Selected coccal green algae are not affected by the humic substance Huminfeed<Superscript>®</Superscript> in term of growth or photosynthetic performance

Humic substances (HSs) have been shown to influence growth, photophysiology, and redox homeostasis in phototrophs. However, many ecological studies deliver controversial results indicating inhibitory or stimulating effects depending on the kind of phototrophic organism or type of HSs applied. Here we analyzed the effect of Huminfeed^® (HF), a preparation from leonardite associated with lignite deposits, on growth and photosynthetic performance of three different coccal green algae. Concentrations of HF in the range of 2–20 mg l^?1 dissolved organic carbon (DOC) did neither affect the growth rate nor the light-adapted photosynthetic electron transport. Even photoinhibitory light intensities of 1,600 μmol photons m^?2 s^?1, representing the tenfold of growth light intensity, did not result in a decline of the maximal photosynthetic rate in HF-treated algae. In HF-grown algae, a very subtle decrease by about 10% could be observed in thermoluminescent light emission, a sensitive method to detect changes in photosystem II (PSII) chemistry. However, thermoluminescence (TL) represents only 3% of the light-induced charge separated states in PSII. Hence, rather small changes will not have significant effects on overall photosynthetic performance and growth. Therefore, the physiological effect of HSs on freshwater phototrophs has to be revisited.     

Identification and characterization of a succinyl-coenzyme A (CoA):benzoate CoA transferase in Geobacter metallireducens

Geobacter metallireducens is a Fe(III)-respiring deltaproteobacterium and serves as a model organism for aromatic compound-degrading, obligately anaerobic bacteria. In this study, a genetic system was established for G. metallireducens using nitrate as an alternative electron acceptor. Surprisingly, disruption of the benzoate-induced bamY gene, encoding a benzoate coenzyme A (CoA) ligase, reproducibly showed an increased biomass yield in comparison to the wild type during growth with benzoate but not during growth with acetate. Complementation of bamY in trans converted the biomass yield back to the wild-type level. Growth of the bamY mutant with benzoate can be rationalized by the identification of a previously unknown succinyl-CoA:benzoate CoA transferase activity; it represents an additional, energetically less demanding mode of benzoate activation. The activity was highly enriched from extracts of cells grown on benzoate, yielding a 50-kDa protein band; mass spectrometric analysis identified the corresponding benzoate-induced gene annotated as a CoA transferase. It was heterologously expressed in Escherichia coli and characterized as a specific succinyl-CoA:benzoate CoA transferase. The newly identified enzyme in conjunction with a benzoate-induced succinyl-CoA synthetase links the tricarboxylic acid cycle to the upper benzoyl-CoA degradation pathway during growth on aromatic growth substrates.     

Effect of thiazole orange doubly labeled thymidine on DNA duplex formation

Nucleic acid oligonucleotides are widely used in hybridization experiments for specific detection of complementary nucleic acid sequences. For design and application of oligonucleotides, an understanding of their thermodynamic properties is essential. Recently, exciton-controlled hybridization-sensitive fluorescent oligonucleotides (ECHOs) were developed as uniquely labeled DNA oligomers containing commonly one thymidine having two covalently linked thiazole orange dye moieties. The fluorescent signal of an ECHO is strictly hybridization-controlled, where the dye moieties have to intercalate into double-stranded DNA for signal generation. Here we analyzed the hybridization thermodynamics of ECHO/DNA duplexes, and thermodynamic parameters were obtained from melting curves of 64 ECHO/DNA duplexes measured by ultraviolet absorbance and fluorescence. Both methods demonstrated a substantial increase in duplex stability (ΔΔG°(37) ～ -2.6 ± 0.7 kcal mol(-1)) compared to that of DNA/DNA duplexes of the same sequence. With the exception of T·G mismatches, this increased stability was mostly unaffected by other mismatches in the position opposite the labeled nucleotide. A nearest neighbor model was constructed for predicting thermodynamic parameters for duplex stability. Evaluation of the nearest neighbor parameters by cross validation tests showed higher predictive reliability for the fluorescence-based than the absorbance-based parameters. Using our experimental data, a tool for predicting the thermodynamics of formation of ECHO/DNA duplexes was developed that is freely available at http://genome.gsc.riken.jp/echo/thermodynamics/ . It provides reliable thermodynamic data for using the unique features of ECHOs in fluorescence-based experiments.     

