Complete RNA inverse folding: computational design of functional hammerhead ribozymes

Nanotechnology and synthetic biology currently constitute one of the most innovative, interdisciplinary fields of research, poised to radically transform society in the 21st century. This paper concerns the synthetic design of ribonucleic acid molecules, using our recent algorithm, RNAiFold, which can determine all RNA sequences whose minimum free energy secondary structure is a user-specified target structure. Using RNAiFold, we design ten cis-cleaving hammerhead ribozymes, all of which are shown to be functional by a cleavage assay. We additionally use RNAiFold to design a functional cis-cleaving hammerhead as a modular unit of a synthetic larger RNA. Analysis of kinetics on this small set of hammerheads suggests that cleavage rate of computationally designed ribozymes may be correlated with positional entropy, ensemble defect, structural flexibility/rigidity and related measures. Artificial ribozymes have been designed in the past either manually or by SELEX (Systematic Evolution of Ligands by Exponential Enrichment); however, this appears to be the first purely computational design and experimental validation of novel functional ribozymes. RNAiFold is available at http://bioinformatics.bc.edu/clotelab/RNAiFold/.Comment: 17 pages, 2 tables, 7 figures, final version to appear in Nucleic Acids Researc

VersaCross Transseptal System for Mitral Transcatheter Edge-To-Edge Repair With the PASCAL Repair Platform

BackgroundVersaCross is a novel radiofrequency transseptal solution that may improve the efficiency and workflow of transseptal puncture (TSP). The aim of this study was to compare the VersaCross transseptal system with mechanical needle systems during mitral transcatheter edge-to-edge repair (M-TEER) with the PASCAL device.MethodsThis is a single-center retrospective study of consecutive patients who underwent M-TEER with the PASCAL. Transseptal puncture was undertaken with either a mechanical needle or the VersaCross wire. The primary endpoints were success of TSP and successful delivery of the Edwards sheath on the chosen delivery wire. Secondary endpoints included number of wires used, tamponade rate, interval from femoral venous access to TSP and first PASCAL device deployment, procedural death, and stroke.ResultsThirty-three consecutive patients (10 with mechanical needle, 23 with VersaCross) who underwent M-TEER with the Edwards PASCAL device were identified. All patients had successful TSP. In the mechanical needle group, the Edwards sheath was successfully delivered on the Superstiff Amplatz wire in all cases. In the VersaCross arm, the radiofrequency wire was used successfully for delivery of the sheath in all cases. There were no cases of pericardial effusion/tamponade in either arm. Interval from femoral venous access to TSP and to deployment of the first PASCAL device was shorter with the VersaCross system. Significantly fewer wires were used with VersaCross. There were no procedural deaths or strokes in either group.ConclusionsVersaCross appears a safe and effective method of TSP and for delivery of the 22Fr sheath for M-TEER with PASCAL

Degradation of spent tea waste by vermicomposting and its effect on growth of Abelmoschus esculentus

Vermicompost is the stable, organic matter that remains after the earthworms feed on the waste materials that occurs due to its decomposition in the gut of the earthworm under controlled conditions. Compost is a rich source of vitamins, hormones, enzymes, macro and micro nutrients which when applied to plants help in efficient growth. Vermicompost was sought to be made by putting spent tea waste as the worm feed. The present study has been carried out to analyze enzymes, physicochemical characteristics, and micro and macro nutrients present in the compost at regular interval of time and also a comparative study was done on the effect of compost on growth parameters namely germination percentage, root length, shoot length and number of leaf count in Abelmoschus esculentus after 30th day of planting. The results of the study revealed that the enzyme activities (amylase, cellulase, protease and invertase) and total macronutrients (N, P, K) and micronutrients (Mn and Cu) showed elevated levels in compost than control. The compost applied plant (Abelmoschus esculentus) showed increased germination percentage, root length, shoot length and number of leaves than the compost untreated plant

Influence of Pyrexia on Pharmacokinetics of Azithromycin and Its Interaction With Tolfenamic Acid in Goats

