Anaerobic metabolism of phenol in proteobacteria and further studies of phenylphosphate carboxylase

Anaerobic phenol metabolism was studied in three facultative aerobic denitrifying bacteria, Thauera aromatica, “Aromatoleum aromaticum” strain EbN1 (Betaproteobacteria), and Magnetospirillum sp. (Alphaproteobacterium). All species formed phenylphosphate and contained phenylphosphate carboxylase but not phenol carboxylase activity. This is in contrast to direct phenol carboxylation by fermenting bacteria. Antisera raised against subunits of the Thauera phenylphosphate synthase and phenylphosphate carboxylase partly cross-reacted with the corresponding proteins in the other species. Some unsolved features of phenylphosphate carboxylase were addressed in T. aromatica. The core sub-complex of this enzyme consists of three different subunits and catalyzes the exchange of ¹⁴CO₂ with the carboxyl group of 4-hydroxybenzoate, but not phenylphosphate carboxylation. It was inactivated by oxygen or by the oxidizing agent thionin and fully reactivated under reducing conditions. The purified recombinant phosphatase subunit alone had only low phenylphosphate phosphatase activity in the absence of the other components. However, activity was strongly enhanced in the presence of the core enzyme resulting in phenylphosphate carboxylation. Hence, a tight interaction of the carboxylase subunits is required for dephosphorylation of phenylphosphate, which is coupled to the concomitant carboxylation of the produced phenolate to 4-hydroxybenzoate, thus preventing a futile cycle.     

Developmental basis for telencephalon expansion in waterfowl: enlargement prior to neurogenesis

Some altricial and some precocial species of birds have evolved enlarged telencephalons compared with other birds. Previous work has shown that finches and parakeets, two species that hatch in an immature (i.e. altricial) state, enlarged their telencephalon by delaying telencephalic neurogenesis. To determine whether species that hatch in a relatively mature (i.e. precocial) state also enlarged their telencephalon by delaying telencephalic neurogenesis, we examined brain development in geese, ducks, turkeys and chickens, which are all precocial. Whereas the telencephalon occupies less than 55 per cent of the brain in chickens and turkeys, it occupies more than 65 per cent in ducks and geese. To determine how these species differences in adult brain region proportions arise during development, we examined brain maturation (i.e. neurogenesis timing) and estimated telencephalon, tectum and medulla volumes from serial Nissl-stained sections in the four species. We found that incubation time predicts the timing of neurogenesis in all major brain regions and that the telencephalon is proportionally larger in ducks and geese before telencephalic neurogenesis begins. These findings demonstrate that the expansion of the telencephalon in ducks and geese is achieved by altering development prior to neurogenesis onset. Thus, precocial and altricial species evolved different developmental strategies to expand their telencephalon.     

Structure of the c14 Rotor Ring of the Proton Translocating Chloroplast ATP Synthase

