Cranial MRI of small rodents using a clinical MR scanner

Increasing numbers of small animal models are in use in the field of neuroscience research. Magnetic resonance imaging (MRI) provides an excellent method for non-invasive imaging of the brain. Using three-dimensional (3D) MR sequences allows lesion volumetry, e.g. for the quantification of tumor size. Specialized small-bore animal MRI scanners are available for high-resolution MRI of small rodents' brain, but major drawbacks of this dedicated equipment are its high costs and thus its limited availability. Therefore, more and more research groups use clinical MR scanners for imaging small animal models. But to achieve a reasonable spatial resolution at an acceptable signal-to-noise ratio with these scanners, some requirements concerning sequence parameters have to be matched. Thus, the aim of this paper was to present in detail a method how to perform MRI of small rodents brain using a standard clinical 1.5 T scanner and clinically available radio frequency coils to keep material costs low and to circumvent the development of custom-made coils.     

Abdominal magnetic resonance imaging in small rodents using a clinical 1.5 T MR scanner

Because of superior soft-tissue contrast compared to other imaging techniques, non-invasive abdominal magnetic resonance imaging (MRI) is ideal for monitoring organ regeneration, tissue repair, cancer stage, and treatment effects in a wide variety of experimental animal models. Currently, sophisticated MR protocols, including technically demanding procedures for motion artefact compensation, achieve an MRI resolution limit of < 100 microm under ideal conditions. However, such a high spatial resolution is not required for most experimental rodent studies. This article describes both a detailed imaging protocol for MR data acquisition in a ubiquitously and commercially available 1.5 T MR unit and 3-dimensional volumetry of organs, tissue components, or tumors. Future developments in MR technology will allow in vivo investigation of physiological and pathological processes at the cellular and even the molecular levels. Experimental MRI is crucial for non-invasive monitoring of a broad range of biological processes and will further our general understanding of physiology and disease.     

Comparative respiratory system mechanics in rodents.

Because of the wide utilization of rodents as animal models in respiratory research and the limited data on measurements of respiratory input impedance (Zrs) in small animals, we measured Zrs between 0.25 and 9.125 Hz at different levels (0-7 hPa) of positive end-expiratory pressure (PEEP) in mice, rats, guinea pigs, and rabbits using a computer-controlled small-animal ventilator (Schuessler TF and Bates JHT, IEEE Trans Biomed Eng 42: 860-866, 1995). Zrs was fitted with a model, including a Newtonian resistance (R) and inertance in series with a constant-phase tissue compartment characterized by tissue damping (Gti) and elastance (Hti) parameters. Inertance was negligible in all cases. R, Gti, and Hti were normalized to body weight, yielding normalized R, Gti, and Hti (NHti), respectively. Normalized R tended to decrease slightly with PEEP and increased with animal size. Normalized Gti had a minimal dependence on PEEP. NHti decreased with increasing PEEP, reaching a minimum at approximately 5 hPa in all species except mice. NHti was also higher in mice and rabbits compared with guinea pigs and rats at low PEEPs, which we conclude is probably due to a relatively smaller air space volume in mice and rabbits. Our data also suggest that smaller rodents have proportionately wider airways than do larger animals. We conclude that a detailed, comparative study of respiratory system mechanics shows some evidence of structural differences among the lungs of various species but that, in general, rodent lungs obey scaling laws similar to those described in other species.     

A yardstick for measuring populations of small rodents

(1) Six-monthly trappings (summer and winter) were done between 1952 and 1969 of Wood mice (Apodemus sylvaticus) and Bank voles (Clethrionomys glareolus) in Wytham Woods, near Oxford. One hundred and fifty Longworth live traps were used on two 2-acre grids in oak-ash-sycamore woodland. (2) The traps were pre-baited for 48 hours and then set. The catch was examined on the evening of the same day and on the following morning. The total of animals caught during the 24 hours was used as an index to the actual numbers present. Animals retrapped in the morning (identified by a simple method of marking) were omitted from the total. (3) Between 1969 and 1972 the same procedure was used but trapping, evening and morning, was continued for 3-4more days until some 75–80% of the catch consisted of marked animals. (4) This enabled estimates to be made of the actual numbers of voles and mice present at each trapping and so to assess the proportion of the total present which was caught ring the first 24 hours. (5) These estimates were made by (Method la) a straight Lincoln Index, (Method lb) a Lincoln Index method as modified by Hayne (1949) and (Method 2) by Hayne's trap-out method. Over six trappings the estimates by these methods showed reasonable agreement. (6) Comparison of the index trapping (i.e. the numbers caught during the first 24 hours) with the estimates of the total numbers present showed that, on all occasions, more than half of the mice and voles present entered the traps during the first 24 hours. With Bank voles there was a tendency for about half of them to be trapped during this time during the winter and about three-quarters of them during the summer. (7) With Wood mice the figures are more variable but, again, never less than half were trapped during the first 24 hours and, on some occasions, nearly the whole of the population. (8) These results show that reasonably accurate estimates of the numbers of these rodents can be achieved within 3–4 days' trapping (estimates that can be cross-checked by different methods) by using a high density of traps (see (1) above). Furthermore, trapping for 24 hours only will always catch at least half of the population present and, on occasions, considerably more than half.     