Azithromycin is a macrolide antimicrobial agent of the azalide group with a broad spectrum of activity against gram-negative and gram-positive bacterial organisms. Tolfenamic acid is a non-steroidal anti-inflammatory drug of the fenamate group, which is used extensively in humans and animals due to its anti-inflammatory, analgesic, and antipyretic properties. There is dearth of literature on any type of drug interaction between azithromycin and tolfenamic acid in any species, including human beings and alteration of its pharmacokinetics by fever. Therefore, the objective of this study was to investigate the alteration of disposition kinetics of azithromycin alone and in the presence of tolfenamic acid in Malabari goats by fever, following an intravenous administration at a dose rate of 20 mg/kg body weight. Blood samples collected from both afebrile and febrile goats at predetermined time intervals after the administration of azithromycin alone and then in combination with tolfenamic acid (2 mg/kg, intravenously), respectively, were analyzed using high-performance liquid chromatography. Non-compartmental analysis was used to determine the peak blood concentration (Cmax), time-to-peak plasma concentration (Tmax), half-life (t1/2λz), area under the curve (AUC 0−t, AUC 0−inf), area under the first moment curve (AUMC 0−inf), mean residence time (MRT0−inf), apparent volume of distribution at steady state (Vss), and the total body clearance of drug from the blood (Cl). In febrile animals, significant differences were noted in the values of Cmax, Cl, and Vss. Thus, azithromycin disappears into an additional compartment in febrile goats, which may be due to its extended cellular penetration into the inflammatory cells, resulting in anti-inflammatory activity. Tolfenamic acid significantly altered the pharmacokinetics of azithromycin in both normal and febrile animals. Tolfenamic acid, being a better anti-inflammatory agent, suppresses the inflammatory mediators, reducing the possibility of increased utilization of azithromycin in febrile condition

Design and development of a field-deployable single-molecule detector (SMD) for the analysis of molecular markers

Single-molecule detection (SMD) has demonstrated some attractive benefits for many types of biomolecular analyses including enhanced processing speed by eliminating processing steps, elimination of ensemble averaging and single-molecule sensitivity. However, it's wide spread use has been hampered by the complex instrumentation required for its implementation when using fluorescence as the readout modality. We report herein a simple and compact fluorescence single-molecule instrument that is straightforward to operate and consisted of fiber optics directly coupled to a microfluidic device. The integrated fiber optics served as waveguides to deliver the laser excitation light to the sample and collecting the resulting emission, simplifying the optical requirements associated with traditional SMD instruments by eliminating the need for optical alignment and simplification of the optical train. Additionally, the use of a vertical cavity surface emitting laser and a single photon avalanche diode serving as the excitation source and photon transducer, respectively, as well as a field programmable gate array (FPGA) integrated into the processing electronics assisted in reducing the instrument footprint. This small footprint SMD platform was tested using fluorescent microspheres and single AlexaFluor 660 molecules to determine the optimal operating parameters and system performance. As a demonstration of the utility of this instrument for biomolecular analyses, molecular beacons (MBs) were designed to probe bacterial cells for the gene encoding Gram-positive species. The ability to monitor biomarkers using this simple and portable instrument will have a number of important applications, such as strain-specific detection of pathogenic bacteria or the molecular diagnosis of diseases requiring rapid turn-around-times directly at the point-of-use.close5

Nanoparticles for Applications in Cellular Imaging

In the following review we discuss several types of nanoparticles (such as TiO2, quantum dots, and gold nanoparticles) and their impact on the ability to image biological components in fixed cells. The review also discusses factors influencing nanoparticle imaging and uptake in live cells in vitro. Due to their unique size-dependent properties nanoparticles offer numerous advantages over traditional dyes and proteins. For example, the photostability, narrow emission peak, and ability to rationally modify both the size and surface chemistry of Quantum Dots allow for simultaneous analyses of multiple targets within the same cell. On the other hand, the surface characteristics of nanometer sized TiO2allow efficient conjugation to nucleic acids which enables their retention in specific subcellular compartments. We discuss cellular uptake mechanisms for the internalization of nanoparticles and studies showing the influence of nanoparticle size and charge and the cell type targeted on nanoparticle uptake. The predominant nanoparticle uptake mechanisms include clathrin-dependent mechanisms, macropinocytosis, and phagocytosis