Structures for the polynucleotide complexes poly(dA) · poly(dT) and poly(dT) · poly(dA) · poly(dT)

X-ray diffraction analyses of fibers of polydeoxyadenylic acid · polydeoxythymidylic acid show that this molecule exists as a 10-fold double-helix with axial rise per nucleotide $\text{h = 3.24}\text{to}\text{3.29}\text{A}\text{?}$. The structure is very similar to B-DNA ($\text{h = 3.37}\text{A}\text{?}$) in having C3-exo furanose rings and base-pairs positioned centrally on the helix axis, but distinctive enough to have two packing modes, neither of which has been observed for B-DNA. Although the triple-stranded poly(dT) · poly(dA) · poly(dT) also has a large value of h(3.26 Å), each of the chains is a 12-fold helix of the A-genus with C3-endo furanose rings and bases displaced several Angstrom units from the helix axis.     

A method for improving Centre for Environmental Studies (CML) characterisation factors for metal (eco)toxicity — the case of zinc gutters and downpipes

Background, aim and scope  

The environmental impact of building products made from heavy metals has been a topic of discussion for some years. This was fuelled by results of life cycle assessments (LCAs), where the emission of heavy metals strongly effected the results. An issue was that the characterisation factors of the Centre for Environmental Studies (CML) 2000 life cycle impact assessment (LCIA) methodology put too much emphasis on the impact of metal emissions. We adjusted Zn characterisation factors according to the most recent insights in the ecotoxicity of zinc and applied them in an LCA using zinc gutters and downpipes as an example.     

Novel α(2)β(1) integrin-targeted peptide probes for prostate cancer imaging

Accumulating experimental evidence indicates that overexpression of α(2)β(1) integrin may correlate with progression in human prostate cancer. The objective of this study was to design a novel imaging probe based on the Asp-Gly-Glu-Ala (DGEA) peptide for near-infrared-fluorescent (NIRF) imaging of α(2)β(1) integrin expression in prostate cancer. The peptides were conjugated with appropriate fluorescent dyes, and the binding affinity of these probes was evaluated by flow cytometry in three human prostate cell lines (PC-3, CWR-22, and LNCaP). In vivo NIRF imaging of the α(2)β(1)-positive PC-3 xenograft model was performed to evaluate the α(2)β(1) targeted probe. In vitro immunofluorescence staining was carried out to confirm the α(2)β(1) integrin expression level. Flow cytometry analysis showed that PC-3 had the highest probe uptake, followed by CWR-22 and LNCaP tumor cells. In the subcutaneous PC-3 model, the tumor demonstrated prominent uptake with good tumor to background contrast. Immunohistochemistry staining also supported the in vivo optical imaging results. DGEA-based optical agents have been developed for specific imaging of α(2)β(1) integrin expression. In vitro and in vivo localization demonstrated the potential of this agent to identify tumor subtypes amenable to anti-α(2)β(1) integrin treatment and potentially provide prognostic information regarding tumor progression.     

Physiological roles for ecto-5’-nucleotidase (CD73)

Nucleotides and nucleosides influence nearly every aspect of physiology and pathophysiology. Extracellular nucleotides are metabolized through regulated phosphohydrolysis by a series of ecto-nucleotidases. The formation of extracellular adenosine from adenosine 5′-monophosphate is accomplished primarily through ecto-5′-nucleotidase (CD73), a glycosyl phosphatidylinositol-linked membrane protein found on the surface of a variety of cell types. Recent in vivo studies implicating CD73 in a number of tissue protective mechanisms have provided new insight into its regulation and function and have generated considerable interest. Here, we review contributions of CD73 to cell and tissue stress responses, with a particular emphasis on physiologic responses to regulated CD73 expression and function, as well as new findings utilizing Cd73-deficient animals.     

Chemical shift assignments for F-plasmid TraI (381–569)

TraI, the F plasmid-encoded nickase, is a 1,756 amino acid protein essential for conjugative transfer of F plasmid DNA from one bacterium to another. While crystal structures of N- and C-terminal domains of F TraI have been determined, central domains of the protein are structurally unexplored. These middle domains (between residues 306 and 1,500) are known to both bind single-stranded DNA (ssDNA) and unwind DNA through a highly processive helicase activity. Of this central region, the more C-terminal portion (~900–1500) appears related to helicase RecD of the E. coli RecBCD complex. The more N-terminal portion (306–900), however, shows limited sequence similarity to other proteins. In an attempt to define the structure of well-folded domains of this middle region and discern their function, we have isolated stable regions of TraI following limited proteolysis. One of these regions, TraI (381–569), was identified and a genetic construct encoding it was engineered. The protein was expressed, purified, and the sequence-specific chemical shifts for it were assigned.     

