Effects of gypsum on the uptake,assimilation and cycling of 15N-labelled ammonium and nitrate-N by perennial ryegrass

Solution culture studies have shown that plant uptake of NH₄ ⁺ and NO₃ ^- can be improved by increasing the concentration of Ca²⁺ in the root environment: the same may be true for grass grown in soil culture. An experiment was set up to see whether gypsum (CaSO₄ 2H₂O) increased the rate at which perennial ryegrass absorbed ¹⁵NH₄ ⁺ and ¹⁵NO₃ ^- from soil.The results demonstrated that gypsum increases the rates of uptake of both NH₄ ⁺ and NO₃ ^- by perennial ryegrass. However because there was little potential for mineral-N loss from the experimental system, either by gaseous emission or by N immobilization, long term improvements in fertilizer efficiency were not observed. Nitrogen cycling from shoots to roots commenced once net uptake of N into plants had ceased. Labelled N transferred thus to roots underwent isotopic exchange with unlabelled soil N. It was suggested that this exchange of N might constitute an energy drain from the plant, if plant organic N was exchanged for soil inorganic N. The fact that the exchange occurred at all cast doubt on the suitability of the ¹⁵N-isotope dilution technique for assessing fertilizer efficiency in medium to long term experiments. There was evidence that the extra NO₃ ^--N taken up by plants on the all-nitrate treatments as a result of gypsum application, was reduced in root tissue rather than in shoots, but to the detriment of subsequent root growth and N uptake.     

Carbon: terrestrial C4 plants

The carbon isotope composition of terrestrial C₄ plants depends on the primary carboxylation of phosphoenolpyruvate (PEP) and on the diffusion of CO₂ to the carboxylation sites, but is also influenced by the final carboxylation of ribulose-1,5-bisphosphate (RuBP). Several models have been used for reproducing this complex situation. In the present review, a particular model is applied as a means to interpret the effects of environmental and genetically determined factors on carbon isotope discrimination during C₄ photosynthesis. As a new feature, the model considers four types of limitation of the overall CO₂ assimilation rate. Both carboxylation reactions are assumed to be limited by either maximum enzyme activity or maximum substrate regeneration rate. The model is applied to experimental data on the effects of CO₂, irradiance and water stress on short-term discrimination by leaves of several C₄ species measured simultaneously with CO₂ gas exchange characteristics. In particular, different patterns of the influence of low irradiances on carbon isotope discrimination are interpreted as due to variations in that irradiance at which a transition from limitation by PEP regeneration rate and RuBP carboxylase activity to limitation by the regeneration rates of both substrates occurs. After discussing literature data on the effects of environmental conditions on carbon isotope discrimination by C₄ plants seasonal and developmental changes in carbon isotope composition, studies on the systematic and geographic distribution of C₄ plants, evolutionary and genetical aspects, and some ecological implications are reviewed.     

Carbon isotope discrimination in C3-C4 intermediates

Carbon isotope discrimination in C₃–C₄ intermediates is determined by fractionations during diffusion and the biochemical fractionations occurring during CO₂ fixation. These biochemical fractionations in turn depend on the fractionation by Rubisco in the mesophyll, the amount of CO₂ fixation. These biochemical fractionations in turn depend on the fractionation by Rubisco in the mesophyll, the amount of CO₂ fixation occurring in the bundle sheath, the extent of bundle-sheath leakiness and the contribution which C₄-cycle activity makes to the CO₂ pool there. In most instances, carbon isotope discrimination in C₃–C₄ intermediates is C₃-like because only a small fraction of the total carbon fixed is fixed in the bundle sheath. In particular, this must be the case for Flaveria intermediates which initially fix substantial amounts of CO₂ into C₄-acids. In C₃–C₄ intermediates that refix photorespiratory CO₂ alone, it is possible for carbon isotope discrimination to be greater than in C₃-species, particularly at low CO₂ pressures or at high leaf temperatures. Short-term measurements of carbon isotope discrimination and gas exchange of leaves can be used to study the photosynthetic pathways of C₃-C₄ intermediates and their hybrids as has recently been done for C₃ and C₄ species.     

