Model-free model elimination: A new step in the model-free dynamic analysis of NMR relaxation data

Model-free analysis is a technique commonly used within the field of NMR spectroscopy to extract atomic resolution, interpretable dynamic information on multiple timescales from the R ₁, R ₂, and steady state NOE. Model-free approaches employ two disparate areas of data analysis, the discipline of mathematical optimisation, specifically the minimisation of a χ² function, and the statistical field of model selection. By searching through a large number of model-free minimisations, which were setup using synthetic relaxation data whereby the true underlying dynamics is known, certain model-free models have been identified to, at times, fail. This has been characterised as either the internal correlation times, τ _e , τ _f , or τ _s , or the global correlation time parameter, local τ _m , heading towards infinity, the result being that the final parameter values are far from the true values. In a number of cases the minimised χ² value of the failed model is significantly lower than that of all other models and, hence, will be the model which is chosen by model selection techniques. If these models are not removed prior to model selection the final model-free results could be far from the truth. By implementing a series of empirical rules involving inequalities these models can be specifically isolated and removed. Model-free analysis should therefore consist of three distinct steps: model-free minimisation, model-free model elimination, and finally model-free model selection. Failure has also been identified to affect the individual Monte Carlo simulations used within error analysis. Each simulation involves an independent randomised relaxation data set and model-free minimisation, thus simulations suffer from exactly the same types of failure as model-free models. Therefore, to prevent these outliers from causing a significant overestimation of the errors the failed Monte Carlo simulations need to be culled prior to calculating the parameter standard deviations.     

NMR solution structure of the acylphosphatase from Escherichia coli

The solution structure of Escherichia coli acylphosphatase (E. coli AcP), a small enzyme catalyzing the hydrolysis of acylphosphates, was determined by (1)H and (15)N NMR and restrained modelling calculation. In analogy with the other members of AcP family, E. coli AcP shows an alpha/beta sandwich domain composed of four antiparallel and one parallel beta-strand, assembled in a five-stranded beta-sheet facing two antiparallel alpha-helices. The pairwise RMSD values calculated for the backbone atoms of E. coli and Sulfolobus solfataricus AcP, Bovine common type AcP and Horse muscle AcP are 2.18, 5.31 and 5.12 A, respectively. No significant differences are present in the active site region and the catalytic residue side chains are consistently positioned in the structures.     

Reciprocal chromosome painting between three laboratory rodent species

The laboratory mouse (Mus musculus, 2n = 40), the Chinese hamster (Cricetulus griseus, 2n = 22), and the golden (Syrian) hamster (Mesocricetus auratus, 2n = 44) are common laboratory animals, extensively used in biomedical research. In contrast with the mouse genome, which was sequenced and well characterized, the hamster species has been set aside. We constructed a chromosome paint set for the golden hamster, which for the first time allowed us to perform multidirectional chromosome painting between the golden hamster and the mouse and between the two species of hamster. From these data we constructed a detailed comparative chromosome map of the laboratory mouse and the two hamster species. The golden hamster painting probes revealed 25 autosomal segments in the Chinese hamster and 43 in the mouse. Using the Chinese hamster probes, 23 conserved segments were found in the golden hamster karyotype. The mouse probes revealed 42 conserved autosomal segments in the golden hamster karyotype. The two largest chromosomes of the Chinese hamster (1 and 2) are homologous to seven and five chromosomes of the golden hamster, respectively. The golden hamster karyotype can be transformed into the Chinese hamster karyotype by 15 fusions and 3 fissions. Previous reconstructions of the ancestral murid karyotype proposed diploid numbers from 2n = 52 to 2n = 54. By integrating the new multidirectional chromosome painting data presented here with previous comparative genomics data, we can propose that syntenies to mouse Chrs 6 and 16 were both present and to hypothesize a diploid number of 2n = 48 for the ancestral Murinae/Cricetinae karyotype.     

Characteristics of the functional state of rat tracheal and bronchial smooth muscle at different stages of alveolitis

In isolated tracheal smooth muscle preparations in normal rats and in rats with experimental fibrotic alveolitis, responses to electrical field stimulation of nervous and muscle fibers were studied. At stimulation of muscles or nerves of tracheal preparations without intramural ganglia in rats with acute alveolitis, parameters of smooth muscle contractions did not practically differ from those in normal rats. In rats with fibrotic alveolitis the amplitude and rate of muscle contraction decreased, while the response latent period (LP) increased. At stimulation of preganglionic nerve fibers of the tracheal preparations with intramural ganglia in rats with acute alveolitis, the value and rate of smooth muscle contraction decreased, while the response LP increased. After transition into chronic phase of the disease (fibrotic alveolitis), a partial restoration of the response parameters took place. In rats with acute alveolitis, the repeated stimulation of the nerve fibers led to an increase of amplitude and a decrease of rate of tracheal smooth muscle contractions. In rats with fibrotic alveolitis, the repeated stimulation caused a decrease of amplitude and rate of contractions and an increase of the response LP.     

