MaGIC: a program to generate targeted marker sets for genome-wide association studies

High-throughput genotyping technologies such as DNA pooling and DNA microarrays mean that whole-genome screens are now practical for complex disease gene discovery using association studies. Because it is currently impractical to use all available markers, a subset is typically selected on the basis of required saturation density. Restricting markers to those within annotated genomic features of interest (e.g., genes or exons) or within feature-rich regions, reduces workload and cost while retaining much information. We have designed a program (MaGIC) that exploits genome assembly data to create lists of markers correlated with other genomic features. Marker lists are generated at a user-defined spacing and can target features with a user-defined density. Maps are in base pairs or linkage disequilibrium units (LDUs) as derived from the International HapMap data, which is useful for association studies and fine-mapping. Markers may be selected on the basis of heterozygosity and source database, and single nucleotide polymorphism (SNP) markers may additionally be selected on the basis of validation status. The import function means the method can be used for any genomic features such as housekeeping genes, long interspersed elements (LINES), or Alu repeats in humans, and is also functional for other species with equivalent data. The program and source code is freely available at http://cogent.iop.kcl.ac.uk/MaGIC.cogx.     

GABAA Modulation of S100B Secretion in Acute Hippocampal Slices and Astrocyte Cultures

Astrocytes are the major glial cells in brain tissue and are involved, among many functions, ionic and metabolic homeostasis maintenance of synapses. These cells express receptors and transporters for neurotransmitters, including GABA. GABA signaling is reportedly able to affect astroglial response to injury, as evaluated by specific astrocyte markers such as glial fibrillary acid protein and the calcium-binding protein, S100B. Herein, we investigated the modulatory effects of the GABA_A receptor on astrocyte S100B secretion in acute hippocampal slices and astrocyte cultures, using the agonist, muscimol, and the antagonists pentylenetetrazol (PTZ) and bicuculline. These effects were analyzed in the presence of tetrodotoxin (TTX), fluorocitrate (FLC), cobalt and barium. PTZ positively modify S100B secretion in hippocampal slices and astrocyte cultures; in contrast, bicuculline inhibited S100B secretion only in hippocampal slices. Muscimol, per se, did not change S100B secretion, but prevented the effects of PTZ and bicuculline. Moreover, PTZ-induced S100B secretion was prevented by TTX, FLC, cobalt and barium indicating a complex GABA_A communication between astrocytes and neurons. The effects of two putative agonists of GABA_A, β-hydroxybutyrate and methylglyoxal, on S100B secretion were also evaluated. In view of the neurotrophic role of extracellular S100B under conditions of injury, our data reinforce the idea that GABA_A receptors act directly on astrocytes, and indirectly on neurons, to modulate astroglial response.

     

Altered temporal characteristics of the rectoanal inhibitory reflex in patients with abdominal distension

The rectoanal inhibitory reflex (RAIR) is important in gas and stool evacuation. We examined RAIR features in patients with chronic constipation who exhibited bloating with and without abdominal distension, to determine whether alterations in RAIR may be a factor in the pathogenesis of abdominal distension. Seventy-five female patients with chronic constipation with or without abdominal distension were included in the study. The presence or absence of abdominal distension was assessed according to the Rome II questionnaire. All patients underwent both RAIR and rectal sensitivity testing, and specific RAIR parameters were analyzed. Patients were divided into two groups: abdominal bloating with distension (D, n = 55) and abdominal bloating without distension (ND, n = 20). D had a longer time to the onset of anal sphincter inhibition (latency of inhibition) (P = 0.03) compared with ND. In logistic regression analysis, a combination of age, latency of inhibition and the time measured from onset of inhibition to the point of maximum inhibition predicted abdominal distension (P = 0.002). There were no differences between groups for the time from point of maximum inhibition to recovery and for the percentage of internal anal sphincter relaxation. This is the first study to examine the role of RAIR in patients with abdominal distension. Female patients with constipation and abdominal distension exhibited differences in the temporal characteristics of, but not in the degree of, anal sphincter relaxation compared with patients without distension. Since this study was uncontrolled, further studies are necessary to determine the contribution of altered anorectal reflexes to abdominal distension.     

