Feeding ecological knowledge: the underutilised power of faecal DNA approaches for carnivore diet analysis

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Effect of heterochiral inversions on the structure of a β-hairpin peptide

We study computationally a family of β-hairpin peptides with systematically introduced chiral inversions, in explicit water, and we investigate the extent to which the backbone structure is able to fold in the presence of heterochiral perturbations. In contrast to the recently investigated case of a helical peptide, we do not find a monotonic change in secondary structure content as a function of the number of L- to D-inversions. The effects of L- to D-inversions are instead found to be highly position-specific. Additionally, in contrast to the helical peptide, some inversions increase the stability of the folded peptide: in such cases, we compute an increase in β-sheet content in the aqueous solution equilibrium ensemble. However, the tertiary structures of the stable (folded) configurations for peptides for which inversions cause an increase in β-sheet content show differences from one another, as well as from the native fold of the nonchirally perturbed β-hairpin. Our results suggest that although some chiral perturbations can increase folding stability, chirally perturbed proteins may still underperform functionally, given the relationship between structure and function.     

Electrostatic interactions determine entrance/release order of substrates in the catalytic cycle of adenylate kinase

Adenylate kinase is a monomeric phosphotransferase with important biological function in regulating concentration of adenosine triphosphate (ATP) in cells, by transferring the terminal phosphate group from ATP to adenosine monophosphate (AMP) and forming two adenosine diphosphate (ADP) molecules. During this reaction, the kinase may undergo a large conformational transition, forming different states with its substrates. Although many structures of the protein are available, atomic details of the whole process remain unclear. In this article, we use both conventional molecular dynamics (MD) simulation and an enhanced sampling technique called parallel cascade selection MD simulation to explore different conformational states of the Escherichia coli adenylate kinase. Based on the simulation results, we propose a possible entrance/release order of substrates during the catalytic cycle. The substrate-free protein prefers an open conformation, but changes to a closed state once ATP·Mg enters into its binding pocket first and then AMP does. After the reaction of ATP transferring the terminal phosphate group to AMP, ADP·Mg and ADP are released sequentially, and finally the whole catalyze cycle is completed. Detailed contact and distance analysis reveals that the entrance/release order of substrates may be largely controlled by electrostatic interactions between the protein and the substrates.     

Low genetic diversity in the vulnerable Goitred Gazelle,Gazella subgutturosa (Cetartiodactyla: Bovidae), in Iran: potential genetic consequence of recent population declines

The Goitered Gazelle, Gazella subgutturosa, is the most widespread gazelle species in the Middle East and central Asia inhabiting desert and semi-desert habitats. Today it is threatened and its geographic range and population size have experienced significant decline in the last decades. In Iran, the remnant populations are confined to fragmented habitats. We aimed to characterise genetic diversity and phylogenetic status of the populations of Goitered Gazelle in Central Iran and to evaluate the potential effect of a historic population bottleneck on the genetic variation of today’s population. We used noninvasive sampling to uncover structure and level of genetic variation in a fragment of the cytochrome-b gene from 170 samples. Genealogical analyses were performed using HKY+I model and phylogenetic trees reconstructed using Bayesian inference and maximum likelihood. We found extremely low levels of genetic variation, with altogether only five haplotypes in samples from different populations. Overall haplotype diversity was 0.081 and nucleotide diversity 0.0003. The mean observed mismatch between any two sequences was 0.093 with the largest peak for small numbers. The mismatch distribution fit the model of population expansion and suggested that gazelles had experienced a sudden expansion. An unrooted median-joining network analysis of mtDNA haplotypes showed a star-like structure which few mutations steps separating the haplotypes from other regions. Our findings strengthen the urgency of preserving the species’ genetic diversity to prevent local extinction.     

Invertebrate Sampling in the Substratum of an Experimental Recirculating Stream

In order to determine the efficacy of sampling benthic invertebrates to a depth of 100 mm as compared with 200 mm, the gravel substratum of an experimental recirculating stream was sampled to both depths. Except for 6 taxa which were significantly more numerous in the shallower samplers, there was no significant difference between the densities determined from the two depths.     

