The potential of reduced tillage in Flanders

Untill recently, modern agriculture was focused on maximum food production without considering the long term impact on soil fertility or environment. As a consequence modern agriculture is nowadays confronted with a number of pressing problems. The main problems agriculture experiences in industrialised societies are the degradation of physical soil structure resulting in erosion and soil compaction, decline in SOM and N losses. Conservation tillage (CsT) agriculture was first introduced on a large scale on fields with mainly cereals, soybean and sunflower in the USA, Latin America and Australia as a very effective measure to reduce erosion and store water into the soil (Arshad, 1999; Six et al., 2002b). To date research on the positive and negative effect of CsT compared to CT agriculture mainly focussed on the soil conditions and crop rotations under the warm and dry climatic of the USA, Latin America and Australia. The climatic and soil conditions and crop rotations in Western Europe are, however, very different. Western Europe has a maritime temperate climate and the crop rotations contain crops that seem less suitable under CsT agriculture because they often include beets and potatoes, resulting in a high disturbance of the soil at the formation of the ridges and at harvest (Anonymous, 2006d). The major erosion problems in Belgium are found with these root and tuber crops and maize in the loess belt (Anonymous, 2000; Geelen, 2006). Nowadays farmers in Western Europe shift more and more to reduced tillage (RT) agriculture, a type of CsT agriculture which refers to tilling the whole soil surface but eliminating one or more of the operations that would otherwise be done in a CT system. This shift can partly be explained by the progress in machines, especially sowing machines, and because of its proven effects on reduction of soil erosion (Vandergeten & Roisin, 2004). However, very little information is available on the evolution of important soil properties e.g. related to C dynamics in RT agriculture under the specific Western European climatic and soil conditions and crop rotations. In this thesis, eighteen fields with a silt loam texture were selected, including the different types of RT agriculture running for a different number of years. In the study area, very little experimental sites exist where CT practices are compared to RT practices. Therefore, we had no choice but to include farmers' fields, where inevitably there is no perfect match between CT and RT fields. Despite the high disturbance of the soil every 2 or 3 years of crop rotations including sugar beets or potatoes, RT agriculture had a positive effect on the measured physical soil properties. The aggregate stability of the upper 10 cm depth layer measured with the method of De Leenheer & De Boodt (1959) and the three methods of Le Bissonnais (1996) were higher a short time after the shift to RT compared to CT agriculture. At each location, bulk density (BD) of the 5-10 cm depth layer was mostly lower and saturated soil water content (θs) was mostly higher under RT than CT agriculture. The penetration resistance (PR) of the upper depth layer under RT by direct drilling (RTDD) is higher than under CT agriculture, while the PR in the 20-30 cm depth layer is only higher under RT agriculture by cultivator or soil loosener (RTC) if the working depth is lower. The trend was a higher field-saturated hydraulic conductivity (Kfs) under RT compared to CT agriculture (chapter 3). RT agriculture resulted in a higher stratification of soil organic carbon (SOC) and total nitrogen (TN) in the soil profile. However, the total SOC and TN stock was not changed, even after a period of 20 years of RT agriculture. The amount of organic carbon and TN in three different particulate organic matter (POM) fractions of the 0-10 cm depth layer were found to be (significantly) higher both on an absolute and relative basis in the RT compared to the CT fields. In general the difference was the highest for the coarse free POM fraction, which is the most labile fraction. The higher SOC, TN and microbial biomass (MB) content in the upper depth layer of RT fields resulted in a higher carbon (C) and nitrogen (N) mineralization rate in undisturbed soil under controlled conditions in the laboratory. Simulating ploughing by disturbing the soil resulted both in lower and higher mineralization rates of the silt loam soils, but due to the large variability of the estimated mineralization parameters, the differences were not significant. It seems that under the specific management and climatic conditions of Western Europe, RT agriculture increase the SOC and TN content and microbial activity in the top layers, but do not result in enhanced sequestration when the entire soil profile is considered (chapter 4 and 5). Nitrous oxide nitrogen (N2O-N) emissions from RT fields tended to be slightly higher than CT fields. The higher N2O-N emissions of RT compared to CT fields were correlated with a higher % TN and MB-N (chapter 6). This study indicates that RTC agriculture is beneficial for the farmers, society and environment. However, the potential for RTDD agriculture in Flanders is probably limited because of the typical crop rotations that are less compatible with this type of agriculture (chapter 7)

