NOD1 mediates interleukin-18 processing in epithelial cells responding to Helicobacter pylori infection in mice.

The interleukin-1 family members, IL-1ß and IL-18, are processed into their biologically active forms by multi-protein complexes, known as inflammasomes. Although the inflammasome pathways that mediate IL-1ß processing in myeloid cells have been defined, those involved in IL-18 processing, particularly in non-myeloid cells, are still not well understood. Here we report that the host defence molecule NOD1 regulates IL-18 processing in mouse epithelial cells in response to the mucosal pathogen, Helicobacter pylori. Specifically, NOD1 in epithelial cells mediates IL-18 processing and maturation via interactions with caspase-1, instead of the canonical inflammasome pathway involving RIPK2, NF-κB, NLRP3 and ASC. NOD1 activation and IL-18 then help maintain epithelial homoeostasis to mediate protection against pre-neoplastic changes induced by gastric H. pylori infection in vivo. Our findings thus demonstrate a function for NOD1 in epithelial cell production of bioactive IL-18 and protection against H. pylori-induced pathology.

Artificial selection on ant female caste ratio uncovers a link between female-biased sex ratios and infection by Wolbachia endosymbionts.

Social insect sex and caste ratios are well-studied targets of evolutionary conflicts, but the heritable factors affecting these traits remain unknown. To elucidate these factors, we carried out a short-term artificial selection study on female caste ratio in the ant Monomorium pharaonis. Across three generations of bidirectional selection, we observed no response for caste ratio, but sex ratios rapidly became more female-biased in the two replicate high selection lines and less female-biased in the two replicate low selection lines. We hypothesized that this rapid divergence for sex ratio was caused by changes in the frequency of infection by the heritable bacterial endosymbiont Wolbachia, because the initial breeding stock varied for Wolbachia infection, and Wolbachia is known to cause female-biased sex ratios in other insects. Consistent with this hypothesis, the proportions of Wolbachia-infected colonies in the selection lines changed rapidly, mirroring the sex ratio changes. Moreover, the estimated effect of Wolbachia on sex ratio (~13% female bias) was similar in colonies before and during artificial selection, indicating that this Wolbachia effect is likely independent of the effects of artificial selection on other heritable factors. Our study provides evidence for the first case of endosymbiont sex ratio manipulation in a social insect.

Mixtures of n-dodecyl-beta-D-maltoside and hexaoxyethylene dodecyl ether--surface properties, bulk properties, foam films, and foams.

Mixtures of the two non-ionic surfactants hexaoxyethylene dodecyl ether (C(12)E(6)) and n-dodecyl-beta-D-maltoside (beta-C(12)G(2)) were studied with regard to surface properties, bulk properties, foam films, and foams. The reason for studying a mixture of an ethylene oxide (C(i)E(j)) and a sugar (C(n)G(m)) based surfactant is that despite being non-ionic, these two surfactants behave quite differently. Firstly, the physico-chemical properties of aqueous solutions of C(n)G(m) surfactants are less temperature-sensitive than those of C(i)E(j) solutions. Secondly, the surface charge density q(0) of foam films stabilized by C(n)G(m) surfactants is pH insensitive down to the so-called isoelectric point, while that of foam films stabilized by C(i)E(j) surfactants changes linearly with the pH. The third difference is related to interaction forces between solid surfaces. Under equilibrium conditions very high forces are needed to expel beta-C(12)G(2) from between thiolated gold surfaces, while for C(12)E(6) low loads are sufficient. Fourthly, the adsorption of C(12)E(6) and beta-C(12)G(2) on hydrophilic silica and titania, respectively, is inverted. While the surface excess of C(12)E(6) is large on silica and negligible on titania, beta-C(12)G(2) adsorbs very little on silica but has a large surface excess on titania. What is the reason for this different behaviour? Under similar conditions and for comparable head group sizes, it was found that the hydration of C(i)E(j) surfactants is one order of magnitude higher but on average much weaker than that of C(n)G(m) surfactants. Moreover, C(n)G(m) surfactants possess a rigid maltoside unit, while C(i)E(j) surfactants have a very flexible hydrophilic part. Indeed, most of the different properties mentioned above can be explained by the different hydration and the head group flexibilities. The intriguing question of how mixtures of C(i)E(j) and C(n)G(m) surfactants would behave arises organically. Thus various properties of C(12)E(6)+beta-C(12)G(2) mixtures in aqueous solution have been studied with a focus on the 1:1 mixture. The results are compared with those of the single surfactants and are discussed accordingly.

