Enrichment of low abundance DNA/RNA by oligonucleotide-clicked iron oxide nanoparticles.

Detection of low abundance target DNA/RNA for clinical or research purposes is challenging because the target sequences can be hidden under a large background of human genomic or non-human metagenomic sequences. We describe a probe-based capture method to enrich for target sequences with DNA-clicked iron oxide nanoparticles. Our method was tested against commercial capture assays using streptavidin beads, on a set of probes derived from a common genotype of the hepatitis C virus. We showed that our method is more specific and sensitive, most likely due to the combination of an inert silica coating and a high density of DNA probes clicked to the nanoparticles. This facilitates target capture below the limits of detection for TaqMan qPCR, and we believe that this method has the potential to transform management of infectious diseases.

An injectable peptide hydrogel for reconstruction of the human trabecular meshwork.

Glaucoma is a leading cause of irreversible blindness worldwide. Current treatments of glaucoma involve lowering the IOP by means of decreasing aqueous humor production or increasing non-trabecular aqueous humor outflow with the help of IOP-lowering eye drops, nanotechnology enabled glaucoma drainage implants, and trabeculectomy. However, there is currently no effective and permanent cure for this disease. In order to investigate new therapeutic strategies, three dimensional (3D) biomimetic trabecular meshwork (TM) models are in demand. Therefore, we adapted MAX8B, a peptide hydrogel system to bioengineer a 3D trabecular meshwork scaffold. We assessed mechanical and bio-instructive properties of this engineered tissue matrix by using rheological analysis, 3D cell culture and imaging techniques. The scaffold material exhibited shear-thinning ability and biocompatibility for proper hTM growth and proliferation indicating a potential utilization as an injectable implant. Additionally, by using a perfusion system, MAX8B scaffold was tested as an in vitro platform for investigating the effect of Dexamethasone (Dex) on trabecular meshwork outflow facility. The physiological response of hTM cells within the scaffold to Dex treatment clearly supported the effectiveness of this 3D model as a drug-testing platform, which can accelerate discovery of new therapeutic targets for glaucoma. STATEMENT OF SIGNIFICANCE: Artificial 3D-TM (3-dimentional Trabecular Meshwork) developed here with hTM (human TM) cells seeded on peptide-hydrogel scaffolds exhibits the mechanical strength and physiological properties mimicking the native TM tissue. Besides serving a novel and effective 3D-TM model, the MAX8B hydrogel could potentially function as an injectable trabecular meshwork implant.

Establishment of human trabecular meshwork cell cultures using nontransplantable corneoscleral rims.

Human trabecular meshwork (hTM) cell isolation in academic settings utilizes the motile nature of these cells, allowing them to migrate away from the explant and proliferate on distal regions of the culture substrate. Corneoscleral rims used for transplantation are a potential source of explants for the establishment of hTM cell cultures. However, cell isolation and the initiation of primary cell cultures from ocular tissues stored in Optisol-GS medium for an extended period of time (>6 days) has proven difficult, since Optisol-GS remarkably reduces cell viability and cellularity. Therefore, explants obtained from ocular tissues stored in Optisol-GS do not often provide adequate cell yield to initiate primary cell cultures if conventional culture techniques are used. Therefore, the majority of the research on primary hTM cell isolation has been accomplished using donor tissue obtained within 72 h postmortem. The goal of this study was to develop an hTM cell isolation procedure from nontransplantable ocular materials, utilizing the anchorage dependency of TM cells. This procedure yielded functionally viable cells, eficiently dissociated from the trabecular meshwork. Isolated cells demonstrated typical hTM cell characteristics including monolayer formation, contact inhibition, phagocytosis, and responses to glucocorticoid exposure. To the best of our knowledge, this is the first time an expired explant has been utilized in the successful isolation of hTM cells. Our results clearly demonstrate the advantage of increasing the anchor points of hTM cells for enhanced cell migration out from the explants, which have limited cell proliferative capacity.

An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications.

