Synthesis of a small library of bivalent α-D-mannopyranosides for lectin cross-linking

A small library of bivalent α-D-mannopyranosides having rigid linkers was constructed in order to evaluate the effects of inter-saccharide distances upon multivalent binding interactions with plant and bacterial lectins. To this end, iodoaryl and propargyl α-D-mannopyranosides were synthesized and the former treated with TMS-acetylene under palladium chemistry to provide their corresponding ethynylaryl derivatives. A library of 15 dimeric members was then obtained using Lewis acid catalyzed glycosidation, aryl-aryl homocoupling, transition metal catalyzed Sonogashira cross-coupling reactions, and oxidative Glaser homocoupling.     

Design of a resilient ring for middle ear’s chamber stapes prosthesis

Abstract

This paper presents the process of designing a new elastic element replacing a membrane in the chamber stapes prosthesis (ChSP). The results of the study are volume displacement characteristics obtained for the prosthesis and physiological stapes. Simulation tests on a 3D CAD model have confirmed that a properly designed ring can stimulate perilymph with the same or greater efficacy as the physiological stapes footplate placed on the elastic annular ligament. The ChSP with a new elastic element creates a good chance of improving hearing in patients suffering from otosclerosis.     

Near-field dosimetry for in vitro exposure of human cells at 60 GHz

Due to the expected mass deployment of millimeter‐wave wireless technologies, thresholds of potential millimeter‐wave‐induced biological and health effects should be carefully assessed. The main purpose of this study is to propose, optimize, and characterize a near‐field exposure configuration allowing illumination of cells in vitro at 60 GHz with power densities up to several tens of mW/cm². Positioning of a tissue culture plate containing cells has been optimized in the near‐field of a standard horn antenna operating at 60 GHz. The optimal position corresponds to the maximal mean‐to‐peak specific absorption rate (SAR) ratio over the cell monolayer, allowing the achievement of power densities up to 50 mW/cm² at least. Three complementary parameters have been determined and analyzed for the exposed cells, namely the power density, SAR, and temperature dynamics. The incident power density and SAR have been computed using the finite‐difference time‐domain (FDTD) method. The temperature dynamics at different locations inside the culture medium are measured and analyzed for various power densities. Local SAR, determined based on the initial rate of temperature rise, is in a good agreement with the computed SAR (maximal difference of 5%). For the optimized exposure setup configuration, 73% of cells are located within the ±3 dB region with respect to the average SAR. It is shown that under the considered exposure conditions, the maximal power density, local SAR, and temperature increments equal 57 mW/cm², 1.4 kW/kg, and 6 °C, respectively, for the radiated power of 425 mW. Bioelectromagnetics 33:55–64, 2012. © 2011 Wiley Periodicals, Inc.     

Design of a PKCδ-specific small peptide as a theragnostic agent for glioblastoma

Glioblastoma is an aggressive malignant brain tumor that starts in the brain or spine and frequently recurs after anticancer treatment. The development of an accurate diagnostic system combined with effective cancer therapy is essential to improve prognosis of glioma patients. Peptides, produced from phage display, are attractive biomolecules for glioma treatment because of their biostability, nontoxicity, and small size. In this study, we employed phage display methodology to screen for peptides that specifically recognize the target PKCδ as a novel biomarker for glioma. The phage library screening yielded four different peptides displayed on phages with a 20- to 200-pM K_d value for the recombinant PKCδ catalytic domain. Among these four phage peptides, we selected one to synthesize and tagged it with fluorescein isothiocyanate (FITC) based on the sequence of the PKCδ-binding phage clone. The synthetic peptide showed a relative binding affinity for antibody and localization in the U373 glioma cell. The kinase activity of PKCδ was inhibited by FITC-labeled peptide with an IC₅₀ of 1.4 μM in vitro. Consequently, the peptide found in this study might be a promising therapeutic agent against malignant brain tumor.     

