Omnivores as plant bodyguards—A model of the importance of plant quality

The importance of omnivores in ecological systems is increasingly being recognized, not least due to their intensified use as biocontrol agents in crop production. We model a simple plant–herbivore–omnivore (predator) system to explore the effects of plant suitability as food for omnivores on the outcome of omnivore–herbivore interactions. The model predicts that increasing plant suitability relative to herbivore suitability for the omnivore will catalyze the extinction of herbivores or omnivores, depending on the relative growth rate of omnivores feeding solely on plants or herbivores. When omnivore growth is higher on plants, either the omnivore or the herbivore goes extinct. When omnivore growth is higher on herbivores, the possible consequences are extinction, stable coexistence, and limit cycles, depending on the combination of species properties. Our results suggest that plants in some situations may evolve towards becoming more suitable to omnivores to escape detrimental herbivores and that breeders could manipulate crop suitability to omnivore species to reach a desired outcome of omnivore–herbivore interactions.     

The folding and stability of human alpha class glutathione transferase A1-1 depend on distinct roles of a conserved N-capping box and hydrophobic staple motif.

An N-capping box and a hydrophobic staple motif are strictly conserved in the core of all known glutathione S-transferases (GST). In the present work, mutations of hGSTA1-1 enzyme residues forming these motifs have been generated. The analysis of S154A, D157A, and S154A/D157A capping mutants indicate that the removal of this local signal destabilizes the protein. The fact that the third helical residue D157A mutation (N-3) was much more destabilizing than the first helical residue S154A mutation (N-cap) suggests that the appropriate conformation of the conserved substructure formed by the alpha 6-helix and preceding loop (GST motif II) is crucial for the overall protein stability. The refolding study of GSTA1-1 variants supports the prediction that this subdomain could represent a nucleation site of refolding. The analysis of L153A, I158A, L153G, and L153A/I158A hydrophobic staple mutants indicate that the removal of this motif destabilizes the GSTA1-1 structure as well as its refolding transition state. The hydrophobic staple interaction favors essential inter-domain contacts and, thereby, in contrast to capping interactions, accelerates the enzyme reactivation. Its strict conservation in the GST system supports the suggestion that this local signal could represent an evolutionarily conserved determinant for rapid folding.     

Titration and subunit localization of active center cysteine in fibrinoligase (thrombin-activated fibrin stabilizing fector)

Fibrinoligase activity, measured in a fully synthetic substrate system, was shown to be inhibited by prior incubation of the enzyme with iodoacetamide. Using 1-¹⁴C-iodoacetamide, the amount of incorporated radio-activity increased in proportion to the loss of enzyme activity. Labelling of the enzyme was totally dependent on the addition of calcium ions and, under the conditions described, occurred predominantly in the $\text{a}\text{′}$ protomer. Acid hydrolysis of labelled fibrinoligase gave rise to S-carboxymethylcysteine as the only radioactive amino acid derivative.     

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Spruce versus Arabidopsis: different strategies of photosynthetic acclimation to light intensity change

Photosynthesis Research - The acclimation of higher plants to different light intensities is associated with a reorganization of the photosynthetic apparatus. These modifications, namely, changes...     

MicroRNAs show a wide diversity of expression profiles in the developing and mature central nervous system

Background  

MicroRNA (miRNA) encoding genes are abundant in vertebrate genomes but very few have been studied in any detail. Bioinformatic tools allow prediction of miRNA targets and this information coupled with knowledge of miRNA expression profiles facilitates formulation of hypotheses of miRNA function. Although the central nervous system (CNS) is a prominent site of miRNA expression, virtually nothing is known about the spatial and temporal expression profiles of miRNAs in the brain. To provide an overview of the breadth of miRNA expression in the CNS, we performed a comprehensive analysis of the neuroanatomical expression profiles of 38 abundant conserved miRNAs in developing and adult zebrafish brain.     

Deficit of CD47 results in a defect of marginal zone dendritic cells, blunted immune response to particulate antigen and impairment of skin dendritic cell migration

