Outbreak of Mycobacterium bovis in a conditioned colony of rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques

We describe a tuberculosis outbreak caused by Mycobacterium bovis in a conditioned colony of rhesus (Macaca mulatta) and cynomolgus (Macaca fascicularis) macaques. Animals in five rooms were exposed, but most (16/27) infections were confined to the room that housed a mixed population of cynomolgus and rhesus macaques. In this room, rhesus (8/8) and cynomolgus (10/11) macaques naturally exposed to M. bovis were infected at nearly identical rates (Fisher exact test, 2-tailed P = 1). The clinical signs of disease and pathologic lesions in infected macaques, however, were moderately different between the two species. Rhesus macaques were more likely (5/8) to exhibit clinical signs of persistent coughing and inappetance, and had more severe pulmonary lesions. By contrast, clinical signs of disease were seen in only 1 of 19 cynomolgus macaques, and overall, the pulmonary lesions were often focal and less severe, although some still had severe involvement of the lungs similar to that seen in rhesus macaques. These differences should be taken into consideration when developing or evaluating a tuberculosis-screening program. On the basis of observations made during this outbreak, we recommend that alternative screening methods such as the PRIMAGAM test and the ESAT-6 ELISA, be incorporated into the screening program to aid in the identification of infected animals.     

Models for the kinetics of biodegradation of organic compounds not supporting growth.

We developed 12 models of kinetics to describe the metabolism of organic substrates that are not supporting bacterial growth. These models can be used to describe the biodegradation of organic compounds that are not supporting growth when the responsible populations are growing logistically, logarithmically, or linearly or are not increasing in numbers. Nonlinear regression analysis was used to fit patterns of mineralization by two bacteria to these kinetic models. Pseudomonas acidovorans mineralized 1 ng of phenol per ml while growing exponentially at the expense of uncharacterized organic carbon in a synthetic medium. Phenol at a concentration of 1 ng/ml did not affect the growth of P. acidovorans. These data were best fit by the model that incorporates the equation for logarithmic growth and assumes a concentration of test substrate well below its Km value. In the absence of a second substrate, glucose at concentrations below those supporting growth was mineralized by Salmonella typhimurium in a manner best described by pseudo first-order kinetics. In the presence of different concentrations of arabinose, however, the kinetics of glucose mineralization by S. typhimurium reflected linear, logistic, or logarithmic growth of the population on arabinose. We conclude that the kinetics of mineralization of organic compounds at concentrations too low to support growth are best described either by the first-order model or by models that incorporate expressions for the kinetics of growth of the metabolizing population on other substrates. When growth is at the expense of other substrates, the kinetics observed reflect such growth, as well as the concentration of the substrate of interest.(ABSTRACT TRUNCATED AT 250 WORDS)     

Functional integrity of fetal rat liver explants cultured in a chemically defined medium.

A technique is described for the rapid preparation of large numbers of fetal rat liver explants for the study of developmental changes. Uniform pieces (1 mm³) of liver at 16 and 20 days of gestation were cultured for 3 days in a chemically defined medium in the absence of serum or exogenous proteins. Explants of both gestational ages appeared morphologically normal at the end of 3 days. Net uptakes of glucose remained relatively constant over the culture period. There was an initial loss of protein and DNA which could be largely accounted for by loss of erythropoietic cells. After the first or second day in culture, the DNA content of the explants remained constant. The amount of nonsedimentable protein (nonerythrocyte) released into the medium was 16 to 20 μ per explant per day. Between 40 and 50% of this protein was identified as albumin and α-fetoprotein by immunologic and electrophoretic techniques. A minor protein component was identified as transferrin. These proteins, normally secreted into amniotic fluid, were released in amounts that markedly exceeded their concentrations in the explant. This release was blocked by the presence of cycloheximide in the culture medium. This technique provides a simple method for maintaining viable fetal liver explants in a chemically defined medium, and should be useful for studying metabolic development in antenatal liver.     

Models for the kinetics of biodegradation of organic compounds not supporting growth

We developed 12 models of kinetics to describe the metabolism of organic substrates that are not supporting bacterial growth. These models can be used to describe the biodegradation of organic compounds that are not supporting growth when the responsible populations are growing logistically, logarithmically, or linearly or are not increasing in numbers. Nonlinear regression analysis was used to fit patterns of mineralization by two bacteria to these kinetic models. Pseudomonas acidovorans mineralized 1 ng of phenol per ml while growing exponentially at the expense of uncharacterized organic carbon in a synthetic medium. Phenol at a concentration of 1 ng/ml did not affect the growth of P. acidovorans. These data were best fit by the model that incorporates the equation for logarithmic growth and assumes a concentration of test substrate well below its Km value. In the absence of a second substrate, glucose at concentrations below those supporting growth was mineralized by Salmonella typhimurium in a manner best described by pseudo first-order kinetics. In the presence of different concentrations of arabinose, however, the kinetics of glucose mineralization by S. typhimurium reflected linear, logistic, or logarithmic growth of the population on arabinose. We conclude that the kinetics of mineralization of organic compounds at concentrations too low to support growth are best described either by the first-order model or by models that incorporate expressions for the kinetics of growth of the metabolizing population on other substrates. When growth is at the expense of other substrates, the kinetics observed reflect such growth, as well as the concentration of the substrate of interest.(ABSTRACT TRUNCATED AT 250 WORDS)     

Two approaches to modeling kinetics of biodegradation by growing cells and application of a two-compartment model for mineralization kinetics in sewage

The patterns of microbial mineralization of 0.3 to 30 ng of glucose, benzoate, and phenol per ml of sewage collected in late fall and winter were analyzed with the integrated Monod equation and a model in which growth of active organisms occurs at the expense of organic compounds other than the test substrate. Either model could be closely fit by nonlinear regression to the data from individual tests with one concentration of substrate added to one dilution of sewage. However, neither model accounted satisfactorily for differences in patterns of mineralization resulting from differences in substrate concentration and cell density between different tests. It is suggested that both the added substrates and other organics present in sewage contributed to the growth of the active organisms. The mineralization of glucose in sewage collected in summer was better described by a two-compartment model than by any other model tested.     