Spatio-temporal distribution and production of calanoid copepods in the central Baltic Sea

The aim of our study was the exploration of species-specificdistribution and production patterns of dominant copepods inthe Central Baltic Sea (Bornholm Basin). Spatio-temporal distribution,egg and secondary production were studied by means of net-samplingand egg production experiments from April to August 1999. Verticaland horizontal distribution patterns appeared to be linked witheach other and were primarily species-dependent. Both Acartiaspp. and Temora longicornis preferentially inhabited the upper30 m of the water column and the shallower marginal regionsof the Bornholm Basin. In contrast, the C4–5 and C6 ofPseudocalanus spp. preferentially inhabited the halocline region(50–70 m) and the deep central part of the area. Observeddifferences in horizontal distribution among these three copepodsappear to result from different depth preferences and depth-dependentwater circulation patterns. Egg production rates (EPR) clearlyexhibited seasonal differences with maximum EPR in May and minimumEPR in July. Mean EPR was significantly different between species,being highest in Acartia spp. and lowest in Pseudocalanus spp.The variability in EPR was related to differences in hydrographyand modelled food environment.     

Assessing the efficacy of vesicle fusion with planar membrane arrays using a mitochondrial porin as reporter

Reconstitution of functionally active membrane protein into artificially made lipid bilayers is a challenge that must be overcome to create a membrane-based biomimetic sensor and separation device. In this study we address the efficacy of proteoliposome fusion with planar membrane arrays. We establish a protein incorporation efficacy assay using the major non-specific porin of Fusobacterium nucleatum (FomA) as reporter. We use electrical conductance measurements and fluorescence microscopy to characterize proteoliposome fusion with an array of planar membranes. We show that protein reconstitution in biomimetic membrane arrays may be quantified using the developed FomA assay. Specifically, we show that FomA vesicles are inherently fusigenic. Optimal FomA incorporation is obtained with a proteoliposome lipid-to-protein molar ratio (LPR) = 50 more than 10⁵ FomA proteins could be incorporated in a bilayer array with a total membrane area of 2 mm² within 20 min. This novel assay for quantifying protein delivery into lipid bilayers may be a useful tool in developing biomimetic membrane applications.     

Accumulation of nano-sized particles in a murine model of angiogenesis

Purpose

To evaluate the ability of nm-scaled iron oxide particles conjugated with Azure A, a classic histological dye, to accumulate in areas of angiogenesis in a recently developed murine angiogenesis model.

Materials and methods

We characterised the Azure A particles with regard to their hydrodynamic size, zeta potential, and blood circulation half-life. The particles were then investigated by Magnetic Resonance Imaging (MRI) in a recently developed murine angiogenesis model along with reference particles (Ferumoxtran-10) and saline injections.

Results

The Azure A particles had a mean hydrodynamic diameter of 51.8 ± 43.2 nm, a zeta potential of −17.2 ± 2.8 mV, and a blood circulation half-life of 127.8 ± 74.7 min. Comparison of MR images taken pre- and 24-h post-injection revealed a significant increase in R₂^* relaxation rates for both Azure A and Ferumoxtran-10 particles. No significant difference was found for the saline injections. The relative increase was calculated for the three groups, and showed a significant difference between the saline group and the Azure A group, and between the saline group and the Ferumoxtran-10 group. However, no significant difference was found between the two particle groups.

Conclusion

Ultrahigh-field MRI revealed localisation of both types of iron oxide particles to areas of neovasculature. However, the Azure A particles did not show any enhanced accumulation relative to Ferumoxtran-10, suggesting the accumulation in both cases to be passive.     

