scholarly journals Variable inhibition of unwinding rates of DNA catalyzed by the SARS-Cov-2 (COV19) helicase nsp13 by structurally distinct single DNA lesions.

2021 ◽  
Author(s):  
Ana H. Sales ◽  
Sam Ciervo ◽  
Tania Lupoli ◽  
Vladimir Shafirovich ◽  
Nicholas E Geacintov
Keyword(s):  
Structural Features ◽  
Dna Lesions ◽  
Pyrimidine Dimer ◽  
Helicase Activity ◽  
Thymine Dimers ◽  
Guanine Adducts ◽  
Bulky Dna Adducts ◽  
A Minor ◽  
The Impact ◽  
Kinetics Of

The SARS 2 (Covid 19) helicase nsp13 plays a critically important role in the replication of the Corona virus by unwinding double-stranded RNA (and DNA) with a 5 prime to 3 prime strand polarity. Here we explored the impact of single, structurally defined covalent DNA lesions on the helicase activity of nsp13 in aqueous solutions, The objectives were to derive mechanistic insights into the relationships between the structures of DNA lesions, the DNA distortions that they engender, and the inhibition of helicase activity. The lesions included two bulky stereoisomeric N2-guanine adducts derived from the reactions of benzo[a]pyrene diol epoxide with DNA. The trans-adduct assumes a minor groove conformation, while the cis-product adopts a base-displaced intercalated conformation. The non-bulky DNA lesions included the intra-strand cross-linked thymine dimers, the cis-syn-cyclobutane pyrimidine dimer, and the pyrimidine (6–4) pyrimidone photoproduct. All four lesions strongly inhibit the helicase activity of nsp13, The UV photolesions feature a 2 - 5-fold smaller inhibition of the nsp13 unwinding activity than the bulky DNA adducts, and the kinetics of these two pairs of DNA lesions are also different. The connections between the structural features of these four DNA lesions and their impact on nsp13 unwinding efficiencies are discussed.

scholarly journals Evaluating polymer interplay after hot water pretreatment to investigate maize stem internode recalcitrance

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Amandine Leroy ◽  
Xavier Falourd ◽  
Loïc Foucat ◽  
Valérie Méchin ◽  
Fabienne Guillon ◽  
...  
Keyword(s):  
Cell Wall ◽  
Negative Impact ◽  
Lignin Content ◽  
Structural Features ◽  
Hot Water ◽  
Condensed State ◽  
Structural Factors ◽  
Water Pretreatment ◽  
Hot Water Pretreatment ◽  
The Impact

Abstract Background Biomass recalcitrance is governed by various molecular and structural factors but the interplay between these multiscale factors remains unclear. In this study, hot water pretreatment (HWP) was applied to maize stem internodes to highlight the impact of the ultrastructure of the polymers and their interactions on the accessibility and recalcitrance of the lignocellulosic biomass. The impact of HWP was analysed at different scales, from the polymer ultrastructure or water mobility to the cell wall organisation by combining complementary compositional, spectral and NMR analyses. Results HWP increased the kinetics and yield of saccharification. Chemical characterisation showed that HWP altered cell wall composition with a loss of hemicelluloses (up to 45% in the 40-min HWP) and of ferulic acid cross-linking associated with lignin enrichment. The lignin structure was also altered (up to 35% reduction in β–O–4 bonds), associated with slight depolymerisation/repolymerisation depending on the length of treatment. The increase in $${T}_{1\rho }^{H}$$ T 1 ρ H , $${T}_{HH}$$ T HH and specific surface area (SSA) showed that the cellulose environment was looser after pretreatment. These changes were linked to the increased accessibility of more constrained water to the cellulose in the 5–15 nm pore size range. Conclusion The loss of hemicelluloses and changes in polymer structural features caused by HWP led to reorganisation of the lignocellulose matrix. These modifications increased the SSA and redistributed the water thereby increasing the accessibility of cellulases and enhancing hydrolysis. Interestingly, lignin content did not have a negative impact on enzymatic hydrolysis but a higher lignin condensed state appeared to promote saccharification. The environment and organisation of lignin is thus more important than its concentration in explaining cellulose accessibility. Elucidating the interactions between polymers is the key to understanding LB recalcitrance and to identifying the best severity conditions to optimise HWP in sustainable biorefineries.