Lack of the mitochondrial protein acylglycerol kinase causes Sengers syndrome

Exome sequencing of an individual with congenital cataracts, hypertrophic cardiomyopathy, skeletal myopathy, and lactic acidosis, all typical symptoms of Sengers syndrome, discovered two nonsense mutations in the gene encoding mitochondrial acylglycerol kinase (AGK). Mutation screening of AGK in further individuals with congenital cataracts and cardiomyopathy identified numerous loss-of-function mutations in an additional eight families, confirming the causal nature of AGK deficiency in Sengers syndrome. The loss of AGK led to a decrease of the adenine nucleotide translocator in the inner mitochondrial membrane in muscle, consistent with a role of AGK in driving the assembly of the translocator as a result of its effects on phospholipid metabolism in mitochondria.     

Structural insight into activation mechanism of Toxoplasma gondii nucleoside triphosphate diphosphohydrolases by disulfide reduction

The intracellular parasite Toxoplasma gondii produces two nucleoside triphosphate diphosphohydrolases (NTPDase1 and -3). These tetrameric, cysteine-rich enzymes require activation by reductive cleavage of a hitherto unknown disulfide bond. Despite a 97% sequence identity, both isozymes differ largely in their ability to hydrolyze ATP and ADP. Here, we present crystal structures of inactive NTPDase3 as an apo form and in complex with the product AMP to resolutions of 2.0 and 2.2 Å, respectively. We find that the enzyme is present in an open conformation that precludes productive substrate binding and catalysis. The cysteine bridge 258–268 is identified to be responsible for locking of activity. Crystal structures of constitutively active variants of NTPDase1 and -3 generated by mutation of Cys²⁵⁸–Cys²⁶⁸ show that opening of the regulatory cysteine bridge induces a pronounced contraction of the whole tetramer. This is accompanied by a 12° domain closure motion resulting in the correct arrangement of all active site residues. A complex structure of activated NTPDase3 with a non-hydrolyzable ATP analog and the cofactor Mg²⁺ to a resolution of 2.85 Å indicates that catalytic differences between the NTPDases are primarily dictated by differences in positioning of the adenine base caused by substitution of Arg⁴⁹² and Glu⁴⁹³ in NTPDase1 by glycines in NTPDase3.     

Simultaneous acquisition of PAR and PAIN spectra

We present a scheme that allows the simultaneous detection of PAR and PAIN correlation spectra in a single two-dimensional experiment. For both spectra, we obtain almost the same signal-to-noise ratio as if a PAR or PAIN spectrum is recorded separately, which in turn implies that one of the spectra may be considered additional information for free. The experiment is based on the observation that in a PAIN experiment, the PAR condition is always also fulfilled. The performance is demonstrated experimentally using uniformly ¹³C,¹⁵N-labeled samples of N–f–MLF–OH and ubiquitin.     

Do arbuscular mycorrhizal fungi affect the allometric partition of host plant biomass to shoots and roots? A meta-analysis of studies from 1990 to 2010

Arbuscular mycorrhizas (AM) are ubiquitous root symbioses with often pervasive effects on the plant host, one of which may be above- and belowground biomass allocation. A meta-analysis was conducted on 516 trials that were described in 90 available articles to examine whether AM colonization could result in a modification of partitioning of plant biomass in shoots and roots. It was hypothesized that alleviating plant nutrient limitations could result in a decrease of root to shoot (R/S) ratio in AM plants or, alternatively, the direction of shifts in the R/S ratio would be determined by the changes in total dry biomass. In our analysis, we considered four types of stresses: drought stress, single heavy metal stress, multiple heavy metal stress, and other potential abiotic plant stress factors. When disregarding any factors that could regulate effects, including stress status and mode of propagation, the overall AM effect was a significant modification of biomass towards shoot growth. However, the responses of stressed and clonally propagated plants differed from those of seed-grown unstressed plants. Our meta-analysis detected a considerable decline in the R/S ratio when plants were grown from seeds in the absence of abiotic stresses. Moreover, we demonstrate that additional regulators of the AM-mediated impact on R/S ratio were presence of competition from other plants, plant growth outcome of the symbiosis, growth substrate volume, experimental duration, and the identities of both plant and AM fungus. Our results indicate that a prediction of AM effects on R/S allocation becomes more accurate when considering regulators, most notably propagation mode and stress. We discuss possible mechanisms through which stress and other regulators may operate.     