Evolution of epitopes on human and nonhuman primate lymphocyte cell surface antigens

The T- and B-cell surface polypeptides detected by an international workshop panel of 100 mouse monoclonal antibodies (M.Ab) were biochemically defined by radioimmunoprecipitation. Eight T-cell-associated molecules and eight B-cell-associated molecules were identified by multiple antibodies in the panel. Clusters of antibodies specific for the same polypeptide were then compared for their reactivity against peripheral blood mononuclear cells (PBMC) from 11 nonhuman primate species. All the major T- and B-cell antigens present in humans were also expressed in some nonhuman primates. M.Ab to the same antigen were found to react with distinct epitope groups that differed in their phylogenetic distribution. Some epitopes were highly conserved, while other epitopes on the same molecule were only expressed in hominoids and were not detected in old world and new world monkeys. Our detailed analysis of the phylogeny of 37 T-cell antigen epitopes on ten different molecules revealed there was no clear correspondence between the number of epitopes shared and evolutionary distance. Rather the data suggest that parallelism with back mutation may be a common mechanism in the evolution of T-cell antigens. The data also show that the tissue distribution of T-cell antigens can differ between primate species; for example, M.Ab to human Tp45 Tla-Qa-like antigens that did not react with human PBMC did react with PBMC from new world monkeys.     

Fabrication and Operation of a Nano-Optical Conveyor Belt

The technique of using focused laser beams to trap and exert forces on small particles has enabled many pivotal discoveries in the nanoscale biological and physical sciences over the past few decades. The progress made in this field invites further study of even smaller systems and at a larger scale, with tools that could be distributed more easily and made more widely available. Unfortunately, the fundamental laws of diffraction limit the minimum size of the focal spot of a laser beam, which makes particles smaller than a half-wavelength in diameter hard to trap and generally prevents an operator from discriminating between particles which are closer together than one half-wavelength. This precludes the optical manipulation of many closely-spaced nanoparticles and limits the resolution of optical-mechanical systems. Furthermore, manipulation using focused beams requires beam-forming or steering optics, which can be very bulky and expensive. To address these limitations in the system scalability of conventional optical trapping our lab has devised an alternative technique which utilizes near-field optics to move particles across a chip. Instead of focusing laser beams in the far-field, the optical near field of plasmonic resonators produces the necessary local optical intensity enhancement to overcome the restrictions of diffraction and manipulate particles at higher resolution. Closely-spaced resonators produce strong optical traps which can be addressed to mediate the hand-off of particles from one to the next in a conveyor-belt-like fashion. Here, we describe how to design and produce a conveyor belt using a gold surface patterned with plasmonic C-shaped resonators and how to operate it with polarized laser light to achieve super-resolution nanoparticle manipulation and transport. The nano-optical conveyor belt chip can be produced using lithography techniques and easily packaged and distributed.     

MicroRNAs in systemic rheumatic diseases

MicroRNAs (miRNAs) are endogenous, non-coding, single-stranded RNAs about 21 nucleotides in length. miRNAs have been shown to regulate gene expression and thus influence a wide range of physiological and pathological processes. Moreover, they are detected in a variety of sources, including tissues, serum, and other body fluids, such as saliva. The role of miRNAs is evident in various malignant and nonmalignant diseases, and there is accumulating evidence also for an important role of miRNAs in systemic rheumatic diseases. Abnormal expression of miRNAs has been reported in autoimmune diseases, mainly in systemic lupus erythematosus and rheumatoid arthritis. miRNAs can be aberrantly expressed even in the different stages of disease progression, allowing miRNAs to be important biomarkers, to help understand the pathogenesis of the disease, and to monitor disease activity and effects of treatment. Different groups have demonstrated a link between miRNA expression and disease activity, as in the case of renal flares in lupus patients. Moreover, miRNAs are emerging as potential targets for new therapeutic strategies of autoimmune disorders. Taken together, recent data demonstrate that miRNAs can influence mechanisms involved in the pathogenesis, relapse, and specific organ involvement of autoimmune diseases. The ultimate goal is the identification of a miRNA target or targets that could be manipulated through specific therapies, aiming at activation or inhibition of specific miRNAs responsible for the development of disease.