CD47 is a ubiquitously expressed cell surface glycoprotein that associates with integrins and regulates chemotaxis, migration, and activation of leukocytes. CD47 is also a ligand for signal regulatory protein alpha, a cell surface receptor expressed on monocytes, macrophages, granulocytes, and dendritic cell (DC) subsets that regulates cell activation, adhesion, and migration. Although the function of CD47 in macrophages and granulocytes has been studied in detail, little is known about the role of CD47 in DC biology in vivo. In this study we demonstrate that CD47(-/-) mice exhibit a selective reduction of splenic CD11c(high)CD11b(high)CD8alpha(-)CD4(+) DCs. These DCs correspond to marginal zone DCs and express signal regulatory protein alpha, possibly explaining their selective deficiency in CD47(-/-) mice. Deficiency of marginal zone DCs resulted in impairment of IgG responses to corpusculate T cell-independent Ags. Although epidermal DCs were present in normal numbers in CD47(-/-) mice, their migration to draining lymph nodes in response to contact sensitization was impaired, while their maturation was intact. In vitro, CD47(-/-) mature DCs showed normal CCR7 expression but impaired migration to CCL-19, whereas immature DC response to CCL-5 was only slightly impaired. These results demonstrate a fundamental role of CD47 in DC migration in vivo and in vitro and in the function of marginal zone DCs.     

Coexpression and Heteromerization of Two Neuronal K-Cl Cotransporter Isoforms in Neonatal Brain

The neuron-specific K-Cl cotransporter KCC2 maintains the low intracellular chloride concentration required for the fast hyperpolarizing actions of inhibitory neurotransmitters. The KCC2 gene codes for two isoforms, KCC2a and KCC2b, which differ in their N termini. The relative expression and cellular distribution of the two KCC2 protein isoforms are unknown. Here, we characterize an antibody against the KCC2a isoform and show that a previously described antibody against KCC2 is specific for the KCC2b isoform (Hubner, C. A., Stein, V., Hermans-Borgmeyer, I., Meyer, T., Ballanyi, K., and Jentsch, T. J. (2001) Neuron 30, 515–524). Immunostaining of dissociated hippocampal cultures confirms that both KCC2 isoforms are neuron-specific. Immunoblot analysis indicates that KCC2b is the major KCC2 isoform in the adult brain, whereas in the neonatal mouse central nervous system, half of total KCC2 protein is KCC2a. At this stage, the two KCC2 isoforms are largely colocalized and show similar patterns of distribution in the brain. When coexpressed in HEK293 cells, KCC2a and KCC2b proteins form heteromeric complexes. Moreover, the two isoforms can be coimmunoprecipitated from the neonatal brain, suggesting the presence of endogenous KCC2a-KCC2b heteromers. Consistent with this, native gel analysis shows that a substantial part of endogenous KCC2 isoforms in the neonatal brain constitute dimers.The neuron-specific K⁺-Cl^- cotransporter KCC2 extrudes potassium and chloride ions from neurons, thus maintaining the low intracellular chloride concentration [Cl]_i necessary for the fast hyperpolarizing actions of inhibitory neurotransmitters γ-aminobutyric acid (GABA) and glycine (1). KCC2 is an ∼140-kDa plasma membrane protein that belongs to the cation chloride cotransporter (CCC)⁴ family (2, 3). CCCs, including KCC2, are thought to exist in the plasma membrane as functional oligomers, although the mechanisms whereby oligomerization affects their transport activity are unclear (4–8).We have recently shown that the KCC2 gene (alias Slc12a5) generates two mRNAs, KCC2a and KCC2b, by an alternative promoter and first exon usage (9). The difference between the KCC2a and KCC2b proteins lies in the most N-terminal part; the 40 unique amino acids in KCC2a include a putative binding sequence for the Ste20-related proline-alanine-rich kinase (SPAK). KCC2 null mutant mice deficient for both KCC2 isoforms show a disrupted breathing rhythm and die immediately after birth (10, 11), whereas selective KCC2b isoform knock-out mice exhibit spontaneous seizures but can survive up to 3 weeks after birth (9, 12). Thus, KCC2a obviously supports some vital functions of lower brain structures.In general, KCC2 expression in the CNS follows neuronal maturation; it is first detected in the postmitotic neurons of the spinal cord and brainstem and is then gradually increased in higher brain structures (13, 14). Our previous work has shown that during postnatal development, KCC2a mRNA expression remains relatively constant, whereas KCC2b mRNA is strongly up-regulated in the cortex during postnatal development (9). This indicates that KCC2b is responsible for the developmental shift from depolarizing to hyperpolarizing GABAergic responses.Here, we study the relative expression and cellular distribution of KCC2a and KCC2b proteins in the mouse brain. We characterize a new antibody specific for the KCC2a isoform and demonstrate that a previously described antibody against KCC2 (11) is specific for the KCC2b isoform. The relative expression of the KCC2 protein isoforms determined by immunoblot analysis correlates well with their mRNA levels (9). KCC2a and KCC2b proteins have a similar level and pattern of expression in the neonatal mouse brain and are colocalized in most neurons in non-cortical lower brain areas. Coimmunoprecipitation (coIP) experiments and coexpression followed by native gel analysis indicate that KCC2a-KCC2b heteromers can form in vitro and may exist in vivo.     