A Historical Perspective for the Catalytic Reaction Mechanism of Glycosidase; So As to Bring about Breakthrough in Confusing Situation

Various catalytic reaction models have been proposed as the reaction mechanisms of glycosidases, but a reasonable and unitary model capable of interpreting both “inverting” and “retaining” glycosidase reactions remains to be established. As for the models proposed to date, the nucleophilic displacement mechanism and the oxocarbenium ion intermediate mechanism are widely known, but recently the former is widely accepted, and so the general tendency of world opinion appears to favor it. This reaction model, however, is considered to comprise some inconsistencies that cannot be neglected from the viewpoint of reactivity in organic chemistry. While the nucleophilic displacement mechanism is often applied to reactions of glycosidases, it appears unlikely that such reactions actually occur. This review argues that the oxocarbenium ion intermediate reaction mechanism is more rational than the nucleophilic displacement reaction mechanism, as the action mode of glycosidases and related enzymes.     

Harmonizing Labeling and Analytical Strategies to Obtain Protein Turnover Rates in Intact Adult Animals

Changes in the abundance of individual proteins in the proteome can be elicited by modulation of protein synthesis (the rate of input of newly synthesized proteins into the protein pool) or degradation (the rate of removal of protein molecules from the pool). A full understanding of proteome changes therefore requires a definition of the roles of these two processes in proteostasis, collectively known as protein turnover. Because protein turnover occurs even in the absence of overt changes in pool abundance, turnover measurements necessitate monitoring the flux of stable isotope–labeled precursors through the protein pool such as labeled amino acids or metabolic precursors such as ammonium chloride or heavy water. In cells in culture, the ability to manipulate precursor pools by rapid medium changes is simple, but for more complex systems such as intact animals, the approach becomes more convoluted. Individual methods bring specific complications, and the suitability of different methods has not been comprehensively explored. In this study, we compare the turnover rates of proteins across four mouse tissues, obtained from the same inbred mouse strain maintained under identical husbandry conditions, measured using either [¹³C₆]lysine or [²H₂]O as the labeling precursor. We show that for long-lived proteins, the two approaches yield essentially identical measures of the first-order rate constant for degradation. For short-lived proteins, there is a need to compensate for the slower equilibration of lysine through the precursor pools. We evaluate different approaches to provide that compensation. We conclude that both labels are suitable, but careful determination of precursor enrichment kinetics in amino acid labeling is critical and has a considerable influence on the numerical values of the derived protein turnover rates.     

Measurement of oxidatively induced DNA damage and its repair,by mass spectrometric techniques

Abstract

Oxidatively induced damage caused by free radicals and other DNA-damaging agents generate a plethora of products in the DNA of living organisms. There is mounting evidence for the involvement of this type of damage in the etiology of numerous diseases including carcinogenesis. For a thorough understanding of the mechanisms, cellular repair, and biological consequences of DNA damage, accurate measurement of resulting products must be achieved. There are various analytical techniques, with their own advantages and drawbacks, which can be used for this purpose. Mass spectrometric techniques with isotope dilution, which include gas chromatography (GC) and liquid chromatography (LC), provide structural elucidation of products and ascertain accurate quantification, which are absolutely necessary for reliable measurement. Both gas chromatography-mass spectrometry (GC-MS) or liquid chromatography-mass spectrometry (LC-MS), in single or tandem versions, have been used for the measurement of numerous DNA products such as sugar and base lesions, 8,5’-cyclopurine-2’-deoxynucleosides, base-base tandem lesions, and DNA-protein crosslinks, in vitro and in vivo. This article reviews these techniques and their applications in the measurement of oxidatively induced DNA damage and its repair.     

Where old meets new: An ecosystem study of methanogenesis in a reflooded agricultural peatland

Reflooding formerly drained peatlands has been proposed as a means to reduce losses of organic matter and sequester soil carbon for climate change mitigation, but a renewal of high methane emissions has been reported for these ecosystems, offsetting mitigation potential. Our ability to interpret observed methane fluxes in reflooded peatlands and make predictions about future flux trends is limited due to a lack of detailed studies of methanogenic processes. In this study we investigate methanogenesis in a reflooded agricultural peatland in the Sacramento Delta, California. We use the stable‐and radio‐carbon isotopic signatures of wetland sediment methane, ecosystem‐scale eddy covariance flux observations, and laboratory incubation experiments, to identify which carbon sources and methanogenic production pathways fuel methanogenesis and how these processes are affected by vegetation and seasonality. We found that the old peat contribution to annual methane emissions was large (~30%) compared to intact wetlands, indicating a biogeochemical legacy of drainage. However, fresh carbon and the acetoclastic pathway still accounted for the majority of methanogenesis throughout the year. Although temperature sensitivities for bulk peat methanogenesis were similar between open‐water (Q₁₀ = 2.1) and vegetated (Q₁₀ = 2.3) soils, methane production from both fresh and old carbon sources showed pronounced seasonality in vegetated zones. We conclude that high methane emissions in restored wetlands constitute a biogeochemical trade‐off with contemporary carbon uptake, given that methane efflux is fueled primarily by fresh carbon inputs.     

