Mathematical models and simulations of bacterial growth and chemotaxis in a diffusion gradient chamber

The diffusion gradient chamber (DGC) is a novel device developed to study the response of chemotactic bacteria to combinations of nutrients and attractants [7]. Its purpose is to characterize genetic variants that occur in many biological experiments. In this paper, a mathematical model which describes the spatial distribution of a bacterial population within the DGC is developed. Mathematical analysis of the model concerning positivity and boundedness of the solutions are given. An ADI (Alternating Direction Implicit) method is constructed for finding numerical solutions of the model and carrying out computer simulations. The numerical results of the model successfully reproduced the patterns that were observed in the experiments using the DGC. Received: 3 June 1997 / Revised version: 15 August 2000 / Published online: 20 December 2000     

Mechanistic similarity and diversity among the guanidine-modifying members of the pentein superfamily

The pentein superfamily is a mechanistically diverse superfamily encompassing both noncatalytic proteins and enzymes that catalyze hydrolase, dihydrolase and amidinotransfer reactions on guanidine substrates. Despite generally low sequence identity, they possess a conserved structural fold and display common mechanistic themes in catalysis. The structurally characterized catalytic penteins possess a conserved core of residues that include a Cys, His and two polar, guanidine-binding residues. All known catalytic penteins use the core Cys to attack the substrate's guanidine moiety to form a covalent thiouronium adduct and all cleave one or more of the guanidine C―N bonds. The mechanistic information compiled to date supports the hypothesis that this superfamily may have evolved divergently from a catalytically promiscuous ancestor.     

Concentrations of organophosphorus pesticides in rice (Oryza sativa) and human health risk assessment from Songhua River,Northeast China

The aim of this study was to investigate organophosphorus pesticides (OPs) concentrations in rice grains and estimate potential health risk to inhabitants. A total of 102 rice samples were collected from the Irrigated Area of Songhua River, located in Jilin province, one of the most important rice production areas and a key agricultural area in China. The twelve OPs were determined by gas chromatography coupled with flame photometric detector. Results showed that OPs concentrations in rice grains did not exceed maximum residue limit. The mean concentrations obtained for the detected twelve OPs in µg kg^?1 were as follows: omethoate (0.60), diazinon (0.56), parathion-methyl (0.54), dimethoate (0.38), isocarbophos (0.38), phorate (0.31), fenitrothion (0.24), parathion (0.23), fenthion (0.23), malathion (0.13), dichlorvos (0.13), and methamidophos (0.08). Diazinon (39.2%), omethoate (31.4%), and parathion-methyl (25.5%) had the highest frequency in the detected twelve OPs. 69.6% of samples contained more than one OP, 24.5% of samples detected one OP, and only 5.9% samples did not find any OPs. The average target hazard quotients were all less than one and average hazard index for adults and children were 0.273 and 0.238, respectively. Overall, results indicated that the intake of rice may be safe for consumers.     

Common structural traits across pathogenic mutants of the human prion protein and their implications for familial prion diseases

Human (Hu) familial prion diseases are associated with about 40 point mutations of the gene coding for the prion protein (PrP). Most of the variants associated with these mutations are located in the globular domain of the protein. We performed 50 ns of molecular dynamics for each of these mutants to investigate their structure in aqueous solution. Overall, 1.6 μs of molecular dynamics data is presented. The calculations are based on the AMBER(parm99) force field, which has been shown to reproduce very accurately the structural features of the HuPrP wild type and a few variants for which experimental structural information is available. The variants present structural determinants different from those of wild-type HuPrP and the protective mutation HuPrP(E219K-129M). These include the loss of salt bridges in α₂-α₃ regions and the loss of π-stacking interactions in the β₂-α₂ loop. In addition, in the majority of the mutants, the α₃ helix is more flexible and Y169 is more solvent exposed. The presence of similar traits in this large spectrum of mutations hints to a role of these fingerprints in their known disease-causing properties. Overall, the regions most affected by disease-linked mutations in terms of structure and/or flexibility are those involved in the pathogenic conversion to the scrapie form of the protein and in the interaction with cellular partners. These regions thus emerge as optimal targets for antibody- and ligand-binding studies.     