A new small-angle X-ray scattering set-up on the crystallography beamline I711 at MAX-lab.

A small-angle X-ray scattering (SAXS) set-up has recently been developed at beamline I711 at the MAX II storage ring in Lund (Sweden). An overview of the required modifications is presented here together with a number of application examples. The accessible q range in a SAXS experiment is 0.009-0.3 A(-1) for the standard set-up but depends on the sample-to-detector distance, detector offset, beamstop size and wavelength. The SAXS camera has been designed to have a low background and has three collinear slit sets for collimating the incident beam. The standard beam size is about 0.37 mm x 0.37 mm (full width at half-maximum) at the sample position, with a flux of 4 x 10(10) photons s(-1) and lambda = 1.1 A. The vacuum is of the order of 0.05 mbar in the unbroken beam path from the first slits until the exit window in front of the detector. A large sample chamber with a number of lead-throughs allows different sample environments to be mounted. This station is used for measurements on weakly scattering proteins in solutions and also for colloids, polymers and other nanoscale structures. A special application supported by the beamline is the effort to establish a micro-fluidic sample environment for structural analysis of samples that are only available in limited quantities. Overall, this work demonstrates how a cost-effective SAXS station can be constructed on a multipurpose beamline.

Elevated level of inhibin-alpha subunit is pro-tumourigenic and pro-metastatic and associated with extracapsular spread in advanced prostate cancer.

The biological function of inhibin-alpha subunit (INH alpha) in prostate cancer (PCa) is currently unclear. A recent study associated elevated levels of INH alpha in PCa patients with a higher risk of recurrence. This prompted us to use clinical specimens and functional studies to investigate the pro-tumourigenic and pro-metastatic function of INH alpha. We conducted a cross-sectional study to determine a link between INH alpha expression and a number of clinicopathological parameters including Gleason score, surgical margin, extracapsular spread, lymph node status and vascular endothelial growth factor receptor-3 expression, which are well-established prognostic factors of PCa. In addition, using two human PCa cell lines (LNCaP and PC3) representing androgen-dependent and -independent PCa respectively, we investigated the biological function of elevated levels of INH alpha in advanced cancer. Elevated expression of INH alpha in primary PCa tissues showed a higher risk of PCa patients being positive for clinicopathological parameters outlined above. Over-expressing INH alpha in LNCaP and PC3 cells demonstrated two different and cell-type-specific responses. INH alpha-positive LNCaP demonstrated reduced tumour growth whereas INH alpha-positive PC3 cells demonstrated increased tumour growth and metastasis through the process of lymphangiogenesis. This study is the first to demonstrate a pro-tumourigenic and pro-metastatic function for INH alpha associated with androgen-independent stage of metastatic prostate disease. Our results also suggest that INH alpha expression in the primary prostate tumour can be used as a predictive factor for prognosis of PCa.

Time-resolved in situ small-angle X-ray scattering study of silica particle formation in nonionic water-in-oil microemulsions.

