Analysis of the sequence and structural features of the left-handed beta-helical fold

The left-handed parallel beta-helix (LbetaH) is a structurally repetitive, highly regular, and symmetrical fold formed by coiling of elongated beta-sheets into helical "rungs." This canonical fold has recently received interest as a possible solution to the fibril structure of amyloid and as a building block of self-assembled nanotubular structures. In light of this interest, we aimed to understand the structural requirements of the LbetaH fold. We first sought to determine the sequence characteristics of the repeats by analyzing known structures to identify positional preferences of specific residues types. We then used molecular dynamics simulations to demonstrate the stabilizing effect of successive rungs and the hydrophobic core of the LbetaH. We show that a two-rung structure is the minimally stable LbetaH structure. In addition, we defined the structure-based sequence preference of the LbetaH and undertook a genome-wide sequence search to determine the prevalence of this unique protein fold. This profile-based LbetaH search algorithm predicted a large fraction of LbetaH proteins from microbial origins. However, the relative number of predicted LbetaH proteins per specie was approximately equal across the genomes from prokaryotes to eukaryotes.     

Aggregation and C and N contents of soil organic matter fractions in a permanent raised-bed planting system in the Highlands of Central Mexico

Permanent raised bed planting with crop residue retention is a form of conservation agriculture that has been proposed as an alternative to conventional tillage for wheat production systems in the Central Highlands of Mexico. A field experiment comparing permanent and tilled raised beds with different residue management under rainfed conditions was started at El Batán (State of Mexico, Mexico) in 1999. The percentage of small and large macroaggregates and mean weight diameter (MWD) was significantly larger in permanent raised beds compared to conventionally tilled raised beds both with full crop residue retention (average for maize and wheat), while the percentages free microaggregates was lower. The percentages of small and large macroaggregates and mean weight diameter (MWD) was significantly larger in permanent raised beds with residue retention compared to permanent raised beds with removal of the residue (average for maize and wheat), while the percentages free microaggregates and silt and clay fraction was lower. Cultivation of maize significantly reduced the large macroaggregates, while wheat reduced the silt and clay fraction (average over all systems). Cultivation of maize reduced the C and N content of the free microaggregates compared to soil cultivated with wheat, while removal of plant residue reduced the C and N content of the silt and clay fraction compared to soil where residue was retained. The C and N content of the coarse particulate organic matter (cPOM) and microaggregates within the macroaggregates was significantly larger in permanent raised beds compared to conventionally tilled raised beds both with full residue retention, while C and N content of the cPOM was significantly lower when residue was removed or partially removed compared to the soil where the residue was retained. The δ ¹³C ‰ signatures of the macroaggregates, microaggregates, the silt and clay fraction, cPOM and microaggregates within the macroaggregates were not affected by tillage or residue management when wheat was the last crop, but removal of residue reduced the δ ¹³C ‰ signatures of the macro-, microaggregates and microaggregates within the macroaggregates significantly compared to soil where the residue was retained. Retaining only 30–50% of the organic residue still improved the soil structure considerably compared to plots where it was removed completely. Permanent raised beds without residue retention, however, is a practice leading to soil degradation. Kelly Lichter and Bram Govaerts contributed equally to this publication.     

Lysine 183 and glutamic acid 157 of the TSH receptor: two interacting residues with a key role in determining specificity toward TSH and human CG

