遮荫条件下绞股蓝光合作用特点的研究

在夏季遮荫条件下栽培绞股蓝的净光合速率日变化呈现不典型的双峰曲线,第1峰值出现在11：00时,达13．8μmolCO2·m^-2·S^-1日净光合速率达到176．97μmol CO2·m^-2,是强光下栽培的3．1倍;净光合速率和光量子通量密度呈正相关,相对湿度对净光合速率的影响小．强光下栽培绞股蓝。光合作用“午休”现象明显,净光合速率日变化呈现双峰曲线,第1峰值出现在10：00时,为3．0μmol CO2·m^-2·s^-1．第2峰值出现在14：00时,为1．25μmol CO2·m^-2·s^-1;相对湿度与净光合速率成正相关,对净光合速率的影响大．当光量子通量超过700μmol·m^-2·s^-1时,净光合速率与光量子通量密度呈负相关．在影响该植物蒸腾速率的诸多因子中,蒸腾速率和气孔导度之间的相关性最为显著．因此绞股蓝属于高度耐荫而怕光的植物．人工栽培应重点考虑光照因子．     

Nitrogen cycle of tropical perennial crops under shade trees

The distribution and fluxes of nitrogen in some parts of a coffee plantation under shade were studied at a typical mountain (1380 m a sl) location in Venezuela. The amounts of nitrogen in the soil to 60 cm depth are by far the largest nitrogen store, reaching a total of 49 000 kg ha^?1. The nitrogen flow associated with litterfall was dominated by the shade-tree fraction accounting for a transfer of 86 kg ha^?1 yr^?1 of the total 189 kg ha^?1 yr^?1. The rapid decomposition of this litter, although showing a phase of nitrogen accumulation, is an important source of nitrogen to the roots of coffee which occupy preferentially the upper 30 cm of soil and even the litter layer itself. Some evidence of synchrony was found between the peaks of nitrogen transfer to the soil by litter and the periods of high nitrogen demand by the crop plants. It is proposed that the system can amply compensate the nitrogen outputs by harvest (17 kg ha^?1 yr^?1) with a subsidy from the shade trees.Erythrina sp. andInga sp. are potential nitrogen fixers although we found no active sites during the dry period sampled. The average litter decomposition constant, k, expressed in terms of nitrogen, was estimated as 4.5, equivalent to a half-life of approximately two months.     

Reproductive efficiency and shade avoidance plasticity under simulated competition

Plant strategy and life‐history theories make different predictions about reproductive efficiency under competition. While strategy theory suggests under intense competition iteroparous perennial plants delay reproduction and semelparous annuals reproduce quickly, life‐history theory predicts both annual and perennial plants increase resource allocation to reproduction under intense competition. We tested (1) how simulated competition influences reproductive efficiency and competitive ability (CA) of different plant life histories and growth forms; (2) whether life history or growth form is associated with CA; (3) whether shade avoidance plasticity is connected to reproductive efficiency under simulated competition. We examined plastic responses of 11 herbaceous species representing different life histories and growth forms to simulated competition (spectral shade). We found that both annual and perennial plants invested more to reproduction under simulated competition in accordance with life‐history theory predictions. There was no significant difference between competitive abilities of different life histories, but across growth forms, erect species expressed greater CA (in terms of leaf number) than other growth forms. We also found that shade avoidance plasticity can increase the reproductive efficiency by capitalizing on the early life resource acquisition and conversion of these resources into reproduction. Therefore, we suggest that a reassessment of the interpretation of shade avoidance plasticity is necessary by revealing its role in reproduction, not only in competition of plants.     

Cool shade and not-so-cool shade: How habitat loss may accelerate thermal stress under current and future climate

Worldwide habitat loss, land-use changes, and climate change threaten biodiversity, and we urgently need models that predict the combined impacts of these threats on organisms. Current models, however, overlook microhabitat diversity within landscapes and so do not accurately inform conservation efforts, particularly for ectotherms. Here, we built and field-parameterized a model to examine the effects of habitat loss and climate change on activity and microhabitat selection by a diurnal desert lizard. Our model predicted that lizards in rock-free areas would reduce summer activity levels (e.g. foraging, basking) and that future warming will gradually decrease summer activity in rocky areas, as even large rocks become thermally stressful. Warmer winters will enable more activity but will require bushes and small rocks as shade retreats. Hence, microhabitats that may seem unimportant today will become important under climate change. Modelling frameworks should consider the microhabitat requirements of organisms to improve conservation outcomes.     