The formation of silica particles by the ammonia-catalyzed hydrolysis of tetraethyl orthosilicate (TEOS) in the polyoxyethylene (5) nonylphenyl ether (NP-5)/cyclohexane/water microemulsion system was investigated by time-resolved small-angle X-ray scattering (SAXS). The SAXS data could be modeled as a combination of two species where one describes the silica-particle containing microemulsion droplets and the other the reverse droplets. The analysis allowed the determination of the evolution of the system of particles of silica and reverse droplets. A model of nucleation and growth of the silica particles is confirmed and the volume fraction versus time data for the silica particles is in agreement with first order kinetics with respect to TEOS concentration. Moreover to describe the long time evolution of the system, a correlation among the silica particles has been taken into account by introducing a structure factor with a local silica volume fraction eta = 0.1. This high local density is 2 orders of magnitude larger than the global silica fraction and can be explained in terms of depleting interaction.

The UCSC Genome Browser Database: 2008 update.

The University of California, Santa Cruz, Genome Browser Database (GBD) provides integrated sequence and annotation data for a large collection of vertebrate and model organism genomes. Seventeen new assemblies have been added to the database in the past year, for a total coverage of 19 vertebrate and 21 invertebrate species as of September 2007. For each assembly, the GBD contains a collection of annotation data aligned to the genomic sequence. Highlights of this year's additions include a 28-species human-based vertebrate conservation annotation, an enhanced UCSC Genes set, and more human variation, MGC, and ENCODE data. The database is optimized for fast interactive performance with a set of web-based tools that may be used to view, manipulate, filter and download the annotation data. New toolset features include the Genome Graphs tool for displaying genome-wide data sets, session saving and sharing, better custom track management, expanded Genome Browser configuration options and a Genome Browser wiki site. The downloadable GBD data, the companion Genome Browser toolset and links to documentation and related information can be found at: http://genome.ucsc.edu/.

The UCSC genome browser database: update 2007.

The University of California, Santa Cruz Genome Browser Database contains, as of September 2006, sequence and annotation data for the genomes of 13 vertebrate and 19 invertebrate species. The Genome Browser displays a wide variety of annotations at all scales from the single nucleotide level up to a full chromosome and includes assembly data, genes and gene predictions, mRNA and EST alignments, and comparative genomics, regulation, expression and variation data. The database is optimized for fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. In the past year, 22 new assemblies and several new sets of human variation annotation have been released. New features include VisiGene, a fully integrated in situ hybridization image browser; phyloGif, for drawing evolutionary tree diagrams; a redesigned Custom Track feature; an expanded SNP annotation track; and many new display options. The Genome Browser, other tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Bone nanostructure near titanium and porous tantalum implants studied by scanning small angle x-ray scattering.

Bone sections including either titanium or porous tantalum implant devices used for interbody spinal fusion were investigated with position-resolved small angle X-ray scattering (sSAXS). The samples were obtained from six-month-old pigs that had undergone surgery three months prior to sacrifice. The aim of the study was to explore the possibility of using sSAXS to obtain information about thickness, orientation and shape/arrangement of the mineral crystals in bone near the implant surfaces. Detailed sSAXS scans were carried out in two different regions of bone adjacent to the implant in each of the implant samples. In the implant vicinity the mineral crystals tended to be aligned with the surface of the implants. The mean crystal thickness was between 2.1 and 3.0 nm. The mineral crystal thickness increased linearly with distance from the implant in both regions of the porous tantalum implant and in one of the regions in the titanium sample. In the second region of the titanium sample the thickest mineral crystals were found close to the implant surface. The observed differences in mineral thickness with distance from the implant surfaces might be explained by differences in mechanical load induced by the implant material and the geometrical design of the implant. The study shows that sSAXS is a powerful tool to characterize the nanostructure of bone near implant surfaces.

The UCSC Genome Browser Database: update 2006.

The University of California Santa Cruz Genome Browser Database (GBD) contains sequence and annotation data for the genomes of about a dozen vertebrate species and several major model organisms. Genome annotations typically include assembly data, sequence composition, genes and gene predictions, mRNA and expressed sequence tag evidence, comparative genomics, regulation, expression and variation data. The database is optimized to support fast interactive performance with web tools that provide powerful visualization and querying capabilities for mining the data. The Genome Browser displays a wide variety of annotations at all scales from single nucleotide level up to a full chromosome. The Table Browser provides direct access to the database tables and sequence data, enabling complex queries on genome-wide datasets. The Proteome Browser graphically displays protein properties. The Gene Sorter allows filtering and comparison of genes by several metrics including expression data and several gene properties. BLAT and In Silico PCR search for sequences in entire genomes in seconds. These tools are highly integrated and provide many hyperlinks to other databases and websites. The GBD, browsing tools, downloadable data files and links to documentation and other information can be found at http://genome.ucsc.edu/.

