Spinal cord stimulation as a tool for physiological research

The use of spinal cord stimulation for alleviation of disabilities due to motor neuron lesions has provided the opportunity to explore a new approach to measurement of spinal cord physiology. Externalized leads of epidural electrodes provide the possibility of recording evoked spinal cord activity, while both externalized or implanted leads can be used to study cortical evoked responses and twitches induced by spinal cord stimulation. The use of such electrophysiological techniques can be expected to expand greatly the applicability of the technique for alleviating motor disabilities, through a better definition of the degree, nature and extent of the lesion.     

Digestive enzymes present in crustacean feces as a tool for biochemical, physiological, and ecological studies

The effect of food composition on the digestive system of Penaeus vannamei shrimp was used to determine the suitability of feces for analysis of class, type, composition of digestive proteinases, and whether alterations in the digestive gland are mirrored in feces composition. Enzymes recovered from feces and the midgut gland of white shrimp P. vannamei were used for comparison purposes. Three groups of shrimp were assembled: two groups fed two different brands of commercial feeds (PI and SC) with different content of protein, and the last group fed 50% PI feed and 50% thawed giant squid. Composition of proteinases in the midgut gland and feces were identical, and trypsin and chymotrypsin paralogues were identified in both samples by substrate-electrophoresis. Total proteolytic, trypsin, and chymotrypsin enzyme activities were higher in both samples from organisms fed SC, than in the other two groups. In the hepatopancreas, trypsin activity was ∼30% higher in SC fed group. Final average weights of shrimp were close in three groups, but hepatopancreas weight was 20% higher in the SC group. The degree of protein hydrolysis (DH) in vitro for the SC and PI was evaluated by the pH-stat method, using enzymes from feces and hepatopancreas of each group. The DH of food was no different, but it was affected by enzyme source, hepatopancreas extract (HPE) or feces extract (FE). DH was always higher when FE was the enzyme source than when HPE was the source. The proposed methods for recovery of enzymes from shrimp feces can be applied to other crustaceans. Measurements were sufficiently sensitive to allow quantifying the effects of feed on digestion physiology and other ecological and physiological applications, without the necessity of killing specimens.     

Stem cells from human adipose tissue: a new tool for pharmacological studies and for clinical applications

Multipotent adult stem cells constitute an unlimited source of differentiated cells that could be used in pharmacological studies and in medicine. The presence of stem cells in different tissues, such as bone marrow, skin, muscle, has been reported. However, stem cells are rare in these tissues, are difficult to isolate and to maintain ex vivo. As adipose tissue allows extraction of a large volume of tissue with limited morbidity, this tissue could be an exciting alternative stem cell source. We have recently identified and isolated multipotent stem cells from adipose tissue of young donors. These cells, named human Multipotent Adipose-Derived Stem (hMADS) cells, exhibit features of stem cells, i.e. a high ability to self-renew and the capacity to differentiate in different lineages at the single cell level. The adipocyte differentiation of hMADS cells has been thoroughly studied and differentiated cells exhibit the unique characteristics of human adipocytes. The effects of HIV drugs on the development of hMADS cells into adipocytes will be discussed. Finally, the therapeutic potential of hMADS cells has been revealed after their transplantation into muscles of mdx mice, an animal model of Duchenne muscular dystrophy. Therefore, hMADS cells provides a powerful cellular model for drug screenings and their regenerative properties suggest that these cells could be an important tool for cell-mediated therapy.     

Retinal dopamine D1 and D2 receptors: Characterization by binding or pharmacological studies and physiological functions

1. In the retinal inner nuclear layer of the majority of species, a dopaminergic neuronal network has been visualized in either amacrine cells or the so-called interplexiform cells. 2. Binding studies of retinal dopamine receptors have revealed the existence of both D1- as well D2-subtypes. The D1-subtype was characterized by labeled SCH 23390 (Kd ranging from 0.175 to 1.6 nM and Bmax from 16 to 482 fmol/mg protein) and the D2-subtype by labelled spiroperidol (Kd ranging from 0.087 to 1.35 nM and Bmax from 12 to 1500 fmol/mg protein) and more selectively by iodosulpiride (Kd 0.6 nM and Bmax 82 fmol/mg protein) or methylspiperone (Kd 0.14 nM and Bmax 223 fmol/mg protein). 3. Retinal dopamine receptors have been also shown to be positively coupled with adenylate cyclase activity in most species, arguing for the existence of D1-subtype, whereas in some others (lower vertebrates and rats), a negative coupling (D2-subtype) has been also detected in peculiar pharmacological conditions implying various combinations of dopamine or a D2-agonist with a D1-antagonist or a D2-antagonist in the absence or presence of forskolin. 4. A subpopulation of autoreceptors of D2-subtype (probably not coupled to adenylate cyclase) also seems to be involved in the modulation of retinal dopamine synthesis and/or release. 5. Light/darkness conditions can affect the sensitivity of retinal dopamine D1 and/or D2-receptors, as studied in binding or pharmacological experiments (cAMP levels, dopamine synthesis, metabolism and release). 6. Visual function(s) of retinal dopamine receptors were connected with the regulation of electrical activity and communication (through gap junctions) between horizontal cells mediated by D1 and D2 receptor stimulation. Movements of photoreceptor cells and migration of melanin granules in retinal pigment epithelial cells as well as synthesis of melatonin in photoreceptors were on the other hand mediated by the stimulation of D2-receptors. 7. Other physiological functions of dopamine D1-receptors respectively in rabbit and in embryonic avian retina would imply the modulation of acetylcholine release and the inhibition of neuronal growth cones.     

