Nucleoside optimization for RNAi: a high-throughput platform

The RNA induced silencing complex (RISC) contains at its core the endonuclease Argonaute (Ago) that allows for guide strand (GS)-mediated sequence-specific cleavage of the target mRNA. Functionalization of the sugar/phosphodiester backbone of the GS, which is in direct contact with Ago, presents a logical opportunity to affect RISC's activity. A systematic evaluation of modified nucleosides requires the synthesis of phosphoramidites corresponding to all four canonical bases (A, U, C, and G) and their sequential evaluation at each position along the 21-nucleotide-long GS. With the use of a platform approach, the sequential replacement of canonical bases with inosine greatly simplifies the problem and defines a new activity baseline toward which the corresponding sugar-modified inosines are compared. This approach was validated using 2'-O-benzyl modification, which demonstrated that positions 5, 8, 15, and 19 can accommodate this large group. Application of this high-throughput methodology now allows for hypothesis-driven rational design of highly potent, immunologically silent and stable siRNAs suitable for therapeutic applications.     

RNAi for Insect Control: Current Perspective and Future Challenges

The research on the RNA interference (RNAi) for the control of insect pests has made significant growth in recent years. The availability of the genomic sequences of insects has further widened the horizons for the testing of this technology to various insect groups. Different modes of application of double-stranded RNA (dsRNA) have been tested; however, the practicability of delivery of dsRNA in insects still remains the biggest challenge. Till date, the oral delivery of dsRNA in insects is one of the efficient approaches for the practical application of this technique. The uptake of dsRNA from the insect gut is mediated either by SID-1/SID-2 transmembrane proteins or by endocytosis; however, the systemic RNAi machinery still remains to be revealed in insect species. The RNAi-mediated gene knockdown has shown striking results in different insect groups, pointing it to be the upcoming technique for insect control. However, before the successful application of this technique for insect control, some potential issues need to be resolved. This review presents the account of prospects and challenges for the use of this technology for insect control.     

Single siRNA Nanocapsules for Enhanced RNAi Delivery

Synthetic siRNA has been considered as a highly promising therapeutic agent for human diseases. However, clinical use of siRNA has been hampered by instability in the body and inability to deliver sufficient RNA interference compounds to the tissues or cells. To address this challenge, we present here a single siRNA nanocapsule delivery technology, which is achieved by encapsulating a single siRNA molecule within a degradable polymer nanocapsule with a diameter around 20 nm and positive surface charge. As proof-of-concept, since CCR5 is considered a major silencing target of HIV therapy, CCR5-siRNA nanocapsules were delivered into 293T cells and successfully downregulated the CCR5 RNA fused with mCherry reporter RNA. In the absence of human serum, nanocapsules and lipofectamine silenced expression of CCR5-mCherry expression to 8% and 15%, respectively. Such nanocapsules maintain the integrity of siRNA inside even after incubation with ribonuclease and serum for 1 h; under the same conditions, siRNA is degraded in the native form or when formulated with lipofectamine. In the presence of serum, CCR5-siRNA nanocapsules knocked down CCR5-mCherry expression to less than 15% while siRNAs delivered through lipofectamine slightly knocked down the expression to 55%. In summary, this work provides a novel platform for siRNA delivery that can be developed for therapeutic purposes.     

Destructive quantum interference in heterocyclic alkanes: the search for ultra-short molecular insulators

Designing highly insulating sub-nanometer molecules is difficult because tunneling conductance increases exponentially with decreasing molecular length. This challenge is further enhanced by the fact that most molecules cannot achieve full conductance suppression with destructive quantum interference. Here, we present results for a series of small saturated heterocyclic alkanes where we show that conductance is suppressed due to destructive interference. Using the STM-BJ technique and density functional theory calculations, we confirm that their single-molecule junction conductance is lower than analogous alkanes of similar length. We rationalize the suppression of conductance in the junctions through analysis of the computed ballistic current density. We find there are highly symmetric ring currents, which reverse direction at the antiresonance in the Landauer transmission near the Fermi energy. This pattern has not been seen in earlier studies of larger bicyclic systems exhibiting interference effects and constitutes clear-cut evidence of destructive σ-interference. The finding of heterocyclic alkanes with destructive quantum interference charts a pathway for chemical design of short molecular insulators using organic molecules.

We present a combined experimental and theoretical study of small saturated heterocyclic alkanes and show that they perform well as insulators with an electronic transmission that is suppressed due to destructive interference.     

