Immunity to systemic Salmonella infections

Salmonella infections are a serious public health problem in developing countries and represent a constant concern for the food industry. The severity and the outcome of a systemic Salmonella infection depends on the "virulence" of the bacteria, on the infectious dose as well as on the genetic makeup and immunological status of the host. The control of bacterial growth in the reticuloendothelial system (RES) in the early phases of a Salmonella infection relies on the NADPH oxidase-dependent anti-microbial functions of resident phagocytes and is controlled by the innate resistance gene Nramp1. This early phase is followed by the suppression of Salmonella growth in the RES due to the onset of an adaptive host response. This response relies on the concerted action of a number of cytokines (TNFalpha, IFNgamma, IL12, IL18, and IL15), on the recruitment of inflammatory phagocytes in the tissues and on the activation of the recruited cells. Phagocytes control bacterial growth in this phase of the infection by producing reactive nitrogen intermediates (RNI) generated via the inducible nitric oxide synthase (iNOS). Clearance of the bacteria from the RES at a later stage of the infection requires the CD28-dependent activation of CD4+ TCR-alphabeta T-cells and is controlled by MHC class II genes. Resistance to re-infection with virulent Salmonella micro-organisms requires the presence of Th1 type immunological memory and anti-Salmonella antibodies. Thus, the development of protective immunity to Salmonella infections relies on the cross-talk between the humoral and cellular branches of the immune system.     

Glycolipids from a colloid chemical point of view

Glycolipids are a group of compounds with a broad range of applications. Two types of glycolipids (alkylpolyglycosides and gangliosides) were examined with regard to their physicochemical properties. Despite their structural differences, they have in common that they are amphiphilic molecules and able to aggregate to form monolayers, bilayers, micelles, lyothropic mesophases or vesicles. The structures of glycolipid micelles were investigated by different experimental techniques in addition to molecular dynamic simulations. The knowledge of the physicochemical properties of gangliosides enables a better understanding of their biological functions. Structural features were obtained for the monosialogangliosides GM1, GM2 and GT1b from bovine brain by means of mass spectrometry. Further the aggregation behaviour was determined by small-angle neutron and dynamic light scattering experiments. Interaction studies of these compounds were carried out by means of surface plasmon resonance using gangliosides incorporated liposomes. They were used as model membranes that interact with the lectins WGA, RCA and HPA. The interaction of lectins immobilized to a modified silicon surface was investigated by in-situ ellipsometry.     

Non-syndromic X-linked mental retardation: from a molecular to a clinical point of view

This review focuses on the 19 identified genes involved in X-linked "non-syndromic" mental retardation (MR) and defines the signaling pathways in which they are involved, focusing on emerging common mechanisms. The majority of proteins are involved in three distinct pathways: (1) Rho GTPases pathway modulating neuronal differentiation and synaptic plasticity; (2) Rab GTPases pathway regulating synaptic vesicle cycling; (3) gene expression regulation. The function of four proteins (ACSL4, AT2, SLC6A8, and SAP102) could not be reconciled to a common pathway. From a clinical point of view, the review discusses whether some common dysmorphic features can be identified even in non-syndromic MR patients and whether it is correct to maintain the distinction between "non-syndromic" and "syndromic" MR.     

Hydrodynamics of larval settlement from a larva's point of view

Many benthic marine invertebrate animals release larvae that are dispersed by ocean currents. These larvae swim and can respond to environmental factors such as chemical cues. However, larvae are so small (generally 0.01-1 mm) that they are often assumed to be passive particles whose trajectories are determined by the motion of the water in which they are riding. Therefore, marine larvae are useful model organisms to study the more general question of how the locomotion of very small animals in complex, variable natural habitats is affected by the motion of the fluid (water or air) around them. Studying larval locomotion under conditions of water flow encountered in nature is challenging because measuring the behavior of an individual microscopic organism requires high magnification imaging that is difficult to do in the field. The purpose of this article is to synthesize in one place the various approaches that we have been using to address the technical challenges of studying the locomotion of microscopic larvae in realistic ambient flow. The steps in our process include: (1) measuring water flow in the field; (2) mimicking realistic water movement in laboratory flumes to measure larval scale fluctuations in velocity of flow and concentration of chemical cues; (3) mimicking fine scale temporal patterns of larval encounters with a dissolved chemical cue to record larval responses; (4) using individual-based models to put larvae back into the larger scale environmental flow to determine trajectories; and (5) mimicking fine scale spatial and temporal patterns of larval encounters with water velocities and shear to determine the instantaneous forces on larvae. We illustrate these techniques using examples from our ongoing research on the settlement of larvae onto fouling communities and from our published work on settlement of larvae onto coral reefs. These examples show that water velocities and concentrations of chemical cues encountered by microscopic organisms can fluctuate in fractions of a second and vary over scales of less than a millimeter.     

Animal models of NAFLD from a hepatologist's point of view

Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disorder closely linked to obesity, hyperlipidemia and type 2 diabetes and is increasingly recognized as a major health problem in many parts of the world. While early stages of NAFLD are characterized by a bland accumulation of fat (steatosis) in hepatocytes, the disease can progress to non-alcoholic steatohepatitis (NASH) which involves chronic liver inflammation, tissue damage and fibrosis and can ultimately lead to end-stage liver disease including cirrhosis and cancer. As no approved pharmacological treatment for NAFLD exists today, there is an urgent need to identify promising pharmacological targets and develop future therapies. For this purpose, basic and translational research in NAFLD animal models is indispensable. While a large number of diverse animal models are currently used in the field, there is an ongoing challenge to identify those models that mirror human pathology the closest to allow good translation of obtained results into further clinical development. This review is meant to provide a concise overview of the most relevant NAFLD animal models currently available and will discuss the strengths and weaknesses of these models with regard to their comparability to human disease conditions.     

