driven metabolism by early organisms; (2) a CISD3-like protein with two CDGSH domains on the same polypeptide appears to represent the ancient archetype of CDGSH proteins; (3) the origin of the human CISD3 protein is linked to the mitochondrial endosymbiotic event; (4) the CISD1/2 type proteins that contain only one CDGSH domain, but function as homodimers, originated after the divergence of bacteria and archaea/eukaryotes from their common ancestor; and (5) the human CISD1 and CISD2 proteins diverged about 650-720 million years ago, and CISD3 and CISD1/2 share their descent from an ancestral CISD about 1-1...
March 19, 2018: Scientific Reports
A Kwiatkowski da Silva, D Ponge, Z Peng, G Inden, Y Lu, A Breen, B Gault, D Raabe
Analysis and design of materials and fluids requires understanding of the fundamental relationships between structure, composition, and properties. Dislocations and grain boundaries influence microstructure evolution through the enhancement of diffusion and by facilitating heterogeneous nucleation, where atoms must overcome a potential barrier to enable the early stage of formation of a phase. Adsorption and spinodal decomposition are known precursor states to nucleation and phase transition; however, nucleation remains the less well-understood step in the complete thermodynamic sequence that shapes a microstructure...
March 19, 2018: Nature Communications
Tahmina Islam, Ajit Ghosh
Reactive carbonyl species, such as methylglyoxal and glyoxal are very toxic in nature and can inactivate various cellular macromolecules such as DNA, RNA, and protein by forming advanced glycation end products. Conventional glyoxalase pathway with two enzymes- glyoxalase I and glyoxalase II, detoxify MG into D-lactate with the help of reduced glutathione. However, DJ-1/PfpI domain(s) containing DJ-1/ Hsp31 proteins do the same in a single step, and thus termed as "glyoxalase III". A comprehensive genome-wide analysis of soybean identified eleven putative glyoxalase III proteins with DJ-1/PfpI domain encoded by seven genes...
March 19, 2018: Scientific Reports
Miguel Ángel Lozada Aguilar, Andrei Khrennikov, Klaudia Oleschko
As was recently shown by the authors, quantum probability theory can be used for the modelling of the process of decision-making (e.g. probabilistic risk analysis) for macroscopic geophysical structures such as hydrocarbon reservoirs. This approach can be considered as a geophysical realization of Hilbert's programme on axiomatization of statistical models in physics (the famous sixth Hilbert problem). In this conceptual paper , we continue development of this approach to decision-making under uncertainty which is generated by complexity, variability, heterogeneity, anisotropy, as well as the restrictions to accessibility of subsurface structures...
April 28, 2018: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
Arunkumar Krishnan, Lakshminarayan M Iyer, Stephen J Holland, Thomas Boehm, L Aravind
AID/APOBEC deaminases (AADs) convert cytidine to uridine in single-stranded nucleic acids. They are involved in numerous mutagenic processes, including those underpinning vertebrate innate and adaptive immunity. Using a multipronged sequence analysis strategy, we uncover several AADs across metazoa, dictyosteliida, and algae, including multiple previously unreported vertebrate clades, and versions from urochordates, nematodes, echinoderms, arthropods, lophotrochozoans, cnidarians, and porifera. Evolutionary analysis suggests a fundamental division of AADs early in metazoan evolution into secreted deaminases (SNADs) and classical AADs, followed by diversification into several clades driven by rapid-sequence evolution, gene loss, lineage-specific expansions, and lateral transfer to various algae...
March 19, 2018: Proceedings of the National Academy of Sciences of the United States of America
Ronald L Eisenberg, Long H Ngo, Benedikt H Heidinger, Alexander A Bankier
RATIONALE AND OBJECTIVES: To analyze the pattern and longitudinal evolution of honorary authorship in major radiology journals. MATERIALS AND METHODS: In this Institutional Review Board-approved study, an electronic survey was sent to first authors of original research articles published in the American Journal of Roentgenology, European Radiology, the Journal of Magnetic Resonance Imaging, and Radiology during 2 years (July 2014 through June 2016). Questions addressed the perception of honorary authorship and contributing factors, as well as demographic information...
March 16, 2018: Academic Radiology
Tridip Phukan, Amar Nath Rai, Mayashree B Syiem
With the intention of getting an insight into the differential effect of UV-C radiation on the N2 -fixing heterocystous cyanobacterium Nostoc muscorum Meg1, various aspects of carbon and nitrogen metabolism was evaluated in the organism. Exposure to different doses of UV-C (6, 12, 18 and 24 mJ/cm2 ) showed that among various photo-absorbing pigments, phycobiliproteins were most sensitive. Oxygen evolving complex (OEC) activity measured as net oxygen evolution rate decreased by 63% upon 24 mJ/cm2 exposure...
July 15, 2018: Ecotoxicology and Environmental Safety
Uzair Ansari, Ibrahim El-Battrawy, Christian Fastner, Michael Behnes, Katherine Sattler, Aydin Huseynov, Stefan Baumann, Erol Tülümen, Martin Borggrefe, Ibrahim Akin
BACKGROUND: Recent hypotheses have suggested the pathophysiological role of catecholamines in the evolution of the Takotsubo syndrome (TTS). The extent of cardiac and circulatory compromise dictates the use of some form of supportive therapy. This study was designed to investigate the clinical outcomes associated with catecholamine use in TTS patients. METHODS: Our institutional database constituted a collective of 114 patients diagnosed with TTS between 2003 and 2015...
March 20, 2018: BMC Cardiovascular Disorders
Martin Davi, Markus Mann, Zili Ma, Felix Schrader, Andreas Drichel, Serhiy Budnyk, Anna Rokicinska, Piotr Kustrowski, Richard Dronskowski, Adam Slabon
CuWO4 is a photoanode candidate in neutral pH, and manganese-based oxygen evolution reaction electrocatalysts are of high interest due to their low price and low toxicity. Considering the unexplored chemistry of transition-metal carbodiimides/cyanamides for the PEC water oxidation, we investigated MnNCN as an electrocatalyst for CuWO4 under AM 1.5G illumination in potassium phosphate electrolyte (pH 7). Surface functionalization of CuWO4 photoanodes with MnNCN increased the photocurrent from 22 to 30 μA cm-2 at 1...
March 19, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Denis Warshan, Anton Liaimer, Eric Pederson, Sea-Yong Kim, Nicole Shapiro, Tanja Woyke, Bjørn Altermark, Katharina Pawlowski, Philip D Weyman, Christopher L Dupont, Ulla Rasmussen
The cyanobacteria belonging to the genus Nostoc comprise free-living strains but also facultative plant-symbionts. Symbiotic strains can enter into symbiosis with taxonomically diverse range of host plants. Little is known about genomic changes associated with evolutionary transition of Nostoc from free-living to plant symbiont. Here we compared the genomes derived from eleven symbiotic Nostoc strains isolated from different host plants and infer phylogenetic relationships between strains. Phylogenetic reconstructions of 89 Nostocales showed that symbiotic Nostoc strains with a broad host range, entering epiphytic and intracellular or extracellular endophytic interactions, form a monophyletic clade indicating a common evolutionary history...
March 15, 2018: Molecular Biology and Evolution
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