Effect of deep and shallow root systems on the dynamics of soil inorganic N during 3-year crop rotations

Unused inorganic nitrogen (N_inorg) left in agricultural soils will typically leach to deeper soil layers. If it moves below the root zone it will be lost from the system, but the depth of the root zone depends on the crop species grown. In this experiment we studied the effect of 3-year crop sequences, with different combinations of deep-rooted and shallow-rooted crops, on soil N_inorg dynamics to 2.5 m soil depth and the possibility of crop utilization of N leached to deep soil layers. We grew ten different crop sequences for 3 years. The crops and catch crops grown were selected to allow different sequences of deep-rooted and shallow-rooted crops. Very different rooting depths were obtained, from only 0.5 m (leek), to ∼1.0 m (ryegrass and barley), 1.5 m (red beet), 2.0 m (fodder radish and white cabbage) and more than 2.5 m by the chicory catch crop. The results showed a significant retention of N_inorg within the 2.5 m soil profile from one year to the next, but the retained N had leached to deeper parts of the profile during the winter season. Only little N_inorg was retained over two winter seasons. The retention in the deeper soil layers allowed N_inorg to be taken up by succeeding deep-rooted main crops or catch crops. The effects of crop rooting depth on N_inorg in the subsoil layers from 1.0 to 2.5 m were striking. White cabbage reduced N_inorg below 1.0 m with up to 113 kg N ha^-1 during its growth. Grown after catch crops, leek and red beet left on average 60 kg N ha⁻¹ less below 1.0 m than leek and red beet grown without a preceding catch crop. We conclude that it is possible to design crop rotations with improved nitrogen use efficiency by using the differences in crop rooting patterns; deep-rooted crops or catch crops can be used to recover N_inorg leached after previous crops, and catch crops can be grown before shallow-rooted crops to lift the deep N_inorg up to layers where these crops have their roots.     

Determination of the binding affinities of plasmid DNA using fluorescent intercalators possessing an acridine skeleton

Novel acridine derivatives, wherein the steric factor has been varied systematically through substitution at the 9 position of the acridine ring, were evaluated as convenient fluorescent probes for nucleic acid detection. The binding affinities of N-(9-acridinylthiocarbamoyl)amino acids (ATA) with plasmid DNA (pUC 19) were investigated using UV-vis spectrophotometry, fluorometric titration and quantum chemical calculations (AM1). From spectrofluorometric analysis, the binding constants for the DNA-ATA complexes were determined. To elucidate its DNA intercalation, the most preferable tautomeric structure of ATA was established by means of AM1 calculations.     

Microarray analysis of butyrate regulated genes in colonic epithelial cells

Butyrate is a naturally occurring product of colonic microbial fermentation of dietary carbohydrates that escape hydrolysis in the small intestine. Butyrate plays a significant role in the maintenance of colonic tissue homeostasis by regulating the expression of genes associated with the processes of proliferation, differentiation, and apoptosis. Using microarray analysis, we assessed changes in the expression of 19,400 genes in response to butyrate in a human colonic epithelial cell line. Among these, we have identified 221 potentially butyrate- responsive genes specifically associated with the processes of proliferation, differentiation, and apoptosis. Of these genes, 59 are upregulated and 162 downregulated, in accordance with the known modes of action of butyrate. The changes in the expression levels (up- or downregulation) of many of these genes were found to be opposite to that reported in colon cancer tissue, where the intracellular concentration of butyrate would be reduced due to the decline in expression of the colonic butyrate transporter, MCT1.     

CCR3, CCR5, CCR8 and CXCR3 expression in memory T helper cells from allergic rhinitis patients, asymptomatically sensitized and healthy individuals

Background

Interleukin 8 (IL8) belongs to the family of chemokines. It mediates the activation and migration of neutrophils from peripheral blood into tissue and hereby plays a pivotal role in the initiation of inflammation. Thus it is important in inflammatory lung diseases like bronchial asthma or severe infections by Respiratory Syncytial Virus (RSV). IL8 acts through binding to the IL8-Receptor alpha (IL8RA). For both genes association with asthma has been described. In addition, IL8 has been found in association with RSV bronchiolitis. The aim of our study was to test both genes for association with asthma and severe RSV infections. In addition we were interested in whether a common genetic background of both diseases exists in regards to these genes.

Methods

We genotyped the two IL8 promotor polymorphisms -251A/T and -781C/T and the three amino acid variants M31R, S276T and R335C in IL8RA on 322 children with asthma, 131 infants with severe RSV associated diseases and 270 controls. Statistical analyses made use of the Armitage's trend test for single polymorphisms and FAMHAP for calculations of haplotypes.

Results

We found association of the IL8 polymorphism -781C/T as well as IL8 haplotypes with asthma (p = 0.011 and p = 0.036, respectively). In addition, direct comparison of the asthmatic population with the RSV population revealed significant differences, both for -781C/T alone (p = 0.034) and IL8 haplotypes (p = 0.005). The amino acid variants in IL8RA were evenly distributed in between all three populations.

Conclusion

We conclude from our data that IL8 might play a role in the genetic predisposition to asthma and that these effects are different or even opposite to the effects on severe RSV diseases. Furthermore, IL8RA is unlikely to play a major role in the genetics of either disease.     

