Gut macrophage phenotype is dependent on the tumor microenvironment in colorectal cancer.

In contrast to many cancers, a high infiltration of macrophages in colorectal cancer (CRC) has been associated with improved prognosis for patients. Cytokines and other stimuli from the tumor microenvironment affect monocyte to macrophage maturation and subsequent phenotype and function. Heterogeneous myeloid populations were identified using a novel flow cytometry panel in both tumor and paired non-tumor bowel (NTB) from CRC patients. The frequency of macrophage subsets with a gut-conditioned phenotype was lower in tumor compared with NTB. We used an in vitro system to show that two of the macrophage populations represented pro-inflammatory and anti-inflammatory phenotypes. Conditioned media that contained high levels of interleukin-6 promoted and maintained an anti-inflammatory phenotype in vitro. This study demonstrates the plasticity and heterogeneity of macrophage subtypes in human CRC, and the feasibility of studying complex populations. Ex vivo experiments demonstrate that macrophage subsets are influenced by the tumor microenvironment.

Distinct immune signatures in the colon of Crohn's disease and ankylosing spondylitis patients in the absence of inflammation.

Crohn's disease (CD) is an inflammatory bowel disease characterized by patchy inflammation of the gastrointestinal tract. Ankylosing spondylitis (AS) is primarily characterized by inflammation of the lower vertebral column, and many patients with AS present with inflammatory gut symptoms. Genome-wide association studies have highlighted significant overlap in short nucleotide polymorphisms for both diseases. We hypothesized that patients with CD and AS have a common intestinal immune signature, characterized by inflammatory T cells, compared with healthy people. We designed a pilot study to determine both the feasibility of defining complex immune signatures from primary tissue, and differences in the local immune signature of people with inflammatory diseases compared with healthy people. Intestinal biopsies were obtained by colonoscopy from healthy patients, non-inflamed regions of CD patients and AS patients with inflammatory gut symptoms. A flow cytometry platform was developed measuring polyfunctional T-cell populations based on cytokines, surface molecules and transcription factors. There was overlap in the immune signature of people with CD or AS, characterized by changes in the frequency of regulatory T cells, compared with healthy people. There were significant differences in frequencies of other polyfunctional T-cell populations-CD patients had an increased frequency of T cells producing interleukin-22 (IL-22) and interferon-γ, whereas AS patients had an increased frequency of T cells producing IL-2; compared with healthy people. These data indicate that the local immune signature could be described in these patients and that distinct immune mechanisms may underlie disease progression.

Multipartite entangled spatial modes of ultracold atoms generated and controlled by quantum measurement.

We show that the effect of measurement backaction results in the generation of multiple many-body spatial modes of ultracold atoms trapped in an optical lattice, when scattered light is detected. The multipartite mode entanglement properties and their nontrivial spatial overlap can be varied by tuning the optical geometry in a single setup. This can be used to engineer quantum states and dynamics of matter fields. We provide examples of multimode generalizations of parametric down-conversion, Dicke, and other states; investigate the entanglement properties of such states; and show how they can be transformed into a class of generalized squeezed states. Furthermore, we propose how these modes can be used to detect and measure entanglement in quantum gases.

Capturing exponential variance using polynomial resources: applying tensor networks to nonequilibrium stochastic processes.

Estimating the expected value of an observable appearing in a nonequilibrium stochastic process usually involves sampling. If the observable's variance is high, many samples are required. In contrast, we show that performing the same task without sampling, using tensor network compression, efficiently captures high variances in systems of various geometries and dimensions. We provide examples for which matching the accuracy of our efficient method would require a sample size scaling exponentially with system size. In particular, the high-variance observable e^{-ßW}, motivated by Jarzynski's equality, with W the work done quenching from equilibrium at inverse temperature ß, is exactly and efficiently captured by tensor networks.

Effect of a GaAsP shell on the optical properties of self-catalyzed GaAs nanowires grown on silicon.

We realize the growth of self-catalyzed core-shell GaAs/GaAsP nanowires (NWs) on Si substrates using molecular-beam epitaxy. Transmission electron microscopy of single GaAs/GaAsP NWs demonstrates their high crystal quality and shows domination of the GaAs zinc-blende phase. Using continuous-wave and time-resolved photoluminescence (PL), we make a detailed comparison with uncapped GaAs NWs to emphasize the effect of the GaAsP capping in suppressing the nonradiative surface states. Significant PL enhancement in the core-shell structures exceeding 3 orders of magnitude at 10 K is observed; in uncapped NWs PL is quenched at 60 K, whereas single core-shell GaAs/GaAsP structures exhibit bright emission even at room temperature. From analysis of the PL temperature dependence in both types of NW we are able to determine the main carrier escape mechanisms leading to the PL quench.