Temporal β-diversity of zooplankton at various time scales in a small mountain lake

Limnology - To examine how compositional changes in a community vary depending on time scales, we estimated temporal β-diversity of zooplankton in Lake Hataya Ohnuma, a small lake in Yamagata,...     

How does a small molecule bind at a cryptic binding site?

Protein-protein interactions (PPIs) are ubiquitous biomolecular processes that are central to virtually all aspects of cellular function. Identifying small molecules that modulate specific disease-related PPIs is a strategy with enormous promise for drug discovery. The design of drugs to disrupt PPIs is challenging, however, because many potential drug-binding sites at PPI interfaces are “cryptic”: When unoccupied by a ligand, cryptic sites are often flat and featureless, and thus not readily recognizable in crystal structures, with the geometric and chemical characteristics of typical small-molecule binding sites only emerging upon ligand binding. The rational design of small molecules to inhibit specific PPIs would benefit from a better understanding of how such molecules bind at PPI interfaces. To this end, we have conducted unbiased, all-atom MD simulations of the binding of four small-molecule inhibitors (SP4206 and three SP4206 analogs) to interleukin 2 (IL2)—which performs its function by forming a PPI with its receptor—without incorporating any prior structural information about the ligands’ binding. In multiple binding events, a small molecule settled into a stable binding pose at the PPI interface of IL2, resulting in a protein–small-molecule binding site and pose virtually identical to that observed in an existing crystal structure of the IL2-SP4206 complex. Binding of the small molecule stabilized the IL2 binding groove, which when the small molecule was not bound emerged only transiently and incompletely. Moreover, free energy perturbation (FEP) calculations successfully distinguished between the native and non-native IL2–small-molecule binding poses found in the simulations, suggesting that binding simulations in combination with FEP may provide an effective tool for identifying cryptic binding sites and determining the binding poses of small molecules designed to disrupt PPI interfaces by binding to such sites.     

Quantitative evaluation of refolding conditions for a disulfide-bond-containing protein using a concise ¹⁸O-labeling technique

A concise method was developed for quantifying native disulfide‐bond formation in proteins using isotopically labeled internal standards, which were easily prepared with proteolytic ¹⁸O‐labeling. As the method has much higher throughput to estimate the amounts of fragments possessing native disulfide arrangements by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOF‐MS) than the conventional high performance liquid chromatography (HPLC) analyses, it allows many different experimental conditions to be assessed in a short time. The method was applied to refolding experiments of a recombinant neuregulin 1‐β1 EGF‐like motif (NRG1‐β1), and the optimum conditions for preparing native NRG1‐β1 were obtained by quantitative comparisons. Protein disulfide isomerase (PDI) was most effective at the reduced/oxidized glutathione ratio of 2:1 for refolding the denatured sample NRG1‐β1 with the native disulfide bonds.     

Nuclear domain ‘knock-in’ screen for the evaluation and identification of small molecule enhancers of CRISPR-based genome editing

CRISPR is a genome-editing platform that makes use of the bacterially-derived endonuclease Cas9 to introduce DNA double-strand breaks at precise locations in the genome using complementary guide RNAs. We developed a nuclear domain knock-in screen, whereby the insertion of a gene encoding the green fluorescent protein variant Clover is inserted by Cas9-mediated homology directed repair (HDR) within the first exon of genes that are required for the structural integrity of subnuclear domains such as the nuclear lamina and promyelocytic leukemia nuclear bodies (PML NBs). Using this approach, we compared strategies for enhancing CRISPR-mediated HDR, focusing on known genes and small molecules that impact non-homologous end joining (NHEJ) and homologous recombination (HR). Ultimately, we identified the small molecule RS-1 as a potent enhancer of CRISPR-based genome editing, enhancing HDR 3- to 6-fold depending on the locus and transfection method. We also characterized U2OS human osteosarcoma cells expressing Clover-tagged PML and demonstrate that this strategy generates cell lines with PML NBs that are structurally and functionally similar to bodies in the parental cell line. Thus, the nuclear domain knock-in screen that we describe provides a simple means of rapidly evaluating methods and small molecules that have the potential to enhance Cas9-mediated HDR.     

