Crystal Structure of the HEAT Domain from the Pre-mRNA Processing Factor Symplekin

The majority of eukaryotic pre-mRNAs are processed by 3′-end cleavage and polyadenylation, although in metazoa the replication-dependent histone mRNAs are processed by 3′-end cleavage but not polyadenylation. The macromolecular complex responsible for processing both canonical and histone pre-mRNAs contains the ∼ 1160-residue protein Symplekin. Secondary-structural prediction algorithms identified putative HEAT domains in the 300 N-terminal residues of all Symplekins of known sequence. The structure and dynamics of this domain were investigated to begin elucidating the role Symplekin plays in mRNA maturation. The crystal structure of the Drosophila melanogaster Symplekin HEAT domain was determined to 2.4 Å resolution with single-wavelength anomalous dispersion phasing methods. The structure exhibits five canonical HEAT repeats along with an extended 31-amino-acid loop (loop 8) between the fourth and fifth repeat that is conserved within closely related Symplekin sequences. Molecular dynamics simulations of this domain show that the presence of loop 8 dampens correlated and anticorrelated motion in the HEAT domain, therefore providing a neutral surface for potential protein-protein interactions. HEAT domains are often employed for such macromolecular contacts. The Symplekin HEAT region not only structurally aligns with several established scaffolding proteins, but also has been reported to contact proteins essential for regulating 3′-end processing. Together, these data support the conclusion that the Symplekin HEAT domain serves as a scaffold for protein-protein interactions essential to the mRNA maturation process.     

Verdoheme formation in Proteus mirabilis catalase

Background

Heme oxidative degradation has been extensively investigated in peroxidases but not in catalases. The verdoheme formation, a product of heme oxidation which inactivates the enzyme, was studied in Proteus mirabilis catalase.

Methods

The verdoheme was generated by adding peracetic acid and analyzed by mass spectrometry and spectrophotometry.

Results

Kinetics follow-up of different catalase reactional intermediates shows that i) the formation of compound I always precedes that of verdoheme, ii) compound III is never observed, iii) the rate of compound II decomposition is not compatible with that of verdoheme formation, and iv) dithiothreitol prevents the verdoheme formation but not that of compound II, whereas NADPH prevents both of them. The formation of verdoheme is strongly inhibited by EDTA but not increased by Fe³⁺ or Cu²⁺ salts. The generation of verdoheme is facilitated by the presence of protein radicals as observed in the F194Y mutated catalase. The inability of the inactive variant (H54F) to form verdoheme, indicates that the heme oxidation is fully associated to the enzyme catalysis.

Conclusion

These data, taken together, strongly suggest that the verdoheme formation pathway originates from compound I rather than from compound II.

General significance

The autocatalytic verdoheme formation is likely to occur in vivo.     

近金线属的分类地位及金线属的鉴别特征(鲤形目:鲤科:亚科)

本文根据系统学原理,提出了建立新类元的依据;并据此从分类和系统发育上论证了近金线属ＡｎｃｈｉｃｙｃｌｏｃｈｅｉｌｕｓＬｉｅｔＬａｎ独立成属的可能性,认为应将近金线属归于金线属;修订了金线属ＳｉｎｏｃｙｃｌｏｃｈｅｉｌｕｓＦａｎｇ的鉴别特征。     

When should we expect early bursts of trait evolution in comparative data? Predictions from an evolutionary food web model

Conceptual models of adaptive radiation predict that competitive interactions among species will result in an early burst of speciation and trait evolution followed by a slowdown in diversification rates. Empirical studies often show early accumulation of lineages in phylogenetic trees, but usually fail to detect early bursts of phenotypic evolution. We use an evolutionary simulation model to assemble food webs through adaptive radiation, and examine patterns in the resulting phylogenetic trees and species' traits (body size and trophic position). We find that when foraging trade-offs result in food webs where all species occupy integer trophic levels, lineage diversity and trait disparity are concentrated early in the tree, consistent with the early burst model. In contrast, in food webs in which many omnivorous species feed at multiple trophic levels, high levels of turnover of species' identities and traits tend to eliminate the early burst signal. These results suggest testable predictions about how the niche structure of ecological communities may be reflected by macroevolutionary patterns.     