In this paper we review the current status of high-performance computing applications in the general area of drug discovery. We provide an introduction to the methodologies applied at atomic and molecular scales, followed by three specific examples of implementation of these tools. The first example describes in silico modeling of the adsorption of small molecules to organic and inorganic surfaces, which may be applied to drug delivery issues. The second example involves DNA translocation through nanopores with major significance to DNA sequencing efforts. The final example offers an overview of computer-aided drug design, with some illustrative examples of its usefulness.

Sporosarcina pasteurii can form nanoscale calcium carbonate crystals on cell surface.

The bacterium Sporosarcina pasteurii (SP) is known for its ability to cause the phenomenon of microbially induced calcium carbonate precipitation (MICP). We explored bacterial participation in the initial stages of the MICP process at the cellular length scale under two different growth environments (a) liquid culture (b) MICP in a soft agar (0.5%) column. In the liquid culture, ex-situ imaging of the cellular environment indicated that S. pasteurii was facilitating nucleation of nanoscale crystals of calcium carbonate on bacterial cell surface and its growth via ureolysis. During the same period, the meso-scale environment (bulk medium) was found to have overgrown calcium carbonate crystals. The effect of media components (urea, CaCl2), presence of live and dead in the growth medium were explored. The agar column method allows for in-situ visualization of the phenomena, and using this platform, we found conclusive evidence of the bacterial cell surface facilitating formation of nanoscale crystals in the microenvironment. Here also the bulk environment or the meso-scale environment was found to possess overgrown calcium carbonate crystals. Extensive elemental analysis using Energy dispersive X-ray spectroscopy (EDS) and X-ray powder diffraction (XRD), confirmed that the crystals to be calcium carbonate, and two different polymorphs (calcite and vaterite) were identified. Active participation of S. pasteurii cell surface as the site of calcium carbonate precipitation has been shown using EDS elemental mapping with Scanning transmission electron microscopy (STEM) and scanning electron microscopy (SEM).

Sporosarcina pasteurii can clog and strengthen a porous medium mimic.

The bacterium Sporosarcina pasteurii can produce significant volumes of solid precipitation in the presence of specific chemical environments. These solid precipitate particles can enter a network of microscale pores and cause long-range clogging. As a result, the medium gains strength and exhibits superior mechanical properties. This concept is also known as Microbiologically Induced Calcite Precipitation (MICP). In this study, we have used sponge blocks as surrogate porous media mimics and analyzed several aspects of MICP. A synergistic approach involving electron microscopy (SEM), computerized X-Ray tomography (µCT), quasi-static compressive load testing and chemical characterization (EDX) has been used to understand several physical and chemical aspects of MICP.

Enhanced overexpression, purification of a channelrhodopsin and a fluorescent flux assay for its functional characterization.

Channelrhodopsins (ChRs) are a group of membrane proteins that allow cation flux across the cellular membrane when stimulated by light. They have been emerged as important tools in optogenetics where light is used to trigger a change in the membrane potential of live cells which induces downstream physiological cascades. There is also increased interest in their applications for generating light-responsive biomaterials. Here we have used a two-step screening protocol to develop a Pichia pastoris strain that produces superior yields of an enhance variant of CaChR2 (from Chlamydomonas reinhardtii), called ChIEF. We have also studied the effect of the co-factor, namely all-trans retinal (ATR), on the recombinant overexpression, folding, and function of the protein. We found that both ChIEF-mCitrine and CaChR2 can be overexpressed and properly trafficked to the plasma membrane in yeast regardless of the presence of the ATR. The purified protein was reconstituted into large unilamellar lipid vesicle using the detergent-assisted method. Using 9-amino-6-chloro-2-methoxyacridine (ACMA) as the fluorescent proton indicator, we have developed a flux assay to verify the light-activated proton flux in the ChIEF-mCitrine vesicles. Hence such vesicles are effectively light-responsive nano-compartments. The results presented in this work lays foundations for creating bio-mimetic materials with a light-responsive function using channelrhodopsins.

Knotty: efficient and accurate prediction of complex RNA pseudoknot structures.

