Body composition of north and southbound migratory blackcaps is influenced by the lay‐of‐the‐land ahead

The annual migration of small birds depends on the optimal management of time and energy. Since refueling at stopovers between flights consumes most of the birds’ time and energy, selection of food‐rich sites, and timely departure therefrom are likely crucial to success. We examined this concept quantifying body composition of 200 migrating blackcaps, Sylvia atricapilla, in Eilat, Israel, using dual‐energy x‐ray absorptiometry and generated a model to predict body composition as it changes with body mass (m_b). We then back‐calculated body composition of > 20 000 blackcaps ringed between 1984 and 2005, and tested the hypothesis that the amount of fuel that a bird stores determines the length of its stopover. We predicted that 1) if time‐constrained in spring, birds at the stopover site carry less than a maximum fuel load, but 2) if not time‐constrained, as in autumn, their fuel load is much higher than in spring. We found the change in body composition of blackcaps to be biphasic and correlated with increasing m_b. At m_b < ? 17.8 g, increasing m_b is due to increasing lean mass (m_l), while at m_b > ? 17.8 g increasing m_b results from increasing fat mass (m_f), which is accompanied by decreasing m_l. Body composition of blackcaps at a spring stopover site indicates that blackcaps leave stopovers as soon as they regain functionality of their digestive systems, but before laying down much m_f. In autumn blackcaps arrive with fuel stores much larger than in spring. For these birds, the Eilat stopover apparently serves to complete fat accumulation before crossing the deserts ahead. We conclude that in spring, the decision to depart is not determined by the bird's fuel stores, especially when early arrival at the breeding site, and therefore time, is of the essence. In autumn, accumulating enough fuel to ensure successful crossing of the deserts ahead probably dictates stopover time.     

Plant antimicrobial peptides

Plant antimicrobial peptides (AMPs) are a component of barrier defense system of plants. They have been isolated from roots, seeds, flowers, stems, and leaves of a wide variety of species and have activities towards phytopathogens, as well as against bacteria pathogenic to humans. Thus, plant AMPs are considered as promising antibiotic compounds with important biotechnological applications. Plant AMPs are grouped into several families and share general features such as positive charge, the presence of disulfide bonds (which stabilize the structure), and the mechanism of action targeting outer membrane structures.     

Characterization of exceptionally thermostable single-stranded DNA-binding proteins from <Emphasis Type="Italic">Thermotoga maritima</Emphasis> and <Emphasis Type="Italic">Thermotoga neapolitana</Emphasis>

Background  

In recent years, there has been an increasing interest in SSBs because they find numerous applications in diverse molecular biology and analytical methods.     

Structural analogues of reactive intermediates as inhibitors of glucosamine-6-phosphate synthase and phosphoglucose isomerase

The active centers of phosphoglucose isomerase (PGI) and the hexose phosphate isomerase domain (HPI) of glucosamine-6-P (GlcN-6-P) synthase demonstrate apparent similarity in spatial arrangement of critical amino acid residues, except Arg272 of the former and Lys603 and Lys485 of the latter. Ten derivatives of d-hexitol-6-P, 5-phosphoarabinoate, or 6-phosphogluconate, structural analogues of putative cis-enolamine or cis-enolate intermediates, were tested as inhibitors of fungal GlcN-6-P synthase and PGI. None of the investigated compounds demonstrated equally high inhibitory potential against both enzymes. 2-Amino-2-deoxy-D-mannitol 6-P was found to be the strongest GlcN-6-P synthase inhibitor in the series, with an inhibition constant equal to 9.0 (+/-1.0) x 10(-6)M. On the contrary, 5-phosphoarabinoate (5PA) exhibited specificity for PGI, with K(i)=2.2 (+/-0.1) x 10(-6) M. N-acetylation substantially lowered the GlcN-6-P synthase inhibitory potential of 2-amino-2-deoxy-D-glucitol-6-P but strongly enhanced inhibitory potential of this compound towards PGI. Molecular modeling studies revealed that interactions of the C1-C2 part of transition state analogue inhibitors with the respective areas demonstrating different distribution of molecular electrostatic potential (MEP) inside HPI and PGI active centers determined enzyme:ligand affinity. In Escherichia coli HPI, a patch of the negative potential created by Glu488 aided by Val399, supposed to stabilize a putative positively charged intermediate, especially attracts ligands containing 2-amino function. The Arg272, Lys210, and Gly271 peptide bond nitrogen system, present in the corresponding space of rabbit PGI, creates an area of positive MEP, stabilizing cis-enolate intermediate and attracting its structural mimics, such as 5PA.     