No evidence of nonlinear effects of predator density,refuge availability,or body size of prey on prey mortality rates

Predator density, refuge availability, and body size of prey can all affect the mortality rate of prey. We assume that more predators will lead to an increase in prey mortality rate, but behavioral interactions between predators and prey, and availability of refuge, may lead to nonlinear effects of increased number of predators on prey mortality rates. We tested for nonlinear effects in prey mortality rates in a mesocosm experiment with different size classes of western mosquitofish (Gambusia affinis) as the prey, different numbers of green sunfish (Lepomis cyanellus) as the predators, and different levels of refuge. Predator number and size class of prey, but not refuge availability, had significant effects on the mortality rate of prey. Change in mortality rate of prey was linear and equal across the range of predator numbers. Each new predator increased the mortality rate by about 10% overall, and mortality rates were higher for smaller size classes. Predator–prey interactions at the individual level may not scale up to create nonlinearity in prey mortality rates with increasing predator density at the population level.     

Two approaches to modeling kinetics of biodegradation by growing cells and application of a two-compartment model for mineralization kinetics in sewage.

The patterns of microbial mineralization of 0.3 to 30 ng of glucose, benzoate, and phenol per ml of sewage collected in late fall and winter were analyzed with the integrated Monod equation and a model in which growth of active organisms occurs at the expense of organic compounds other than the test substrate. Either model could be closely fit by nonlinear regression to the data from individual tests with one concentration of substrate added to one dilution of sewage. However, neither model accounted satisfactorily for differences in patterns of mineralization resulting from differences in substrate concentration and cell density between different tests. It is suggested that both the added substrates and other organics present in sewage contributed to the growth of the active organisms. The mineralization of glucose in sewage collected in summer was better described by a two-compartment model than by any other model tested.     

Microbial growth rates and local external mass transfer coefficients in a porous bed biofilm system measured by 19F magnetic resonance imaging of structure,oxygen concentration,and flow velocity

¹⁹F nuclear magnetic resonance (NMR) oximetry and ¹H NMR velocimetry were used to noninvasively map oxygen concentrations and hydrodynamics in space and time in a model packed bed biofilm system in the presence and absence of flow. The development of a local oxygen sink associated with a single gel bead inoculated with respiring Escherichia coli was analyzed with a phenomenological model to determine the specific growth rate of the bacteria in situ, returning a value (0.66 hr⁻¹) that was close to that measured independently in planktonic culture (0.62 hr⁻¹). The decay of oxygen concentration in and around the microbiologically active bead was delayed and slower in experiments conducted under continuous flow in comparison to no-flow experiments. Concentration boundary layer thicknesses were determined and Sherwood numbers calculated to quantify external mass transfer resistance. Boundary layers were thicker in no-flow experiments compared to experiments with flow. Whereas the oxygen concentration profile across a reactive biofilm particle was symmetric in no-flow experiments, it was asymmetric with respect to flow direction in flow experiments with Sherwood numbers on the leading edge (Sh = 7) being larger than the trailing edge (Sh = 3.5). The magnitude of the experimental Sh was comparable to values predicted by a variety of correlations. These spatially resolved measurements of oxygen distribution in a geometrically complex model reveal in innovative detail the local coupling between microbial growth, oxygen consumption, and external mass transfer.     

Identification and quantification of protecting groups remaining in commercial oligonucleotide products using monoclonal antibodies

Quality control is paramount to reproducibly achieving oligonucleotide therapeutics and diagnostics of superior value. However, incomplete deprotection of nucleoside reactive groups after the automated chemical synthesis of oligonucleotides would result in diminished antisense activity and in erroneous array analysis of gene expression. Mass spectrometry and capillary electrophoresis are used to detect aborted sequences of oligonucleotides, but not to identify and quantify incompletely deprotected oligonucleotides. To address this problem, monoclonal antibodies (MAbs), ELISA, and dot-blot assays were developed for the specific identification and quantification of the commonly used nucleic acid base- and sugar-protecting groups: benzoyl, isobutyryl, isopropylphenoxyacetyl, and dimethoxytrityl. Each MAb was capable of reproducibly detecting 8-32 pmol of the respectively protected nucleoside in an intact DNA or RNA sample composed of 320-640 nmol of the deprotected nucleoside. In a direct comparison, HPLC nucleoside composition analysis of enzyme-hydrolyzed DNA was limited to the detection of 2-5 nmol of protected nucleoside. Using the MAb dot-blot assay, 5 of 16 commercial DNA products obtained from eight different companies were found to have 1.0-5.2% of the benzoyl and isopropylphenoxyacetyl protecting groups remaining. Thus, MAbs selectively identify and quantify picomoles of remaining protecting groups on antisense therapeutics and oligonucleotide diagnostics.