荒漠河岸胡杨林生态系统能量分配及蒸散发

生态输水工程使得黑河下游地区荒漠河岸林的面积得到了恢复,为进一步巩固生态恢复的成果,非常有必要深入研究胡杨林生态系统的水热交换过程及其对环境因子和人类活动的响应机理。基于涡度相关技术,对2013-2016年荒漠河岸胡杨林生态系统的水热交换过程进行了研究,得出的主要结论如下：（1）生长季生态系统的能量消耗以潜热通量为主,波文比为0.21;非生长季则以感热通量为主,波文比为3.61;春季和秋季的灌水过程,使得胡杨生长前期和后期的潜热通量值较高,直接影响着胡杨林生态系统的能量分配。（2）灌水的时间改变了潜热通量和蒸散发的季节变化过程,而灌水的量决定着春季和秋季潜热通量和蒸散量的年际差异。（3）2014-2016年,生态系统的年蒸散量和生长季蒸散量平均分别为1092 mm和932 mm。荒漠河岸胡杨林生态系统的蒸散量主要受系统水分状况（灌水量）及植物生长状况的影响。     

Cold and hungry: combined effects of low temperature and resource scarcity on an edge-of-range temperate primate,the golden snub-nose monkey

Both biotic and abiotic factors play important roles in influencing ecological distributions and niche limits. Where biotic and abiotic stressors co-occur in space and time, homeostatic systems face a scenario in which stressors can compound to impose a challenge that is greater than the sum of the separate factors. We studied the homeostatic strategies of the golden snub-nosed monkey Rhinopithecus roxellana, a species living in temperate deciduous forests at the edge of the global distribution range for folivorous primates, to cope with the co-occurrence of cold temperatures and resource scarcity during winter. We discovered that in winter the monkeys experience a dietary energy deficit of 101 kJ mbm⁻¹ d⁻¹ compared with calculated needs, despite increased feeding. This is partly offset by behavioral changes (reduced locomotion and increased resting) and reducing skin temperature by an average of 3.2°C through a cutaneous vasoconstriction to decrease heat loss. However, their major strategy is ingesting surplus energy and accumulating fat reserves when food was not limiting during summer and autumn. Their 14% of body mass lost over the winter represented an energy yield of 102 kJ mbm⁻¹ d⁻¹, which closely matched the calculated winter energy deficit of 101 kJ mbm⁻¹ d⁻¹. However, the latter value assumes that all the 75.41 kJ mbm⁻¹ d⁻¹ of protein ingested in winter was available for energy metabolism. This is almost certainly an over-estimate, suggesting that the study population was in negative energy balance over the study period. Our study therefore suggests that despite its suit of integrated homeostatic responses, the confluence of low temperatures and resource limitation during winter places this edge-of-range primate close the threshold of what is energetically viable. It also provides a framework for quantitative models predicting the vulnerability of temperate primates to global change.     

Conformational diversity of the quercetin molecule: a quantum-chemical view

Abstract

This paper focuses on the comprehensive conformational analysis of the quercetin molecule with a broad range of the therapeutic and biological actions. All possible conformers of these molecule, corresponding to the local minima on the potential energy hypersurface, have been obtained by the sequential rotation of its five hydroxyl groups and also by the rotation of its (A?+?C) and B rings relatively each other. Altogether, it was established 48 stable conformers, among which 24 conformers possess planar structure and 24 conformers – nonplanar structure. Their structural, symmetrical, energetical and polar characteristics have been investigated in details. Quantum-mechanical calculations indicate that conformers of the quercetin molecule are polar structures with a dipole moment, which varies within the range from 0.35 to 9.87 Debay for different conformers. Relative Gibbs free energies of these conformers are located within the range from 0.0 to 25.3?kcal·mol^?1 in vacuum under normal conditions. Impact of the continuum with ε?=?4 leads to the decreasing of the Gibbs free energies (–0.19–18.15?kcal·mol^?1) and increasing of the dipole moment (0.57–12.48?D). It was shown that conformers of the quercetin molecule differ from each other by the intramolecular specific contacts (two or three), stabilizing all possible conformers of the molecule – H-bonds (both classical ОН…О and so-called unusual С′Н…О and ОН…С′) and attractive van-der-Waals contacts О…О. Obtained conformational analysis for the quercetin molecule enables to provide deeper understanding of the ‘structure-function’ relationship and also to suggest its mechanisms of the therapeutic and biological actions.