Hypertonic Saline Attenuates Colonic Tumor Cell Metastatic Potential by Activating Transmembrane Sodium Conductance

Hypertonic saline (HTS) suppresses tumor cell-endothelial interactions by reducing integrin expression. This translates into reduced adhesion, migration and metastatic potential. This study determined the relative contributions of hyperosmolarity and sodium-specific hypertonicity on the inhibitory effects of HTS, the intracellular pH and sodium responses to HTS and the role of cytoskeletal remodeling in these changes. Human colonic tumor cells (LS174T) were exposed to lipopolysaccharide under isotonic, hypertonic, sodium-free (N-methyl- D-glucamine), hyperosmolar (mannitol or urea), disrupted cytoskeletal (10 μg/ml cytochalasin D) conditions or in the presence of 5-(N-ethyl-N-isopropyl)amiloride (EIPA). β₁ integrin expression was measured flow-cytometrically. Intracellular sodium and pH were measured with confocal laser microscopic imaging. Statistical analysis was performed with analysis of variance, and P < 0.05 was considered significant. Data are represented as mean ± SEM. Hypertonic exposure attenuated integrin expression (62.03 ± 4.7% of control, P < 0.04). No discernible effect was observed with sodium-free or hyperosmolar solutions. HTS evoked a cellular alkalinization (by a mean 0.2 pH units) and an increase in cytosolic sodium concentration (by a mean 12.4 mM, P < 0.001) via upregulation of sodium-hydrogen exchange. Disassembly of actin microfilaments by cytochalasin D and antiporter inhibition with EIPA abrogated the effect of hypertonicity on integrin expression and intracellular sodium and pH (P < 0.05). HTS downregulates adhesion molecule expression via a hypertonic, sodium-specific, cytoskeletally mediated mechanism that involves activation of sodium-hydrogen exchange with associated changes in intracellular pH and sodium concentrations.     

Application of principal component analysis and self-organizing map to the analysis of 2D fluorescence spectra and the monitoring of fermentation processes

2D fluorescence sensors produce a great deal of spectral data during fermentation processes, which can be analyzed using a variety of statistical techniques. Principal component analysis (PCA) and a self-organizing map (SOM) were used to analyze these 2D fluorescence spectra and to extract useful information from them. PCA resulted in scores and loadings that were visualized in the score-loading plots and used to monitor various fermentation processes with recombinantEscherichia coli andSaccharomyces cerevisiae. The SOM was found to be a useful and interpretative method of classifying the entire gamut of 2D fluorescence spectra and of selecting some significant combinations of excitation and emission wavelengths. The results, including the normalized weights and variances, indicated that the SOM network is capable of being used to interpret the fermentation processes monitored by a 2D fluorescence sensor.     

Biodegradability of end-groups of the biocide polyhexamethylene biguanide (PHMB) assessed using model compounds

Polyhexamethylene biguanide (PHMB), a biocide used in a wide variety of disinfection and preservation applications, is a polydisperse mixture in which the end-groups may be any combination of amine, guanidine and cyanoguanidine. Using PHMB model compounds (1,6-diaminohexane; 1,6-diguanidinohexane; 1,6-di(cyanoguanidino)hexane; 4-guanidinobutyric acid), we have determined the biodegradation characteristics of each end-group in several strains of bacteria isolated for their ability to utilise PHMB as a sole source of nitrogen. Bacteria were screened for growth at the expense of each model compound (at non-inhibitory concentrations) as sole nitrogen source. None of the isolated bacteria was capable of utilising a cyanoguanidine end-group as growth substrate, whereas several bacteria were shown to utilise amine or guanidine end-groups. In particular, a strain of Pseudomonas putida was capable of extensive growth with 1,6-diguanidinohexane as a sole nitrogen source, with complete removal of guanidine groups from culture medium within 2 days, and with concomitant formation of unsubstituted urea, which in turn was also utilised by the organism. We conclude that whilst amine and guanidine end-groups in PHMB are likely to be susceptible to biodegradation, cyanoguanidine end-groups are likely to be recalcitrant.     

