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https://www.readbyqxmd.com/read/29457815/hydrogen-bonding-effect-between-active-site-and-protein-environment-on-catalysis-performance-in-h-2-producing-nife-hydrogenases
#1
Siyao Qiu, Luis Miguel Azofra, Douglas R MacFarlane, Chenghua Sun
The interaction between the active site and the surrounding protein environment plays a fundamental role in the hydrogen evolution reaction (HER) in [NiFe] hydrogenases. Our density functional theory (DFT) findings demonstrate that the reaction Gibbs free energy required for the rate determining step decreases by 7.1 kcal mol-1 when the surrounding protein environment is taken into account, which is chiefly due to free energy decreases for the two H+ /e- addition steps (the so-called Ni-SIa to I1, and Ni-C to Ni-R), being the largest thermodynamic impediments of the whole reaction...
February 19, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29457717/oedometric-small-angle-neutron-scattering-in-situ-nano-pore-structure-during-bentonite-consolidation-and-swelling-in-co2-environments
#2
Thomas Dewers, Jason E Heath, Charles R Bryan, Joseph T Mang, Rex Paul Hjelm, Mei Ding, Mark Taylor
Results of oedometric consolidation experiments linked with small-angle neutron scattering (SANS) measurements are presented, using SWy-2 Wyoming bentonite clay in dry and water-bearing N2 and CO2 atmospheres. Oedometric SANS involves deforming a porous sample under uniaxial strain conditions with applied axial force and internal pore pressure control, and combines with SANS for in situ observation of pore structure evolution and interaction. Scattering from both interlayer (clay intra-aggregate) and free (inter-aggregate) pores is observed, showing decreasing pore size with dry consolidation and interactions between interlayer and free pore types with swelling and consolidation...
February 19, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/29457336/high-school-biology-students-use-of-visual-molecular-dynamics-as-an-authentic-tool-for-learning-about-modeling-as-a-professional-scientific-practice
#3
Stephen R Burgin, Jennifer Oramous, Michael Kaminski, Linda Stocker, Mahmoud Moradi
Modeling is a practice of science that is underemphasized in biology classrooms in comparison to its central focus in the physical sciences. Visualizations of the submicroscopic world of molecules are becoming increasingly sophisticated with the evolution of new technologies. With this in mind, we introduced high school biology classrooms to a professional molecular modeling software program used by research biochemists to visualize proteins and other macromolecules. Analysis of surveys completed before and after the use of the program revealed significant student gains in their understandings of the nature of models...
February 19, 2018: Biochemistry and Molecular Biology Education
https://www.readbyqxmd.com/read/29457135/oceanic-crustal-carbon-cycle-drives-26-million-year-atmospheric-carbon-dioxide-periodicities
#4
R Dietmar Müller, Adriana Dutkiewicz
Atmospheric carbon dioxide (CO2 ) data for the last 420 million years (My) show long-term fluctuations related to supercontinent cycles as well as shorter cycles at 26 to 32 My whose origin is unknown. Periodicities of 26 to 30 My occur in diverse geological phenomena including mass extinctions, flood basalt volcanism, ocean anoxic events, deposition of massive evaporites, sequence boundaries, and orogenic events and have previously been linked to an extraterrestrial mechanism. The vast oceanic crustal carbon reservoir is an alternative potential driving force of climate fluctuations at these time scales, with hydrothermal crustal carbon uptake occurring mostly in young crust with a strong dependence on ocean bottom water temperature...
February 2018: Science Advances
https://www.readbyqxmd.com/read/29456146/a-comprehensive-and-dated-phylogenomic-analysis-of-butterflies
#5
Marianne Espeland, Jesse Breinholt, Keith R Willmott, Andrew D Warren, Roger Vila, Emmanuel F A Toussaint, Sarah C Maunsell, Kwaku Aduse-Poku, Gerard Talavera, Rod Eastwood, Marta A Jarzyna, Robert Guralnick, David J Lohman, Naomi E Pierce, Akito Y Kawahara
Butterflies (Papilionoidea), with over 18,000 described species [1], have captivated naturalists and scientists for centuries. They play a central role in the study of speciation, community ecology, biogeography, climate change, and plant-insect interactions and include many model organisms and pest species [2, 3]. However, a robust higher-level phylogenetic framework is lacking. To fill this gap, we inferred a dated phylogeny by analyzing the first phylogenomic dataset, including 352 loci (> 150,000 bp) from 207 species representing 98% of tribes, a 35-fold increase in gene sampling and 3-fold increase in taxon sampling over previous studies [4]...
