Spermiogenesis in the Australian cockatiel Nymphicus hollandicus

Information on the ultrastructure of parrot spermatids and spermatozoa is limited to only four species with no comprehensive study of spermiogenesis conducted within the order Psittaciformes. The present study was undertaken to describe the development of the cockatiel spermatid using electron microscopy. Four phases of spermatid maturation were documented on the basis of nuclear morphology, development of the acrosome, perforatorium, and axial filament. These phases included 1) round nuclei, 2) irregular nuclei, 3) elongated nuclei with granular chromatin, and 4) elongated nuclei with homogenous chromatin. While development of the cockatiel spermatid was comparable to that of other domestic avian species, we have noted the hollow nature of some chromatin granules, an abnormal formation of the axoneme, the absence of the fibrous sheath around the axoneme of the principal piece, and the absence of an annulus. J. Morphol. , 2012. © 2012 Wiley Periodicals, Inc.     

Conformational Space Comparison of GnRH and lGnRH-III using Molecular Dynamics,Cluster Analysis and Monte Carlo Thermodynamic Integration

Abstract

The conformational space available to GnRH and 1GnRH-III was compared using 5.2 ns constant temperature and pressure molecular dynamics simulations with explicit TIP3P solvation and the AMBER v. 5.0 force field. Cluster analysis of both trajectories resulted in two groups of conformations. Results of free energy calculations, in agreement with previous experimental data, indicate that a conformation with a turn from residues 5 through 8 is preferred for GnRH in an aqueous environment. By contrast, a conformation with a helix from residues 2 through 7 with a bend from residues 6 through 10 is preferred for 1GnRH-III in an aqueous environment. The side chains of His² and Trp³ in 1GnRH-III occupy different regions of phase space and participate in weakly polar interactions different from those in GnRH. The unique conformational properties of 1GnRH-III may account for its specific anti cancer activity.     

Roadside verges and cemeteries: Comparative analysis of anthropogenic orchid habitats in the Eastern Mediterranean

Several important habitats have become threatened in the last few centuries in the Mediterranean Basin due to major changes adopted in land‐use practices. The consequent loss of natural and seminatural orchid habitats leads to the appreciation of small anthropogenic habitats, such as cemeteries and roadside verges. Colonization of cemeteries and roadside verges by orchids has long been known, but no study to date compared the suitability of these two anthropogenic habitats for orchids. Therefore, in this paper our aim was to survey cemeteries and roadside verges and to compare these two habitats regarding their role in conserving Mediterranean terrestrial orchids. We conducted field surveys in three Mediterranean islands, Cyprus, Crete, and Lesbos, where both cemeteries and roadside verges were sampled on a geographically representative scale. We found a total of almost 7,000 orchid individuals, belonging to 77 species in the two anthropogenic habitat types. Roadside verges hosted significantly more individuals than cemeteries in Crete and Lesbos, and significantly more species across all three islands. Our results suggest that although cemeteries have a great potential conservation value in other parts of the world, intensive maintenance practices that characterized cemeteries in these three islands renders them unable to sustain valuable plant communities. On the other hand, roadside verges play a prominent role in the conservation of Mediterranean orchids in Cyprus and Greece. The pioneer status of roadside verges facilitates their fast colonization, while roads serve as ecological corridors in fragmented landscapes.     

Molecular Dynamics Simulations of β-turn Forming Tetra- and Hexapeptides

Abstract

It was previously shown that the structural ensemble of model peptides DDKG and GKDG (H. Ishii et al. Biopolymers 24, 2045–2056, 1985), DEKS (A. Otter et al. J. Biomol. Struct. Dyn. 7, 455–476, 1989) NPGQ (F. R. Carbone et al. Int. J. Pept. Protein. Res. 26, 498–508, 1985), SALN (H. Santa et al. J. Biomol. Struct. Dyn. 16, 1033–1041, 1999), SYPFDV and SYPYDV (J. Yao et al. J. Mol. Biol. 243, 736–753, 1994), VP^DAH and VP^DSH (B. Imperiali et al. J. Am. Chem. Soc. 114, 3182–3188, 1992) in solution contains a significant—or in some cases dominant—proportion of β-turn conformation. In this study, a protein database was searched for the above, unprotected sequences which incorporate only L-amino acid residues. Simulated annealing and 25 ns MD simulations of structures were also performed. The DSSP and STRIDE secondary structure-assigning algorithms and clustering were used to analyze trajectories and i, i+3 hydrogen bonds were also sought. The DSSP analysis showed a fluctuation between β-turn and random meander structure, although bend structures were not detected because of the insufficient length of peptide chains. This alternating trend was confirmed when the STRIDE algorithm was used to analyze trajectories, but STRIDE assigned more turn structures. The population of the strongest clusters was above 40% and the middle structures adopted β-turn structure for most sequences. These results are in good agreement with previous experimental results and support the idea of the ultra-marginal stability of turns in the absence of stabilizing long-range interactions of the neighboring segments of a polypeptide chain. However, interactions between the side-chains in tetrapeptides could also contribute to turn stability and result in unusual stability in some cases. Our observations suggest that such interactions are the consequence rather than the driving force of turn formation.     

