Solvent Effects are Important in Elucidating Radical-Scavenging Mechanisms of Antioxidants. A Case Study on Genistein

Abstract

In two recent researches on antioxidant mechanisms of flavonoids and isoflavonoids, quantum chemical method was employed to calculate the proton dissociation energies, the bond dissociation energies and the ionization potentials for the phenols and derived radicals to help determine the radical-scavenging mechanisms. As the solvent effect was left out of consideration, the conclusion drawn from the calculation incurred some controversies. In the current study, we re-calculated the parameters for genistein and its anion by employing a B3LYP/6–311+G(d,p)//6–31G(d,p) method with solvent effect. Accordingly, a more reasonable explanation on the experimentally observed behavior of genistein as a radical scavenger was obtained. Therefore, solvent effect should be considered in the investigation of radical-scavenging mechanisms of antioxidants in polar solvents.     

Biodiversity and Nutrition in Rice-Based Ecosystems; the Case of Lao PDR

This paper presents results from a year-long household survey in which the aquatic resource collection and consumption activities of 240 households across Lao PDR were studied to assess the diversity of species used, their role in household food security and the overall importance of ricefield habitats in this respect. Results show that aquatic biodiversity, under threat in rice-based ecosystems, plays a larger role in household consumption than previous estimates. More than 90 % of these resources are collected by households themselves and the greatest quantities from ricefield habitats. This seasonal aquatic environment is therefore the principal habitat from which households acquire aquatic animals, both to eat fresh and to process and store for use during nutritionally vulnerable times of year. The importance of these habitats therefore goes far beyond their use for rice production and this multi-functionality needs to be understood and addressed in agricultural, conservation and food security policy.     

Gravel Bars Can Be Critical for Biodiversity Conservation: A Case Study on Scaly-Sided Merganser in South China

Gravel bars are characteristic components of river landscapes and are increasingly recognized as key sites for many waterbirds, though detailed studies on the ecological function of gravel bars for waterbirds are rare. In this study, we surveyed the endangered Scaly-sided Merganser Mergus squamatus along a 40 km river section of Yuan River, in Central China, for three consecutive winters. We derived the landscape metrics of river gravel bars from geo-rectified fine resolution (0.6 m) aerial image data. We then built habitat suitability models (Generalized Linear Models—GLMs) to study the effects of landscape metrics and human disturbance on Scaly-sided Merganser presence probability. We found that 1) the Scaly-sided Merganser tended to congregate at river segments with more gravel patches; 2) the Scaly-sided Merganser preferred areas with larger and more contiguous gravel patches; and 3) the number of houses along the river bank (a proxy for anthropogenic disturbance) had significantly negative impacts on the occurrence of the Scaly-sided Merganser. Our results suggest that gravel bars are vital to the Scaly-sided Merganser as shelters from disturbance, as well as sites for feeding and roosting. Therefore, maintaining the exposure of gravel bars in regulated rivers during the low water period in winter might be the key for the conservation of the endangered species. These findings have important implications for understanding behavioral evolution and distribution of the species and for delineating between habitats of different quality for conservation and management.     

Analysis of Photosynthetic Activity at the Leaf and Canopy Levels from Reflectance Measurements: A Case Study

The photochemical reflectance index (PRI), based on reflectance signatures at 531 and 570 nm, and associated with xanthophyll pigment inter-conversion and related thylakoid energisation, was evaluated as an indicator of photosynthetic function in a Mediterranean holm oak (Quercus ilex L.) coppice. The chlorophyll fluorescence pulse-amplitude-modulation and the eddy correlation techniques were used to estimate the photosystem 2 photochemical efficiency of leaves and the CO₂ flux over the canopy, respectively. The reflectance and fluorescence techniques yielded identical estimates of the photosynthetic activity in leaves exposed to dark-light-dark cycles or to a variable irradiance in laboratory. However, there was no such correlation between photosynthetic performance and PRI when applied to a sun-exposed canopy in field conditions. Fluorescence profiles inside the canopy and especially a helpful use of multispectral reflectance imaging highlight the limitations of such method.     

