Exposure of the promonocytic cell line THP-1 to Escherichia coli induces IFN-gamma-inducible lysosomal thiol reductase expression by inflammatory cytokines

IFN-gamma-inducible lysosomal thiol reductase (GILT), which plays a role in MHC class II-restricted processing and presentation of Ags containing disulfide bonds, can be induced in various cell types by the cytokine IFN-gamma. APCs, including circulating macrophages, constitutively express high levels of GILT, although the pathways regulating its expression in these cells have not been characterized. In this study, we used the promonocytic cell line THP-1, an established model for monocyte to macrophage differentiation, to investigate the induction of GILT upon exposure to bacteria. We show that contact with LPS or intact Escherichia coli causes THP-1 cells to undergo programmed differentiation, characterized by adhesion, cytokine secretion, and up-regulation of Ag processing and presentation components, including GILT. Unlike GILT induction in response to IFN-gamma treatment, induction by bacteria is dependent on new protein synthesis, NF-kappaB signaling, and secretion of the inflammatory cytokines TNF and IL-1beta. Furthermore, we show that both cytokines are sufficient for GILT induction in the absence of a microbial stimulus. The majority of GILT synthesized by differentiated THP-1 cells is secreted as the precursor form rather than being transported to, and maturing in, lysosomes, suggesting a novel role for GILT in cells of the macrophage lineage.     

The Src homology 2 domain-containing leukocyte protein of 76-kDa adaptor links integrin ligation with p44/42 MAPK phosphorylation and podosome distribution in murine dendritic cells

The Src homology 2 domain-containing leukocyte protein of 76 kDa (SLP-76) is an important molecular intermediate in multiple signaling pathways governing immune cell function. In this study, we report that SLP-76 is expressed in CD11c+ B220- dendritic cells (DCs) isolated from murine thymus or spleen, and that SLP-76 is rapidly phosphorylated on tyrosine residues upon plating of bone marrow-derived DCs (BMDCs) on integrin agonists. SLP-76 is not required for the in vitro or in vivo generation of DCs, but SLP-76-deficient BMDCs adhere poorly to fibronectin, suggesting impaired integrin function. Consistent with impaired adhesion, cutaneous SLP-76-deficient DCs leave ear tissue at an elevated frequency compared with wild-type DCs. In addition, the pattern and distribution of actin-based podosome formation are visibly altered in BMDCs lacking SLP-76 following integrin engagement. SLP-76-deficient BMDCs manifest multiple signaling defects following integrin ligation, including reduced global tyrosine phosphorylation and markedly impaired phosphorylation of p44/42 MAPK (ERK1/2). These data implicate SLP-76 as an important molecular intermediate in the signaling pathways regulating multiple integrin-dependent DC functions, and add to the growing body of evidence that hemopoietic cells may use unique molecular intermediates and mechanisms for regulating integrin signaling.     

The stacked-X DNA Holliday junction and protein recognition

The crystal structure of the four-stranded DNA Holliday junction has now been determined in the presence and absence of junction binding proteins, with the extended open-X form of the junction seen in all protein complexes, but the more compact stacked-X structure observed in free DNA. The structures of the stacked-X junction were crystallized because of an unexpected sequence dependence on the stability of this structure. Inverted repeat sequences that contain the general motif NCC or ANC favor formation of stacked-X junctions, with the junction cross-over occurring between the first two positions of the trinucleotides. This review focuses on the sequence dependent structure of the stacked-X junction and how it may play a role in structural recognition by a class of dimeric junction resolving enzymes that themselves show no direct sequence recognition.     

