Development of a novel tobramycin dependent riboswitch

We herein report the selection and characterization of a new riboswitch dependent on the aminoglycoside tobramycin. Its dynamic range rivals even the tetracycline dependent riboswitch to be the current best performing, synthetic riboswitch that controls translation initiation. The riboswitch was selected with RNA Capture-SELEX, a method that not only selects for binding but also for structural changes in aptamers on binding. This study demonstrates how this method can fundamentally reduce the labour required for the de novo identification of synthetic riboswitches. The initially selected riboswitch candidate harbours two distinct tobramycin binding sites with KDs of 1.1 nM and 2.4 μM, respectively, and can distinguish between tobramycin and the closely related compounds kanamycin A and B. Using detailed genetic and biochemical analyses and 1H NMR spectroscopy, the proposed secondary structure of the riboswitch was verified and the tobramycin binding sites were characterized. The two binding sites were found to be essentially non-overlapping, allowing for a separate investigation of their contribution to the activity of the riboswitch. We thereby found that only the high-affinity binding site was responsible for regulatory activity, which allowed us to engineer a riboswitch from only this site with a minimal sequence size of 33 nt and outstanding performance.

Tapping the potential of synthetic riboswitches: reviewing the versatility of the tetracycline aptamer

Synthetic riboswitches are a versatile class of regulatory elements that are becoming increasingly established in synthetic biology applications. They are characterized by their compact size and independence from auxiliary protein factors. While naturally occurring riboswitches were mostly discovered in bacteria, synthetic riboswitches have been designed for all domains of life. Published design strategies far exceed the number of riboswitches found in nature. A core element of any riboswitch is a binding domain, called an aptamer, which is characterized by high specificity and affinity for its ligand. Aptamers can be selected de novo, allowing the design of synthetic riboswitches against a broad spectrum of targets. The tetracycline aptamer has proven to be well suited for riboswitch engineering. Since its selection, it has been used in a variety of applications and is considered to be well established and characterized. Using the tetracycline aptamer as an example, we aim to discuss a large variety of design approaches for synthetic riboswitch engineering and their application. We aim to demonstrate the versatility of riboswitches in general and the high potential of synthetic RNA devices for creating new solutions in both the scientific and medical fields.

Relationship between fatigue and cytokine levels in patients age 50+ with acute myeloid leukemia (AML)

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Background: Fatigue is the most common and disabling symptom affecting patients with AML; effective prevention or treatment measures have yet to be found. Cytokines, biological markers of inflammation, may represent a major cause of fatigue, but published data are limited. Methods: Patients age 50 or older with AML were recruited between May and September 2006. All patients were fluent in English, within one year of diagnosis, and free of any other active malignancy. Fatigue was measured using the Functional Assessment of Cancer Therapy (FACT) Fatigue subscale, a single-item global fatigue scale, and the European Organization for the Research and Treatment of Cancer (EORTC) QLQ-C30. Blood was simultaneously drawn for quantitative measurement of a panel of 13 cytokines. Repeat measurements were done 4–6 weeks later. Correlational analysis was used to examine relationships between individual cytokines and fatigue scores. Changes in fatigue scores between time points were correlated with changes in cytokine levels. Results: 34 patients (23 men; 11 women) were enrolled (mean age 67 y; range 52–84). 27% had not started chemotherapy or were receiving best supportive care, while the rest were undergoing active chemotherapy. At baseline, a weak correlation (r=0.332, p=0.059) was seen with interleukin (IL)-6 and at least one fatigue measure. No correlations (r<0.30) were observed with any of the other cytokines (interferon (IFN)-?, IL-1β, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12, IP-10, MCP-1, MiG, and tumor necrosis factor-a) and any fatigue measure. Follow-up data were available for 29 patients. A statistically significant correlation with fatigue was seen with IL-2 (r=0.407, p=0.032), and clinically-important correlations that did not achieve conventional statistical significance were seen with IFN-? (r=0.331, p=0.085), IL-5 (r=0.344, p=0.073), and IL-10 (r=0.326, p=0.091). Conclusions: Based on these data, the most promising cytokine-fatigue relationship was noted with IL-2. However, IFN-?, IL-5, IL-6, and IL-10 also showed potentially important relationships with fatigue. Given our small sample size and patient enrolment at differing time points during their treatment course, further controlled studies are warranted.

