生态系统稳态转换检测研究进展

在气候变化、人类活动等影响下,生态系统结构和功能可能发生大规模的突变,导致生态系统从一个相对稳定的状态进入另一个稳定状态,这种现象称为稳态转换。由于生态系统的复杂性,准确刻画生态系统多稳态并界定其临界点尚存在挑战,提升对生态系统稳态转换的检测和预测能力依旧是生态学领域研究的热点和难题。基于多稳态理论和稳态转换经典概念框架,阐释了稳态转换检测的理论基础;归纳总结出四种稳态转换检测方法的原理和优劣势;鉴于稳态转换的尺度依赖性,梳理了单一生态系统、区域综合生态系统和全球生态系统不同尺度下的稳态转换检测方法、研究思路和应用案例。基于研究进展和问题现状,提出在未来研究中,亟待发展适应复杂系统的综合检测方法;创新稳态转换多尺度分析的技术方法体系;深化生态系统稳态转换驱动机制研究,构建多元耦合机理模型;进而深化稳态转换检测结果链接生态系统管理的实践研究;解析生态系统服务和可持续发展机制。     

具有两个状态脉冲控制的害虫治理模型的阶一周期解的存在性和吸引性

在文献[10]的基础上,基于害虫治理问题,建立具有两个状态脉冲控制的HollingⅡ功能性反应的害虫治理模型,利用所定义的后继函数和分析的方法研究了系统阶一周期解的存在性和吸引性.     

不同预处理对小鼠粪样菌群高通量测序分析结果的影响

应用高通量测序技术比较不同预处理对小鼠粪样菌群结构的影响,以期为后续相关研究提供参考依据。采集昆明小鼠新鲜粪样,分为原始粪样组、生理盐水处理组和PBS处理组,提取粪样DNA,采用Illumina MiSeq平台进行测序对3组样本的16S rRNA V3~V4区基因文库进行生物信息学分析。结果显示,3组样本拥有共同的OTUs 188个,不同预处理对粪样微生物多样性和丰度产生影响,生理盐水处理组、PBS处理组和原始粪样组分别检出14、11、12个门,3组样本共有门11个;分别检出24、21、21个纲,3组样本共有纲20个;分别检出62、55、59个科,3组样本共有科26个;分别检出147、126、137个属,3组样本共有属117个。总体来看,生理盐水处理组微生物多样性和丰度相对最高,原始粪样组次之,PBS处理组最低。粪样经生理盐水处理后,能在一定程度上提高肠道菌群检测的准确性。     

分布时滞竞争模型的周期解

研究了分布时滞竞争模型周期解,利用Gaines与Mawhin的重合度理论,通过构造恰当的Lyapunov函数得到模型正周期解的存在性、唯一性及全局稳定性。     

Influence of non-bonded parameters on the quality of NMR structures: A new force field for NMR structure calculation

The effects of different non-bonded parameters of force fields for NMR structure calculation on the quality of the resulting NMR solution structures were investigated using Interleukin 4 as a model system. NMR structure ensembles were calculated with an ab initio protocol using torsion angle dynamics. The calculations were repeated with five different non-bonded energy functions and parameters. The resulting ensembles were compared with the available X-ray structures, and their quality was assessed with common structure validation programs. In addition, the impact of torsion angle restraints and dihedral energy terms for the sidechains and the backbone was studied. The further improvement of the quality by refinement in explicit solvent was demonstrated. The optimal parameters, including those necessary for water refinement, are available in the new version of the PARALLHDG force field.     

NMR solution structure and dynamics of motilin in isotropic phospholipid bicellar solution

The structure and dynamics of the gastrointestinal peptide hormone motilin, consisting of 22 amino acid residues, have been studied in the presence of isotropic q=0.5 phospholipid bicelles. The NMR solution structure of the peptide in acidic bicelle solution was determined from 203 NOE-derived distance constraints and six backbone torsion angle constraints. Dynamic properties for the ¹³C-¹H vector in Leu10 were determined for motilin specifically labeled with ¹³C at this position by analysis of multiple-field relaxation data. The structure reveals an ordered -helical conformation between Glu9 and Lys20. The N-terminus is also well structured with a turn resembling that of a classical -turn. The ¹³C dynamics clearly show that motilin tumbles slowly in solution, with a correlation time characteristic of a large object. It was also found that motilin has a large degree of local flexibility as compared with what has previously been reported in SDS micelles. The results show that motilin interacts with the bicelle, displaying motional properties of a peptide bound to a membrane. In comparison, motilin in neutral bicelles seems less structured and more flexible. This study shows that the small isotropic bicelles are well suited for use as membrane-mimetic for structural as well as dynamical investigations of membrane-bound peptides by high-resolution NMR.     

