Exploratory analysis of excitation-emission matrix fluorescence spectra with self-organizing maps—A tutorial

Large datasets are common in chemical and environmental engineering applications and tools for their analysis are in great demand. Here, the outputs of a series of fluorescence spectroscopy analyses are utilised to demonstrate the application of the self-organising map (SOM) technique for data analysis. Fluorescence spectroscopy is a well-established technique of organic matter fingerprinting in water. The technique can provide detailed information on the physico-chemical properties of water. However, analysis of fluorescence spectra requires the application of robust statistical and computational data pre-processing and analysis tools.This paper presents a tutorial for training engineering postgraduate researchers in the use of SOM techniques using MATLAB^®. Via a tutorial, the application of SOM to fluorescence spectra and, in particular, the characterisation of organic matter removal in water treatment, is presented. The tutorial presents a step-by-step example of the application of SOM to fluorescence data analysis and includes the source code for MATLAB^®, together with presentation and discussion of the results. With this tutorial we hope to popularise this robust pattern recognition technique for fluorescence data analysis and large data sets in general, and also to provide educational practitioners with a novel tool with which to train engineering students in SOM.     

RAFT-derived polymer-drug conjugates: poly(hydroxypropyl methacrylamide) (HPMA)-7-ethyl-10-hydroxycamptothecin (SN-38) conjugates

A series of well‐defined polymer–drug conjugates were prepared in order to modify the physical properties of a known cytotoxic drug, 7‐ethyl‐10‐hydroxycamptothecin (SN‐38), the active metabolite of irinotecan (CPT‐11). Reversible addition–fragmentation chain transfer (RAFT) polymerisation was used to covalently and site‐specifically append a defined N‐(2‐hydroxypropyl)methacrylamide (HPMA) polymer to SN‐38 using a graft‐from process. These poly‐HPMA–SN‐38 conjugates displayed excellent aqueous solubility and stability, whilst retaining the cytotoxic activity of the parent SN‐38. In vitro co‐culture assays containing both cancer and noncancer cell lines demonstrated the specificity of RAFT‐derived poly‐HPMA–SN‐38 conjugates for cancerous cells. The concept of post‐optimisation modification of small‐molecule drugs through a graft‐from polymer conjugation method is introduced.     

Evaluating the In Vitro Metabolism of Docosahexaenoic Acid in Sheep Rumen Fluid

Rumen metabolism (e.g., biohydrogenation) of dietary unsaturated fatty acids (FA) is one of the main reasons why ruminant fats tend to be highly saturated and contain many isomerized FA intermediates. The process by which long-chain (20- to 24-carbon FA) polyunsaturated FA (LC-PUFA) are metabolized by rumen bacteria is not as well understood as that of linoleic or linolenic acids. In order to better understand the fate of LC-PUFA in the rumen several concentrations of docosahexaenoic acid (DHA) were evaluated in in vitro batch incubations ranging from 100 to 1,500 μg per 6 mL of incubation volume using rumen fluid from sheep and incubated for 0, 1, 2, 3, and 6 h. From the results, it was shown that DHA was extensively metabolized at low (100 to 300 μg/6 mL incubation volume), but not at high level of inclusion (800 μg). At 300 μg of DHA most of the depleted DHA was recovered as LC-DHA metabolites within the first 6 h of incubation, and at the lowest levels (100 μg of incubation volume) further metabolism is apparent at 6 h. Using SP-2560 GC columns several LC-DHA metabolites were shown to elute after 24:0 and just past DHA, a region generally free of interfering FA. The present in vitro study would appear to be a useful method to evaluate the production of DHA metabolites in combination with its depletion.     

Identification of the first known inhibitors of O-acetylpeptidoglycan esterase: a potential new antibacterial target

The O‐acetylation of peptidoglycan (PG) is now known to occur in 53 species, including numerous human pathogens such as, Staphylococcus aureus, Bacillus anthracis, species of Enterococcus, Campylobacter jejuni, Helicobacter pylori, Neisseria gonorrhoeae and N. meningitidis. This modification, which occurs at the C‐6 hydroxyl of N‐acetylmuramoyl residues within PG, serves to regulate autolytic activity during PG metabolism and contributes to pathogenesis and persistence within a host. O‐Acetylpeptidoglycan esterase (Ape) was recently discovered as an enzyme responsible for the removal of O‐acetyl groups from PG, thus permitting the continued maintenance and metabolism of the sacculus. Recombinant Ape1 from N. gonorrhoeae was purified to apparent homogeneity and optimal storage conditions for the enzyme were determined. Using 4‐methylumbelliferyl acetate as substrate, a fluorogenic assay amenable for the high‐throughput screening for potential inhibitors was developed and Ape1 was screened against a subset of compounds of the Canadian Compound Collection. The overall Z′ score for the screen was 0.62, indicative of a well‐suited assay with a sufficient signal window, and the threshold was set at 65 %. After eliminating a number of false‐positives, seven compounds were identified as true inhibitors of Ape1, the first to be identified for this class of enzyme. Dose–response curves were generated leading to the identification of five of these compounds with IC₅₀ values ranging between 0.3 and 23 μM . Of these, purpurin was selected for further analysis and it was found to inhibit the growth of both Gram‐positive and Gram‐negative bacteria that produce both O‐acetylated PG and Ape.     