Synthesis and Structure-Activity Relationship of [Nle10]Neurokinin A (4–10) Analogs with Constraint in the Backbone and at Position Six

Steric requirements of binding [Nle¹⁰]NKA(4–10) to NK-2 receptor were studied by introducing conformationally constrained amino acid analogs into its sequence. Two series of [Nle¹⁰]NKA(4–10) analogs were synthesized to investigate (i) the significance of a putative β-turn in the receptor-ligand interaction by insertion of either (S)- or (R)-Gly⁸{ANC-2}Leu⁹ γ-lactams to mimic a β-turn constraint, and (ii) the effect of hindered rotation in the Φ, χ¹ and χ² dihedral angle space of the crucially important Phe⁶ which was replaced systematically with d-Phe, d- and l-Tyr, as well as with their conformationally constrained analogs, Tic, HOTic and β-MePhe. Competition binding experiments with [³H]NKA were performed using cloned human NK-2 receptors expressed in CHO cells. The analog possessing only an (R)-Gly⁸{ANC-2}Leu⁹ constraint, had the same binding affinity as that of the parent peptide. The rank order of potency of the other analogs showed a cumulative effect of different structural modifications in decreasing the binding affinity, i.e., when changing the configuration of the lactam ring to S, replacing Phe⁶ with constrained analogs, Tic or β-MePhe, changing the configuration of the amino acid at position six to d, and introducing a hydroxyl group on the aromatic ring. Ferenc ?tv?s and Dmitry S. Gembitsky - Made an equal contribution. Abbreviations used for amino acids and peptides follow the recommendations of the IUPAC-IUB Commission of Biochemical Nomenclature, Eur. J. Biochem. (1984) 138, 9–37     

Shorebirds as important vectors for plant dispersal in Europe

Shorebirds (Charadriiformes) undergo rapid migrations with potential for long‐distance dispersal (LDD) of plants. We studied the frequency of endozoochory by shorebirds in different parts of Europe covering a broad latitudinal range and different seasons. We assessed whether plants dispersed conformed to morphological dispersal syndromes. A total of 409 excreta samples (271 faeces and 138 pellets) were collected from redshank Tringa totanus, black‐winged stilt Himantopus himantopus, pied avocet Recurvirostra avosetta, northern lapwing Vanellus vanellus, Eurasian curlew Numenius arquata and black‐tailed godwit Limosa limosa in south‐west Spain, north‐west England, southern Ireland and Iceland in 2005 and 2016, and intact seeds were extracted and identified. Godwits were sampled just before or after migratory movements between England and Iceland. The germinability of seeds was tested. Intact diaspores were recovered from all bird species and study areas, and were present in 13% of samples overall. Thirteen plant families were represented, including Charophyceae and 26 angiosperm taxa. Only four species had an ‘endozoochory syndrome’. Four alien species were recorded. Ellenberg values classified three species as aquatic and 20 as terrestrial. Overall, 89% of seeds were from terrestrial plants, and 11% from aquatic plants. Average seed length was higher in redshank pellets than in their faeces. Six species were germinated, none of which had an endozoochory syndrome. Seeds were recorded during spring and autumn migration. Plant species recorded have broad latitudinal ranges consistent with LDD via shorebirds. Crucially, morphological syndromes do not adequately predict LDD potential, and more empirical work is required to identify which plants are dispersed by shorebirds. Incorporating endozoochory by shorebirds and other migratory waterbirds into plant distribution models would allow us to better understand the natural processes that facilitated colonization of oceanic islands, or to improve predictions of how plants will respond to climate change, or how alien species spread.     

