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https://www.readbyqxmd.com/read/28107414/multifractality-and-network-analysis-of-phase-transition
#1
Longfeng Zhao, Wei Li, Chunbin Yang, Jihui Han, Zhu Su, Yijiang Zou
Many models and real complex systems possess critical thresholds at which the systems shift dramatically from one sate to another. The discovery of early-warnings in the vicinity of critical points are of great importance to estimate how far the systems are away from the critical states. Multifractal Detrended Fluctuation analysis (MF-DFA) and visibility graph method have been employed to investigate the multifractal and geometrical properties of the magnetization time series of the two-dimensional Ising model...
2017: PloS One
https://www.readbyqxmd.com/read/28107392/upon-accounting-for-the-impact-of-isoenzyme-loss-gene-deletion-costs-anticorrelate-with-their-evolutionary-rates
#2
Christopher Jacobs, Luke Lambourne, Yu Xia, Daniel Segrè
System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism's genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene's fitness contribution to an organism "here and now" and the same gene's historical importance as evidenced by its accumulated mutations over millions of years of evolution...
2017: PloS One
https://www.readbyqxmd.com/read/28107009/nmr-and-computation-reveal-a-pressure-sensitive-folded-conformation-of-trp-cage
#3
Soichiro Kitazawa, Martin J Fossat, Scott A McCallum, Angel E Garcia, Catherine Ann Royer
Beyond defining the structure and stability of folded states of proteins, primary amino acid sequences determine all of the features of their conformational landscapes. Characterizing how sequence modulates the population of protein excited states or folding pathways requires atomic level detailed structural and energetic information. Such insight is essential for improving protein design strategies, as well as for interpreting protein evolution. Here, high pressure NMR and molecular dynamics simulations were combined to probe the conformational landscape of a small model protein, the tryptophan cage variant, Tc5b...
January 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28106912/the-phycocyanobilin-chromophore-of-streptophyte-algal-phytochromes-is-synthesized-by-hy2
#4
Nathan C Rockwell, Shelley S Martin, Fay-Wei Li, Sarah Mathews, John Clark Lagarias
Land plant phytochromes perceive red and far-red light to control growth and development, using the linear tetrapyrrole (bilin) chromophore phytochromobilin (PΦB). Phytochromes from streptophyte algae, sister species to land plants, instead use phycocyanobilin (PCB). PCB and PΦB are synthesized by different ferredoxin-dependent bilin reductases (FDBRs): PΦB is synthesized by HY2, whereas PCB is synthesized by PcyA. The pathway for PCB biosynthesis in streptophyte algae is unknown. We used phylogenetic analysis and heterologous reconstitution of bilin biosynthesis to investigate bilin biosynthesis in streptophyte algae...
January 20, 2017: New Phytologist
https://www.readbyqxmd.com/read/28106144/electronic-and-atomic-structures-of-the-sr3ir4sn13-single-crystal-a-possible-charge-density-wave-material
#5
H-T Wang, M K Srivastava, C-C Wu, S-H Hsieh, Y-F Wang, Y-C Shao, Y-H Liang, C-H Du, J-W Chiou, C-M Cheng, J-L Chen, C-W Pao, J-F Lee, C N Kuo, C S Lue, M-K Wu, W-F Pong
X-ray scattering (XRS), x-ray absorption near-edge structure (XANES) and extended x-ray absorption fine structure (EXAFS) spectroscopic techniques were used to study the electronic and atomic structures of the high-quality Sr3Ir4Sn13 (SIS) single crystal below and above the transition temperature (T(*) ≈ 147 K). The evolution of a series of modulated satellite peaks below the transition temperature in the XRS experiment indicated the formation of a possible charge density wave (CDW) in the (110) plane...
January 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28106042/diverse-feather-shape-evolution-enabled-by-coupling-anisotropic-signalling-modules-with-self-organizing-branching-programme
#6
Ang Li, Seth Figueroa, Ting-Xin Jiang, Ping Wu, Randall Widelitz, Qing Nie, Cheng-Ming Chuong
Adaptation of feathered dinosaurs and Mesozoic birds to new ecological niches was potentiated by rapid diversification of feather vane shapes. The molecular mechanism driving this spectacular process remains unclear. Here, through morphology analysis, transcriptome profiling, functional perturbations and mathematical simulations, we find that mesenchyme-derived GDF10 and GREM1 are major controllers for the topologies of rachidial and barb generative zones (setting vane boundaries), respectively, by tuning the periodic-branching programme of epithelial progenitors...