Radiation absorption and growth of Viciafaba under shade at two densities

Faba beans were grown under various shading treatments at densities of 20 and 60 plants m^-2. The amount of PAR absorbed by each treatment was estimated from measured leaf area index. The conversion factor (E, g MJ^-1) relating dry matter production to absorbed PAR increased as shading increased. Application or removal of shade changed E rapidly, though there was some evidence for an increased value of ? persisting after removal of shade. Differences in dry matter production between the two years were due to as much to differences in ? as to changes in the amount of light absorbed. Increased plant density increased PAR absorbed but hardly affected e.     

Function prediction of uncharacterized proteins

Function prediction of uncharacterized protein sequences generated by genome projects has emerged as an important focus for computational biology. We have categorized several approaches beyond traditional sequence similarity that utilize the overwhelmingly large amounts of available data for computational function prediction, including structure-, association (genomic context)-, interaction (cellular context)-, process (metabolic context)-, and proteomics-experiment-based methods. Because they incorporate structural and experimental data that is not used in sequence-based methods, they can provide additional accuracy and reliability to protein function prediction. Here, first we review the definition of protein function. Then the recent developments of these methods are introduced with special focus on the type of predictions that can be made. The need for further development of comprehensive systems biology techniques that can utilize the ever-increasing data presented by the genomics and proteomics communities is emphasized. For the readers' convenience, tables of useful online resources in each category are included. The role of computational scientists in the near future of biological research and the interplay between computational and experimental biology are also addressed.     

COP1 re‐accumulates in the nucleus under shade

Shade‐avoider plants typically respond to shade‐light signals by increasing the rate of stem growth. CONSTITTUTIVE PHOTOMORPHOGENESIS 1 (COP1) is an E3 ligase involved in the ubiquitin labelling of proteins targeted for degradation. In dark‐grown seedlings, COP1 accumulates in the nucleus and light exposure causes COP1 migration to the cytosol. Here, we show that in Arabidopsis thaliana, COP1 accumulates in the nucleus under natural or simulated shade, despite the presence of far‐red light. In plants grown under white light, the transfer to shade‐light conditions triggers an unexpectedly rapid re‐accumulation of COP1 in the nucleus. The partial simulation of shade by lowering either blue or red light levels (maintaining far‐red light) caused COP1 nuclear re‐accumulation. Hypocotyl growth of wild‐type seedlings is more sensitive to afternoon shade than to morning shade. A residual response to shade was observed in the cop1 mutant background, but these seedlings showed inverted sensitivity as they responded to morning shade and not to afternoon shade. COP1 overexpression exaggerated the wild‐type pattern by enhancing afternoon sensitivity and making morning shade inhibitory of growth. COP1 nuclear re‐accumulation also responded more strongly to afternoon shade than to morning shade. These results are consistent with a signalling role of COP1 in shade avoidance. We propose a function of COP1 in setting the daily patterns of sensitivity to shade in the fluctuating light environments of plant canopies.     

过氧化物氧还蛋白家族的功能及调节机制

过氧化物氧还蛋白(peroxiredoxin,Prx)家族是细胞中一类高丰度蛋白质,作为过氧化物酶对维持体内过氧化氢水平发挥着重要的作用,并且通过调控蛋白激酶的氧化还原状态参与细胞信号转导调控过程。Prx家族根据其参与催化反应的半胱氨酸残基数目分为典型双半胱氨酸型(2-Cys)、非典型双半胱氨酸型(atypical 2-Cys)和单半胱氨酸型(1-Cys)。Prx的活性受到寡聚化状态、磷酸化以及蛋白质水解的调控。     

Function and regulation of Rnd proteins

The Rnd proteins, which form a distinct sub-group of the Rho family of small GTP-binding proteins, have been shown to regulate the organization of the actin cytoskeleton in several tissues. In the brain, they participate in neurite extension, whereas in smooth muscle, they modulate contractility. Recent evidence has shown that Rnd3 (RhoE) is also involved in the regulation of cell-cycle progression and transformation, indicating that these proteins might have other, as yet unexplored roles.     