基于稳定氧同位素确定植物水分来源不同方法的比较

利用稳定同位素技术确定植物水分来源,对提高生态水文过程的认识和对干旱半干旱区的生态管理至关重要。目前基于稳定同位素技术确定植物水分来源的方法众多,但不同方法之间对比的研究较少。本研究基于原位样品采集,室内实验测试,利用直接对比法、多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)和吸水深度模型分析植物水分来源,并对比各方法的优缺点。结果表明:相对于多元线性混合模型(IsoSource)而言,贝叶斯混合模型(MixSIR、MixSIAR)具有更好的水源区分性能,但对数据要求较高,且植物木质部水和潜在水源同位素组成的标准差越小,模型运行结果的可信度更高。本研究中贝叶斯混合模型(MixSIR)为最优解。在利用稳定氢氧同位素技术确定植物水分来源时,可先通过直接对比法定性判断植物可能利用的潜在水源,然后再用多元线性混合模型(IsoSource)、贝叶斯混合模型(MixSIR、MixSIAR)计算出各潜在水源对植物的贡献率和贡献范围,必要时可评估模型性能,选择出最优模型,定量分析植物的水分来源。若植物主要吸收利用不同土层深度的土壤水,可结合吸水深度模型计算出植物吸收土壤水的平均深度。本研究为干旱半干旱地区利用同位素技术确定植物水分来源方法的选择提供了理论依据。     

特定化合物同位素分析技术在树木非结构性碳水化合物研究中的应用

特定化合物同位素分析(CSIA)可以实现对复杂基质中特定化合物稳定碳同位素组成(δ¹³C)的精确测定。应用此方法测定树木非结构性碳水化合物(NSC)中特定成分(如糖类、有机酸和糖醇)的δ¹³C,不仅能够追踪新同化的光合产物在树木中的运移及与外界的碳交换,还能够更敏感地指示树木生理状况对环境变化的响应。本文首先系统介绍了CSIA从样品采集、处理到δ¹³C测定的方法,然后综述了树木NSC中各成分之间及各成分在不同器官之间的δ¹³C差异,阐述了树木NSC的δ¹³C时间动态变化特征及内在机制,最后分析了NSC作为主要呼吸底物,其δ¹³C与树木呼吸释放CO₂的δ¹³C(δ¹³C_R)之间的联系,并针对CSIA分析技术在后光合分馏、树木逆境生理和年轮δ¹³C形成机制等研究的应用前景提出了展望。     

箱式通量观测技术和方法的理论假设及其应用进展

碳(CO₂、CH₄)、氮(N₂O)和水汽(H₂O)等温室气体的交换通量是生态系统物质循环的核心, 是地圈-生物圈-大气圈相互作用的纽带。稳定同位素光谱和质谱技术和方法的进步使碳稳定同位素比值(δ ¹³C)和氧稳定同位素比值(δ ¹⁸O)(CO₂)、δ ¹³C (CH₄)、氮稳定同位素比值(δ ¹⁵N)和δ ¹⁸O (N₂O)、氢稳定同位素比值(δD)和δ ¹⁸O (H₂O)的观测成为可能, 与箱式通量观测技术和方法结合可以实现土壤、植物乃至生态系统尺度温室气体及其同位素通量观测研究。该综述以CO₂及其δ ¹³C通量的箱式观测技术和方法为例, 概述了箱式通量观测系统的基本原理及分类, 阐述了系统设计的理论要求和假设, 综述了从野外到室内土壤、植物叶-茎-根以及生态系统尺度箱式通量观测研究的应用进展及问题, 展望了气体分析精度和准确度、观测数据精度和准确度以及观测数据的代表性评价在箱式通量观测研究中的重要性。