Fourier transform infrared microspectroscopy as a new tool for nematode studies

We report the results of a microspectroscopy study on the Fourier transform infrared (FT-IR) absorption spectra of Caenorhabditis elegans, collected from the different parts of a single intact specimen--pharynx, intestine and tail regions. The principal absorption bands were assigned to the molecular species present in C. elegans, with an excellent reproducibility for the pharynx spectrum. These results enabled us to explore if FT-IR microspectroscopy could offer a new tool for nematode identification. As an example, the discrimination among four well characterised nematode taxa is reported. The FT-IR results completely match those obtained by Blaxter and colleagues through molecular biology [Nature 392 (1998) 71].     

Q-factor analysis as a tool for phylogenetic studies of morphometric data

The statistical procedure of Q-factor analysis was applied with the aim to detect complex morphological characters, which clearly separate taxonomic groups. Since Q-factor analysis, unlike cluster analysis, does not prescribe a hierarchical grouping, the results can be interpreted phylogenetically using an outgroup comparison. The essential steps of the approach are demonstrated by an empirical study on the phylogeny of Callitrichinae. Except for some complications concerning the determination of the number of relevant factors and factor rotation, the procedure proved to be a suitable instrument for phylogenetic research.     

In silico model as a tool for interpretation of intestinal infection studies

In nutrition research the number of human in vivo experiments is limited because of the many restrictions and the high costs of testing in humans. Up to now predictive computer models aiming to enhance research have been rare or too complex, with many nonmeasurable adjustable parameters. This study aimed to develop a basic physicochemical computer model for a first quantitative interpretation of results obtained from in vivo intestinal experiments with bacteria. This new modeling approach is validated with results obtained from gut infection studies in vivo. The design of the model is described, and its ability to reproduce experimental data is evaluated. The model predictions are compared with new experimental data. The phenomena that take place in the gastrointestinal tract are summarized by model constants for growth, adherence, and release of bacteria. Although the model is far from describing all details and many processes in the intestine are combined, the model calculation results lead to reasonable conclusions and interesting hypotheses. One of these hypotheses concluded from the model outcomes is that Escherichia coli bacteria have a much lower intestinal growth rate in humans than in rats. Extra laboratory validation experiments proved the reliability of this hypothesis predicted by the model. In addition, the known protective effect of dietary calcium and detrimental effect of clindamycin on the growth and adherence of Salmonella bacteria could be quantified. From these results it is clear that the model enhances the interpretation of in vivo gastrointestinal experiments and will facilitate research trajectories towards new functional foods that improve resistance to pathogenic bacteria in humans.     

Small angle X-ray scattering as a complementary tool for high-throughput structural studies

Structural crystallography and nuclear magnetic resonance (NMR) spectroscopy are the predominant techniques for understanding the biological world on a molecular level. Crystallography is constrained by the ability to form a crystal that diffracts well and NMR is constrained to smaller proteins. Although powerful techniques, they leave many soluble, purified structurally uncharacterized protein samples. Small angle X-ray scattering (SAXS) is a solution technique that provides data on the size and multiple conformations of a sample, and can be used to reconstruct a low-resolution molecular envelope of a macromolecule. In this study, SAXS has been used in a high-throughput manner on a subset of 28 proteins, where structural information is available from crystallographic and/or NMR techniques. These crystallographic and NMR structures were used to validate the accuracy of molecular envelopes reconstructed from SAXS data on a statistical level, to compare and highlight complementary structural information that SAXS provides, and to leverage biological information derived by crystallographers and spectroscopists from their structures. All the ab initio molecular envelopes calculated from the SAXS data agree well with the available structural information. SAXS is a powerful albeit low-resolution technique that can provide additional structural information in a high-throughput and complementary manner to improve the functional interpretation of high-resolution structures.     

