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1.
Breeding rice for a changing climate by improving adaptations to water saving technologies.
Heredia, MC, Kant, J, Prodhan, MA, Dixit, S, Wissuwa, M
TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik. 2022;(1):17-33
Abstract
Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.
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2.
The role of water coordination in the pH-dependent gating of hAQP10.
Truelsen, SF, Missel, JW, Gotfryd, K, Pedersen, PA, Gourdon, P, Lindorff-Larsen, K, Hélix-Nielsen, C
Biochimica et biophysica acta. Biomembranes. 2022;(1):183809
Abstract
Human aquaporin 10 (hAQP10) is an aquaglyceroporin that assists in maintaining glycerol flux in adipocytes during lipolysis at low pH. Hence, a molecular understanding of the pH-sensitive glycerol conductance may open up for drug development in obesity and metabolically related disorders. Control of hAQP10-mediated glycerol flux has been linked to the cytoplasmic end of the channel, where a unique loop is regulated by the protonation status of histidine 80 (H80). Here, we performed unbiased molecular dynamics simulations of three protonation states of H80 to unravel channel gating. Strikingly, at neutral pH, we identified a water coordination pattern with an inverted orientation of the water molecules in vicinity of the loop. Protonation of H80 results in a more hydrophobic loop conformation, causing loss of water coordination and leaving the pore often dehydrated. Our results indicate that the loss of such water interaction network may be integral for the destabilization of the loop in the closed configuration at low pH. Additionally, a residue unique to hAQP10 (F85) reveals structural importance by flipping into the channel in correlation with loop movements, indicating a loop-stabilizing role in the closed configuration. Taken together, our simulations suggest a unique gating mechanism combining complex interaction networks between water molecules and protein residues at the loop interface. Considering the role of hAQP10 in adipocytes, the detailed molecular insights of pH-regulation presented here will help to understand glycerol pathways in these cells and may assist in drug discovery for better management of human adiposity and obesity.
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3.
Dynamics and energetics of water transport through aquaporin mutants causing nephrogenic diabetes insipidus (NDI): A molecular dynamics study.
Hadidi, H, Kamali, R, Binesh, A
Journal of biomolecular structure & dynamics. 2022;(3):1273-1284
Abstract
Human aquaporin-2 (AQP2) is the principal water channel in the human kidney. Any alteration of its physiological functioning may lead to the water imbalance and consequently diseases in humans, especially nephrogenic diabetes insipidus (NDI). Although many of the mutations associated with NDI are experimentally discovered and examined, a molecular level characterization of the structure and transport mechanism is still missing. In this paper, the gating effects of selectivity filter (SF) as wide/narrow states on the mechanism and dynamics of water permeation within the wild-type AQP2 and two NDI causing mutants as AQP2-V168M and AQP2-G64R are studied for the first time. The analysis of the 200 ns trajectory shows that the SF region in AQP2 is not only a selectivity filter, as previously reported but also it performs as a gating site depending on the side-chain conformation of His172. The assignment of the wide/narrow states of SF is supported by computing the free energy and permeability through the AQP2. Moreover, by exploring the effects of V168M and G64R mutants on the AQP2 structure during 200 ns trajectories, remarkable increases of energy barriers are observed in the middle and cytoplasmic side of the pore, respectively. Interestingly, it is found that due to the variable conformations of the SF region as wide/narrow, the effect of the NDI causing mutants on the average water permeability can be revealed with notably better accuracy by finding the wide states in the wild-type and mutated types of AQP2 and comparing the osmotic permeabilities for this state.Communicated by Ramaswamy H. Sarma.
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4.
A microscopic study on scattering in tissue section of Alternanthera philoxeroides under polarized light.