Latent class model diagnosis from a frequentist point of view

This is in response to Garrett and Zeger (2000, Biometrics 56, 1055-1067) who, within the Bayesian framework, developed mainly graphical methods for latent class model diagnosis. Possible problems with this approach, and with its application to both generated and empirical data, are pointed out. The impact of the proposed tools cannot be understood by their reader, as no comparisons are made to results obtainable using established methods for latent class model diagnosis; this applies especially to overall goodness-of-fit tests, for which alternatives (bootstrap, Rudas-Clogg-Lindsay index of fit) are mentioned. Further, in one case of generated data, the methods proposed by Garrett and Zeger seem to give problematic results as to identifiability; in the case of the empirical data on major depression, they lead to accepting a suboptimal three-class model. In the latter case, one can be rather sure that an identifiable, well-fitting latent class model could have been identified--if Garrett and Zeger had also considered restricted latent class models.     

Sparse canonical correlation analysis from a predictive point of view

Canonical correlation analysis (CCA) describes the associations between two sets of variables by maximizing the correlation between linear combinations of the variables in each dataset. However, in high‐dimensional settings where the number of variables exceeds the sample size or when the variables are highly correlated, traditional CCA is no longer appropriate. This paper proposes a method for sparse CCA. Sparse estimation produces linear combinations of only a subset of variables from each dataset, thereby increasing the interpretability of the canonical variates. We consider the CCA problem from a predictive point of view and recast it into a regression framework. By combining an alternating regression approach together with a lasso penalty, we induce sparsity in the canonical vectors. We compare the performance with other sparse CCA techniques in different simulation settings and illustrate its usefulness on a genomic dataset.     

Genetic code from tRNA point of view

The possible codon-anticodon pairings follow the standard genetic code, yet in a different mode. The corresponding rules for decoding sequence of the codons in mRNA with tRNA may be called "tRNA code". In this paper we analyse the mutational and translational stability of such tRNA code. Our approach is based on the model of "ambiguous intermediate" and on the study of underlying block structure and Eulerean graph technique. It is shown that the wobble rules and the reduced number of tRNA anticodons strongly affect the mutational and translational stability of the code. The selection of tRNA anticodons, besides the optimization of translation, also ensures the more reliable start and, to a lesser extent, the stop of translation. The attribution of tRNA anticodons to the groups [WWW, WWS, SWW, SWS] and [SSS, SSW, WSS, WSW] as well as [MMM, MMK, KMM, KMK] and [KKK, KKM, MKK, MKM] clearly correlates with class I and class II aminoacyl-tRNA synthetases and obeys the principle of the optimal coding in both cases. Both W-S and M-K groupings also refer to the encoding of amino acids with the large and small side-chain volumes, which may provide such an attribution. The higher variability of tRNA code agrees with the suggestions that the variations in an assignment of tRNA anticodons may serve as the driving force generating the different variants of the genetic code.     

Immunity to Intracellular Salmonella Depends on Surface-associated Antigens

Invasive Salmonella infection is an important health problem that is worsening because of rising antimicrobial resistance and changing Salmonella serovar spectrum. Novel vaccines with broad serovar coverage are needed, but suitable protective antigens remain largely unknown. Here, we tested 37 broadly conserved Salmonella antigens in a mouse typhoid fever model, and identified antigen candidates that conferred partial protection against lethal disease. Antigen properties such as high in vivo abundance or immunodominance in convalescent individuals were not required for protectivity, but all promising antigen candidates were associated with the Salmonella surface. Surprisingly, this was not due to superior immunogenicity of surface antigens compared to internal antigens as had been suggested by previous studies and novel findings for CD4 T cell responses to model antigens. Confocal microscopy of infected tissues revealed that many live Salmonella resided alone in infected host macrophages with no damaged Salmonella releasing internal antigens in their vicinity. In the absence of accessible internal antigens, detection of these infected cells might require CD4 T cell recognition of Salmonella surface-associated antigens that could be processed and presented even from intact Salmonella. In conclusion, our findings might pave the way for development of an efficacious Salmonella vaccine with broad serovar coverage, and suggest a similar crucial role of surface antigens for immunity to both extracellular and intracellular pathogens.     

Uncoupling proteins: the issues from a biochemist point of view

The functional characteristics of uncoupling proteins (UCP) are reviewed, with the main focus on the results with isolated and reconstituted proteins. UCP1 from brown adipose tissue, the paradigm of the UCP subfamily, is treated in more detail. The issues addressed are the role and mechanism of fatty acids, the nucleotide binding, the regulation by pH and the identification by mutagenesis of residues involved in these functions. The transport and regulatory functions of UCP2 and 3 are reviewed in comparison to UCP1. The inconsistencies of a proposed nucleotide insensitive H(+) transport by these UCPs as concluded from the expression in yeast and Escherichia coli are elucidated. In both expression system UCP 2 and 3 are not in or cannot be converted to a functionally native state and thus also for these UCPs a nucleotide regulated H (+) transport is postulated.     

Disease from the point of view of evolution

In the process of evolution, such compensatory reactions as enhanced absorption of sodium chloride and an increase of arterial pressure could be formed only for compensation of acute pathological states (blood loss, dehydration). At present they remain similarly adequate in acute disturbances of blood circulation and of water-electrolyte balance. However, in severe chronic pathology of heart and kidney they often lose their compensatory function and even become dangerous. Evolution of man and of human society has created novel social conditions of adaptation. They are of humanitarian and technogenic character by promoting prevention and treatment of diseases.