Differential roles of the co-stimulatory molecules GITR and CTLA-4 in the immune response to Trichinella spiralis

We investigated the roles of the regulatory molecules glucocorticoid-induced TNF receptor family-related protein (GITR) and cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) in murine infection with the nematode parasite Trichinella spiralis. Expression of GITR and CTLA-4 was rapidly upregulated on cells in the mesenteric lymph nodes and spleen, with approximately 80% of CD4+ lymphocytes expressing GITR by day 7 post-infection, coinciding with release and dissemination of newborn larvae. As the infection progressed to the chronic muscle phase, expression of GITR returned to normal, whereas CTLA-4 was sustained as late as day 60. Mice treated with anti-GITR antibodies rapidly developed higher titres of parasite-specific IgG1, IgG2a, IgG2b and IgM than controls. This was accompanied by elevated background lymphocyte proliferation, but parasite establishment in the intestine or the muscle was unaffected. In contrast, treatment with anti-CTLA-4 antibody resulted in elevated serum IgE, enhanced production of interleukin-4 and interleukin-10, and lower numbers of parasites recovered from skeletal muscle. These results reveal different temporal and regulatory roles for CTLA-4 and GITR in immune responses to helminth infection.     

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation

Pyrrolo-C (PC), or 3-[beta-D-2-ribofuranosyl]-6-methylpyrrolo[2,3-d]pyrimidin-2(3H)-one, is a fluorescent analog of the nucleoside cytidine that retains its Watson-Crick base-pairing capacity with G. Due to its red-shifted absorbance, it can be selectively excited in the presence of natural nucleosides, making it a potential site-specific probe for RNA structure and dynamics. Similar to 2-aminopurine nucleoside, which base-pairs with uridine (or thymidine), PC's fluorescence becomes reversibly quenched upon base-pairing, most likely due to stacking interactions with neighboring bases. To test its utility as an RNA probe, we examined PC's fluorescent properties over a wide range of ionic strengths, pH, organic cosolvents, and temperatures. Incorporation of PC into a single-stranded RNA results in an approximately 60% reduction of fluorescence intensity, while duplex formation reduces the fluorescence by approximately 75% relative to the free ribonucleoside. We find that the fluorescence intensity of PC is only moderately affected by ionic strength, pH, and temperature, while it is slightly enhanced by organic cosolvents, making it a versatile probe for a broad range of buffer conditions. We demonstrate two applications for PC: fluorescent measurements of the kinetics of formation and dissociation of an RNA/DNA complex, and fluorescent monitoring of the thermal denaturation of the central segment of an RNA duplex. Taken together, our data showcase the potential of pyrrolo-C as an effective fluorescent probe to study RNA structure, dynamics, and function, complementary to the popular 2-aminopurine ribonucleoside.     

Making water flow: a comparison of the hydrodynamic characteristics of 12 different benthic biological flumes

Flume tanks are becoming increasingly important research tools in aquatic ecology, to link biological to hydrodynamical processes. There is no such thing as a “standard flume tank”, and no flume tank is suitable for every type of research question. A series of experiments has been carried out to characterise and compare the hydrodynamic characteristics of 12 different flume tanks that are designed specifically for biological research. These facilities are part of the EU network BioFlow. The flumes could be divided into four basic design types: straight, racetrack, annular and field flumes. In each facility, two vertical velocity profiles were measured: one at 0.05 m s⁻¹ and one at 0.25 m s⁻¹. In those flumes equipped with Acoustic Doppler Velocimeters (ADV), time series were also recorded for each velocity at two heights above the bottom: 0.05 m and 20% of the water depth. From these measurements turbulence characteristics, such as TKE and Reynolds stress, were derived, and autocorrelation spectra of the horizontal along-stream velocity component were plotted. The flume measurements were compared to two sets of velocity profiles measured in the field.Despite the fact that some flumes were relatively small, turbulence was fully developed in all channels. Straight and racetrack flumes generally produced boundary layers with a clearly definable logarithmic layer, similar to measurements in the field taken under steady flow conditions. The two annular flumes produced relatively thin boundary layers, presumably due to secondary flows developing in the curved channels. The profiles in the field flumes also differed considerably from the expected log profile. This may either have been due the construction of the flume, or due to unsteady conditions during measurement. Constraints imposed by the different flume designs on the suitability for different types of boundary layer research, as well as scaling issues are discussed.     