January 20, 2017: Nature Communications
https://www.readbyqxmd.com/read/28105941/the-loss-of-photosynthetic-pathways-in-the-plastid-and-nuclear-genomes-of-the-non-photosynthetic-mycoheterotrophic-eudicot-monotropa-hypopitys
#7
Nikolai V Ravin, Eugeny V Gruzdev, Alexey V Beletsky, Alexander M Mazur, Egor B Prokhortchouk, Mikhail A Filyushin, Elena Z Kochieva, Vitaly V Kadnikov, Andrey V Mardanov, Konstantin G Skryabin
BACKGROUND: Chloroplasts of most plants are responsible for photosynthesis and contain a conserved set of about 110 genes that encode components of housekeeping gene expression machinery and photosynthesis-related functions. Heterotrophic plants obtaining nutrients from other organisms and their plastid genomes represent model systems in which to study the effects of relaxed selective pressure on photosynthetic function. The most evident is a reduction in the size and gene content of the plastome, which correlates with the loss of genes encoding photosynthetic machinery which become unnecessary...
November 16, 2016: BMC Plant Biology
https://www.readbyqxmd.com/read/28105939/evolution-of-mitochondrial-genomes-in-baikalian-amphipods
#8
Elena V Romanova, Vladimir V Aleoshin, Ravil M Kamaltynov, Kirill V Mikhailov, Maria D Logacheva, Elena A Sirotinina, Alexander Yu Gornov, Anton S Anikin, Dmitry Yu Sherbakov
BACKGROUND: Amphipods (Crustacea) of Lake Baikal are a very numerous and diverse group of invertebrates generally believed to have originated by adaptive radiation. The evolutionary history and phylogenetic relationships in Baikalian amphipods still remain poorly understood. Sequencing of mitochondrial genomes is a relatively feasible way for obtaining a set of gene sequences suitable for robust phylogenetic inferences. The architecture of mitochondrial genomes also may provide additional information on the mechanisms of evolution of amphipods in Lake Baikal...
December 28, 2016: BMC Genomics
https://www.readbyqxmd.com/read/28105921/simba-a-web-tool-for-managing-bacterial-genome-assembly-generated-by-ion-pgm-sequencing-technology
#9
Diego C B Mariano, Felipe L Pereira, Edgar L Aguiar, Letícia C Oliveira, Leandro Benevides, Luís C Guimarães, Edson L Folador, Thiago J Sousa, Preetam Ghosh, Debmalya Barh, Henrique C P Figueiredo, Artur Silva, Rommel T J Ramos, Vasco A C Azevedo
BACKGROUND: The evolution of Next-Generation Sequencing (NGS) has considerably reduced the cost per sequenced-base, allowing a significant rise of sequencing projects, mainly in prokaryotes. However, the range of available NGS platforms requires different strategies and software to correctly assemble genomes. Different strategies are necessary to properly complete an assembly project, in addition to the installation or modification of various software. This requires users to have significant expertise in these software and command line scripting experience on Unix platforms, besides possessing the basic expertise on methodologies and techniques for genome assembly...
December 15, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/28105829/gastight-hydrodynamic-electrochemistry-design-for-a-hermetically-sealed-rotating-disk-electrode-cell
#10
Suho Jung, Ruud Kortlever, Ryan J R Jones, Michael F Lichterman, Theodor Agapie, Charles C L McCrory, Jonas C Peters
Rotating disk electrodes (RDEs) are widely used in electrochemical characterization to analyze the mechanisms of various electrocatalytic reactions. RDE experiments often make use of or require collection and quantification of gaseous products. The combination of rotating parts and gaseous analytes makes the design of RDE cells that allow for headspace analysis challenging due to gas leaks at the interface of the cell body and the rotator. In this manuscript we describe a new, hermetically sealed electrochemical cell that allows for electrode rotation while simultaneously providing a gastight environment...