外源EBR对NaCl胁迫下燕麦幼苗无机离子吸收、运输和分配的影响

为了探讨外源2,4-表油菜素内酯(2,4-epibrassinolide,EBR)诱导燕麦(Avena sativa L.)幼苗抗盐性的效果及其生理调节机制,以"青引2号"和"加燕2号"燕麦为材料,研究NaCl胁迫下施用外源EBR对燕麦幼苗无机离子吸收、运输和分配的影响。结果表明:100mmol·L-1NaCl胁迫下,"青引2号"和"加燕2号"燕麦幼苗叶片和根系中的Na+、Cl-含量均显著升高,对阳离子的吸收产生了拮抗作用,导致燕麦幼苗叶片和根系中的K+、Ca2+、Mg2+、Mn2+、Fe2+、Zn2+、Cu2+含量显著降低,离子稳态平衡被打破; 100 mmol·L-1NaCl胁迫下,施用0.01μmol·L-1外源EBR后,"青引2号"和"加燕2号"燕麦幼苗叶片和根系中的Na+和Cl-含量显著降低,促进了燕麦幼苗根系对K+、Ca2+、Mg2+、Fe2+、Mn2+、Cu2+和Zn2+的吸收,叶片和根系中K+/Na+、Cl-/Na+、Ca2+/Na+、Mg2+/Na+、Fe2+/Na+、Mn2+/Na+、Cu2+/Na+和Zn2+/Na+显著升高,并且有效调控燕麦幼苗体内无机离子的运输...     

The role of temperature in determining distributions and coexistence of three species of Plestiodon

The Common Five-Lined Skink (Plestiodon fasciatus), Southeastern Five-Lined Skink (P. inexpectatus), and Broadheaded Skink (P. laticeps) are all found in forested ecosystems of the southeastern United States and occur in apparent sympatry. No aspect of their ecology has been quantitatively shown to be different. Differences in their natural history, such as northern extent of geographic range, observations of differences in habitat preference, and differing physiological responses to temperature, implicate the thermal environment as a potential niche dimension by which these organisms partition resources. Here we show that the northernmost extent of each species' range can be adequately discriminated by temperature extremes and that their preferred habitats differ in canopy cover, mean temperature, and daily maximum temperatures. These differences are supported by observations in the field. Based upon these findings and observations, we conclude that these species may be able to exist in such close proximity due to differences in their thermal niche, particularly the two like-sized species, P. fasciatus and P. inexpectatus. P. laticeps is a much larger lizard as an adult and functionally coexists with its congeners, potentially by partitioning resources along a different axis.     

Assessing the scale-specific importance of niches and other spatial processes on beta diversity: a case study from a temperate forest

Niche processes and other spatial processes, such as dispersal, may simultaneously control beta diversity, yet their relative importance may shift across spatial and temporal scales. Although disentangling the relative importance of these processes has been a continuing methodological challenge, recent developments in multi-scale spatial and temporal modeling can now help ecologists estimate their scale-specific contributions. Here we present a statistical approach to (1) detect the presence of a space–time interaction on community composition and (2) estimate the scale-specific importance of environmental and spatial factors on beta diversity. To illustrate the applicability of this approach, we use a case study from a temperate forest understory where tree seedling abundances were monitored during a 9-year period at 40 permanent plots. We found no significant space–time interaction on tree seedling composition, which means that the spatial abundance patterns did not vary over the study period. However, for a given year the relative importance of niche processes and other spatial processes was found to be scale-specific. Tree seedling abundances were primarily controlled by a broad-scale environmental gradient, but within the confines of this gradient the finer scale patchiness was largely due to other spatial processes. This case study illustrates that these two sets of processes are not mutually exclusive and can affect abundance patterns in a scale-dependent manner. More importantly, the use of our methodology for future empirical studies should help in the merging of niche and neutral perspectives on beta diversity, an obvious next step for community ecology. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Response of wetland plant species to hydrologic conditions