Synthesis and evaluation of a 18F-curcumin derivate for β-amyloid plaque imaging

IntroductionCurcumin is a neuroprotective compound that inhibits the formation of amyloid oligomers and fibrils and binds to β-amyloid plaques in Alzheimer’s disease (AD). We aimed to synthesize an ¹⁸F-labeled curcumin derivate ([¹⁸F]4) and to characterize its positron emission tomography (PET) tracer-binding properties to β-amyloid plaques in a transgenic APP23 mouse model of AD.MethodsWe utilized facile one-pot synthesis of [¹⁸F]4 using nucleophilic ¹⁸F-fluorination and click chemistry. Binding of [¹⁸F]4 to β-amyloid plaques in the transgenic APP23 mouse brain cryosections was studied in vitro using heterologous competitive binding against PIB. [¹⁸F]4 uptake was studied ex vivo in rodents and in vivo using PET/computed tomography of transgenic APP23 and wild-type control mice.ResultsThe radiochemical yield of [¹⁸F]4 was 21 ± 11%, the specific activity exceeded 1 TBq/μmol, and the radiochemical purity exceeded 99.3% at the end of synthesis. In vitro studies of [¹⁸F]4 with the transgenic APP23 mouse revealed high β-amyloid plaque binding. In vivo and ex vivo studies demonstrated that [¹⁸F]4 has fast clearance from the blood, moderate metabolism but low blood–brain barrier (BBB) penetration.Conclusions[¹⁸F]4 was synthesized in high yield and excellent quality. In vitro studies, metabolite profile, and fast clearance from the blood indicated a promising tracer for Aβ imaging. However, [¹⁸F]4 has low in vivo BBB penetration and thus further studies are needed to reveal the reason for this and to possibly overcome this issue.     

FERN – a Java framework for stochastic simulation and evaluation of reaction networks

Background  

Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary.     

Development and evaluation of a trehalose-contained solution formula to preserve hUC-MSCs at 4°C

Human mesenchymal stem cells (hMSCs) hold great promise in cell therapy and regenerative medicine. Various preclinical and clinical trials have been carried out to illustrate the therapeutic potential of these cells. However, one major challenge for manufacturing clinical grade hMSCs is the requisition of current good manufacturing practice (cGMP) grade practices in cell isolation, processing, storage, and distribution. Development of non-toxic and animal serum-free preservation medium is critical for storage and distribution of mesenchymal stem cells (MSCs). In this study, we developed a solution formula that could preserve MSCs at 4°C for up to 3 weeks. In the solution, trehalose is a key ingredient for maintaining survival of MSCs. Among the concentrations investigated, 40 mM trehalose showed the best outcome with the viability maintained more than 92.7 ± 1.5% for 7 days. Cells preserved in the solution formula for 3 weeks still remained about 70% viability, and produced results similar to those of freshly harvested hMSCs in terms of growth kinetics, expression profile of cell surface antigens, and differentiation potential. In summary, storage of MSCs in the medium makes it far easier for transporting the cells from processing units to clinical sites.     

What measurements are necessary for a comprehensive evaluation of the peripheral arterial circulation?

