Neutron radiography as a tool for revealing root development in soil: capabilities and limitations

Chronic atmospheric nitrogen deposition affects the cycling of carbon (C) and nitrogen (N) in forest ecosystems, and thereby alters the stable C isotopic abundance of plant and soil. Three successional stages, disturbed, rehabilitated and mature forests were studied for their responses to different nitrogen input levels. N-addition manipulative experiments were conducted at low, medium and high N levels. To study the responses of C cycling to N addition, the C concentration and ¹³C natural abundances for leaf, litter and soil were measured. Labile organic carbon fractions in mineral soils were measured to quantify the dynamics of soil organic C (SOC). Results showed that three-year continuous N addition did not significantly increase foliar C and N concentration, but decreased C/N ratio and enriched ¹³C in N-rich forests. In addition, N addition significantly decreased microbial biomass C, and increased water soluble organic C in surface soils of N-rich forests. This study suggests that N addition enhances the water consumption per unit C assimilation of dominant plant species, restricts SOC turnover in N-poor forests at early and medium successional stages (thus favored SOC sequestration), and vice versa for N-rich mature forests.     

A dimanganese(II) complex with bridging chlorides: Synthesis, electrochemistry, magnetic behavior, structure and bonding

The synthesis of dimeric [Mn₂Cl₂(μ-Cl)₂(dipa)₂]·MeOH (3) (dipa = dipyridylmethylamine) from [MnCl₂(H₂O)₄] (1) and dipa (2) and its structural characterization is reported. In the solid state complex 3 is dimeric and possesses crystallographically imposed C₂ symmetry, which differs from similar dimanganese(II) complexes showing an inversion symmetry for the central Mn(μ-Cl)₂Mn arrangement. Each manganese atom is thereby bound by three nitrogen atoms from a facially coordinated dipa ligand, and three chlorides (1 terminal and 2 μ-bridging) in an octahedrally distorted fashion.The cylovoltammogram of 3 displays that the two manganese(II) ions can independently be oxidized. The magnetic properties of 3 were determined by susceptibility measurements versus temperature. The intramolecular J parameter was determined to a value of J = (−5.2 ± 0.5) cm⁻¹.     

Metalloprotease meprin beta generates nontoxic N-terminal amyloid precursor protein fragments in vivo

Identification of physiologically relevant substrates is still the most challenging part in protease research for understanding the biological activity of these enzymes. The zinc-dependent metalloprotease meprin β is known to be expressed in many tissues with functions in health and disease. Here, we demonstrate unique interactions between meprin β and the amyloid precursor protein (APP). Although APP is intensively studied as a ubiquitously expressed cell surface protein, which is involved in Alzheimer disease, its precise physiological role and relevance remain elusive. Based on a novel proteomics technique termed terminal amine isotopic labeling of substrates (TAILS), APP was identified as a substrate for meprin β. Processing of APP by meprin β was subsequently validated using in vitro and in vivo approaches. N-terminal APP fragments of about 11 and 20 kDa were found in human and mouse brain lysates but not in meprin β(-/-) mouse brain lysates. Although these APP fragments were in the range of those responsible for caspase-induced neurodegeneration, we did not detect cytotoxicity to primary neurons treated by these fragments. Our data demonstrate that meprin β is a physiologically relevant enzyme in APP processing.     

DARPins recognizing the tumor-associated antigen EpCAM selected by phage and ribosome display and engineered for multivalency

Designed Ankyrin Repeat Proteins (DARPins) represent a novel class of binding molecules. Their favorable biophysical properties such as high affinity, stability and expression yields make them ideal candidates for tumor targeting. Here, we describe the selection of DARPins specific for the tumor-associated antigen epithelial cell adhesion molecule (EpCAM), an approved therapeutic target on solid tumors. We selected DARPins from combinatorial libraries by both phage display and ribosome display and compared their binding on tumor cells. By further rounds of random mutagenesis and ribosome display selection, binders with picomolar affinity were obtained that were entirely monomeric and could be expressed at high yields in the cytoplasm of Escherichia coli. One of the binders, denoted Ec1, bound to EpCAM with picomolar affinity (K_d = 68 pM), and another selected DARPin (Ac2) recognized a different epitope on EpCAM. Through the use of a variety of bivalent and tetravalent arrangements with these DARPins, the off-rate on cells was further improved by up to 47-fold. All EpCAM-specific DARPins were efficiently internalized by receptor-mediated endocytosis, which is essential for intracellular delivery of anticancer agents to tumor cells. Thus, using EpCAM as a target, we provide evidence that DARPins can be conveniently selected and rationally engineered to high-affinity binders of various formats for tumor targeting.     