A naturally occurring mutation in the ectodomain of the TSH receptor (TSHr), K183R, has been described recently in a familial case of gestational hyperthyroidism. Hyperthyroidism was explained by the widening of the specificity of the mutant receptor toward human CG (hCG). In the present study, we attempted to understand in molecular terms the structure-phenotype relationships of this mutant in light of the available structural model of TSHr ectodomain established on the template of the atomic structure of the porcine ribonuclease inhibitor. To this aim, we studied by site-directed mutagenesis and functional assays in transfected COS cells the effects of substituting amino acids with different physicochemical properties for lysine 183. Unexpectedly, all TSHr mutants displayed widening of their specificity toward hCG. Molecular dynamics simulations suggested that the gain of function would be secondary to the release of a nearby glutamate residue (E157) from a salt bridge with K183. This hypothesis was supported by further site-directed mutagenesis experiments showing that the presence of an acidic residue in position 157, or in its vicinity, was required to observe the increase in sensitivity to hCG (an acidic residue in position 183 can partially fulfill the role of a free acidic residue in position 157 when tested on the background of a E157A mutant). Our results suggest also that additional natural mutations (especially K183M, N, or Q) in position 183 of TSHr are expected to be found in gestational hyperthyroidism.     

Bioanalysis of tobramycin for therapeutic drug monitoring by solid-phase extraction and capillary zone electrophoresis

A method based on solid-phase extraction (SPE) and capillary zone electrophoresis (CZE) for the analysis of tobramycin in human serum is presented. An off-line SPE employing a carboxypropyl bonded phase (CBA) cartridge was used for the extraction of tobramycin from human serum. Adsorbed tobramycin was eluted from the CBA cartridge using a mixture of NH(3) (25%, w/v)-methanol (30:70, v/v). After evaporation, the analyte was reconstituted and derivatized with o-phthaldialdehyde (OPA)/3-mercaptopropionic acid (MPA). The resulting tobramycin-OPA/MPA derivative was purified, and then identified by mass spectrometry. The tobramycin-OPA/MPA derivative was then analysed by CZE with a background electrolyte (BGE) comprising of 30 mM sodium tetraborate pH 10.0-acetonitrile (ACN) (80:20, v/v) with ultraviolet detection at 230 nm. A linear response was observed in the range of 0.3-30 microg/ml with r(2) = 0.992. The sensitivity of the method was determined by its limit of quantitation (LOQ) and limit of detection (LOD) of 0.3 microg/ml and 0.1 microg/ml, respectively. SPE recovery ranged from 68 to 79% at the trough levels to 98% at the peak levels found in serum. Furosemide has been added as internal standard (IS) to improve precision. For the therapeutic range of tobramycin in serum (2-10 microg/ml) the relative standard deviation (R.S.D.) was less than 11% for the entire SPE/CE process. The method demonstrated excellent selectivity as shown by the lack of interference from a total of 20 drugs investigated. The method was then used in therapeutic drug monitoring of patients receiving the drug.     

Activation of CCR5 by chemokines involves an aromatic cluster between transmembrane helices 2 and 3

CCR5 is a G protein-coupled receptor responding to four natural agonists, the chemokines RANTES (regulated on activation normal T cell expressed and secreted), macrophage inflammatory protein (MIP)-1 alpha, MIP-1 beta, and monocyte chemotactic protein (MCP)-2, and is the main co-receptor for the macrophage-tropic human immunodeficiency virus strains. We have previously identified a structural motif in the second transmembrane helix of CCR5, which plays a crucial role in the mechanism of receptor activation. We now report the specific role of aromatic residues in helices 2 and 3 of CCR5 in this mechanism. Using site-directed mutagenesis and molecular modeling in a combined approach, we demonstrate that a cluster of aromatic residues at the extracellular border of these two helices are involved in chemokine-induced activation. These aromatic residues are involved in interhelical interactions that are key for the conformation of the helices and govern the functional response to chemokines in a ligand-specific manner. We therefore suggest that transmembrane helices 2 and 3 contain important structural elements for the activation mechanism of chemokine receptors, and possibly other related receptors as well.     