No significant financial relationships to disclose.

Spleen autotransplantation in mice: a novel experimental model for immunology study

The aim of the experimental model to develop a spleen transplant model in mice to study the role of spleen in autoimmune and transplant rejection. After a midline incision, splenectomy was performed. Four tiny segments were cut from the removed spleen and were rinsed at room temperature in physiological salt solution. The greater omentum was lifted and four omental pockets were created; four thin segments were then placed into the "nests," subsequently marked, and fixed using 8-0 suture. The abdomen was then closed. The duration of the survival time was different among the nine groups (n = 3-3). Tissue samples were taken from the marked areas for histological examination stained with hematoxylin and eosin (H&E). H&E staining demonstrated large, well-circumscribed splenic nests with lymphoid zone and red pulp and well-formed trabecules in the spleen. Among the possible applications of this novel model is the ability to study the role of spleen in autoimmune and organ rejection.

The human hematopoietic stem cell compartment is heterogeneous for CXCR4 expression

The chemokine stromal derived factor-1alpha (SDF-1alpha) has been implicated recently in the chemotaxis of primitive human hematopoietic cells, suggesting that pluripotent human stem cells express the SDF-1alpha receptor, CXCR4. By using flow cytometry and confocal microscopy, we have identified and isolated primitive subsets of human CXCR4(+) and CXCR4(-) cells. Distinctions in the progenitor content and response to SDF-1alpha in vitro indicate that CXCR4(+) and CXCR4(-) cells represent discrete populations of primitive blood cells. The i.v. transplantation of these subfractions into immune-deficient mice established that both possess comparable engraftment capacity in vivo. Human myeloid, lymphoid, and primitive CD34(+) CXCR4(+) cells were present in chimeric animals transplanted with either subset, indicating that CXCR4(+) and CXCR4(-) stem cells have equivalent proliferative and differentiative abilities. Our study indicates that the human stem cell compartment is heterogeneous for CXCR4 expression, suggesting that the relationship between CXCR4 expression and stem cell repopulating function is not obligatory.

Characterization of chemokine receptors expressed in primitive blood cells during human hematopoietic ontogeny

Chemokines are capable of regulating a variety of fundamental processes of hematopoietic cells that include proliferation, differentiation, and migration. To evaluate potential chemokine signaling pathways important to the regulation of primitive human hematopoietic cells, we examined chemokine receptor expression of highly purified subpopulations of uncommitted human blood cells. CXCR1-, CXCR2-, CXCR4-, and CCR5-expressing cells were detected by flow cytometry among human blood subsets depleted of lineage-restricted cells (Lin(-)) derived from adult bone marrow, mobilized peripheral blood, cord blood (CB), and circulating fetal blood. Although these chemokine receptors could be detected on Lin(-) cells throughout human development, only CXCR4 could be detected in CD34(-)CD38(-)Lin(-) and CD34(+)CD38(-)Lin(-) subfractions enriched for stem cell function, suggesting that independent of ontogeny, CXCR4-mediated signals are critical to primitive hematopoiesis. Distinct to other stages of human hematopoietic development, primitive CB cells expressed higher levels of CXCR1, CXCR2, CCR5, and CXCR4 on both CD34(-)CD38(-)Lin(-) and CD34(+)CD38(-)Lin(-) subsets. Isolation of these fractions revealed expression of additional chemokine receptors CCR7, CCR8, and Bonzo (STRL133), whereas BOB (GPR15) could not be detected. Our study illustrates that rare uncommitted hematopoietic cells express chemokine receptors not previously associated with primitive human blood cells. Based on these results, we suggest that signaling pathways mediated by chemokine receptors identified here may play a fundamental role in hematopoietic stem cell regulation and provide alternative receptor targets for retroviral pseudotyping for genetic modification of repopulating cells.