Role of heme-protein covalent bonds in mammalian peroxidases. Protection of the heme by a single engineered heme-protein link in horseradish peroxidase

Oxidation of SCN-, Br-, and Cl- (X-) by horseradish peroxidase (HRP) and other plant and fungal peroxidases results in the addition of HOX to the heme vinyl group. This reaction is not observed with lactoperoxidase (LPO), in which the heme is covalently bound to the protein via two ester bonds between carboxylic side chains and heme methyl groups. To test the hypothesis that the heme of LPO and other mammalian peroxidases is protected from vinyl group modification by the hemeprotein covalent bonds, we prepared the F41E mutant of HRP in which the heme is attached to the protein via a covalent bond between Glu41 and the heme 3-methyl. We also examined the E375D mutant of LPO in which only one of the two normal covalent heme links is retained. The prosthetic heme groups of F41E HRP and E375D LPO are essentially not modified by the HOBr produced by these enzymes. The double E375D/D225E mutant of LPO that can form no covalent bonds is inactive and could not be examined. These results unambiguously demonstrate that a single heme-protein link is sufficient to protect the heme from vinyl group modification even in a protein (HRP) that is normally highly susceptible to this reaction. The results directly establish that one function of the covalent heme-protein bonds in mammalian peroxidases is to protect their prosthetic group from their highly reactive metabolic products.     

Prediction of Secondary Ionization of the Phosphate Group in Phosphotyrosine Peptides

A computational approach, based on a continuum molecular electrostatics model, for the calculation of the pK_a values of secondary ionization of the phosphate group in phenyl phosphate derivatives is described. The method uses the ESP atomic charges of the mono-anionic and di-anionic forms of the ionizable phosphate group, computed with the use of the density functional method, and applies a new concept of the model group, being the reference state for the pK_a calculations. Both conformational flexibility and tautomeric degrees of freedom are taken into account in the calculations. The method was parameterized using experimentally available pK_a values of four derivatives of phenyl phosphates, and phosphotyrosine. Subsequently this parameterization was used to predict pK_a of the phosphate group in a short peptide Gly-Gly-Tyr(P)-Ala, and in a longer peptide consisting of 12 residues, the latter in water, and in a complex with a protein—phospholipase. The agreement between the computed and the experimental pK_a values is better than ±0.3 pH units for the optimized solute dielectric constant of 11–13. This approach is promising and its extension to other phospho-amino acids is in progress.     

Morphology heterogeneity within a Campylobacter jejuni helical population: the use of calcofluor white to generate rod‐shaped C. jejuni 81‐176 clones and the genetic determinants responsible for differences in morphology within 11168 strains

Campylobacter jejuni helical shape is important for colonization and host interactions with straight mutants having altered biological properties. Passage on calcofluor white (CFW) resulted in C. jejuni 81‐176 isolates with morphology changes: either a straight morphology from frameshift mutations and single nucleotide polymorphisms in peptidoglycan hydrolase genes pgp1 or pgp2 or a reduction in curvature due a frameshift mutation in cjj81176_1105, a putative peptidoglycan endopeptidase. Shape defects were restored by complementation. Whole genome sequencing of CFW‐passaged strains showed no specific changes correlating to CFW exposure. The cjj81176_1279 (recR; recombinational DNA repair) and cjj81176_1449 (unknown function) genes were highly variable in all 81‐176 strains sequenced. A frameshift mutation in pgp1 of our laboratory isolate of the straight genome sequenced variant of 11168 (11168‐GS) was also identified. The PG muropeptide profile of 11168‐GS was identical to that of Δpgp1 in the original minimally passaged 11168 strain (11168‐O). Introduction of wild type pgp1 into 11168‐GS did not restore helical morphology. The recR gene was also highly variable in 11168 strains. Microbial cell‐to‐cell heterogeneity is proposed as a mechanism of ensuring bacterial survival in sub‐optimal conditions. In certain environments, changes in C. jejuni morphology due to genetic heterogeneity may promote C. jejuni survival.