DNA molecules and human therapeutics

Nucleic acid molecules are championing a new generation of reverse engineered biopharmaceuticals. In terms of potential application in gene medicine, plasmid DNA (pDNA) vectors have exceptional therapeutic and immunological profiles as they are free from safety concerns associated with viral vectors, display non-toxicity and are simpler to develop. This review addresses the potential applications of pDNA molecules in vaccine design/development and gene therapy via recombinant DNA technology as well as a staged delivery mechanism for the introduction of plasmid-borne gene to target cells via the nasal route.

DNA molecules and future blockbuster therapeutics

Deoxyribonucleic acid molecules are heralding a new generation of reverse - engineered biopharmaceuticals. In terms of potential application in gene medicine, plasmid DNA (pDNA) vectors have exceptional therapeutic and immunological profiles as they are free from safety concerns associated with viral vectors, display non-toxicity and are simpler to develop. This presentation will discuss the potential applications of pDNA molecules in vaccine development and gene therapy, pilot-scale production of pDNA-based biopharmaceuticals and the controlled delivery of therapeutic sequences in biodegradable polymers to different target cells via the nasal route.

To sonicate or not to sonicate PM filters: Reactive Oxygen Species generation upon ultrasonic irradiation

In aerosol research, a common approach for the collection of particulate matter (PM) is the use of filters in order to obtain sufficient material to undertake analysis. For subsequent chemical and toxicological analyses, in most of cases the PM needs to be extracted from the filters. Sonication is commonly used to most efficiently extract the PM from the filters. Extraction protocols generally involve 10 - 60 min of sonication. The energy of ultrasonic waves causes the formation and collapse of cavitation bubbles in the solution. Inside the collapsing cavities the localised temperatures and pressures can reach extraordinary values. Although fleeting, such conditions can lead to pyrolysis of the molecules present inside the cavitation bubbles (gases dissolved in the liquid and solvent vapours), which results in the production of free radicals and the generation of new compounds formed by reactions with these free radicals. For example, simple sonication of pure water will result in the formation of detectable levels of hydroxyl radicals. As hydroxyl radicals are recognised as playing key roles as oxidants in the atmosphere the extraction of PM from filters using sonication is therefore problematic. Sonication can result in significant chemical and physical changes to PM through thermal degradation and other reactions. In this article, an overview of sonication technique as used in aerosol research is provided, the capacity for radical generation under these conditions is described and an analysis is given of the impact of sonication-derived free radicals on three molecular probes commonly used by researchers in this field to detect Reactive Oxygen Species in PM.

Design of redox/radical sensing molecules via Nitrile Imine-Mediated Tetrazole-ene Cycloaddition (NITEC)

The current study introduces a novel synthetic avenue for the preparation of profluorescent nitroxides via nitrile imine-mediated tetrazole-ene cycloaddition (NITEC). The photoinduced cycloaddition was performed under metal-free, mild conditions allowing the preparation of a library of the nitroxide functionalized pyrazolines and corresponding methoxyamines. High reaction rates and full conversion were observed, with the presence of the nitroxide having no significant impact on the cycloaddition performance. The formed products were investigated with respect to their photophysical properties in order to quantify their “switch on/off” behavior. The fluorescence quenching performance is strongly dependent on the distance between the chromophore and the free radical spin as demonstrated theoretically and experimentally. Highest levels of fluorescence quenching were achieved for pyrazolines with the nitroxide directly fused to the chromophore. Importantly, the pyrazoline profluorescent nitroxides were shown to efficiently act as sensors for redox/radical processes.

Analysis of complex molecular systems: The impact of multivariate analysis for resolving the interactions of small molecules with biopolymers - a review

This review is focused on the impact of chemometrics for resolving data sets collected from investigations of the interactions of small molecules with biopolymers. These samples have been analyzed with various instrumental techniques, such as fluorescence, ultraviolet–visible spectroscopy, and voltammetry. The impact of two powerful and demonstrably useful multivariate methods for resolution of complex data—multivariate curve resolution–alternating least squares (MCR–ALS) and parallel factor analysis (PARAFAC)—is highlighted through analysis of applications involving the interactions of small molecules with the biopolymers, serum albumin, and deoxyribonucleic acid. The outcomes illustrated that significant information extracted by the chemometric methods was unattainable by simple, univariate data analysis. In addition, although the techniques used to collect data were confined to ultraviolet–visible spectroscopy, fluorescence spectroscopy, circular dichroism, and voltammetry, data profiles produced by other techniques may also be processed. Topics considered including binding sites and modes, cooperative and competitive small molecule binding, kinetics, and thermodynamics of ligand binding, and the folding and unfolding of biopolymers. Applications of the MCR–ALS and PARAFAC methods reviewed were primarily published between 2008 and 2013.