ADI1, a methionine salvage pathway enzyme,is required for Drosophila fecundity

Background

Methionine, an essential amino acid, is required for protein synthesis and normal cell metabolism. The transmethylation pathway and methionine salvage pathway (MTA cycle) are two major pathways regulating methionine metabolism. Recently, methionine has been reported to play a key role in Drosophila fecundity.

Results

Here, we revealed that the MTA cycle plays a crucial role in Drosophila fecundity using the mutant of aci-reductone dioxygenase 1 (DADI1), an enzyme in the MTA cycle. In dietary restriction condition, the egg production of adi1 mutant flies was reduced compared to that of control flies. This fecundity defect in mutant flies was rescued by reintroduction of Dadi1 gene. Moreover, a functional homolog of human ADI1 also recovered the reproduction defect, in which the enzymatic activity of human ADI1 is required for normal fecundity. Importantly, methionine supply rescued the fecundity defect in Dadi1 mutant flies. The detailed analysis of Dadi1 mutant ovaries revealed a dramatic change in the levels of methionine metabolism. In addition, we found that three compounds namely, methionine, SAM and Methionine sulfoxide, respectively, may be required for normal fecundity.

Conclusions

In summary, these results suggest that ADI1, an MTA cycle enzyme, affects fly fecundity through the regulation of methionine metabolism.     

Coupling of the polyamine and iron metabolism pathways in the regulation of proliferation: Mechanistic links to alterations in key polyamine biosynthetic and catabolic enzymes

Many biological processes result from the coupling of metabolic pathways. Considering this, proliferation depends on adequate iron and polyamines, and although iron-depletion impairs proliferation, the metabolic link between iron and polyamine metabolism has never been thoroughly investigated. This is important to decipher, as many disease states demonstrate co-dysregulation of iron and polyamine metabolism. Herein, for the first time, we demonstrate that cellular iron levels robustly regulate 13 polyamine pathway proteins. Seven of these were regulated in a conserved manner by iron-depletion across different cell-types, with four proteins being down-regulated (i.e., acireductone dioxygenase 1 [ADI1], methionine adenosyltransferase 2α [MAT2α], Antizyme and polyamine oxidase [PAOX]) and three proteins being up-regulated (i.e., S-adenosyl methionine decarboxylase [AMD1], Antizyme inhibitor 1 [AZIN1] and spermidine/spermine-N¹-acetyltransferase 1 [SAT1]). Depletion of iron also markedly decreased polyamine pools (i.e., spermidine and/or spermine, but not putrescine). Accordingly, iron-depletion also decreased S-adenosylmethionine that is essential for spermidine/spermine biosynthesis. Iron-depletion additionally reduced ³H-spermidine uptake in direct agreement with the lowered levels of the polyamine importer, SLC22A16. Regarding mechanism, the “reprogramming” of polyamine metabolism by iron-depletion is consistent with the down-regulation of ADI1 and MAT2α, and the up-regulation of SAT1. Moreover, changes in ADI1 (biosynthetic) and SAT1 (catabolic) partially depended on the iron-regulated changes in c-Myc and/or p53. The ability of iron chelators to inhibit proliferation was rescuable by putrescine and spermidine, and under some conditions by spermine. Collectively, iron and polyamine metabolism are intimately coupled, which has significant ramifications for understanding the integrated role of iron and polyamine metabolism in proliferation.     

