Simulating Fluid–Solid Equilibrium with the Gibbs Ensemble

The Gibbs ensemble is employed to simulate fluid–solid equilibrium for a shifted-force Lennard-Jones system. This is achieved by generating an accurate canonical Helmholtz free-energy model of the (defect-free) solid phase. This free-energy model is easily generated, with accuracy limited only by finite-size effects, by a single isothermal–isobaric simulation at a pressure not too far from coexistence for which the chemical potential is known. We choose to illustrate this method at the known triple-point because the chemical potential is easily calculated from the coexisting gas. Alternatively, our methods can be used to locate fluid–solid coexistence and the triple-point of pure systems if the chemical potential of the solid phase can be efficiently calculated at a pressure not too far from the actual coexistence pressure. Efficient calculation of the chemical potential of solids would also enable the Gibbs ensemble simulation of bulk solid–solid equilibrium and the grand-canonical ensemble simulation of bulk solids.     

Products of Vitamin D3 or 7-Dehydrocholesterol Metabolism by Cytochrome P450scc Show Anti-Leukemia Effects,Having Low or Absent Calcemic Activity

Background

Cytochrome P450scc metabolizes vitamin D3 to 20-hydroxyvitamin D3 (20(OH)D3) and 20,23(OH)₂D3, as well as 1-hydroxyvitamin D3 to 1α,20-dihydroxyvitamin D3 (1,20(OH)₂D3). It also cleaves the side chain of 7-dehydrocholesterol producing 7-dehydropregnenolone (7DHP), which can be transformed to 20(OH)7DHP. UVB induces transformation of the steroidal 5,7-dienes to pregnacalciferol (pD) and a lumisterol-like compounds (pL).

Methods and Findings

To define the biological significance of these P450scc-initiated pathways, we tested the effects of their 5,7-diene precursors and secosteroidal products on leukemia cell differentiation and proliferation in comparison to 1α,25-dihydroxyvitamin D3 (1,25(OH)₂D3). These secosteroids inhibited proliferation and induced erythroid differentiation of K562 human chronic myeloid and MEL mouse leukemia cells with 20(OH)D3 and 20,23(OH)₂D3 being either equipotent or slightly less potent than 1,25(OH)₂D3, while 1,20(OH)₂D3, pD and pL compounds were slightly or moderately less potent. The compounds also inhibited proliferation and induced monocytic differentiation of HL-60 promyelocytic and U937 promonocytic human leukemia cells. Among them 1,25(OH)₂D3 was the most potent, 20(OH)D3, 20,23(OH)₂D3 and 1,20(OH)₂D3 were less active, and pD and pL compounds were the least potent. Since it had been previously proven that secosteroids without the side chain (pD) have no effect on systemic calcium levels we performed additional testing in rats and found that 20(OH)D3 had no calcemic activity at concentration as high as 1 µg/kg, whereas, 1,20(OH)₂D3 was slightly to moderately calcemic and 1,25(OH)₂D3 had strong calcemic activity.

Conclusions

We identified novel secosteroids that are excellent candidates for anti-leukemia therapy with 20(OH)D3 deserving special attention because of its relatively high potency and lack of calcemic activity.     

Cubicle Refusal and Rearing Accommodation as Possible Mastitis Risk Factors in Cubicle-Housed Dairy Heifers

Fifty-nine of the 65 dairy farms with cubicle sheds in the Norwegian county of Oppland in 1990 were included in a study of rearing accommodation, cubicle refusal and mastitis incidence. The farmers recorded the favoured resting location of the individual cows and heifers throughout the final week of pregnancy as well as during calving. The observations were matched with individual records of mastitis cases during the first 30 days after calving. Mastitis incidence in the heifers was analysed by logistic regression using rearing accommodation and cubicle refusal as independent variables, controlling for herd as a clustering factor. Cubicle refusal was found in 29% of the heifers, but in only 3% of older cows. The results of the analysis indicated a tendency for cubicle refusal to be associated with an increased mastitis incidence among the heifers (OR = 2.2, c.i._95%OR = 0.9–5.4, P = 0.08). Cubicle refusal accounted for 21% (0–32%) of the mastitis cases in the study population (PAF = 0.21).     