scholarly journals Ice Coverage Induced by Depositing a Water Drop onto the Supercooled Substrate at Extreme Low Vapor Pressure

Crystals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 691
Author(s):  
Yugang Zhao ◽  
Zichao Zuo ◽  
Haibo Tang ◽  
Xin Zhang
Keyword(s):  
Vapor Pressure ◽  
Substrate Temperature ◽  
Water Drop ◽  
Industrial Processes ◽  
Aircraft Icing ◽  
Ice Coverage ◽  
Fundamental Understanding ◽  
Order Of Magnitude ◽  
The Impact ◽  
Kinetics Of

Icing/snowing/frosting is ubiquitous in nature and industrial processes, and the accretion of ice mostly leads to catastrophic consequences. The existing understanding of icing is still limited, particularly for aircraft icing, where direct observation of the freezing dynamics is inaccessible. In this work, we investigate experimentally the impact and freezing of a water drop onto the supercooled substrate at extremely low vapor pressure, to mimic an aircraft passing through clouds at a relatively high altitude, engendering icing upon collisions with pendant drops. Special attention is focused on the ice coverage induced by an impinging drop, from the perimeter pointing outward along the radial direction. We observed two freezing regimes: (I) spread-recoil-freeze at the substrate temperature of Ts = −15.4 ± 0.2 °C and (II) spread (incomplete)-freeze at the substrate temperature of Ts = −22.1 ± 0.2 °C. The ice coverage is approximately one order of magnitude larger than the frozen drop itself, and counterintuitively, larger supercooling yields smaller ice coverage in the range of interest. We attribute the variation of ice coverage to the kinetics of vapor diffusion in the two regimes. This fundamental understanding benefits the design of new anti-icing technologies for aircraft.

scholarly journals The Impact of Metabolic Scion–Rootstock Interactions in Different Grapevine Tissues and Phloem Exudates

Metabolites ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 349
Author(s):  
Sara Tedesco ◽  
Alexander Erban ◽  
Saurabh Gupta ◽  
Joachim Kopka ◽  
Pedro Fevereiro ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Phloem Exudate ◽  
Graft Union ◽  
Reciprocal Effect ◽  
Metabolic Markers ◽  
Interaction Studies ◽  
Metabolic Interactions ◽  
A Minor ◽  
The Impact ◽  
Related Compounds

In viticulture, grafting is used to propagate Phylloxera-susceptible European grapevines, thereby using resistant American rootstocks. Although scion–rootstock reciprocal signaling is essential for the formation of a proper vascular union and for coordinated growth, our knowledge of graft partner interactions is very limited. In order to elucidate the scale and the content of scion–rootstock metabolic interactions, we profiled the metabolome of eleven graft combination in leaves, stems, and phloem exudate from both above and below the graft union 5–6 months after grafting. We compared the metabolome of scions vs. rootstocks of homografts vs. heterografts and investigated the reciprocal effect of the rootstock on the scion metabolome. This approach revealed that (1) grafting has a minor impact on the metabolome of grafted grapevines when tissues and genotypes were compared, (2) heterografting affects rootstocks more than scions, (3) the presence of a heterologous grafting partner increases defense-related compounds in both scion and rootstocks in shorter and longer distances from the graft, and (4) leaves were revealed as the best tissue to search for grafting-related metabolic markers. These results will provide a valuable metabolomics resource for scion–rootstock interaction studies and will facilitate future efforts on the identification of metabolic markers for important agronomic traits in grafted grapevines.

scholarly journals Theoretical Studies of the Interaction between Screw Surface and Material in the Mixer