Loss of Wolbachia infection during colonisation in the invasive Argentine ant Linepithema humile.

WOLBACHIA are maternally inherited bacteria, which are very common in arthropods and nematodes. Wolbachia infection may affect host reproduction through feminisation, parthenogenesis, male-killing, cytoplasmic incompatibility and increased fecundity. Previous studies showing discrepancies between the phylogenies of Wolbachia and its arthropod hosts indicate that infection is frequently lost, but the causes of symbiont extinction have so far remained elusive. Here, we report data showing that colonisation of new habitats is a possible mechanism leading to the loss of infection. The presence and prevalence of Wolbachia were studied in three native and eight introduced populations of the Argentine ant Linepithema humile. The screening shows that the symbiont is common in the three native L. humile populations analysed. In contrast, Wolbachia was detected in only one of the introduced populations. The loss of infection associated with colonisation of new habitats may result from drift (founder effect) or altered selection pressures in the new habitat. Furthermore, a molecular phylogeny based on sequences of the Wolbachia wsp gene indicates that L. humile has been infected by a single strain. Horizontal transmission of the symbiont may be important in ants as suggested by the sequence similarity of strains in the three genera Linepithema, Acromyrmex, and Solenopsis native from South and Central America.

Convergent development of low-relatedness supercolonies in Myrmica ants.

Many ant species have independently evolved colony structures with multiple queens and very low relatedness among nestmate workers, but it has remained unclear whether low-relatedness kin structures can repeatedly arise in populations of the same species. Here we report a study of Danish island populations of the red ant Myrmica sulcinodis and show that it is likely that such repeated developments occur. Two microsatellite loci were used to estimate genetic differentiation (F(ST)) among three populations and nestmate relatedness within these populations. The F(ST) values were highly significant due to very different allele frequencies among the three populations with relatively few common alleles and relatively many rare alleles, possibly caused by single queen foundation and rare subsequent immigration. Given the isolation of the islands and the low investment in reproduction, we infer that each of the populations was most likely established by a single queen, even though all three extant populations now have within-colony relatedness 95%), and the genetic differentiation of nests showed a significantly positive correlation with the distance between them. Both male-biased sex-ratio and genetic viscosity are expected characteristics of populations where queens have very local dispersal and where new colonies are initiated through nest-budding. Based on a comparison with other M. sulcinodis populations we hypothesise a distinct succession of population types and suggest that this may be a possible pathway to unicoloniality, ie, development towards a complete lack of colony kin structure and unrelated nestmate workers.

Phase II clinical trial of preoperative combined chemoradiation for T3 and T4 resectable rectal cancer: preliminary results.