A Case Study on Human Upper Limb Modelling for Dynamic Simulation

Modelling consists of developing a representation of the properties of an object or a phenomenon with respect to the goals of its analysis. In this paper, the procedure presented is that followed in the CHARM project for human upper limb modelling with respect to the project constraints on the model implementation and simulation. The objective is to develop a Comprehensive Human Animation Resource Model allowing the simulation of human motion, including the finite element simulation of soft tissue deformation and muscular contraction. Generally, models are presented based on assumptions left for a fortiori validation. The a priori considerations which lead to these assumptions are rarely detailed. Here, the aim is to form a basis for the choices and assumptions which are to be made prior to the validation. The analysis is based on the general approach for the modelling of multi-body deformable systems as well as on previous studies on the human upper limb.     

Risk Assessment of Human Activities on Protected Areas: A Case Study

No study has been done on the impact of anthropogenic risks on protected areas. This may be due to complexity and diversity of risk assessment indices. In this research, using multicriteria decision-making methods, qualitative and complex indices were converted to simple and quantitative indices by which anthropogenic risks affecting the Helleh Protected Area in Iran were analyzed. To this end, a questionnaire was prepared and delivered to Delphi panelists consisting of environmental expertise. In order to prioritize the identified risks, Technique for Order Preference by Similarity to Ideal Solution (TOPSIS), Analytical Hierarchy Process (AHP), and Simple Additive Weighting Technique (SAW) were used as a subset of Multiple Attribute Decision-making methods (MADM). In this study, risk factors were evaluated using three criteria of severity, probability of occurrence, and sensitivity of the recipient environment. In order to reach enough transcendence (consensus on priority of risks), an integrated approach comprising average, Borda, and Copeland methods was used. The obtained results suggested that “dam inundation upstream of the study area” is a top-priority risky factor threatening the wetland. “Stopping water pumps from the wetland” and “use of modern irrigation systems” were recommended as the most effective managerial strategies to control the identified risk.     

Past Climate Change and Plant Evolution in Western North America: A Case Study in Rosaceae

Species in the ivesioid clade of Potentilla (Rosaceae) are endemic to western North America, an area that underwent widespread aridification during the global temperature decrease following the Mid-Miocene Climatic Optimum. Several morphological features interpreted as adaptations to drought are found in the clade, and many species occupy extremely dry habitats. Recent phylogenetic analyses have shown that the sister group of this clade is Potentilla section Rivales, a group with distinct moist habitat preferences. This has led to the hypothesis that the ivesioids (genera Ivesia, Horkelia and Horkeliella) diversified in response to the late Tertiary aridification of western North America. We used phyloclimatic modeling and a fossil-calibrated dated phylogeny of the family Rosaceae to investigate the evolution of the ivesioid clade. We have combined occurrence- and climate data from extant species, and used ancestral state reconstruction to model past climate preferences. These models have been projected into paleo-climatic scenarios in order to identify areas where the ivesioids may have occurred. Our analysis suggests a split between the ivesioids and Potentilla sect. Rivales around Late Oligocene/Early Miocene (∼23 million years ago, Ma), and that the ivesioids then diversified at a time when summer drought started to appear in the region. The clade is inferred to have originated on the western slopes of the Rocky Mountains from where a westward range expansion to the Sierra Nevada and the coast of California took place between ∼12-2 Ma. Our results support the idea that climatic changes in southwestern North America have played an important role in the evolution of the local flora, by means of in situ adaptation followed by diversification.     

Effects of Litter Inputs on N<Subscript>2</Subscript>O Emissions from a Tropical Rainforest in Southwest China

Litter inputs are expected to have a strong impact on soil N₂O efflux. This study aimed to assess the effects of the litter decomposition process and nutrient efflux from litter to soil on soil N₂O efflux in a tropical rainforest. A paired study with a control (L) treatment and a litter-removed (NL) treatment was followed for 2 years, continuously monitoring the effects of these treatments on soil N₂O efflux, fresh litter input, decomposed litter carbon (LCI) and nitrogen (LNI), soil nitrate (NO₃ ^?–N), ammonium (NH₄ ⁺–N), dissolved organic carbon (DOC), and dissolved nitrogen (DN). Soil N₂O flux was 0.48 and 0.32 kg N₂O–N ha^?1 year^?1 for the L and NL treatments, respectively. Removing the litter caused a decrease in the annual soil N₂O emission by 33%. The flux values from the litter layer were higher in the rainy season as compared to the dry season (2.10 ± 0.28 vs. 1.44 ± 0.35 μg N m^?2 h^?1). The N₂O fluxes were significantly correlated with the soil NO₃ ^?–N contents (P < 0.05), indicating that the N₂O emission was derived mainly from denitrification as well as other NO₃ ^? reduction processes. Suitable soil temperature and moisture sustained by rainfall were jointly attributed to the higher soil N₂O fluxes of both treatments in the rainy season. The N₂O fluxes from the L were mainly regulated by LCI, whereas those from the NL were dominated jointly by soil NO₃ ^? content and temperature. The effects of LCI and LNI on the soil N₂O fluxes were the greatest in the 2 months after litter decomposition. Our results show that litter may affect not only the variability in the quantity of N₂O emitted, but also the mechanisms that govern N₂O production. However, further studies are still required to elucidate the impacting mechanisms of litter decomposition on N₂O emission from tropical forests.     