Automated MEMS-based Drosophila embryo injection system for high-throughput RNAi screens

We have developed an automated system based on microelectromechanical systems (MEMS) injectors for reliable mass-injection of Drosophila embryos. Targeted applications are high-throughput RNA interference (RNAi) screens. Our injection needles are made of silicon nitride. The liquid to be injected is stored in an integrated 500 nl reservoir, and an externally applied air pressure pulse precisely controls the injected volume. A steady-state water flow rate per applied pressure of 1.2 nl s(-1) bar(-1) was measured for a needle with channel width, height and length of 6.1 microm, 2.3 microm and 350 microm, respectively. A typical volume of 60 pl per embryo can be reliably and rapidly delivered within tens of milliseconds. Theoretical predictions of flow rates match measured values within +/-10%. Embryos are attached to a glass slide surface and covered with oil. Packages with the injector chip and the embryo slide are mounted on motorized xyz-stages. Two cameras allow the user to quickly align the needle tip to alignment marks on the glass slide. Our system then automatically screens the glass slide for embryos and reliably detects and injects more than 98% of all embryos. Survival rates after deionized (DI) water injection of 80% and higher were achieved. A first RNAi experiment was successfully performed with double-stranded RNA (dsRNA) corresponding to the segment polarity gene armadillo at a concentration of 0.01 microM. Almost 80% of the injected embryos expressed an expected strong loss-of-function phenotype. Our system can replace current manual injection technologies and will support systematic identification of Drosophila gene functions.     

Branched RNA nanostructures for RNA interference

Branched RNAs with three- or four-way junctions were designed by assembling single-stranded RNA for RNA interference. Human Dicer transformed branched RNAs into about 20 base pairs of double-stranded RNA, which is a standard siRNA species. Our tetramer design provides a potent silencing effect over a period of 5 days.     

Label-free characterization of cell adhesion using reflectometric interference spectroscopy (RIfS)

Reflectometric interference spectroscopy (RIfS) is a label-free, time-resolved technique for detecting interactions of molecules immobilized on a surface with ligands in solution. Here we show that RIfS also permits the detection of the adhesion of tissue culture cells to a functionalized surface in a flow system. Interactions of T cells with other leukocytes or epithelial cells of blood vessels are crucial steps in the regulating immune response and inflammatory reactions. Jurkat T cell leukemia cells rapidly attached to a transducer functionalized with a monoclonal antibody directed against the T cell receptor (TCR)/CD3 complex, followed by activation-dependent cell spreading. RIfS curves were obtained for the Jurkat derivative JCaM 1.6 (which lacks the key signaling protein Lck), cells preincubated with cytochalasin D (an inhibitor of actin polymerization), and for surfaces functionalized with an antibody directed against the coreceptor CD28. These curves differed with respect to the maximum signal and the initial slope of the increase in optical thickness. The testing of chemical inhibitors, cell surface molecules and gene products relevant to a key event in T cell immunity illustrates the potential of label-free techniques for the analysis of activation-dependent cell-surface contacts. The first two authors contributed equally to this paper     

Return to the RNAi world: rethinking gene expression and evolution (Nobel Lecture)

It's wonderful to be here today, I would like to start with the most important part, by saying thank you. First of all, I want to thank Andy Fire for being such a tremendous colleague, friend, and collaborator going back over the years. Without Andy I definitely wouldn't be here today. I need to thank the University of Massachusetts for providing for my laboratory, for believing in me, and for giving me not only a place and money, but great colleagues with whom to pursue my research. Without UMass and the great environment provided for me there, I probably would not be here today. And, of course my family; I'm not going to spend time now thanking them individually, but they know how important they are.     

Intrinsically conducting polymers for electromagnetic interference shielding

This paper summarizes and reviews the research on electromagnetic interference (EMI) shielding with intrinsically conducting polymers (ICPs), mainly polyaniline (PANI) and polypyrrole (PPY), and their composites in various frequency ranges. ICPs are new alternative candidates for EMI shielding applications due to their lightweight, corrosion resistance, ease of processing, and tunable conductivities as compared with typical metals. More importantly, the dominant shielding characteristic of absorption other than that of reflection for metals render ICPs more promising materials in applications requiring not only high EMI shielding effectiveness but also shielding by absorption, such as in stealth technology. Copyright © 2005 John Wiley & Sons, Ltd.     

Engineering Multifunctional RNAi Nanomedicine To Concurrently Target Cancer Hallmarks for Combinatorial Therapy

Cancer hallmarks allow the complexity and heterogeneity of tumor biology to be better understood, leading to the discovery of various promising targets for cancer therapy. An amorphous iron oxide nanoparticle (NP)‐based RNAi strategy is developed to co‐target two cancer hallmarks. The NP technology can modulate the glycolysis pathway by silencing MCT4 to induce tumor cell acidosis, and concurrently exacerbate oxidative stress in tumor cells via the Fenton‐like reaction. This strategy has the following features for systemic siRNA delivery: 1) siRNA encapsulation within NPs for improving systemic stability; 2) effective endosomal escape through osmotic pressure and/or endosomal membrane oxidation; 3) small size for enhancing tumor tissue penetration; and 4) triple functions (RNAi, Fenton‐like reaction, and MRI) for combinatorial therapy and in vivo tracking.     

