Reconciling Carbon-cycle Concepts, Terminology, and Methods

Recent projections of climatic change have focused a great deal of scientific and public attention on patterns of carbon (C) cycling as well as its controls, particularly the factors that determine whether an ecosystem is a net source or sink of atmospheric carbon dioxide (CO₂). Net ecosystem production (NEP), a central concept in C-cycling research, has been used by scientists to represent two different concepts. We propose that NEP be restricted to just one of its two original definitions—the imbalance between gross primary production (GPP) and ecosystem respiration (ER). We further propose that a new term—net ecosystem carbon balance (NECB)—be applied to the net rate of C accumulation in (or loss from [negative sign]) ecosystems. Net ecosystem carbon balance differs from NEP when C fluxes other than C fixation and respiration occur, or when inorganic C enters or leaves in dissolved form. These fluxes include the leaching loss or lateral transfer of C from the ecosystem; the emission of volatile organic C, methane, and carbon monoxide; and the release of soot and CO₂ from fire. Carbon fluxes in addition to NEP are particularly important determinants of NECB over long time scales. However, even over short time scales, they are important in ecosystems such as streams, estuaries, wetlands, and cities. Recent technological advances have led to a diversity of approaches to the measurement of C fluxes at different temporal and spatial scales. These approaches frequently capture different components of NEP or NECB and can therefore be compared across scales only by carefully specifying the fluxes included in the measurements. By explicitly identifying the fluxes that comprise NECB and other components of the C cycle, such as net ecosystem exchange (NEE) and net biome production (NBP), we can provide a less ambiguous framework for understanding and communicating recent changes in the global C cycle.     

Microbial degradation of styrene: biochemistry, molecular genetics, and perspectives for biotechnological applications

Large quantities of the potentially toxic compound styrene are produced and used annually by the petrochemical and polymer-processing industries. It is as a direct consequence of this that significant volumes of styrene are released into the environment in both the liquid and the gaseous forms. Styrene and its metabolites are known to have serious negative effects on human health and therefore, strategies to prevent its release, remove it from the environment, and understand its route of degradation were the subject of much research. There are a large number of microbial genera capable of metabolizing styrene as a sole source of carbon and energy and therefore, the possibility of applying these organisms to bioremediation strategies was extensively investigated. From the multitude of biodegradation studies, the application of styrene-degrading organisms or single enzymes for the synthesis of value-added products such as epoxides has emerged.     

Identification and characterization of two related murine genes, Eat2a and Eat2b, encoding single SH2-domain adapters

Human EAT-2 (SH2D1B) and SLAM-associated protein (SAP) (SH2D1A) are single SH2-domain adapters, which bind to specific tyrosine residues in the cytoplasmic tail of six signaling lymphocytic activation molecule (SLAM) (SLAMF1)-related receptors. Here we report that, unlike in humans, the mouse and rat Eat2 genes are duplicated with an identical genomic organization. The coding regions of the mouse Eat2a and Eat2b genes share 91% identity at the nucleotide level and 84% at the protein level; similarly, segments of introns are highly conserved. Whereas expression of mouse Eat2a mRNA was detected in multiple tissues, Eat2b was only detectable in mouse natural killer cells, CD8⁺ T cells, and ovaries, suggesting a very restricted tissue expression of the latter. Both the EAT-2A and EAT-2B coimmunoprecipitated with mouse SLAM in transfected cells and augmented tyrosine phosphorylation of the cytoplasmic tail of SLAM. Both EAT-2A and EAT-2B bind to the Src-like kinases Fyn, Hck, Lyn, Lck, and Fgr, as determined by a yeast two-hybrid assay. However, unlike SAP, the EAT-2 proteins bind to their kinase domains and not to the SH3 domain of these kinases. Taken together, the data suggest that both EAT-2A and EAT-2B are adapters that recruit Src kinases to SLAM family receptors using a mechanism that is distinct from that of SAP. Electronic supplementary material Supplementary material is available for this article at and accessible for authorised users. S. Calpe and E. Erdős contributed equally to this work     

Protein structural motif prediction in multidimensional phi-psi space leads to improved secondary structure prediction.