Improving the reliability and throughput of mass spectrometry-based proteomics by spectrum quality filtering

In contemporary peptide-centric or non-gel proteome studies, vast amounts of peptide fragmentation data are generated of which only a small part leads to peptide or protein identification. This motivates the development and use of a filtering algorithm that removes spectra that contribute little to protein identification. Removal of unidentifiable spectra reduced both the amount of computational and human time spent on analyzing spectra as well as the chances of obtaining false identifications. Thorough testing on various proteome datasets from different instruments showed that the best suggested machine-learning classifier is, on average, able to recognize half of the unidentified spectra as bad spectra. Further analyses showed that several unidentified spectra classified as good were derived from peptides carrying unanticipated amino acid modifications or contained sequence tags that allowed peptide identification using homology searches. The implementation of the classifiers is available under the GNU General Public License at http://www.bioinfo.no/software/spectrumquality.     

The transfer function of a target limits the jitter detection threshold with signals of echolocating FM-bats

The delay jitter discrimination threshold in bats is a disputed subject. Some investigators have obtained results indicating that bats are able to discriminate alternations in delay down to 10 ns, which appears incredible for purely physical reasons. Using actual bat echolocation sequences recorded during an easy detection task to measure simulated delay jitter, it is shown here that jitter detection thresholds in the order of some tens of nanoseconds are actually physically realizable. However, if the transfer function of the target simulating apparatus is not perfect, the lowest thresholds are in the order of hundreds of nanoseconds and variable between individual bats. This phenomenon is shown to arise as a consequence of the variation in signal parameters from call to call. When the transfer function from a real jitter experiment was artificially applied to the echoes, the jitter detection thresholds again were several hundred nanoseconds. This is the first study to point out a limiting role of the transfer function of a system faced with variations in echolocation signal parameters, something that should be considered in evaluating all sonar systems with variable signal structure.     

The TSG-6/HC2-mediated Transfer Is a Dynamic Process Shuffling Heavy Chains between Glycosaminoglycans

The heavy chain (HC) subunits of the bikunin proteins are covalently attached to a single chondroitin sulfate (CS) chain originating from bikunin and can be transferred to different hyaluronan (HA) molecules by TSG-6/HC2. In the present study, we demonstrate that HCs transferred to HA may function as HC donors in subsequent transfer reactions, and we show that the CS of bikunin may serve as an HC acceptor, analogous to HA. Our data suggest that TSG-6/HC2 link HCs randomly on the CS chain of bikunin, in contrast to the ordered attachment observed during the biosynthesis. Moreover, the results show that the transfer activity is indifferent to the new HC position, and the relocated HCs are thus prone to further TSG-6/HC2-induced transfer reactions. The data suggest that HCs may be transferred directly from HA to HA without the involvement of the bikunin CS chain. The results demonstrate reversibility of the interactions between HCs and glycosaminoglycans and suggest that a dynamic shuffling of the HCs occur in vivo.     

Vitronectin binds to the head region of Moraxella catarrhalis ubiquitous surface protein A2 and confers complement‐inhibitory activity

The serum resistance of the common respiratory pathogen Moraxella catarrhalis is mainly dependent on ubiquitous surface proteins (Usp) A1 and A2 that interact with complement factor 3 (C3) and complement inhibitor C4b binding protein (C4BP) preventing the alternative and classical pathways of the complement system respectively. UspA2 also has the capacity to attract vitronectin that in turn binds C9 and hereby inhibits membrane attack complex (MAC) formation. We found UspA2 as a major vitronectin binding protein and hence the UspA2/vitronectin interaction was studied in detail. The affinity constant (K_D) for vitronectin binding to UspA2 was 2.3 × 10^?8 M, and the N‐terminal region encompassing residues UspA2 30–170 bound vitronectin with a K_D of 7.9 × 10^?8 M. Electron microscopy verified that the active binding domain (UspA2^30–177) was located at the head region of UspA2. Experiments with recombinantly expressed vitronectin also revealed that UspA2^30–177 bound to the C‐terminal region of vitronectin residues 312–396. Finally, when human serum was pre‐incubated with UspA2, bacteria showed significantly less serum resistance. Our study directly reveals the binding mode between the N‐terminal domain of UspA2 and the C‐terminal part of vitronectin and thus sheds light upon the mechanism of M. catarrhalis‐dependent serum resistance.     

Characterization and kinetic analysis of a thermostable GH3 β-glucosidase from Penicillium brasilianum

A GH3 β-glucosidase (BGL) from Penicillium brasilianum was purified to homogeneity after cultivation on a cellulose and xylan rich medium. The BGL was identified in a genomic library, and it was successfully expressed in Aspergillus oryzae. The BGL had excellent stability at elevated temperatures with no loss in activity after 24 h of incubation at 60°C at pH 4–6, and the BGL was shown to have significantly higher stability at these conditions in comparison to Novozym 188 and to other fungal GH3 BGLs reported in the literature. The BGL had significant lower affinity for cellobiose compared with the artificial substrate para-nitrophenyl-β-d-glucopyranoside (pNP-Glc) and further, pronounced substrate inhibition using pNP-Glc. Kinetic studies demonstrated the high importance of using cellobiose as substrate and glucose as inhibitor to describe the inhibition kinetics of BGL taking place during cellulose hydrolysis. A novel assay was developed to characterize this glucose inhibition on cellobiose hydrolysis. The assay uses labelled glucose-¹³C₆ as inhibitor and subsequent mass spectrometry analysis to quantify the hydrolysis rates.