Spatial modulation microscopy for real-time imaging of plasmonic nanoparticles and cells.

Spatial modulation microscopy (SMM) is a technique originally developed for quantitative spectroscopy of individual nano-objects. Here, a parallel implementation of the SMM technique is demonstrated based on a line detector capable of demodulation at kHz frequencies. The capabilities of the imaging system are shown using an array of plasmonic nanoantennas and dendritic cells incubated with gold nanoparticles.

Phylogenetic evidence of noteworthy microflora from the subsurface of the former Homestake gold mine, Lead, South Dakota.

Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil-like sample. Geochemical analyses indicated that both samples were high in sulphur, rich in nitrogen and salt, but with significantly different metal concentrations. Microbial diversity comparisons unexpectedly revealed three distinct operational taxonomic units (OTUs) belonging to the archaeal phylum Thaumarchaeota, typically identified from marine environments, and one OTU belonging to a potentially novel phylum that fell sister to Thaumarchaeota. To our knowledge this is only the second report of Thaumarchaeota in a terrestrial environment. The majority of the clones from Archaea sequence libraries fell into two closely related OTUs and were grouped most closely to an ammonia-oxidizing, carbon-fixing and halophilic thaumarchaeote genus, Nitrosopumilus. The two samples showed neither Euryarchaeota nor Crenarchaeota members that have often been identified from other subsurface terrestrial ecosystems. Bacteria OTUs containing the highest percentage of sequences were related to sulphur-oxidizing bacteria of the orders Chromatiales and Thiotrichales. Community members of Bacteria from individual Homestake ecosystems were heterogeneous and distinctive to each community, with unique phylotypes identified within each sample.

Evaluation of agrobacterium-mediated transformation of Agaricus bisporus using a range of promoters linked to hygromycin resistance.

There is interest in establishing genetic modification technologies for the cultivated mushroom Agaricus bisporus, both for improved crop characteristics and for molecular pharming. For these methods to be successful, it is necessary to establish a set of transformation systems that include robust and reliable vectors for gene manipulation. In this article, we report the evaluation of a series of promoters for driving expression of the Escherichia coli hph gene encoding hygromycin phosphotransferase. This was achieved using the Aspergillus nidulans gpdA and the A. bisporus gpdII and trp2 promoters. The Coprinus cinereus beta-tubulin promoter gave contrasting results depending on the size of promoter used, with a 393-bp region being effective, whereas the longer 453-bp fragment failed to yield any hygromycin-resistant transformants. The C. cinereus trp1 and the A. bisporus lcc1 promoters both failed to yield transformants. We also show that transformation efficiency may be improved by careful selection of both appropriate Agrobacterium strains, with AGL-1 yielding more than LBA1126 and by the choice of the binary vectors used to mobilize the DNA, with pCAMBIA vectors appearing to be more efficient than either pBIN19- or pGREEN-based systems.

Efficient GFP expression in the mushrooms Agaricus bisporus and Coprinus cinereus requires introns.

We have developed a "Molecular Toolkit" comprising interchangeable promoters and marker genes to facilitate transformation of homobasidiomycete mushrooms. We describe the evaluation of a range of promoters in the homobasidiomycetes Agaricus bisporus and Coprinus cinereus using green fluorescent protein (GFP) as a reporter gene; the C. cinereus trp1 promoter and A. bisporus trp2 and gpdII promoters proving successful in driving expression in C. cinereus, with the gpdII promoter also functioning in A. bisporus. Our investigations demonstrate that a prerequisite for GFP expression in C. cinereus and A. bisporus is the presence of an intron. This is the first reported expression of GFP in either C. cinereus or A. bisporus.

RAPD discrimination of Agaricus bisporus mushroom cultivars.

Cultivars of the white button mushroom Agaricus bisporus are difficult to differentiate, which has made strain protection problematic for this crop species. We have used RAPDs to discriminate between 26 strains of A. bisporus, 24 of which were commercial cultivars, and to characterise the genetic relatedness of these strains. Using 20 primers, 211 RAPD markers were identified and used in hierarchical cluster, patristic distance and parsimony analyses. All strains could be differentiated using the aggregated primer data. Although no one primer could differentiate all 26 strains, several individual primers yielded unique fingerprints for a variety of strains. The greatest differences (up to 28% variation) were observed in comparisons with or between two wild collections of A. bisporus. Quondam cultivars, commercial brown and off-white varieties proved more variable than the widely grown 'hybrid' types. Of the 15 hybrid varieties analysed, only one differed substantially (20% or more variable). The patristic and parsimony analyses both demonstrated the gross similarity of the hybrids, many of which appear to be essentially derived varieties from two original hybrid cultivars. RAPD analyses can assist mushroom strain identification and could play a role in the protection of novel cultivars.