Zebrafish xenografts as a tool for in vivo studies on human cancer

The zebrafish has become a powerful vertebrate model for genetic studies of embryonic development and organogenesis and increasingly for studies in cancer biology. Zebrafish facilitate the performance of reverse and forward genetic approaches, including mutagenesis and small molecule screens. Moreover, several studies report the feasibility of xenotransplanting human cells into zebrafish embryos and adult fish. This model provides a unique opportunity to monitor tumor-induced angiogenesis, invasiveness, and response to a range of treatments in vivo and in real time. Despite the high conservation of gene function between fish and humans, concern remains that potential differences in zebrafish tissue niches and/or missing microenvironmental cues could limit the relevance and translational utility of data obtained from zebrafish human cancer cell xenograft models. Here, we summarize current data on xenotransplantation of human cells into zebrafish, highlighting the advantages and limitations of this model in comparison to classical murine models of xenotransplantation.     

Chemostat cultivation as a tool for studies on sugar transport in yeasts.

Chemostat cultivation enables investigations into the effects of individual environmental parameters on sugar transport in yeasts. Various means are available to manipulate the specific rate of sugar uptake (qs) in sugar-limited chemostat cultures. A straightforward way to manipulate qs is variation of the dilution rate, which, in substrate-limited chemostat cultures, is equal to the specific growth rate. Alternatively, qs can be varied independently of the growth rate by mixed-substrate cultivation or by variation of the biomass yield on sugar. The latter can be achieved, for example, by addition of nonmetabolizable weak acids to the growth medium or by variation of the oxygen supply. Such controlled manipulation of metabolic fluxes cannot be achieved in batch cultures, in which various parameters that are essential for the kinetics of sugar transport cannot be controlled. In sugar-limited chemostat cultures, yeasts adapt their sugar transport systems to cope with the low residual sugar concentrations, which are often in the micromolar range. Under the conditions, yeasts with high-affinity proton symport carriers have a competitive advantage over yeasts that transport sugars via facilitated-diffusion carriers. Chemostat cultivation offers unique possibilities to study the energetic consequences of sugar transport in growing cells. For example, anaerobic, sugar-limited chemostat cultivation has been used to quantify the energy requirement for maltose-proton symport in Saccharomyces cerevisiae. Controlled variation of growth conditions in chemostat cultures can be used to study the differential expression of genes involved in sugar transport and as such can make an important contribution to the ongoing studies on the molecular biology of sugar transport in yeasts.     

BjalphaIT: a novel scorpion alpha-toxin selective for insects--unique pharmacological tool

Long-chain neurotoxins derived from the venom of the Buthidae scorpions, which affect voltage-gated sodium channels (VGSCs) can be subdivided according to their toxicity to insects into insect-selective excitatory and depressant toxins (beta-toxins) and the alpha-like toxins which affect both mammals and insects. In the present study by the aid of reverse-phase HPLC column chromatography, RT-PCR, cloning and various toxicity assays, a new insect selective toxin designated as BjalphaIT was isolated from the venom of the Judean Black Scorpion (Buthotus judaicus), and its full primary sequence was determined: MNYLVVICFALLLMTVVESGRDAYIADNLNCAYTCGSNSYCNTECTKNGAVSGYCQWLGKYGNACWCINLPDKVPIRIPGACR (leader sequence is underlined). Despite its lack of toxicity to mammals and potent toxicity to insects, BjalphaIT reveals an amino acid sequence and an inferred spatial arrangement that is characteristic of the well-known scorpion alpha-toxins highly toxic to mammals. BjalphaITs sharp distinction between insects and mammals was also revealed by its effect on sodium conductance of two cloned neuronal VGSCs heterloguously expressed in Xenopus laevis oocytes and assayed with the two-electrode voltage-clamp technique. BjalphaIT completely inhibits the inactivation process of the insect para/tipE VGSC at a concentration of 100 nM, in contrast to the rat brain Na(v)1.2/beta1 which is resistant to the toxin. The above categorical distinction between mammal and insect VGSCs exhibited by BjalphaIT enables its employment in the clarification of the molecular basis of the animal group specificity of scorpion venom derived neurotoxic polypeptides and voltage-gated sodium channels.     

Fish gut content from biological collections as a tool for long-term environmental impact studies

Most of the world’s fish fauna is suffering from different types of human impacts and new conservation tools are required. The fish diet analysis is a tool that has been used to evaluate degradation processes of aquatic environments, however, few long-term studies are performed by several reasons (e.g., lack of funding, opportunity). Our aim was to test whether the fish gut content from biological collections can be used for comparisons with current data and, consequently, be used as a tool for long-term environmental impact studies. We compared the gut content of fish preserved for fifteen years in a biological collection with recently sampled fish, considering the factors size of the specimen, preservation time and preservation form. We did not find differences in the gut content percentage of preservation between fish size classes and preservation time. However, we found differences between preservation form, in which the fish fixed in formalin kept the digestive content preserved while the fish preserved directly in alcohol did not. Thus, we encourage the use of fish gut content from biological collections fixed in formalin for long-term ecological studies. Our findings may help elucidate some long-term effects of human impacts on fish fauna.     