Evidence that human histidine triad nucleotide binding protein 3 (Hint3) is a distinct branch of the histidine triad (HIT) superfamily

Human Hint3 (hHint3) has been classified as a member of the histidine triad nucleotide (Hint) binding protein subfamily. While Hint1 is ubiquitously expressed by both eukaryotes and prokaryotes, Hint3 is found only in eukaryotes. Previously, our laboratory has characterized and compared the aminoacyl-adenylate and nucleoside phosphoramidate hydrolase activity of hHint1 and Escherichia coli hinT. In this study, hHint3-1(Ala36) and its single nucleotide polymorphism, hHint3-2 (A36G variant), were cloned, overexpressed, and purified. Steady-state kinetic studies with a synthetic fluorogenic indolepropinoic acyl-adenylate (AIPA) and with a series of fluorogenic tryptamine nucleoside phosphoramidates revealed that hHint3-1 and hHint3-2 are adenylate and phosphoramidate hydrolases with apparent second-order rate constants (kcat/Km) ranging from 10(2) to 10(6) s(-1) M(-1). Unlike hHint1, hHint3-1 and hHint3-2 prefer AIPA over tryptamine adenosine phosphoramidate by factors of 33- and 16-fold, respectively. In general, hHint3s hydrolyze phosphoramidate 370- to 2000-fold less efficiently than hHint1. Substitution of the potential active-site nucleophile, His145, by Ala was shown to abolish the adenylate and phosphoramidate hydrolase activity for hHint3-1. However, 0.2-0.4% residual activity was observed for the H145A mutant of hHint3-2. Both hHint3-1 and hHint3-2 were found to hydrolyze lysyl-adenylate generated by human lysyl-tRNA synthetase (hLysRS) by proceeding through an adenylated protein intermediate. hLysRS-dependent labeling of hHint3-1 and hHint3-2 was found to depend on His145, which aligns with the His112 of the Hint1 active site. The extent of active-site His145-AMP labeling was shown to be similar to His112-AMP labeling of hHint1. In contrast to all previously characterized members of the histidine triad superfamily, which have been shown to exist exclusively as homodimers, wild type and the H145A of hHint3-1 were found to exist across a range of multimeric states, from dimers to octamers and even larger oligomers, while wild type and the H145A of hHint3-2 exist predominantly in a monomeric state. The differences in oligomeric state may be important in vivo, because unlike tetracysteine-tagged Hint1, which was found along linear arrays exclusively in the cytoplasm in transfected HeLa cells, tagged Hint3-1 and Hint3-2 were found as aggregates both in the cytosol and in the nucleus. Taken together, these results imply that while Hint3 and Hint1 prefer aminoacyl-adenylates as substrates and catalytically interact with aminoacyl-tRNA synthetases, the significant differences in phosphoramidase activity, oligomeric state, and cellular localization suggest that Hint3s should be placed in a distinct branch of the histidine triad superfamily.     

Solution structure of inhibitor-free human metalloelastase (MMP-12) indicates an internal conformational adjustment

