Seasonal variation in diet quality: antioxidants,invertebrates and blue tits Cyanistes caeruleus

Breeding success is often dictated by the degree to which parents can synchronize the maximum food requirements of offspring to the peak in abundance of invertebrate prey. Less studied is how the nutritional quality of individual diet items impacts on breeding. In the present study, we assessed the abundance and antioxidant concentrations of arboreal arthropods from oak woodland and provisioning behaviour of the blue tit Cyanistes caeruleus. Dietary antioxidants are important during development because they defend against oxidative stress. Operophtera caterpillars, Erannis caterpillars, and spiders contained significantly different levels of individual carotenoids and α‐tocopherol. Concentrations of lutein and β‐carotene in Operophtera caterpillars did not vary seasonally, although concentrations of zeaxanthin declined and α‐tocopherol increased with date. Blue tit broods hatched later in the season received significantly fewer caterpillars and more spiders per chick compared to earlier broods. Reflecting changes in prey composition, blue tit nestling plasma showed decreases in zeaxanthin and increases in α‐tocopherol with date. Thus, processes that shift the timing of breeding in birds and/or prey composition are likely to alter antioxidant intake and thus potentially influence the oxidative stress status of animals. The data obtained in the present study suggest a mechanism by which environmental change as a result of human activities could influence the health and fitness of individuals in natural populations. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 99 , 708–717.     

Recombinant expression of a unique chloromuconolactone dehalogenase ClcF from Rhodococcus opacus 1CP and identification of catalytically relevant residues by mutational analysis

Chloromuconolactone dehalogenase ClcF plays a unique role in 3-chlorocatechol degradation by Rhodococcus opacus 1CP by compensating the inability of its chloromuconate cycloisomerase ClcB2 to dechlorinate the chemically stable cycloisomerization product (4R,5S)-5-chloromuconolactone (5CML). High sequence similarities showed relatedness of ClcF to muconolactone isomerases (MLIs, EC 5.3.3.4) of the 3-oxoadipate pathway. Although both enzyme types share the ability to dechlorinate 5CML, comparison of kcat/Km indicated a significant extent of specialization of ClcF for dechlorination. This assumption was substantiated by an almost complete inability of ClcF to convert (4S)-muconolactone and the exclusive formation of cis-dienelactone from 5CML. Mutational analysis of ClcF by means of variants E27D, E27Q, Y50A, N52A, and A89S indicated relevance of some highly conserved residues for substrate binding and catalysis. Based on the putative isomerization mechanism of MLI, evidence was provided for a role of E27 in initial proton abstraction as well as of Y50 and N52 in substrate binding. In case of N52 substrate binding is likely to occur to the carboxylic group of 5CML as indicated by a significant change of product specificity. Expression in Escherichia coli BL21-CP(DE)-RIL followed by a three-step purification procedure with heat treatment is a convenient strategy to obtain recombinant ClcF and variants thereof.     

Effects of Rotational Grazing on Nesting Ducks in California

Abstract: Grazing is thought to be incompatible with nesting by dabbling ducks (Anas spp.), but this belief is based on little data. We therefore conducted a 2-year, replicated field experiment to determine whether the habitat requirements of nesting ducks could be met on uplands managed by rotational grazing (1 Jul-1 Nov) in the northern San Joaquin Valley, California, USA. Grazed fields had shorter vegetation than ungrazed fields throughout the winter, but vegetation height did not differ by the beginning of the nesting season in late March, and by the end of the nesting season in late May, previously grazed fields had taller vegetation than did ungrazed fields. In 1996, densities of duck nests were >3 times higher in grazed than in ungrazed fields (least-squares means [± 1 SE]: grazed = 2.18 [0.34] nests/ha, ungrazed = 0.59 [0.34] nests/ha), but nest densities were substantially lower in 1997 and did not differ between treatment groups (grazed = 0.65 [0.32] nests/ha, ungrazed = 0.39 [0.32] nests/ha). Mayfield nest success did not differ between grazed fields (5.3%) and ungrazed fields (2.9%). We conclude that rotational grazing was successful in providing summer nesting habitat for dabbling ducks, and we recommend that it be considered for other managed habitats within the Central Valley, California, USA.     

Waterfowl Use of Dense Nesting Cover in the Canadian Parklands

ABSTRACT Dense nesting cover (DNC) has been a conspicuous component of habitat management for upland-nesting ducks for >30 years, but its benefits for nesting ducks have been contentious. During 1994–1999 we monitored 3,058 dabbling duck (Anas spp.) nests in 84 DNC fields located throughout the Canadian Parklands to examine sources of among-field variation in nest density and nesting success. Nest density averaged 1.51 (SE=0.15) nests/ha and overall nesting success was 20.4%, but there was pronounced annual variation in both estimates. Nesting success increased with increasing field size (range = 6–111 ha), but nest density remained constant. Nest density increased with percent wetland habitat within DNC fields and declined with percent perennial cover in the surrounding 2.4 × 2.4-km landscape, but these variables were not important for predicting nesting success. Nest abundance and nesting success roughly doubled in fields seeded with alfalfa (Medicago sativa) or sweet clovers (Melilotus spp.), but there was no benefit from using native as opposed to tame grasses. We recommend that waterfowl managers in the Canadian Parklands establish DNC with alfalfa in large fields in landscapes with abundant wetlands but minimal competing cover.     