Root growth and litter decomposition in a coffee plantation under shade trees

In a non-fertilized coffee plantation under shade trees the root biomass was excavated to estimate its distribution in the soil profile. One third of total fine (less than 1 mm) roots was found in the first 10 cm of soil; the cumulative total to 30 cm reached 73%. A highly variable and transient amount of fine roots colonized the litter layer. Root production both in the litter and in the first 7.5 cm of mineral soil was estimated from sequential samplings and was 10 g m^–2 yr^–1 and 660 g m^–2 yr^–1 respectively. The decomposition rate of weighed averages of litter fractions in the coffee plantation, calculated as the ratio of litter fall rate to the amount found in the soil was k=4.8. Shade tree leaves, the major component of litter descomposed slower than coffee leaves and these slower than flowers and fruits. Litter bag experiments showed considerable slower rates when mesh was 0.03 mm than 0.5 mm. Nitrogen and phosphorous showed increases in concentrations as decomposition progressed while potassium, calcium and magnesium followed a decrease in concentration that paralleled that of dry weight loss. In comparing the decomposition rate for litter with or without coffee roots growing in the bags, a tendency to show faster decomposition rates was found for the treatment with roots. These differences were however, only significant for one month for shade tree leaves litter. Nitrogen amounts remaining in shade tree leaves litter was lower in the treatment with roots that without roots. Potassium concentration in roots was positively correlated with potassium concentration in decomposing leaf litter where roots were growing. These results suggest that while roots growing attached to decomposing litter had little or no effect in speeding the decomposition process, the superficial roots seem to play an important role in absorbing very efficiently the mineralized nutrients from litter. The anatomical study of roots showed that the plantation is intensely infected with V-A mycorrhiza. External mycorrhizal hyphae did not to play a role in attachment of roots to decomposing litter while root hairs were found to grow in profusion on root surfaces oriented toward litter.     

Habitat preference of wormlions and their behavioural repeatability under illumination/shade conditions

1. Animal personality is defined as the repeatable between‐individual differences in behaviour over time and contexts. Some personality traits, such as activity or aggression, have received much attention while other behaviours, such as habitat preference or learning, have been neglected. 2. Wormlion larvae are sit‐and‐wait dipteran predators that inhabit shaded microhabitats in the field and also prefer shade in the laboratory. The aim of the present study was to examine wormlion larvae behavioural repeatability in general and specifically in the context of habitat preference. In order to achieve this, three experiments were conducted to determine whether, to what extent and under which conditions wormlion preference for shaded microhabitats is repeatable. 3. Individual tendency to relocate when the environment conditions deteriorate was also assessed, by switching between shaded and illuminated conditions, either with or without pit destruction. 4. Larvae showed a highly repeatable preference for shade. Repeatability was detected in additional behavioural traits: pit construction, pit area and tendency to relocate. 5. This behavioural repeatability was demonstrated under constant microhabitat conditions, with distinct behaviours in each setting. Under constant illumination, wormlions constructed smaller pits, moved over longer distances and were found at the tray edges more frequently than under constant shade conditions, suggesting that illuminated environments are perceived as risky or unsuitable. 6. Switching between the two microhabitat conditions without pit destruction induced fewer relocations than switching with pit destruction, suggesting that wormlions do not tend to abandon their pits, even if their microhabitat conditions deteriorate.     

