Yeast as a model to study apoptosis?

Programmed cell death (PCD) serves as a major mechanism for the precise regulation of cell numbers, and as a defense mechanism to remove unwanted and potentially dangerous cells. Despite the striking heterogeneity of cell death induction pathways, the execution of the death program is often associated with characteristic morphological and biochemical changes termed apoptosis. Although for a long time the absence of mitochondrial changes was considered as a hallmark of apoptosis, mitochondria appear today as the central executioner of programmed cell death. This crucial position of mitochondria in programmed cell death control is not due to a simple loss of function (deficit in energy supplying), but rather to an active process in the regulation of effector mechanisms.The large diversity of regulators of apoptosis in mammals and their numerous interactions complicate the analysis of their individual functions. Yeast, eukaryotic but unicellular organism, lack the main regulators of apoptosis (caspases, Bcl-2 family members, . . .) found in mammals. This absence render them a powerful tool for heterologous expression, functional studies, and even cloning of new regulators of apoptosis.Great advances have thus been made in our understanding of the molecular mechanisms of Bcl-2 family members interactions with themselves and other cellular proteins, specially thanks to the two hybrid system and the easy manipulation of yeast (molecular biology and genetics).This review will focus on the use of yeast as a tool to identify new regulators and study function of mammalian apoptosis regulators.     

Salmonid fish: model organisms to study cardiovascular morphogenesis in conjoined twins?

Background

There is a gap in knowledge regarding the cardiovascular system in fish conjoined twins, and regarding the cardiovascular morphogenesis of conjoined twins in general. We examined the cardiovascular system in a pair of fully developed ventrally conjoined salmonid twins (45.5 g body weight), and the arrangement of the blood vessels during early development in ventrally conjoined yolk sac larvae salmonid twins (<0.5 g body weight).

Results

In the fully developed twins, one twin was normal, while the other was small and severely malformed. The mouth of the small twin was blocked, inhibiting respiration and feeding. Both twins had hearts, but these were connected through a common circulatory system. They were joined by the following blood vessels: (i) arteria iliaca running from arteria caudalis of the large twin to the kidney of the small twin; (ii) arteria subclavia running from aorta dorsalis of the large twin to aorta dorsalis of the small twin; (iii) vena hepatica running from the liver of the small twin into the sinus venosus of the large twin. Among the yolk sac larvae twins investigated, distinct vascular connections were found in some individuals through a joined v. vitellina hepatica.

Conclusions

Ventrally conjoined fish twins can develop cardiovascular connections during early development, enabling a normal superior twin to supply a malfunctioning twin with oxygen and nutrients. Since the yolk sac in salmonids is transparent, twinning in salmonids may be a useful model in which to study cardiovascular morphogenesis in conjoined twins.

     

The bleomycin animal model: a useful tool to investigate treatment options for idiopathic pulmonary fibrosis?

Different animal models of pulmonary fibrosis have been developed to investigate potential therapies for idiopathic pulmonary fibrosis (IPF). The most common is the bleomycin model in rodents (mouse, rat and hamster). Over the years, numerous agents have been shown to inhibit fibrosis in this model. However, to date none of these compounds are used in the clinical management of IPF and none has shown a comparable antifibrotic effect in humans. We performed a systematic review of publications on drug efficacy studies in the bleomycin model to evaluate the value of this model regarding transferability to clinical use. Between 1980 and 2006 we identified 240 experimental studies describing beneficial antifibrotic compounds in the bleomycin model. 222 of those used a preventive regimen (drug given < or =7 days after last bleomycin application), only 13 were therapeutic trials (>7 days after last bleomycin application). In 5 studies we did not find enough details about the timing of drug application to allow inter-study comparison. It is critical to distinguish between drugs interfering with the inflammatory and early fibrogenic response from those preventing progression of fibrosis, the latter likely much more meaningful for clinical application. All potential antifibrotic compounds should be evaluated in the phase of established fibrosis rather than in the early period of bleomycin-induced inflammation for assessment of its antifibrotic properties. Further care should be taken in extrapolation of drugs successfully tested in the bleomycin model due to partial reversibility of bleomycin-induced fibrosis over time. The use of alternative and more robust animal models, which better reflect human IPF, is warranted.     

Arabidopsis, a model to study biological functions of isoprene emission?