Animal models in xenotransplantation

The severe shortage of donor organs has provided a strong impetus to push the investigation into the use of animal organs for humans. Xenotransplantation will not only benefit patients, but also represents a unique and potentially profitable business opportunity. However, there are many barriers to successful clinical xenotransplantation, including immunological barriers, physiological incompatibility, zoonosis and ethical concerns. This overview will focus on currently available animal models used in attempts to break through the immunological barriers to xenotransplantation. There are many advantages to using small animal, namely rodent, models in xenotransplantation research. For example, the use of the mouse model allows the use of knockout mice and careful dissection of rejection mechanisms at the molecular level. The following models can be used to study hyperacute rejection (HAR): guinea-pig-to-rat, mouse-to-rabbit, guinea-pig-to-mouse, rat-to-presensitised mouse and rat-to-alpha-Gal knockout mouse. The hamster-to-rat, mouse-to-rat and rat-to-mouse models are commonly used to study acute vascular rejection. Large animal models are complex and expensive, but they are more relevant to clinical xenotransplantation. Based on experiments using transgenic pig-to-primate models, HAR can be overcome. However, acute vascular rejection remains a major barrier at the present time. A pig cartilage-to-monkey model has been developed to study chronic rejection. Other novel models such as pig venous segment-to-monkey model and rat-to-primate model may represent viable options to study immunological barriers following xenotransplantation. Like many other medical breakthroughs, animal research will continue to make enormous contributions towards the eventual success of xenotransplantation.

Allograft tolerance induced by cyclophosphamide without prior inoculation of donor cells--immune suppression and redirection

OBJECTIVES

To determine the possibility and cellular mechanism of inducing allograft tolerance by multiple injection of a lower dose of cyclophosphamide without prior infusion of donor cells.

METHODS AND RESULTS

Heterotopic heart grafts were performed in MHC mismatched strain combinations (C57/B6 vs. BALB/c). Cyclophosphamide (40 mg/kg) was given intravenously on days 0, 2, 4 and 7 without prior infusion of donor cells. Long-term (> 100 days) allograft survival with normal histology was achieved. The long-term survivors accepted the donor skin grafts, but rejected the third-party skin grafts. Cyclophosphamide treatment initially led to profound lymphocytopenia, inhibition of spontaneous blastogenesis and low levels of lymphocyte proliferation response to both donor and third-party antigens. Ultimately, donor-specific tolerance occurred demonstrated by normal levels of peripheral lymphocytes, spontaneous blastogenesis and lymphocyte proliferation response to third-party antigens, and low levels of lymphocyte proliferation response to donor antigen. A switch of cytokines from IFNgamma dominant to IL-4 dominant, a low level of IgM and a high level of IgG1 were found in tolerant mice.

CONCLUSIONS

Allograft tolerance can be induced by a short course of cyclophosphamide without prior donor cell inoculation. Tolerance induced is characterized initially by non-specific immunosuppression, which progresses to donor-specific hyporesponsiveness associated with the development of a Th2 dominant cytokine response.

New strategies for chemokine inhibition and modulation: you take the high road and I'll take the low road

Chemokines are low molecular weight cytokines that induce extravasation, chemotaxis, and activation of a wide variety of leukocytes. Members of the different chemokine families are defined by the orientation of specific critical cysteine residues, and are designated as C-X-C (e.g. interleukin-8), C-C (e.g. regulated upon activation normally T cell expressed and secreted, RANTES), or C (lymphotactin). All chemokines bind to members of a G-protein coupled serpentine receptor superfamily that span the leukocyte cell surface membrane seven times and mediate the biological activities of the individual ligands. Most chemokines possess two major binding surfaces: a high affinity site responsible for specific ligand/receptor interactions and a lower affinity site, also called the heparin-binding or glycosaminoglycan-binding domain, believed to be responsible for the establishment and presentation of chemokine gradients on the surface of endothelial cells and within the extracellular matrix. Although chemokines are clearly beneficial in wound healing, hemopoiesis, and the clearance of infectious organisms, the continued expression of chemokines is associated with chronic inflammation. Therefore, this class of cytokines are attractive targets for the creation of antagonists that abrogate one or more chemokine functions. It is envisioned that such antagonists could serve as a new class of anti-inflammatory drugs. In this commentary, we will discuss two different but related strategies for antagonizing chemokine-induced functions, namely, disruption of the low and high affinity binding sites.