Expanding the Clinical Indications for α(1)-Antitrypsin Therapy

α(1)-Antitrypsin (AAT) is a 52-kDa circulating serine protease inhibitor. Production of AAT by the liver maintains 0.9-1.75 mg/mL circulating levels. During acute-phase responses, circulating AAT levels increase more than fourfold. In individuals with one of several inherited mutations in AAT, low circulating levels increase the risk for lung, liver and pancreatic destructive diseases, particularly emphysema. These individuals are treated with lifelong weekly infusions of human plasma-derived AAT. An increasing amount of evidence appears to suggest that AAT possesses not only the ability to inhibit serine proteases, such as elastase and proteinase-3 (PR-3), but also to exert antiinflammatory and tissue-protective effects independent of protease inhibition. AAT modifies dendritic cell maturation and promotes T regulatory cell differentiation, induces interleukin (IL)-1 receptor antagonist and IL-10 release, protects various cell types from cell death, inhibits caspases-1 and -3 activity and inhibits IL-1 production and activity. Importantly, unlike classic immunosuppressants, AAT allows undeterred isolated T-lymphocyte responses. On the basis of preclinical and clinical studies, AAT therapy for nondeficient individuals may interfere with disease progression in type 1 and type 2 diabetes, acute myocardial infarction, rheumatoid arthritis, inflammatory bowel disease, cystic fibrosis, transplant rejection, graft versus host disease and multiple sclerosis. AAT also appears to be antibacterial and an inhibitor of viral infections, such as influenza and human immunodeficiency virus (HIV), and is currently evaluated in clinical trials for type 1 diabetes, cystic fibrosis and graft versus host disease. Thus, AAT therapy appears to have advanced from replacement therapy, to a safe and potential treatment for a broad spectrum of inflammatory and immune-mediated diseases.     

Cystine-knot peptides engineered with specificities for α(IIb)β(3) or α(IIb)β(3) and α(v)β(3) integrins are potent inhibitors of platelet aggregation

A truncated form of the Agouti‐related protein (AgRP), a member of the cystine‐knot family, has shown promise as a scaffold for engineering novel peptides with new molecular recognition properties. In this study, we replaced a constrained six amino acid loop in AgRP with a nine amino acid loop containing an Arg–Gly–Asp integrin recognition motif, and randomized the neighboring residues to create a library of ～20 million AgRP variants. We displayed the AgRP mutants as fusions on the surface of yeast and used high‐throughput fluorescence‐activated cell sorting (FACS) to isolate peptides that bound specifically to the platelet integrin α_IIbβ₃, a clinically important target for the prevention and treatment of thrombosis. These AgRP peptides had equilibrium dissociation (K_D) constants for α_IIbβ₃ integrin ranging from 60 to 90 nM, and did not bind to α_vβ₃, α_vβ₅, or α₅β₁ integrins. Using an alternate library screening strategy, we identified AgRP peptides that bound to both α_IIbβ₃ and α_vβ₃ integrins with K_D values ranging from 40 to 70 nM and 20 to 30 nM, respectively, and did not bind to α_vβ₅ or α₅β₁ integrins. Unique consensus sequences were identified within both series of AgRP peptides suggesting alternative molecular recognition events that dictate different integrin binding specificities. In addition, the engineered AgRP peptides prevented platelet aggregation as well as or slightly better than the FDA‐approved cyclic peptide eptifibatide. Collectively, these data demonstrate that cystine‐knot peptides can be generated with high affinity and specificity to closely‐related integrins, and provide insights into molecular interactions between small, structured peptide ligands and their receptors. Copyright © 2010 John Wiley & Sons, Ltd.     

Relativistic MS-Xα calculations for some thallium(I) compounds

Ionization energies for TlF, TlC1, TlBr, TlI, Tl₂O, Tl₂S, and TlNO₃ have been obtained using relativistic overlapping spheres multiple-scattering Xα transition state calculations. The results are compared with other theoretical and experimental ionization energies. It was found that the present results are in agreement with the experimental ionization energies. However, the results of these calculations and other recent calculations strongly suggest that the assignment of the origin of the bands in the photoelectron spectra of thallium(I) compounds has been erroneous. A uniform interpretation for the monovalent compounds of group IIIA and divalent compounds of group IVA is proposed.     

