Differences in root architecture influence attraction of fishes to mangroves: A field experiment mimicking roots of different length, orientation, and complexity

Benthic structure plays an important role as shelter and feeding habitat for demersal fauna. While many studies have investigated the relationship between structural complexity of aquatic vegetation and the number of species or abundance of motile organisms, little is known of the attractiveness of submerged mangrove roots. We tested the importance of various root attributes in attracting fish species in a field experiment using different artificial mangrove units (AMUs) with PVC pipes mimicking roots to exclude interaction with other environmental and biotic factors. We manipulated length, vertical orientation, and three-dimensional structural complexity of root mimics in the AMUs to explore their effects on the fish community variables: fish abundance, number of species and community composition. Pipe length and three-dimensional structure did not have an effect on fish community variables. Vertical pipe orientation had a significant effect and AMUs with standing pipes showed higher total fish abundances and number of species than AMUs with hanging pipes. Also community composition differed greatly between AMUs with standing versus hanging pipes. At species level, demersal fish species mainly occupied AMUs with standing pipes and occurred only at very low abundances when hanging pipes dominated in the AMUs; in contrast, the semi-pelagic swimmer Sphyraena barracuda showed a trend of higher abundance in AMUs with mainly hanging pipes. When analyzed across all AMUs, fish abundances of demersal as well as semi-pelagic species decreased significantly with increasing interspatial pipe distance among AMUs, suggesting that distance to refuge may be the underlying mechanism for the observed patterns. The above findings are important in the context of the worldwide degradation of mangroves, because human alteration to mangrove vegetation affects its structure and thus composition and size of fish communities.     

不同生境条件下滨海芦苇湿地C、N、P化学计量特征

为阐明不同生境对黄河三角洲滨海芦苇湿地土壤和植物碳(C)氮(N)磷(P)含量及生态化学计量特征的影响,选取新生湿地和退耕湿地两种湿地类型为研究对象,对土壤和植物体C、N、P含量及其化学计量特征进行研究。研究表明:1)退耕芦苇湿地土壤TC、TN的含量明显增加,TP的含量变化不大。2)新生湿地和退耕湿地土壤R_(C、N、P)分别为42.6:1.6:1、71.2:2.0:1,R_(NP)低于全球平均水平(13.1)和我国平均水平(5.2),土壤表现为N限制。新生湿地土壤剖面中,R_(CN)和R_(CP)变化剧烈;R_(NP)值随深度的增加而减小;退耕湿地土壤R_(C、N、P)值规律性较好,R_(CN)随深度的增加而变大,R_(CP)和R_(NP)值随深度的增加而减小。3)新生湿地和退耕湿地中芦苇整株R_(CN)、R_(CP)和R_(NP)平均值分别为78.2、1753、22.4;67.0、1539、23.0。开垦活动可以降低芦苇植物体R_(CN)和R_(CP)值,但由于芦苇植物体本身对R_(NP)的约束性较高,对R_(NP)值的影响不大,芦苇植株R_(NP)约为23。以上结论可以为黄河三角洲国家级自然保护区正在进行的湿地保护与恢复工作提供借鉴和参考。     

Solvent effects on the conformational transition of a model polyalanine peptide

We have investigated the folding of polyalanine by combining discontinuous molecular dynamics simulation with our newly developed off-lattice intermediate-resolution protein model. The thermodynamics of a system containing a single Ac-KA(14)K-NH(2) molecule has been explored by using the replica exchange simulation method to map out the conformational transitions as a function of temperature. We have also explored the influence of solvent type on the folding process by varying the relative strength of the side-chain's hydrophobic interactions and backbone hydrogen bonding interactions. The peptide in our simulations tends to mimic real polyalanine in that it can exist in three distinct structural states: alpha-helix, beta-structures (including beta-hairpin and beta-sheet-like structures), and random coil, depending upon the solvent conditions. At low values of the hydrophobic interaction strength between nonpolar side-chains, the polyalanine peptide undergoes a relatively sharp transition between an alpha-helical conformation at low temperatures and a random-coil conformation at high temperatures. As the hydrophobic interaction strength increases, this transition shifts to higher temperatures. Increasing the hydrophobic interaction strength even further induces a second transition to a beta-hairpin, resulting in an alpha-helical conformation at low temperatures, a beta-hairpin at intermediate temperatures, and a random coil at high temperatures. At very high values of the hydrophobic interaction strength, polyalanines become beta-hairpins and beta-sheet-like structures at low temperatures and random coils at high temperatures. This study of the folding of a single polyalanine-based peptide sets the stage for a study of polyalanine aggregation in a forthcoming paper.     