Reversible blockade of rodent whisking: Botulinum toxin as a tool for developmental studies

Studies of sensorimotor systems such as the whisking system of rodents have suggested that associations between body movements and their sensory consequences during development may make an important contribution to the functional organization of the system. In the present study we have explored the possible utility of Botulinum toxin for developmental studies of whisking. Botox selectively blocks whisking-generated afference leaving other sources of whisker afference intact. We describe appropriate modes of injection, define dosage levels, and assess the effects of prolonged whisking paralysis during development upon the basic motor competency of the adult rat. Our findings indicate that: (a) Botulinum toxin may be used to block whisking behavior in adult and developing rats, (b) that the duration of the whisking paralysis produced by Botox treatment blockade is dose dependent in both developing and adult animals, (c) that the blockade is functionally reversible and (d) that Botox treatment during development does not impair either the kinematics or the rhythmic patterning of adult whisking behavior. Botox may be a useful tool for studying the role of experiential factors in the development of "active touch" in rodents.     

Exploring whole genome amplification as a DNA recovery tool for molecular genetic studies.

The whole genome amplification (WGA) protocol evaluated during this study, GenomiPhi DNA amplification kit, is a novel method that is not based on polymerase chain reaction but rather relies on the highly processive and high fidelity Phi29 DNA polymerase to replicate linear genomic DNA by multiple strand displacement amplification. As little as 1 ng of genomic DNA template is sufficient to produce microgram quantities of high molecular weight DNA. The question explored during this study is whether such a WGA method is appropriate to reliably replenish and even recover depleted DNA samples that can be used for downstream genetic analysis. A series of human DNA samples was tested in our laboratory and validated using such analytical methods as gene-specific polymerase chain reaction, direct sequencing, microsatellite marker analysis, and single nucleotide polymorphism allelic discrimination using TaqMan and Pyrosequencing chemistries. Although degraded genomic DNA is not a good template for Phi29 WGA, this method is a powerful tool to replenish depleted DNA stocks and to increase the amount of sample for which biological tissue availability is scarce. The testing performed during the validation phase of the study indicates no discernable difference between WGA samples and the original DNA templates. Thus, GenomiPhi WGA can be used to increase precious or depleted DNA stocks, thereby extending the life of a family-based linkage analysis project and increasing statistical power.     

Long-term monitoring studies as a powerful tool in marine ecosystem research

The EU-funded research project WISER (“Water bodies in Europe: Integrative Systems to assess Ecological status and Recovery”) developed new assessment methods required by the EU Water Framework Directive (WFD) for lakes, coastal and transitional waters. WISER also addressed the recovery of biotic assemblages from degradation. The results are summarised in five key messages, supported by papers in this special issue and by WISER results published elsewhere: (1) Response to stress differs between organism groups, water types and stressors; a conceptual model is proposed summarising how the individual organism groups respond to different types of degradation in rivers, lakes, transitional and coastal waters. (2) The sources of uncertainty differ between BQEs and water types, leading to methodological suggestions on how to design WFD sampling programmes. (3) Results from about 300 current assessment methods indicate geographical variations in metrics but assessments are comparable at an aggregated level (“ecological status”). (4) Scale and time matter; restoration requires action at (sub)-basin levels and recovery may require decades. (5) Long-term trends require consideration; the effects of both degradation and restoration at the water body or river basin scales is increasingly superimposed by multiple stressors acting at large scales, in particular by climate change.     

Evaluation of laser microdissection as a tool in cancer glycomic studies

Laser microdissection (LMD) is a recent development that enables the isolation of specific cell populations from tissue sections. This study focuses on the potential of LMD as a tool in cancer glycomics using colon cancer as a model. LMD was performed on hematoxylin and eosin stained frozen tissue sections. Tumor cells and normal epithelial cells were selectively microdissected. N-Glycans from the LMD- and the bulk tissue-derived samples were liberated by hydrazinolysis and then labeled with 2-aminopyridine. After sialidase digestion, the resulting asialo-N-glycans were analyzed by normal and reversed phase HPLC combined with mass spectrometry. Comparison of the various N-glycan profiles with the aid of LMD identified seven characteristic N-glycans with significantly different expression profiles between normal and cancerous cells that could not be detected by conventional analysis. Thus, LMD is a potent and useful tool for analyzing variations in the expression of N-glycans by overcoming the problem of tissue sample heterogeneity.