The volatile hemiterpene isoprene is emitted from plants and can affect atmospheric chemistry. Although recent studies indicate that isoprene can enhance thermotolerance or quench oxidative stress, the underlying physiological mechanisms are largely unknown. In this work, Arabidopsis (Arabidopsis thaliana), a natural nonemitter of isoprene and the model plant for functional plant analyses, has been constitutively transformed with the isoprene synthase gene (PcISPS) from Grey poplar (Populus x canescens). Overexpression of poplar ISPS in Arabidopsis resulted in isoprene-emitting rosettes that showed transiently enhanced growth rates compared to the wild type under moderate thermal stress. The findings that highest growth rates, higher dimethylallyl diphosphate levels, and enzyme activity were detected in young plants during their vegetative growth phase indicate that enhanced growth of transgenic plants under moderate thermal stress is due to introduced PcISPS. Dynamic gas-exchange studies applying transient cycles of heat stress to the wild type demonstrate clearly that the prime physiological role of isoprene formation in Arabidopsis is not to protect net assimilation from damage against thermal stress, but may instead be to retain the growth potential or coordinated vegetative development of the plant. Hence, this study demonstrates the enormous potential but also the pitfalls of transgenic Arabidopsis (or other nonnatural isoprenoid emitters) in studying isoprene biosynthesis and its biological function(s).     

Are fusion peptides a good model to study viral cell fusion?

Fusion peptides are hydrophobic and conserved sequences located within glycoprotein ectodomains that protrude from the virion surface. Direct participation of fusion peptides in the viral membrane fusion phenomenon has been inferred from genetic analyses showing that even a single residue substitution or a deletion within these sequences may completely block the process. However, the specific fusion peptide activities associated to the multi-step fusion mechanism are not well defined. Based on the assumption that fusion peptides are transferred into target membranes, biophysical methodologies have been applied to study integration into model membranes of synthetic fragments representing functional and non-functional sequences. From these studies, it is inferred that, following insertion, functional sequences generate target membrane perturbations and adopt specific structural arrangements within. Further characterization of these artificial systems may help in understanding the molecular processes that bring initial bilayer destabilizations to the eventual opening of a fusion pore.     

Are fusion peptides a good model to study viral cell fusion?

Fusion peptides are hydrophobic and conserved sequences located within glycoprotein ectodomains that protrude from the virion surface. Direct participation of fusion peptides in the viral membrane fusion phenomenon has been inferred from genetic analyses showing that even a single residue substitution or a deletion within these sequences may completely block the process. However, the specific fusion peptide activities associated to the multi-step fusion mechanism are not well defined. Based on the assumption that fusion peptides are transferred into target membranes, biophysical methodologies have been applied to study integration into model membranes of synthetic fragments representing functional and non-functional sequences. From these studies, it is inferred that, following insertion, functional sequences generate target membrane perturbations and adopt specific structural arrangements within. Further characterization of these artificial systems may help in understanding the molecular processes that bring initial bilayer destabilizations to the eventual opening of a fusion pore.     

Is the sheep a suitable model to study the mechanical alterations of disc degeneration in humans? A probabilistic finite element model study

Intervertebral disc degeneration is one major source of low back pain, which because of its complex multifactorial nature renders the treatment challenging and thus necessitates extensive research. Experimental animal models have proven valuable in improving our understanding of degenerative processes and potentially promising therapies. Currently, the sheep is the most frequently used large animal in vivo model in intervertebral disc research. However, despite its undoubted value for investigations of the complex biological and cellular aspects, to date, it is unclear whether the sheep is also suited to study the mechanical aspects of disc degeneration in humans.A parametric finite element (FE) model of the L4–5 spinal motion segment was developed. Using this model, the geometry and the material properties of both the human and the ovine spinal segment as well as different appearances of disc degeneration can be depicted. Under pure and combined loads, it was investigated whether degenerative changes to both the human and the ovine model equivalent caused the same mechanical response.Different patterns of degeneration resulted in large variations in the ranges of motion, intradiscal pressure, ligament and facet loads. In the human, but not in the ovine model, all these results differed significantly between different degrees of degeneration.This FE model study highlighted possible differences in the mechanical response to disc degeneration between human and ovine intervertebral discs and indicates the necessity of further, more detailed, investigations.     

Malondialdehyde in benign prostate hypertrophy: a useful marker?

Benign prostate hypertrophy (BPH) is the most common benign tumor in men due to obstruction of the urethra and, finally, uremia. Malondialdehyde (MDA) is a product derived from peroxidation of polyunsaturated fatty acids and related esters. Evaluation of MDA in serum represents a non-invasive biomarker of oxidative stress. Prostate-specific antigen (PSA) is a sensitive marker for prostatic hypertrophy and cancer. We analyzed MDA serum levels to evaluate the oxidative stress in BPH. To this end, 22 BPH patients and 22 healthy donors were enrolled. Data show an increase of MDA level in BPH patients and a positive correlation between PSA and MDA levels. In conclusion, we describe a previously unknown relationship between PSA and MDA as an index of inflammation and oxidative stress in BPH.     

