Causality,transfer entropy,and allosteric communication landscapes in proteins with harmonic interactions

A fast and approximate method of generating allosteric communication landscapes in proteins is presented by using Schreiber's entropy transfer concept in combination with the Gaussian Network Model of proteins. Predictions of the model and the allosteric communication landscapes generated show that information transfer in proteins does not necessarily take place along a single path, but an ensemble of pathways is possible. The model emphasizes that knowledge of entropy only is not sufficient for determining allosteric communication and additional information based on time delayed correlations should be introduced, which leads to the presence of causality in proteins. The model provides a simple tool for mapping entropy sink‐source relations into pairs of residues. By this approach, residues that should be manipulated to control protein activity may be determined. This should be of great importance for allosteric drug design and for understanding the effects of mutations on function. The model is applied to determine allosteric communication in three proteins, Ubiquitin, Pyruvate Kinase, and the PDZ domain. Predictions are in agreement with molecular dynamics simulations and experimental evidence. Proteins 2017; 85:1056–1064. © 2017 Wiley Periodicals, Inc.     

The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review

Among different conversion processes for biomass, biological anaerobic digestion is one of the most economic ways to produce biogas from various biomass substrates. In addition to hydrolysis of polymeric substances, the activity and performance of the methanogenic bacteria is of paramount importance during methanogenesis. The aim of this paper is primarily to review the recent literature about the occurrence of both acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of particulate biomass to methane (not wastewater treatment), while this review does not cover the activity of the acetate oxidizing bacteria. Both acetotrophic and hydrogenotrophic methanogens are essential for the last step of methanogenesis, but the reports about their roles during this phase of the process are very limited. Despite, some conclusions can still be drawn. At low concentrations of acetate, normally filamentous Methanosaeta species dominate, e.g., often observed in sewage sludge. Apparently, high concentrations of toxic ionic agents, like ammonia, hydrogen sulfide (H₂S) and volatile fatty acids (VFA), inhibit preferably Methanosaetaceae and especially allow the growth of Methanosarcina species consisting of irregular cell clumps, e.g., in cattle manure. Thermophilic conditions can favour rod like or coccoid hydrogenotrophic methanogens. Thermophilic Methanosarcina species were also observed, but not thermophilic Methanosaetae. Other environmental factors could favour hydrogentrophic bacteria, e.g., short or low retention times in a biomass reactor. However, no general rules regarding process parameters could be derivated at the moment, which favours hydrogenotrophic methanogens. Presumably, it depends only on the hydrogen concentration, which is generally not mentioned in the literature.     

Comparison of partial excision with simple section of the transverse carpal ligament in the treatment of carpal tunnel syndrome

In the surgical treatment of carpal tunnel syndrome, debate has commonly focused on whether decompression should be performed by open or blind techniques. Contrarily, the goal of the present study was to determine whether instead of simple section, partial excision of the transverse carpal ligament has contributed to better results. Because complete healing of the transverse carpal ligament observed during reoperations has been reported elsewhere, the charts of 75 carpal tunnel syndrome patients who had been treated with open technique at Dokuz Eylül University were reviewed. Statistical analysis was performed using the Fisher's exact test and Student's t test when appropriate. Thirty-five patients had been treated with simple section of the transverse carpal ligament, whereas 40 had been treated with partial excision. Internal neurolysis was also performed in 19 of the patients, 11 of whom were treated with partial excision. The average follow-up time was 3.8 years. The comparisons regarding the overall operative outcomes did not show any significant difference between the two different techniques of releasing the transverse carpal ligament. In patients treated without neurolysis, results of partial excision of the transverse carpal ligament improved when compared with those of simple section, but this superiority was not statistically significant. There seemed to be statistically higher reoperation rates and worse outcomes after neurolysis (p < 0.05). Reoperation was required in eight patients (11 percent). Five of the patients who underwent reoperation had initially been treated with partial excision and neurolysis, whereas two had been treated with simple section and neurolysis. Another patient who had undergone reoperation had initially undergone only simple section. The mean time to return to work or daily activities did not differ between the types of applied technique for releasing the transverse carpal ligament. However, neurolysis lengthened these periods significantly when performed (p < 0.05). In the present study, partial excision of the transverse carpal ligament without adding neurolysis offered relatively better results than simple section. Verification of this finding endoscopically, if applicable, may improve the success rate of surgical therapy in patients with carpal tunnel syndrome.     