February 14, 2018: Current Biology: CB
https://www.readbyqxmd.com/read/29455315/mitogenomes-of-two-neotropical-bird-species-and-the-multiple-independent-origin-of-mitochondrial-gene-orders-in-passeriformes
#6
Renato Caparroz, Amanda V Rocha, Gustavo S Cabanne, Pablo Tubaro, Alexandre Aleixo, Emily M Lemmon, Alan R Lemmon
At least four mitogenome arrangements occur in Passeriformes and differences among them are derived from an initial tandem duplication involving a segment containing the control region (CR), followed by loss or reduction of some parts of this segment. However, it is still unclear how often duplication events have occurred in this bird order. In this study, the mitogenomes from two species of Neotropical passerines (Sicalis olivascens and Lepidocolaptes angustirostris) with different gene arrangements were first determined...
February 17, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29455142/cereal-powdery-mildew-effectors-a-complex-toolbox-for-an-obligate-pathogen
#7
REVIEW
Salim Bourras, Coraline R Praz, Pietro D Spanu, Beat Keller
Cereal powdery mildews are major pathogens of cultivated monocot crops, and all are obligate biotrophic fungi that can only grow and reproduce on living hosts. This lifestyle is combined with extreme host specialization where every mildew subspecies (referred to as forma specialis) can only infect one plant species. Recently there has been much progress in our understanding of the possible roles effectors play in this complex host-pathogen interaction. Here, we review current knowledge on the origin, evolution, and mode of action of cereal mildew effectors, with a particular focus on recent advances in the identification of bona fide effectors and avirulence effector proteins from wheat and barley powdery mildews...
February 15, 2018: Current Opinion in Microbiology
https://www.readbyqxmd.com/read/29454373/subclinical-hypothyroidism-in-children-is-it-always-subclinical
#8
R Gallizzi, C Crisafulli, T Aversa, G Salzano, F De Luca, M Valenzise, G Zirilli
Aim of this commentary is to report current knowledges on the main clinical and metabolic abnormalities which might be observed in children with longstanding and untreated subclinical hypothyroidism (SH) and to comment the most recent views about natural evolution of thyroid function in the cases with either idiopathic or Hashimoto's thyroiditis-related SH. On the basis of these preliminary remarks, the essential guidelines for an appropriate and tailored management of SH children are also proposed.
February 17, 2018: Italian Journal of Pediatrics
https://www.readbyqxmd.com/read/29453274/select-and-resequence-reveals-relative-fitness-of-bacteria-in-symbiotic-and-free-living-environments
#9
Liana T Burghardt, Brendan Epstein, Joseph Guhlin, Matt S Nelson, Margaret R Taylor, Nevin D Young, Michael J Sadowsky, Peter Tiffin
Assays to accurately estimate relative fitness of bacteria growing in multistrain communities can advance our understanding of how selection shapes diversity within a lineage. Here, we present a variant of the "evolve and resequence" approach both to estimate relative fitness and to identify genetic variants responsible for fitness variation of symbiotic bacteria in free-living and host environments. We demonstrate the utility of this approach by characterizing selection by two plant hosts and in two free-living environments (sterilized soil and liquid media) acting on synthetic communities of the facultatively symbiotic bacterium Ensifer meliloti We find ( i ) selection that hosts exert on rhizobial communities depends on competition among strains, ( ii ) selection is stronger inside hosts than in either free-living environment, and ( iii ) a positive host-dependent relationship between relative strain fitness in multistrain communities and host benefits provided by strains in single-strain experiments...
February 16, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29453273/evolution-of-a-holistic-systems-approach-to-planning-and-managing-road-safety-the-victorian-case-study-1970-2015
#10
Carlyn Muir, Ian R Johnston, Eric Howard
BACKGROUND: The Victorian Safe System approach to road safety slowly evolved from a combination of the Swedish Vision Zero philosophy and the Sustainable Safety model developed by the Dutch. The Safe System approach reframes the way in which road safety is viewed and managed. METHODS: This paper presents a case study of the institutional change required to underpin the transformation to a holistic approach to planning and managing road safety in Victoria, Australia...
February 16, 2018: Injury Prevention: Journal of the International Society for Child and Adolescent Injury Prevention
https://www.readbyqxmd.com/read/29451780/using-i-in-vitro-i-evolution-and-whole-genome-analysis-iviewga-to-discover-next-generation-targets-for-antimalarial-drug-discovery
#11
Madeline R Luth, Purva Gupta, Sabine Ottilie, Elizabeth A Winzeler
Although many new anti-infectives have been discovered and developed solely using phenotypic cellular screening and assay optimization, most researchers recognize that structure-guided drug design is more practical and less costly. In addition, a greater chemical space can be interrogated with structure-guided drug design. The practicality of structure-guided drug design has launched a search for the targets of compounds discovered in phenotypic screens. One method that has been used extensively in malaria parasites for target discovery and chemical validation is in vitro evolution and whole genome analysis (IVIEWGA)...