Roy, S, Bhattacharya, B, Bal, B, Ghosh, K
Journal of biosciences. 2021
Abstract
Like any other biological tissue, plant tissue also exhibits optical properties like refraction, transmission, absorption, coloration, scattering and so on. Several studies have been conducted using different parts of plants such as leaves, seedlings, roots, stems and so on, and their optical properties have been analyzed to study plant physiology, influence of environmental cues on plant metabolism, light propagation through plant parts and the like. Thus, it is essential to study in detail the optical properties of several plant parts to determine their structural relationship. In this backdrop, an experimental study was conducted to observe and analyze the optical properties of node and inter-nodal tissue cross-sections of the plant Alternanthera philoxeroides under a polarizing microscope constructed and standardized in the laboratory. The observed optical properties of the microscopic tissue sections have been then studied to determine a significant structural relationship between nodal and inter-nodal tissue arrangement patterns as a whole. Tissue sections that have undergone a sort of biological perturbation like loss of water (dried in air for 15 min) have also been studied to study the change in the pattern of tissue optical property when compared with that of normal plant-tissue cross-sections under a polarizing microscope. This type of biological perturbation was chosen for the study because water plays an important role in maintenance of the normal physiological processes in plants and most other forms of life.
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5.
Advances in deep eutectic solvents and water: applications in metal- and biocatalyzed processes, in the synthesis of APIs, and other biologically active compounds.
Cicco, L, Dilauro, G, Perna, FM, Vitale, P, Capriati, V
Organic & biomolecular chemistry. 2021;(12):2558-2577
Abstract
Owing to a growing awareness towards environmental impact, the search for "greener", safer, and cost-effective solvents able to replace petroleum-derived solvents has never been greater today. In this context, the use of environmentally responsible solvents like water and the so-called deep eutectic solvents (DESs), constructed from bio-based compounds, has recently experienced important growth in several fields of sciences. This short review highlights the key features of the chemistry of water and (hydrated) DESs when applied to metal- and biocatalyzed transformations as well as to the synthesis of active pharmaceutical ingredients (APIs) and other biologically relevant compounds by providing, through discussion of all relevant literature over the past five years, a comparison of the outcomes of the reactions when carried out in one or the other solvent.
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6.
Proton Hopping in Living Systems.
Kier, LB
Current computer-aided drug design. 2021;(3):333-336
Abstract
This review focuses on the two-century-old concept of proton hopping. Introduced in 1806 by Grotthuss, it has evolved into an explanation of great diversity in describing many functions in living systems. It is a process involving water, which expands on the belief that life exists only in the presence of water. This review describes the mechanism of the process as it carries information through the water. A focus is initially made on the process of water in the nerve systems. The nature of the process in these systems is described as the passage of proton hopping in living systems. In drug-receptor encounters, proton hopping is initiated, carrying specific information from these specialized encounters. The review continues with an explanation of sleep, arising from an alteration in proton hopping. A similar phenomenon of the effect of general anesthetic agents is described, as they interfere with by proton hopping. Finally, memory functions are addressed in the realm of events carried by proton hopping.
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7.
Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water.
Roeters, SJ, Golbek, TW, Bregnhøj, M, Drace, T, Alamdari, S, Roseboom, W, Kramer, G, Šantl-Temkiv, T, Finster, K, Pfaendtner, J, et al
Nature communications. 2021;(1):1183
Abstract
Ice-nucleation active (INA) bacteria can promote the growth of ice more effectively than any other known material. Using specialized ice-nucleating proteins (INPs), they obtain nutrients from plants by inducing frost damage and, when airborne in the atmosphere, they drive ice nucleation within clouds, which may affect global precipitation patterns. Despite their evident environmental importance, the molecular mechanisms behind INP-induced freezing have remained largely elusive. We investigate the structural basis for the interactions between water and the ice-nucleating protein InaZ from the INA bacterium Pseudomonas syringae. Using vibrational sum-frequency generation (SFG) and two-dimensional infrared spectroscopy, we demonstrate that the ice-active repeats of InaZ adopt a β-helical structure in solution and at water surfaces. In this configuration, interaction between INPs and water molecules imposes structural ordering on the adjacent water network. The observed order of water increases as the interface is cooled to temperatures close to the melting point of water. Experimental SFG data combined with molecular-dynamics simulations and spectral calculations show that InaZ reorients at lower temperatures. This reorientation can enhance water interactions, and thereby the effectiveness of ice nucleation.
