Applicability of new spin trap agent, 2-diphenylphosphinoyl-2-methyl-3,4-dihydro-2H-pyrrole N-oxide, in biological system

Electron spin resonance using spin-trapping is a useful technique for detecting direct reactive oxygen species, such as superoxide (). However, the widely used spin trap 2,2-dimethyl-3,4-dihydro-2H-pyrrole N-oxide (DMPO) has several fundamental limitations in terms of half-life and stability. Recently, the new spin trap 2-diphenylphosphinoyl-2-methyl-3,4-dihydro-2H-pyrrole N-oxide (DPhPMPO) was developed by us. We evaluated the biological applicability of DPhPMPO to analyze in both cell-free and cellular systems. DPhPMPO had a larger rate constant for and formed more stable spin adducts for than DMPO in the xanthine/xanthine oxidase (X/XO) system. In the phorbol myristate acetate-activated neutrophil system, the detection potential of DPhPMPO for was significantly higher than that of DMPO (k_DMPO = 13.95 M⁻¹ s⁻¹, k_DPhPMPO = 42.4 M⁻¹ s⁻¹). These results indicated that DPhPMPO is a potentially good candidate for trapping in a biological system.     

Plant Community Composition as a Predictor of Regional Soil Carbon Storage in Alaskan Boreal Black Spruce Ecosystems

The boreal forest is the largest terrestrial biome in North America and holds a large portion of the world’s reactive soil carbon. Therefore, understanding soil carbon accumulation on a landscape or regional scale across the boreal forest is useful for predicting future soil carbon storage. Here, we examined the relationship between floristic composition and ecosystem parameters, such as soil carbon pools, the carbon-to-nitrogen (C/N) ratio of live black spruce needles, and normalized basal area increment (NBAI) of trees in black spruce communities, the most widespread forest type in the boreal forest of Alaska. Variability in ecosystem properties among black spruce stands was as large as that which had previously been documented among all forest types in the central interior of Alaska; we found an eightfold range in NBAI and fivefold range in mineral soil carbon and nitrogen pools. Acidic black spruce communities had significantly more carbon in the organic soil horizon than did nonacidic black spruce communities, but did not differ in any other measured ecosystem parameter. We explained 48% of the variation in total soil carbon with a combination of plant community indices and abiotic and biotic factors. Plant community composition was at least as effective as any single environmental factor or stand characteristic in predicting soil C pools in Alaskan black spruce ecosystems. We conclude that among the community properties analyzed, the presence of key groups of species, overall species composition, and diversity of certain functional types, especially Sphagnum moss species, are important predictors of soil carbon sequestration in the black spruce forest type.     

Scion and Rootstock Effects on ABA-mediated Plant Growth Regulation and Salt Tolerance of Acclimated and Unacclimated Potato Genotypes

Tolerance of salt stress in potato (Solanum tuberosum L.) increased when the plants were pre-exposed to low concentrations of salt (salt acclimation). This acclimation was accompanied by increased levels of abscisic acid (ABA) in the shoot. To further study the role of roots and shoots in this acclimation process, reciprocal grafts were made between a salt-tolerant (9506) and salt-sensitive ABA(−) mutant and its ABA(+) normal sibling potato genotype. The grafted plants were acclimated with 75 or 100 mM NaCl for 3 weeks and then exposed to 150–180 mM NaCl, depending on the salt tolerance of the rootstock. After 2 weeks of exposure to the salt stress, the acclimated and unacclimated plants were compared for physiologic and morphologic parameters. The response to the salt stress was strongly influenced by the rootstock. The salt-tolerant 9506 rootstock increased the salt tolerance of scions of both the ABA-deficient mutant and its ABA(+) sibling. This salt tolerance induced by the rootstock was primarily modulated by salt acclimation and manifested in the scion via increased plant water content, stem diameter, dry matter accumulation, stomatal conductivity, and osmotic potential, and is associated with a reduction in leaf necrosis. There was also a pronounced scion effect on the rootstock. Using 9506 as a scion significantly increased root fresh and dry weights, stem diameter, and root water content of ABA(−) mutant rootstocks. Specific evidence was found of the role of exogenous ABA in the enhancement of water status in grafted plants under salt stress beyond that of grafting alone. This was verified by more positive stomatal conductivity and upward water flow in ABA-treated grafted and nongrafted plants and the absence of upward water flow in nontreated grafted plants through NMR imaging. Grafting using either salt-tolerant scions or rootstocks with inherently high ABA levels may positively modify subsequent responses of the plant under salt stress.     