January 3, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28105808/evolution-of-the-structural-and-electronic-properties-of-medium-sized-sodium-clusters-a-honeycomb-like-na20-cluster
#11
Wei Guo Sun, Jing Jing Wang, Cheng Lu, Xin Xin Xia, Xiao Yu Kuang, Andreas Hermann
Sodium is one of the best examples of a free-electron-like metal and of a certain technological interest. However, an unambiguous determination of the structural evolution of sodium clusters is challenging. Here, we performed an unbiased structure search among neutral and anionic sodium clusters in the medium size range of 10-25 atoms, using the Crystal structure AnaLYsis by Particle Swarm Optimization (CALYPSO) method. Geometries are determined by CALYPSO structure searches, followed by reoptimization of a large number of candidate structures...
January 20, 2017: Inorganic Chemistry
https://www.readbyqxmd.com/read/28104924/the-adaptive-nature-of-culture-a-cross-cultural-analysis-of-the-returns-of-local-environmental-knowledge-in-three-indigenous-societies
#12
Victoria Reyes-García, Maximilien Guèze, Isabel Díaz-Reviriego, Romain Duda, Álvaro Fernández-Llamazares, Sandrine Gallois, Lucentezza Napitupulu, Martí Orta-Martínez, Aili Pyhälä
Researchers have argued that the behavioral adaptations that explain the success of our species are partially cultural, i.e., cumulative and socially transmitted. Thus, understanding the adaptive nature of culture is crucial to understand human evolution. We use a cross-cultural framework and empirical data purposely collected to test whether culturally transmitted and individually appropriated knowledge provides individual returns in terms of hunting yields and health and, by extension, to nutritional status, a proxy for individual adaptive success...
December 2016: Current Anthropology
https://www.readbyqxmd.com/read/28104494/thoughts-on-interactions-between-pgrmc1-and-diverse-attested-and-potential-hydrophobic-ligands
#13
REVIEW
Michael A Cahill, Amy E Medlock
Progesterone Receptor Membrane Component 1 (PGRMC1) is located in many different subcellular locations with many different attested and probably location-specific functions. PGRMC1 was recently identified in the mitochondrial outer membrane where it interacts with ferrochelatase, the last enzyme in the heme synthetic pathway. It has been proposed that PGRMC1 may act as a chaperone to shuttle newly synthesized heme from the mitochondrion to cytochrome P450 (cyP450) enzymes. Here we consider potential roles that PGRMC1 may play in transferring heme, and other small hydrophobic ligands such as cholesterol and steroids, between the hydrophobic compartment of the membrane lipid bilayer interior to aqueous proteins, and perhaps to the membranes of other organelles...
January 16, 2017: Journal of Steroid Biochemistry and Molecular Biology
https://www.readbyqxmd.com/read/28103977/-differential-textual-research-and-analysis-on-the-evolution-of-fritillaria-species-in-successive-dynasties
#14
L Qiu
Rhizoma bolbostemmae was the earliest applied fritillaria species during the period of pre-Qin to Han Dynasties in China. In the period of Wei-Jin, the fritillaria species presented diversities, with Zhejiang-fritillary also appeared for the first time. During the period of the Tang Dynasty to late Ming Dynasty, the fritillaria species kept expanding, Fritillaria hupehensis and Zhejiang-fritillary were deemed authentic species all the time. To the end of the Ming Dynasty, Fritillaria hupehensis withdrew from the stage of history gradually, Fritillaria cirrhosa came into being and then Fritillaria cirrhosa and Zhejiang-fritillary both appeared and became two important species of medicinal fritillarias after late Ming dynasty until today...
November 28, 2016: Zhonghua Yi Shi za Zhi, Chinese Journal of Medical History
https://www.readbyqxmd.com/read/28103803/variational-inference-for-rare-variant-detection-in-deep-heterogeneous-next-generation-sequencing-data
#15
Fan Zhang, Patrick Flaherty
BACKGROUND: The detection of rare single nucleotide variants (SNVs) is important for understanding genetic heterogeneity using next-generation sequencing (NGS) data. Various computational algorithms have been proposed to detect variants at the single nucleotide level in mixed samples. Yet, the noise inherent in the biological processes involved in NGS technology necessitates the development of statistically accurate methods to identify true rare variants. RESULTS: We propose a Bayesian statistical model and a variational expectation maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations...