Communicated by Ramaswamy H. Sarma     

The investigation of the G-quadruplex aptamer selectivity to Pb2+ ion: a joint molecular dynamics simulation and density functional theory study

Abstract

The aptamers with the ability to form a G-quadruplex structure can be stable in the presence of some ions. Hence, study of the interactions between such aptamers and ions can be beneficial to determine the highest selective aptamer toward an ion. In this article, molecular dynamics (MD) simulations and quantum mechanics (QM) calculations have been applied to investigate the selectivity of the T30695 aptamer toward Pb²⁺ in comparison with some ions. The Free Energy Landscape (FEL) analysis indicates that Pb²⁺ has remained inside the aptamer during the MD simulation, while the other ions have left it. The Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) binding energies prove that the conformational stability of the aptamer is the highest in the presence of Pb²⁺. According to the compaction parameters, the greatest compressed ion-aptamer complex, and hence, the highest ion-aptamer interaction have been induced in the presence of Pb²⁺. The contact maps clarify the closer contacts between the nucleotides of the aptamer in the presence of Pb²⁺. The density functional theory (DFT) results show that Pb²⁺ forms the most stable complex with the aptamer, which is consistent with the MD results. The QM calculations reveal that the N-H bonds and the O…H distances are the longest and the shortest, respectively, in the presence of Pb²⁺. The obtained results verify that the strongest hydrogen bonds (HBs), and hence, the most compressed aptamer structure are induced by Pb²⁺. Besides, atoms in molecules (AIM) and natural bond orbital (NBO) analyses confirm the results.

Communicated by Ramaswamy H. Sarma     

Binding mechanism of spinosine and venenatine molecules with p300 HAT enzyme: Molecular screening,molecular dynamics and free-energy analysis

The chromatin modification is regulated by the histone acetyltransferase (HAT) and histone deacetyltransferase (HDAC) enzymes; abnormal function of these enzymes leads to several malignant diseases. The inhibition of these enzymes using natural ligand molecules is an emerging technique to cure these diseases. The in vitro analysis of natural molecules, venenatine, spinosine, palmatine and taxodione are giving the best inhibition rate against p300 HAT enzyme. However, the detailed understanding of binding and the stability of these molecules with p300 HAT is not yet known. The aim of the present study is focused to determine the binding strength of the molecules from molecular dynamics simulation analysis. The docking analysis confirms that, the venenatine (−6.97 kcal/mol - conformer 8), spinosine (−6.52 kcal/mol conformer −10), palmatine (−5.72 kcal/mol conformer-3) and taxodione (−4.99 kcal/mol conformer-4) molecules form strong hydrogen bonding interactions with the key amino acid residues (Arg1410, Thr1411 and Trp1466) present in the active site of p300. In the molecular dynamics (MD) simulation, the spinosine retain these key interactions with the active site amino acid residues (Arg1410, Thr1411, and Trp1466) than venenatine and are stable throughout the simulation. The RMSD value of spinosine (0.5 to 1.3 Å) and venenatine (0.3 to 1.3 Å) are almost equal during the MD simulation. However, during the MD simulation, the intermolecular interaction between venenatine and the active site amino acid residues (Arg1410, Thr1411, and Trp1466) decreased on comparing with the spinosine-p300 interaction. The binding free energy of the spinosine (−15.30 kcal/mol) is relatively higher than the venenatine (−11.8 kcal/mol); this increment is attributed to the strong hydrogen bonding interactions of spinosine molecule with the active site amino acid residues of p300.     

Protonation state of the selectivity filter of bacterial voltage-gated sodium channels is modulated by ions

The selectivity filter (SF) of bacterial voltage-gated sodium channels consists of four glutamate residues arranged in a C₄ symmetry. The protonation state population of this tetrad is unclear. To address this question, we simulate the pore domain of bacterial voltage-gated sodium channel of Magnetococcus sp. (Na_vMs) through constant pH methodology in explicit solvent and free energy perturbation calculations. We find that at physiological pH the fully deprotonated as well as singly and doubly protonated states of the SF appear feasible, and that the calculated pKa decreases with each additional bound ion, suggesting that a decrease in the number of ions in the pore can lead to protonation of the SF. Previous molecular dynamics simulations have suggested that protonation can lead to a decrease in the conductance, but no pKa calculations were performed. We confirm a decreased ionic population of the pore with protonation, and also observe structural symmetry breaking triggered by protonation; the SF of the deprotonated channel is closest to the C₄ symmetry observed in crystal structures of the open state, while the SF of protonated states display greater levels of asymmetry which could lead to transition to the inactivated state which possesses a C₂ symmetry in the crystal structure. We speculate that the decrease in the number of ions near the mouth of the channel, due to either random fluctuations or ion depletion due to conduction, could be a self-regulatory mechanism resulting in a nonconducting state that functionally resembles inactivated states.     