Regulation of insulin gene expression by the IDDM associated, insulin locus haplotype.

A 4.1 kb genomic region, spanning the insulin (INS) gene, confers genetic susceptibility to Type 1 or insulin-dependent diabetes mellitus (IDDM). Ten polymorphisms within this region form two predominant, complementary haplotypes. We have been studying the effects of these polymorphisms on the levels of insulin mRNA. Cloned genomic DNA fragments representing these two separate haplotypes were transiently transfected into a rodent pancreatic beta cell line, HIT-T15. These studies revealed that insulin mRNA levels were consistently higher in the transfectants expressing the diabetic haplotype. Over-expression of insulin mRNA may provide the basic mechanism for the diabetic susceptibility encoded at the INS locus.

Expression of A mating type genes of Coprinus cinereus in a heterologous basidiomycete host.

The A mating factor of Coprinus cinereus determines compatibility in mating by regulating part of a developmental sequence that leads to dikaryon formation. The A genes that trigger development encode two different classes of homeodomain proteins, and for a successful mating, a protein of one class, HD1, must interact with a protein of the other class, HD2. In this report we show that C. cinereus A genes that encode HD2 proteins, a2-1 and b2-1, can elicit A-regulated development in the heterologous host C. bilanatus. Transformation rates were very low, suggesting that the genes were poorly transcribed. The fact that the HD2 genes are functionally expressed implies successful heteromultimeric association of putative DNA-binding proteins coded by the two Coprinus species. This interaction was sufficient to satisfy the need for different A factors in the formation of a fertile C. bilanatus dikaryon, but fertile dikaryons were more readily produced in matings with the a2-1 gene transformants. The C. cinereus A genes, b1-1 and d1-1, which encode HD1 proteins, were either not expressed or their proteins were non-functional in C. bilanatus. These experiments raise some interesting questions regarding HD1-HD2 protein interactions.

Antigen presentation and the association of class-I molecules.

We have identified two mutant cell lines which are not able to present epitopes of influenza virus synthesized in the cytoplasm but can present the same epitope when exposed to it as a peptide in the extracellular medium. The cell lines also have a defect in class-I assembly, with reduced expression of assembled alpha chain: beta 2M heterodimers at their cell surface. This led to the suggestion that the two traits were the result of the same mutation and that stable assembly of class-I molecules is dependent on peptide binding. Consistent with this idea was the finding that exposure to specific peptides in the extracellular fluid promotes stable association of class-I heavy chains with beta 2M and restores expression of class-I at the cell surface. We have gone on to show that stable assembly of class-I molecules can be supported in detergent extracts of the mutant cells when specific peptides are added. Peptides stabilized a conformational change in the class-I heavy chain and association with beta 2M by binding to the complexes. This effect is apparent at peptide concentrations around 100-fold lower than required in "peptide feeding" experiments with whole cells. We have also demonstrated that the conformational change induced in heavy chain is influenced by the concentration of beta 2M, and consequently have been able to demonstrate the formation of empty class-I molecules.

A multicenter validation study of Doppler ultrasound versus angiography.

The establishment of 60% or greater diameter stenosis by Doppler ultrasound is an eligibility requirement of the Asymptomatic Carotid Atherosclerosis Study (ACAS). We used a uniform statistical approach for each of 30 Doppler devices to establish a cutpoint for the peak systolic flow to insure a positive predictive value of 90% in predicting a 60%+ stenosis by angiography. Data were analyzed by device; however, performance relates to the device-sonographer-reader system. For those devices reporting in peak systolic velocity, cutpoints ranged from 151 to 390 cm/s, and for those reporting a peak systolic frequency from 5,400 to 11,250 Hz. Eighteen devices had a sensitivity above 60%, and nine devices had a sensitivity above 80%. However, for six instruments, the relationship between Doppler and angiography was too weak to establish any cutpoint. In addition, for one instrument a value could be established, but the associated sensitivity was only 18%. This remarkable variability in the performance is at odds with the high sensitivity uniformly published in the literature, suggesting (a) that the high reported sensitivity for Doppler may represent an overestimate of average performance, perhaps due to publication bias, (b) the paramount need for documented quality control measures within local laboratories to insure that Doppler examinations are performed reliably, and (c) the need for caution in the generalization of results among laboratories.

Cytotoxic T lymphocytes recognize a reconstituted class I histocompatibility antigen (HLA-A2) as an allogeneic target molecule.