Over-expression of a scopoletin glucosyltransferase in Nicotiana tabacum leads to precocious lesion formation during the hypersensitive response to tobacco mosaic virus but does not affect virus resistance

Nicotiana tabacum Togt encodes a scopoletin glucosyltransferase (UDPglucose:scopoletin O -beta-D-glucosyltrans- ferase, EC 2.4.1.128) known to act in vitro on many different substrates including the 6-methoxy-7-hydroxy- coumarin scopoletin. This phenolic compound accumulates in vast amounts, essentially in its glucosylated form scopolin, in tobacco during the hypersensitive response (HR) to tobacco mosaic virus (TMV). To identify the physiological role of this pathogen-inducible UDP-Glc glucosyltransferase (UGT), we generated TOGT over-expressing transgenic plants. Although no endogenous scopoletin or scopolin could be detected before infection, the accumulation of both the aglycone and the glucoside was found to be 2-fold higher in transgenic plants after inoculation with TMV than in wild-type plants. Scopoletin UGT activity in plants over-expressing Togt was significantly higher during the HR than in control plants. This up-regulated activity was associated with a strong increase of the bright blue fluorescence surrounding the HR-necrotic lesions under UV light, which is known to correlate with scopoletin and scopolin abundance. Necrosis appeared sooner in transgenic plants and lesions developed faster, suggesting an accelerated HR. Unexpectedly, the viral content in each lesion was not significantly different in transgenic and in wild-type plants. These results are discussed in relation to the role of TOGT as the major UDP-Glc: scopoletin glucosyltransferase and to the importance of scopoletin accumulation during the HR.     

Energetic approach to the folding of alpha/beta barrels

The folding of a polypeptide into a parallel (alpha/beta)8 barrel (which is also called a circularly permuted beta 8 alpha 8 barrel) has been investigated in terms of energy minimization. According to the arrangement of hydrogen bonds between two neighboring beta-strands of the central barrel therein, such an alpha/beta barrel structure can be folded into six different types: (1) left-tilted, left-handed crossover; (2) left-tilted, right-handed crossover; (3) nontilted, left-handed crossover; (4) nontilted, right-handed crossover; (5) right-tilted, left-handed crossover; and (6) right-tilted, right-handed crossover. Here "tilt" refers to the orientational relation of the beta-strands to the axis of the central beta-barrel, and "crossover" to the beta alpha beta folding connection feature of the parallel beta-barrel. It has been found that the right-tilted, right-handed crossover alpha/beta barrel possesses much lower energy than the other five types of alpha/beta barrels, elucidating why the observed alpha/beta barrels in proteins always assume the form of right tilt and right-handed crossover connection. As observed, the beta-strands in the energy-minimized right-tilted, right-handed crossover (alpha/beta)8-barrel are of strong right-handed twist. The value of root-mean-square fits also indicates that the central barrel contained in the lowest energy (alpha/beta)8 structure thus found coincides very well with the observed 8-stranded parallel beta-barrel in triose phosphate isomerase (TIM). Furthermore, an energetic analysis has been made demonstrating why the right-tilt, right-handed crossover barrel is the most stable structure. Our calculations and analysis support the principle that it is possible to account for the main features of frequently occurring folding patterns in proteins by means of conformational energy calculations even for very complicated structures such as (alpha/beta)8 barrels.     

Chelicerae as male grasping organs in scorpions: sexual dimorphism and associated behaviour

Specialised structures that enable males to grasp females during sexual interactions are highly susceptible to selection and thus diverge relatively rapidly over evolutionary time. These structures are often used to test hypotheses regarding sexual selection such as sexually antagonistic co-evolution and sexual selection by female choice. In the present study, we determine whether there is a relationship between a novel record of scorpion sexual dimorphism, the sexual dimorphism of chelicerae (CSD), and the presence of the mating behaviour termed “cheliceral grip” (CG). The presence of both traits in the order Scorpiones is also reviewed from a phylogenetic perspective. The results confirm a strong relationship between CSD and the presence of CG. The morphological and behavioural patterns associated with “CSD–CG” are opposed to the predictions postulated by the hypothesis of sexually antagonistic co-evolution. However, if the female shows resistance after the deposition of the spermatophore, the possibility that the male exerts pressure as a “cryptic form” of coercion to prevent the interruption of mating cannot be ruled out completely. Female choice by “mechanical fit” could be another explanation for some aspects of the CG's contact zone. The possibility that the “CG–CSD” complex has evolved under natural selection in order to ensure sperm transfer is also considered.     

Tracing Primordial Protein Evolution through Structurally Guided Stepwise Segment Elongation

The understanding of how primordial proteins emerged has been a fundamental and longstanding issue in biology and biochemistry. For a better understanding of primordial protein evolution, we synthesized an artificial protein on the basis of an evolutionary hypothesis, segment-based elongation starting from an autonomously foldable short peptide. A 10-residue protein, chignolin, the smallest foldable polypeptide ever reported, was used as a structural support to facilitate higher structural organization and gain-of-function in the development of an artificial protein. Repetitive cycles of segment elongation and subsequent phage display selection successfully produced a 25-residue protein, termed AF.2A1, with nanomolar affinity against the Fc region of immunoglobulin G. AF.2A1 shows exquisite molecular recognition ability such that it can distinguish conformational differences of the same molecule. The structure determined by NMR measurements demonstrated that AF.2A1 forms a globular protein-like conformation with the chignolin-derived β-hairpin and a tryptophan-mediated hydrophobic core. Using sequence analysis and a mutation study, we discovered that the structural organization and gain-of-function emerged from the vicinity of the chignolin segment, revealing that the structural support served as the core in both structural and functional development. Here, we propose an evolutionary model for primordial proteins in which a foldable segment serves as the evolving core to facilitate structural and functional evolution. This study provides insights into primordial protein evolution and also presents a novel methodology for designing small sized proteins useful for industrial and pharmaceutical applications.