Stochastic Binary Modeling of Cells in Continuous Time as an Alternative to Biochemical Reaction Equations

We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic process, while reducing each biochemical quantity to a binary value at the level of individual cells. The system can be analytically represented by a finite set of ordinary linear differential equations, which provides a continuous time course prediction of each molecular state. In this letter, we introduce our formalism and demonstrate it with several examples.Comment: 10pages, 3 figure

Structures and Magnetic Properties of Tm1-yYyMn1-xCoxO3

The structure and magnetic properties of Tm1−y Y y Mn1−x Co x O3 with 0 ≦ x ≦ 0.5 and 0 ≦ y ≦ 0.3 were investigated by X-ray diffraction, specific heat and magnetization measurements. Thulium manganite TmMnO3 prepared by solid-state synthesis at ambient pressure is hexagonal and antiferromagnetic with a Nèel temperature T N of 86 K. The substitution of Y for Tm in TmMnO3 does not greatly affect the fundamental hexagonal structure. The magnetization and specific heat measurement results for Tm1−y Y y MnO3 can be qualitatively explained in terms of the dilution effect of Tm by Y. On the other hand, the structure of TmMn1−x Co x O3 changes gradually from hexagonal to orthorhombic with the substitution of Co for Mn; hexagonal and orthorhombic phases coexist in samples for x ≦ 0.3 whereas TmMn0.6Co0.4O3 is almost a single orthorhombic phase. The magnetization of TmMn0.6Co0.4O3 in a field of 250 Oe increases rapidly at about 60K with decreasing temperature. The difference between zero-field-cooled (ZFC) and field-cooled (FC) magnetizations increases remarkably at about 60 K. Moreover, the temperature dependences of the ZFC and the FC magnetizations exhibit peaks at about 40 and 30K, respectively. Thus, TmMn1−x Co x O3 exhibits complex magnetic properties

Impact of carotid atherosclerosis on long-term mortality in chronic hemodialysis patients

Impact of carotid atherosclerosis on long-term mortality in chronic hemodialysis patients.BackgroundCardiovascular event is the major cause of mortality in patients on maintenance hemodialysis. We prospectively tested the predictive values of atherosclerotic parameters for all-cause and cardiovascular outcomes in 219 hemodialysis patients (age, 58 ± 13 years; time on hemodialysis, 13 ± 7 years; male/female, 144/75).MethodsWe measured blood homocysteine (Hcy), ultrasound carotid artery intima media thickness (IMT) and % aortic wall calcification at L2/3 region [% of calcification index in the abdominal aortic wall (%ACI)] by computed tomography (CT) scan, and followed all patients for 5 years.ResultsDuring the follow-up periods, 54 patients (25%) died, 40 (74%) of them of cardiovascular causes. IMT was significantly higher in patients who expired (0.75 ± 0.02mm) than in those who survived (0.62 ± 0.01mm). IMT was significantly correlated with age (r = 0.47, P < 0.01) and %ACI (r = 0.27, P < 0.01). The survival rate during the observation was significantly lower in the final IMT third (58%) than in the first (90%) and the middle IMT third (80%) (P < 0.01). Multivariate Cox proportional hazards analysis revealed that diabetes and IMT became independent determinants of all-cause and cardiovascular death. Adjusted hazards ratios of all-cause and cardiovascular mortality for an increase of 0.1mm in IMT were 1.31 (95% CI, 1.07 to 1.59) and 1.41 (95% CI, 1.12 to 1.76). In contrast, %ACI at abdominal aorta and blood Hcy did not affect their 5-year mortality.ConclusionThese findings suggested that measurement of carotid artery IMT is useful for predicting long-term mortality in patients receiving maintenance hemodialysis

Carbon footprint assessment of a whole dairy farming system with a biogas plant and the use of solid fraction of digestate as a recycled bedding material

Biogas generated from livestock manure is a renewable energy source and the digestate is used as a fertilizer. Moreover, dewatered biogas digestate can be used as a bedding material (recycled bedding material). The aims of the present study were to model a whole dairy system with a biogas plant using recycled bedding material and to assess the life cycle greenhouse gas (GHG) emissions. Emissions from the material flow of dairy cattle production, manure treatment and organic fertilizer application to on-farm crops were evaluated. In the emissions from organic fertilizer storage and recycled bedding material production, CH4 emission was decreased by 43.0%, and consequently the system with a biogas plant reduced total GHG emissions by 6.8% compared with conventional slurry storage and straw bedding. The use of recycled bedding material from a biogas plant has the potential to create a resource cycle and to be beneficial as a GHG mitigation strategy

A bacterial platform for fermentative production of plant alkaloids

The secondary metabolites of higher plants include diverse chemicals, such as alkaloids, isoprenoids and phenolic compounds (phenylpropanoids and flavonoids). Although these compounds are widely used in human health and nutrition, at present they are mainly obtained by extraction from plants and extraction yields are low because most of these metabolites accumulate at low levels in plant cells. Recent advances in synthetic biology and metabolic engineering have enabled tailored production of plant secondary metabolites in microorganisms, but these methods often require the addition of expensive substrates. Here we develop an Escherichia coli fermentation system that yields plant alkaloids from simple carbon sources, using selected enzymes to construct a tailor-made biosynthetic pathway. In this system, engineered cells cultured in growth medium without additional substrates produce the plant benzylisoquinoline alkaloid, (S)-reticuline (yield, 46.0 mg l−1 culture medium). The fermentation platform described here offers opportunities for low-cost production of many diverse alkaloids

Bis[μ-3,5-bis­(2-pyrid­yl)pyrazolato]bis­(hydrogensulfato)­dicopper(II) methanol disolvate

The title compound, [Cu2(C13H9N4)2(HSO4)2]·2CH3OH, consists of discrete centrosymmetric dinuclear complex mol­ecules and methanol solvent mol­ecules. The CuII atom shows a square-pyramidal coordination geometry and is bonded to four N atoms of the two bis-chelating 3,5-bis­(2-pyrid­yl)pyrazol­ate ions (bpypz−) and one O atom of the hydrogensulfate ion. The bpypz− ligands in the complex mol­ecule are virtually coplanar [dihedral angle between the mean ligand planes = 0.000(1)°] with the CuII atom deviating in opposite directions from their best plane by 0.2080 (12) Å. π–π stacking inter­actions between the pyridyl and pyrazole rings [centroid–centroid distance = 3.391 (3) Å] and strong O—H⋯O hydrogen bonds between the hydrogensulfate ligands and the methanol mol­ecules assemble the mol­ecules into a one-dimensional polymeric structure extending along the a axis. The methanol mol­ecule acts both as an accepter and a donor in the hydrogen bonding