Method for avoiding the interference of formamide with the Karl Fischer titration

 The Karl Fischer titration is based on a specific chemical reaction. Several measures exist to make all the water of insoluble samples accessible for the chemical reactants. The most efficient are the titration at elevated temperatures, the use of a homogenizer in the titration vessel and the modification of the polarity of the working medium (essentially methanol) by the addition of appropriate solvents like chloroform or formamide. It is known however that formamide interferes with the Karl Fischer reaction and so causes more or less false results. This effect increases with higher temperatures. A method is therefore presented to avoid this interference, even when working at the boiling point of the working medium. It takes advantage of the fact that the side reaction has a practically constant velocity, at least as long as usual titrations last. Thus, a constant additional consumption of Karl Fischer reagent is observed. This can be accounted for by measuring this effect before the start of the determination and by deducting the additional reagent consumption, which is proportional to the duration of the titration, from the totally added volume. With certain modern titrators this can even be carried out automatically. They can continuously measure the so-called drift, the titration rate necessary to keep the titration cell dry, and have the capability to use this drift as stop criterion for the titration. This means that the analysis is terminated when the drift existing before the titration is reached again. The additional consumption of reagent, to be deducted from the total volume, can (automatically) be calculated from the drift rate and the titration time. The proposed procedure allows the use of formamide as additional solvent, even at high temperatures, in order to shorten determination times considerably. It avoids false results due to the interference, which has so far prevented its use when exact results were desired and when the duration of the analysis was long. Received: 30 May 1996 / Revised: 26 July 1996/Accepted: 30 July 1996     

Real-time dynamics of label-free single mast cell granules revealed by differential interference contrast microscopy

We demonstrate the capability of differential interference contrast (DIC) microscopy as a simple and useful tool for studying cellular events without fluorescence labeling. By coupling an advanced DIC microscope to a computer-controlled motorized vertical stage and a high-speed, high-resolution CCD camera, real-time three-dimensional monitoring is possible in a high-throughput manner. The performance among three modes of microscopy, bright-field, dark-field and DIC, in terms of horizontal resolving power and vertical sectioning was investigated. As a model, exocytosis of rat peritoneal mast cells was recorded on the subsecond time scale. Three-dimensional tracking of granules during degranulation was achieved and granule–granule fusion before plasma membrane fusion was recorded. Electronic Supplementary Material Supplementary material is available for this article at     

Dissipaton equation of motion for system-and-bath interference dynamics

In this review we give a comprehensive account on the dissipaton equation of motion(DEOM) approach to quantum mechanics of open systems. This approach provides a statistical quasi-particle(dissipaton) picture for the environment, as it participates in the correlated system-and-bath dynamics. The underlying dissipaton algebra is de facto established via a close comparison with the celebrated hierarchical equations of motion formalism that is rooted at the Feynman-Vernon influence functional path integral formalism. As a quasi-particle generalization, DEOM identifies unambiguously the physical meanings of all involving dynamical variables as many-dissipaton configurations. It addresses the dynamics of not only systems but also hybridizing bath degrees of freedom. We demonstrate these features of DEOM via its real-time evaluation of the Fano interference of an analytically solvable model system, with the highlight that the statistical quasi-particle picture is ubiquitous, implied even in those commonly used quantum master equations.     

An Effective Platform for SARS-CoV-2 Prevention by Combining Neutralization and RNAi Technology

At present, the coronavirus disease 2019(COVID-19) pandemic is a global health crisis. Scientists all over the globe are urgently looking forward to an effective solution to prevent the spread of the epidemic and avoid more casualties at an early date. In this study, we establish an effective platform for the prevention of SARS-CoV-2 by combining the neutralization strategy and RNAi technology. To protect normal cells from infection, the customized cells are constructed to stably express viral a...     

Determination of uranium fission interference factors for INAA

Instrumental neutron activation analysis (INAA) is a very suitable technique for the determination of several elements in different kinds of matrices. However, when the sample contains high uranium concentration this method presents interference problems of uranium fission products. The same radioisotopes used in INAA are formed in uranium fission. Among these radioisotopes are ¹⁴¹Ce, ¹⁴³Ce, ¹⁴⁰La, ⁹⁹Mo, ¹⁴⁷Nd, ¹⁵³Sm and ⁹⁵Zr. The purpose of this study was to evaluate uranium fission interference factors to be used in the INAA of environmental and geological samples containing high levels of U. The obtained interference factors agreed with literature reported values. The results point to the viability of using these experimentally determined interference factors for the correction of uranium fission products.     

Two-layer reflectometric interference spectroscopy-based immunosensing for C-reactive protein

Microchimica Acta - We report on dual interference layers for use in reflectometric interference spectroscopy (RIfS)-based immunosensing. The layers consist of (a) an antibody-embedded...     

RNA interference silencing the transcriptional message

We developed the microbial immobilization particle with curdlan and activated carbon, which has great adsorption capacity. The characteristics of porosity and mechanical strength of these supporting particles are dependent on manufacturing method. The supporting particle showed the best performance when the ratio of curdlan and activated carbon was 30 to 6 g/L. Brumauer-Emmett-Teller (specific surface area) and swelling capacity of the carrier were 52.63 m²/g and 17 (w/w), respectively. The immobilization characteristics of iron-oxidizing bacteria on supporting particles were observed using a scanning electron microscope. The concentration of micro-organism on the surface of supporting particle was increased with reaction time. As the number of iron oxidation batch cycles increased, the iron oxidation rate increased.