Global dynamics of Escherichia coli phosphoproteome in central carbon metabolism under changing culture conditions

Little is known about the role of global phosphorylation events in the control of prokaryote metabolism. By performing a detailed analysis of all protein phosphorylation events previously reported in Escherichia coli, dynamic changes in protein phosphorylation were elucidated under three different culture conditions. Using scheduled reaction monitoring, the phosphorylation ratios of 82 peptides corresponding to 71 proteins were quantified to establish whether serine (S), threonine (T) and tyrosine (Y) phosphorylation events displayed a dynamic profile under changing culture conditions. The ratio of phosphorylation for 23 enzymes from central carbon metabolism was found to be dynamic. The data presented contributes to our understanding of the global role of phosphorylation in bacterial metabolism and highlight that phosphorylation is an important, yet poorly understood, regulatory mechanism of metabolism control in bacteria

Orientation-dependent ionization yields from strong-field ionization of fixed-in-space linear and asymmetric top molecules

The yield of strong-field ionization, by a linearly polarized probe pulse, is studied experimentally and theoretically, as a function of the relative orientation between the laser field and the molecule. Experimentally, carbonyl sulfide, benzonitrile and naphthalene molecules are aligned in one or three dimensions before being singly ionized by a 30 fs laser pulse centered at 800 nm. Theoretically, we address the behaviour of these three molecules. We consider the degree of alignment and orientation and model the angular dependence of the total ionization yield by molecular tunneling theory accounting for the Stark shift of the energy level of the ionizing orbital. For naphthalene and benzonitrile the orientational dependence of the ionization yield agrees well with the calculated results, in particular the observation that ionization is maximized when the probe laser is polarized along the most polarizable axis. For OCS the observation of maximum ionization yield when the probe is perpendicular to the internuclear axis contrasts the theoretical results.Comment: 14 pages, 4 figure

Effect of physical training on function of chronically painful muscles: A randomized controlled trial

Udgivelsesdato: 2008-Oct-23Purpose: Pain and tenderness of the upper trapezius muscle is frequent in several occupational groups. The objective of this study is to investigate the effect of three contrasting interventions on muscle function and pain in women with trapezius myalgia. Methods: A group of employed women (n=42) with a clinical diagnosis of trapezius myalgia participated in a 10 week randomized controlled intervention; specific strength training of the neck/shoulder muscles (SST), general fitness training performed as leg-bicycling (GFT), or a reference intervention without physical activity (REF). Torque and electromyography (EMG) were recorded during maximal shoulder abductions in an isokinetic dynamometer at -60, 60, 0 and 180 degrees (.)s(-1). Further, a submaximal reference contraction with only the load of the arms was performed. Results: Significant changes were observed only in SST. Pain decreased 42-49% (P<0.01-0.05). While EMG activity of the unaffected deltoid remained unchanged during the maximal contractions, an increase in EMG amplitude (42-86%, P<0.001-0.05) and median power frequency (19%, P<0.001) were observed for the painful trapezius muscle. Correspondingly, torque increased 18-53% (P<0.001-0.05). EMG during the reference contraction decreased significantly for both the trapezius and deltoid muscles (P<0.01). Conclusion: In conclusion, specific strength training relieves pain and increases maximal activity specifically of the painful trapezius muscle, leading to increased shoulder abduction strength in women with trapezius myalgia. Further, decreased relative workload may indirectly augment pain reduction. Key words: isokinetic, isometric, torque, neck pain

Modelling diverse root density dynamics and deep nitrogen uptake — a simple approach

We present a 2-D model for simulation of root density and plant nitrogen (N) uptake for crops grown in agricultural systems, based on a modification of the root density equation originally proposed by Gerwitz and Page in J Appl Ecol 11:773–781, (1974). A root system form parameter was introduced to describe the distribution of root length vertically and horizontally in the soil profile. The form parameter can vary from 0 where root density is evenly distributed through the soil profile, to 8 where practically all roots are found near the surface. The root model has other components describing root features, such as specific root length and plant N uptake kinetics. The same approach is used to distribute root length horizontally, allowing simulation of root growth and plant N uptake in row crops. The rooting depth penetration rate and depth distribution of root density were found to be the most important parameters controlling crop N uptake from deeper soil layers. The validity of the root distribution model was tested with field data for white cabbage, red beet, and leek. The model was able to simulate very different root distributions, but it was not able to simulate increasing root density with depth as seen in the experimental results for white cabbage. The model was able to simulate N depletion in different soil layers in two field studies. One included vegetable crops with very different rooting depths and the other compared effects of spring wheat and winter wheat. In both experiments variation in spring soil N availability and depth distribution was varied by the use of cover crops. This shows the model sensitivity to the form parameter value and the ability of the model to reproduce N depletion in soil layers. This work shows that the relatively simple root model developed, driven by degree days and simulated crop growth, can be used to simulate crop soil N uptake and depletion appropriately in low N input crop production systems, with a requirement of few measured parameters