Testing the Wyart-Cates model for non-Brownian shear thickening using bidisperse suspensions

There is a growing consensus that shear thickening of concentrated dispersions is driven by the formation of stress-induced frictional contacts. The Wyart-Cates (WC) model of this phenomenon, in which the microphysics of the contacts enters solely via the fraction $f$ of contacts that are frictional, can successfully fit flow curves for suspensions of weakly polydisperse spheres. However, its validity for "real-life", polydisperse suspensions has yet to be seriously tested. By performing systematic simulations on bidisperse mixtures of spheres, we show that the WC model applies only in the monodisperse limit and fails when substantial bidispersity is introduced. We trace the failure of the model to its inability to distinguish large-large, large-small and small-small frictional contacts. By fitting our data using a polydisperse analogue of $f$ that depends separately on the fraction of each of these contact types, we show that the WC picture of shear thickening is incomplete. Systematic experiments on model shear-thickening suspensions corroborate our findings, but highlight important challenges in rigorously testing the WC model with real systems. Our results prompt new questions about the microphysics of thickening for both monodisperse and polydisperse systems.Comment: 9 pages, 8 figures, ancillary informatio

Reliability and Short-Term Intra-Individual Variability of Telomere Length Measurement Using Monochrome Multiplexing Quantitative PCR

Studies examining the association between telomere length and cancer risk have often relied on measurement of telomere length from a single blood draw using a real-time PCR technique. We examined the reliability of telomere length measurement using sequential samples collected over a 9-month period.Relative telomere length in peripheral blood was estimated using a single tube monochrome multiplex quantitative PCR assay in blood DNA samples from 27 non-pregnant adult women (aged 35 to 74 years) collected in 7 visits over a 9-month period. A linear mixed model was used to estimate the components of variance for telomere length measurements attributed to variation among women and variation between time points within women. Mean telomere length measurement at any single visit was not significantly different from the average of 7 visits. Plates had a significant systematic influence on telomere length measurements, although measurements between different plates were highly correlated. After controlling for plate effects, 64% of the remaining variance was estimated to be accounted for by variance due to subject. Variance explained by time of visit within a subject was minor, contributing 5% of the remaining variance.Our data demonstrate good short-term reliability of telomere length measurement using blood from a single draw. However, the existence of technical variability, particularly plate effects, reinforces the need for technical replicates and balancing of case and control samples across plates

NANOG Reporter Cell Lines Generated by Gene Targeting in Human Embryonic Stem Cells

Background: Pluripotency and self-renewal of human embryonic stem cells (hESCs) is mediated by a complex interplay between extra- and intracellular signaling pathways, which regulate the expression of pluripotency-specific transcription factors. The homeodomain transcription factor NANOG plays a central role in maintaining hESC pluripotency, but the precise role and regulation of NANOG are not well defined. Methodology/Principal Findings: To facilitate the study of NANOG expression and regulation in viable hESC cultures, we generated fluorescent NANOG reporter cell lines by gene targeting in hESCs. In these reporter lines, the fluorescent reporter gene was co-expressed with endogenous NANOG and responded to experimental induction or repression of the NANOG promoter with appropriate changes in expression levels. Furthermore, NANOG reporter lines facilitated the separation of hESC populations based on NANOG expression levels and their subsequent characterization. Gene expression arrays on isolated hESC subpopulations revealed genes with differential expression in NANOG high and NANOG low hESCs, providing candidates for NANOG downstream targets hESCs. Conclusion/Significance: The newly derived NANOG reporter hESC lines present novel tools to visualize NANOG expression in viable hESCs. In future applications, these reporter lines can be used to elucidate the function and regulation of NANO

Quantitative PCR of ear discharge from Indigenous Australian children with acute otitis media with perforation supports a role for Alloiococcus otitidis as a secondary pathogen

Otitis media is endemic in remote Indigenous communities of Australia’s Northern Territory. Alloiococcus otitidis is an outer ear commensal and putative middle ear pathogen that has not previously been described in acute otitis media (AOM) in this population. The aims of this study were to determine the presence, antibiotic susceptibility and bacterial load of A. otitidis in nasopharyngeal and ear discharge swabs collected from Indigenous Australian children with AOM with perforation.Financial support for this study was provided by the Channel 7 Children’s Research Foundation; The Trust Foundation; and the National Health and Medical Research Council (Australia)