The structure of the membrane integral rotor ring of the proton translocating F₁F₀ ATP synthase from spinach chloroplasts was determined to 3.8 Å resolution by x-ray crystallography. The rotor ring consists of 14 identical protomers that are symmetrically arranged around a central pore. Comparisons with the c₁₁ rotor ring of the sodium translocating ATPase from Ilyobacter tartaricus show that the conserved carboxylates involved in proton or sodium transport, respectively, are 10.6–10.8 Å apart in both c ring rotors. This finding suggests that both ATPases have the same gear distance despite their different stoichiometries. The putative proton-binding site at the conserved carboxylate Glu⁶¹ in the chloroplast ATP synthase differs from the sodium-binding site in Ilyobacter. Residues adjacent to the conserved carboxylate show increased hydrophobicity and reduced hydrogen bonding. The crystal structure reflects the protonated form of the chloroplast c ring rotor. We propose that upon deprotonation, the conformation of Glu⁶¹ is changed to another rotamer and becomes fully exposed to the periphery of the ring. Reprotonation of Glu⁶¹ by a conserved arginine in the adjacent a subunit returns the carboxylate to its initial conformation.ATP synthases found in the energy-transducing membranes of bacteria, mitochondria, and chloroplasts catalyze ATP synthesis and ATP hydrolysis coupled with transmembrane proton or sodium ion transport. The enzymes are multi-subunit complexes composed of an extra-membranous catalytic F₁ domain and an interconnected integral membrane F₀ domain. The hydrophilic F₁ domain consists of five different polypeptides with a stoichiometry of α₃β₃γδϵ. Detailed structural information obtained with the mitochondrial enzyme (1–3) in combination with biochemical (4), biophysical (5), and single molecule studies (6–9) revealed that synthesis or hydrolysis of ATP in the F₁ domain is accomplished via a rotary catalytic mechanism. In addition to information on the catalytic mechanism, structure analysis and single molecule studies of the mitochondrial or the chloroplast F₁ complex have also unraveled the molecular mechanism of several F₁-specific inhibitors (10–14). Less detailed information is available on the integral membrane F₀ domain, which consists of three different polypeptides (a, b, and c) and mediates the transfer of protons or sodium ions across the membrane. Subunits a and b were shown to reside at the periphery of a cylindrical complex formed by multiple copies of the c subunit (15–18). The number of c subunits in the cylindrical subcomplex shows substantial variation in different organisms. Ten protomers are found in ATP synthases from yeast, Escherichia coli and Bacillus PS3 (19–21), 11 in Ilyobacter tartaricus, Propionigenium modestum, and Clostridium paradoxum (22–24), 13 in the thermoalkalophilic Bacillus TA2.TA1 (25), 14 in spinach chloroplasts (26), and 15 in the cyanobacterium Spirulina platensis (27). The structure of isolated subunits a, b, and c from E. coli has been studied by mutagenesis analysis and by NMR spectroscopy in a mixed solvent that was suggested to mimic the membrane environment (28–32). These studies showed that subunit a folds with five membrane-spanning helices. The fourth of these helices directly interacts with subunit c and contains a conserved arginine (Arg²¹⁰), which is thought to be involved in proton transfer (33). Subunit b, which is present in two copies in the intact F₀, contains a single transmembrane helix. Cross-linking data support a direct interaction of the two copies of the b subunit (29). Subunit c was studied at two different pH values to obtain the protonated and deprotonated form of a conserved carboxylate (Asp⁶¹ in E. coli) that was shown to be essential for proton transport (34). NMR spectroscopy revealed that the isolated c subunit consists of two long hydrophobic membrane spanning segments connected by a short hydrophilic loop (30, 35). This loop is located close to the γ and ϵ subunit on the F₁ side of the membrane (36, 37). Low resolution x-ray crystallography, cryo-electron microscopy, and atomic force microscopy showed that the membrane-spanning helices of the multiple copies of subunit c in the intact F₀ complex are tightly packed in two concentric rings (19, 22, 26). Atomic resolution of the c ring was recently provided for the Na⁺-translocating F-type ATPase from I. tartaricus (38) and the related Na⁺-translocating V-type ATPase from Enterococcus hirae (39). Rotation of the c ring was demonstrated by cross-linking (18), fluorescence studies (40), and single molecule visualization (41, 42). Based on the structural and biochemical information on F₁ and F₀, different mechanical models have been proposed describing how the rotation of the c ring is coupled to the rotation of the F₁ rotor subunits. This rotation in turn drives sequential conformational shifts at the three catalytic β subunits that result in ATP synthesis (43–45). Vice versa hydrolysis of ATP in the F₁ domain is thought to drive rotation of the γϵc_10–15 subcomplex and transports protons or sodium ions across the membrane.Here we describe the crystal structure of the chloroplast c₁₄ rotor, which is the first structure of an isolated c ring rotor from a proton driven ATPase. The structure was solved by molecular replacement using a tetradecameric search model that was generated from a monomer taken from the I. tartaricus c₁₁ structure. The imposition of noncrystallographic symmetry restraints during refinement substantially improved electron density and structure determination.     

Tissue-specific Short Chain Fatty Acid Metabolism and Slow Metabolic Recovery after Ischemia from Hyperpolarized NMR in Vivo

Mechanistic details of mammalian metabolism in vivo and dynamic metabolic changes in intact organisms are difficult to monitor because of the lack of spatial, chemical, or temporal resolution when applying traditional analytical tools. These limitations can be addressed by sensitivity enhancement technology for fast in vivo NMR assays of enzymatic fluxes in tissues of interest. We apply this methodology to characterize organ-specific short chain fatty acid metabolism and the changes of carnitine and coenzyme A pools in ischemia reperfusion. This is achieved by assaying acetyl-CoA synthetase and acetyl-carnitine transferase catalyzed transformations in vivo. The fast and predominant flux of acetate and propionate signal into acyl-carnitine pools shows the efficient buffering of free CoA levels. Sizeable acetyl-carnitine formation from exogenous acetate is even found in liver, where acetyl-CoA synthetase and acetyl-carnitine transferase activities have been assumed sequestered in different compartments. In vivo assays of altered acetate metabolism were applied to characterize pathological changes of acetate metabolism upon ischemia. Coenzyme pools in ischemic skeletal muscle are reduced in vivo even 1 h after disturbing muscle perfusion. Impaired mitochondrial metabolism and slow restoration of free CoA are corroborated by assays employing fumarate to show persistently reduced tricarboxylic acid (TCA) cycle activity upon ischemia. In the same animal model, anaerobic metabolism of pyruvate and tissue perfusion normalize faster than mitochondrial bioenergetics.     

