Selection of thermodynamic models for combinatorial control of multiple transcription factors in early differentiation of embryonic stem cells

<p>Abstract</p> <p>Background</p> <p>Transcription factors (TFs) have multiple combinatorial forms to regulate the transcription of a target gene. For example, one TF can help another TF to stabilize onto regulatory DNA sequence and the other TF may attract RNA polymerase (RNAP) to start transcription; alternatively, two TFs may both interact with both the DNA sequence and the RNAP. The different forms of TF-TF interaction have different effects on the probability of RNAP's binding onto the promoter sequence and therefore confer different transcriptional efficiencies.</p> <p>Results</p> <p>We have developed an analytical method to identify the thermodynamic model that best describes the form of TF-TF interaction among a set of TF interactions for every target gene. In this method, time-course microarray data are used to estimate the steady state concentration of the transcript of a target gene, as well as the relative changes of the active concentration for each TF. These estimated concentrations and changes of concentrations are fed into an inference scheme to identify the most compatible thermodynamic model. Such a model represents a particular way of combinatorial control by multiple TFs on a target gene.</p> <p>Conclusions</p> <p>Applying this approach to a time-course microarray dataset of embryonic stem cells, we have inferred five interaction patterns among three regulators, Oct4, Sox2 and Nanog, on ten target genes.</p

Finite iterative algorithms for solving generalized coupled Sylvester systems – Part I: One-sided and generalized coupled Sylvester matrix equations over generalized reflexive solutions

AbstractThe generalized coupled Sylvester systems play a fundamental role in wide applications in several areas, such as stability theory, control theory, perturbation analysis, and some other fields of pure and applied mathematics. The iterative method is an important way to solve the generalized coupled Sylvester systems. In this two-part article, finite iterative methods are proposed for solving one-sided (or two-sided) and generalized coupled Sylvester matrix equations and the corresponding optimal approximation problem over generalized reflexive solutions (or reflexive solutions). In part I, an iterative algorithm is constructed to solve one-sided and coupled Sylvester matrix equations (AY−ZB,CY−ZD)=(E,F) over generalized reflexive matrices Y and Z. When the matrix equations are consistent, for any initial generalized reflexive matrix pair [Y1,Z1], the generalized reflexive solutions can be obtained by the iterative algorithm within finite iterative steps in the absence of round-off errors, and the least Frobenius norm generalized reflexive solution pair can be obtained by choosing a special kind of initial matrix pair. The unique optimal approximation generalized reflexive solution pair [Y^,Z^] to a given matrix pair [Y0,Z0] in Frobenius norm can be derived by finding the least-norm generalized reflexive solution pair [Y∼∗,Z∼∗] of two new corresponding generalized coupled Sylvester matrix equations (AY∼-Z∼B,CY∼-Z∼D)=(E∼,F∼), where E∼=E-AY0+Z0B,F∼=F-CY0+Z0D. Several numerical examples are given to show the effectiveness of the presented iterative algorithm

Signaling Molecule Hydrogen Sulfide Improves Seed Germination and Seedling Growth of Maize (Zea mays L.) Under High Temperature by Inducing Antioxidant System and Osmolyte Biosynthesis

Hydrogen sulfide (H2S) is a novel type signaling molecule in plants. Seed germination is a key stage of life cycle of plants, which is vulnerable to environmental stress including high temperature. However, under high temperature stress, whether pre-soaking of maize seeds with NaHS (a H2S donor) could improve seed germination and seedling growth and the possible mechanisms are not completely clear. In this study, maize seeds pre-soaked with NaHS enhanced germination percentage, sprout length, root length, and fresh weight compared with the control without NaHS treatment, illustrating that H2S could improve maize seed germination and seedling growth under high temperature. In addition, in comparison to the control, NaHS pre-soaking stimulated antioxidant enzymes [ascorbate peroxidase (APX), glutathione reductase (GR), guaiacol peroxidase (GPX), superoxide dismutase (SOD), and catalase (CAT)] activities and the contents of water soluble non-enzymatic antioxidants [ascorbic acid (AsA) and glutathione (GSH)], as well as the ratio of reduced antioxidant to oxidized antioxidant. Moreover, pre-soaking with NaHS activated Δ1-pyrroline-5-carboxylate synthetase (P5CS) and ornithine aminotransferase [OAT; both are rate-limiting enzymes in proline (Pro) synthesis], betaine aldehyde dehydrogenase [BADH; a key enzyme in glycine betaine (GB)], and trehalose (Tre)-6-phosphate phosphatase (a key step in Tre synthesis), which in turn accumulated Pro, GB, and Tre in germinating seeds compared with the control. Also, an improved germination by NaHS under high temperature was reinforced by the above osmotic adjustment substances (osmolytes) alone, while deteriorated by the inhibitors of osmolyte biosynthesis [gabaculine (GAB), disulfiram (DSF), and sodium citrate (SC)]. These results imply that H2S could improve maize seed germination and seedling growth under high temperature by inducing antioxidant system and osmolyte biosynthesis

4-(1-Cyclo­propyl-6-fluoro-4-oxo-1,4-dihydro­quinolin-7-yl)piperazin-1-ium 2,4,5-tricarb­oxy­benzene-1-carboxyl­ate monohydrate

In the crystal of title compound, C16H19FN3O+·C10H5O8 −·H2O, the water mol­ecule and the ions are connected by inter­molecular N—H⋯O and O—H⋯O hydrogen bonds and π–π stacking [centroid–centroid separation = 3.602 (1) Å] between the benzene ring and the pyridine ring, generating a three-dimensional supra­molecular structure

A Capacitive Humidity Sensor Based on Multi-Wall Carbon Nanotubes (MWCNTs)

A new type of capacitive humidity sensor is introduced in this paper. The sensor consists of two plate electrodes coated with MWCNT films and four pieces of isolating medium at the four corners of the sensor. According to capillary condensation, the capacitance signal of the sensor is sensitive to relative humidity (RH), which could be transformed to voltage signal by a capacitance to voltage converter circuit. The sensor is tested using different saturated saline solutions at the ambient temperature of 25 °C, which yielded approximately 11% to 97% RH, respectively. The function of the MWCNT films, the effect of electrode distance, the temperature character and the repeatability of the sensor are discussed in this paper

Flavonoids from Saussurea stella Maxim as superoxide scavengers and antioxidants

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ZIF-67 In Situ Grown on Attapulgite: A Flame Retardant Synergist for Ethylene Vinyl Acetate/Magnesium Hydroxide Composites.

ZIF-67@ATP was prepared by the in situ growth of the zeolite imidazole frame (ZIF-67) on the surface of attapulgite (ATP). The structure and surface morphology of ZIF-67@ATP were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and transmission electron microscopy (TEM). Different mass fractions of ATP and ZIF-67@ATP were added to ethylene vinyl acetate (EVA)/magnesium hydroxide (MH) composites as flame retardant synergists. The flame retardancy of EVA composites was evaluated by the limiting oxygen index (LOI) test, UL-94 test and cone calorimeter test. Composites containing 3 wt% of ZIF-67@ATP reached an LOI value of 43% and a V-0 rating in the UL-94 test, and the ignition time of the composite increased from 38 s to 56 s. The tensile strength and impact strength of the composites did not change significantly, but the elongation at break increased greatly. Typically, for composites containing 4 wt% of ZIF-67@ATP, the elongation at break of the composites increased from 69.5% to 522.2% compared to the samples without the synergist. This study provides novel insights into the application of attapulgite in the field of flame retardant polymer materials.post-print3999 K