January 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28103796/phylogenomic-analysis-of-copepoda-arthropoda-crustacea-reveals-unexpected-similarities-with-earlier-proposed-morphological-phylogenies
#16
Seong-Il Eyun
BACKGROUND: Copepods play a critical role in marine ecosystems but have been poorly investigated in phylogenetic studies. Morphological evidence supports the monophyly of copepods, whereas interordinal relationships continue to be debated. In particular, the phylogenetic position of the order Harpacticoida is still ambiguous and inconsistent among studies. Until now, a small number of molecular studies have been done using only a limited number or even partial genes and thus there is so far no consensus at the order-level...
January 19, 2017: BMC Evolutionary Biology
https://www.readbyqxmd.com/read/28103318/static-and-evolving-norovirus-genotypes-implications-for-epidemiology-and-immunity
#17
Gabriel I Parra, R Burke Squires, Consolee K Karangwa, Jordan A Johnson, Cara Lepore, Stanislav V Sosnovtsev, Kim Y Green
Noroviruses are major pathogens associated with acute gastroenteritis worldwide. Their RNA genomes are diverse, with two major genogroups (GI and GII) comprised of at least 28 genotypes associated with human disease. To elucidate mechanisms underlying norovirus diversity and evolution, we used a large-scale genomics approach to analyze human norovirus sequences. Comparison of over 2000 nearly full-length ORF2 sequences representing most of the known GI and GII genotypes infecting humans showed a limited number (≤5) of distinct intra-genotypic variants within each genotype, with the exception of GII...
January 19, 2017: PLoS Pathogens
https://www.readbyqxmd.com/read/28103252/comparative-and-evolutionary-analysis-of-grass-pollen-allergens-using-brachypodium-distachyon-as-a-model-system
#18
Akanksha Sharma, Niharika Sharma, Prem Bhalla, Mohan Singh
Comparative genomics have facilitated the mining of biological information from a genome sequence, through the detection of similarities and differences with genomes of closely or more distantly related species. By using such comparative approaches, knowledge can be transferred from the model to non-model organisms and insights can be gained in the structural and evolutionary patterns of specific genes. In the absence of sequenced genomes for allergenic grasses, this study was aimed at understanding the structure, organisation and expression profiles of grass pollen allergens using the genomic data from Brachypodium distachyon as it is phylogenetically related to the allergenic grasses...
2017: PloS One
https://www.readbyqxmd.com/read/28103245/anaerobically-grown-escherichia-coli-has-an-enhanced-mutation-rate-and-distinct-mutational-spectra
#19
Sonal Shewaramani, Thomas J Finn, Sinead C Leahy, Rees Kassen, Paul B Rainey, Christina D Moon
Oxidative stress is a major cause of mutation but little is known about how growth in the absence of oxygen impacts the rate and spectrum of mutations. We employed long-term mutation accumulation experiments to directly measure the rates and spectra of spontaneous mutation events in Escherichia coli populations propagated under aerobic and anaerobic conditions. To detect mutations, whole genome sequencing was coupled with methods of analysis sufficient to identify a broad range of mutational classes, including structural variants (SVs) generated by movement of repetitive elements...
January 19, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28103105/evolution-of-earth-like-extrasolar-planetary-atmospheres-assessing-the-atmospheres-and-biospheres-of-early-earth-analog-planets-with-a-coupled-atmosphere-biogeochemical-model
#20
S Gebauer, J L Grenfell, J W Stock, R Lehmann, M Godolt, P von Paris, H Rauer
Understanding the evolution of Earth and potentially habitable Earth-like worlds is essential to fathom our origin in the Universe. The search for Earth-like planets in the habitable zone and investigation of their atmospheres with climate and photochemical models is a central focus in exoplanetary science. Taking the evolution of Earth as a reference for Earth-like planets, a central scientific goal is to understand what the interactions were between atmosphere, geology, and biology on early Earth. The Great Oxidation Event in Earth's history was certainly caused by their interplay, but the origin and controlling processes of this occurrence are not well understood, the study of which will require interdisciplinary, coupled models...
January 2017: Astrobiology
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