The relation between the specific absorption rate and electromagnetic field intensity for heterogeneous exposure conditions at mobile communications frequencies

The relation between the incident electromagnetic field strength and both the whole‐body and the local specific absorption rate (SAR) was investigated for typical heterogeneous exposure scenarios for frequencies relevant for mobile communication. The results were compared to results from plane wave exposure. Heterogeneous exposure arises from multiple path propagation of the electromagnetic waves to the location of interest. It is shown that plane wave exposure does not represent worst‐case exposure conditions. When the electric field strength arising at plane wave exposure is compared to the electric field strength averaged over the volume of the human body occurring during multipath exposure, 12% of all heterogeneous cases examined represent worse exposure conditions than plane wave exposure for whole‐body exposure at 946 MHz, 15% at 1840 MHz, and 22% at 2140 MHz. The deviation between plane wave and heterogeneous whole‐body SAR ranges from ?54% to 54%. For partial‐body SAR averaged over 10 g of tissue, a range from ?93% to 209% was found when comparing multiple wave exposure to single incoming plane waves. The investigations performed using the Visible Human as phantom showed that the basic restrictions are met as long as the reference levels are not exceeded. However, this must not be necessarily the case when different phantoms are used to perform similar investigations because recent studies demonstrated that reference levels might not be conservative when phantoms of children are used. Therefore, the results of this work indicate the need to extend the investigations to numerical simulations with additional human phantoms representing parts of the human population having different anatomy and morphology compared to the phantom used within the frame of this project. This also applies to phantoms of children. Bioelectromagnetics 30:651–662, 2009. © 2009 Wiley‐Liss, Inc.     

Dynamics and structural changes of an oak dominated Natural Forest Reserve in Austria

Natural forest reserves provide a rare opportunity to study forest dynamics after the cessation of human management. Inventories were carried out in 1996 and 2006 in an oak (Quercus spp.) dominated forest reserve formerly managed as coppice forest using the Bitterlich sampling method, an inventory method with a fixed angle of sight to select trees based on their stem diameter. The total living stand volume increased from 245.2 to 276.5 m³/ha (+12.8%) over the 10-year period. This net increase resulted from the growth of individual trees (+3.7%), the ingrowths of young trees (+17.7%) and tree mortality between 1996 and 2006 (−8.6%). Tree mortality included 14.8 m³/ha of standing deadwood and 6.2 m³/ha of fallen deadwood. Stand dynamics differed among tree species: the volume of oak (Quercus spp.) increased due to strong growth and low mortality, whereas hornbeam (Carpinus betulus) showed a decrease in stand volume due to high mortality and low growth. The findings suggest an increase in oak dominance at the expense of hornbeam although inventories repeated over longer time periods would be needed for confirmation. Our data indicate that the Bitterlich sampling method can be used for assessing tree species dynamics and structural changes in natural forest reserves, but some important processes (seedling recruitment, wood decomposition) would need to be investigated separately.

---

Zusammenfassung  In einem von Eiche (Quercus spp.) dominierten Naturwaldreservat wurde in den Jahren 1996 und 2006 auf einer Fl?che von 29 ha eine Inventur mittels der Winkelz?hlprobe nach Bitterlich durchgeführt. Der Gesamtvorrat erh?hte sich in der 10-j?hrigen Beobachtungsperiode von 245.2 m³/ha auf 276.5 m³/ha. Im Durchschnitt konnten 14.8 m³/ha stehendes Totholz und 6.2 m³/ha liegendes Totholz ermittelt werden. Die Mortalit?tsrate lag zwischen 1996 und 2006 bei 8.6%. Hainbuche (Carpinus betulus) zeigte aufgrund der hohen Mortalit?t und dem geringen Einwuchs im Vergleich zur Eiche und den anderen Baumarten eine Abnahme im Gesamtvorrat. Die Ergebnisse erlauben einen Einblick in die dynamischen Prozesse unter nahezu natürlichen Bedingungen. Die Eignung der Winkelz?hlprobe für die Beurteilung der Dynamik und die Analyse von strukturellen Ver?nderungen wird kritisch diskutiert.