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8.
Metabolic engineering: Towards water deficiency adapted crop plants.
Yoshida, T, Yamaguchi-Shinozaki, K
Journal of plant physiology. 2021;:153375
Abstract
Water deficiency caused by drought is one of the severe environmental conditions limiting plant growth, development, and yield. In this review article, we will summarize the changes in transcription, metabolism, and phytohormones under drought stress conditions and show the key transcription factors in these processes. We will also highlight the recent attempts to enhance stress tolerance without growth retardation and discuss the perspective on the development of stress adapted crops by engineering transcription factors.
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9.
Sulfurous-arsenical-ferruginous thermal water nasal inhalation and irrigation in children with recurrent upper respiratory tract infections: Clinical outcomes and predictive factors.
Franz, L, Manica, P, Claudatus, J, Frigo, AC, Marioni, G, Staffieri, A
American journal of otolaryngology. 2021;(6):103083
Abstract
PURPOSE Recurrent upper respiratory disorders (RURD) are among the most common problems diagnosed in pediatric otolaryngology practice. Although several preliminary studies have demonstrated beneficial effects of thermal water inhalations for RURD, inhalation of thermal water has not been included among validated management protocols. The effects of sulfurous-arsenical-ferruginous thermal water nasal irrigations have been confirmed also in prospective, randomized studies. The main aim of this explorative, retrospective, observational study has been to compare the clinical outcome in pediatric patients with RURD treated with sulfurous-arsenical-ferruginous thermal water inhalation versus combined inhalation and nasal irrigation. METHODS Two hundred and fifty-three pediatric patients with RURD were considered; 231 underwent thermal water inhalations (inhalation of hot humid air and aerosol) only, while 22 underwent nasal irrigations combined with inhalations. Subjective overall efficacy perception and treatment tolerability were scored as categorical variables (from 0 = no efficacy/worst tolerability to 3 = maximal efficacy/best tolerability). RESULTS Nasal obstruction, sneezing, serous, mucous, and purulent rhinorrhea, cough, and snoring improved respectively in 80.2%, 72.9%, 79.0%, 93.8%, 92.3%, 64.8%, and 60.4% of patients referring these symptoms at presentation, respectively. No statistically significant differences between inhalations alone and combined inhalations and irrigations emerged. The median overall efficacy perception score was 2 while the median treatment tolerability score was 3. CONCLUSIONS This investigation found that sulfurous-arsenical-ferruginous water treatment was a well-tolerated therapeutic option for selected pediatric patients with RURD. These promising preliminary results should be confirmed in prospective, randomized, double-blind settings, also using minimally invasive but objective and quantitative evaluation methods.
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10.
Application of Monolayer Graphene and Its Derivative in Cryo-EM Sample Preparation.
Wu, K, Wu, D, Zhu, L, Wu, Y
International journal of molecular sciences. 2021;(16)
Abstract
Cryo-electron microscopy (Cryo-EM) has become a routine technology for resolving the structure of biological macromolecules due to the resolution revolution in recent years. The specimens are typically prepared in a very thin layer of vitrified ice suspending in the holes of the perforated amorphous carbon film. However, the samples prepared by directly applying to the conventional support membranes may suffer from partial or complete denaturation caused by sticking to the air-water interface (AWI). With the application in materials, graphene has also been used recently to improve frozen sample preparation instead of a suspended conventional amorphous thin carbon. It has been proven that graphene or graphene oxide and various chemical modifications on its surface can effectively prevent particles from adsorbing to the AWI, which improves the dispersion, adsorbed number, and orientation preference of frozen particles in the ice layer. Their excellent properties and thinner thickness can significantly reduce the background noise, allowing high-resolution three-dimensional reconstructions using a minimum data set.