Expanding our scientific horizons: utilization of unique model organisms in biological research

During the past century, research studies using animal models have contributed to numerous scientific discoveries and have been vital for the understanding of numerous biological processes, including disease. Over the past decades, the scientific community has defined a small number of model organisms that includes a few mammals, fish (mainly zebrafish), birds (mainly chicken), frogs, flies, and nematodes. Rodents are by far the most commonly employed laboratory animals in biomedical research. Mice share many biological similarities to humans and can be genetically manipulated to express mutations linked to human diseases. Mice and rats reproduce relatively quickly and have a short life span, which allows scientists to study progressive disorders, including aging. A large range of inbred mice strains enables accurate and reproducible experiments by decreasing the variability often associated with animal models and biological systems in general. Finally, mice are cost‐effective, small, and relatively easy to handle, transport, and house. All of these advantages combine to make mice the major species for recapitulating and studying human diseases. However, focusing exclusively on one or very few animal models may lead researchers to lose sight of other species with vastly different biology that might inform and affect our understanding of disease pathogenesis.     

Redox control bioreactor: a unique biological water processor

The redox control bioreactor (RCB) is a new hollow fiber membrane bioreactor (HFMBR) design in which oxygen and hydrogen gases are provided simultaneously through separate arrays of juxtaposed hollow fiber (HF) membranes. This study applied the RCB for completely autotrophic conversion of ammonia to N(2) through nitrification with O(2) and denitrification using hydrogen as an electron donor (i.e., autohydrogentrophic denitrification). The hypothesis of this research was that efficient biofilm utilization of O(2) and H(2) at respective HFs would limit transport of these gases to bulk fluid, thereby enabling completely autotrophic ammonia conversion to N(2) through the co-occurrence of ammonia oxidation (O(2)-HF biofilms) and autohydrogenotrophic denitrification (H(2)-HF biofilms). A prototype RCB was fabricated and operated for 215 days on a synthetic, organic-free feedstream containing 217 mg L(-1) NH(4)(+)-N. When O(2) and H(2) were simultaneously supplied, the RCB achieved a steady NH(4)(+)-N removal flux of 5.8 g m(-2) day(-1) normalized to O(2)-HF surface area with a concomitant removal flux of 4.4 g m(-2) day(-1) (NO(3)(-))+NO(2)(-))-N based on H(2)-HF surface area. The significance of H(2) supply was confirmed by an increase in effluent NO(3)(-)-N when H(2) supply was discontinued and a decline in NO(3)(-)-N when H(2) supply was restarted. Increases in H(2) pressure caused decreased ammonia utilization, suggesting that excess H(2) interfered with nitrification. Microprobe profiling across radial transects revealed significant gradients in dissolved O(2) on spatial scales of 1 mm or less. Physiological and molecular analysis of biofilms confirmed that structurally and functionally distinct biofilms developed on adjacent, juxtaposed fibers.     

Structure for energy cycle: a unique status of the second law of thermodynamics for living systems

Distinguishing things from beings, or matters from lives, is a fundamental question. Extending E. Schr?dinger's neg-entropy and I. Prigogine's dissipative structure, we propose a chemical kinetic view that the earliest "live" process is embedded essentially in a special interaction between a pair of specific components under a particular, corresponding environmental conditions. The interaction exists as an inter-molecular-force-bond complex(IMFBC) that couples two separate chemical processes: one is the spontaneous formation of the IMFBC driven by a decrease of Gibbs free energy as a dissipative process; while the other is the disassembly of the IMFBC driven thermodynamically by free energy input from the environment. The two chemical processes coupled by the IMFBC originated independently and were considered non-living on Earth, but the IMFBC coupling of the two can be considered as the earliest form of metabolism: the first landmark on the path from things to a being. The dynamic formation and disassembly of the IMFBC, as a composite individual, follows a principle designated as "… structure for energy for structure for energy…", the cycle continues; and for short it will be referred to as "structure for energy cycle". With additional features derived from this starting point, the IMFBC-centered "live" process spontaneously evolved into more complex living organisms with the characteristics currently known.     

Design of a description language for generating wrapper to collect biological data

The biological data are scattered in various areas with various formats and they are changing continuously. Therefore, data integration becomes an important issue to provide researcher a dynamic access of data. In the data integration process, the method of extracting heterogeneous data dynamically from the data source is an essential part. Data extraction method using wrapper can provide flexibility and extensibility to an integration system.     