Natural occurrence of mycotoxins and mycoflora of argentinien popcorn

Argentina is the first popcorn exporting country worldwide. In 1997-1998 harvest season, 40,000 ha were sown with a production of 125,000 tons; 120,000 tons of this production were exported to more than 40 countries. The objectives of this study were to isolate and to identify the fungi present in this cereal and to assess the occurrence of mycotoxins in freshly harvested popcorn in Buenos Aires province, Argentina, in 1999. All popcorn samples showed fungal contamination. A total of 4,211 isolates were recovered from popcorn kernel samples. The prevalent species isolated wasFusarium verticillioides followed byPenicillium funiculosum, F. graminearum andAlternaria alternata. No aflatoxins, zearalenone, deoxynivalenol or ochratoxin A were detected in the 42 popcorn simples. All samples but one were contaminated with fumonisins (FB) in a range in ug/kg of (not detected-529) for FB₁; (not detected-216) for FB₂ and (not detected-103) for FB₃. Fumonisin contamination levels in Argentinean popcorn were lower than observed in flint corn. No significant differences in fungal and fumonisins contamination levels were observed in the different tested hybrids.     

Frequency responses of cat rapidly adapting mechanoreceptive fibers

The frequency responses of 11 rapidly adapting (RA) fibers in cat were studied by representing the average firing rate as a function of sinusoidal stimulus amplitude and stimulus frequency. Specifically, rate-intensity functions at different stimulation frequencies were fitted by four-parameter (a0, a1, a2, a3), piece-wise linear functions using nonlinear regression (n = 59; R2 > 0.877). Rate-intensity functions at intermediate frequencies were found by linear interpolation. The result of this analysis is rate-amplitude-frequency functions plotted as two-dimensional surfaces. The surfaces consist of five regions separated and sufficiently defined by four space curves. At 14 different frequencies, the statistical distribution of each rate-intensity-function parameter could be approximated by a particular lognormal distribution (n = 56; R2 > 0.796). The Kolmogorov-Smirnov test fails to reject this hypothesis for each combination of frequency and parameter (56 tests; p > 0.39). Therefore, at a given frequency, the variation of the parameters can be represented by lognormal distributions with specific means and standard deviations. Responses of six RA fibers, which are different from the data-set used for modeling, were compared with the stochastic model at different frequencies. The parameters of those fibers were tested against the null hypotheses that they were sampled from the particular parameter distributions dictated by the model. The Kolmogorov-Smirnov test fails to reject all the hypotheses at the alpha = 0.05 level (44 tests). At the alpha = 0.10 level, only a few test parameters were found to be departing from the model (a0 and a1 at 5 Hz; a2 at 20 Hz; a2 and a3 at 50 Hz). The remaining test parameters could be accurately described by the model. Having confirmed the validity of the model, the logarithmic means and the logarithmic standard deviations of the lognormally distributed rate-intensity-function parameters were estimated in the frequency range of 4-200 Hz. The rate-amplitude-frequency surfaces sampled from the established stochastic model completely characterize the rate responses of RA fibers to sinusoidal stimuli and are superior to tuning curves which require selecting criterion responses. The current rate-response model is promising for future computational work, especially on population modeling.     

Thermal ablation therapeutics based on CN(x) multi-walled nanotubes

We demonstrate that nitrogen doped, multi-walled carbon nanotubes (CN(x)-MWNT) result in photo-ablative destruction of kidney cancer cells when excited by near infrared (NIR) irradiation. Further, we show that effective heat transduction and cellular cytotoxicity depends on nanotube length: effective NIR coupling occurs at nanotube lengths that exceed half the wavelength of the stimulating radiation, as predicted in classical antenna theory. We also demonstrate that this radiation heats the nanotubes through induction processes, resulting in significant heat transfer to surrounding media and cell killing at extraordinarily small radiation doses. This cell death was attributed directly to photothermal effect generated within the culture, since neither the infrared irradiation itself nor the CN(x)-MWNT were toxic to the cells.