Diffusion weighted imaging in small rodents using clinical MRI scanners

Diffusion weighted imaging (DWI) has emerged as a unique and powerful non-invasive magnetic resonance imaging (MRI) technique with a major potential impact on imaging-based diagnosis in a variety of clinical applications including oncology and tissue viability assessment. In light of increasing demand for applying this technique in preclinical investigations using small animals, we have explored the potentials of a clinical magnet for acquiring the DWI in rats and mice with either cerebral ischemia or solid tumors. Through technical adaptation and optimization, we have been able to perform a series of clinically relevant animal studies with conclusions based on DWI quantification. Focusing more on practical aspects and cross-referencing with the current literature, this paper is aimed to summarize our ongoing DWI studies on small rodents with stroke and tumors, and to provide protocols for researchers to replicate similar techniques in their own preclinical and clinical studies.     

A robust platform for chemical genomics in bacterial systems

While genetic perturbation has been the conventional route to probing bacterial systems, small molecules are showing great promise as probes for cellular complexity. Indeed, systematic investigations of chemical-genetic interactions can provide new insights into cell networks and are often starting points for understanding the mechanism of action of novel chemical probes. We have developed a robust and sensitive platform for chemical-genomic investigations in bacteria. The approach monitors colony volume kinetically using transmissive scanning measurements, enabling acquisition of growth rates and conventional endpoint measurements. We found that chemical-genomic profiles were highly sensitive to concentration, necessitating careful selection of compound concentrations. Roughly 20,000,000 data points were collected for 15 different antibiotics. While 1052 chemical-genetic interactions were identified using the conventional endpoint biomass approach, adding interactions in growth rate resulted in 1564 interactions, a 50–200% increase depending on the drug, with many genes uncharacterized or poorly annotated. The chemical-genetic interaction maps generated from these data reveal common genes likely involved in multidrug resistance. Additionally, the maps identified deletion backgrounds exhibiting class-specific potentiation, revealing conceivable targets for combination approaches to drug discovery. This open platform is highly amenable to kinetic screening of any arrayable strain collection, be it prokaryotic or eukaryotic.     

A tunable multivariable nonlinear robust observer for biological systems

This paper presents a robust nonlinear asymptotic observer with adjustable convergence rate with a great potential of applicability for biological systems in which the main state variables are difficult and expensive to measure or such measurements do not exist. This observer scheme is based on the classical asymptotic observer, which is modified to allow the tuning of the convergence rate. It is shown that the proposed observer provides fast and satisfactory estimates when facing load disturbances, system failures and parameter uncertainty while maintaining the excellent robustness and stability properties of the classical asymptotic observer. The implementation of the tunable observer is carried out by numerical simulations of a mathematical model of an anaerobic digestion process used for wastewater treatment. The key results are examined and further developed.     

Aerobic and anaerobic metabolism during activity in small rodents.

Analysis of oxygen consumption and lactic acid formation during five minutes of maximal activity by the rodents Microtus montanus (Cricetidae) and Dipodomys merriami (Hetermyidae) indicates that: (1) anaerobiosis provides approximately 10% of total energy utilized during the 5-minute activity period; (2) anaerobiosis may account for as much as one-third of total energy utilized during the first 30 seconds of activity. In addition, these data indicate at least one species of lizard may be capable of a higher total rate of metabolism during "burst" activity than are the rodents investigated here.     

A perturbed two-level model for exciton trapping in small photosynthetic systems.

The study of exciton trapping in photosynthetic systems provides significant information about migration kinetics within the light harvesting antenna (LHA) and the reaction center (RC). We discuss two random walk models for systems with weakly coupled pigments, with a focus on the application to small systems (10-40 pigments/RC). Details of the exciton transfer to and from the RC are taken into consideration, as well as migration within the LHA and quenching in the RC. The first model is obtained by adapting earlier local trap models for application to small systems. The exciton lifetime is approximated by the sum of three contributions related to migration in the LHA, trapping by the RC, and quenching within the RC. The second model is more suitable for small systems and regards the finite rate of migration within the LHA as a perturbation of the simplified model, where the LHA and the RC are each represented by a single pigment level. In this approximation, the exciton lifetime is the sum of a migration component and a single nonlinear expression for the trapping and quenching of the excitons. Numerical simulations demonstrate that both models provide accurate estimates of the exciton lifetime in the intermediate range of 20-50 sites/RC. In combination, they cover the entire range of very small to very large photosynthetic systems. Although initially intended for regular LHA lattices, the models can also be applied to less regular systems. This becomes essential as more details of the structure of these systems become available. Analysis with these models indicates that the excited state decay in LH1 is limited by the average rate at which excitons transfer to the RC from neighboring sites in the LHA. By comparing this to the average rate of transfer within the LHA, various structural models that have been proposed for the LH1 core antenna are discussed.     