Panorama Ab Microarray Cell Signaling kit: a unique tool for protein expression analysis

Antibody arrays are a promising new tool for mass analysis of protein level changes in cells responding to different stimuli. Here we describe a novel antibody array system called Panorama Ab Microarray Cell Signaling, that contains 224 antibodies spotted on FAST nitrocellulose-coated slides that can detect protein levels as low as a few nanograms per mL. The antibodies spotted are specific for proteins important in various areas of cell signaling such as phosphorylation, cell cycle, apoptosis, nuclear signaling and cytoskeleton proteins. Furthermore, for some of the protein targes, the Panorama Ab Microarray can detect phosphorylated and nonphosphorylated forms of the traget protein. We found that treatment of the slides post-spotting is important for the array performance (ratio of signal to background) and its stability. Panorama Ab Microarray was used to analyze changes in protein expression in F9 embryonic carcinoma cells stimulated to differentiate by all-trans retinoic acid. We found that the level of several proteins, among them cell cycle regulators and kineases, was either up- or down-regulated. For more than ten protein targets, the results obtained by the Panorama Ab Microarray were confirmed by immunoblotting.     

Bio-electrosprays: a novel electrified jetting methodology for the safe handling and deployment of primary living organisms

Electrohydrodynamic jetting (EHDJ) which is also known as electrosprays (ES) has recently been elucidated as a unique electrified biotechnique for the safe handling and deployment of living organisms. This high intensity electric field driven jetting methodology is now referred to as "bioelectrosprays" (BES). Previously these charged jets have only been shown to jet-process immortalized cells which have undergone expected cellular behavior when compared with control cells. In this paper we demonstrate the ability to jet process primary living organisms in the stable conejetting mode. Finally the viability of the bio-electrosprayed living organisms has been assessed employing a flow cytometry approach which forms the discussion in this paper. Our findings further establish BES as a competing biotechnique, which could be employed for the deposition of primary living organisms according to a predetermined active cellular architecture. One day this could be used for the fabrication of viable tissues and organs for repair or replacement. These advanced studies carried out on BES have direct widespread applications ranging from developmental biology to regenerative and therapeutic medicine, which are a few amongst several other areas of study within the life sciences.     

BODIPY-cholesterol: a new tool to visualize sterol trafficking in living cells and organisms

Analysis of sterol distribution and transport in living cells has been hampered by the lack of bright, photostable fluorescent sterol derivatives that closely resemble cholesterol. In this study, we employed atomistic simulations and experiments to characterize a cholesterol compound with fluorescent boron dipyrromethene difluoride linked to sterol carbon-24 (BODIPY-cholesterol). This probe packed in the membrane and behaved similarly to cholesterol both in normal and in cholesterol-storage disease cells and with trace amounts allowed the visualization of sterol movement in living systems. Upon injection into the yolk sac, BODIPY-cholesterol did not disturb zebrafish development and was targeted to sterol-enriched brain regions in live fish. We conclude that this new probe closely mimics the membrane partitioning and trafficking of cholesterol and, because of its excellent fluorescent properties, enables the direct monitoring of sterol movement by time-lapse imaging using trace amounts of the probe. This is, to our knowledge, the first cholesterol probe that fulfills these prerequisites.     

Characterizing biological aerosol in a chamber: an approach to estimation of viable organisms in a single biological particle

There are practical and valid reasons topresent biological field trial referenceresults as agent containing particles per literof air (ACPLA). However, workers in biologicalaerosol research have a need to know how manyviable individual organisms are contained in asingle particle of a given diameter. Anecdotalevidence may exist suggesting that the task hasbeen accomplished but without a way toreplicate the measurements, it is difficult toaccept unsubstantiated claims. It is verydifficult to declare a finite number thatsatisfies all the experimental requirements, asthe problem is a statistical probability issue. This paper describes a method for estimatingthe number with practical instructions forreplicating the work in other laboratories.The test aerosol was contained in a 90 m³chamber at concentrations as low as 5 ACPLA. Amodified version of slit sampler collectedviable particles. A statistical method was usedto demonstrate sampling predictability at 95%confidence level. By using glass fiber filtersmounted in a dichotomous sampler, samplingefficiencies were estimated for a variety ofcommon aerosol collectors. The accumulated datapermitted the estimation of the number ofviable spores per particle. For a 2.5 to4 µm particle, arguments have beenpresented for considering 4.5 as the mostprobable ACPLA value.     