Biochemical and spectroscopic characterization of the membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617

Membrane-bound nitrate reductase from Marinobacter hydrocarbonoclasticus 617 can be solubilized in either of two ways that will ultimately determine the presence or absence of the small (Ι) subunit. The enzyme complex (NarGHI) is composed of three subunits with molecular masses of 130, 65, and 20 kDa. This enzyme contains approximately 14 Fe, 0.8 Mo, and 1.3 molybdopterin guanine dinucleotides per enzyme molecule. Curiously, one heme b and 0.4 heme c per enzyme molecule have been detected. These hemes were potentiometrically characterized by optical spectroscopy at pH 7.6 and two noninteracting species were identified with respective midpoint potentials at E _m = +197 mV (heme c) and −4.5 mV (heme b). Variable-temperature (4–120 K) X-band electron paramagnetic resonance (EPR) studies performed on both as-isolated and dithionite-reduced nitrate reductase showed, respectively, an EPR signal characteristic of a [3Fe–4S]⁺ cluster and overlapping signals associated with at least three types of [4Fe–4S]⁺ centers. EPR of the as-isolated enzyme shows two distinct pH-dependent Mo(V) signals with hyperfine coupling to a solvent-exchangeable proton. These signals, called “low-pH” and “high-pH,” changed to a pH-independent Mo(V) signal upon nitrate or nitrite addition. Nitrate addition to dithionite-reduced samples at pH 6 and 7.6 yields some of the EPR signals described above and a new rhombic signal that has no hyperfine structure. The relationship between the distinct EPR-active Mo(V) species and their plausible structures is discussed on the basis of the structural information available to date for closely related membrane-bound nitrate reductases. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Variable oligomerization modes in coronavirus non-structural protein 9

Non-structural protein 9 (Nsp9) of coronaviruses is believed to bind single-stranded RNA in the viral replication complex. The crystal structure of Nsp9 of human coronavirus (HCoV) 229E reveals a novel disulfide-linked homodimer, which is very different from the previously reported Nsp9 dimer of SARS coronavirus. In contrast, the structure of the Cys69Ala mutant of HCoV-229E Nsp9 shows the same dimer organization as the SARS-CoV protein. In the crystal, the wild-type HCoV-229E protein forms a trimer of dimers, whereas the mutant and SARS-CoV Nsp9 are organized in rod-like polymers. Chemical cross-linking suggests similar modes of aggregation in solution. In zone-interference gel electrophoresis assays and surface plasmon resonance experiments, the HCoV-229E wild-type protein is found to bind oligonucleotides with relatively high affinity, whereas binding by the Cys69Ala and Cys69Ser mutants is observed only for the longest oligonucleotides. The corresponding mutations in SARS-CoV Nsp9 do not hamper nucleic acid binding. From the crystal structures, a model for single-stranded RNA binding by Nsp9 is deduced. We propose that both forms of the Nsp9 dimer are biologically relevant; the occurrence of the disulfide-bonded form may be correlated with oxidative stress induced in the host cell by the viral infection.     

Solution structure of a cyanobacterial phytochrome GAF domain in the red-light-absorbing ground state

The unique photochromic absorption behavior of phytochromes (Phys) depends on numerous reversible interactions between the bilin chromophore and the associated polypeptide. To help define these dynamic interactions, we determined by NMR spectroscopy the first solution structure of the chromophore-binding cGMP phosphodiesterase/adenylcyclase/FhlA (GAF) domain from a cyanobacterial Phy assembled with phycocyanobilin (PCB). The three-dimensional NMR structure of Synechococcus OS-B′ cyanobacterial Phy 1 in the red-light-absorbing state of Phy (Pr) revealed that PCB is bound to Cys138 of the GAF domain via the A-ring ethylidene side chain and is buried within the GAF domain in a ZZZsyn,syn,anti configuration. The D ring of the chromophore sits within a hydrophobic pocket and is tilted by approximately 80° relative to the B/C rings by contacts with Lys52 and His169. The solution structure revealed remarkable flexibility for PCB and several adjacent amino acids, indicating that the Pr chromophore has more freedom in the binding pocket than anticipated. The propionic acid side chains of rings B and C and Arg101 and Arg133 nearby are especially mobile and can assume several distinct and energetically favorable conformations. Mutagenic studies on these arginines, which are conserved within the Phy superfamily, revealed that they have opposing roles, with Arg101 and Arg133 helping stabilize and destabilize the far-red-light-absorbing state of Phy (Pfr), respectively. Given the fact that the Synechococcus OS-B′ GAF domain can, by itself, complete the Pr → Pfr photocycle, it should now be possible to determine the solution structure of the Pfr chromophore and surrounding pocket using this Pr structure as a framework.     