Motivation: The computational prediction of RNA secondary structure by free energy minimization has become an important tool in RNA research. However in practice, energy minimization is mostly limited to pseudoknot-free structures or rather simple pseudoknots, not covering many biologically important structures such as kissing hairpins. Algorithms capable of predicting sufficiently complex pseudoknots (for sequences of length n) used to have extreme complexities, e.g. Pknots has O(n6) time and O(n4) space complexity. The algorithm CCJ dramatically improves the asymptotic run time for predicting complex pseudoknots (handling almost all relevant pseudoknots, while being slightly less general than Pknots), but this came at the cost of large constant factors in space and time, which strongly limited its practical application (∼200 bases already require 256 GB space). Results: We present a CCJ-type algorithm, Knotty, that handles the same comprehensive pseudoknot class of structures as CCJ with improved space complexity of Θ(n3+Z)-due to the applied technique of sparsification, the number of 'candidates', Z, appears to grow significantly slower than n4 on our benchmark set (which include pseudoknotted RNAs up to 400 nt). In terms of run time over this benchmark, Knotty clearly outperforms Pknots and the original CCJ implementation, CCJ 1.0; Knotty's space consumption fundamentally improves over CCJ 1.0, being on a par with the space-economic Pknots. By comparing to CCJ 2.0, our unsparsified Knotty variant, we demonstrate the isolated effect of sparsification. Moreover, Knotty employs the state-of-the-art energy model of 'HotKnots DP09', which results in superior prediction accuracy over Pknots. Availability and implementation: Our software is available at https://github.com/HosnaJabbari/Knotty. Supplementary information: Supplementary data are available at Bioinformatics online.

Light-induced ATP driven self-assembly of actin and heavy-meromyosin in proteo-tubularsomes as a step toward artificial cells.

In this work, we studied the light induced self-assembly of F-actin and heavy meromyosin (HMM) in tubular vesicles or "tubularsomes" during initiation by ATP. To mimic nature, light-induced ATP synthesis was used for the F-actin/HMM self-assembly inside these vesicles created from a triblock copolymer reconstituted with the membrane protein bacteriorhodopsin (bR) and F1F0-ATPase along with F-actin and HMM in the core.

Facile fabrication of microparticles with pH-responsive macropores for small intestine targeted drug formulation.

Oral drugs present the most convenient, economical, and painless route for self-administration. Despite commercialization of multiple technologies relying on micro- and nanocrystalline drugs, research on microparticles (MPs) based oral biopharmaceuticals delivery systems has still not culminated well enough in commercial products. This is largely due to the drugs being exposed to the destabilizing environment during MP synthesis process, and partly because of complicated process conditions. Hence, we developed a solvent swelling-evaporation method of producing pH-responsive MPs with micron-sized macropores using poly(methacrylic acid-co-ethyl acrylate) in 1:1 ratio (commercial name: Eudragit® L100-55 polymer). We investigated the effects of temperature and evaporation time on pore formation, freeze-drying induced pore closure, and the release profile of model drugs (fluorescent beads, lactase, and pravastatin sodium) encapsulated MPs in simulated gastrointestinal tract conditions. Encapsulated lactase/pravastatin maintained >60% of their activity due to the preservation of pore closure, which proved the potential of this proof-of-concept microencapsulation system. Importantly, the presence of macropores on MPs can be beneficial for easy drug loading, and solve the problem of bioactivity loss during the conventional MP fabrication-drug encapsulation steps. Therefore, pH-sensing MPs with macropores can contribute to the development of oral drug formulations for a wide variety of drugs and bio-macromolecules, having a various size ranging from genes to micron-sized ingredients with high therapeutic efficacy.

RNA secondary structure prediction with pseudoknots: Contribution of algorithm versus energy model.