Several methods are available to detect atherosclerotic lesions with a severe degree of stenosis (>70%), but the diagnosis of atherosclerotic lesions with no stenosis or with a minor degree of stenosis (<20%), is problematic. Hemodynamics associated with stenotic lesions are well described by the relationship of blood pressure and blood flow velocity, both as a function of time and localization (along the length and cross-section of the vessel). The use of this relationship in the clinic is difficult because no precise information is available about the geometry and branching of arteries, blood viscosity, and the velocity distribution over the cross-sectional area of the blood vessel. Besides, the invasiveness of the technique to measure arterial pressure as a function of time and localization does not allow routine application in patients. Because of these limitations, alternative methods have been developed. The degree and extensiveness of atherosclerotic disease can, for instance, be estimated from the changes in maximum blood flow velocity and in velocity profile, i.e., velocity distribution along the cross-section of the vessel. Moreover, the delay between simultaneously recorded arterial blood flow velocity tracings (pulse-wave velocity determination) is used to assess the elastic properties of the vessel. Changes in velocity profile occur at relatively slight degrees of arterial stenosis (around 20%), so that determination of these profiles along diseased arteries may contribute to the early diagnosis of atherosclerotic lesions. In man, transcutaneous information about the maximum and mean blood flow velocities over the cross-sectional area of the artery as an instantaneous function of time as well as the flow pattern can be obtained online with continuous wave Doppler flowmeters, at least when audio spectrum analysis is used as a processing technique. Velocity profiles can be determined with multichannel pulsed Doppler systems if the resolution of the system is adequate and a sufficient number of sample volumes can be obtained, limiting the interpolation between these samples. The on-line recording of velocity profiles can be facilitated by combining the pulsed Doppler device with either a velocity imaging system or a B-mode scan. In systems with a high resolution (sample distance 0.5 mm), one should be able to detect local disturbances in the velocity profile at the site of the lesion (due to local increases in shear stress) and proximal to the lesion (due to reflections), so that lesions with a minor degree of stenosis can be detected. In resistive systems (e.g., internal carotid arteries) in which the relationship between pressure and velocity changes during the cardiac cycle is relatively simple, the elasticity of the arterial wall can be determined by relating the relative diameter changes of the vessel, determined on-line with multichannel pulsed Doppler systems, to the instantaneous velocity pulse. Although the detection of atherosclerotic lesions at an early stage of the disease with sophisticated Doppler devices looks promising, further clinical evaluation is required.     

Emission of alfvén waves from a nonuniform MHD waveguide

The efficiency of the wave energy loss from a nonuniform MHD waveguide due to the conversion of the trapped magnetosonic waveguide modes into runaway Alfvén waves is estimated theoretically. It is shown that, if the waveguide parameters experience a jumplike change along the waveguide axis, the interaction between the waveguide modes and Alfvén waves occurs precisely at this “jump.” This effect is incorporated into the boundary conditions. A set of coupled integral equations with a singular kernel is derived in order to determine the transmission and reflection coefficients for the waveguide modes. The poles in the kernels of the integral operators correspond to the surface waves. When the jump in the waveguide parameters is small, analytic expressions for the frequency dependence of the transformation coefficients are obtained by using a model profile of the Alfvén velocity along the magnetic field. For the jump characterized by the small parameter value ε=0.3, the wave-amplitude transformation coefficient can amount to 5–10%. Under the phase synchronization condition (when the phase velocities of the waveguide modes on both sides of the jump are the same), the wave-energy transformation coefficient is much higher: it increases from a fraction of one percent to tens of percent. The transformation of fast magnetosonic waves into Alfvén waves is resonant in character, which ensures the frequency and wavelength filteringof the emitted Alfvén perturbations.     

Stability and evaluation of siRNAs labeled at the sense strand with a 3′-azobenzene unit

siRNAs bearing a 3′-azobenzene derivative on the sense strand were evaluated for their gene silencing ability in mammalian cell culture and nuclease stability in nuclease-rich media. Azobenzene can be isomerized between cis and trans isomers through the incubation of UV (cis isomer) and visible light (trans isomer). It was demonstrated that subtle differences in nuclease stability and activity were observed. These small changes can be used to photochemically fine-tune the activity of an siRNA for gene-silencing applications.     