PURPOSE: Although preoperative chemoradiation for high-risk rectal cancer may improve survival and local recurrence rate, its adverse effects are not well defined. This prospective study evaluated the use of preoperative chemoradiation for T3 and T4 resectable rectal cancer, with special emphasis on treatment morbidity, pathologic remission rate, quality of life, and anorectal function. METHODS: Forty-two patients (30 men, 12 women) were enrolled in the study. Median distance of the distal tumor margin from the anal verge was 6.5 cm. Preoperative staging was based on digital rectal examination, endorectal ultrasound, and computed tomography. None of the patients had distant metastases. All patients had 45 Gy (1.8 Gy/day in 25 fractions) over five weeks, plus 5-fluorouracil (350 mg/m(2)/day) and leucovorin (20 mg/m(2)/day) bolus on days 1 to 5 and 29 to 33. Quality of life was assessed with the European Organization for Research and Treatment of Cancer 30-item quality-of-life questionnaire (QLQ-C30) and its colorectal cancer-specific module (QLQ-CR38) questionnaires. Objective anorectal function was assessed by anorectal manometry and pudendal nerve terminal motor latency. Surgery was performed 46 (range, 24-63) days after completion of adjuvant therapy. RESULTS: Nineteen patients (45 percent) had Grade 3 or 4 chemoradiation-induced toxic reactions. Four patients developed intercurrent distant metastases or intraperitoneal carcinomatosis at completion of chemoradiation. Thirty-eight patients underwent surgical resection: abdominoperineal resection, anterior resection, and Hartmann's procedure were performed in 55 percent, 39 percent (11 of 15 patients had a diverting stoma), and 5 percent, respectively. Major surgical complications occurred in 7 patients (18 percent) and included anastomotic leak (n = 1), pelvic abscess (n = 1), small-bowel obstruction (n = 3), and wound breakdown (n = 2). Final pathology was Stage 0 (no residual disease), I, II, and III in 6 (16 percent), 7 (18 percent), 9 (24 percent), and 16 (42 percent) patients, respectively. There was a deterioration, after chemoradiation and surgery, in the quality of life on all subscales assessed, with physical, role, and social function being most severely affected. The symptoms most adversely affected were micturition, defecation, and gastrointestinal problems. Body image and sexual enjoyment deteriorated in both men and women. Chemoradiation alone led to prolonged pudendal nerve terminal motor latency in 57 percent of 7 patients assessed. CONCLUSION: Preliminary results have identified defined costs with preoperative chemoradiation, which included treatment-induced toxicity, a high stoma rate, and adverse effects on quality of life and anorectal function.

Block copolymer micelle coronas as quasi-two-dimensional dilute or semidilute polymer solutions.

Chain-chain interactions in a corona of polymers tethered to a spherical core under good solvent conditions are studied using Monte Carlo simulations. The total scattering function of the corona as well as different partial contributions are sampled. By combining the different contributions in a self-consistent approach, it is demonstrated that the corona can be regarded as a quasi-two-dimensional polymer solution, with a concentration dependence analogous to that of an ordinary polymer solution. Scattering due to the corona profile and density fluctuation correlations are separated in this approach. The osmotic compressibility is extracted from the latter, and it is shown to be a universal function of surface coverage, with some deviations at high coverage due to surface curvature effects.

Droplet polydispersity and shape fluctuations in AOT [bis(2-ethylhexyl)sulfosuccinate sodium salt] microemulsions studied by contrast variation small-angle neutron scattering.

Microemulsions consisting of AOT water, and decane or iso-octane are studied in the region of the phase diagram where surfactant covered water droplets are formed. The polydispersity and shape fluctuations of the microemulsion droplets are determined and compared in the two different alkane types. Conductivity measurements show that there is a pronounced dependence of the temperature behavior of the microemulsion on the type of alkane used. In both cases the microemulsion droplets start to form larger aggregates when the temperature increases. But in the system with decane this aggregation temperature occurs at a temperature about 10 degrees C lower than in a similar system with iso-octane. Aggregation phenomena are avoided and the two systems are at approximately the same reduced temperature with respect to the aggregation temperature when the temperature of the AOT/D(2)O/decane microemulsion is 10 degrees C and the temperature of the AOT/D(2)O/iso-octane microemulsion is 20 degrees C. Contrast variation small-angle neutron scattering measurements are performed at these temperatures on systems with volume fractions of 5% D2O+AOT by varying the scattering length density of the alkane. The small-angle scattering for 11 different contrasts evenly distributed around the match points are studied for each sample. The scattering data for the different contrasts are analyzed using a molecular constrained model for ellipsoidal droplets of water covered by AOT, interacting as polydisperse hard spheres. All contrasts are fitted simultaneously by taking the different contrast factors into account. The analysis show that at the same reduced temperature with respect to the aggregation temperature the droplet size, polydispersity index, the size of the shape fluctuations are similar in the two systems. A polydispersity index (sigma/R of the Gaussian size distribution) of 16% and an average axis ratio of the droplets of 1.56 is found in the AOT/D(2)O/decane microemulsion. In the AOT/D(2)O/iso-octane system the polydispersity index is also 16% while the axis ratio is 1.72. The bending elastic constant kappa and the Gaussian bending elastic constant kappa; can be estimated from these numbers. For AOT/D(2)O/decane we find kappa=3.4 k(B)T and kappa=-5.9 k(B)T and for AOT/D(2)O/iso-octane we find kappa=2.35k(B)T and kappa=-3.8k(B)T, where k(B) is the Boltzmann constant and T is the absolute temperature.