Molecular cytogenetic analysis of eight inversion duplications of human chromosome 13q that each contain a neocentromere

Neocentromeres are fully functional centromeres that have arisen in previously noncentromeric chromosomal locations on rearranged chromosomes. The formation of neocentromeres results in the mitotic stability of chromosomal fragments that do not contain endogenous centromeres and that would normally be lost. Here we describe a unique collection of eight independent patient-derived cell lines, each of which contains a neocentromere on a supernumerary inversion duplication of a portion of human chromosome 13q. Findings in these patients reveal insight into the clinical manifestations associated with polysomy for portions of chromosome 13q. The results of FISH and immunofluorescent analysis of the neocentromeres in these chromosomes confirm the lack of alpha-satellite DNA and the presence of CENtromere proteins (CENP)-C, -E, and hMAD2. The positions of the inversion breakpoints in these chromosomes have been placed onto the physical map of chromosome 13, by means of FISH mapping with cosmid probes. These cell lines define, within chromosome 13q, at least three distinct locations where neocentromeres have formed, with five independent neocentromeres in band 13q32, two in band 13q21, and one in band 13q31. The results of examination of the set of 40 neocentromere-containing chromosomes that have thus far been described, including the 8 neocentromere-containing chromosomes from chromosome 13q that are described in the present study, suggest that chromosome 13q has an increased propensity for neocentromere formation, relative to some other human chromosomes. These neocentromeres will provide the means for testing hypotheses about sequence requirements for human centromere formation.     

Electron crystallography of the scrapie prion protein complexed with heavy metals

The insolubility of the disease-causing isoform of the prion protein (PrP^Sc) has prevented studies of its three-dimensional structure at atomic resolution. Electron crystallography of two-dimensional crystals of N-terminally truncated PrP^Sc (PrP 27-30) and a miniprion (PrP^Sc106) provided the first insights at intermediate resolution on the molecular architecture of the prion. Here, we report on the structure of PrP 27-30 and PrP^Sc106 negatively stained with heavy metals. The interactions of the heavy metals with the crystal lattice were governed by tertiary and quaternary structural elements of the protein as well as the charge and size of the heavy metal salts. Staining with molybdate anions revealed three prominent densities near the center of the trimer that forms the unit cell, coinciding with the location of the β-helix that was proposed for the structure of PrP^Sc. Differential staining also confirmed the location of the internal deletion of PrP^Sc106 at or near these densities.     

Evaluating spatial within plot crop variability for different management practices with an optical sensor?

Subsoil constraints to root growth exacerbate frequent water and nutrient limitations to crop yields in Mediterranean-type environments. Amelioration of subsoil constraints can relieve these limitations by opening root-access to subsoil water and nutrients. However, decisions in subsoil amelioration are hampered by seasonally variable yield responses in these environments. We used the APSIM model to analyse the impact of subsoil constraints on yield and yield variability. The simulated yield data were used to calculate the financial benefits of subsoil amelioration across several scenarios. There was a strong yield-dependence on accessible soil water governed by root depth. Root depth development was limited to a minimum of either the effect of subsoil constraints or the weather-dependent depth of the soil wetting front. Insufficient rainfall in dry years or in a drier region often resulted in shallow soil wetting fronts and correspondingly shallow roots even in the absence of subsoil compaction. In these situations, there is little response to subsoil amelioration. Positive yield responses and positive financial returns to subsoil amelioration are therefore greater in good rainfall years and are more likely in a wetter region. A yield response to amelioration is also greater in coarser textured sand than finer textured sandy loam in an average rainfall season because the same amount of rainfall results in a deeper wetting front in sand than in sandy loam. Hence, roots in a sand are required to grow deeper compared to a sandy loam to access the same amount of water and therefore benefited more from subsoil amelioration in an average rainfall year. In wet years, sands leach more nitrate than sandy loam, which decreases yields and the response to subsoil amelioration in sands is more than in the sandy loam. Environmental threats occur along with yield loss when roots cannot access subsoil water. These include increased nitrate leaching and deep drainage due to unused water remaining in the soil profile. By allowing roots to access deep soil water, ameliorating subsoil is expected to yield financial gains in average to good rainfall seasons and decrease the environmental risk of drainage and leaching loss. The financial gains are expected to offset potential financial losses in dry and dry finish seasons especially in coarser textured soils and wetter environment. Responsible Editor: Jan Vos.