Soil Resources Influence Spatial Patterns of Denitrifying Communities at Scales Compatible with Land Management

Knowing spatial patterns of functional microbial guilds can increase our understanding of the relationships between microbial community ecology and ecosystem functions. Using geostatistical modeling to map spatial patterns, we explored the distribution of the community structure, size, and activity of one functional group in N cycling, the denitrifiers, in relation to 23 soil parameters over a 44-ha farm divided into one organic and one integrated crop production system. The denitrifiers were targeted by the nirS and nirK genes that encode the two mutually exclusive types of nitrite reductases, the cd₁ heme-type and copper reductases, respectively. The spatial pattern of the denitrification activity genes was reflected by the maps of the abundances of nir genes. For the community structure, only the maps of the nirS community were related to the activity. The activity was correlated with nitrate and dissolved organic nitrogen and carbon, whereas the gene pools for denitrification, in terms of size and composition, were influenced by the soil structure. For the nirS community, pH and soil nutrients were also important in shaping the community. The only unique parameter related to the nirK community was the soil Cu content. However, the spatial pattern of the nirK denitrifiers corresponded to the division of the farm into the two cropping systems. The different community patterns, together with the spatial distribution of the nirS/nirK abundance ratio, suggest habitat selection on the nirS- and nirK-type denitrifiers. Our findings constitute a first step in identifying niches for denitrifiers at scales relevant to land management.Soil microorganisms are abundant and diverse (46), drive key processes in biogeochemical cycles, and, thus, play crucial roles in ecosystem functioning (2). They are not randomly distributed but exhibit spatial patterns at different scales (26). Spatial patterns ranging from the micrometer up to the meter scale have been reported (19, 20, 32, 37), and an understanding of such patterns can give clues to how microbial communities are generated and maintained (17). Spatial patterns of microorganisms at the field and landscape scales warrant special attention, since they could be associated with land use and aid in creating knowledge-based management strategies for agricultural production (5, 42). However, our understanding of key habitat-selective factors is limited, and few studies have specified which factors influence the spatial patterns of soil microbial communities at larger scales. Lauber et al. (30) recently demonstrated that pH could predict the community composition of soil bacteria at the continental scale. The importance of pH as a key edaphic driver of bacterial community structure has also been shown in other studies (11, 47). Another major, but complex, factor pointed out in a few studies is the soil type (4, 5, 14). Most studies have included only a limited number of properties that are easy to measure; most often, carbon and nitrogen pools and soil physical factors have been neglected in microbial community ecology. Since these factors delineate soil oxygen and water content, they may exert a stronger impact on microbial communities than other soil resources.Reports on the field or landscape scale spatial distribution of soil bacteria have had a taxon-centered perspective at either the species or total-community level, but there is emerging interest in the biogeography of functional traits possessed by microorganisms (18). Bacterial species composition is likely important for soil ecosystem functions, but species affiliation rarely predicts in which way. In addition, the fuzzy species concept of bacteria makes it all the more difficult to link species to niches. Analysis of functional guilds, i.e., assemblages of populations sharing certain traits, can bridge this gap, and one guild of global concern that has been suggested and recently used as a model in functional ecology is the denitrifiers (39, 49). Denitrification is an anaerobic respiration pathway during which NO₃⁻ is reduced to N₂ by a wide range of unrelated taxa. The process is an essential route for N loss from agricultural soil and a major source of the greenhouse gas N₂O. It was recently shown that the spatial distribution of the relative abundances of denitrifiers with the genetic capacity to perform the last step in the denitrification pathway, reduction of N₂O to N₂, is linked to areas with high denitrification rates and low N₂O emissions (38). Adding field scale predicted patterns of the denitrifier community structure to the abundance and activity would not only give insight into the mechanisms shaping the community, but also deepen our understanding of the relationships between the ecology of denitrifiers, N loss, and the agroecosystems'' impact on climate change.We hypothesize that spatial autocorrelations of the structures, sizes, and activities of communities of denitrifying bacteria is governed by soil-based resources at a scale compatible with land management. To test this, and to elucidate the effects of crop production systems and the importance of soil physical and chemical factors in the denitrifying community, we explored the spatial distribution of community structure, size, and activity in relation to 23 soil parameters at a 44-ha farm divided into one organic and one integrated crop production system. The denitrifier community was described in terms of the signature genes that encode the two different types of nitrite reductases in the denitrification pathway, the cd₁ heme-type reductase (NirS), encoded by the nirS gene, and the copper oxidoreductase (NirK), encoded by nirK. The spatial patterns were mapped by geostatistical modeling, and correlation structures were explored.