February 16, 2018: ACS Infectious Diseases
https://www.readbyqxmd.com/read/29449576/lizards-ran-bipedally-110-million-years-ago
#12
Hang-Jae Lee, Yuong-Nam Lee, Anthony R Fiorillo, Junchang Lü
Four heteropod lizard trackways discovered in the Hasandong Formation (Aptian-early Albian), South Korea assigned to Sauripes hadongensis, n. ichnogen., n. ichnosp., which represents the oldest lizard tracks in the world. Most tracks are pes tracks (N = 25) that are very small, average 22.29 mm long and 12.46 mm wide. The pes tracks show "typical" lizard morphology as having curved digit imprints that progressively increase in length from digits I to IV, a smaller digit V that is separated from the other digits by a large interdigital angle...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29449551/mutations-in-cfap43-and-cfap44-cause-male-infertility-and-flagellum-defects-in-trypanosoma-and-human
#13
Charles Coutton, Alexandra S Vargas, Amir Amiri-Yekta, Zine-Eddine Kherraf, Selima Fourati Ben Mustapha, Pauline Le Tanno, Clémentine Wambergue-Legrand, Thomas Karaouzène, Guillaume Martinez, Serge Crouzy, Abbas Daneshipour, Seyedeh Hanieh Hosseini, Valérie Mitchell, Lazhar Halouani, Ouafi Marrakchi, Mounir Makni, Habib Latrous, Mahmoud Kharouf, Jean-François Deleuze, Anne Boland, Sylviane Hennebicq, Véronique Satre, Pierre-Simon Jouk, Nicolas Thierry-Mieg, Beatrice Conne, Denis Dacheux, Nicolas Landrein, Alain Schmitt, Laurence Stouvenel, Patrick Lorès, Elma El Khouri, Serge P Bottari, Julien Fauré, Jean-Philippe Wolf, Karin Pernet-Gallay, Jessica Escoffier, Hamid Gourabi, Derrick R Robinson, Serge Nef, Emmanuel Dulioust, Raoudha Zouari, Mélanie Bonhivers, Aminata Touré, Christophe Arnoult, Pierre F Ray
Spermatogenesis defects concern millions of men worldwide, yet the vast majority remains undiagnosed. Here we report men with primary infertility due to multiple morphological abnormalities of the sperm flagella with severe disorganization of the sperm axoneme, a microtubule-based structure highly conserved throughout evolution. Whole-exome sequencing was performed on 78 patients allowing the identification of 22 men with bi-allelic mutations in DNAH1 (n = 6), CFAP43 (n = 10), and CFAP44 (n = 6). CRISPR/Cas9 created homozygous CFAP43/44 male mice that were infertile and presented severe flagellar defects confirming the human genetic results...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29449486/natural-selection-and-the-predictability-of-evolution-in-timema-stick-insects
#14
Patrik Nosil, Romain Villoutreix, Clarissa F de Carvalho, Timothy E Farkas, Víctor Soria-Carrasco, Jeffrey L Feder, Bernard J Crespi, Zach Gompert
Predicting evolution remains difficult. We studied the evolution of cryptic body coloration and pattern in a stick insect using 25 years of field data, experiments, and genomics. We found that evolution is more difficult to predict when it involves a balance between multiple selective factors and uncertainty in environmental conditions than when it involves feedback loops that cause consistent back-and-forth fluctuations. Specifically, changes in color-morph frequencies are modestly predictable through time ( r 2 = 0...
February 16, 2018: Science
https://www.readbyqxmd.com/read/29448656/tuneable-physicochemical-properties-of-thermally-annealed-graphene-oxide-powder-and-thin-films
#15
Manjri Singh, Pooja Saini, Bhanu P Singh, Priti Singh, Ram P Tandon, Ajit K Mahapatro, Surinder P Singh
The tuneability of oxygen containing groups in graphene oxide (GO) that controls physicochemical properties is highly desirable for device applications. In this context, the thermally reduced graphene oxide (r-GO) powders and spin coated thin films with varying sp2/sp3 carbon network have been prepared using highly exfoliated GO (synthesized using modified Hummer's method with an innovative conjunction of lyophilisation). The additional step of lyophilisation results in the formation of highly exfoliated and monodispersed GO nanosheets as evidenced from FESEM, TEM, XRD, and Raman, FT-IR and UV-Vis spectroscopy...
