StructureSelector: A web‐based software to select and visualize the optimal number of clusters using multiple methods

Inferences of population genetic structure are of great importance to the fields of ecology and evolutionary biology. The program structure has been widely used to infer population genetic structure. However, previous studies demonstrated that uneven sampling often leads to wrong inferences on hierarchical structure. The most widely used ΔK method tends to identify the uppermost hierarchy of population structure. Recently, four alternative statistics (medmedk , medmeak , maxmedk and maxmeak ) were proposed, which appear to be more accurate than the previously used methods for both even and uneven sampling data. However, the lack of easy‐to‐use software limits the use of these appealing new estimators. Here, we developed a web‐based user‐friendly software structureselector to calculate the four appealing alternative statistics together with the commonly used Ln Pr(X|K) and ΔK statistics. structureselector accepts the result files of structure , admixture or faststructure as input files. It reports the “best” K for each estimator, and the results are available as HTML or tab separated tables. The program can also generate graphical representations for specific K, which can be easily downloaded from the server. The software is freely available at http://lmme.qdio.ac.cn/StructureSelector/ .     

Characterization of the molecular properties of KtrC,a second RCK domain that regulates a Ktr channel in Bacillus subtilis

RCK (regulating conductance of K⁺) domains are common regulatory domains that control the activity of eukaryotic and prokaryotic K⁺ channels and transporters. In bacteria these domains play roles in osmoregulation, regulation of turgor and membrane potential and in pH homeostasis. Whole-genome sequencing unveiled RCK gene redundancy, however the biological role of this redundancy is not well understood. In Bacillus subtilis, there are two closely related RCK domain proteins (KtrA and KtrC) that regulate the activity of the Ktr cation channels. KtrA has been well characterized but little is known about KtrC. We have characterized the structural and biochemical proprieties of KtrC and conclude that KtrC binds ATP and ADP, just like KtrA. However, in solution KtrC exist in a dynamic equilibrium between octamers and non-octameric species that is dependent on the bound ligand, with ATP destabilizing the octameric ring relative to ADP. Accordingly, KtrC-ADP crystal structures reveal closed octameric rings similar to those in KtrA, while KtrC-ATP adopts an open assembly with RCK domains forming a super-helix. In addition, both KtrC-ATP and -ADP octamers are stabilized by the signaling molecule cyclic-di-AMP, which binds to KtrC with high affinity. In contrast, c-di-AMP binds with 100-fold lower affinity to KtrA. Despite these differences we show with an E. coli complementation assay that KtrC and KtrA are interchangeable and able to form functional transporters with both KtrB and KtrD. The distinctive properties of KtrC, in particular ligand-dependent assembly/disassembly, suggest that this protein has a specific physiological role that is distinct from KtrA.     

Crystal structure determination of a neutral neurotoxin BmK M4 from Buthus martensii Karsch at 0.20 nm

BmK M4 is a neutral neurotoxin in the BmK toxin series.It is medially toxic and belongs to group III α-toxins.The purified sample was crystallized in rhombic space group P61.Using an X-ray diffraction technique,the crystal structure of BmK M4 was revealed by molecular replacement at 0.20 nm resolution.The model was refined.The final crystallographic R factor was 0.142 and the free R factor was 0.173.The root mean square deviation is 0.001 5 nm for the bond length and 1.753°for the bond angles.64 water molecules were added to the asymmetric unit.The refined structure showed an unusual non-prolyl cis peptide bond at residue 10.The structure was compared with group II α-toxin BmK M8 (an acidic,weak toxin).The potential structural implications of the cis peptide bond were discussed.     

EFFECTS OF DISTURBANCE ON EPIPHYTIC COMMUNITY ARCHITECTURE1

Microdistributional patterns of attached algal communities on Cladophora and glass slides were compared under varying disturbance regimes in the Upper Mississippi River, using light and scanning electron microscopy. Localized physical disturbance, induced by boat traffic and wind-generated wave action in the main channel, inhibited development of complex attached algal communities and maintained an adnate flora with two-dimensional architecture. In contrast, communities protected from disturbance developed a more complex, three-dimensional architecture. A high degree of architectural similarity was observed between communities on Cladophora and glass substrates exposed to similar levels of disturbance. Communities exposed to severe disturbance resembled ones in early stages of colonization and development, whereas less disturbed communities were similar to ones in advanced stages of development. These results demonstrated that turbulence strongly influences the community structure of periphyton on both micro and macro scale levels.     

Phylogenetic scale in ecology and evolution

Aim

Many important patterns and processes vary across the phylogeny and depend on phylogenetic scale. Nonetheless, phylogenetic scale has never been formally conceptualized, and its potential remains largely unexplored. Here, we formalize the concept of phylogenetic scale, review how phylogenetic scale has been considered across multiple fields and provide practical guidelines for the use of phylogenetic scale to address a range of biological questions.