Umbilical cord fibroblasts: Could they be considered as mesenchymal stem cells?

In cell therapy protocols, many tissues were proposed as a source of mesenchymal stem cells (MSC) isolation. So far, bone marrow (BM) has been presented as the main source of MSC despite the invasive isolation procedure related to this source. During the last years, the umbilical cord (UC) matrix was cited in different studies as a reliable source from which long term ex vivo proliferating fibroblasts were isolated but with contradictory data about their immunophenotype, gene expression profile, and differentiation potential. Hence, an interesting question emerged: Are cells isolated from cord matrix (UC-MSC) different from other MSCs? In this review, we will summarize different studies that isolated and characterized UC-MSC. Considering BM-MSC as gold standard, we will discuss if UC-MSC fulfill different criteria that define MSC, and what remain to be done in this issue.     

Protein microarrays: a chance to study microorganisms?

Within the last 5 years, protein microarrays have been developed and applied to multiple approaches: identification of protein–protein interactions or protein–small molecule interactions, cancer profiling, detection of microorganisms and toxins, and identification of antibodies due to allergens, autoantigens, and pathogens. Protein microarrays are small size (typically in the microscopy slide format) planar analytical devices with probes arranged in high density to provide the ability to screen several hundred to thousand known substrates (e.g., proteins, peptides, antibodies) simultaneously. Due to their small size, only minute amounts of spotted probes and analytes (e.g., serum) are needed; this is a particularly important feature, for these are limited or expensive. In this review, different types of protein microarrays are reviewed: protein microarrays (PMAs), with spotted proteins or peptides; antibody microarrays (AMAs), with spotted antibodies or antibody fragments (e.g., scFv); reverse phase protein microarrays (RPMAs), a special form of PMA where crude protein mixtures (e.g., cell lysates, fractions) are spotted; and nonprotein microarrays (NPMAs) where macromolecules other than proteins and nucleic acids (e.g., carbohydrates, monosaccharides, lipopolysaccharides) are spotted. In this study, exemplary experiments for all types of protein arrays are discussed wherever applicable with regard to investigations of microorganisms.     

Applying GPS to the study of primate ecology: A useful tool?

Data on the spatiotemporal distribution of resources can be collected and plotted using GPS (global positioning system) and GIS (geographical information system) technologies. By combining such data with information on foraging and ranging behavior of nonhuman primates, one can analyze the influence of resource distribution on social organization and group cohesion. We investigated the abilities of a three-channel GPS receiver to collect location data under varying canopy densities in both temperate and tropical forests. Eighty randomly selected points were sampled in a beech–maple forest in northeast Ohio, USA; 65 points also were sampled at several tropical forests in Costa Rica and Trinidad. At each point we attempted to obtain a GPS position fix; we also determined the speed of satellite acquisition and measured canopy density using a spherical densiometer. The ability to obtain a reading differed greatly between the two forest types (χ² = 53.79, P < 0.001). Ninety-seven percent of all attempts were successful in the temperate forest, whereas only a 34% acquisition rate was obtained in the tropical forests. Logistic regression showed that the probability of obtaining a reading in Neotropical forests was 75% but only when canopy cover was less than 20%. Thus, these minimal-channel GPS units may be of limited utility for behavioral ecologists working in closed-canopy Neotropical forests. Am. J. Primatol. 46:167–172, 1998. © 1998 Wiley-Liss, Inc.     

Adverse cardiac responses to alpha-lipoic acid in a rat-diabetic model: possible mechanisms?

