Microboring organisms in living stylasterid corals (Cnidaria,Hydrozoa)

Microboring or euendolithic microorganisms, which colonize and penetrate various carbonate substrates, are abundant in coral reef ecosystems and play a major role in reef carbonate dissolution. A few studies reported the presence of euendoliths in stylasterid coral skeletons but the biological identity, distribution and abundance of these microorganisms remain largely unknown. Observations of over 100 stylasterid colonies, collected in the Indo-Pacific area, revealed for the first time that the association between these corals and euendolith organisms appears to be quite common in shallow tropical waters. The most abundant euendolith was identified as a cryptic stage in the development of the rhodophyte Porphyra (Conchocelis stage). The euendoliths were observed in the skeletons of seven species of three genera (four Stylaster, two Distichopora and one Lepidotheca). The presence of euendoliths inside skeletons conferred a particular colour to the studied stylasterid corals. Distribution and abundance of microborings varied significantly among stylasterid species and among branches of a single colony and so did the colour of their skeletons. Colonization of skeletons and the associated colour distribution were almost uniform in some stylasterids, forming an upward gradually diminishing or sharply limited gradient. This study shows that patterns of euendolith colonization and growth in stylasterid skeletons may depend on the stage of the euendolith development as well as on their environmental requirements such as light exposure.     

Diverse mechanisms of metaeffector activity in an intracellular bacterial pathogen,Legionella pneumophila

Pathogens deliver complex arsenals of translocated effector proteins to host cells during infection, but the extent to which these proteins are regulated once inside the eukaryotic cell remains poorly defined. Among all bacterial pathogens, Legionella pneumophila maintains the largest known set of translocated substrates, delivering over 300 proteins to the host cell via its Type IVB, Icm/Dot translocation system. Backed by a few notable examples of effector–effector regulation in L. pneumophila, we sought to define the extent of this phenomenon through a systematic analysis of effector–effector functional interaction. We used Saccharomyces cerevisiae, an established proxy for the eukaryotic host, to query > 108,000 pairwise genetic interactions between two compatible expression libraries of ~330 L. pneumophila‐translocated substrates. While capturing all known examples of effector–effector suppression, we identify fourteen novel translocated substrates that suppress the activity of other bacterial effectors and one pair with synergistic activities. In at least nine instances, this regulation is direct—a hallmark of an emerging class of proteins called metaeffectors, or “effectors of effectors”. Through detailed structural and functional analysis, we show that metaeffector activity derives from a diverse range of mechanisms, shapes evolution, and can be used to reveal important aspects of each cognate effector's function. Metaeffectors, along with other, indirect, forms of effector–effector modulation, may be a common feature of many intracellular pathogens—with unrealized potential to inform our understanding of how pathogens regulate their interactions with the host cell.     

Deciphering structure-activity relationships in a series of Tat/TAR inhibitors

A series of pentameric “Polyamide Amino Acids” (PAAs) compounds derived from the same trimeric precursor have been synthesized and investigated as HIV TAR RNA ligands, in the absence and in the presence of a Tat fragment. All PAAs bind TAR with similar sub-micromolar affinities but their ability to compete efficiently with the Tat fragment strongly differs, IC₅₀ ranging from 35 nM to >2 μM. While NMR and CD studies reveal that all PAA interact with TAR at the same site and induce globally the same RNA conformational change upon binding, a comparative thermodynamic study of PAA/TAR equilibria highlights distinct TAR binding modes for Tat competitor and non-competitor PAAs. This led us to suggest two distinct interaction modes that have been further validated by molecular modeling studies. While the binding of Tat competitor PAAs induces a contraction at the TAR bulge region, the binding of non-competitor ones widens it. This could account for the distinct PAA ability to compete with Tat fragment. Our work illustrates how comparative thermodynamic studies of a series of RNA ligands of same chemical family are of value for understanding their binding modes and for rationalizing structure-activity relationships.     