Silicon,a required nutrient for Cladophora glomerata (L) Kütz. (Chlorophyta)

Summary Physiological and ultrastructural studies of unialgal cultures demonstrated that silicon is a required nutrient and a component of the cell walls of Cladophora glomerata. Addition of silicon promoted growth of the alga, and the addition of germanium, an analogue of silicon, inhibited growth of C. glomerata in culture. An electron-dense outer layer was a conspicuous part of the cell walls of filaments taken from silicon rich medium.Abbreviation SWE soil water extract     

Near-infrared fluorescent divalent RGD ligand for integrin α(v)β(3)-targeted optical imaging

A new near-infrared fluorescent compound containing two cyclic RGD motifs, cypate-[c(RGDfK)](2) (1), was synthesized based on a carbocyanine fluorophore bearing two carboxylic acid groups (cypate) for integrin α(v)β(3)-targeting. Compared with its monovalent counterpart cypate-c(RGDfK) (2), 1 exhibited remarkable improvements in integrin α(v)β(3) binding affinity and tumor uptake in nude mice of A549. The results suggest that cypate-linked divalent ligands can serve as an important molecular platform for exploring receptor-targeted optical imaging and treatment of various diseases.     

Cooperation of p40(phox) with p47(phox) for Nox2-based NADPH oxidase activation during Fcγ receptor (FcγR)-mediated phagocytosis: mechanism for acquisition of p40(phox) phosphatidylinositol 3-phosphate (PI(3)P) binding

During activation of the phagocyte (Nox2-based) NADPH oxidase, the cytoplasmic Phox complex (p47(phox)-p67(phox)-p40(phox)) translocates and associates with the membrane-spanning flavocytochrome b(558). It is unclear where (in cytoplasm or on membranes), when (before or after assembly), and how p40(phox) acquires its PI(3)P-binding capabilities. We demonstrated that in addition to conformational changes induced by H(2)O(2) in the cytoplasm, p40(phox) acquires PI(3)P-binding through direct or indirect membrane targeting. We also found that p40(phox) is essential when p47(phox) is partially phosphorylated during FcγR-mediated oxidase activation; however, p40(phox) is less critical when p47(phox) is adequately phosphorylated, using phosphorylation-mimicking mutants in HEK293(Nox2/FcγRIIa) and RAW264.7(p40/p47KD) cells. Moreover, PI binding to p47(phox) is less important when the autoinhibitory PX-PB1 domain interaction in p40(phox) is disrupted or when p40(phox) is targeted to membranes. Furthermore, we suggest that high affinity PI(3)P binding of the p40(phox) PX domain is critical during its accumulation on phagosomes, even when masked by the PB1 domain in the resting state. Thus, in addition to mechanisms for directly acquiring PI(3)P binding in the cytoplasm by H(2)O(2), p40(phox) can acquire PI(3)P binding on targeted membranes in a p47(phox)-dependent manner and functions both as a "carrier" of the cytoplasmic Phox complex to phagosomes and an "adaptor" of oxidase assembly on phagosomes in cooperation with p47(phox), using positive feedback mechanisms.     

Social aspects for sustainability assessment of technologies—challenges for social life cycle assessment (SLCA)

Purpose

Technologies can contribute to sustainable development (e.g., improving living conditions) and at the same time cause sustainability problems (e.g., emissions). Decisions on alternative technologies should thus ideally be based on the principle to minimize the latter. Analyzing environmental, economic, and social aspects related to technologies supports decisions by identifying the “more sustainable” technology. This paper focuses on social issues. First, it discusses the applicability of the social life cycle assessment (SLCA) guidelines for a comparative technology analysis, taking the example of two case studies in developing countries. Indicating technologies as “sustainable” also means that they are indeed operated over the expected lifetime, which, in development projects, is often not guaranteed. Consequently, social aspects related to implementation conditions should be considered in an SLCA study as well. Thus, a second focus is laid on identifying appropriate indicators to address these aspects.

Methods

First, the SLCA guidelines were examined with regard to applying this product-related approach to two real case studies (analysis of technologies/plants for water supply and for decentralized fuel production) for a comparative technology analysis. Suitable indicators are proposed. To address the second focus, a literature research on technology assessment and implementation in developing countries was conducted. Moreover, socioeconomic studies in the investigation areas of the case studies were consulted. Based on this, indicators addressing implementation conditions were identified from the SLCA guidelines and additional literature.

Results and discussion

The study shows social issues and indicators found in the SLCA guidelines and considered suitable for a comparative technology analysis in the case studies. However, for a sustainability assessment of technologies, especially in developing countries, further indicators are required to address technology implementation conditions. A set of additional social indicators like reported trust in institutions or fluctuation of personnel is proposed. Though these indicators were derived based on specific case studies, they can also be suggested to other technologies and are not necessarily limited to developing countries.