Recent findings suggest that peptide fragments of newly synthesized proteins may associate intracellularly with nascent chains of class I histocompatibility antigens (termed MHC-I proteins because they are encoded by genes of the major histocompatibility complex) and that these peptide adducts may be required for the folding or stability and perhaps even the transport of these proteins to the cell surface. To determine whether these proteins can be reconstituted from their separated subunits into ostensibly native molecules in the absence of added peptides, we denatured a purified human MHC-I protein (HLA-A2) with 4 M NaSCN, separated its heavy (alpha) and light (beta 2-microglobulin) chains by gel filtration, and then mixed them in the presence of a 3-fold molar excess of beta 2-microglobulin and absence of added peptides. The reconstituted protein, recovered in 10% yield, was indistinguishable from native A2 in its reactivity with a monoclonal antibody (BB7.7) and its ability to specifically activate A2-specific CD8+ T cells. Inasmuch as the reconstituted A2 contained no detectable peptide adducts (we estimate less than 1 per 100 on a molar basis, assuming peptides of 2-5 kDa), the results suggest that peptide-free A2 can be recognized by CD8+ T cells and that peptide adducts are not essential for the MHC-I protein to maintain an ostensibly native structure.

Segregation of genetic markers in the two-spored secondarily homothallic basidiomycete Coprinus bilanatus.

Secondarily homothallic basidiomycetes, of which the cultivated mushroom Agaricus bisporus is an example, produce both self-fertile and non self-fertile spores. The random migration of nuclei from the basidia to give binucleate spores provides the simplest explanation for the regulation of breeding behaviour in this group of fungi. To test the predictions of the random migration hypothesis, the segregation of mating-type, auxotrophy and antimetabolite resistance has been determined in the secondarily homothallic ink-cap fungus, Coprinus bilanatus. In 41 of a total of 56 spore progenies tested, the segregation ratios conformed to the predictions of the random migration hypothesis. Poor fits to the predicted ratios were, in many instances, associated with an adenine auxotrophy. On the basis of the data reported, random migration can be regarded as the primary control of secondary homothallism.

Target cell lysis by cytotoxic T lymphocytes that lack detectable hemolytic perforin activity.

When mouse target cells are subjected to cytolytic attack by mouse CTL cell lines that have been cultured for many months in high levels of IL-2, and have abundant perforin-rich secretory granules, they exhibit two prominent changes: 1) rapid and massive increase (greater than 10-fold) in intracellular Ca2+ concentration and 2) fragmentation of DNA into nucleosome-sized fragments. We show here that when the same target cells are subjected to cytolytic attack by perforin-deficient CTL, either human CTL or primary mouse CTL from peritoneal exudates, the same changes are observed, suggesting that perforin-rich and perforin-deficient CTL kill their target cells by similar (if not identical) mechanisms. It is possible that perforin-deficient CTL produce enough perforin to destroy target cells but not enough to be detected by currently available methods.

Allorecognition of purified major histocompatibility complex glycoproteins by cytotoxic T lymphocytes.

To investigate how T cells recognize allogeneic class I proteins encoded by the major histocompatibility complex (MHC), we examined the human cytotoxic T lymphocytes (CTL) elicited in a mixed lymphocyte reaction against a lymphoblastoid B-cell line (JY) whose MHC-class I proteins are HLA-A2 and -B7. By panning the responding T cells on plates that were coated with purified HLA-A2, an essentially pure population of CD8+ anti-HLA-A2 CTL was isolated in a single step and established as a cell line designated A2p. In addition to lysing HLA-A2+ target cells, the A2p cells lysed HLA-A2- cells, including mouse cells (P815), when purified native HLA-A2 was attached to them, but not when denatured HLA-A2 was attached. Thus, contrary to the general rule that T cells recognize sequential antigenic determinants in denatured protein antigens, the alloreactive CTLs appear to recognize determinants that depend upon the native configuration of HLA-A2; however, the possibility that these T cells recognize a peptide adduct persistently associated with purified, soluble HLA-A2 has not been ruled out.

DNA polymorphisms in commercial and wild strains of the cultivated mushroom, Agaricus bisporus.

DNA from the cultivated mushroom, Agaricus bisporus, was cloned into the bacteriophage lambda vector EMBL3 creating a partial genomic library. Ten random clones from the library were used to probe for restriction fragment length polymorphisms (RFLPs). Six of the ten probes detected polymorphisms and were used to demonstrate variation in wild and cultivated strains of the mushroom. These results suggest that RFLPs could form a basis for genetic finger-printing and subsequent strain protection in A. bisporus. In single spore progeny, RFLPs were used to demonstrate normal meiotic segregation and to differentiate between homokaryons and heterokaryons. RFLPs therefore have great potential in the development of the genetics and breeding of this commercially important species.