Resonance energy transfer methods of RNA detection

Quantitation of RNA is important in diagnostics, environmental science, and basic biomedical research. RNA is considered a signature for pathogen identification, and its expression profile is linked with disease pathogenesis, allowing for biomarker identification. RNA-based diagnostics is an emerging field of research. This expansion of interest in studying RNA has generated demand for its accurate and sensitive detection. Several methods have therefore been developed to detect RNA. Resonance energy transfer methods of RNA detection are highly promising in terms of simplicity and high sensitivity. In this review, we have focused on the latest developments in resonance energy transfer methods of RNA detection that utilize various probe designs. The probe designs discussed here are molecular beacons, quenched autoligation probes, and linear oligonucleotide probes. Resonance energy transfer methods based on both fluorescence and bioluminescence detection are discussed.     

Correction of CT burst array errors in the generalized-lee-RT spaces

In [Jain, S.： Array codes in the generalized-Lee-RT-pseudo-metric （the GLRTP-metric）, to appear in Algebra Colloq.], Jain introduced a new pseudo-metric on the space Matm×s（Zq）, the module space of all m × s matrices with entries from the finite ring Zq, generalized the classical Lee metric [Lee, C. Y.： Some properties of non-binary error correcting codes. IEEE Trans. Inform. Theory, IT-4, 77- 82 （1958）] and array RT-metric [Rosenbloom, M. Y., Tsfasman, M. A.： Codes for m-metric. Prob. Inf. Transm., 33, 45-52 （1997）] and named this pseudo-metric as the Generalized-Lee-RT-Pseudo-Metric （or the GLRTP-Metric）. In this paper, we obtain some lower bounds for two-dimensional array codes correcting CT burst array errors [Jain, S.： CT bursts from classical to array coding. Discrete Math., 308-309, 1489-1499 （2008）] with weight constraints under the GLRTP-metric.     

Luminescence-based whole-cell-sensing systems for cadmium and lead using genetically engineered bacteria

Whole-cell-based sensing systems that respond to cadmium and lead ions have been designed and developed using genetically engineered bacteria. These systems take advantage of the ability of certain bacteria to survive in environments polluted with cadmium and lead ions. The bacteria used in this investigation have been genetically engineered to produce reporter proteins in response to the toxic ions. This was achieved by modifying a strain of Escherichia colito harbor plasmids pYSC1 and pYS2/pYSG1. In these dual-plasmid-based sensing systems, the expression of the reporters beta-galactosidase and red-shifted green fluorescent protein (rs-GFP) was controlled by CadC, the regulatory protein of the cad operon. Regulation of the expression of the reporter proteins is related to the amount of cadmium and lead ions employed to induce the bacteria. The bacterial sensing systems were found to respond to cadmium, lead, and zinc ions, and had no significant response to nickel, copper, manganese, and cobalt.     

Bioluminescence resonance energy transfer from aequorin to a fluorophore: an artificial jellyfish for applications in multianalyte detection

In nature, the green light emission observed in the jellyfish Aequorea victoria is a result of a non-radiative energy transfer from the excited-state aequorin to the green fluorescent protein. In this work, we have modified the photoprotein aequorin by attaching selected fluorophores at a unique site on the protein. This will allow for in vitro transfer of bioluminescent energy from aequorin to the fluorophore thus creating an artificial jellyfish. The fluorophores are selected such that the excitation spectrum of the fluorophore overlaps with the emission spectrum of aequorin. By modifying aequorin with different fluorophores, bioluminescent labels with different emission maxima are produced, which will allow for the simultaneous detection of multiple analytes. By examining the X-ray crystal structure of the protein, four different sites for introduction of the unique cysteine residue were evaluated. Two fluorophores with differing emission maxima were attached individually to the mutants through the sulfhydryl group of the cysteine molecule. Two of the fluorophore-labeled mutants showed a peak corresponding to fluorophore emission thus indicating resonance energy transfer from aequorin to the fluorophore.     

CT bursts—from classical to array coding

R.T. Chien and D.T. Tang [On definition of a burst, IBM J. Res. Develop. 9 (1965) 292-293] introduced the concept of Chien and Tang bursts (CT bursts) for classical coding systems where codes are subsets (or subspaces) of the space , the space of all n-tuples with entries from a finite field F_q. In this paper, we extend the notion of CT bursts for array coding systems where array codes are subsets (or subspaces) of the space Mat_m×s(F_q), the linear space of all m×s matrices with entries from a finite field F_q, endowed with a non-Hamming metric [M.Yu. Rosenbloom, M.A. Tsfasman, Codes for m-metric, Problems Inform. Transmission 33 (1997) 45-52]. We also obtain some bounds on the parameters of array codes for the detection and correction of CT burst errors.     

Recovery and Reuse of Composite Cathode Binder in Lithium Ion Batteries

Here, we investigate the recovery and reuse of polyvinylidene fluoride (PVDF) binders from both homemade and commercial cathode films in Li ion batteries. We find that PVDF solubility depends on whether the polymer is an isolated powder or cast into a composite film. A mixture of tetrahydrofuran:N-methyl-2-pyrrolidone (THF : NMP, 50 : 50 v/v) at 90 °C delaminates composite cathodes from Al current collectors and yields pure PVDF as characterized by ¹H nuclear magnetic resonance (NMR), gel permeation chromatography (GPC), wide-angle X-ray scattering (WAXS), and scanning electron microscopy (SEM). PVDF recovered from Li ion cells post-cycling exhibits similar performance to pristine PVDF. These data suggest that PVDF can be extracted and reused during Li ion battery recycling while simultaneously eliminating the formation of HF etchants, providing an incentive for use in direct cathode recycling.     

Campopiano-type bounds in non-Hamming array coding

Campopiano [C.N. Campopiano, Bounds on burst error correcting codes, IRE Trans. IT-8 (1962) 257-259] obtained an upper bound for burst error correction in classical coding systems where codes are subsets/subspaces of the space , the space of all n-tuples with entries from a finite field F_q equipped with the Hamming metric. In [S. Jain, Bursts in m-metric array codes, Linear Algebra Appl., in press], the author introduced the notion of burst errors for m-metric array coding systems where m-metric array codes are subsets/subspaces of the space Mat_m×s(F_q), the linear space of all m × s matrices with entries from a finite field F_q, endowed with a non-Hamming metric and obtained some lower bounds for burst error correction. In this paper, we obtain various construction upper bounds on the parameters of m-metric array codes for the detection and correction of burst errors.