Structure and expression of a hybrid proline-rich protein gene in the solanaceous species,Solanum brevidens, Solanum tuberosum, andLycopersicum esculentum

The full-length cDNA of a previously identified Solanum brevidens gene was isolated and characterised. DNA sequence analysis revealed an open reading frame that encodes a hybrid proline-rich cell wall protein of 407 amino acids. The putative protein was designated SbrPRP. The SbrPRP harbours three parts, an N-terminal signal peptide followed by a repetitive proline-rich domain and a cysteine-rich C-terminus resembling non-specific lipid-transfer proteins. The repetitive proline-rich domain contains two repeated motifs, PPHVKPPSTPK and PTPPIVSPP extended with TPKYP and TPKPPS motifs, respectively, at their N- or C-terminal. The SbrPRP gene of the non-tuberising Solanum species, Solanum brevidens, possesses highly homologous counterparts in the tuberising species, Solanum tuberosum (StPRP) and in the related species, Lycopersicum esculentum (TFM7). All three genes are present in single- or low copy number in the corresponding genome. Organ-specific expression of the genes, however, is different in the three solanaceous species.     

Effects of force fields on the conformational and dynamic properties of amyloid β(1‐40) dimer explored by replica exchange molecular dynamics simulations

The conformational space and structural ensembles of amyloid beta (Aβ) peptides and their oligomers in solution are inherently disordered and proven to be challenging to study. Optimum force field selection for molecular dynamics (MD) simulations and the biophysical relevance of results are still unknown. We compared the conformational space of the Aβ(1‐40) dimers by 300 ns replica exchange MD simulations at physiological temperature (310 K) using: the AMBER‐ff99sb‐ILDN, AMBER‐ff99sb*‐ILDN, AMBER‐ff99sb‐NMR, and CHARMM22* force fields. Statistical comparisons of simulation results to experimental data and previously published simulations utilizing the CHARMM22* and CHARMM36 force fields were performed. All force fields yield sampled ensembles of conformations with collision cross sectional areas for the dimer that are statistically significantly larger than experimental results. All force fields, with the exception of AMBER‐ff99sb‐ILDN (8.8 ± 6.4%) and CHARMM36 (2.7 ± 4.2%), tend to overestimate the α‐helical content compared to experimental CD (5.3 ± 5.2%). Using the AMBER‐ff99sb‐NMR force field resulted in the greatest degree of variance (41.3 ± 12.9%). Except for the AMBER‐ff99sb‐NMR force field, the others tended to under estimate the expected amount of β‐sheet and over estimate the amount of turn/bend/random coil conformations. All force fields, with the exception AMBER‐ff99sb‐NMR, reproduce a theoretically expected β‐sheet‐turn‐β‐sheet conformational motif, however, only the CHARMM22* and CHARMM36 force fields yield results compatible with collapse of the central and C‐terminal hydrophobic cores from residues 17‐21 and 30‐36. Although analyses of essential subspace sampling showed only minor variations between force fields, secondary structures of lowest energy conformers are different.     

A cytochrome b561 with ferric reductase activity from the parasitic blood fluke, Schistosoma japonicum

Background

Iron has an integral role in numerous cellular reactions and is required by virtually all organisms. In physiological conditions, iron is abundant in a largely insoluble ferric state. Ferric reductases are an essential component of iron uptake by cells, reducing iron to the soluble ferrous form. Cytochromes b561 (cyts-b561) are a family of ascorbate reducing transmembrane proteins found in most eukaryotic cells. The identification of the ferric reductase duodenal cytochrome b (dcytb) and recent observations that other cyts-b561 may be involved in iron metabolism have opened novel perspectives for elucidating their physiological function.

Methodology/Principal Findings

Here we have identified a new member of the cytochrome b561 (Sjcytb561) family in the pathogenic blood fluke Schistosoma japonicum that localises to the outer surface of this parasitic trematode. Heterologous expression of recombinant Sjcyt-b561 in a Saccharomyces cerevisiae mutant strain that lacks plasma membrane ferrireductase activity demonstrated that the molecule could rescue ferric reductase activity in the yeast.

Significance/Conclusions

This finding of a new member of the cytochrome b561 family further supports the notion that a ferric reductase function is likely for other members of this protein family. Additionally, the localisation of Sjcytb561 in the surface epithelium of these blood-dwelling schistosomes contributes further to our knowledge concerning nutrient acquisition in these parasites and may provide novel targets for therapeutic intervention.