Organismic sets: Outline of a general theory of biological and social organisms

The discussion as to whether societies are organisms andvice versa has been going on for a long time. The question is meaningless unless a clear definition of the term “organism” is made. Once such a definition is made, the question may be answered by studying whether there exists any relational isomorphism between what the biologist calls an organism and what the sociologist calls society. Such a study should also include animal societies studied by ecologists. Both human and animal societies are sets of individuals together with certain other objects which are the products of their activities. A multicellular organism is a set of cells together with some products of their activities. A cell itself may be regarded as a set of genes together with the products of their activities because every component of the cell is either directly or indirectly the result of the activities of the genes. Thus it is natural to define both biological and social organisms as special kinds of sets. A number of definitions are given in this paper which define what we call here organismic sets. Postulates are introduced which characterize such sets, and a number of conclusions are drawn. It is shown that an organismic set, as defined here, does represent some basic relational aspects of both biological organisms and societies. In particular a clarification and a sharpening of the Postulate of Relational Forces given previously (Bull. Math. Biophysics,28, 283–308, 1966) is presented. It is shown that from the basic definitions and postulates of the theory of organismic sets, it folows that only such elements of those sets will aggregate spontaneously, which are not completely “specialized” in the performance of only one activity. It is further shown that such “non-specialized” elements undergo a process of specialization, and as a result of it their spontaneous aggregation into organismic sets becomes impossible. This throws light on the problem of the origin of life on Earth and the present absence of the appearance of life by spontaneous generation. Some applications to problems of ontogenesis and philogenesis are made. Finally the relation between physics, biology, and sociology is discussed in the light of the theory of organismic sets.     

Direct observation of single MuB polymers: evidence for a DNA-dependent conformational change for generating an active target complex

MuB, an ATP-dependent DNA binding protein, is critical for selection of target sites on the host chromosome during Mu transposition. We have developed a system for observing the behavior of single MuB polymers bound to an immobilized molecule of DNA. We show that the individual polymers display a broad distribution of disassembly rates and exhibit regional variations in DNA binding. Additionally, ATP hydrolysis was obligatorily coupled to dissociation of MuB subunits from the DNA during polymer disassembly. We propose a model in which the formation of an active target complex is mediated by a conformational change within the MuB polymer that is influenced by the sequence of the DNA.     

Cell recognition and adhesiveness: a possible biological role for the sulfated mucopolysaccharides.

The sulfated mucopolysaccharide composition of different neonate, adult and tumoral tissues is reported. It is shown that each tissue has a characteristic composition with respect to the relative amount, type and molecular size of chondroitin sulfate $\text{A}\text{C}$, chondroitin sulfate B and heparitin sulfate. Neonate and tumor tissues contain large amounts of chondrotin sulfate $\text{A}\text{C}$ which is nearly absent in most adult and normal tissues respectively. Based on these and other results a possible role for the sulfated mucopolysaccharides in cell recognition and adhesiveness is proposed.     

Experimental evolution and the Krogh principle: generating biological novelty for functional and genetic analyses

August Krogh counseled the careful selection of the best subject organism on which to undertake mechanistic physiological research. But what if an organism with the desired properties does not exist? It is now within our power to engineer organisms genetically to achieve novel combinations of traits. I propose that it is a logical extension of the Krogh principle that we use biological methodologies to create novel organisms ideally suited for particular physiological studies. Transgenics may first come to mind as the method for such transformations, but here I suggest that an alternative and complementary technique for generating biological novelty is experimental evolution. The latter has several advantages, including modification of multiple characters in one experiment, the production of advantageous traits, the testing of evolutionary hypotheses, and the identification of previously unsuspected factors involved in adaptation. Three experiments are reviewed, each of which examined the evolution of different physiological characters in different environments and organisms: locomotor performance in mice, desiccation tolerance in fruit flies, and high temperature adaptation in bacteria. While diverse in experimental type and subject, all resulted in the successful production of new variants with enhanced function in their new environments. Each experiment successfully tested hypotheses concerning physiological evolution, and in each case, unanticipated results emerged, which suggests previously unsuspected adaptive pathways and mechanisms. In addition, replicate populations in each experiment adjusted to their common environments by several different means, which indicates that physiological evolution may follow diverse stochastic pathways during adaptation. Experimental evolution can be a valuable method to produce and investigate new physiological variants and traits. The choice of experimental subjects, according to the Krogh principle, is no longer limited to currently existing organisms but is open to our imaginations and our ingenuity.     

Imaging of light emission from the expression of luciferases in living cells and organisms: a review

Luciferases are enzymes that emit light in the presence of oxygen and a substrate (luciferin) and which have been used for real‐time, low‐light imaging of gene expression in cell cultures, individual cells, whole organisms, and transgenic organisms. Such luciferin–luciferase systems include, among others, the bacterial lux genes of terrestrial Photorhabdus luminescens and marine Vibrio harveyi bacteria, as well as eukaryotic luciferase luc and ruc genes from firefly species (Photinus) and the sea panzy (Renilla reniformis), respectively. In various vectors and in fusion constructs with other gene products such as green fluorescence protein (GFP; from the jellyfish Aequorea), luciferases have served as reporters in a number of promoter search and targeted gene expression experiments over the last two decades. Luciferase imaging has also been used to trace bacterial and viral infection in vivo and to visualize the proliferation of tumour cells in animal models. Copyright © 2002 John Wiley & Sons, Ltd.