Analysis of repeating oligonucleotide sequences in ribonucleic acids using an Apple II microcomputer

A simple computer program has been developed to locate repeating subsequences of all possible lengths in a given nucleic acid. The observed number of repeats of subsequences was compared with the expected number of such repeats in several RNAs. The analysis showed that, in the case of rRNAs, there are no constraints in the choice of the fourth and the higher order nucleotides, while the selection is maximum at the level of nearest neighbour. This is, however, not true for RNAs coding for proteins, where the constraints are also found at the level of nucleotides containing five or more bases.     

Data-dependent-systems and Fourier-transform methods for single-interferogram analysis

Results of wave-front phase detection obtained from a spatial method based on data-dependent-systems (DDS) methodology are compared with those obtained from the Fourier-transform method. DDS is a novel approach that extends and improves the way the stochastic autoregressive moving-average models are obtained and interpreted. The methodology is robust to noise influence and insensitive to the errors commonly associated with the Fourier transform. Both the Fourier-transform and the DDS methods use one interference pattern, and both offer means for filtering out disturbances such as noise and background variations. We present a brief review of the two methods to compare them theoretically, and then we describe their experimental implementation. The methods were applied to the same interferometric data sets, and the results are presented and compared to discuss relative advantages and disadvantages. In particular, it is shown that the DDS method preserves the detailed surface texture because a convolution of the component that represents the surface dynamic aspect with the component that corresponds to the independent and dynamic-free aspect is able to recover the original details. In contrast the Fourier-transform method smooths such details to an extent that depends on the subjective choice of filters.     

Interferogram analysis based on the data-dependent systems method for nanometrology applications

A spatial method of wave-front phase detection from an interferogram is presented. The method uses data-dependent systems methodology, an approach that extends and improves the way the stochastic autoregressive moving average models are obtained and interpreted. Its application to interference data addresses the fundamental problem of recovering the self-coherence function commonly used to retrieve the wave-front phase. The self-coherence function is efficiently computed by means of a complex autoregressive model and is used for surface reconstruction. The method is shown to be robust and suitable for surface testing. The correspondence of the data-dependent systems methodology and its physical meaning as related to the classical interferometry are presented. The theoretical development is illustrated by experimental implementation, with the results obtained from one- and two-dimensional interferometric fringe analysis of a computer hard disk.     

Biogenic fabrication of CuNPs,Cu bioconjugates and in vitro assessment of antimicrobial and antioxidant activity

In the present study, the authors synthesised copper nanoparticles (CuNPs) by using extract of Zingiber officinale (ginger) and later the NPs were bioconjugated with nisin, which shows antimicrobial activity against food spoilage microorganisms. CuNPs and its bioconjugate were characterised by ultraviolet–vis spectroscopy, NP tracking analysis, Zetasizer, transmission electron microscopy analysis, X‐ray diffraction and Fourier transform infra‐red (FTIR) spectroscopy. Zeta potential of CuNPs and its bioconjugate were found to be very stable. They evaluated in vitro efficacy of CuNPs and its bioconjugate against selected food spoilage bacteria: namely, Staphylococcus aureus, Pseudomonas fluorescens, Listeria monocytogenes and fungi including Fusarium moniliforme and Aspergillus niger. Antimicrobial activity of CuNPs was found to be maximum against F. moniliforme (18 mm) and the least activity was noted against L. monocytogenes (13 mm). Antioxidant activity of CuNPs and ginger extract was performed by various methods such as total antioxidant capacity reducing power assay, 1‐1‐diphenyl‐2‐picryl‐hydrazyl free radical scavenging assay and hydrogen peroxide assay. Antioxidant activity of CuNPs was higher as compared with ginger extract. Hence, CuNPs and its bioconjugate can be used against food spoilage microorganisms.Inspec keywords: antibacterial activity, biomedical materials, copper, nanoparticles, nanofabrication, nanomedicine, microorganisms, ultraviolet spectra, visible spectra, electrokinetic effects, transmission electron microscopy, X‐ray diffraction, Fourier transform infrared spectra, free radical reactions, food technologyOther keywords: biogenic fabrication, Cu bioconjugates, in vitro assessment, antimicrobial activity, antioxidant activity, copper nanoparticles, Zingiber officinale, ultraviolet‐visible spectroscopy, NP tracking analysis, Zetasizer, transmission electron microscopy, X‐ray diffraction, Fourier transform infrared spectroscopy, FTIR, zeta‐potential, food spoilage bacteria, Staphylococcus aureus, Pseudomonas fluorescens, Listeria monocytogenes, fungi, Fusarium moniliforme, Aspergillus niger, F. moniliforme, L. monocytogenes, ginger extract, total antioxidant capacity, power assay, 1‐1‐diphenyl‐2‐picryl‐hydrazyl free radical scavenging assay, hydrogen peroxide assay, food spoilage microorganisms, Cu     

Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence

Statistical analysis of 12 unstable and 32 stable proteins revealedthat there are certain dipeptides, the occurrence of which issignificantly different in the unstable proteins compared withthose in the stable ones. Based on the impact of these dipeptideson the unstable proteins over the stable ones, a weight valueof instability is assigned to each of the dipeptides. For agiven protein the summation of these weight values normalizedto the length of its sequence helps to distinguish between unstableand stable proteins. Results suggest that the in vivo instabilityof proteins is possibly determined by the order of certain aminoacids in its sequence. An attempt is made to correlate metabolicstability of proteins with features of their primary sequencewhere weight values of instability for a protein of known sequencecould thus be used as an index for predicting its stabilitycharacteristics.     

A stochastic approach to the mode of deformation and contact between rough surfaces

The real area of contact between a rough and an ideally flat surface is evaluated from the spectral moments of the profile of the rough surface. A stochastic criterion for plastic deformation of the asperities is developed and applied to determine the percentage of plastic and elastic deformation in the total area of contact at a given separation. An illustration is given to delineate the theory through experimental profile data obtained from a ground surface.     

Effect of Secondary Structure and Side Chain Length of Hydrophobic Amino Acid Residues on the Antimicrobial Activity and Toxicity of 14-Residue-Long de novo AMPs

Herein we report the efficacy and toxicity of three de novo designed cationic antimicrobial peptides (AMPs) LL-14, VV-14 and ββ-14, where side chains of the hydrophobic amino acids were reduced gradually. The AMPs showed broad-spectrum antimicrobial activity against three pathogens from the ESKAPE group and two fungal strains. This study showed that side chains which are either too long or too short increase toxicity and lower antimicrobial activity, respectively. VV-14 was found to be non-cytotoxic and highly potent under physiological salt concentrations against several pathogens, especially Salmonella typhi TY2. These AMPs acted via membrane deformation, depolarization, and lysis. The activity of the AMPs is related to their ability to take on amphipathic helical conformations in the presence of microbial membrane mimics. Among AMPs with the same charge, hydrophobic interactions between the side chains of the residues with cell membrane lipids determine their antimicrobial potency and cytotoxicity. Strikingly, an optimum hydrophobic interaction is the crux of generating highly potent non-cytotoxic AMPs.