Alpha-lipoic acid (ALA) is widely used as an antioxidant for the treatment of diabetes and its complications; however, the pro-oxidant potential of ALA has recently been reported. This study was designed to investigate whether ALA supplementation could have pro-oxidant effects on cardiac tissues in normal and diabetic rats. Diabetes was induced by a single dose of streptozotocin (STZ; 55 mg/kg (intraperitoneal). Diabetic and normal rats were treated with ALA (100 mg kg^?1 day^?1) for 45 days. ALA supplementation resulted in oxidative protein damage as evident by significant reduction in the cardiac levels of protein thiol in ALA-treated normal rats (P?<?0.01) together with a significant elevation (P?<?0.001) in the plasma levels of advanced oxidation protein products in ALA-treated normal rats and in ALA?+?STZ-diabetic rats compared with the normal control rats. Nicotinamide adenine dinucleotide phosphate (NADPH) oxidase has emerged as the major source of superoxide anion and enhanced oxidative damage in heart failure. ALA supplementation increased the myocardial immunoreactivity of p47phox subunit of NADPH oxidase in both normal nondiabetic and diabetic rats reflecting its pro-oxidant effect. Data showed that ALA supplementation failed to prevent cardiac complications in diabetic rats and led to cardiac toxicity in normal rats as indicated by pathological changes (cellular infiltration, fibrosis, and degeneration) and by the elevation of serum cardiac biomarkers compared with normal controls. The pro-oxidant effects of ALA suggest that careful selection of appropriate doses of ALA in reactive oxygen species-related diseases are critical.     

What is in a model?

After reading contradictory claims of model status for some insect species, we feel a brief discussion of the topic may be useful. Here, we document a few examples where clarity on model status seems to be lacking, briefly review work on widely recognized models, and offer criteria for including any given species as a model organism.     

Alfalfa infection model: is it a potential alternative for mouse pneumonia model to study pathogenesis of Stenotrophomonas maltophilia?

The objective of this study was to develop a new, inexpensive and simple plant model to study the virulence potential of Stenotrophomonas maltophilia. The alfalfa seedlings were visually monitored for disease symptoms till 7 days post infection with 10⁵ cfu/ml of five different strains (Sm1–Sm5) of S. maltophilia. Symptoms including yellowing of leaves, stunted roots, and brown necrotic regions on seedlings were considered as disease symptoms. Sm5 and Sm2 appeared to be most virulent in alfalfa infection model, whereas Sm3 and Sm4 were moderately virulent. Strain Sm1 was found to be weakly virulent. A comparison of alfalfa infection model was carried out with mouse pneumonia model to compare the virulence of different strains of S. maltophilia in both models. Although there was variability in the level of infection caused by different strains, in both models of study, strains Sm5 and Sm2 appeared to be most virulent and were able to cause a comparatively more severe infection. We conclude that both the models can be used to study the pathogenesis of S. maltophilia and to analyze the preliminary virulence potential of this bacterium. However, clearly, to study the virulence factors, a mouse pneumonia model would be desirable.     

Marine metapopulations: a useful concept?

We discuss the potential and limitations of the metapopulation concept in marine ecology. The usefulness of the concept in terrestrial ecology is neither based on its simplicity or generality nor on overwhelming empirical evidence. The usefulness is in the questions which are asked when the metapopulation concept is applied. These questions address spatial phenomena and processes on different spatial scales. They help in acknowledging that every population, be it terrestrial or marine, has a spatial organization. Understanding this spatial organization is also important for tackling specific applied problems, i.e. to avoid overexploitation of living marine resources or for configuring marine reserves. The 'openness' of coastal populations, whose larvae enter larval pools or which are holoplanktonic, is no reason for not asking the questions implied by the metapopulation concept. For marine ecology, the real problem is to delineate populations, which then may possibly correspond to the 'local populations' of metapopulations. Thus, the answer to the question in the title of this paper, whether 'marine metapopulation' is a useful concept, is 'yes', if the concept is considered a working hypotheses, if the concept is explicitly defined, and if the questions linked to the concept are clearly stated. Even if it eventually transpires that only very few marine metapopulations actually exist, marine ecology would still have gained some important new insights. Electronic Publication     

Biomass: Is it a useful tool in paleocommunity reconstruction?

In general, more of the biomass of the community is preserved than is its numerical abundance. Thus, the paleontologist, on the average, works with more of the community when biomass is used. Community characteristics such as taxon dominance and habitat proportions are at least as accurately derived from biomass as numerical abundance. The use of biomass is clearly more appropriate in describing energy flow and trophic proportions. Whenever possible, biomass should be used as a complement to numerical abundance in future paleoecologic reconstructions.     

Monoamines activate neuropeptide signaling cascades to modulate nociception in C. elegans: a useful model for the modulation of chronic pain?

Monoamines and neuropeptides interact to modulate key behaviors in most organisms. This review is focused on the interaction between octopamine (OA) and an array of neuropeptides in the inhibition of a simple, sensory-mediated aversive behavior in the C. elegans model system and describes the role of monoamines in the activation of global peptidergic signaling cascades. OA has been often considered the invertebrate counterpart of norepinephrine, and the review also highlights the similarities between OA inhibition in C. elegans and the noradrenergic modulation of pain in higher organisms.