Directed Evolution of Scanning Unnatural‐Protease‐Resistant (SUPR) Peptides for in Vivo Applications

Peptides typically have poor biostabilities, and natural sequences cannot easily be converted into drug‐like molecules without extensive medicinal chemistry. We have adapted mRNA display to drive the evolution of highly stable cyclic peptides while preserving target affinity. To do this, we incorporated an unnatural amino acid in an mRNA display library that was subjected to proteolysis prior to selection for function. The resulting “SUPR (scanning unnatural protease resistant) peptide” showed ≈500‐fold improvement in serum stability (t =160 h) and up to 3700‐fold improvement in protease resistance versus the parent sequence. We extended this approach by carrying out SUPR peptide selections against Her2‐positive cells in culture. The resulting SUPR4 peptide showed low‐nanomolar affinity toward Her2, excellent specificity, and selective tumor uptake in vivo. These results argue that this is a general method to design potent and stable peptides for in vivo imaging and therapy.     

Sulfide-induced nitrate reduction in the sludge of an anaerobic digester of a zero-discharge recirculating mariculture system

The anaerobic digester is a vital component in a zero-discharge mariculture system as therein most of the organic matter is mineralized and nitrogen-containing compounds are converted to gaseous N₂. Although denitrification is a major respiratory process in this nitrate-rich treatment stage, also sulfate respiration takes place and may cause undesirable high sulfide concentrations in the effluent water. To examine the effect of sulfide on nitrate reduction, in situ depth profiles of inorganic nitrogen and sulfur compounds were determined. Additionally, nitrate reduction was examined as a function of ambient sulfide concentrations in sludge collected from different locations in the anaerobic reactor. Depth profiles showed high concentrations of nitrate and low concentrations of sulfide and ammonia in the aqueous layer of the reactor. A sharp decrease of nitrate and an increase in sulfide and ammonia concentrations was measured at the water-sludge interface. Nitrate reduction was highest in this interface zone with rates of up to 8.05 ± 0.57 μmol NO₃⁻ h⁻¹ g_(sludge)⁻¹. Addition of sulfide increased the nitrate reduction rate at all sludge depths, pointing to the important role of autotrophic denitrification in the anaerobic reactor. Dissimilatory nitrate reduction to ammonia (DNRA) was found to be low in all sludge layers but was enhanced when sludge was incubated at high sulfide concentrations. Although nitrate reduction rates increased as a result of sulfide addition to sludge samples, no differences in nitrate reduction rates were observed between the samples incubated with different initial sulfide concentrations. This as opposed to sulfide oxidation rates, which followed Michaelis-Menten enzymatic kinetics. Partial oxidation of sulfide to elemental sulfur instead of a complete oxidation to sulfate, could explain the observed patterns of nitrate reduction and sulfide oxidation in sludge incubated with different initial sulfide concentrations.     

Genetically Encoded Biotin Analogues: Incorporation and Application in Bacterial and Mammalian Cells

The biotin–streptavidin interaction is among the strongest known in nature. Herein, the site-directed incorporation of biotin and 2-iminobiotin composed of noncanonical amino acids (ncAAs) into proteins is reported. 2-Iminobiotin lysine was employed for protein purification based on the pH-dependent dissociation constant to streptavidin. By using the high-affinity binding of biotin lysine, the bacterial protein RecA could be specifically isolated and its interaction partners analyzed. Furthermore, the biotinylation approach was successfully transferred to mammalian cells. Stringent control over the biotinylation site and the tunable affinity between ncAAs and streptavidin of the different biotin analogues make this approach an attractive tool for protein interaction studies, protein immobilization, and the generation of well-defined protein–drug conjugates.     

Metallic nanobowls by galvanic replacement reaction on heterodimeric nanoparticles

Well-defined metallic nanobowls can be prepared by extending the concept of a protecting group to colloidal synthesis. Magnetic nanoparticles are employed as "protecting groups" during the galvanic replacement of silver with gold. The replacement reaction is accompanied by spontantous dissociation of the protecting groups, leaving behind metallic nanobowls.     

Intact implicit memory for newly formed verbal associations in amnesic patients following single study trials.