碧桃朝鲜球坚蚧的出蛰若虫空间格局及应用

采用多种聚集度指标、Iwao法和Taylor幂函数法分析朝鲜球坚蚧出蛰若虫在碧桃上的空间格局。结果表明,出蛰若虫在碧桃上呈聚集分布,分布以个体群形式存在。碧桃不同段位上的聚集度指标和Iwao法均表明其为聚集分布,而Taylor幂函数法测定为上、中段均匀分布,下段聚集分布,综合分析其成因是各样地受害程度及垂直方向虫口密度差异显著所致。聚集均数λ值的测定结果表明,该虫的聚集原因主要由出蛰若虫自身的生物学习性和环境因素所引起。此外,利用空间格局参数确定了理论抽样数和序贯抽样模型。     

广西热带稀有濒危植物迁地保护地域探讨

对广西热带稀有濒危植物在广西及邻近省份植物园的引种保育进行对比研究。结果表明:大部分树种在热带和南亚热带可以正常生长,通过适当的保护措施,部分树种在中亚热带的桂林可以保存。低温和霜冻是广西热带稀有濒危树种能否成功保存的主要限制因素,因此,在引种保存过程中要注意防寒和树种的选择,以提高迁地保护的有效性。     

The Impact of Seeding Method on Diversity and Plant Distribution in Two Restored Grasslands

Previous studies have compared grassland restoration techniques based on resulting species richness and composition. However, none have determined if different techniques generate different plant distributions in space, which may further impact restoration success. This study tests if there are quadrat‐scale (1 m²) differences between paired drilled and broadcast plantings in diversity, composition, and plant distributions. Higher competition intensity in and more contiguous spaces between rows in drill‐seeded restorations were hypothesized to result in larger patches of native grasses and exotic species. Two paired drill‐ and broadcast‐seeded plantings were sampled in June 2007 in Iowa, U.S.A. Within 10 quadrats in each planting, we measured species abundance with point intercept sampling and plant distributions by dividing the quadrat into 64 cells and recording the most abundant species in each cell. Drilled and broadcast plantings at both sites had similar Simpson’s diversity and evenness. However, the effect of planting type on species richness, composition, and plant distribution was site dependent. Native warm‐season grasses in one site, and exotic species in the second, occupied more space and were distributed in larger patches in drilled plantings. Furthermore, drilled canopies consistently captured more light than broadcast canopies. This suggests that initial differences in seed placement can affect resulting plant distributions, resource use, and potentially long‐term species turnover. Mechanisms structuring vegetation in these communities need to be further investigated to determine if this approach can provide more information on long‐term diversity maintenance in restorations than traditional measures.     

Effects of sampling protocol on the shapes of species richness curves

Aim Scheiner (Journal of Biogeography, 2009, 36 , 2005–2008) criticized several issues regarding the typology and analysis of species richness curves that were brought forward by Dengler (Journal of Biogeography, 2009, 36 , 728–744). In order to test these two sets of views in greater detail, we used a simulation model of ecological communities to demonstrate the effects of different sampling schemes on the shapes of species richness curves and their extrapolation capability. Methods We simulated five random communities with 100 species on a 64 × 64 grid using random fields. Then we sampled species–area relationships (SARs, contiguous plots) as well as species–sampling relationships (SSRs, non‐contiguous plots) from these communities, both for the full extent and the central quarter of the grid. Finally, we fitted different functions (power, quadratic power, logarithmic, Michaelis–Menten, Lomolino) to the obtained data and assessed their goodness‐of‐fit (Akaike weights) and their extrapolation capability (deviation of the predicted value from the true value). Results We found that power functions gave the best fit for SARs, while for SSRs saturation functions performed better. Curves constructed from data of 32² grid cells gave reasonable extrapolations for 64² grid cells for SARs, irrespective of whether samples were gathered from the full extent or the centre only. By contrast, SSRs worked well for extrapolation only in the latter case. Main conclusions SARs and SSRs have fundamentally different curve shapes. Both sampling strategies can be used for extrapolation of species richness to a target area, but only SARs allow for extrapolation to a larger area than that sampled. These results confirm a fundamental difference between SARs and area‐based SSRs and thus support their typological differentiation.     

Technological properties of Oenococcus oeni strains isolated from typical southern Italian wines

Aims: To isolate indigenous Oenococcus oeni strains suitable as starters for malolactic fermentation (MLF), using a reliable polyphasic approach. Methods and Results: Oenococcus oeni strains were isolated from Nero di Troia wines undergoing spontaneous MLF. Samples were taken at the end of alcoholic fermentation and during MLF. Wine samples were diluted in a sterile physiological solution and plated on MRS and on modified FT80. Identification of O. oeni strains was performed by a polymerase chain reaction (PCR) experiment using strain‐specific primers. Strains were further grouped using a multiplex RAPD‐PCR analysis. Then, six strains were inoculated in two wine‐like media with two different ethanol concentrations (11 and 13% vol/vol) with a view to evaluate their capacity to grow and to perform MLF. In addition, a quantitative PCR (qRT‐PCR) approach was adapted to monitor the physiological state of the strains selected. Conclusion: A positive correlation between the malolactic activity performance and the ability to develop and tolerate stress conditions was observed for two selected O. oeni strains. Significance and Impact of the Study: The results reported are useful for the selection of indigenous MLF starter cultures with desired oenological traits from typical regional wines. It should be the base for the improvement in organoleptic quality of typical red wine.