A Systematic Review on the Contributions of Edible Plant and Animal Biodiversity to Human Diets

The sustainable use of natural and agricultural biodiversity in the diet can be instrumental to preserve existing food biodiversity, address malnutrition, and mitigate adverse effects of dietary changes worldwide. This systematic review of literature summarizes the current evidence on the contribution of plant and animal biodiversity to human diets in terms of energy intake, micronutrient intake, and dietary diversification. Peer-reviewed studies were searched in ten databases using pre-defined search terms. Only original studies assessing food biodiversity and dietary intake were included, resulting in a total of 34 studies. 7, 14, and 17 studies reported information in relation to energy intake, micronutrient intake, and dietary diversification, respectively. In general, locally available foods were found to be important sources of energy, micronutrients, and dietary diversification in the diet of particularly rural and forest communities of highly biodiverse ecosystems. The current evidence shows local food biodiversity as important contributor of nutritious diets. Findings are, however, limited to populations living in highly biodiverse areas. Research on the contribution of biodiversity in diets of industrialized and urban settings needs more attention. Instruments are needed that would more appropriately measure the dietary contribution of local biodiversity.     

Conservation Planning for Offsetting the Impacts of Development: A Case Study of Biodiversity and Renewable Energy in the Mojave Desert

Balancing society’s competing needs of development and conservation requires careful consideration of tradeoffs. Renewable energy development and biodiversity conservation are often considered beneficial environmental goals. The direct footprint and disturbance of renewable energy, however, can displace species’ habitat and negatively impact populations and natural communities if sited without ecological consideration. Offsets have emerged as a potentially useful tool to mitigate residual impacts after trying to avoid, minimize, or restore affected sites. Yet the problem of efficiently designing a set of offset sites becomes increasingly complex where many species or many sites are involved. Spatial conservation prioritization tools are designed to handle this problem, but have seen little application to offset siting and analysis. To address this need we designed an offset siting support tool for the Desert Renewable Energy Conservation Plan (DRECP) of California, and present a case study of hypothetical impacts from solar development in the Western Mojave subsection. We compare two offset scenarios designed to mitigate a hypothetical 15,331 ha derived from proposed utility-scale solar energy development (USSED) projects. The first scenario prioritizes offsets based precisely on impacted features, while the second scenario offsets impacts to maximize biodiversity conservation gains in the region. The two methods only agree on 28% of their prioritized sites and differ in meeting species-specific offset goals. Differences between the two scenarios highlight the importance of clearly specifying choices and priorities for offset siting and mitigation in general. Similarly, the effects of background climate and land use change may lessen the durability or effectiveness of offsets if not considered. Our offset siting support tool was designed specifically for the DRECP area, but with minor code modification could work well in other offset analyses, and could provide continuing support for a potentially innovative mitigation solution to environmental impacts.     

Investigating the Use of Fractional Replication and Taguchi Techniques in Cryopreservation: A Case Study Using Orthodox Seeds of a Tropical Rainforest Tree Species