This study examines the ability of amnesic patients to recover newly formed associations implicitly after a single study trial. Fifteen amnesic patients with various etiologies studied pairs by forming a sentence containing both words. At test, all participants saw 40 intact pairs, 40 rearranged pairs, and 40 new words. All pairs appeared side by side both at study and at test. For the implicit lexical-decision task, 40 nonwords were intermixed with the other pairs, and participants indicated whether both items were words. For the explicit speeded recognition test, participants were asked to indicate whether both words had appeared at study. Despite being severely impaired on the explicit test, amnesic patients performed like healthy controls on the implicit test, with faster and more accurate responses to intact pairs than to recombined pairs. Contrary to existing theories, the results suggest that amnesic patients can form and retain new associations. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

von Willebrand factor-cleaving protease in thrombotic thrombocytopenic purpura and the hemolytic-uremic syndrome

BACKGROUND: Thrombotic thrombocytopenic purpura and the hemolytic-uremic syndrome are severe microvascular disorders of platelet clumping with similar signs and symptoms. Unusually large multimers of von Willebrand factor, capable of agglutinating circulating platelets under high shear stress, occur in the two conditions. We investigated the prevalence of von Willebrand factor-cleaving protease deficiency in patients with familial and nonfamilial forms of these disorders. METHODS: Plasma samples were obtained from 53 patients with thrombotic thrombocytopenic purpura or hemolytic-uremic syndrome. Von Willebrand factor-cleaving protease was assayed in diluted plasma samples with purified normal von Willebrand factor as the substrate. The extent of the degradation of von Willebrand factor was assessed by electrophoresis in sodium dodecyl sulfate-agarose gels and immunoblotting. To determine whether an inhibitor of von Willebrand factor-cleaving protease was present, we measured the protease activity in normal plasma after incubation with plasma from the patients. RESULTS: We examined 30 patients with thrombotic thrombocytopenic purpura and 23 patients with the hemolytic-uremic syndrome. Of 24 patients with nonfamilial thrombotic thrombocytopenic purpura, 20 had severe and 4 had moderate protease deficiency during an acute event. An inhibitor found in 20 of these patients was shown to be IgG in five of five tested plasma samples. Of 13 patients with nonfamilial hemolytic-uremic syndrome, 11 had normal levels of activity of von Willebrand factor-cleaving protease during the acute episode, whereas in 2 patients, the activity was slightly decreased. All 6 patients with familial thrombotic thrombocytopenic purpura lacked von Willebrand factor-cleaving protease activity but had no inhibitor, whereas all 10 patients with familial hemolytic-uremic syndrome had normal protease activity. In vitro proteolytic degradation of von Willebrand factor by the protease was studied in 5 patients with familial and 7 patients with nonfamilial hemolytic-uremic syndrome and was normal in all 12 patients. CONCLUSIONS: Nonfamilial thrombotic thrombocytopenic purpura is due to an inhibitor of von Willebrand factor-cleaving protease, whereas the familial form seems to be caused by a constitutional deficiency of the protease. Patients with the hemolyticuremic syndrome do not have a deficiency of von Willebrand factor-cleaving protease or a defect in von Willebrand factor that leads to its resistance to protease.     

Perceptual integrality of sex and identity of faces: Further evidence for the single-route hypothesis.

According to current face-recognition models, sex (gender) and identity of faces are processed in independent routes. Using Garner's speeded-classification task, the authors provide evidence that sex and identity are processed within a single route. In 4 experiments, participants judged the sex or the familiarity of faces while the other dimension remained constant or varied randomly. The results of Experiments 1, 2, and 4 showed that participants could not selectively attend to either sex or familiarity without being influenced by the other, irrelevant dimension. Thus, identity and sex are integral dimensions. Experiment 3 provided evidence that when sex judgments are based on hairstyle heuristics, false separability can emerge. The findings support the claim that identity and sex are processed within a single route. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Space-time completion of video

This paper presents a new framework for the completion of missing information based on local structures. It poses the task of completion as a global optimization problem with a well-defined objective function and derives a new algorithm to optimize it. Missing values are constrained to form coherent structures with respect to reference examples. We apply this method to space-time completion of large space-time "holes" in video sequences of complex dynamic scenes. The missing portions are filled in by sampling spatio-temporal patches from the available parts of the video, while enforcing global spatio-temporal consistency between all patches in and around the hole. The consistent completion of static scene parts simultaneously with dynamic behaviors leads to realistic looking video sequences and images. Space-time video completion is useful for a variety of tasks, including, but not limited to: 1) sophisticated video removal (of undesired static or dynamic objects) by completing the appropriate static or dynamic background information. 2) Correction of missing/corrupted video frames in old movies. 3) Modifying a visual story by replacing unwanted elements. 4) Creation of video textures by extending smaller ones. 5) Creation of complete field-of-view stabilized video. 6) As images are one-frame videos, we apply the method to this special case as well