MOTIVATION: RNA is a biopolymer with various applications inside the cell and in biotechnology. Structure of an RNA molecule mainly determines its function and is essential to guide nanostructure design. Since experimental structure determination is time-consuming and expensive, accurate computational prediction of RNA structure is of great importance. Prediction of RNA secondary structure is relatively simpler than its tertiary structure and provides information about its tertiary structure, therefore, RNA secondary structure prediction has received attention in the past decades. Numerous methods with different folding approaches have been developed for RNA secondary structure prediction. While methods for prediction of RNA pseudoknot-free structure (structures with no crossing base pairs) have greatly improved in terms of their accuracy, methods for prediction of RNA pseudoknotted secondary structure (structures with crossing base pairs) still have room for improvement. A long-standing question for improving the prediction accuracy of RNA pseudoknotted secondary structure is whether to focus on the prediction algorithm or the underlying energy model, as there is a trade-off on computational cost of the prediction algorithm versus the generality of the method. RESULTS: The aim of this work is to argue when comparing different methods for RNA pseudoknotted structure prediction, the combination of algorithm and energy model should be considered and a method should not be considered superior or inferior to others if they do not use the same scoring model. We demonstrate that while the folding approach is important in structure prediction, it is not the only important factor in prediction accuracy of a given method as the underlying energy model is also as of great value. Therefore we encourage researchers to pay particular attention in comparing methods with different energy models.

Biomining of MoS2 with Peptide-based Smart Biomaterials.

Biomining of valuable metals using a target specific approach promises increased purification yields and decreased cost. Target specificity can be implemented with proteins/peptides, the biological molecules, responsible from various structural and functional pathways in living organisms by virtue of their specific recognition abilities towards both organic and inorganic materials. Phage display libraries are used to identify peptide biomolecules capable of specifically recognizing and binding organic/inorganic materials of interest with high affinities. Using combinatorial approaches, these molecular recognition elements can be converted into smart hybrid biomaterials and harnessed for biotechnological applications. Herein, we used a commercially available phage-display library to identify peptides with specific binding affinity to molybdenite (MoS2) and used them to decorate magnetic NPs. These peptide-coupled NPs could capture MoS2 under a variety of environmental conditions. The same batch of NPs could be re-used multiple times to harvest MoS2, clearly suggesting that this hybrid material was robust and recyclable. The advantages of this smart hybrid biomaterial with respect to its MoS2-binding specificity, robust performance under environmentally challenging conditions and its recyclability suggests its potential application in harvesting MoS2 from tailing ponds and downstream mining processes.

Immobilization of membrane proteins on solid supports using functionalized ß-sheet peptides and click chemistry.

We have developed two functionalized ß-sheet peptides (FBPs) and demonstrated that they can stabilize a variety of integral membrane proteins (IMPs), and most importantly allow covalent crosslinking of the IMPs onto solid supports via the highly selective click chemistry. The FBPs are promising tools for the preparation of IMP-based biomaterials or biosensors.

Emulsion Electrospinning of Polytetrafluoroethylene (PTFE) Nanofibrous Membranes for High-Performance Triboelectric Nanogenerators.

Electrospinning is a simple, versatile technique for fabricating fibrous nanomaterials with the desirable features of extremely high porosities and large surface areas. Using emulsion electrospinning, polytetrafluoroethylene/polyethene oxide (PTFE/PEO) membranes were fabricated, followed by a sintering process to obtain pure PTFE fibrous membranes, which were further utilized against a polyamide 6 (PA6) membrane for vertical contact-mode triboelectric nanogenerators (TENGs). Electrostatic force microscopy (EFM) measurements of the sintered electrospun PTFE membranes revealed the presence of both positive and negative surface charges owing to the transfer of positive charge from PEO which was further corroborated by FTIR measurements. To enhance the ensuing triboelectric surface charge, a facile negative charge-injection process was carried out onto the electrospun (ES) PTFE subsequently. The fabricated TENG gave a stabilized peak-to-peak open-circuit voltage (Voc) of up to ∼900 V, a short-circuit current density (Jsc) of ∼20 mA m-2, and a corresponding charge density of ∼149 µC m-2, which are ∼12, 14, and 11 times higher than the corresponding values prior to the ion-injection treatment. This increase in the surface charge density is caused by the inversion of positive surface charges with the simultaneous increase in the negative surface charge on the PTFE surface, which was confirmed by using EFM measurements. The negative charge injection led to an enhanced power output density of ∼9 W m-2 with high stability as confirmed from the continuous operation of the ion-injected PTFE/PA6 TENG for 30 000 operation cycles, without any significant reduction in the output. The work thus introduces a relatively simple, cost-effective, and environmentally friendly technique for fabricating fibrous fluoropolymer polymer membranes with high thermal/chemical resistance in TENG field and a direct ion-injection method which is able to dramatically improve the surface negative charge density of the PTFE fibrous membranes.