A homologue of the breast cancer-associated gene BARD1 is involved in DNA repair in plants

hBRCA1 and hBARD1 are tumor suppressor proteins that are involved as heterodimer via ubiquitinylation in many cellular processes, such as DNA repair. Loss of BRCA1 or BARD1 results in early embryonic lethality and chromosomal instability. The Arabidopsis genome carries a BRCA1 homologue, and we were able to identify a BARD1 homologue. AtBRCA1 and the putative AtBARD1 protein are able to interact with each other as indicated by in vitro and in planta experiments. We have identified T-DNA insertion mutants for both genes, which show no visible phenotype under standard growth conditions and are fully fertile. Thus, in contrast to animals, both genes have no indispensable role during development and meiosis in plants. The two single as well as the double mutant are to a similar extent sensitive to mitomycin C, indicating an epistatic interaction in DNA crosslink repair. We could further demonstrate that in Arabidopsis BARD1 plays a prominent role in the regulation of homologous DNA repair in somatic cells.     

Prostate-specific membrane antigen regulates angiogenesis by modulating integrin signal transduction

The transmembrane peptidase prostate-specific membrane antigen (PSMA) is universally upregulated in the vasculature of solid tumors, but its functional role in tumor angiogenesis has not been investigated. Here we show that angiogenesis is severely impaired in PSMA-null animals and that this angiogenic defect occurs at the level of endothelial cell invasion through the extracellular matrix barrier. Because proteolytic degradation of the extracellular matrix is a critical component of endothelial invasion in angiogenesis, it is logical to assume that PSMA participates in matrix degradation. However, we demonstrate a novel and more complex role for PSMA in angiogenesis, where it is a principal component of a regulatory loop that is tightly modulating laminin-specific integrin signaling and GTPase-dependent, p21-activated kinase 1 (PAK-1) activity. We show that PSMA inhibition, knockdown, or deficiency decreases endothelial cell invasion in vitro via integrin and PAK, thus abrogating angiogenesis. Interestingly, the neutralization of beta(1) or the inactivation of PAK increases PSMA activity, suggesting that they negatively regulate PSMA. This negative regulation is mediated by the cytoskeleton as the disruption of interactions between the PSMA cytoplasmic tail and the anchor protein filamin A decreases PSMA activity, integrin function, and PAK activation. Finally, the inhibition of PAK activation enhances the PSMA/filamin A interaction and, thus, boosts PSMA activity. These data imply that PSMA participates in an autoregulatory loop, wherein active PSMA facilitates integrin signaling and PAK activation, leading to both productive invasion and downregulation of integrin beta(1) signaling via reduced PSMA activity. Therefore, we have identified a novel role for PSMA as a true molecular interface, integrating both extracellular and intracellular signals during angiogenesis.     

Modelling multivariate outcomes in hierarchical data, with application to cluster randomised trials

In the cluster randomised study design, the data collected have a hierarchical structure and often include multivariate outcomes. We present a flexible modelling strategy that permits several normally distributed outcomes to be analysed simultaneously, in which intervention effects as well as individual-level and cluster-level between-outcome correlations are estimated. This is implemented in a Bayesian framework which has several advantages over a classical approach, for example in providing credible intervals for functions of model parameters and in allowing informative priors for the intracluster correlation coefficients. In order to declare such informative prior distributions, and fit models in which the between-outcome covariance matrices are constrained, priors on parameters within the covariance matrices are required. Careful specification is necessary however, in order to maintain non-negative definiteness and symmetry between the different outcomes. We propose a novel solution in the case of three multivariate outcomes, and present a modified existing approach and novel alternative for four or more outcomes. The methods are applied to an example of a cluster randomised trial in the prevention of coronary heart disease. The modelling strategy presented would also be useful in other situations involving hierarchical multivariate outcomes.