Ecophysiology parameters of four Brazilian Atlantic Forest species under shade and drought stress

The Brazilian Atlantic Forest has experienced a reduction in its original area since the discovery of Brazil. Over the last 30 years, studies and techniques for forest recovery have advanced. Establishing a self-sustainable reforested area with adequate biodiversity is the main parameter for any reforestation program. Thus, knowledge of the ecophysiological behavior of the species to be used is crucial. Our hypothesis is that certain tools are efficient in determining the ecophysiological characterization of native species within different functional groups. Filling group plants show fast growth, intense gas exchange, present mechanisms of water deficit tolerance and show high efficiency in radiation capture, so they are first planted in a reforestation area. While plants pertaining to the diversity group do not exhibit these characteristics, thus are plants after the establishment of the first group of species. To test this hypothesis, two experiments were installed using young plants of four species native to the Atlantic Forest, grown in 9-L pots. Leaf water potential, gas exchange, chlorophyll fluorescence and certain biochemical parameters of leaf metabolism were evaluated. In the first experiment, plants were maintained under two forms of light availability for 15 days, full light (control) and shaded (shade). The species Inga sp. and Brosimum guianensis presented the most contrasting responses on day 15, principally in the variables leaf water potential, gas exchange, leaf soluble sugar content, F_\textv^￠ /F_\textm^￠ F_{\text{v}}^{\prime } /F_{\text{m}}^{\prime } and F _v/F _m. In the second experiment, plants were divided into two groups: a well-hydrated group (control) and one that underwent irrigation suspension for 7 days (drought); measurements were performed on day 8 of drought. Again, Inga sp. and Brosimum guianensis plants showed responses characterizing them as pertaining to distinct functional groups for the experimental parameters previously described. Thus, Inga sp. was classified as pertaining to the filling group and B. guianensis to the diversity group. The performance of the species Cinnamomum zeylancium and Tapirira guianensis under the conditions studied suggests that these are intermediate species with potential for use as filling group species.     

Function of small hydrophobic proteins of paramyxovirus

Mumps virus (MuV), a rubulavirus of the paramyxovirus family, causes acute infections in humans. MuV has seven genes including a small hydrophobic (SH) gene, which encodes a type I membrane protein of 57 amino acid residues. The function of the SH protein is not clear, although its expression is not necessary for growth of MuV in tissue culture cells. It is speculated that MuV SH plays a role in viral pathogenesis. Simian virus 5 (SV5), a closely related rubulavirus, encodes a 44-amino-acid-residue SH protein. Recombinant SV5 lacking the SH gene (rSV5DeltaSH) is viable and has no growth defect in tissue culture cells. However, rSV5DeltaSH induces apoptosis in tissue culture cells and is attenuated in vivo. Neutralizing antibodies against tumor necrosis factor alpha (TNF-alpha) and TNF-alpha receptor 1 block rSV5DeltaSH-induced apoptosis, suggesting that SV5 SH plays an essential role in blocking the TNF-alpha-mediated apoptosis pathway. Because MuV is closely related to SV5, we hypothesize that the SH protein of MuV has a function similar to that of SV5, even though there is no sequence homology between them. To test this hypothesis and to study the function of MuV SH, we have replaced the open reading frame (ORF) of SV5 SH with the ORF of MuV SH in a SV5 genome background. The recombinant SV5 (rSV5DeltaSH+MuV-SH) was analyzed in comparison with SV5. It was found that rSV5DeltaSH+MuV-SH was viable and behaved like wild-type SV5, suggesting that MuV SH has a function similar to that of SV5 SH. Furthermore, both ectopically expressed SV5 SH and MuV SH blocked activation of NF-kappaB by TNF-alpha in a reporter gene assay, suggesting that both SH proteins can inhibit TNF-alpha signaling.     