Photochromic Paper Indicators for Acidic Food Spoilage Detection.

A photoresponsive microstructured composite is fabricated through the impregnation of cellulosic filter paper (FP) with a spiropyran-modified acrylic polymer. The polymer enwraps uniformly each individual cellulose fiber, increases the thermal stability of cellulose, and ensures the preservation of the composite functionalities even upon removal of the surface layers through mechanical scratching. The photochromic spiropyran moieties of the polymer, even while embedded in the cellulosic sheet, can reversibly interconvert between the colorless spiropyran and the pink merocyanine isomeric states upon irradiation with UV and visible light, respectively. Moreover, the photochromic polymer presents a faster photochromic response and a higher resistance to photodegradation, with an outstanding reusability for more than 100 switching cycles when it is incorporated in the cellulose network. Most importantly, the acidochromism of the modified FP, attributed to the spiropyran molecules after UV activation, allows the real-time optical and visual detection of acidity changes and spoilage in food products, such as wine and milk. Spoilage due to bacterial degradation and oxidation processes generates acidic vapors that induce the protonation of the merocyanine. This results in a visually detectable chromic transition from pink to white of the treated cellulose fibers, corresponding to a blue shift in the absorption spectrum. The developed photoresponsive cellulose composite can serve as cost-effective robust optical component in integrated functional platforms and consumer-friendly indicators for smart food packaging, as well as portable on demand acidoresponsive interfaces for gas monitoring in industrial and environmental applications.

Biofunctionalized silicon nitride platform for sensing applications.

Silicon nitride (SiNx) based biosensors have the potential to converge on the technological achievements of semiconductor microfabrication and biotechnology. Development of biofunctionalized SiNx surface and its integration with other devices will allow us to integrate the biosensing capability with probe control, data acquisition and data processing. Here we use the hydrogen plasma generated by inductively coupled plasma-reactive ion etching (ICP-RIE) technique to produce amino-functionality on the surface of SiNx which can then be readily used for biomolecule immobilization. ICP-RIE produces high-density hydrogen ions/radicals at low energy, which produces high-density amino group on the SiNx surface within a short duration of time and with minimal surface damage. In this work, we have demonstrated selective amination of SiNx surface as compared to Si surface. The as-activated SiNx surface can be readily biofunctionalized with both protein and oligonucleotide through covalent immobilization. N-5-azido-2-nitrobenzoyloxysuccinimide, a photoactivable amino reactive bifunctional crosslinker, was used and greater than 90% surface coverage was achieved for protein immobilization. In addition, ssDNA immobilization and hybridization with its complemented strand was shown. Thus, we demonstrate a uniform, reliable, fast and economical technique for creating biofunctionalized SiNx surface that can be used for developing compact high-sensitivity biosensors.

Single-molecule study of full-length NaChBac by planar lipid bilayer recording.

Planar lipid bilayer device, alternatively known as BLM, is a powerful tool to study functional properties of conducting membrane proteins such as ion channels and porins. In this work, we used BLM to study the prokaryotic voltage-gated sodium channel (Nav) NaChBac in a well-defined membrane environment. Navs are an essential component for the generation and propagation of electric signals in excitable cells. The successes in the biochemical, biophysical and crystallographic studies on prokaryotic Navs in recent years has greatly promoted the understanding of the molecular mechanism that underlies these proteins and their eukaryotic counterparts. In this work, we investigated the single-molecule conductance and ionic selectivity behavior of NaChBac. Purified NaChBac protein was first reconstituted into lipid vesicles, which is subsequently incorporated into planar lipid bilayer by fusion. At single-molecule level, we were able to observe three distinct long-lived conductance sub-states of NaChBac. Change in the membrane potential switches on the channel mainly by increasing its opening probability. In addition, we found that individual NaChBac has similar permeability for Na+, K+, and Ca2+. The single-molecule behavior of the full-length protein is essentially highly stochastic. Our results show that planar lipid bilayer device can be used to study purified ion channels at single-molecule level in an artificial environment, and such studies can reveal new protein properties that are otherwise not observable in in vivo ensemble studies.