The purified myxoma virus gamma interferon receptor homolog M-T7 interacts with the heparin-binding domains of chemokines

The myxoma virus T7 protein M-T7 is a functional soluble gamma interferon receptor homolog that has previously been shown to bind gamma interferon and inhibit its antiviral activities in a species-specific manner, but gene knockout analysis has suggested a further role for M-T7 in blocking leukocyte influx into infected lesions. We purified M-T7 to apparent homogeneity and showed that M-T7 is an N-linked glycoprotein that appears to be a stable homotrimer with a molecular mass of approximately 113 kDa in solution. M-T7, in addition to forming inhibitory complexes with rabbit gamma interferon, was also shown to bind to human interleukin-8, a prototypic member of the chemokine superfamily. Moreover, M-T7 was able to interact promiscuously with all members of the CXC, CC, and C chemokine subfamilies tested. Binding of human RANTES to M-T7 can be competed by rabbit gamma interferon and also by cold RANTES competitor with a 50% inhibitory concentration of 900 nM. Although M-T7 retains binding to a number of interleukin-8 N-terminal (ELR) deletion mutants, binding to mutants containing deletions in the C-terminal heparin-binding domain of interleukin-8 is abrogated. Furthermore, heparin effectively competes the interaction of M-T7 with the chemokine RANTES but not with rabbit gamma interferon. We propose that this novel M-T7 interaction with members of the chemokine superfamily may be facilitated through the conserved heparin-binding domains found in a wide spectrum of chemokines and that M-T7 may function by modulating chemokine-glycosaminoglycan interactions in virus-infected tissues.

Bone marrow-derived murine mast cells migrate, but do not degranulate, in response to chemokines

We have determined that several chemokines induce mast cell migration in vitro. This directed migration is dependent on the presence of particular extracellular matrix proteins and the activation status of the cells. Mast cell haptotactic responses were observed in response to various chemokines on vitronectin-, laminin-, and fibronectin-coated filters. Unstimulated mast cells were chemoattracted only by monocyte chemotactic protein-1 and RANTES on vitronectin-coated and, to a lesser extent, laminin-coated filters, whereas IgE-activated mast cells migrated in response to monocyte chemotactic protein-1, regulated on activation normal T expressed and secreted, platelet factor-4, and macrophage inflammatory protein-1 alpha on all three matrix proteins. No significant migration was observed on collagen type IV-coated or uncoated filters. Mast cell migration in response to chemokines on extracellular matrices and its enhancement by IgE-dependent activation provide a mechanism by which cells may be drawn to sites of inflammation. Chemokine-induced mast cell recruitment may be particularly relevant in host defense responses to parasitic infections, allergic reactions, Jones-Mote reactions, and in wound healing.

Bone marrow-derived murine mast cells migrate, but do not degranulate, in response to chemokines

We have determined that several chemokines induce mast cell migration in vitro. This directed migration is dependent on the presence of particular extracellular matrix proteins and the activation status of the cells. Mast cell haptotactic responses were observed in response to various chemokines on vitronectin-, laminin-, and fibronectin-coated filters. Unstimulated mast cells were chemoattracted only by monocyte chemotactic protein-1 and RANTES on vitronectin-coated and, to a lesser extent, laminin-coated filters, whereas IgE-activated mast cells migrated in response to monocyte chemotactic protein-1, regulated on activation normal T expressed and secreted, platelet factor-4, and macrophage inflammatory protein-1 alpha on all three matrix proteins. No significant migration was observed on collagen type IV-coated or uncoated filters. Mast cell migration in response to chemokines on extracellular matrices and its enhancement by IgE-dependent activation provide a mechanism by which cells may be drawn to sites of inflammation. Chemokine-induced mast cell recruitment may be particularly relevant in host defense responses to parasitic infections, allergic reactions, Jones-Mote reactions, and in wound healing.

Assignment of genes for interleukin-8 receptors (IL8R) A and B to human chromosome band 2q35

The human genes encoding the interleukin 8 receptors type A and B were assigned to chromosome 2 by polymerase chain reaction amplification and by Southern analysis of a panel of human x rodent somatic cell hybrid DNAs. The IL8R genes were further localized by in situ hybridization to band 2q35.