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Ining Jou, Murugappan Muthukumar
We have investigated the dynamics of single-stranded DNA as it translocates through charge-mutated protein nanopores. Translocation of DNA is a crucial step in nanopore-based sequencing platforms, where control over translocation speed remains one of the main challenges. Taking advantage of the interactions between negatively charged DNA and positively charged amino acid residues, the translocation speed of DNA can be manipulated by deliberate charge decorations inside the nanopore. We employed coarse-grained Langevin dynamics simulations to monitor the step-by-step movement of DNA through different mutations of α-hemolysin protein nanopores...
October 17, 2017: Biophysical Journal
Caroline M Williams, Gregory J Ragland, Gustavo Betini, Lauren B Buckley, Zachary A Cheviron, Kathleen Donohue, Joe Hereford, Murray M Humphries, Simeon Lisovski, Katie E Marshall, Paul S Schmidt, Kimberly S Sheldon, Øystein Varpe, Marcel E Visser
Seasonality is a critically important aspect of environmental variability, and strongly shapes all aspects of life for organisms living in highly seasonal environments. Seasonality has played a key role in generating biodiversity, and has driven the evolution of extreme physiological adaptations and behaviors such as migration and hibernation. Fluctuating selection pressures on survival and fecundity between summer and winter provide a complex selective landscape, which can be met by a combination of three outcomes of adaptive evolution: genetic polymorphism, phenotypic plasticity, and bet-hedging...
October 16, 2017: Integrative and Comparative Biology
Boon Huat Cheah, Sudhir Jadhao, Madavan Vasudevan, Ratnam Wickneswari, Kalaivani Nadarajah
A cross between IR64 (high-yielding but drought-susceptible) and Aday Sel (drought-tolerant) rice cultivars yielded a stable line with enhanced grain yield under drought screening field trials at International Rice Research Institute. The major effect qDTY4.1 drought tolerance and yield QTL was detected in the IR77298-14-1-2-10 Backcrossed Inbred Line (BIL) and its IR87705-7-15-B Near Isogenic Line (NIL) with 93.9% genetic similarity to IR64. Although rice yield is extremely susceptible to water stress at reproductive stage, currently, there is only one report on the detection of drought-responsive microRNAs in inflorescence tissue of a Japonica rice line...
2017: PloS One
Melania Figueroa, Kim E Hammond-Kosack, Peter S Solomon
Wheat is one of the primary staple foods throughout the planet. Significant yield gains in wheat production over the past 40 years have resulted in a steady balance of supply versus demand. However, predicted global population growth rates and dietary changes necessitate substantial yield gains over the next several decades to meet this escalating demand. A key component to meeting this challenge is better management of fungal incited diseases, which can be responsible for 15-20% yield losses per annum. Prominent diseases of wheat that currently contribute to these losses include the rusts, the blotches and head blight/scab...
October 18, 2017: Molecular Plant Pathology
Craig R Yendrek, Gorka Erice, Christopher M Montes, Tiago Tomaz, Crystal A Sorgini, Patrick J Brown, Lauren M McIntyre, Andrew D B Leakey, Elizabeth A Ainsworth
Exposure to elevated tropospheric ozone concentration ([O3 ]) accelerates leaf senescence in many C3 crops. However, the effects of elevated [O3 ] on C4 crops including maize (Zea mays L.) are poorly understood in terms of physiological mechanism and genetic variation in sensitivity. Using free air gas concentration enrichment, we investigated the photosynthetic response of 18 diverse maize inbred and hybrid lines to season-long exposure to elevated [O3 ] (~100 nl L(-1) ) in the field. Gas exchange was measured on the leaf subtending the ear throughout the grain filling period...
October 17, 2017: Plant, Cell & Environment
Rachel S Lane, F Michael Haller, Anais A E Chavaroche, Andrew Almond, Paul L DeAngelis
Liposomal encapsulation is a useful drug delivery strategy for small molecules, especially chemotherapeutic agents such as doxorubicin. Doxil® is a doxorubicin-containing liposome ("dox-liposome") that passively targets drug to tumors while reducing side effects caused by free drug permeating and poisoning healthy tissues. Polyethylene glycol (PEG) is the hydrophilic coating of Doxil® that protects the formulation from triggering the mononuclear phagocyte system (MPS). Evading the MPS prolongs dox-liposome circulation time thus increasing drug deposition at the tumor site...
November 1, 2017: Glycobiology
Taliane L Soares, Onildo N Jesus, Everton H Souza, Mônica L Rossi, Eder J Oliveira
The genus Passiflora is the most diversified of the Passifloraceae, and its palynology presents wide morphological variability. The objective of the study was to evaluate the pollen morphology of 18 Passiflora species in order to identify informative pollinic characteristics to contribute to the taxonomic classification of the genus. The morphology of the pollen grains and the exine structure were investigated using light microscopy and scanning electron microscopy. Differences in the pollen morphology were found in the studied species, mainly in terms of shape, pollen aperture and ornamentation pattern of the exine...