March 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29447752/retracted-the-revised-stratigraphy-of-the-hominin-bearing-site-of-kromdraai-gauteng-south-africa-and-associated-perspectives
#16
Laurent Bruxelles, Richard Maire, Amélie Beaudet, Raymond Couzens, Francis Duranthon, Jean-Baptiste Fourvel, Dominic Stratford, Francis Thackeray, José Braga
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the co-Editors-in-Chief and the authors. The Results and Discussion of this article duplicate significant parts of book chapter "A revised stratigraphy of Kromdraai", published by L.B., R.M., R.C., F.T. and J.B. in Braga, J. and Thackeray, J.F. (Eds.), "Kromdraai. A Birthplace of Paranthropus in the Cradle of Humankind" (2016, SUN MeDIA MeTRO, pp...
January 2018: Journal of Human Evolution
https://www.readbyqxmd.com/read/29447175/modelling-human-hard-palate-shape-with-b%C3%A3-zier-curves
#17
Rick Janssen, Scott R Moisik, Dan Dediu
People vary at most levels, from the molecular to the cognitive, and the shape of the hard palate (the bony roof of the mouth) is no exception. The patterns of variation in the hard palate are important for the forensic sciences and (palaeo)anthropology, and might also play a role in speech production, both in pathological cases and normal variation. Here we describe a method based on Bézier curves, whose main aim is to generate possible shapes of the hard palate in humans for use in computer simulations of speech production and language evolution...
2018: PloS One
https://www.readbyqxmd.com/read/29446925/visible-light-driven-photosystems-using-heteroleptic-cu-i-photosensitizers-and-rh-iii-catalysts-to-produce-h-2
#18
Bradley J McCullough, Bertrand J Neyhouse, Briana R Schrage, Demi T Reed, Allen J Osinski, Christopher J Ziegler, Travis A White
The synthesis of two new heteroleptic Cu(I) photosensitizers (PS), [Cu(Xantphos)(NN)]PF 6 (NN = biq = 2,2'-biquinoline, dmebiq = 2,2'-biquinoline-4,4'-dimethyl ester; Xantphos = 4,5-bis(diphenylphosphino)-9,9-dimethylxanthene), along with the associated structural, photophysical, and electrochemical properties, are described. The biquinoline diimine ligand extends the PS light absorbing properties into the visible with a maximum absorption at 455 and 505 nm for NN = biq and dmebiq, respectively, in CH 2 Cl 2 solvent...
February 15, 2018: Inorganic Chemistry
https://www.readbyqxmd.com/read/29446510/use-of-t-1-relaxation-time-in-rotating-frame-t-1-%C3%AF-and-apparent-diffusion-coefficient-to-estimate-cerebral-stroke-evolution
#19
Yuefa Tan, Jun Xu, Ruiying Chen, Bin Chen, Juan Xu, Daokun Ren, Queenie Chan, Yingjie Mei, Yuankui Wu, Yikai Xu
BACKGROUND: The major factor for the appropriate treatment strategies for ischemia patients is its onset timing. PURPOSE/HYPOTHESIS: To study to evaluate the diagnostic accuracy of T 1 relaxation time in a rotating frame (T 1 ρ) and apparent diffusion coefficient (ADC) from MRI to estimate ischemia stages. STUDY TYPE: Prospective. POPULATION/SUBJECTS/PHANTOM/SPECIMEN/ANIMAL MODEL: In all, 73 patients (49 males, aged 29-78 years and 24 females, aged 22-94 years) with ischemia were prospectively imaged with T 1 ρ and diffusion MRI during the postischemic period...
February 15, 2018: Journal of Magnetic Resonance Imaging: JMRI
https://www.readbyqxmd.com/read/29446223/evolution-and-development-of-scyphozoan-jellyfish
#20
Rebecca R Helm
Scyphozoan jellyfish, or scyphomedusae, are conspicuous members of many ocean ecosystems, and have large impacts on human health and industry. Most scyphomedusae are the final stage in a complex life cycle that also includes two intermediate stages: the larval planula and benthic polyp. In species with all three life-cycle stages, the metamorphosis of a polyp into a juvenile scyphomedusa (ephyra) is termed strobilation, and polyps can produce one ephyra (termed monodisc strobilation) or many ephyrae (termed polydisc strobilation)...
February 14, 2018: Biological Reviews of the Cambridge Philosophical Society
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