System-level feedbacks control cell cycle progression

Repetitive cell cycles, which are essential to the perpetuation of life, are orchestrated by an underlying biochemical reaction network centered around cyclin-dependent protein kinases (Cdks) and their regulatory subunits (cyclins). Oscillations of Cdk1/CycB activity between low and high levels during the cycle trigger DNA replication and mitosis in the correct order. Based on computational modeling, we proposed that the low and the high kinase activity states are alternative stable steady states of a bistable Cdk-control system. Bistability is a consequence of system-level feedback (positive and double-negative feedback signals) in the underlying control system. We have also argued that bistability underlies irreversible transitions between low and high Cdk activity states and thereby ensures directionality of cell cycle progression.     

Solid Tryptophan as a Pseudoracemate: Physicochemical and Crystallographic Characterization

The crystalline nature of solid tryptophan has been characterized by X‐ray single crystal and powder diffraction analyses, differential scanning calorimetry, as well as measurement of solid–liquid equilibrium in water/isopropanol solution. Both the thermodynamic and crystallographic investigations have demonstrated unambiguously that solid tryptophan crystallizes in the form of a pseudoracemate (i.e., solid solution) with maximum melting over the entire enantiomeric composition range. Comparative single‐crystal X‐ray studies show that the crystal structures of racemic and enantiomeric tryptophan give very similar solid‐state packing geometries dictated by hydrogen bonding interactions. Our results indicate that the insignificant difference between homochiral and heterochiral interactions accounts for the formation of a pseudoracemate for this system. Chirality 27:88–94, 2015. © 2014 Wiley Periodicals, Inc.     

Early Prediction of COVID-19 Patient Survival by Targeted Plasma Multi-Omics and Machine Learning

The recent surge of coronavirus disease 2019 (COVID-19) hospitalizations severely challenges healthcare systems around the globe and has increased the demand for reliable tests predictive of disease severity and mortality. Using multiplexed targeted mass spectrometry assays on a robust triple quadrupole MS setup which is available in many clinical laboratories, we determined the precise concentrations of hundreds of proteins and metabolites in plasma from hospitalized COVID-19 patients. We observed a clear distinction between COVID-19 patients and controls and, strikingly, a significant difference between survivors and nonsurvivors. With increasing length of hospitalization, the survivors’ samples showed a trend toward normal concentrations, indicating a potential sensitive readout of treatment success. Building a machine learning multi-omic model that considers the concentrations of 10 proteins and five metabolites, we could predict patient survival with 92% accuracy (area under the receiver operating characteristic curve: 0.97) on the day of hospitalization. Hence, our standardized assays represent a unique opportunity for the early stratification of hospitalized COVID-19 patients.     

Mixed monolayers of dipalmitoylglycerophosphocholine,distearoylglycerophosphocholine and 1-palmitoylglycerol

Mixed monolayer systems of dipalmitoylglycerophosphocholine (DPPC)-distearoylglycerophosphocholine (DSPC), palmitoylglycerol-DPPC, and palmitoylglycerol-DSPC have been investigated by a previously described thermodynamic treatment. The surface pressures of these systems were measured at various compositions and temperatures. The two-dimensional phase diagrams and the apparent molar entropy and energy changes were evaluated. It was found that the phase diagrams of the DPPC-DSPC, palmitoylglycerol-DSPC and palmitoylglycerol-DPPC systems are all of different types. According to our phase diagram classification, DPPC-DSPC, palmitoylglycerol-DSPC, and palmitoylglycerol-DPPC systems exhibited a modified cigar type, a eutectic type, and a negative azeotropic type, respectively.     

The nucleolus as a polarized coaxial cable in which the rDNA axis is surrounded by dynamic subunit-specific phases

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A comparative analysis of developmental profiles for DNA methylation in 5-azacytidine-induced early-flowering flax lines and their control

Earlier experiments demonstrated that DNA from young plants of 5-azacytidine-induced flax (Linum usitatissimum) lines that flower earlier-than-normal is hypomethylated relative to DNA from their control lines and detected differences in methylation level between plants sampled at different ages, which suggested that the methylation level in flax changes during development. To investigate this possibility, and its potential impact on the difference in methylation level between early-flowering and control lines, developmental profiles were established for the cytosine methylation levels in DNA from post-germination seedlings and from the shoot tips of main stems and the cotyledons sampled throughout vegetative phase. The methylation profiles for two early-flowering lines and their control lines were compared. The methylation profiles were then compared to profiles for DNA content, tissue weight and chlorophyll content (green tissues); these additional parameters provided information on tissue status in terms of cell division, tissue expansion and/or photosynthetic maturity. With one exception, methylation levels were either static or increased with plant age and/or tissue maturity; the highest methylation levels were seen in senescent cotyledons. Although DNA from immature plants or tissues of the early-flowering lines was usually hypomethylated, the hypomethylation was not always apparent in tissues from older plants.     

Analytical and preparative chromatographic procedures for obtaining pure cresyl violet and cresyl red from commercial cresyl violet

Abstract

Cresyl violet and cresyl red, components of commercial cresyl violet acetate, were separated and purified using preparative column liquid chromatography. The stationary phase was silica gel and gradient elution was carried out using chloroform:methanol. The purified dyes were obtained in high yield; 51% of the original lot was recovered as cresyl violet and 40% as cresyl red. Separated materials were characterized by nuclear magnetic resonance and mass spectroscopy; UV-visible and Fourier-transform infrared spectra also were obtained for samples of pure cresyl violet and cresyl red. The colored constituents of the commercial dye lot were identified using thin layer chromatography and reverse phase high performance liquid chromatography. Both methodologies were suitable for routine testing; reverse phase high performance liquid chromatography is an appropriate tool for quality control and high resolution identification of these compounds.     

Removing radionuclides from wound fluids using chemical speciation and chelation lavage

Abstract

The relative efficacy of a range of chelating agents for dissolving plutonium(IV) hydroxide precipitated in wounds is assessed by computing the chemical speciation prevailing in the wound fluid and wound lavage solution. The most promising ligand for mobilisation is DTPA when used under mildly acid (approx. pH 6.4) conditions. If the Pu(IV) oxide has been formed, none of the ligands are effective.     

Lipid phase transitions in fatty acid-homogeneous membranes of Acholeplasma laidlawii B

The thermotropic behaviour of fatty acid-homogeneous membranes of Acholeplasma laidlawii B was investigated by Fourier transform infrared spectroscopy. The organism was grown at 37°C in the presence of avidin, an inhibitor of fatty acid synthesis, in a medium supplemented with pentadecanoic acid-d₂₉; the enrichment of the membranes with this fatty acid was 95%. The temperature-dependent phase behaviour of the membranes was studied via the C–D stretching vibrational modes of the membrane lipids and was compared with that of the lipid extract. The high level of fatty acid homogeneity results in a sharp (for natural membranes) gel to liquid crystalline phase transition. The transition, in both the membranes and extracted lipids, is centered at about 6°C above the growth temperature. During the transition two principal liquid states are evident, one being more conformationally ordered than the other. The effect of proteins on the principal lipid phase transition is minimal. However, in the intact membranes there is evident a weaker, lower temperature transition, which is not evident in the extracted lipids.