October 16, 2017: Anais da Academia Brasileira de Ciências
Rajendra Sharma, David De Sancho, Victor Muñoz
Proteins that fold upon binding to their partners exhibit complex binding behavior such as induced-fit. But the connections between the folding mechanism and the binding mode remain unknown. Here we focus on the high affinity complex between the physiologically and marginally unstable, fast folder PSBD and the E1 subunit of pyruvate dehydrogenase. Using coarse-grained simulations we investigate the binding to E1 of a partially disordered PSBD under two folding scenarios: two-state and downhill. Our simulations show that induced-fit binding requires that PSBD folds-unfolds in the downhill folding regime...
October 18, 2017: Physical Chemistry Chemical Physics: PCCP
Xiakun Chu, Victor Muñoz
Transcription factors are thought to efficiently search for their target DNA site via a combination of conventional 3D diffusion and 1D diffusion along the DNA molecule mediated by non-specific electrostatic interactions. This process requires the DNA-binding protein to quickly exchange between a search competent and a target recognition mode, but little is known as to how these two binding modes are encoded in the conformational properties of the protein. Here, we investigate this issue on the engrailed homeodomain (EngHD), a DNA-binding domain that folds ultrafast and exhibits a complex conformational behavior consistent with the downhill folding scenario...
October 18, 2017: Physical Chemistry Chemical Physics: PCCP
Adrian Duba, Klaudia Goriewa, Urszula Wachowska, Marian Wiwart
The saprotrophic fungus Alternaria alternata is widespread in the agro-environment and produces more than ten allergenic proteins, mostly protein Alt a 1. The frequency of the Alt a 1 gene was analyzed in a group of A. alternata isolates from winter wheat kernels obtained in Poland, and the effectiveness of various fungicides targeting the pathogen was evaluated. The Alt a 1 gene was identified in four of the seven tested isolates. A. alternata colonized 35.67% kernels on average, but its frequency increased in stored grain where the presence of epiphytes was noted on 23...
October 18, 2017: Environmental Science and Pollution Research International
Satyabrata Maiti, Dhananjay Bhattacharyya
The G:A basepair, stabilized by hydrogen bonding through the sugar edge of guanine and Hoogsteen edge of adenine in trans orientation (G:A S:HT), appears very frequently in the solved RNA structures and is very stable. We have carried out stacking energy analyses of two sequences, namely C:G W:WC::G:A S:HT and G:C W:WC::G:A S:HT (':' represents basepairing and '::' represents stacking interactions), formed by this non-Watson-Crick basepair, by DFT-D. We have scanned nearly the complete phase space by modeling structures of these sequences using different values of the basepair orientation parameters to determine the most stable conformations...
October 18, 2017: Physical Chemistry Chemical Physics: PCCP
Zhuoran Zeng, Jian-Feng Nie, Shi-Wei Xu, Chris H J Davies, Nick Birbilis
Magnesium, the lightest structural metal, is difficult to form at room temperature due to an insufficient number of deformation modes imposed by its hexagonal structure and a strong texture developed during thermomechanical processes. Although appropriate alloying additions can weaken the texture, formability improvement is limited because alloying additions do not fundamentally alter deformation modes. Here we show that magnesium can become super-formable at room temperature without alloying. Despite possessing a strong texture, magnesium can be cold rolled to a strain at least eight times that possible in conventional processing...
October 17, 2017: Nature Communications
Jinjuan Gao, Huahong Shi, Zhijun Dai, Xuefei Mei, Haibo Zong, Hongwei Yang, Lingling Hu, Shushi Li
Anthropogenic activities are driving an increase in sediment contamination in coastal areas. This poses significant challenges for the management of estuarine ecosystems and their adjacent seas worldwide. However, few studies have been conducted on how dynamic mechanisms affect the sediment toxicity in the estuarine environment. This study was designed to investigate the linkages between sediment toxicity and hydrodynamics in the Yangtze River Estuary (YRE) area. High sediment toxicity was found in the Yangtze River mouth (Region I), the depocenter of the Yangtze River Delta (Region II), and the southeastern area of the adjacent sea (Region III), while low sediment toxicity was found in the northeastern offshore region (Region IV)...
October 14, 2017: Environmental Pollution
Yunlong Meng, Wei Lin, Chenglin Li, Shih-Chi Chen
We present a new two-snapshot structured light illumination (SLI) reconstruction algorithm for fast image acquisition. The new algorithm, which only requires two mutually π phase-shifted raw structured images, is implemented on a custom-built temporal focusing fluorescence microscope (TFFM) to enhance its axial resolution via a digital micromirror device (DMD). First, the orientation of the modulated sinusoidal fringe patterns is automatically identified via spatial frequency vector detection. Subsequently, the modulated in-focal-plane images are obtained via rotation and subtraction...