Isostructural co-crystals derived from molecules with different supramolecular topologies

In this article, we report the crystal structures of five halogen bonded co-crystals comprising quaternary ammonium cations, halide anions (Cl– and Br–), and one of either 1,2-, 1,3-, or 1,4-diiodotetrafluorobenzene (DITFB). Three of the co-crystals are chemical isomers: 1,4-DITFB[TEA-CH2Cl]Cl, 1,2-DITFB[TEA-CH2Cl]Cl, and 1,3-DITFB[TEA-CH2Cl]Cl (where TEA-CH2Cl is chloromethyltriethylammonium ion). In each structure, the chloride anions link DITFB molecules through halogen bonds to produce 1D chains propagating with (a) linear topology in the structure containing 1,4-DITFB, (b) zigzag topology with 60° angle of propagation in that containing 1,2-DITFB, and (c) 120° angle of propagation with 1,3-DITFB. While the individual chains have highly distinctive and different topologies, they combine through π-stacking of the DITFB molecules to produce remarkably similar overall arrangements of molecules. Structures of 1,4-DITFB[TEA-CH2Br]Br and 1,3-DITFB[TEA-CH2Br]Br are also reported and are isomorphous with their chloro/chloride analogues, further illustrating the robustness of the overall supramolecular architecture. The usual approach to crystal engineering is to make structural changes to molecular components to effect specific changes to the resulting crystal structure. The results reported herein encourage pursuit of a somewhat different approach to crystal engineering. That is, to investigate the possibilities for engineering the same overall arrangement of molecules in crystals while employing molecular components that aggregate with entirely different supramolecular connectivity.

A model to explain specific cellular communications and cellular harmony: - a hypothesis of coupled cells and interactive coupling molecules

Background The various cell types and their relative numbers in multicellular organisms are controlled by growth factors and related extracellular molecules which affect genetic expression pathways. However, these substances may have both/either inhibitory and/or stimulatory effects on cell division and cell differentiation depending on the cellular environment. It is not known how cells respond to these substances in such an ambiguous way. Many cellular effects have been investigated and reported using cell culture from cancer cell lines in an effort to define normal cellular behaviour using these abnormal cells. A model is offered to explain the harmony of cellular life in multicellular organisms involving interacting extracellular substances. Methods A basic model was proposed based on asymmetric cell division and evidence to support the hypothetical model was accumulated from the literature. In particular, relevant evidence was selected for the Insulin-Like Growth Factor system from the published data, especially from certain cell lines, to support the model. The evidence has been selective in an attempt to provide a picture of normal cellular responses, derived from the cell lines. Results The formation of a pair of coupled cells by asymmetric cell division is an integral part of the model as is the interaction of couplet molecules derived from these cells. Each couplet cell will have a receptor to measure the amount of the couplet molecule produced by the other cell; each cell will be receptor-positive or receptor-negative for the respective receptors. The couplet molecules will form a binary complex whose level is also measured by the cell. The hypothesis is heavily supported by selective collection of circumstantial evidence and by some direct evidence. The basic model can be expanded to other cellular interactions. Conclusions These couplet cells and interacting couplet molecules can be viewed as a mechanism that provides a controlled and balanced division-of-labour between the two progeny cells, and, in turn, their progeny. The presence or absence of a particular receptor for a couplet molecule will define a cell type and the presence or absence of many such receptors will define the cell types of the progeny within cell lineages.

Two-dimensional self-assembly of a symmetry-reduced tricarboxylic acid

Investigations of the self-assembly of simple molecules at the solution/solid interface can provide useful insight into the general principles governing supramolecular chemistry in two dimensions. Here, we report on the assembly of 3,4′,5-biphenyl tricarboxylic acid (H3BHTC), a small hydrogen bonding unit related to the much-studied 1,3,5-benzenetricarboxylic acid (trimesic acid, TMA), which we investigate using scanning tunneling microscopy (STM) and density functional theory (DFT) calculations. STM images show that H3BHTC assembles by itself into an offset zigzag chain structure that maximizes the surface molecular density in favor of maximizing the number density of strong cyclic hydrogen bonds between the carboxylic groups. The offset geometry creates “sticky” pores that promote solvent coadsorption. Adding coronene to the molecular solution produces a transformation to a high-symmetry host–guest lattice stabilized by a dimeric/trimeric hydrogen bonding motif similar to the TMA flower structure. Finally, we show that the H3BHTC lattice firmly immobilizes the guest coronene molecules, allowing for high-resolution imaging of the coronene structure.