Understanding hydrologic requirements of native and introduced species is critical to sustaining native plant communities in wetlands of disturbed landscapes. We examined plant assemblages, and 31 of the most common species comprising them, from emergent wetlands in an urbanizing area of the Pacific Northwest, USA, in relation to in situ, fine-scale hydrology. Percent cover by plant species was estimated in 2208 1-m² plots across 43 sites, with water depth at time of vegetation sampling measured in 432 plots. Three years of bi-weekly hydrologic data from each of the 43 sites were used to estimate mean surface water level and mean absolute difference (MAD) in surface water level for every plot. Nine assemblages of plant species that co-occur in the field were identified using TWINSPAN. The assemblage richest in native species occurred under intermediate hydrologic conditions and was bracketed by pasture grass dominated assemblages at drier conditions with low water level variability, and Phalaris arundinacea L. assemblages with higher mean water levels and variability. Results suggest minor changes in average water levels (10 cm) or in variability (±2 cm in MAD) could promote a shift from assemblages dominated by natives to those dominated by invasive or alien taxa. Canonical correspondence analysis segregated the species into four groups related to hydrologic gradients. Each species response group was typified by taxa with similar optima for a given environmental variable, with each group related to a characteristic suite of hydrologic conditions. The most common species (P. arundinacea, Juncus effusus L., and Typha latifolia L.), each representing a different response group, exhibited unique responses in occurrence/abundance in relation to water level variability, but were abundant over a wide range of water depth. The realized niches of other species in each response group were more restricted, with peaks in cover confined to narrower ranges of water depth and variability.     

Fragment Propagation and Colonization Ability Enhanced and Varied at Node Level after Escaping from Apical Dominance in Submerged Macrophytes

Aquatic plants develop strong fragment propagation and colonization ability to endure the natural disturbances. However, detailed research of ability to endure the natural disturbances has been lacking to date. Therefore, reproduction （shoot） and colonization （root） of shoot fragments of Potamogeton crispus L. with or without apices were investigated for the effect of apical dominance, and the growth of decapitated shoot fragments at three lengths （2, 4, 6 cm） was compared. Meanwhile, fragment propagation at levels of bud position was studied for bud position effect after escaping from apical dominance. The results showed significant increases occurred in the outgrowth of lateral branches on fragments decapitated compared with the fragments with apices, implying that apical dominance exists. Different lengths of fragments showed little difference in biomass allocations, but significant differences were noted in their propagation. Meanwhile, the effect of bud position was verified, due to the significant difference of average reproduction per node among the three length groups. Thus, the present study has made progress in the current understanding of aquatic plant dispersion among natural systems and contributes to improve methods of in vitro propagation for re-implantation purposes.     

黄土沟壑区狼牙刺群落优势种群生态位研究

运用Levin公式和百分率相似公式,对狼牙刺群落中13个优势种群的生态位宽度、生态位相似性比例及其生态位重叠值进行了研究.结果表明,生态位宽度依次为狼牙刺(0.964)、茭蒿(0.77)、铁杆蒿(0.664)、黄背草(0.08)、远志(0.48)、狗尾草(0.472)、狗牙根(0.399)、白羊草(0.393)、达乌里胡枝子(0.327)、长芒草(0.321)、杠柳(0.292)、灌木铁线莲(0.21)、糙隐子草(0.234).狼牙刺与其他种群的生态位相似比在0.21～0.76之间,生态位重叠值较高,其他种群与狼牙刺之间的重叠值较低,表明狼牙刺与其他种群之间对资源的竞争并不十分激烈,因而能成为黄土沟壑区狼牙刺群落中利用资源能力和生态适应性最强的优势种群,并在维持群落的物种多样性和相对稳定性中发挥重要作用.