3'-O-Caged 2'-Deoxynucleoside Triphosphates for Light-Mediated, Enzyme-Catalyzed, Template-Independent DNA Synthesis.

Synthesis, purification, and characterization of 3'-O-caged 2'-deoxyribonucleoside triphosphates (dNTPs), namely 3'-O-(2-nitrobenzyl)-2'-deoxy ribonucleoside triphosphates (NB-dNTPs) and 3'-O-(4,5-dimethoxy-2-nitrobenzyl)-2'-deoxy ribonucleoside triphosphates (DMNB-dNTPs), are discussed in detail. A total of eight 3'-O-caged dNTPs are synthesized with specific protocols depending on the nitrogenous base on the first carbon, i.e., adenine, guanine, thymine, and cytosine, as well as the photo-cleavable group, i.e, 2-nitrobenzyl and 4,5- dimethoxy-2-nitrobenzyl, to be attached in the 3'-O position. The purification of the synthesized compounds is done using ion-exchange and flash chromatography; this is followed by structural confirmation by nuclear magnetic resonance (NMR) and mass spectroscopy (MS). The efficiency of the designed compounds is tested by conducting and evaluating UV-cleaving experiments at 365 nm with proton NMR and LC-MS curves. Finally, the application of the 3'-O-cagged dNTPs in template-independent, enzyme-catalyzed, photo-mediated oligonucleotide synthesis is demonstrated. © 2017 by John Wiley & Sons, Inc.

Peptides for targeting ßB2-crystallin fibrils.

Crystallins are a major family of proteins located within the lens of the eye. Cataracts are thought to be due to the formation of insoluble fibrillar aggregates, which are largely composed of proteins from the crystallin family. Today the only cataract treatment that exists is surgery and this can be difficult to access for individuals in the developing world. Development of novel pharmacotherapeutic approaches for the treatment of cataract rests on the specific targeting of these structures. ßB2-crystallin, a member of ß-crystallin family, is a large component of the crystallin proteins within the lens, and as such was used to form model fibrils in vitro. Peptides were identified, using phage display techniques, that bound to these fibrils with high affinity. Fibrillation of recombinantly expressed human ßB2-crystallin was performed in 10% (v/v) trifluoroethanol (TFE) solution (pH 2.0) at various temperatures, and its amyloid-like structure was confirmed using Thioflavin-T (ThT) assay, transmission electron microscopy (TEM), and X-ray fiber diffraction (XRFD) analysis. Affinity of identified phage-displayed peptides were analyzed using enzyme-linked immunosorbent assay (ELISA). Specific binding of a cyclic peptide (CKQFKDTTC) showed the highest affinity, which was confirmed using a competitive inhibition assay.

Antifouling Cellulose Hybrid Biomembrane for Effective Oil/Water Separation.

Oil/water separation has been of great interest worldwide because of the increasingly serious environmental pollution caused by the abundant discharge of industrial wastewater, oil spill accidents, and odors. Here, we describe simple and economical superhydrophobic hybrid membranes for effective oil/water separation. Eco-friendly, antifouling membranes were fabricated for oil/water separation, waste particle filtration, the blocking of thiol-based odor materials, etc., by using a cellulose membrane (CM) filter. The CM was modified from its original superhydrophilic nature into a superhydrophobic surface via a reversible addition-fragmentation chain transfer technique. The block copolymer poly{[3-(trimethoxysilyl)propyl acrylate]-block-myrcene} was synthesized using a "grafting-from" approach on the CM. The surface contact angle that we obtained was >160°, and absorption tests of several organic contaminants (oils and solvents) exhibited superior levels of extractive activity and excellent reusability. These properties rendered this membrane a promising surface for oil/water separation. Interestingly, myrcene blocks thiol (through "-ene-" chemistry) contaminants, thereby bestowing a pleasant odor to polluted water by acting as an antifouling material. We exploited the structural properties of cellulose networks and simple chemical manipulations to fabricate an original material that proved to be effective in separating water from organic and nano/microparticulate contaminants. These characteristics allowed our material to effectively separate water from oily/particulate phases as well as embed antifouling materials for water purification, thus making it an appropriate absorber for chemical processes and environmental protection.