Cryopreservation is increasingly important for conserving endangered species including tropical rain forest germplasm where optimal cryopreservation protocols must be established rapidly sacrificing little germplasm. Currently, full factorial experiments analysed by ANOVA establish optimal conditions. However, these experiments can contain many treatment combinations whilst ANOVA identifies significant effects without guaranteeing to find robust optimal conditions. Taguchi optimization techniques efficiently identify robust conditions through fractional factorial experiments with an appropriate signal to noise ratio (SNR). This paper reports for the first time the use of Taguchi techniques in cryopreservation. An orthodox seed (Cassia siamea Lam.) was used to guarantee sufficient data to compare full and fractionally replicated experiments analysed using both ANOVA and SNR. For sprouting day (smaller is better), identical significant main effects were found for all experimental sizes for ANOVA and SNR. The 1/4 replicate did not allow investigation of interaction terms, but the significant main effects were the same for larger experiments. For shoot to root ratio (nominal is best), a significant main effect was found for all experimental sizes using ANOVA. This was also found using SNR, which identified additional significant main effect and interactions. No significant effects were found for dry weight (larger is better). We show smaller experiments are possible, provided important two level interactions are analysed. Differences determining the optimal treatment combination were found between ANOVA and SNR; with the Taguchi choice provides more robust solutions. Taguchi optimization techniques are recommended when germplasm is scarce and/or the experiment needs to be conducted rapidly.     

四平转山湖水库地区昆虫多样性的初步研究

昆虫个体虽小,但种类繁多,全世界约有140万种生物,而昆虫约占53.57%.昆虫与人类有着极为密切的关系,如害虫对人类健康和国民经济有着重要影响,但绝大多数种类的昆虫对人类是有益或中性的,有的是显花植物的传粉者;有的是害虫的天敌;生活在土壤内的昆虫能促进腐殖质形成与土壤通气,提高土地的肥力;而有些昆虫的产物,如蜂蜜、丝、白蜡等是食品、医药及工业原料;还有许多昆虫用于环境净化和科学研究等多个领域[1].     

Speciation Progress: A Case Study on the Bushcricket Poecilimon veluchianus

Different mechanisms such as selection or genetic drift permitted e.g. by geographical isolation can lead to differentiation of populations and could cause subsequent speciation. The two subspecies of Poecilimon veluchianus, a bushcricket endemic to central Greece, show a parapatric distribution and are partially reproductively isolated. Therefore, P. veluchianus is suitable to investigate an ongoing speciation process. We based our analysis on sequences of the internal transcribed spacer (ITS) and the mitochondrial control region (CR). The population genetic analysis based on the nuclear marker ITS revealed a barrier to gene flow within the range of Poecilimon veluchianus, which corresponds well to the described subspecies. In contrast to the results based on the nuclear ITS marker, the mitochondrial CR marker does not clearly support the separation into two subspecies with restricted gene flow and a clear contact zone. Furthermore, we could identify isolation by distance (IBD) as one important mechanism responsible for the observed genetic structure (based on the ITS marker). The population genetic analysis based on the nuclear marker ITS also suggests the existence of hybrids in the wild. Furthermore, the simultaneous lack of strong prezygotic barriers and the presence of postzygotic mating barriers, observed in previous laboratory experiments, suggest that a secondary contact after an allopatric phase is more likely than parapatric speciation.     

Integrated Human and Ecological Risk Assessment: A Case Study of Organophosphorous Pesticides in the Environment

This study was chosen as an example of integrated risk assessment because organophosphorous esters (OPs) share exposure characteristics for different species, including human beings and because a common mechanism of action can be identified. The “Framework for the integration of health and ecological risk assessment” is being tested against a deterministic integrated environmental health risk assessment for OPs used in a typical farming community. It is argued that the integrated approach helps both the risk manager and the risk assessor in formulating a more holistic approach toward the risk of the use of OP-esters. It avoids conclusions based on incomplete assessments or on separate assessments. The database available can be expanded and results can be expressed in a more coherent manner. In the integrated exposure assessment of OPs, the risk assessments for human beings and the environment share many communalities with regards to sources and emissions, distribution routes and exposure scenarios. The site of action of OPs, acetylcholinesterase, has been established in a vast array of species, including humans. It follows that in the integrated approach the effects assessment for various species will show communalities in reported effects and standard setting approaches. In the risk characterization, a common set of evidence, common criteria, and common interpretations of those criteria are used to determine the cause of human and ecological effects that co-occur or are apparently associated with exposure to OPs. Results of health and ecological risk assessments are presented in a common format that facilitates comparison of results. It avoids acceptable risk conclusions with regard to the environment, which are unacceptable with regard to human risk and vice versa. Risk managers will be prompted to a more balanced judgement and understanding and acceptance of risk reduction measures will be facilitated.     