Effects of termite mounds on composition,functional types and traits of plant communities in Pendjari Biosphere Reserve (Benin,West Africa)

Understanding the role of termite mounds in biodiversity and ecosystem functioning is a priority for the management of tropical terrestrial protected areas dominated by savannahs. This study aimed to assess the effects of termite mounds on the diversity of plant functional types (PFTs) and herbaceous’ net aboveground primary productivity (NAPP) in plant communities (PCs) of the Pendjari Biosphere Reserve. PCs were identified through canonical correspondence analysis performed on 96 phytosociological ‘relevés’ realized in plots of 900 m². PFTs’ diversity was compared between savannahs and mounds’ plots using generalized linear models. In each plot, 7 m² subplots were harvested and NAPP was determined. Linear mixed models were performed to assess change in herbaceous NAPP regarding species richness, graminoids’ richness, specific leaf area and termite mounds. There is no specific plant community related to mounds. However, the occurrence of termite mounds induced an increase of woody and forbs diversity while the diversity of legumes and graminoids decreased. These diversity patterns led to decreasing of PCs’ NAPP. This study confirms that termite‐induced resource heterogeneity supports niche differentiation theory and increased savannah encroachment by woody species.     

Revisiting the Holy Grail: using plant functional traits to understand ecological processes

One of ecology's grand challenges is developing general rules to explain and predict highly complex systems. Understanding and predicting ecological processes from species' traits has been considered a ‘Holy Grail’ in ecology. Plant functional traits are increasingly being used to develop mechanistic models that can predict how ecological communities will respond to abiotic and biotic perturbations and how species will affect ecosystem function and services in a rapidly changing world; however, significant challenges remain. In this review, we highlight recent work and outstanding questions in three areas: (i) selecting relevant traits; (ii) describing intraspecific trait variation and incorporating this variation into models; and (iii) scaling trait data to community‐ and ecosystem‐level processes. Over the past decade, there have been significant advances in the characterization of plant strategies based on traits and trait relationships, and the integration of traits into multivariate indices and models of community and ecosystem function. However, the utility of trait‐based approaches in ecology will benefit from efforts that demonstrate how these traits and indices influence organismal, community, and ecosystem processes across vegetation types, which may be achieved through meta‐analysis and enhancement of trait databases. Additionally, intraspecific trait variation and species interactions need to be incorporated into predictive models using tools such as Bayesian hierarchical modelling. Finally, existing models linking traits to community and ecosystem processes need to be empirically tested for their applicability to be realized.     

Contrasting effects of plant inter‐ and intraspecific variation on community trait responses to restoration of a sandy grassland ecosystem

Changes in plant community traits along an environmental gradient are caused by interspecific and intraspecific trait variation. However, little is known about the role of interspecific and intraspecific trait variation in plant community responses to the restoration of a sandy grassland ecosystem. We measured five functional traits of 34 species along a restoration gradient of sandy grassland (mobile dune, semi‐fixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China. We examined how community‐level traits varied with habitat changes and soil gradients using both abundance‐weighted and non‐weighted averages of trait values. We quantified the relative contribution of inter‐ and intraspecific trait variation in specific leaf area (SLA), leaf dry matter content (LDMC), leaf carbon content (LCC), leaf nitrogen content (LNC), and plant height to the community response to habitat changes in the restoration of sandy grassland. We found that five weighted community‐average traits varied significantly with habitat changes. Along the soil gradient in the restoration of sandy grassland, plant height, SLA, LDMC, and LCC increased, while LNC decreased. For all traits, there was a greater contribution of interspecific variation to community response in regard to habitat changes relative to that of intraspecific variation. The relative contribution of the interspecific variation effect of an abundance‐weighted trait was greater than that of a non‐weighted trait with regard to all traits except LDMC. A community‐level trait response to habitat changes was due largely to species turnover. Though the intraspecific shift plays a small role in community trait response to habitat changes, it has an effect on plant coexistence and the maintenance of herbaceous plants in sandy grassland habitats. The context dependency of positive and negative covariation between inter‐ and intraspecific variation further suggests that both effects of inter‐ and intraspecific variation on a community trait should be considered when understanding a plant community response to environmental changes in sandy grassland ecosystems.