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 962
Author(s):  
Andrzej Marczuk ◽  
Vasily Sysuev ◽  
Alexey Aleshkin ◽  
Petr Savinykh ◽  
Nikolay Turubanov ◽  
...  
Keyword(s):  
Friction Coefficient ◽  
High Efficiency ◽  
Animal Feed ◽  
Structural Features ◽  
Power Demand ◽  
Friction Coefficients ◽  
Length Unit ◽  
Mixing Chamber ◽  
Size Of Particles ◽  
The Impact

Mixing is one of the most commonly used processes in food, animal feed, chemical, cosmetic, etc., industries. It is supposed to provide high-quality homogenous, nutritious mixtures. To provide appropriate mixing of materials while maintaining the process high efficiency and low energy consumption it is crucial to explore and describe the material flow caused by the movement of mixing elements and the contact between particles. The process of mixing is also affected by structural features of the machine components and the mixing chamber, speed of mixing, and properties of the mixed materials, such as the size of particles, moisture, friction coefficients. Thus, modeling of the phenomena that accompany the process of mixing using the above-listed parameters is indispensable for appropriate implementation of the process. The paper provides theoretical power calculations that take into account the material speed change, the impact of the material friction coefficient on the screw steel surface and the impact of the friction coefficient on the material, taking into account the loading height of the mixing chamber and the chamber loading value. Dependencies between the mixer power and the product degree of fineness, rotational speed of screw friction coefficients, the number of windings per length unit, and width of the screw tape have been presented on the basis of a developed model. It has been found that power increases along with an increase in the value of these parameters. Verification of the theoretical model indicated consistence of the predicted power demand with the power demand determined in tests performed on a real object for values of the assumed, effective loading, which was 65–75%.

scholarly journals Morphology and crystallization kinetics of Rubber-modified Nylon 6 Prepared by Anionic In-situ Polymerization

2020 ◽  
Vol 27 (1) ◽  
pp. 204-215
Author(s):  
Hongkai Zhao ◽  
Dengchao Zhang ◽  
Yingshuang Li
Keyword(s):  
Crystallization Kinetics ◽  
In Situ Polymerization ◽  
Good Description ◽  
Nylon 6 ◽  
Avrami Equation ◽  
Infrared Analysis ◽  
Chain Segment ◽  
The Impact ◽  
Kinetics Of

AbstractIn this work, we modified nylon 6 with liquid rubber by in-situ polymerization. The infrared analysis suggested that HDI urea diketone is successfully blocked by caprolactam after grafting on hydroxyl of HTPB, and the rubber-modified nylon copolymer is generated by the anionic polymerization. The impact section analysis indicated the rubber-modified nylon 6 resin exhibited an alpha crystal form.With an increase in the rubber content, nylon 6 was more likely to generate stable α crystal. Avrami equation was a good description of the non-isothermal crystallization kinetics of nylon-6 and rubber-modified nylon-6 resin. Moreover, it is found that the initial crystallization temperature of nylon-6 chain segment decreased due to the flexible rubber chain segment. n value of rubber-modified nylon-6 indicated that its growth was the coexistence of two-dimensional discoid and three-dimensional spherulite growth. Finally, the addition of the rubber accelerated the crystallization rate of nylon 6.

scholarly journals Experimental and theoretical studies on thymine photodimerization mediated by oxidatively generated DNA lesions and epigenetic intermediates

2020 ◽  
Vol 22 (44) ◽  
pp. 25661-25668
Author(s):  
Mauricio Lineros-Rosa ◽  
Antonio Francés-Monerris ◽  
Antonio Monari ◽  
Miguel Angel Miranda ◽  
Virginie Lhiaubet-Vallet
Keyword(s):  
Dna Lesions ◽  
Theoretical Studies ◽  
Computational Studies ◽  
Thymine Dimers ◽  
Different Types ◽  
Experimental And Theoretical Studies

Combined spectroscopic and computational studies reveal that, in spite of their structural similarities, 5-formyluracil and 5-formylcytosine photosensitize cyclobutane thymine dimers through two different types of mechanisms.