Molecular Cloning and Copy Number Variation of a Ferritin Subunit (Fth1) and Its Association with Growth in Freshwater Pearl Mussel Hyriopsis cumingii

Iron is one of the most important minor elements in the shells of bivalves. This study was designed to investigate the involvement of ferritin, the principal protein for iron storage, in shell growth. A novel ferritin subunit (Fth1) cDNA from the freshwater pearl mussel (Hyriopsis cumingii) was isolated and characterized. The complete cDNA contained 822 bp, with an open reading frame (ORF) of 525 bp, a 153 bp 5′ untranslated region (UTR) and a 144 bp 3′ UTR. The complete genomic DNA was 4125 bp, containing four exons and three introns. The ORF encoded a protein of 174 amino acids without a signal sequence. The deduced ferritin contained a highly conserved motif for the ferroxidase center comprising seven residues of a typical vertebrate heavy-chain ferritin. It contained one conserved iron associated residue (Try27) and iron-binding region signature 1 residues. The mRNA contained a 27 bp iron-responsive element with a typical stem-loop structure in the 5′-UTR position. Copy number variants (CNVs) of Fth1 in two populations (PY and JH) were detected using quantitative real-time PCR. Associations between CNVs and growth were also analyzed. The results showed that the copy number of the ferritin gene of in the diploid genome ranged from two to 12 in PY, and from two to six in JH. The copy number variation in PY was higher than that in JH. In terms of shell length, mussels with four copies of the ferritin gene grew faster than those with three copies (P<0.05), suggesting that CNVs in the ferritin gene are associated with growth in shell length and might be a useful molecular marker in selective breeding of H. cumingii

A genome-wide association scan in admixed Latin Americans identifies loci influencing facial and scalp hair features

We report a genome-wide association scan in over 6,000 Latin Americans for features of scalp hair (shape, colour, greying, balding) and facial hair (beard thickness, monobrow, eyebrow thickness). We found 18 signals of association reaching genome-wide significance (P values 5 × 10−8 to 3 × 10−119), including 10 novel associations. These include novel loci for scalp hair shape and balding, and the first reported loci for hair greying, monobrow, eyebrow and beard thickness. A newly identified locus influencing hair shape includes a Q30R substitution in the Protease Serine S1 family member 53 (PRSS53). We demonstrate that this enzyme is highly expressed in the hair follicle, especially the inner root sheath, and that the Q30R substitution affects enzyme processing and secretion. The genome regions associated with hair features are enriched for signals of selection, consistent with proposals regarding the evolution of human hair

Targeting vascular endothelial growth factor receptor 2 and protein kinase d1 related pathways by a multiple kinase inhibitor in angiogenesis and inflammation related processes in vitro.

Emerging evidence suggests that the vascular endothelial growth factor receptor 2 (VEGFR2) and protein kinase D1 (PKD1) signaling axis plays a critical role in normal and pathological angiogenesis and inflammation related processes. Despite all efforts, the currently available therapeutic interventions are limited. Prior studies have also proved that a multiple target inhibitor can be more efficient compared to a single target one. Therefore, development of novel inflammatory pathway-specific inhibitors would be of great value. To test this possibility, we screened our molecular library using recombinant kinase assays and identified the previously described compound VCC251801 with strong inhibitory effect on both VEGFR2 and PKD1. We further analyzed the effect of VCC251801 in the endothelium-derived EA.hy926 cell line and in different inflammatory cell types. In EA.hy926 cells, VCC251801 potently inhibited the intracellular activation and signaling of VEGFR2 and PKD1 which inhibition eventually resulted in diminished cell proliferation. In this model, our compound was also an efficient inhibitor of in vitro angiogenesis by interfering with endothelial cell migration and tube formation processes. Our results from functional assays in inflammatory cellular models such as neutrophils and mast cells suggested an anti-inflammatory effect of VCC251801. The neutrophil study showed that VCC251801 specifically blocked the immobilized immune-complex and the adhesion dependent TNF-alpha -fibrinogen stimulated neutrophil activation. Furthermore, similar results were found in mast cell degranulation assay where VCC251801 caused significant reduction of mast cell response. In summary, we described a novel function of a multiple kinase inhibitor which strongly inhibits the VEGFR2-PKD1 signaling and might be a novel inhibitor of pathological inflammatory pathways