September 18, 2017: Optics Express
Gitanjali Kolhatkar, Julien Plathier, Alain Pignolet, Andreas Ruediger
The effect of gold tip crystallinity on their spectral amplification characteristics, monitored through the luminescence enhanced by surface plasmon resonance (SPR), is investigated experimentally. As the tip radius increases, the grains composing polycrystalline tips become larger, resulting in a blueshift of the emission while a redshift of the SPR was predicted for monocrystalline gold. This reveals that the effect of the grain size, a parameter that has not been considered so far, is dominant over that of the tip radius...
October 16, 2017: Optics Express
Gustavo Haquin, Zohar Yungrais, Danielle Ilzycer, Hovav Zafrir, Noam Weisbrod
The dependency of radon emanation on soil texture was investigated using the closed chamber method. Ground phosphate rock with a large specific surface area was analyzed, and the presence of inner pores, as well as a high degree of roughness and heterogeneity in the phosphate particles, was found. The average radon emanation of the dry phosphate was 0.145 ± 0.016. The emanation coefficient was highest (0.169 ± 0.019) for the smallest particles (<25 μm), decreasing to a constant value (0.091 ± 0...
October 14, 2017: Journal of Environmental Radioactivity
Hongyuan Zhou, Saji George, Caixia Li, Subramaniam Gurusamy, Xiulan Sun, Zhiyuan Gong, He Qian
While, Aflatoxin B1 (AFB1), deoxynivalenol (DON) and zearalenone (ZEN) are the most prevalent mycotoxins co-existing in grain products and animal feeds, little is known about their combinatorial toxicities on aquatic life-forms. We studied the individual and combined effects of these mycotoxins in a fish cell line (BF-2) and zebrafish larvae (wild-type and transgenic). The types of interactions in mycotoxins combinations on cell viability were determined by using Chou-Talalay model. Induction of oxidative stress pathway in mycotoxins-exposed BF-2 cells was assessed using high content screening (HCS)...
October 3, 2017: Aquatic Toxicology
Kensuke Kusumi, Ayana Hashimura, Yoshiko Yamamoto, Juntaro Negi, Koh Iba
Rice production depends on water availability and carbon fixation by photosynthesis. Therefore, optimal control of stomata, which regulate leaf transpiration and CO2 absorption, is important for high productivity. SLAC1 is an S-type anion channel protein that controls stomatal closure in response to elevated CO2. Rice slac1 mutants showed significantly increased stomatal conductance (gs) and enhanced CO2 assimilation. To discern the contribution of stomatal regulation to rice growth, we compared gs among wild-type (WT) and two mutants, slac1 and the dominant-positive mutant SLAC1-F461A, which expresses a point mutation causing an amino acid substitution (F461A) in SLAC1, at different growth stages...
October 5, 2017: Plant & Cell Physiology
Marialaura Bonaccio, Augusto Di Castelnuovo, George Pounis, Simona Costanzo, Mariarosaria Persichillo, Chiara Cerletti, Maria Benedetta Donati, Giovanni de Gaetano, Licia Iacoviello
Background: It is uncertain whether the cardiovascular benefits associated with Mediterranean diet (MD) may differ across socioeconomic groups. Methods: Prospective analysis on 18991 men and women aged ≥35 years from the general population of the Moli-sani cohort (Italy). Adherence to MD was appraised by the Mediterranean diet score (MDS). Household income (euros/year) and educational level were used as indicators of socioeconomic status. Hazard ratios (HR) were calculated by multivariable Cox proportional hazard models...
August 1, 2017: International Journal of Epidemiology
Angela Bechthold, Heiner Boeing, Carolina Schwedhelm, Georg Hoffmann, Sven Knüppel, Khalid Iqbal, Stefaan De Henauw, Nathalie Michels, Brecht Devleesschauwer, Sabrina Schlesinger, Lukas Schwingshackl
BACKGROUND: Despite growing evidence for food-based dietary patterns' potential to reduce cardiovascular disease risk, knowledge about the amounts of food associated with the greatest change in risk of specific cardiovascular outcomes and about the quality of meta-evidence is limited.Therefore, the aim of this meta-analysis was to synthesize the knowledge about the relation between intake of 12 major food groups (whole grains, refined grains, vegetables, fruit, nuts, legumes, eggs, dairy, fish, red meat, processed meat, and sugar-sweetened beverages [SSB]) and the risk of coronary heart disease (CHD), stroke and heart failure (HF)...
October 17, 2017: Critical Reviews in Food Science and Nutrition
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