Biosynthesis of bacterial glycogen: purification and characterization of ADPglucose pyrophosphorylase with modified regulatory properties from Escherichia coli B mutant CL1136-504

The l-thyroxine binding site in human serum thyroxine-binding globulin was investigated by affinity labeling with N-bromoacetyl-l-thyroxine (BrAcT₄). Competitive binding studies showed that, in the presence of 100 molar excess of BrAcT₄, binding of thyroxine to thyroxine-binding globulin was nearly totally abolished. The reaction of BrAcT₄ to form covalent binding was inhibited in the presence of thyroxine and the affinity-labeled thyroxinebinding globulin lost its ability to bind thyroxine. These results indicate BrAcT₄ and thyroxine competed for the same binding site. Affinity labeling with 2 mol of BrAcT₄/mol of thyroxine-binding globulin resulted in the covalent attachment of 0.7 mol of ligand. By amino acid analysis and high voltage paper electrophoresis, methionine was identified as the major residue labeled (75%). Lysine, tyrosine, and histidine were also found to be labeled to the extent of 8, 8, and 5%, respectively.     

Identifying essential genes in bacterial metabolic networks with machine learning methods

Background  

Identifying essential genes in bacteria supports to identify potential drug targets and an understanding of minimal requirements for a synthetic cell. However, experimentally assaying the essentiality of their coding genes is resource intensive and not feasible for all bacterial organisms, in particular if they are infective.     

State-of-the art data normalization methods improve NMR-based metabolomic analysis

Extracting biomedical information from large metabolomic datasets by multivariate data analysis is of considerable complexity. Common challenges include among others screening for differentially produced metabolites, estimation of fold changes, and sample classification. Prior to these analysis steps, it is important to minimize contributions from unwanted biases and experimental variance. This is the goal of data preprocessing. In this work, different data normalization methods were compared systematically employing two different datasets generated by means of nuclear magnetic resonance (NMR) spectroscopy. To this end, two different types of normalization methods were used, one aiming to remove unwanted sample-to-sample variation while the other adjusts the variance of the different metabolites by variable scaling and variance stabilization methods. The impact of all methods tested on sample classification was evaluated on urinary NMR fingerprints obtained from healthy volunteers and patients suffering from autosomal polycystic kidney disease (ADPKD). Performance in terms of screening for differentially produced metabolites was investigated on a dataset following a Latin-square design, where varied amounts of 8 different metabolites were spiked into a human urine matrix while keeping the total spike-in amount constant. In addition, specific tests were conducted to systematically investigate the influence of the different preprocessing methods on the structure of the analyzed data. In conclusion, preprocessing methods originally developed for DNA microarray analysis, in particular, Quantile and Cubic-Spline Normalization, performed best in reducing bias, accurately detecting fold changes, and classifying samples.

     

Toll-like receptor 4 deficiency: Smaller infarcts,but nogain in function

Backgound  

It has been reported that Toll-like receptor 4 (TLR4) deficiency reduces infarct size after myocardial ischemia/reperfusion (MI/R). However, measurement of MI/R injury was limited and did not include cardiac function. In a chronic closed-chest model we assessed whether cardiac function is preserved in TLR4-deficient mice (C3H/HeJ) following MI/R, and whether myocardial and systemic cytokine expression differed compared to wild type (WT).     

Motion parallax and figural properties of depth control flight speed in an insect

Male gypsy moths (Lymantria dispar L.) are able to control their forward flight speed solely by means of optical cues derived from the lateral parts of their visual field. Thereby, relative motion of the objects is required, which under free flight conditions would derive from the self-induced motion of the stationary objects within a surrounding structured in depth. Besides this motion parallax, however, the control system for forward flight speed demands figural properties of the objects such as differences in their angular extension or contrast. In a natural surround, the images of objects closer to the moth have higher angular velocity and, in addition, are usually larger and have higher contrast than those of objects farther away. The experiments have shown that this natural pairing of angular velocity and figural properties is essential to induce a thrust response which appears suitable to counteract involuntary changes in forward flight speed, as e.g. caused by changes in wind speed under free flight conditions. Inverse pairing of the visual stimuli caused the moths to either enlarge the error signal according to positive feedback within the control circuit, or to increase thrust to a maximum as always found in experiments without motion parallax or in the absence of differences in figural properties. The open-loop experiments furthermore established that the set point of angular velocity of the closer objects lies within the range of 4.5–9°/s, and that pattern speed modulation has to cover this range in order to induce a compensatory thrust modulation. The response is largely independent of the magnitude of relative motion as long as it is present; the response amplitude, however, strongly depends on the amplitude of pattern speed modulation.The results are discussed with regard to other visual cues used for the control of forward flight speed in insects, the algorithm underlying the figure-ground discrimination in flies, and the perception of depth in man as known from psychophysical experiments.