scholarly journals Single entity electrochemistry and the electron transfer kinetics of hydrazine oxidation

Nano Research ◽  
2021 ◽  
Author(s):  
Ruiyang Miao ◽  
Lidong Shao ◽  
Richard G. Compton
Keyword(s):  
Electron Transfer ◽  
Bulk Solution ◽  
Relative Contribution ◽  
Rate Determining Step ◽  
Multistep Process ◽  
Ph Range ◽  
Electro Catalytic Oxidation ◽  
Single Particle Impact ◽  
The Impact ◽  
Kinetics Of

AbstractThe mechanism and kinetics of the electro-catalytic oxidation of hydrazine by graphene oxide platelets randomly decorated with palladium nanoparticles are deduced using single particle impact electrochemical measurements in buffered aqueous solutions across the pH range 2–11. Both hydrazine, N2H4, and protonated hydrazine N2H5+ are shown to be electroactive following Butler-Volmer kinetics, of which the relative contribution is strongly pH-dependent. The negligible interconversion between N2H4 and N2H5+ due to the sufficiently short timescale of the impact voltammetry, allows the analysis of the two electron transfer rates from impact signals thus reflecting the composition of the bulk solution at the pH in question. In this way the rate determining step in the oxidation of each specie is deduced to be a one electron step in which no protons are released and so likely corresponds to the initial formation of a very short-lived radical cation either in solution or adsorbed on the platelet. Overall the work establishes a generic method for the elucidation of the rate determining electron transfer in a multistep process free from any complexity imposed by preceding or following chemical reactions which occur on the timescale of conventional voltammetry.

scholarly journals Dissecting the impact of target-binding kinetics of protein binders on tumor localization

iScience ◽  
2021 ◽  
Vol 24 (2) ◽  
pp. 102104
Author(s):  
Yunjin Song ◽  
Hoibin Jeong ◽  
Song-Rae Kim ◽  
Yiseul Ryu ◽  
Jonghwi Baek ◽  
...  
Keyword(s):  
Binding Kinetics ◽  
Tumor Localization ◽  
Protein Binders ◽  
Target Binding ◽  
The Impact ◽  
Kinetics Of

scholarly journals A Study of the Impact of Graphite on the Kinetics of SPS in Nano- and Submicron WC-10%Co Powder Compositions

Ceramics ◽  
2021 ◽  
Vol 4 (2) ◽  
pp. 331-363
Author(s):  
Eugeniy Lantcev ◽  
Aleksey Nokhrin ◽  
Nataliya Malekhonova ◽  
Maksim Boldin ◽  
Vladimir Chuvil'deev ◽  
...  
Keyword(s):  
Activation Energy ◽  
Solid Phase ◽  
Continuous Heating ◽  
Diffusion Creep ◽  
Hard Alloys ◽  
Fine Grained ◽  
Plasma Sintering ◽  
Spark Plasma ◽  
The Impact ◽  
Kinetics Of

This study investigates the impact of carbon on the kinetics of the spark plasma sintering (SPS) of nano- and submicron powders WC-10wt.%Co. Carbon, in the form of graphite, was introduced into powders by mixing. The activation energy of solid-phase sintering was determined for the conditions of isothermal and continuous heating. It has been demonstrated that increasing the carbon content leads to a decrease in the fraction of η-phase particles and a shift of the shrinkage curve towards lower heating temperatures. It has been established that increasing the graphite content in nano- and submicron powders has no significant effect on the SPS activation energy for “mid-range” heating temperatures, QS(I). The value of QS(I) is close to the activation energy of grain-boundary diffusion in cobalt. It has been demonstrated that increasing the content of graphite leads to a significant decrease in the SPS activation energy, QS(II), for “higher-range” heating temperatures due to lower concentration of tungsten atoms in cobalt-based γ-phase. It has been established that the sintering kinetics of fine-grained WC-Co hard alloys is limited by the intensity of diffusion creep of cobalt (Coble creep).

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