Morphological respiratory diffusion capacity of the lungs of ball pythons (Python regius)

This study aims at a functional and morphological characterization of the lung of a boid snake. In particular, we were interested to see if the python's lungs are designed with excess capacity as compared to resting and working oxygen demands. Therefore, the morphological respiratory diffusion capacity of ball pythons (Python regius) was examined following a stereological, hierarchically nested approach. The volume of the respiratory exchange tissue was determined using computed tomography. Tissue compartments were quantified using stereological methods on light microscopic images. The tissue diffusion barrier for oxygen transport was characterized and measured using transmission electron micrographs. We found a significant negative correlation between body mass and the volume of respiratory tissue; the lungs of larger snakes had relatively less respiratory tissue. Therefore, mass-specific respiratory tissue was calculated to exclude effects of body mass. The volume of the lung that contains parenchyma was 11.9±5.0mm(3)g(-1). The volume fraction, i.e., the actual pulmonary exchange tissue per lung parenchyma, was 63.22±7.3%; the total respiratory surface was, on average, 0.214±0.129m(2); it was significantly negatively correlated to body mass, with larger snakes having proportionally smaller respiratory surfaces. For the air-blood barrier, a harmonic mean of 0.78±0.05μm was found, with the epithelial layer representing the thickest part of the barrier. Based on these findings, a median diffusion capacity of the tissue barrier ( [Formula: see text] ) of 0.69±0.38ml O(2)min(-1)mmHg(-1) was calculated. Based on published values for blood oxygen concentration, a total oxygen uptake capacity of 61.16mlO(2)min(-1)kg(-1) can be assumed. This value exceeds the maximum demand for oxygen in ball pythons by a factor of 12. We conclude that healthy individuals of P. regius possess a considerable spare capacity for tissue oxygen exchange.     

LCA of energetic biomass utilization: actual projects and new developments—April 23, 2012, Berne, Switzerland

Introduction

In the last years, the use of biomass for energy purposes has been seen as a promising option to reduce the use of nonrenewable energy sources and the emissions of fossil carbon. However, LCA studies have shown that the energetic use of biomass also causes impacts on climate change and, furthermore, that different environmental issues arise, such as land use and agricultural emissions. While biomass is renewable, it is not an unlimited resource. Its use, to whatever purpose, must therefore be well studied to promote the most efficient option with the least environmental impacts. The 47th LCA Discussion Forum gathered several national and international speakers who provided a broad and qualified view on the topic.

Summary of the topics presented in DF 47

Several aspects of energetic biomass use from a range of projects financed by the Swiss Federal Office of Energy (SFOE) were presented in this Discussion Forum. The first session focused on important aspects of the agricultural biogas production like the use of high energy crops or catch crops as well as the influence of plant size on the environmental performance of biogas. In the second session, other possibilities of biomass treatment like direct combustion, composting, and incineration with municipal waste were presented. Topic of the first afternoon session was the update and harmonization of biomass inventories and the resulting new assessment of biofuels. The short presentations investigated some further aspects of the LCA of bioenergy like the assessment of spatial variation of greenhouse gas (GHG) emissions from bioenergy production in a country, the importance of indirect land use change emissions on the overall results, the assessment of alternative technologies to direct spreading of digestate or the updates of the car operation datasets in ecoinvent.

Conclusions

One main outcome of this Discussion Forum is that bioenergy is not environmentally friendly per se. In many cases, energetic use of biomass allows a reduction of GHG and fossil energy use. However, there is often a tradeoff with other environmental impacts linked to agricultural production like eutrophication or ecotoxicity. Methodological challenges still exist, like the assessment of direct and indirect land use change emissions and their attribution to the bioenergy production, or the influence of heavy metal flows on the bioenergy assessment. Another challenge is the implementation of a life cycle approach in certification or legislation schemes, as shown by the example of the Renewable Energy Directive of the European Union.