A significant step towards establishing the structure and function of a protein is the prediction of the local conformation of the polypeptide chain. In this article, we present systems for the prediction of three new alphabets of local structural motifs. The motifs are built by applying multidimensional scaling (MDS) and clustering to pair-wise angular distances for multiple phi-psi angle values collected from high-resolution protein structures. The predictive systems, based on ensembles of bidirectional recurrent neural network architectures, and trained on a large non-redundant set of protein structures, achieve 72%, 66%, and 60% correct motif prediction on an independent test set for di-peptides (six classes), tri-peptides (eight classes) and tetra-peptides (14 classes), respectively, 28-30% above baseline statistical predictors. We then build a further system, based on ensembles of two-layered bidirectional recurrent neural networks, to map structural motif predictions into a traditional 3-class (helix, strand, coil) secondary structure. This system achieves 79.5% correct prediction using the "hard" CASP 3-class assignment, and 81.4% with a more lenient assignment, outperforming a sophisticated state-of-the-art predictor (Porter) trained in the same experimental conditions. The structural motif predictor is publicly available at: http://distill.ucd.ie/porter+/.     

Herbivore control of annual grassland composition in current and future environments

Selective consumption by herbivores influences the composition and structure of a range of plant communities. Anthropogenically driven global environmental changes, including increased atmospheric carbon dioxide (CO₂), warming, increased precipitation, and increased N deposition, directly alter plant physiological properties, which may in turn modify herbivore consumption patterns. In this study, we tested the hypothesis that responses of annual grassland composition to global changes can be predicted exclusively from environmentally induced changes in the consumption patterns of a group of widespread herbivores, the terrestrial gastropods. This was done by: (1) assessing gastropod impacts on grassland composition under ambient conditions; (2) quantifying environmentally induced changes in gastropod feeding behaviour; (3) predicting how grassland composition would respond to global-change manipulations if influenced only by herbivore consumption preferences; and (4) comparing these predictions to observed responses of grassland community composition to simulated global changes. Gastropod herbivores consume nearly half of aboveground production in this system. Global changes induced species-specific changes in plant leaf characteristics, leading gastropods to alter the relative amounts of different plant types consumed. These changes in gastropod feeding preferences consistently explained global-change-induced responses of functional group abundance in an intact annual grassland exposed to simulated future environments. For four of the five global change scenarios, gastropod impacts explained > 50% of the quantitative changes, indicating that herbivore preferences can be a major driver of plant community responses to global changes.     

Interannual and between species comparison of the lipids, fatty acids and sterols of Antarctic krill from the US AMLR Elephant Island survey area

Antarctic euphausiids, Euphausia superba, E. tricantha, E. frigida and Thysanoessa macrura were collected near Elephant Island ¦ during 1997 and 1998. Total lipid was highest in E. superba small juveniles (16 mg g⁻¹ wet mass), ranging from 12 to 15 mg in other euphausiids. Polar lipid (56–81% of total lipid) and triacylglycerol (12–38%) were the major lipids with wax esters (6%) only present in E. tricantha. Cholesterol was the major sterol (80–100% of total sterols) with desmosterol second in abundance (1–18%). 1997 T. macrura and E. superba contained a more diverse sterol profile, including 24-nordehydrocholesterol (0.1–1.7%), trans-dehydrocholesterol (1.1–1.5%), brassicasterol (0.5–1.7%), 24-methylenecholesterol (0.1–0.4%) and two stanols (0.1–0.2%). Monounsaturated fatty acids included primarily 18:1(n−9)c (7–21%), 18:1(n−7)c (3–13%) and 16:1(n−7)c (2–7%). The main saturated fatty acids in krill were 16:0 (18–29%), 14:0 (2–15%) and 18:0 (1–13%). Highest eicosapentaenoic acid [EPA, 20:5(n−3)] and docosahexaenoic acid [DHA, 22:6(n−3)] occurred in E. superba (EPA, 15–21%; DHA, 9–14%), and were less abundant in other krill. E. superba is a good source of EPA and DHA for consideration of direct or indirect use as a food item for human consumption. Lower levels of 18:4(n−3) in E. tricantha, E. frigida and T. macrura (0.4–0.7% of total fatty acids) are more consistent with a carnivorous or omnivorous diet as compared with herbivorous E. superba (3.7–9.4%). The polyunsaturated fatty acid (PUFA) 18:5(n−3) and the very-long chain (VLC-PUFA), C₂₆ and C₂₈ PUFA, were not present in 1997 samples, but were detected at low levels in most 1998 euphausiids. Interannual differences in these biomarkers suggest greater importance of dinoflagellates or some other phytoplankton group in the Elephant Island area during 1998. The data have enabled between year comparisons of trophodynamic interactions of krill collected in the Elephant Island region, and will be of use to groups using signature lipid methodology.     