Kinetic and stoichiometric characterisation of streptavidin-binding aptamers

Aptamers are oligonucleotide ligands that are selected for high-affinity binding to molecular targets. Only limited knowledge relating to relations between structural and kinetic properties that define aptamer-target interactions is available. To this end, streptavidin-binding aptamers were isolated and characterised by distinct analytical techniques. Binding kinetics of five broadly similar aptamers were determined by surface plasmon resonance (SPR); affinities ranged from 35-375 nM with large differences in association and dissociation rates. Native mass spectrometry showed that streptavidin can accommodate up to two aptamer units. In a 3D model of one aptamer, conserved regions are exposed, strongly suggesting that they directly interact with the biotin-binding pockets of streptavidin. Mutational studies confirmed both conserved regions to be crucial for binding. An important result is the observation that the most abundant aptamer in our selections is not the tightest binder, emphasising the importance of having insight into the kinetics of complex formation. To find the tightest binder it might be better to perform fewer selection rounds and to focus on post-selection characterisation, through the use of complementary approaches as described in this study.     

Biomimetic monolayer-protected gold nanoparticles for immunorecognition

Gold nanoparticles (AuNPs) protected by self-assembled monolayers (SAMs) are capable of presenting precisely engineered surfaces at the nanoscale, allowing the mimicry of biomacromolecules on an artificial platform. Here we review the generation, characterization, and applications of monolayer-protected AuNPs that have been designed for immunorecognition by the integration of an oligopeptide epitope into the protecting monolayer. The resulting peptide-AuNP conjugate is an effective platform for biomimesis, as demonstrated by multiple studies. Recent work is presented and future directions for this field of research are discussed.     

Capillary bending of Janus carbon nanotube micropillars

We present a scalable process for the fabrication of slanted carbon nanotube micropillar arrays by inclined metal deposition and capillary self-assembly. Local control of the micropillar angle from vertical to nearly horizontal is achieved, and is explained using a finite element model. These structures may be useful for microscale contacts and anisotropic smart surfaces.     

Deliberately Losing Control of C−H Activation Processes in the Design of Small-Molecule-Fragment Arrays Targeting Peroxisomal Metabolism

Combined photochemical arylation, “nuisance effect” (S_NAr) reaction sequences have been employed in the design of small arrays for immediate deployment in medium-throughput X-ray protein–ligand structure determination. Reactions were deliberately allowed to run “out of control” in terms of selectivity; for example the ortho-arylation of 2-phenylpyridine gave five products resulting from mono- and bisarylations combined with S_NAr processes. As a result, a number of crystallographic hits against NUDT7, a key peroxisomal CoA ester hydrolase, have been identified.     

Evaluation of expanded gamut software solutions for spot color reproduction

Expanded gamut printing is an approach in color reproduction that expands the color gamut of conventional CMYK printing processes via the use of additional colorants, such as Orange, Green, and Violet inks. This study evaluates the ability of commercial color management software to create an accurate solution for an expanded gamut printing system. In this study, two printing processes were used, an Epson SureColor P9000 inkjet printer/proofer and an HP Indigo 7900 digital production press, both with 7-color expanded gamut ink sets. Software solutions from Alwan, CGS ORIS, ColorLogic, GMG Color, Heidelberg, and Kodak were evaluated. The systems were tested to see how well they could reproduce the colors in the entire PANTONE+ Solid Coated spot color library. It is shown that the solutions are able to reproduce 89% to 94% of the spot colors on the Epson P9000 inkjet printer and 77% to 87% of the library on the Indigo 7900, both to less than two CIEDE2000 (a typical tolerance in label and packaging work). The number of color patches in expanded gamut characterization test charts was noted, as this is still an area of proprietary, nonstandardized working practice. There are many different colorant combinations that can make the same color in expanded gamut printing. The ink build created by the different software solutions was studied, as it relates to press stability through appropriate choice of colorants. Pantone and Adobe provide everyday commercial tools for expanded color workflows. The study identified some issues with products from these companies that could confuse a less-skilled user in a busy production environment. The conclusion of the study is that expanded gamut solutions for spot color printing produce totally acceptable results for digital printing processes; expanded gamut printing is ready, here and now. The findings show that expanded gamut printing can replace cumbersome conventional spot color workflows creating considerable savings and advantages, especially for label and packaging printers.     

Emergency egress for the elderly in care home fire situations

Practitioners are continuing to develop egress modelling software for the design of the built environment. These models require data about human behaviour and factors for calibration, validation and verification. This study aims to address the specific data and knowledge gap: emergency egress of the elderly. Such data are difficult to collect given privacy and consent concerns, with strong relationships generally being required between residences and researchers. Through the observation of nine fire drills at six Canadian long-term care (LTC) and retirement homes, specific evacuation actions and behaviour were observed for 37 staff members and information about the evacuation of 56 residents was collected. These drills demonstrated that emergency egress in LTC and retirement homes is highly staff dependent with 72% of residents recorded requiring full assistance at all stages of movement in evacuation, and that the type of announced/unannounced drill and level of resident care will affect the type of data collected. The development of travel speed and pre-movement is discussed subject to limitation with qualitative behavioural insights of residents that were observed. This study provides valuable methodological discussion on how to conduct behavioural studies in similar highly restricted research environments. Specific attention is given to understanding the considerations that must be made when using fire drills as data sources, and the impact that these can have on using such data for modelling. This study may inform the initial setup and programming of evacuation models from an actions and behavioural perspectives of staff members and residents.