Comparison of serum pools and oral fluid samples for detection of porcine circovirus type 2 by quantitative real-time PCR in finisher pigs

Abstract Background Porcine circovirus type 2 (PCV2) diagnostics in live pigs often involves pooled serum and/or oral fluid samples for group-level determination of viral load by quantitative real-time polymerase chain reaction (qPCR). The purpose of the study was to compare the PCV2 viral load determined by qPCR of paired samples at the pen level of pools of sera (SP) from 4 to 5 pigs and the collective oral fluid (OF) from around 30 pigs corresponding to one rope put in the same pen. Pigs in pens of 2 finishing herds were sampled by cross-sectional (Herd 1) and cross-sectional with follow-up (Herd 2) study designs. In Herd 1, 50 sample pairs consisting of SP from 4 to 5 pigs and OF from around 23 pigs were collected. In Herd 2, 65 sample pairs consisting of 4 (SP) and around 30 (OF) pigs were collected 4 times at 3-week intervals. Results A higher proportion of PCV2-positive pens (86% vs. 80% and 100% vs. 91%) and higher viral loads (mean difference: 2.10 and 1.83 log(10) PCV2 copies per ml) were found in OF versus SP in both herds. The OF cut-off value corresponding to a positive SP (>3 log(10) PCV2 copies per ml) was estimated to 6.5 and 7.36 log(10) PCV2 copies per ml for Herds 1 and 2, respectively. Significant correlations between SP and OF results were found in Herd 1 (rho = 0.69) and the first sampling in Herd 2 (rho = 0.39), but not for the subsequent consecutive 3 samplings in Herd 2. Conclusions The proportion and viral loads of PCV2 positive pens were higher in collective OF (including up to 30 pigs) compared to SP (including 4–5 pigs) of the same pens. Also, OF seemed to detect the PCV2 infection earlier with OF values just below 6.5 (Herd 1) and 7.36 (Herd 2) log(10) being associated with a negative SP for the same pen. Nevertheless, a statistically significant correlation between SP and OF could not be found for all sampling time points, probably due to a high within-pen variation in individual pig viral load becoming very evident in SP of only four or five pigs. Consequently, the results imply that OF is well suited for detecting presence of PCV2 but less so for determining the specific viral load of pigs in a pen

Recon 2.2: from reconstruction to model of human metabolism.

IntroductionThe human genome-scale metabolic reconstruction details all known metabolic reactions occurring in humans, and thereby holds substantial promise for studying complex diseases and phenotypes. Capturing the whole human metabolic reconstruction is an on-going task and since the last community effort generated a consensus reconstruction, several updates have been developed.ObjectivesWe report a new consensus version, Recon 2.2, which integrates various alternative versions with significant additional updates. In addition to re-establishing a consensus reconstruction, further key objectives included providing more comprehensive annotation of metabolites and genes, ensuring full mass and charge balance in all reactions, and developing a model that correctly predicts ATP production on a range of carbon sources.MethodsRecon 2.2 has been developed through a combination of manual curation and automated error checking. Specific and significant manual updates include a respecification of fatty acid metabolism, oxidative phosphorylation and a coupling of the electron transport chain to ATP synthase activity. All metabolites have definitive chemical formulae and charges specified, and these are used to ensure full mass and charge reaction balancing through an automated linear programming approach. Additionally, improved integration with transcriptomics and proteomics data has been facilitated with the updated curation of relationships between genes, proteins and reactions.ResultsRecon 2.2 now represents the most predictive model of human metabolism to date as demonstrated here. Extensive manual curation has increased the reconstruction size to 5324 metabolites, 7785 reactions and 1675 associated genes, which now are mapped to a single standard. The focus upon mass and charge balancing of all reactions, along with better representation of energy generation, has produced a flux model that correctly predicts ATP yield on different carbon sources.ConclusionThrough these updates we have achieved the most complete and best annotated consensus human metabolic reconstruction available, thereby increasing the ability of this resource to provide novel insights into normal and disease states in human. The model is freely available from the Biomodels database (http://identifiers.org/biomodels.db/MODEL1603150001)