The evolutionary history of the allopolyploid Squalius alburnoides (Cyprinidae) complex in the northern Iberian Peninsula

Understanding the population structure, population dynamics and processes that give rise to polyploidy and helps to maintain it is central to our knowledge of the evolution of asexual vertebrates. Previous studies revealed high genetic diversity and several reproductive pathways in the southern populations of the Squalius alburnoides hybrid complex. In contrast, lower genetic variability and the associated limited chance of introducing new genetic combinations may threaten the survival of the northern Mondego populations. We analysed the genetic diversity and structure of nine populations of S. alburnoides in the Iberian Peninsula using microsatellite loci to provide further insights on the evolutionary history of this complex. Special attention was given to the less-studied northern populations (Mondego and Douro basins). Marked population structure, a high frequency of private alleles and a high diversity of some biotypes in the Douro basin indicate that some northern populations may not be at high risk of extinction, contrary to what was expected. The genetic diversity found in the northern Douro populations contradicts the general trend of remarkable genetic impoverishment northwards that occurs in other species and regions. The results indicate the possible existence of a glacial refugium in the Rabaçal River, corroborating findings in other species of this region. Historical events seem to have affected the geographical patterns of genetic variability found among and within the northern and southern populations of this complex and contributed to different patterns of genome composition. Therefore, historical events might have a major role in the long-term persistence of some polyploid hybrid taxa.     

Structural, photophysical and theoretical studies of two dodecachlorinated porphyrins

Two dodecachlorinated porphyrins, 2,3,7,8,12,13,17,18-octachloro-5,10,15,20-tetra(4-chlorophenyl)porphyrin free base (TCl₁₂PPH₂) and its nickel compound (TCl₁₂PPNi), have been synthesized. Single-crystal X-ray diffraction analysis shows that porphyrin rings are heavily distorted and exhibit saddled conformations. The Soret and Q bands of two compounds are red-shifted compared to their non-chlorinated counterparts. Theoretical calculations reveal that the optical band gap of TCl₁₂PPH₂ is reduced, whereas that of TCl₁₂PPNi remains almost the same as to its non-chlorinated nickel compound due to the concurrent lowering of HOMO and LUMO energy levels. The frontier molecular orbitals are degenerated due to the decrease of symmetry of the molecules.     

Synthesis and structures of mono and binuclear nickel(II) thiolate complexes of a dicompartmental pseudo-macrocycle with N(imine)2S2 and N(oxime)2S2 metal-binding sites

The reaction of [Ni(pftp)] [pftp = N,N-propane-1,3-diyl-(6-formyl-4-methyliminatothiophenolato)] with hydroxylamine hydrochloride in the presence potassium acetate in MeOH resulted in the formation of the complex [Ni(LH₂)] [L = N,N-propane-1,3-diyl-(4-methyl-2-methyliminato-6-methyloxime-thiophenolato)] in good yield. A single crystal X-ray diffraction structural determination showed a mononuclear nickel(II) complex with the new acyclic ligand LH₂ that had been functionalised with two oxime groups containing an empty N(oxime)₂S₂ pocket to which another metal ion could be added. A further reaction of [Ni(LH₂)] with NiCl₂·6H₂O, triethylamine and ammonium hexafluorophosphate in MeOH gave a dark red product that yielded red crystals of [Ni₂(LH)]PF₆·DMF via slow recrystallisation from a DMF/PrⁱOH solvent mixture. A single crystal X-ray diffraction study of these crystals confirmed the presence of a dinuclear nickel(II) complex linked by a dithiolato-bridge. Both nickel(II) ions exhibited square-planar geometry where the metal centres are coordinated in two distinct cis-S₂N(imine)₂ and cis-S₂N(oxime)₂ binding sites provided by the new dicompartmental oxime/thiolate-containing ligand LH.     

A critique of the utility of the prediction of protein secondary structure

The Chou-Fasman predictive algorithm for determining the secondary structure of proteins from the primary sequence is reviewed. Many examples of its use are presented which illustrate its wide applicability, such as predicting (a) regions with the potential for conformational change, (b) sequences which are capable of assuming several conformations in different environments, (c) effects of single amino acid mutations, (d) amino acid replacements in synthesis of peptides to bring about a change in conformation, (e) guide to the synthesis of polypeptides with definitive secondary structure,e.g. signal sequences, (f) conformational homologues from varying sequences and (g) the amino acid requirements for amphiphilicα-helical peptides.     

Structural analysis of the N‐terminal fragment of the antiangiogenic protein endostatin: A molecular dynamics study

Endostatin is a potent antiangiogenic protein derived from the noncollagenous domain 1 (NC1) of collagen XVIII. The mechanism by which endostatin exerts its antiangiogenic effect is still incompletely understood. It has been shown that the 27 amino acid N‐terminal fragment of murine endostatin has antitumor, antimigration, and antipermeability activities comparable to the full soluble protein. To understand how this peptide can exert such elaborate function, we performed structural analysis using molecular dynamics to evaluate the behavior of this fragment in aqueous environment. Here, we show that the N‐terminal peptide of murine endostatin is able to assume a well‐defined structure, folding into a zinc‐dependent β‐hairpin conformation. Analyzing the folding mechanism, we were able to understand why the N‐terminal peptide of human endostatin with the same length failed to acquire a stable conformation. Conversely, we were able to predict the successful folding of the R4Q mutant and of a shorter form of the human peptide with 25 residues. Finally, we show that the β‐hairpin conformation assumed by the zinc‐bound peptide of murine endostatin has a high structural similarity with fragments of another family of angiogenesis inhibitors: the integrin‐binding portion of the NC1 domain of collagen IV. Indeed, our docking simulations show that arresten, canstatin, and the endostatin peptide bind to the same spot of αVβ3 integrin, suggesting similar interactions via a common binding site on this receptor. Proteins 2011;. © 2011 Wiley‐Liss, Inc.     