Practical performance evaluation of a 10k × 10k CCD for electron cryo-microscopy

Electron cryo-microscopy (cryo-EM) images are commonly collected using either charge-coupled devices (CCD) or photographic film. Both film and the current generation of 16 megapixel (4k × 4k) CCD cameras have yielded high-resolution structures. Yet, despite the many advantages of CCD cameras, more than two times as many structures of biological macromolecules have been published in recent years using photographic film. The continued preference to film, especially for subnanometer-resolution structures, may be partially influenced by the finer sampling and larger effective specimen imaging area offered by film. Large format digital cameras may finally allow them to overtake film as the preferred detector for cryo-EM. We have evaluated a 111-megapixel (10k × 10k) CCD camera with a 9 μm pixel size. The spectral signal-to-noise ratios of low dose images of carbon film indicate that this detector is capable of providing signal up to at least 2/5 Nyquist frequency potentially retrievable for 3D reconstructions of biological specimens, resulting in more than double the effective specimen imaging area of existing 4k × 4k CCD cameras. We verified our estimates using frozen-hydrated ε15 bacteriophage as a biological test specimen with previously determined structure, yielding a ～7 ? resolution single particle reconstruction from only 80 CCD frames. Finally, we explored the limits of current CCD technology by comparing the performance of this detector to various CCD cameras used for recording data yielding subnanometer resolution cryo-EM structures submitted to the electron microscopy data bank (http://www.emdatabank.org/).     

Synthesis and evaluation of a netropsin–proximicin-hybrid library for DNA binding and cytotoxicity

The proximicins A–C (1–3) are novel naturally occurring γ-peptides with a hitherto unknown 2,4-disubstituted furan amino acid as a core structure. They show a moderate cytotoxic activity and induce upregulation of cell cycle regulating proteins (p53 and p21) and lead to cell cycle arrest in G0/G1-phase. Hybrid molecules combining structural motifs of the proximicins and of netropsin (4), a structurally related natural product, seem to have similar effects. Herein we describe the synthesis of a netropsin–proximicin-hybrid library and its evaluation regarding cytotoxicity and minor groove binding activity.     

Preparation and evaluation of a 99mTcN–PNP complex of sanazole analogue for detecting tumor hypoxia

A sanazole derivative, having a favorable single electron reduction potential (SERP) value compared to that of misonidazole, was synthesized and radiolabeled with [^99mTcN(PNP)] precursor to evaluate its potential as a hypoxia imaging agent. The complex, which was lipophilic, could be prepared in good yields and challenging studies with cysteine showed stability of the complex against trans-chelation. However, despite being lipophilic as well as possessing favorable SERP value, biodistribution studies of this complex in fibrosarcoma tumor bearing Swiss mice showed low uptake in tumor. This observation is possibly attributed to fast clearance of the complex from blood, whereby the complex spends insufficient time in tumor to get reduced and trapped. Though uptake in tumor was low, slow clearance of activity from tumor suggests reduction and trapping of the complex in hypoxic cells. The present ^99mTc-complex demonstrated acceptable values of tumor to blood (TBR) and tumor to muscle (TMR) ratios. However, low uptake in tumor which may not be indicative of the actual hypoxic status of the tumor, limit the utility of the complex to detect tumor hypoxia.     

Synthesis,structure, and evaluation of a β-cyclodextrin-artificial carbohydrate conjugate for use as a doxorubicin-carrying molecule

This paper describes the synthesis of a β-cyclodextrin (β-CyD) derivative conjugated with a C,C-glucopyranoside containing a benzene unit. Its doxorubicin-inclusion ability and structure are also discussed. SPR analysis revealed that the β-CyD conjugate had a high inclusion association value of 3.8 × 10⁶ M⁻¹ for immobilized doxorubicin. NMR structural analysis suggested that its high doxorubicin-inclusion ability was due to the formation of the inclusion complex as a result of the π–π stacking interaction between the benzene ring of the conjugate and the A ring of doxorubicin.