Lipidic phase membrane protein serial femtosecond crystallography

X-ray free electron laser (X-FEL)-based serial femtosecond crystallography is an emerging method with potential to rapidly advance the challenging field of membrane protein structural biology. Here we recorded interpretable diffraction data from micrometer-sized lipidic sponge phase crystals of the Blastochloris viridis photosynthetic reaction center delivered into an X-FEL beam using a sponge phase micro-jet.     

Three-dimensional visualization and quantification of water content in the rhizosphere

? Despite the importance of rhizosphere properties for water flow from soil to roots, there is limited quantitative information on the distribution of water in the rhizosphere of plants. ? Here, we used neutron tomography to quantify and visualize the water content in the rhizosphere of the plant species chickpea (Cicer arietinum), white lupin (Lupinus albus), and maize (Zea mays) 12 d after planting. ? We clearly observed increasing soil water contents (θ) towards the root surface for all three plant species, as opposed to the usual assumption of decreasing water content. This was true for tap roots and lateral roots of both upper and lower parts of the root system. Furthermore, water gradients around the lower part of the roots were smaller and extended further into bulk soil compared with the upper part, where the gradients in water content were steeper. ? Incorporating the hydraulic conductivity and water retention parameters of the rhizosphere into our model, we could simulate the gradual changes of θ towards the root surface, in agreement with the observations. The modelling result suggests that roots in their rhizosphere may modify the hydraulic properties of soil in a way that improves uptake under dry conditions.     

Bacteriocyte dynamics during development of a holometabolous insect,the carpenter ant <Emphasis Type=Italic>Camponotus floridanus</Emphasis>

Background  

The carpenter ant Camponotus floridanus harbors obligate intracellular mutualistic bacteria (Blochmannia floridanus) in specialized cells, the bacteriocytes, intercalated in their midgut tissue. The diffuse distribution of bacteriocytes over the midgut tissue is in contrast to many other insects carrying endosymbionts in specialized tissues which are often connected to the midgut but form a distinct organ, the bacteriome. C. floridanus is a holometabolous insect which undergoes a complete metamorphosis. During pupal stages a complete restructuring of the inner organs including the digestive tract takes place. So far, nothing was known about maintenance of endosymbionts during this life stage of a holometabolous insect. It was shown previously that the number of Blochmannia increases strongly during metamorphosis. This implicates an important function of Blochmannia in this developmental phase during which the animals are metabolically very active but do not have access to external food resources. Previous experiments have shown a nutritional contribution of the bacteria to host metabolism by production of essential amino acids and urease-mediated nitrogen recycling. In adult hosts the symbiosis appears to degenerate with increasing age of the animals.     

Demography and natural selection have shaped genetic variation in Drosophila melanogaster: a multi-locus approach

Demography and selection have been recognized for their important roles in shaping patterns of nucleotide variability. To investigate the relative effects of these forces in the genome of Drosophila melanogaster, we used a multi-locus scan (105 fragments) of X-linked DNA sequence variation in a putatively ancestral African and a derived European population. Surprisingly, we found evidence for a recent size expansion in the African population, i.e., a significant excess of singletons at a chromosome-wide level. In the European population, such an excess was not detected. In contrast to the African population, we found evidence for positive natural selection in the European sample: (i) a large number of loci with low levels of variation and (ii) a significant excess of derived variants at the low-variation loci that are fixed in the European sample but rare in the African population. These results are consistent with the hypothesis that the European population has experienced frequent selective sweeps in the recent past during its adaptation to new habitats. Our study shows the advantages of a genomic approach (over a locus-specific analysis) in disentangling demographic and selective forces.