Phosphorylation of mitochondrial phospholipid scramblase 3 by protein kinase C-delta induces its activation and facilitates mitochondrial targeting of tBid

Phospholipid scramblase 3 (PLS3) is a member of the phospholipid scramblase family present in mitochondria. PLS3 plays an important role in regulation of mitochondrial morphology, respiratory function, and apoptotic responses. PLS3 is phosphorylated by PKC-delta at Thr21 and is the mitochondrial target of PKC-delta-induced apoptosis. Cells with overexpression of PLS3, but not the phosphoinhibitory mutant PLS3(T21A), are more susceptible to apoptosis induced by AD198, an extranuclear targeted anthracycline that activates PKC-delta. Here we report that the phosphomimetic mutant of PLS3(T21D) by itself can induce apoptosis in HeLa cells. Using proteoliposomes with addition of pyrene-labeled phosphatidylcholine (PC) at the outer leaflet, we measured the lipid flip-flop activity of PLS3 and its phosphorylation mutant. PLS3(T21D) is more potent than wild-type PLS3 or PLS3(T21A) to transfer pyrene-PC from the outer leaflet to the inner leaflet of liposomes. Based on our previous finding that PLS3 enhances tBid-induced mitochondrial damages, we tested the hypothesis that PLS3 enhances cardiolipin translocation to mitochondrial surface and facilitates tBid targeting. Fluorescein-labeled tBid(G94E) was used as a probe to quantify cardiolipin on the surface of mitochondria. Mitochondria from cells treated with AD198 or cells expressing PLS3(T21D) had a higher level of tBid-binding capacity than control cells or cells expressing wild-type PLS3. These findings indicate that phosphorylation of PLS3 by PKC-delta induces PLS3 activation to facilitate mitochondrial targeting of tBid and apoptosis.     

Maintenance of Y receptor dimers in epithelial cells depends on interaction with G-protein heterotrimers

Treatment of CHO cells expressing human Y receptors (Y₁, Y₂ or Y4 subtype) with pertussis toxin results in a large decrease in functional receptors, with a preferential loss of heteropentameric assemblies of receptor dimers and G-protein trimers. This occurs in parallel to inactivation of the nucleotide site of Gi α subunits, with a half period of about 4 h. The loss could be mainly due to proteolysis at the level of recycling/perinuclear endosomes, and of receptor completion in the ER, since it is reduced by co-treatment with ammonium chloride, an inhibitor of particulate proteinases. Antagonists do not strongly decrease the heteropentameric fraction. These findings indicate that the upkeep of Y receptor dimers in epithelial cell lines depends on the association of receptor oligomers with functional Gi α subunits. This interaction could use the juxtamembrane helix 8 in the fourth intracellular domain, and could also be supported by the C-terminal helix of the third intracellular loop, as outlined in the companion review (Parker et al., Amino Acids, doi:, 2010).     

An overview of the serpin superfamily

Serpins are a broadly distributed family of protease inhibitors that use a conformational change to inhibit target enzymes. They are central in controlling many important proteolytic cascades, including the mammalian coagulation pathways. Serpins are conformationally labile and many of the disease-linked mutations of serpins result in misfolding or in pathogenic, inactive polymers.     

A field study of fish predation on juvenile crown-of-thorns starfish

To test whether commercially exploited fishes could regulate populations of crown-of-thorns starfish, laboratory reared juvenile Acanthaster planci were planced on small habitat units in an area of a lagoon where a number of species of fish that feed on benthic invertebrates occurred. Predators were excluded from half the units using wire mesh. In 35 days, losses were low and there was no statistically significant difference between caged and uncaged units. A difference in mortality rate of 1% of individuals per day would have been detected with >85% probability.However, the observed mean difference, the maximum estimate of predatory mortality, was 0.13% of starfish per day. It thus seems unlikely that predation by any large fishes was important in the population dynamics of juvenile A. planci at that site at the time of this experiment. Juvenile starfish were presented to lethrinids in the field at two reefs. Thirteen percent of juvenile A. planci presented at one reef were eaten, but in no presentation did lethrinids eat all the available starfish and those that were eaten were often mouthed and rejected by several fish before being swallowed. No juveniles were taken in a smaller number of trials at the second reef. These results do not favour the hypothesis that predation on juveniles by large fish is important in the population dynamics of A. planci but experiments at more sites will be required before this conclusion can be generalized.     