Marked depletion of polar lipid and non-essential fatty acids following settlement by post-larvae of the spiny lobster Jasus verreauxi

The development from the non-feeding post-larva (puerulus) to the first instar juvenile of spiny lobsters is highly energetically demanding. These demands may greatly compromise the energy reserves of the lobsters following settlement, leading to reduced growth and survival in the wild, and also in aquaculture. Therefore, the lipid class and fatty acid composition of wild caught pueruli and first instar juveniles of the spiny lobster Jasus verreauxi (H. Milne Edwards, 1851) were analysed by thin layer chromatography-flame ionisation detection and capillary gas chromatography. Pueruli contained substantially more lipid than first instar juveniles (mean difference =3.5 mg, or 41.9%) and most of this difference was due to the presence of greater amounts of polar lipid (mean difference =3.9 mg or 49.2%) in pueruli. First instar juveniles contained significantly more triacylglycerol (mean =0.2 mg), consistent with the polar lipid being converted to a more readily metabolised lipid class in the hepatopancreas. These results indicate that polar lipid is the major energy store during the non-feeding puerulus stage of spiny lobsters from the genus Jasus. Overall, the essential, polyunsaturated linoleic, docosahexaenoic and eicosapentaenoic acids did not show a significant decrease between the two developmental stages, despite the absence of feeding. However, significant reductions in the abundance of both saturated and monounsaturated fatty acids between the two stages were identified (decrease of 811 and 783 microg per individual, respectively). This suggested that selective depletion of non-essential fatty acids may be occurring, with resultant sparing of the essential fatty acids. Supplying diets rich in these depleted fatty acids, and in particular the essential fatty acids, preferably in polar lipid, is likely to result in increased survival and growth of J. verreauxi and other spiny lobsters from first instar juveniles in aquaculture.     

Carbon isotope ratio measurements of succulent plants in southern Africa

Summary Succulent plants representing 16 families and a variety of growth forms originating from winter, summer, and year-round rainfall regimes in southern Africa were analyzed for carbon isotope ratios. Most families had species with ¹³C values indicative of CAM, particularly those from winter and year-round rainfall regimes. Plants with ¹³C values intermediate between CAM and C₃, indicating flexible photosynthetic pathways, were generally leafy perennials subject to seasonal tissue dehydration. Reproductive tissue tended to have less negative ¹³C values than vegetative tissue on the same plant, indicating drought-season origin of the former.CIW-DPB Publication No. 609     

Deafening drives cell-type-specific changes to dendritic spines in a sensorimotor nucleus important to learned vocalizations

Hearing loss prevents vocal learning and causes learned vocalizations to deteriorate, but how vocalization-related auditory feedback acts on neural circuits that control vocalization remains poorly understood. We deafened adult zebra finches, which rely on auditory feedback to maintain their learned songs, to test the hypothesis that deafening modifies synapses on neurons in a sensorimotor nucleus important to song production. Longitudinal in vivo imaging revealed that deafening selectively decreased the size and stability of dendritic spines on neurons that provide input to a striatothalamic pathway important to audition-dependent vocal plasticity, and changes in spine size preceded and predicted subsequent vocal degradation. Moreover, electrophysiological recordings from these neurons showed that structural changes were accompanied by functional weakening of both excitatory and inhibitory synapses, increased intrinsic excitability, and changes in spontaneous action potential output. These findings shed light on where and how auditory feedback acts within sensorimotor circuits to shape learned vocalizations.