Structural and functional domains of cellobiohydrolase I from trichoderma reesei

Limited proteolysis (papain) of the cellobiohydrolase I (CBH I, 65 kDa) from Trichoderma reesei led to the seperation of two functional domains: a core protein (55 kDa) containing the active site, and a C-terminal glycopeptide (10 kDa) implicated in binding to the insoluble matrix (cellulose). The quaternary structures of the intact CBH I and its core in solution are now compared by small angle X-ray scattering (SAXS) measurements. The molecular parameters derived for the core (Rg=2.09 nm, D_max=6.5 nm) and for the intact enzyme (Rg=4.27 nm, D_max=18 nm) indicate very different shapes. The resulting models show a tadpole-like structure for the intact enzyme where the isotropic part coincides with the core protein and the flexible tail part should be identified with the C-terminal glycopeptide. Thus in this enzyme, functional differentiation is reflected in structural peculiarities.Abbreviations SAXS small angle X-ray scattering - SDS-PAGE SDS-polyacrylamide gel electrophoresis - IEF-PAG polyacrylamide gel isoelectric focusing; cellobiohydrolase (CBH, 1,4--glucan cellobio hydrolase (E.C.3.2.1.91)) - D_max maximum diameter - Rg radius of gyration     

Dimerisation and an increase in active site aromatic groups as adaptations to high temperatures: X-ray solution scattering and substrate-bound crystal structures of Rhodothermus marinus endoglucanase Cel12A

Cellulose, a polysaccharide consisting of beta-1,4-linked glucose, is the major component of plant cell walls and consequently one of the most abundant biopolymers on earth. Carbohydrate polymers such as cellulose are molecules with vast diversity in structure and function, and a multiplicity of hydrolases operating in concert are required for depolymerisation. The bacterium Rhodothermus marinus, isolated from shallow water marine hot springs, produces a number of carbohydrate-degrading enzymes including a family 12 cellulase Cel12A. The structure of R.marinus Cel12A in the ligand-free form (at 1.54 angstroms) and structures of RmCel12A after crystals were soaked in cellopentaose for two different lengths of time, have been determined. The shorter soaked complex revealed the conformation of unhydrolysed cellotetraose, while cellopentaose had been degraded more completely during the longer soak. Comparison of these structures with those of mesophilic family 12 cellulases in complex with inhibitors and substrate revealed that RmCel12A has a more extensive aromatic network in the active site cleft which ejects products after hydrolysis. The substrate structure confirms that during hydrolysis by family 12 cellulases glucose does not pass through a (2,5)B conformation. Small-angle X-ray scattering analysis of RmCel12A showed that the enzyme forms a loosely associated antiparallel dimer in solution, which may target the enzyme to the antiparallel polymer strands in cellulose.     

弓形革囊星虫组织结构和超微结构观察

弓形革囊星虫(Phascolosoma arcuatum)是近年兴起的水产养殖品种,目前已形成一定养殖规模,但是其生物学特性相关的研究只有零星报道。本文主要采用石蜡切片苏木精-伊红(H.E)染色和扫描电镜方法对弓形革囊星虫的整体形态和各主要器官的结构进行研究。结果表明,弓形革囊星虫主要由吻部和躯干部构成,躯干部有乳突分布;吻部由触手和项器构成,伸长可达躯干部的两倍,具有感光性。其消化系统由口、食道、肠、肛门四个部分构成,不同部分的肌肉组织存在明显差异;收吻肌一端与吻相连,另一端分成4支,分别连于背部两侧(背收吻肌)和腹部两侧(腹收吻肌);食道贴于收吻肌,后连接肠。肠分为肠下回环与肠上回环,肠上回环与肠下回环缠绕盘旋,肠上回环后接直肠。直肠具有盲囊,后连接肛门;两条肾管分布在腹侧。     

A tetracopper(II) complex with N,N′-bis(picolinoyl)hydrazine

Synthesis, physical properties and X-ray structure of a hydrated tetranuclear copper(II) complex [Cu₄(μ-diph)₂(μ-H₂O)₂(O₂CCH₃)₄(H₂O)₂]·4H₂O with N,N′-bis(picolinoyl)hydrazine (H₂diph) are reported. The centrosymmetric complex has two types of copper(II) centres with distorted square-pyramidal N₂O₃ coordination spheres. The dinucleating trans planar diph²⁻ ligands are parallel to each other and act as N₂O-donor to one metal centre and N₂-donor to the other metal centre. The complex has a rectangular {Cu₄(μ-N-N)₂(μ-OH₂)₂} core with Cu···Cu distances as 4.834(1) and 3.762(1) Å. Solid state as well as solution electronic spectra show several transitions in the wavelength range 700-280 nm. The room temperature (298 K) solid state magnetic moment is 3.55 μ_B. The powder EPR spectra at 298 and 130 K are very similar and axial (g_∥ = 2.25 and g_⊥ = 2.08) in character.