Scientific basis for uncertainty factors used to establish occupational exposure limits for pharmaceutical active ingredients

The traditional “safety factor”; method has been used for years to establish occupational exposure limits (OELs) for active ingredients used in drugs. In the past, a single safety factor was used to address all sources of uncertainty in the limit setting process. The traditional 100‐fold safety factor commonly used to derive an acceptable daily intake value incorporates a default factor of 10 each to account for interindividual variability and interspecies extrapolation. Use of these defaults can lead to overly conservative health‐based limits, especially when they are combined with other (up to 10‐fold) factors to adjust for inadequacies in the available database. In recent years, attempts have been made to quantitate individual sources of uncertainty and variability to improve the scientific basis for OELs. In this paper we discuss the science supporting reductions in the traditional default uncertainty factors. A number of workplace‐specific factors also support reductions in these factors. Recently proposed alternative methodologies provide a framework to make maximum use of preclinical and clinical information, e.g., toxicokinetic and toxicodynamic data, to reduce uncertainties when establishing OELs for pharmaceutical active ingredients.     

The combination of ADI-PEG20 and TRAIL effectively increases cell death in melanoma cell lines

Current treatment for advanced, metastatic melanoma is not very effective, and new modalities are needed. ADI-PEG20 is a drug that specifically targets ASS-negative malignant melanomas while sparing the ASS-expressing normal cells. Although laboratory research and clinical trials showed promising results, there are some ASS-negative cell lines and patients that can develop resistance to this drug. In this report, we combined ADI-PEG20 with another antitumor drug TRAIL to increase the killing of malignant melanoma cells. This combination can greatly inhibit cell growth (to over 80%) and also enhanced cell death (to over 60%) in four melanoma cell lines tested compared with control. We found that ADI-PEG20 could increase the cell surface receptors DR4/5 for TRAIL and that caspase activity correlated with the increased cell death. These two drugs could also increase the level of Noxa while decrease that of survivin. We propose that these two drugs can complement each other by activating the intrinsic and extrinsic apoptosis pathways, thus enhance the killing of melanoma cells.     

Rationale for the Chemical-Specific Adjustment Factors Used to Derive an Occupational Exposure Limit for Timolol Maleate

Timolol maleate is a non-selective beta-adrenergic blocking agent currently used primarily to reduce intraocular pressure in the treatment of glaucoma. It also produces effects on the heart and bronchial smooth muscle and all of these effects are of potential concern in workers handling this active pharmaceutical ingredient. The disposition of timolol maleate is influenced by a polymorphism in oxidative metabolism by CYP2D6 and two distinct phenotypes have been identified (i.e., poor and extensive metabolizers). These properties of timolol maleate provided an opportunity to use the compound as a case study to demonstrate the derivation of chemical-specific adjustment factors for pharmacokinetics and pharmacodynamics to replace the default uncertainty factor for interindividual variability. Overall, the available data on the pharmacodynamic endpoints showed very little variability and most pharmacokinetic studies failed to discern significant differences in relatively small groups of healthy volunteers or patients. Reports of bradycardia and bronchoconstriction in patients receiving therapeutic doses are relatively rare. In one study, there was a significant reduction in heart rate 24 hours post-dose that was associated with elevated area under the curve (AUC) values. A chemical-specific adjustment factor (CSAF) for kinetics of 9.8 based on these AUC data was combined with a CSAF for dynamics of 1.2 and applied to the extrapolated no-effect level for clinically significant cardiovascular effects (with correction for oral bioavailability) to establish an occupational exposure limit (OEL) for timolol maleate which is expected to be protective of workers that may be poor metabolizers or asthmatics.     

Arginine catabolism by Thermanaerovibrio acidaminovorans

The arginine catabolism of Thermanaerovibrio acidaminovorans was investigated. T. acidaminovorans was able to produce approximately 0.4--0.5 mol citrulline and 0.5--0.6 mol ornithine from 1 mol of arginine. However, in a methanogenic coculture with Methanobacterium thermoautotrophicum Z245 1 mol arginine was converted to approximately 1 mol of propionate, 0.5 mol acetate, 4 mol ammonia and 4 mol hydrogen; citrulline and ornithine were not formed. Enzyme measurements indicated the presence of the arginine deiminase pathway (ADI) in cells of T. acidaminovorans growing on arginine.