Macrophage metalloelastase or matrix metalloproteinase-12 (MMP-12) appears to exacerbate atherosclerosis, emphysema, aortic aneurysm, rheumatoid arthritis, and inflammatory bowel disease. An inactivating E219A mutation, validated by crystallography and NMR spectra, prevents autolysis of MMP-12 and allows us to determine its NMR structure without an inhibitor. The structural ensemble of the catalytic domain without an inhibitor is based on 2813 nuclear Overhauser effects (NOEs) and has an average RMSD to the mean structure of 0.25 Å for the backbone and 0.61 Å for all heavy atoms for residues Trp109-Gly263. Compared to crystal structures of MMP-12, helix B (hB) at the active site is unexpectedly more deeply recessed under the β-sheet. This opens a pocket between hB and β-strand IV in the active-site cleft. Both hB and an internal cavity are shifted toward β-strand I, β-strand III, and helix A on the back side of the protease. About 25 internal NOE contacts distinguish the inhibitor-free solution structure and indicate hB's greater depth and proximity to the sheet and helix A. Line broadening and multiplicity of amide proton NMR peaks from hB are consistent with hB undergoing a slow conformational exchange among subtly different environments. Inhibitor-binding-induced perturbations of the NMR spectra of MMP-1 and MMP-3 map to similar locations across MMP-12 and encompass the internal conformational adjustments. Evolutionary trace analysis suggests a functionally important network of residues that encompasses most of the locations adjusting in conformation, including 18 residues with NOE contacts unique to inhibitor-free MMP-12. The conformational change, sequence analysis, and inhibitor perturbations of NMR spectra agree on the network they identify between structural scaffold and the active site of MMPs.     

Importance of seed Zn content for wheat growth on Zn-deficient soil

Eggplants (Solanum melongena L. cv. Bonica) were grown in a glasshouse during summer under natural light with one unbranched shoot or one shoot with 3 to 4 branches and with or without fruit in quartz sand buffered and not buffered with 0.5% CaCO₃ (w : v), respectively. Nutrient solutions supplied contained nitrate or ammonium as the sole nitrogen source. Compared with nutrient solutions containing nitrate (10 mM), solutions containing ammonium (10 mM) caused a decrease in net photosynthesis of eggplants during early stages of vegetative growth when grown in quartz sand not buffered with CaCO₃. The decrease was not observed before leaves showed interveinal chlorosis. In contrast, net photosynthesis after bloom at first increased more rapidly in eggplants supplied with ammonium than with nitrate nitrogen. However, even in this case, net photosynthesis decreased four weeks later when ammonium nutrition was continued. The decrease was accompanied by epinasty and interveinal chlorosis on the lower leaves and later by severe wilting, leaf drop, stem lesions, and hampered growth of stems, roots, and fruits. These symptoms appeared later on plants not bearing fruits than on plants bearing fruits. If nutrient solutions containing increasing concentrations of ammonium (0.5–30 mM) were supplied after the time of first fruit ripening, shoot growth and set of later flowers and fruits were promoted. In contrast, vegetative growth and reproduction was only slightly affected by increasing the concentration of nitrate in the nutrient solutions. In quartz sand buffered with CaCO₃ ammonium nutrition caused deleterious effects only under low light conditions (shade) and on young plants during rapid fruit growth. If eggplants were supplied with ammonium nitrogen before bloom, vegetative growth was promoted, and set of flowers and fruit occurred earlier than on plants supplied with nitrate. Furthermore, the number of flowers and fruit yield increased. These effects of ammonium nutrition were more pronounced when plants were grown with branched shoots than with unbranched shoots. The results indicate that vegetative and reproductive growth of eggplants may be manipulated without causing injury to the plants by supplying ammonium nitrogen as long as the age of the plants, carbohydrate reserves of the roots, quantity of ammonium nitrogen supplied, and pH of the growth medium are favourable. T W Rufty Section editor     

Alterations in the structure of the electrical double layer adjacent to a charged membrane arising from electromagnetically induced changes in the activity of membrane bound enzymes

Electromagnetic fields of very low amplitude have been reported to influence a number of cellular functions. Many of these effects have a high degree of frequency specificity. Herein it is suggested that some of these reported results could be explained by a fieldinduced alteration in the enzymic activity of integral membrane proteins. It is shown that such a field-induced transition from an initial nonequilibrium steady-state to a final nonequilibrium steady-state can lead to an alteration in the concentration profiles of those charged species in the cell's ambient electrolyte that comprise the so-called electrical double layer. Examples of variations in the concentration profiles of those ions that react with a membrane-bound enzyme, as well as nonreacting ionic species, are given. The modulation of such effects by systematic variations in extracellular pH and ionic strength is discussed.