Innovation

We summarize how phylogenetic scale has been treated in macroevolution, community ecology, biogeography and macroecology, illustrating how it can inform, and possibly resolve, some of the longstanding controversies in these fields. To promote the concept empirically, we define phylogenetic grain and extent, scale dependence, scaling and the domains of phylogenetic scale. We illustrate how existing phylogenetic data and statistical tools can be used to investigate the effects of scale on a variety of well‐known patterns and processes, including diversification rates, community structure, niche conservatism or species‐abundance distributions.

Main conclusions

Explicit consideration of phylogenetic scale can provide new and more complete insight into many longstanding questions across multiple fields (macroevolution, community ecology, biogeography and macroecology). Building on the existing resources and isolated efforts across fields, future research centred on phylogenetic scale might enrich our understanding of the processes that together, but over different scales, shape the diversity of life.     

Crystallographic analysis of the pH-dependent binding of iminobiotin by streptavidin.

Streptavidin binds 2'-iminobiotin in a pH-dependent fashion--affinity decreases as the pH is lowered. This property makes the purification of compounds conjugated to streptavidin or immobiotin possible under mild conditions by affinity chromatography. In order to understand the molecular details of this pH-dependent binding, we analyzed the crystal structures of the complex of core streptavidin with 2'-iminobiotin at pH values 4.0 and 7.5. The two structures are very similar to each other even at their binding sites. Although the relative abundance of the protonated species of the ligand is increased more than 3,000-fold on going from pH 7.5 to pH 4.0, both structures contain only the nonprotonated from of the ligand. Streptavidin selects the nonprotonated form, which, at pH 4.0, is one part in 7.9 x 10(7).     

The spiral glands of Nereis

Summary The spiral organs of Nereis have been shown to be compound glands and not photoreceptors. The ducts of two or three types of secretory cells attach themselves in a serial manner to a spirally wound axial columella which lies just below the cuticle. The large intra-cellular ducts terminate in a number of fine ducts which penetrate the columella and open through it into the lumen of the gland. This communicates to the outside through a pore in the cuticle. The secretions are muco-polysaccharides which are probably mixed in the lumen before discharge.We should like to acknowledge the support of this work by the Science Research Council.     

Distinguishing enzyme structures from non-enzymes without alignments

The ability to predict protein function from structure is becoming increasingly important as the number of structures resolved is growing more rapidly than our capacity to study function. Current methods for predicting protein function are mostly reliant on identifying a similar protein of known function. For proteins that are highly dissimilar or are only similar to proteins also lacking functional annotations, these methods fail. Here, we show that protein function can be predicted as enzymatic or not without resorting to alignments. We describe 1178 high-resolution proteins in a structurally non-redundant subset of the Protein Data Bank using simple features such as secondary-structure content, amino acid propensities, surface properties and ligands. The subset is split into two functional groupings, enzymes and non-enzymes. We use the support vector machine-learning algorithm to develop models that are capable of assigning the protein class. Validation of the method shows that the function can be predicted to an accuracy of 77% using 52 features to describe each protein. An adaptive search of possible subsets of features produces a simplified model based on 36 features that predicts at an accuracy of 80%. We compare the method to sequence-based methods that also avoid calculating alignments and predict a recently released set of unrelated proteins. The most useful features for distinguishing enzymes from non-enzymes are secondary-structure content, amino acid frequencies, number of disulphide bonds and size of the largest cleft. This method is applicable to any structure as it does not require the identification of sequence or structural similarity to a protein of known function.     

Substrate-binding loop interactions with pseudouridine trigger conformational changes that promote catalytic efficiency of pseudouridine kinase PUKI

Pseudouridine, one major RNA modification, is catabolized into uracil and ribose-5′-phosphate by two sequential enzymatic reactions. In the first step, pseudouridine kinase (PUKI) phosphorylates pseudouridine to pseudouridine 5′-monophosphate. High-fidelity catalysis of pseudouridine by PUKI prevents possible disturbance of in vivo pyrimidine homeostasis. However, the molecular basis of how PUKI selectively phosphorylates pseudouridine over uridine with >100-fold greater efficiency despite minor differences in their K_m values has not been elucidated. To investigate this selectivity, in this study we determined the structures of PUKI from Escherichia coli strain B (EcPUKI) in various ligation states. The structure of EcPUKI was determined to be similar to PUKI from Arabidopsis thaliana, including an α/β core domain and β-stranded small domain, with dimerization occurring via the β-stranded small domain. In a binary complex, we show that Ser30 in the substrate-binding loop of the small domain mediates interactions with the hallmark N1 atom of pseudouridine nucleobase, causing conformational changes in its quaternary structure. Kinetic and fluorescence spectroscopic analyses also showed that the Ser30-mediated interaction is a prerequisite for conformational changes and subsequent catalysis by EcPUKI. Furthermore, S30A mutation or EcPUKI complexed with other nucleosides homologous to pseudouridine but lacking the pseudouridine-specific N1 atom did not induce such conformational changes, demonstrating the catalytic significance of the proposed Ser30-mediated interaction. These analyses provide structural and functional evidence for a pseudouridine-dependent conformational change of EcPUKI and its functional linkage to catalysis.