Evidence from molecules and morphology expands Podonomopsis Brundin (Diptera: Chironomidae: Podonominae) to include ‘genus Chile'

The informal taxon ‘genus Chile’ of Brundin, based solely on pupal exuviae of a podonomine Chironomidae, has remained inadequately known for half a century. New collections reveal life associations, and provide molecular data to hypothesise a precise phylogenetic placement in the austral Podonominae. A densely sampled molecular phylogeny based on two nuclear and one mitochondrial DNA markers shows ‘genus Chile’ to be the sister group to Podonomopsis Brundin, 1966. Within Podonomopsis a clade of South American species is sister to all Australian species. We discuss how to rank such a sister group taxon and treat ‘genus Chile’ as a new subgenus Araucanopsis, subg. nov. with the new species, Podonomopsis (Araucanopsis) avelasse, sp. nov. from Chile and Argentina as genotype of the monotypic subgenus. We describe P. (A.) avelasse in all stages and provide an expanded diagnosis and description of Podonomopsis to include Araucanopsis. A dated biogeographic hypothesis (chronogram) infers the most recent common ancestor (tmcra) of expanded Podonomopsis at 95 million years ago (Mya) (68–122 Mya 95% highest posterior density), ‘core’ Podonomopsis at 83 Mya (58–108) and Australian Podonomopsis at 65 Mya (44–87). All dates are before the South America–Australia geological separation through Antarctica, supporting previous conclusions that the taxon distribution is ‘Gondwanan’ in origin. Podonomopsis, even as expanded here, remains unknown from New Zealand or elsewhere on extant Zealandia.

Optimisation of in-cell accelerated solvent extraction technique for the determination of organochlorine pesticides in river sediments

Organochlorine pesticides (OCPs) are ubiquitous environmental contaminants with adverse impacts on aquatic biota, wildlife and human health even at low concentrations. However, conventional methods for their determination in river sediments are resource intensive. This paper presents an approach that is rapid and also reliable for the detection of OCPs. Accelerated Solvent Extraction (ASE) with in-cell silica gel clean-up followed by Triple Quadrupole Gas Chromatograph Mass Spectrometry (GCMS/MS) was used to recover OCPs from sediment samples. Variables such as temperature, solvent ratio, adsorbent mass and extraction cycle were evaluated and optimised for the extraction. With the exception of Aldrin, which was unaffected by any of the variables evaluated, the recovery of OCPs from sediment samples was largely influenced by solvent ratio and adsorbent mass and, to some extent, the number of cycles and temperature. The optimised conditions for OCPs extraction in sediment with good recoveries were determined to be 4 cycles, 4.5 g of silica gel, 105 ᴼC, and 4:3 v/v DCM: hexane mixture. With the exception of two compounds (α-BHC and Aldrin) whose recoveries were low (59.73 and 47.66 % respectively), the recovery of the other pesticides were in the range 85.35 – 117.97% with precision < 10 % RSD. The method developed significantly reduces sample preparation time, the amount of solvent used, matrix interference, and is highly sensitive and selective.

Ratios of T-cell immune-effectors with tumour associated macrophages and PD-1/PD-L1 axis immune-checkpoint molecules, as prognosticators in diffuse large B cell lymphoma: A population-based study

Background Risk-stratification of diffuse large B-cell lymphoma (DLBCL) requires identification of patients with disease that is not cured despite initial R-CHOP. Although the prognostic importance of the tumour microenvironment (TME) is established, the optimal strategy to quantify it is unknown. Methods The relationship between immune-effector and inhibitory (checkpoint) genes was assessed by NanoString™ in 252 paraffin-embedded DLBCL tissues. A model to quantify net anti-tumoural immunity as an outcome predictor was tested in 158 R-CHOP treated patients, and validated in tissue/blood from two independent R-CHOP treated cohorts of 233 and 140 patients respectively. Findings T and NK-cell immune-effector molecule expression correlated with tumour associated macrophage and PD-1/PD-L1 axis markers consistent with malignant B-cells triggering a dynamic checkpoint response to adapt to and evade immune-surveillance. A tree-based survival model was performed to test if immune-effector to checkpoint ratios were prognostic. The CD4*CD8:(CD163/CD68)*PD-L1 ratio was better able to stratify overall survival than any single or combination of immune markers, distinguishing groups with disparate 4-year survivals (92% versus 47%). The immune ratio was independent of and added to the revised international prognostic index (R-IPI) and cell-of-origin (COO). Tissue findings were validated in 233 DLBCL R-CHOP treated patients. Furthermore, within the blood of 140 R-CHOP treated patients immune-effector:checkpoint ratios were associated with differential interim-PET/CT+ve/-ve expression.