Molecular dissection of arginyltransferases guided by similarity to bacterial peptidoglycan synthases

Post-translational protein arginylation is essential for cardiovascular development and angiogenesis in mice and is mediated by arginyl-transfer RNA-protein transferases Ate1-a functionally conserved but poorly understood class of enzymes. Here, we used sequence analysis to detect the evolutionary relationship between the Ate1 family and bacterial FemABX family of aminoacyl-tRNA-peptide transferases, and to predict the functionally important residues in arginyltransferases, which were then used to construct a panel of mutants for further molecular dissection of mouse Ate1. Point mutations of the residues in the predicted regions of functional importance resulted in changes in enzymatic activity, including complete inactivation of mouse Ate1; other mutations altered its substrate specificity. Our results provide the first insights into the mechanisms of Ate1-mediated arginyl transfer reaction and substrate recognition, and define a new protein superfamily called Dupli-GNAT to reflect its origin by the duplication of the GNAT acetyltransferase domain.     

Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms

MOTIVATION: Periodic patterns in time series resulting from biological experiments are of great interest. The commonly used Fast Fourier Transform (FFT) algorithm is applicable only when data are evenly spaced and when no values are missing, which is not always the case in high-throughput measurements. The choice of statistic to evaluate the significance of the periodic patterns for unevenly spaced gene expression time series has not been well substantiated. METHODS: The Lomb-Scargle periodogram approach is used to search time series of gene expression to quantify the periodic behavior of every gene represented on the DNA array. The Lomb-Scargle periodogram analysis provides a direct method to treat missing values and unevenly spaced time points. We propose the combination of a Lomb-Scargle test statistic for periodicity and a multiple hypothesis testing procedure with controlled false discovery rate to detect significant periodic gene expression patterns. RESULTS: We analyzed the Plasmodium falciparum gene expression dataset. In the Quality Control Dataset of 5080 expression patterns, we found 4112 periodic probes. In addition, we identified 243 probes with periodic expression in the Complete Dataset, which could not be examined in the original study by the FFT analysis due to an excessive number of missing values. While most periodic genes had a period of 48 h, some had a period close to 24 h. Our approach should be applicable for detection and quantification of periodic patterns in any unevenly spaced gene expression time-series data.     

Antidepressant effects of mono- and combined non-drug treatments for seasonal and non-seasonal depression

The involvement of chronobiological mechanisms in the antidepressant response to such non-drug treatments as bright light, physical exercise and sleep deprivation still remain to be clarified. We compare the efficacy of several treatment strategies for seasonal and non-seasonal depression and discuss possible the contribution of chronobiological and psychological mechanisms in antidepressant response. The therapeutic effects were tested at the medical academic hospital near Novosibirsk (55 degrees North) in 138 subjects, either with winter depression or with non-seasonal depression or without depression (n = 41, 64 and 33, respectively). One-week monotreatments were either 2-hour 2500 lux cool-white incandescent light from 14:00 (n = 9, 9, 9, respectively) or 1-hour physical exercise from 13:00 (n = 9, 9, 9, respectively). One-week combined treatments included a night of total sleep deprivation followed by either 2-hour bright light from 14:00 (n = 8, 12, 0, respectively) or 1-hour physical exercise either under ordinary room light from 13:00 (n = 0, 12, 0, respectively) or under bright light from 12:00 (n = 5, 11, 0, respectively). The results indicate that, in subjects left without antidepressant treatment for a week (n = 10, 11, and 15, respectively), the 21-item Hamilton Depression Rating Scale score did not change significantly. The beneficial effects of total sleep deprivation were similar in seasonal and non-seasonal depression. The seasonals exhibited better response to bright light compared to non-seasonals. After sleep deprivation the substantial further improvements were produced by either lighting or exercising. Compared to the patients exercising under ordinary room light, the patients exercising under bright light did not gain an additional benefit. In general, winter depression was well-treated with either exercise or light, while the most promising treatment for non-seasonal depression was physical exercise combined with sleep deprivation. Bright light or physical exercise administered in the middle of the day were not less favorable compared to the treatments in the morning hours, although it is unlikely that they considerably challenged patient's chronobiology. It was concluded that the placebo effect would account for a large portion of clinical response to open non-pharmacological treatments. Therapeutic hops and visibility of such treatments would explain their high antidepressant efficacy in comparison with pharmacological trials applying a double blind cross-over design. In particular, the excellent response of patients with winter depression to light therapy might be related to their tendency to attribute a high symbolic value to bright light and associate their bad mood with a dark season.     

Age-related changes in the association of sleep satisfaction with sleep quality and sleep–wake pattern

Sleep and Biological Rhythms - Age-specific relationship of sleep–wake pattern with night sleep satisfaction was examined to address a question of why sleep satisfaction does not accurately...     

Empirical evaluation of a model-driven approach to enlargement of multi-dimensional questionnaires for assessing adaptability of the sleep–wake cycle

The spherical cube model was earlier proposed for explaining interrelationships between scales of multidimensional questionnaires designed for assessing adaptability of the human sleep–wake cycle. The purpose of this report was to use the model’s predictions for identification of new items associated with yet unassessed sub-traits of the sleep–wake adaptability. The 72-item Sleep–Wake Pattern Assessment Questionnaire (SWPAQ) and an initial 320-item list created for a new inventory were administered to 139 respondents. Results of correlating the responses to these items with scores on six SWPAQ’ scales were used for classification of items in accord with the nomenclature proposed by the model and for selection of 120 items for the new inventory that allowed the assessment of the majority (more than 24) of the sleep–wake adaptability sub-traits predicted by the model. Some of these newly assessed sub-traits reflect individual variation in the success of biological adaptation to night and shift work.     

Quod erat demonstrandum? The mystery of experimental validation of apparently erroneous computational analyses of protein sequences

Background  

Computational predictions are critical for directing the experimental study of protein functions. Therefore it is paradoxical when an apparently erroneous computational prediction seems to be supported by experiment.