An Under-appreciated Component of Biodiversity in Plankton Communities: The Role of Protozoa in Lake Michigan (A Case Study)

Recent technological advances have led to the discovery that free-living, planktonic protozoa are ubiquitous in nature and appear to be important components of pelagic food webs (e.g., fluorescent straining, flow cytometry). Despite this, limited information exists tying their seasonality to rate processes that drive succession patterns. The abundance, and seasonal growth and grazing loss of an entire protozoan assemblage were evaluated in Lake Michigan. The protozoan assemblage was species-rich (100 taxa) and abundant throughout the year in Lake Michigan. Nano-sized protozoa (Hnano and Pnano, <20 μm in size) ranged in abundance from 10² to 10³ cells ml⁻¹, while micro-protozoa (Hmicro and Pmico, >20 and <200 μm in size) ranged in abundance from 4 to 17 cells ml⁻¹. The biomass of Hnano and Hmicro by itself represented more than 70–80% of crustacean zooplankton biomass, while Pnano and Pmicro constituted nearly 50% of phytoplankton biomass. Protozoa exhibited growth rates comparable to other components of the plankton in Lake Michigan, and some populations grew at rates similar to maximum rates determined in the laboratory (rates of 1–2 day⁻¹). Overall, it appears that macro-zooplankton predation is a major loss factor counter-balancing growth with only small differences between the two rate processes (<0.1 day⁻¹). Discrepancies between growth and grazing loss in the spring were likely attributed to sedimentation losses for larger species of tintinnids and dinoflagellates (Codonella, Tintinnidium, and Gymnodinium) that can account for their occurrence in the deep chlorophyll layer. In the summer, carnivory among similar sized species (Chromulina and small ciliates) may be additional loss factors impinging on the protozoan assemblage.     

Buffer Interference with Protein Dynamics: A Case Study on Human Liver Fatty Acid Binding Protein

Selection of suitable buffer types is often a crucial step for generating appropriate protein samples for NMR and x-ray crystallographic studies. Although the possible interaction between MES buffer (2-(N-morpholino)ethanesulfonic acid) and proteins has been discussed previously, the interaction is usually thought to have no significant effects on the structures of proteins. In this study, we demonstrate the direct, albeit weak, interaction between MES and human liver fatty acid binding protein (hLFABP). Rather than affecting the structure of hLFABP, we found that the dynamics of hLFABP, which were previously proposed to be relevant to its functions, were significantly affected by the binding of hLFABP with MES. Buffer interference with protein dynamics was also demonstrated with Bis-Tris buffer, which is quite different from MES and fatty acids in terms of their molecular structures and properties. This result, to our knowledge, is the first published report on buffer interference with protein dynamics on a microsecond to millisecond timescale and could represent a generic problem in the studies of functionally relevant protein dynamics. Although being a fortuity, our finding of buffer-induced changes in protein dynamics offers a clue to how hLFABP accommodates its ligands.     

Conformational Effects on the Circular Dichroism of Human Carbonic Anhydrase II: A Multilevel Computational Study

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions.     

Effects of Pleistocene climate change on genetic structure and diversity of <Emphasis Type="Italic">Shorea macrophylla</Emphasis> in Kalimantan Rainforest

The island of Borneo is the diversity center of the Dipterocarpaceae, the most important family of tropical rainforest trees in Southeast Asia. However, changes in land use and climate have affected dipterocarp distributions on the island, raising concerns about the vulnerability (inter alia) of the endemic riparian species Shorea macrophylla. Thus, to aid conservation efforts, we have investigated the genetic diversity, structure, and demographic history of S. macrophylla. The species’ genetic diversity and structure in Kalimantan (part of Indonesia, covering 75% of the island) were explored by examining genotypes of 377 individuals representing 13 populations in three regions (Northeast, Central, and West Kalimantan) using 14 newly developed microsatellite loci. Higher genetic diversity was found, at all loci, in samples from Northeast Kalimantan than in samples from the other regions. Moderate genetic differentiation between populations was detected (F_ST 0.093). Bayesian clustering, principal coordinate, and neighbor joining tree analyses of the population structure consistently identified two genetically distinct groups, one in the Northeast and the other in the Central and West regions. The higher diversity of the diverged populations in Northeast Kalimantan indicates that the region may have hosted rainforest refugia during the ice age. Accordingly, analysis using DIY ABC software indicated that the Northeast and Central-West Kalimantan groups diverged 194,000 years ago. We conclude that global climate change during the Pleistocene strongly influenced the genetic diversity and structure of S. macrophylla populations in Kalimantan.