Molecular and morphological examination of Cyrtobagous sp. collected from Argentina, Paraguay, Brazil, Australia, and Florida

Two members of the floating fern genus Salvinia (Salviniaceae), S. minima Baker and S. molesta Mitchell, have established in the United States. Cyrtobagous salviniae Calder and Sands (Coleoptera: Curculionidae), long established on Florida S. minima, was released in Texas and Louisiana as a biocontrol agent for both species. Subsequently, sequence analysis of the 28S rRNA D2 expansion domain suggested that the Florida and Brazilian populations (used worldwide for biocontrol) of C. salviniae might constitute two cryptic species. In response, the Brazilian weevil was imported from Australia and released instead onto S. molesta. We sampled C. singularis Hustache and C. salviniae from their native ranges in Brazil, Argentina, and Paraguay and sequenced them (D2) along with Australian and Florida samples. The genetic distance between C. singularis and C. salviniae samples is much greater (almost 5×) than the distance between either the Florida and Brazilian samples or the Brazilian and Argentinean/ Paraguayan C. salviniae samples. Since C. singularis and C. salviniae are cryptic species, the Florida and Brazilian populations (or for that matter Brazilian and Argentinean/Paraguayan) could reasonably be described as demes or ecotypes. Occurrence data indicates that, in parts of their ranges, C. salviniae and C. singularis are not only sympatric but also feed on the same plant species at the same site. While host adaptation (species preferences) likely occurs within local demes, both species seem capable of adapting to the available resource (Salvinia species). Finally, a polymerase chain reaction (PCR) primer was developed to distinguish the Florida and Brazilian/Australian types.     

Human Impacts on the Fire Regime of Interior Alaska: Interactions among Fuels, Ignition Sources, and Fire Suppression

Wildfire is the major natural agent of disturbance in interior Alaska. We examined the magnitude of human impact on fire by comparing fire regime between individual 1-km² grid cells designated for fire suppression with lands where fires are allowed to burn naturally. Two-thirds of interior Alaska has an essentially natural fire regime, with few human ignitions, negligible suppression activity, and many large lightning-caused fires. In the 17% of land that is designated for fire suppression due to its proximity to communities and roads, there was a 50% reduction in the proportion of area burned from 1992–2001, relative to areas without suppression. The remaining 16% of land serves as a buffer, receives some suppression, and has an intermediate fire regime. Even though there were 50 times more fires and the fire season began two months earlier in lands designated for suppression, most of these fires were lit by people and remained small because fires tended to occur at times and places less favorable for fire spread and were more accessible to fire fighters compared to lands not designated for suppression. Even in the absence of fire suppression, human-caused fires were less likely to exceed 400 ha compared to lightning-caused fires. Fire suppression reduced area burned in all fuel types but was somewhat more effective in less flammable (non-forest) vegetation. Alaska’s fire policy of focusing suppression efforts on a small proportion of the fire-prone region maximizes the ecological and social benefits associated with fire-dependent ecosystem services, while minimizing the social and ecological costs of suppression. Application of this policy to other areas would require well-informed managers and stakeholders to make difficult decisions about the relative costs and benefits of fire across ecologically and culturally variable landscapes.     

Role of RepB in the replication of plasmid pJB01 isolated from Enterococcus faecium JC1

The plasmid pJB01 (GenBank Accession No. AY425961) isolated from the pathogenic bacterium, Enterococcus faecium JC1, is 2235 base pairs in length and consists of a putative double-strand origin (dso), a single-strand origin, a counter-transcribed RNA, and three open reading frames. A comparison of a few replication factors and motifs, bind and nic regions, for replication initiation on the nucleotide sequence level revealed that it belongs to the pMV158 family among RC-replicating plasmids. A runoff DNA synthesis assay demonstrated that nicking occurred between G525 and A526, which is located on the internal loop of a putative secondary structure in the dso. Unlike all the other plasmids of the pMV158 family having two or three direct repeats, pJB01 has three non-tandem direct repeats of 5'-CAACAAA-3' separated by four nucleotides, as the RepB-binding site in the dso. Moreover, the nick site on the internal loop is located at 77 nucleotides upstream from the RepB-binding region. Irrespective of the structural difference of direct repeats from other members of the pMV158 family, we think, it is still a new member of this plasmid family. The introduction of mutations in conserved regions of RepB confirmed that RepB N-moiety is important for nicking/nick-closing activity. Within N-moiety, especially all of the motif R-III, the Y100 in R-IV and Y116 in R-V residues, played particularly critical roles in this activity, however, for its binding, both of the N- and C-moieties of RepB were needed.