Conclusions

The study pointed out that an application of the SLCA guidelines considering the whole life cycle was not (yet) feasible for the case studies considered. This is mainly due to the lack of data. Regarding technology implementation, it was examined which indicators are available in this SLCA approach and which could additionally be integrated and applied. This is relevant as a potential contribution of technologies to sustainable development can only be achieved when the technologies are successfully implemented.     

Kinetic models for the dynamical behavior of polyacrylamide (PAAm)–κ-carrageenan (κC) composite gels

A fluorescence method was employed for studying the drying and swelling of PAAm–κC composite gels, which were formed from acrylamide (AAm) and N, N’- methylenebisacrylamide (BIS) with various κ–carrageenan (κC) contents by free radical crosslinking copolymerization in water. Composite gels were prepared at 80 °C with pyranine (Py) as a fluorescence probe. Scattered light, I_sc, and fluorescence emission intensities, I_em, were monitored during drying and swelling of these gels. The fluorescence intensity of pyranine increased and decreased as drying and swelling time are increased, respectively, for all gel samples. The Stern–Volmer equation combined with moving boundary and Li-Tanaka models were used to explain the behavior of I_em during drying and swelling processes respectively. It is found that the desorption coefficient D_d decreased as κC contents were increased for a given temperature during drying. However, the cooperative diffusion coefficient, D_s presented exactly the opposite case. Conventional gravimetrical and volumetric experiments were also carried out during drying and swelling of PAAm–κC composite gels. It was observed that D_d and D_s values measured with the fluorescence method were found to be much larger than they were measured with the conventional methods.     

Selective assay for endotoxin using poly(ε-lysine)-immobilized Cellufine and Limulus amoebocyte lysate (LAL)

We developed a selective endotoxin (lipopolysaccharide; LPS) assay using poly(ε-lysine)-immobilized cellulose beads (PL-Cellufine) and Limulus amoebocyte lysate (LAL). First, LPS was selectively adsorbed on the beads in a solution containing various LAL-inhibiting or LAL-enhancing compounds (e.g., amino acids, enzymes) and the LPS adsorbed on the beads was separated from the compounds by centrifugation. Second, the LPS adsorbed on the beads directly reacted with the LAL reagent, and the LPS concentration was determined by a turbidimetric time assay. The accuracy of the adsorption method with PL-Cellufine was high compared with that of a common solution method. Apparent recovery of LPS from compound solution was 88-120%.     

Chitosan IFN-γ-pDNA Nanoparticle (CIN) Therapy for Allergic Asthma

Background  

Allergic subjects produce relatively low amounts of IFN-γ, a pleiotropic Th-1 cytokine that downregulates Th2-associated airway inflammation and hyperresponsiveness (AHR), the hallmarks of allergic asthma. Adenovirus-mediated IFN-γ gene transfer reduces AHR, Th2 cytokine levels and lung inflammation in mice, but its use would be limited by the frequency of gene delivery required; therefore, we tested chitosan/IFN-γ pDNA nanoparticles (CIN) for in situ production of IFN-γ and its in vivo effects.     

Bis-Fe(IV): nature’s sniper for long-range oxidation

Iron-dependent enzymes are prevalent in nature and participate in a wide range of biological redox activities. Frequently, high-valence iron intermediates are involved in the catalytic events of iron-dependent enzymes, especially when the activation of peroxide or molecular oxygen is involved. Building on the fundamental framework of iron–oxygen chemistry, these reactive intermediates constantly attract significant attention from the enzymology community. During the past few decades, tremendous efforts from a number of laboratories have been dedicated to the capture and characterization of these intermediates to improve mechanistic understandings. In 2008, an unprecedented bis-Fe(IV) intermediate was reported in a c-type diheme enzyme, MauG, which is involved in the maturation of a tryptophan tryptophylquinone cofactor of methylamine dehydrogenase. This intermediate, although chemically equivalent to well-characterized high-valence iron intermediates, such as compound I, compound ES, and intermediate Q in methane monooxygenase, as well as the hypothetical Fe(V) species in Rieske non-heme oxygenases, is orders of magnitude more stable than these other high-valence species in the absence of its primary substrate. It has recently been discovered that the bis-Fe(IV) intermediate exhibits a unique near-IR absorption feature which has been attributed to a novel charge-resonance phenomenon. This review compares the properties of MauG with structurally related enzymes, summarizes the current knowledge of this new high-valence iron intermediate, including its chemical origin and structural basis, explores the formation and consequences of charge resonance, and recounts the long-range catalytic mechanism in which bis-Fe(IV) participates. Biological strategies for storing oxidizing equivalents with iron ions are also discussed.