A mechanistic study on SMOB-ADP1: an NADH:flavin oxidoreductase of the two-component styrene monooxygenase of Acinetobacter baylyi ADP1

Two styrene monooxygenase types, StyA/StyB and StyA1/StyA2B, have been described each consisting of an epoxidase and a reductase. A gene fusion which led to the chimeric reductase StyA2B and the occurrence in different phyla are major differences. Identification of SMOA/SMOB-ADP1 of Acinetobacter baylyi ADP1 may enlighten the gene fusion event since phylogenetic analysis indicated both proteins to be more related to StyA2B than to StyA/StyB. SMOB-ADP1 is classified like StyB and StyA2B as HpaC-like reductase. Substrate affinity and turnover number of the homo-dimer SMOB-ADP1 were determined for NADH (24 µM, 64 s^?1) and FAD (4.4 µM, 56 s^?1). SMOB-ADP1 catalysis follows a random sequential mechanism, and FAD fluorescence is quenched upon binding to SMOB-ADP1 (K _d = 1.8 µM), which clearly distinguishes that reductase from StyB of Pseudomonas. In summary, this study confirmes made assumptions and provides phylogenetic and biochemical data for the differentiation of styrene monooxygenase-related flavin reductases.     

Structural Characteristics Determine the Cause of the Low Enzyme Activity of Two Thiopurine S-Methyltransferase Allelic Variants: A Biophysical Characterization of TPMT*2 and TPMT*5

The enzyme thiopurine S-methyltransferase (TPMT) is involved in the metabolism of thiopurine drugs used to treat acute lymphoblastic leukemia and inflammatory bowel disease. Thus far, at least 29 variants of the TPMT gene have been described, many of which encode proteins that have low enzyme activity and in some cases become more prone to aggregation and degradation. Here, the two naturally occurring variants, TPMT*2 (Ala80 → Pro) and TPMT*5 (Leu49 → Ser), were cloned and expressed in Escherichia coli. Far-UV circular dichroism spectroscopy showed that TPMT*2 was substantially destabilized whereas TPMT*5 showed much greater stability comparable to that of wild-type TPMT (TPMTwt). The extrinsic fluorescent molecule anilinonaphthalene sulfonate (ANS) was used to probe the tertiary structure during thermal denaturation. In contrast to TPMTwt, neither of the variants bound ANS to a large extent. To explore the morphology of the TPMT aggregates, we performed luminescent conjugated oligothiophene staining and showed fibril formation for TPMT*2 and TPMT*5. The differences in the flexibility of TPMTwt, TPMT*2, and TPMT*5 were evaluated in a limited proteolysis experiment to pinpoint stable regions. Even though there is only one amino acid difference between the analyzed TPMT variants, a clear disparity in the cleavage patterns was observed. TPMT*2 displays a protected region in the C-terminus, which differs from TPMTwt, whereas the protected regions in TPMT*5 are located mainly in the N-terminus close to the active site. In conclusion, this in vitro study, conducted to probe structural changes during unfolding of TPMT*2 and TPMT*5, demonstrates that the various causes of the low enzyme activity in vivo could be explained on a molecular level.     

MTMDAT: Automated analysis and visualization of mass spectrometry data for tertiary and quaternary structure probing of proteins

In structural biology and -genomics, nuclear magnetic resonance (NMR) spectroscopy and crystallography are the methods of choice, but sample requirements can be hard to fulfil. Valuable structural information can also be obtained by using a combination of limited proteolysis and mass spectrometry, providing not only knowledge of how to improve sample conditions for crystallization trials or NMR spectrosopy by gaining insight into subdomain identities but also probing tertiary and quaternary structure, folding and stability, ligand binding, protein interactions and the location of post-translational modifications. For high-throughput studies and larger proteins, however, this experimentally fast and easy approach produces considerable amounts of data, which until now has made the evaluation exceedingly laborious if at all manually possible. MTMDAT, equipped with a browser-like graphical user interface, accelerates this evaluation manifold by automated peak picking, assignment, data processing and visualization. AVAILABILITY: MTMDAT can be downloaded from the following page: http://www.cms.liu.se/chemistry/molbiotech/maria_sunnerhagens_group/mtmdat by clicking on the corresponding links (windows- or unix-based) together with the manual and example files. The program is free for academic/non-commercial purposes only.     

Regulation of Raf-1 kinase activity by the 14-3-3 family of proteins.

We have identified the beta (beta) isoform of the 14-3-3 family of proteins as an activator of the Raf-1 protein kinase. 14-3-3 was isolated in a yeast two-hybrid screen for Raf-1 kinase domain binding proteins. Purified bovine brain 14-3-3 interacted specifically with both c-Raf-1 and the isolated Raf-1 kinase domain. Association was sensitive to the activation status of Raf-1; 14-3-3 bound to unactivated Raf-1, but not Raf-1 activated by protein kinase C alpha or Ras and Lck. The significance of these interactions under physiological conditions was demonstrated by co-immunoprecipitation of Raf-1 and 14-3-3 from extracts of quiescent, but not mitogen-stimulated, NIH 3T3 cells. 14-3-3 was not a preferred Raf-1 substrate in vitro and did not significantly affect Raf-1 kinase activity in a purified system. However, in cell-free extracts 14-3-3 acted as a Ras-independent activator of both c-Raf-1 and the Raf-1 kinase domain. The same results were obtained in vivo using transfection assays; 14-3-3 enhanced both c-Raf-1- and Raf-1 kinase domain-stimulated expression of AP-1- and NF-kappa B-dependent reporter genes and accelerated Raf-1 kinase domain-triggered differentiation of PC12 cells. We conclude that 14-3-3 is a latent co-activator bound to unactivated Raf-1 in quiescent cells and mediates mitogen-triggered but Ras-independent regulatory effects aimed directly at the kinase domain.