Redesigning the stereospecificity of tyrosyl‐tRNA synthetase

d ‐Amino acids are largely excluded from protein synthesis, yet they are of great interest in biotechnology. Unnatural amino acids have been introduced into proteins using engineered aminoacyl‐tRNA synthetases (aaRSs), and this strategy might be applicable to d ‐amino acids. Several aaRSs can aminoacylate their tRNA with a d ‐amino acid; of these, tyrosyl‐tRNA synthetase (TyrRS) has the weakest stereospecificity. We use computational protein design to suggest active site mutations in Escherichia coli TyrRS that could increase its d ‐Tyr binding further, relative to l ‐Tyr. The mutations selected all modify one or more sidechain charges in the Tyr binding pocket. We test their effect by probing the aminoacyl‐adenylation reaction through pyrophosphate exchange experiments. We also perform extensive alchemical free energy simulations to obtain l ‐Tyr/d ‐Tyr binding free energy differences. Agreement with experiment is good, validating the structural models and detailed thermodynamic predictions the simulations provide. The TyrRS stereospecificity proves hard to engineer through charge‐altering mutations in the first and second coordination shells of the Tyr ammonium group. Of six mutants tested, two are active towards d ‐Tyr; one of these has an inverted stereospecificity, with a large preference for d ‐Tyr. However, its activity is low. Evidently, the TyrRS stereospecificity is robust towards charge rearrangements near the ligand. Future design may have to consider more distant and/or electrically neutral target mutations, and possibly design for binding of the transition state, whose structure however can only be modeled. Proteins 2016; 84:240–253. © 2015 Wiley Periodicals, Inc.     

Species–habitat associations and demographic rates of forest trees

Niche‐driven effects on demographic processes generated in response to habitat heterogeneity partly shape local distributions of species. Thus, tree distributions are commonly studied in relation to habitat conditions to understand how niche differentiation contributes to species coexistence in forest communities. Many such studies implicitly assume that local abundance reflects habitat suitability, and that abundance is relatively stable over time. We compared models based on abundance with those based on demographic performance for making inferences about habitat association for 287 tree species from three large dynamic plots located in tropical, subtropical and temperate forests. The correlation between the predictions of the abundance‐based models and the demography‐based models varied widely, with correlation coefficients ranging nearly from ?1 to 1.This suggests that the two types of models capture different information about species–habitat associations. Demography‐based models evaluate habitat quality by focusing on population processes and thus should be preferred for understanding responses of tree species to habitat conditions, especially when habitat conditions are changing and species–habitat interactions cannot be considered to be at equilibrium.     

Stand density and species richness affect carbon storage and net primary productivity in early and late successional temperate forests differently

How stand density and species richness affect carbon (C) storage and net primary productivity (NPP) changes with forest succession is poorly understood. We quantified the C storage of trees and the aboveground NPP in an early successional secondary birch forest (birch forest) and a late successional mixed broadleaf-Korean pine (Pinus koraiensis) forest (mixed forest) in northeastern China. We found that: 1) tree C storage in the mixed forest (120.3 Mg C ha^?1) was significantly higher than that in the birch forest (78.5 Mg C ha^?1), whereas the aboveground NPP was not different between the two forest types; and 2) only stand density had a positive linear relationship with tree C storage and aboveground NPP in the birch forest. In the mixed forest, both tree C storage and aboveground NPP were significantly affected by the combination of the stand density and species richness. The tree C storage to stand density and species richness relationships were hump-shaped. The aboveground NPP increased with increasing stand density, but its relationship to species richness was hump-shaped. We conclude that the effect of stand density and species richness on tree C storage and aboveground NPP was influenced by forest stand succession, and such effects should be considered in studying stand density- and species richness- ecosystem function (e.g., C storage and NPP) relationships in temperate forest ecosystems.     

Natural triploid Lilium leichtlinii var. maximowiczii populations in Korea

To clarify the ploidy and distribution of Lilium leichtlinii var. maximowiczii populations in Korea, we inspected several mountains and northern valleys and almost all of the sea coast of South Korea. We found nine diploid populations and 19 triploid populations. Many large and small populations were distributed around northern Chungcheongbook‐do and Gyunggi‐do and all over Kangwon‐do. The diploid plants were smaller than the triploid plants in almost all of their morphological characteristics. This is the second report of natural polyploid complexes of diploids and triploids in the genus Lilium.     

氯己定联合联苯苄唑对念珠菌的协同抗菌活性

本文用两种方法评价了联苯苄唑与氯己定联用对临床分离念珠菌的抑菌活性。微量液基稀释法显示,氯己定单独作用于念珠菌时,对念珠菌没有明显的抑制作用,最低抑菌浓度均大于16μg/mL;与联苯苄唑联合应用时,对17株念珠菌均表现为协同抑菌作用。纸片扩散法也观察到,含氯己定和联苯苄唑的纸片对4种念珠菌均能产生直径大于单药纸片的抑菌圈。结果显示,联苯苄唑联合低浓度氯己定对多种念珠菌具有协同抑菌作用。