Association behavior of native beta-lactoglobulin.

The association behavior of beta-lactoglobulin has been studied by small-angle neutron scattering as a function of protein concentration, temperature, pH, and NaCl concentration of the solution. By indirect Fourier transformation of the spectra, pair-distance distribution functions for the various samples were obtained. These functions provided information on the maximum size, the weight-averaged molecular mass, and the z-averaged radius of gyration of the beta-lactoglobulin particles. At room temperature and pH values below 4 and above 5.2 the protein consists predominantly of monomers and dimers, consistent with literature. In these pH regimes the formation of dimers is favored upon increasing ionic strength and decreasing protein charge (pH values closer to the isoelectric point of the protein). Around pH 4.7, larger oligomeric structures are formed, enhanced by a decrease in temperature and a decrease in ionic strength. beta-Lactoglobulin A associates more strongly than beta-lactoglobulin B. Surprisingly, at pH 6.9 larger structures than dimers seem to be formed at high protein concentrations (> 30 mg mL-1).

Loss of the expression and localization of inhibin alpha-subunit in high grade prostate cancer.

Serum inhibin levels are elevated in postmenopausal women with granulosa and mucinous epithelial tumors of the ovary. In contrast, functional deletion of the inhibin alpha gene in male and female mice results in the development of primary gonadal granulosa/Sertoli cell tumors. The aim of this study was to determine whether inhibin alpha-subunit gene and protein expression are altered in prostate cancer. Messenger ribonucleic acid expression was studied by in situ hybridization, and protein localization was studied by immunohistochemistry. Inhibin alpha-subunit messenger ribonucleic acid expression and protein localization were observed in the epithelium of tissues from men with benign prostatic hyperplasia, in regions of basal cell hyperplasia, and in nonmalignant regions of tissue from men with high grade prostate cancer. In the malignant regions of tissue from men with high grade prostate cancer, the expression of the inhibin alpha-subunit gene was suppressed and was not detectable in poorly differentiated tumor cells. These results demonstrate that in contrast to ovarian granulosa cell tumors, inhibin alpha gene expression is down-regulated in poorly differentiated prostate cancer.

Ancient conservation of trinucleotide microsatellite loci in polistine wasps.

Microsatellites have proven to be very useful genetic markers for studies of kinship, parentage, and gene mapping. If microsatellites are conserved among species, then those developed for one species can be used on related species, which would save the time and effort of developing new loci. We evaluated conservation of 27 trinucleotide loci that were derived from 2 species of Polistes wasps in cross-species applications on 27 species chosen from the major lineages of the Vespidae, which diverged as much as 144 million years ago. We further investigated cross-species polymorphism levels for 18 of the loci. There was a clear relationship between cladistic distance and both conservation of the priming sites and heterozygosity. However the loci derived from P. bellicosus were much more widely conserved and polymorphic than were those derived from P. annularis. The disparity in cross-species utility between these sets of loci means that caution should be used in generalizing from conservation rates derived from single species. We found no relationship between locus conservation or heterozygosity and GC content of flanks, repeat motif, repeat length, or heterozygosity in the original species, which suggests that generalizations from other studies reporting such patterns are premature.