     

Allelic ladders and reference genotypes for a rigorous standardization of poplar microsatellite data

A correct identification of members of the poplar hybrid complex Populus × canadensis is essential in breeding programs and studies in introgressive gene flow. Molecular marker protocols have been developed for this purpose. However, due to missing standards, these techniques have so far not been suited to the transfer of results between different laboratories. We present here a powerful system of nuclear microsatellite DNA (nSSR) fingerprints, standardized by allelic ladders and reference genotypes. Seven nSSR loci provided fingerprints of 65 commercial poplar clones. Their alleles were used to construct allelic ladders. Thus, a first standardized register of poplar clones is now available. All procedures were optimized according to simplified DNA extraction protocols, multiplexed PCR and electrophoresis procedures. Corresponding data originating from two different electrophoretic platforms in different laboratories were congruent when the allelic ladder was used. Unambiguous differentiation of the clones was based on a very low probability of identity (PI) of 1.95 × 10⁻⁸. Our results revealed discrepancies between clone denotations and genetic fingerprints. This suggests that, potentially, members of the clone collection could have been mixed up, thus confirming the demand for rigorous standards. The protocol presented can be exploited in a manifold way, e.g. to enlarge the present clonal molecular data base, or to use it for purposes of certification and control. Furthermore, the allelic ladders are recommended for use in poplar population genetic studies across different laboratories. The allelic ladders and single sample reference genotypes can be obtained on demand.     

Electrical microarrays for highly sensitive detection of multiplex PCR products from biological agents

For the sensitive detection of amplicons derived from diagnostic PCR, a novel electrical low-density microarray is applied and compared to state-of-the-art quantitative real-time PCR. The principle of the electrochemical method and the effective use for analysis are described. Interdigitated array gold electrodes (IDA-E) embedded into a silicon chip are the core technology of the fully automated compact biosensor system, basing on enzyme coupled electrochemical detection. The biointerface is built up with thiol-modified capture oligonucleotides on gold and mediates the specific recognition of hybridised target DNA amplified with uniplex or multiplex PCR. In here we show the potential of the designed electrical microarray to function as an advanced screening method for the parallel detection of a panel of the four pathogens Bacillus anthracis, Yersinia pestis, Francisella tularensis and ortho pox viruses (genus), which are among the most relevant biowarfare agents. PCR products, generated from 10 to 50 gene equivalents, have been detected reproducibly. The experiments with varying pathogen amounts showed the good reliability and the high sensitivity of the method, equivalent to optical real-time PCR detection systems. Without PCR the total assay time amounts to 27 min. The advantage of the combination of multiplex-PCR with electrical microarray detection avoiding intensive PCR probe labelling strategies is illustrated.     

Does vacuum-packaging or co-delivered amendments enhance shelf-life of Striga-mycoherbicidal products containing Fusarium oxysporum f. sp. strigae during storage?

The effect of vacuum packaging on the shelf-life and handling of Pesta granules and seed treatment made with chlamydospores of Fusarium oxysporum strains Foxy2, PSM197 or their mixture was studied at 4°C and 22±3°C over 1 year. In addition, the effects of co-incorporated amendments [urea in Pesta or co-delivered fungicides (Ridomil Gold®, Apron XL®) on coated sorghum seeds], and coating material (Arabic gum ‘AG’, SUET Binder ‘SB’) on the viability of Striga-mycoherbicides were evaluated. Storage under vacuum packaging did not enhance shelf-life of the formulated Striga-mycoherbicidal products after 12 months of storage regardless of the treatment used. The co-incorporated urea into Pesta granules significantly reduced the viability of mycoherbicides, but less so at 4°C (58% strain-stability after 12 months). No significant differences between the coating materials in maintaining the viability of mycoherbicides were observed. The shelf-life of isolates on coated seeds significantly decreased when adding Ridomil Gold®. However, at 4°C, the fungicide Apron XL® allowed better survival of Foxy2 and PSM197 by maintaining their averaged half-lives (t _0.5) by an additional 6 months compared to Ridomil Gold®. In general, Striga-mycoherbicidal product combinations exhibited a significantly higher shelf-life when stored at 4°C than at 22±3°C. The absence of a positive effect of vacuum packaging on shelf-life of Striga-mycoherbicidal products reflects the tolerance of the formulated fungal propagules (chlamydospores) to withstand an oxygen enriched environment and allows their handling and distribution through ordinary packaging systems in Africa. The high compatibility between Striga-mycoherbicides and the co-delivered fungicide Apron XL®, and the fungal storage stability allows simultaneous control of Striga and fungal cereal diseases within an integrated pest management (IPM).