Function of tubulin binding proteins in vivo

Overexpression of the beta-tubulin binding protein Rbl2p/cofactor A is lethal in yeast cells expressing a mutant alpha-tubulin, tub1-724, that produces unstable heterodimer. Here we use RBL2 overexpression to identify mutations in other genes that affect formation or stability of heterodimer. This approach identifies four genes-CIN1, CIN2, CIN4, and PAC2-as affecting heterodimer formation in vivo. The vertebrate homologues of two of these gene products-Cin1p/cofactor D and Pac2p/cofactor E-can catalyze exchange of tubulin polypeptides into preexisting heterodimer in vitro. Previous work suggests that both Cin2p or Cin4p act in concert with Cin1p in yeast, but no role for vertebrate homologues of either has been reported in the in vitro reaction. Results presented here demonstrate that these proteins can promote heterodimer formation in vivo. RBL2 overexpression in cin1 and pac2 mutant cells causes microtubule disassembly and enhanced formation of Rbl2p-beta-tubulin complex, as it does in the alpha-tubulin mutant that produces weakened heterodimer. Significantly, excess Cin1p/cofactor D suppresses the conditional phenotypes of that mutant alpha-tubulin. Although none of the four genes is essential for viability under normal conditions, they become essential under conditions where the levels of dissociated tubulin polypeptides increase. Therefore, these proteins may provide a salvage pathway for dissociated tubulin heterodimers and so rescue cells from the deleterious effects of free beta-tubulin.     

Function and structure of inherently disordered proteins

The application of bioinformatics methodologies to proteins inherently lacking 3D structure has brought increased attention to these macromolecules. Here topics concerning these proteins are discussed, including their prediction from amino acid sequence, their enrichment in eukaryotes compared to prokaryotes, their more rapid evolution compared to structured proteins, their organization into specific groups, their structural preferences, their half-lives in cells, their contributions to signaling diversity (via high contents of multiple-partner binding sites, post-translational modifications, and alternative splicing), their distinct functional repertoire compared to that of structured proteins, and their involvement in diseases.     

Effects of trampling and vegetation removal on species diversity and micro-environment under different shade conditions

Abstract. The effects of disturbance by trampling and vegetation removal on herbaceous communities and their micro-environments were examined at two sites with different levels of shade. The dominant species of the original vegetation were the perennial herb Artemisia princeps at the sunny site and the dwarf-bamboo Pleioblastus chino at the shady site. With no disturbance and marked dominance of these species, diversity was low. After vegetation removal there was a rapid recovery, leading to a more diverse vegetation with many more species, each with a lower dominance. Continuous trampling induced a short vegetation while the light intensity under the foliage was increased. At the sunny site, species richness was depressed by trampling because the soil water potential decreased markedly during summer and only the stress-tolerant annual Digitaria adscendens grew vigorously. Thus, the lowest species diversity was observed in the heavily trampled vegetation in late summer. At the shady site, soil water availability was not affected by trampling. This allowed the survival of many species and prevented a strong decline in diversity. The results suggest that the pattern of change in diversity in communities subjected to various disturbances, was always determined by the original environments.     

Non-linear effects of drought under shade: reconciling physiological and ecological models in plant communities

The combined effects of shade and drought on plant performance and the implications for species interactions are highly debated in plant ecology. Empirical evidence for positive and negative effects of shade on the performance of plants under dry conditions supports two contrasting theoretical models about the role of shade under dry conditions: the trade-off and the facilitation hypotheses. We performed a meta-analysis of field and greenhouse studies evaluating the effects of drought at two or more irradiance levels on nine response variables describing plant physiological condition, growth, and survival. We explored differences in plant response across plant functional types, ecosystem types and methodological approaches. The data were best fit using quadratic models indicating a humped-back shape response to drought along an irradiance gradient for survival, whole plant biomass, maximum photosynthetic capacity, stomatal conductance and maximal photochemical efficiency. Drought effects were ameliorated at intermediate irradiance, becoming more severe at higher or lower light levels. This general pattern was maintained when controlling for potential variations in the strength of the drought treatment among light levels. Our quantitative meta-analysis indicates that dense shade ameliorates drought especially among drought-intolerant and shade-tolerant species. Wet tropical species showed larger negative effects of drought with increasing irradiance than semiarid and cold temperate species. Non-linear responses to irradiance were stronger under field conditions than under controlled greenhouse conditions. Non-linear responses to drought along the irradiance gradient reconciliate opposing views in plant ecology, indicating that facilitation is more likely within certain range of environmental conditions, fading under deep shade, especially for drought-tolerant species.