Migratory Disturbance Thresholds with Mule Deer and Energy Development

Fine-scale movement data has transformed our knowledge of ungulate migration ecology and now provides accurate, spatially explicit maps of migratory routes that can inform planning and management at local, state, and federal levels. Among the most challenging land use planning issues has been developing energy resources on public lands that overlap with important ungulate habitat, including the migratory routes of mule deer (Odocoileus hemionus). We generally know that less development is better for minimizing negative effects and maintaining habitat function, but we lack information on the amount of disturbance that animals can tolerate before reducing use of or abandoning migratory habitat. We used global positioning system data from 56 deer across 15 years to evaluate how surface disturbance from natural gas well pads and access roads in western Wyoming, USA, affected habitat selection of mule deer during migration and whether any disturbance threshold(s) existed beyond which use of migratory habitat declined. We used resource and step selection functions to examine disturbance thresholds at 3 different spatial scales. Overall, migratory use by mule deer declined as surface disturbance increased. Based on the weight of evidence from our 3 independent but complementary metrics, declines in migratory use related to surface disturbance were non-linear, where migratory use sharply declined when surface disturbance from energy development exceeded 3%. Disturbance thresholds may vary across regions, species, or migratory habitats (e.g., stopover sites). Such information can help with management and land use decisions related to mineral leasing and energy development that overlap with the migratory routes of ungulates. © 2020 The Wildlife Society.     

Anthropogenic and Natural Disturbance Differentially Affect Sagebrush Bird Habitat Use

North American sagebrush (Artemisia spp.)-obligate birds are experiencing steep population declines due in part to increased disturbance, mainly human-caused, across their range. At the eastern edge of the sagebrush steppe, this issue may potentially be exacerbated because of natural disturbance by black-tailed prairie dogs (Cynomys ludovicianus). Our goal was to compare local and landscape models of habitat use by greater sage-grouse (Centrocercus urophasianus), Brewer's sparrow (Spizella breweri), and sage thrasher (Oreoscoptes montanus) with models including effects of natural (i.e., prairie dog) and anthropogenic disturbance. We used a combination of field data collection, and state and national datasets for the Thunder Basin National Grassland, eastern Wyoming, USA, to understand the factors that influence lek attendance by sage-grouse and habitat use by 2 passerines in this system. For all 3 species, models including big sagebrush (Artemisia tridentata) cover at local and landscape scales were the most competitive among univariate models, supporting the paradigm that sagebrush is key for these species. Models including anthropogenic disturbance (well density, road density) explained more variation than models of prairie dog disturbance alone for 2 of the 3 species, but long-term disturbance by prairie dogs did reduce abundance of Brewer's sparrows. Although long-term prairie dog disturbance has the potential to reduce sagebrush cover for sagebrush-obligate birds, such events are likely rare because outbreaks of plague (Yersina pestis) and lethal control on borders with private land reduce prairie dog disturbance. Conversely, anthropogenic disturbance is slated to increase in this system, suggesting potentially accelerated declines for sagebrush birds into the future. © 2020 The Wildlife Society.     

Use of Upland and Riparian Areas by Wintering Bald Eagles and Implications for Wind Energy

Weather can shape movements of animals and alter their exposure to anthropogenic threats. Bald eagles (Haliaeetus leucocephalus) are increasingly at risk from collision with turbines used in onshore wind energy generation. In the midwestern United States, development of this energy source typically occurs in upland areas that bald eagles use only intermittently. Our objective was to determine the factors that cause wintering bald eagles to occupy riparian areas and riskier, upland areas. We tracked 20 bald eagles using telemetry in the Upper Midwest (MN, IA, MO, WI, IL, USA) during winter 2014–2015 and 2015–2016 and evaluated habitat use by eagles in response to variation in weather and time of year. Eagles used riparian areas more when wind speed and atmospheric pressure were low. Exclusive use of uplands was more frequent during weather systems with low pressure and high humidity and after long periods of cold weather. There was a non-linear response to time of year (measured by days before migration) in the frequency of exclusive use of uplands or riparian areas. Probability of exclusive use of either landscape was generally constant within 95 days prior to migration. The probability of use of riparian areas, however, was markedly less during dates >100 days before migration. Our results suggest that eagles are most likely to be exposed to wind energy developments located in upland areas during low pressure systems, after long periods of cold weather, and several months before the onset of spring migration. This information helps to better understand the factors influencing bald eagle habitat use in winter and will be useful to managers and developers wishing to establish effective strategies to avoid, minimize, and mitigate take, and to survey for mortalities at wind energy developments. © 2020 The Wildlife Society.     

Metabolomics meets lipidomics: Assessing the small molecule component of metabolism

Metabolomics, including lipidomics, is emerging as a quantitative biology approach for the assessment of energy flow through metabolism and information flow through metabolic signaling; thus, providing novel insights into metabolism and its regulation, in health, healthy ageing and disease. In this forward-looking review we provide an overview on the origins of metabolomics, on its role in this postgenomic era of biochemistry and its application to investigate metabolite role and (bio)activity, from model systems to human population studies. We present the challenges inherent to this analytical science, and approaches and modes of analysis that are used to resolve, characterize and measure the infinite chemical diversity contained in the metabolome (including lipidome) of complex biological matrices. In the current outbreak of metabolic diseases such as cardiometabolic disorders, cancer and neurodegenerative diseases, metabolomics appears to be ideally situated for the investigation of disease pathophysiology from a metabolite perspective.