ABE production from corn: a recent economic evaluation

This article details an economic assessment of butanol production from corn using the newly developed hyper-butanol-producing strain of Clostridium beijerinckii BA101. Butanol is produced in batch reactors and recovered by distillation. For a plant with 153,000 metric tons of acetone, butanol, and ethanol (ABE) production capacity, the production equipment cost and total working capital cost is US$33.47×10⁶ and US$110.46×10⁶, respectively. Based on a corn price (C _p) of US$79.23 ton⁻¹ (US$2.01 bushel⁻¹), an ABE yield of 0.42 (g ABE/g glucose) butanol price is projected to be US$0.34 kg⁻¹. An improved yield of 0.50 will reduce this price to US$0.29 kg⁻¹. Assumptions, such as by-product credit for gases and complete conversion of corn steep liquor (CSL) to fermentation by-products, have been taken into consideration. An increased price of corn to US$197.10 ton⁻¹ would result in a butanol price of US$0.47 kg⁻¹. A grass-rooted plant would result in a butanol price of US$0.73 kg⁻¹ (C _p US$79.23 ton⁻¹). In a worst case scenario, the price of butanol would increase to US$1.07 kg⁻¹ (C _p 197.10 ton⁻¹ for a grass-rooted plant and assuming no credit for gases). This is based on the assumption that corn price would not increase to more than US$197.10 ton⁻¹. Journal of Industrial Microbiology & Biotechnology (2001) 27, 292–297. Received 12 September 2000/ Accepted in revised form 12 January 2001     

Development of a multivariate statistical model to predict peroxisome proliferation in the rat, based on urinary 1H-NMR spectral patterns.

A previous report of this work (Ringeissen et al. 2003) described the use of nuclear magnetic resonance (NMR) spectroscopy coupled with multivariate statistical data analysis (MVDA) to identify novel biomarkers of peroxisome proliferation (PP) in Wistar Han rats. Two potential biomarkers of peroxisome proliferation in the rat were described, N-methylnicotinamide (NMN) and N-methyl-4-pyridone-3-carboxamide (4PY). The inference from these results was that the tryptophan-nicotinamide adenine dinucleotide (NAD(+)) pathway was altered in correlation with peroxisome proliferation, a hypothesis subsequently confirmed by TaqMan analysis of the relevant genes encoding two key enzymes in the pathway, aminocarboxymuconate-semialdehyde decarboxylase (EC 4.1.1.45) and quinolinate phosphoribosyltransferase (EC 2.4.2.19). The objective of the present study was to investigate these data further and identify other metabolites in the NMR spectrum correlating equally with PP. MVDA Partial Least Squares (PLS) models were constructed that provided a better prediction of PP in Wistar Han rats than levels of 4PY and NMN alone. The resulting Wistar Han rat predictive models were then used to predict PP in a test group of Sprague Dawley rats following administration of fenofibrate. The models predicted the presence or absence of PP (above on arbitrary threshold of >2-fold mean control) in all Sprague Dawley rats in the test group.     

The [FeFe] hydrogenase of Nyctotherus ovalis has a chimeric origin

Background

The hydrogenosomes of the anaerobic ciliate Nyctotherus ovalis show how mitochondria can evolve into hydrogenosomes because they possess a mitochondrial genome and parts of an electron-transport chain on the one hand, and a hydrogenase on the other hand. The hydrogenase permits direct reoxidation of NADH because it consists of a [FeFe] hydrogenase module that is fused to two modules, which are homologous to the 24 kDa and the 51 kDa subunits of a mitochondrial complex I.

Results

The [FeFe] hydrogenase belongs to a clade of hydrogenases that are different from well-known eukaryotic hydrogenases. The 24 kDa and the 51 kDa modules are most closely related to homologous modules that function in bacterial [NiFe] hydrogenases. Paralogous, mitochondrial 24 kDa and 51 kDa modules function in the mitochondrial complex I in N. ovalis. The different hydrogenase modules have been fused to form a polyprotein that is targeted into the hydrogenosome.

Conclusion

The hydrogenase and their associated modules have most likely been acquired by independent lateral gene transfer from different sources. This scenario for a concerted lateral gene transfer is in agreement with the evolution of the hydrogenosome from a genuine ciliate mitochondrion by evolutionary tinkering.