A personal computer system for observation and analysis of copulatory behavior in small rodents

A personal computer system was developed for measuring values of copulatory behavior of small laboratory rodents. This system enabled us to get the analysis data of copulatory behavior of male rats as soon as possible after observation. This present system could be useful to measure other reproductive behavior of small rodents.     

Nonrebreathing valve system for small animal respiratory measurements.

Flow resistence, frequency response, and backflow characteristics of a nonrebreathing valve system applicable to measuring small animal respiratory volumes are described. Unidirectional valves, molded from liquid resin, were fitted into a modified Y tube for direct use on an endotracheal tube or face mask. Valve size and dead space volume can be scaled to fit several small animal species. In this system, valve resistance was 2.0 and 5.6 mm of water for steady flow rates of 0.5 and 3.0 1/min, respectively.     

A label-free optical technique for detecting small molecule interactions

A novel approach for the label-free detection of molecular interactions is presented in which a colorimetric resonant grating is used as a surface binding platform. The grating, when illuminated with white light, is designed to reflect only a single wavelength. When molecules are attached to the surface, the reflected wavelength (color) is shifted due to the change of the optical path of light that is coupled into the grating. By linking receptor molecules to the grating surface, complementary binding molecules can be detected without the use of any kind of fluorescent probe or radioactive label. The detection technique is capable of detecting the addition and removal of small molecules as they interact with receptor molecules on the sensor surface or enzymes in the solution surrounding the sensor. Two assays are presented to exemplify the detection of small molecule interactions with the biosensor. First, an avidin receptor layer is used to detect 244 Da biotin binding. Second, a protease assay is performed in which a 136 Da p-nitroanilide (pNA) moeity is cleaved from an immobilized substrate. Because the sensor structure can be embedded in the plastic surfaces of microtiter plates or the glass surfaces of microarray slides, it is expected that this technology will be most useful in applications where large numbers of biomolecular interactions are measured in parallel, particularly when molecular labels will alter or inhibit the functionality of the molecules under study. Screening of pharmaceutical compound libraries with protein targets, and microarray screening of protein-protein interactions for proteomics are examples of applications that require the sensitivity and throughput afforded by this approach.     

Towards ecologically based baiting strategies for rodents in agricultural systems

Rodents are a major pest in Australian agricultural systems where they periodically irrupt (outbreak) and cause serious damage to crops. These irruptions still occur despite extensive baiting campaigns. Most of the economic losses caused by rodents occur in cereal and oilseed crops, although significant damage occurs annually in both sugar cane and macadamia orchards. Currently, attempts to control rodent outbreaks rely heavily upon baiting with rodenticides. As these are normally applied in an emergency situation and without adequate scientific insight or planning, they are usually not cost effective. We present strategies aimed at reducing agricultural losses in the event of an outbreak that take into consideration important population processes such as: (a) the stage of development of the rodent population; (b) the likely course of population trends given prevailing environmental conditions; (c) the spatial relationship between the available habitat types; (d) the role of refuge areas in seeding adjacent areas and sustaining a high population in the absence of a crop habitat type; (e) the likely dispersal strategy of the population given the landscape of the area; (f) the consequences of dispersal into areas that do not yet sustain a high population, and for crops that will be harvested late in the season. A process, presented in the form of a flow diagram, has been developed to tailor rodent control programs to specific outbreak conditions. Initially, the extent of a reported rodent problem and the scope of a control program are determined. Where a control program is required, this is developed for each region individually and is based on results of extensive population and crop surveys. Bait application rates are specifically determined for each rodent outbreak, reducing the probability of under- or over-baiting. Two baiting strategies have been developed for inclusion into the control program, a protection strategy and a control strategy. The former is designed to frustrate responsive dispersal into crops at harvest, whilst the latter will reduce numbers and maintain them at a low level until harvest. The procedure is reiterated for as long as the problem persists allowing control procedures to be modified as population and crop changes occur. Using Australian examples to illustrate the ecological concepts underpinning rodent management in an emergency situation, the control processes outlined will have universal application in the management of rodent outbreaks in agricultural systems.