An introduction to biological nuclear magnetic resonance spectroscopy

ABSTRACT Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful analytical techniques available to biology. This review is an introduction to the potential of this method and is aimed at readers who have little or no experience in acquiring or analyzing NMR spectra. We focus on spectroscopic applications of the magnetic resonance effect, rather than imaging ones, and explain how various aspects of the NMR phenomenon make it a versatile tool with which to address a number of biological problems. Using detailed examples, we discuss the use of 1H NMR spectroscopy in mixture analysis and metabolomics, the use of 13C NMR spectroscopy in tracking isotopomers and determining the flux through metabolic pathways (‘fluxomics’) and the use of 31P NMR spectroscopy in monitoring ATP generation and intracellular pH homeotasis in vivo. Further examples demonstrate how NMR spectroscopy can be used to probe the physical environment of a cell by measuring diffusion and the tumbling rates of individual metabolites and how it can determine macromolecular structures by measuring the bonds and distances which separate individual atoms. We finish by outlining some of the key challenges which remain in NMR spectroscopy and we highlight how recent advances— such as increased magnet field strengths, cryogenic cooling, microprobes and hyperpolarisation—are opening new avenues for today’s biological NMR spectroscopists.

Endocrine disrupting effects of zearalenone, alpha- and beta-zearalenol at the level of nuclear receptor binding and steroidogenesis.

The mycotoxin zearalenone (ZEN) is a secondary metabolite of fungi which is produced by certain species of the genus Fusarium and can occur in cereals and other plant products. Reporter gene assays incorporating natural steroid receptors and the H295R steroidogenesis assay have been implemented to assess the endocrine disrupting activity of ZEN and its metabolites -zearalenol (-ZOL) and -zearalenol (-ZOL). -ZOL exhibited the strongest estrogenic potency (EC50 0.022 ± 0.001 nM), slightly less potent than 17- estradiol (EC50 0.015 ± 0.002 nM). ZEN was ~70 times less potent than -ZOL and twice as potent as -ZOL. Binding of progesterone to the progestagen receptor was shown to be synergistically increased in the presence of ZEN, -ZOL or -ZOL. ZEN, -ZOL or -ZOL increased production of progesterone, estradiol, testosterone and cortisol hormones in the H295R steroidogenesis assay, with peak productions at 10 M. At 100 M, cell viability decreased and levels of hormones were significantly reduced except for progesterone. -ZOL increased estradiol concentrations more than -ZOL or ZEN, with a maximum effect at 10 M, with -ZOL (562 ± 59 pg/ml) > -ZOL (494 ± 60 pg/ml) > ZEN (375 ± 43 pg/ml). The results indicate that ZEN and its metabolites can act as potential endocrine disruptors at the level of nuclear receptor signalling and by altering hormone production.

DENSE GAS IN NEARBY GALAXIES .6. A LARGE C-12/C-13 RATIO IN A NUCLEAR STARBURST ENVIRONMENT

Toward the starburst nucleus of NGC 253, C-12/C-13 line intensity ratios from six carbon bearing molecules (CO, CN, CS, HCN, HCO+, and HNC) are used to confine the possible range of carbon and oxygen isotope ratios. A detailed analysis yields C-12/C-13 approximately 40 and O-16/O-18 approximately 200. Also reported are first detections of (CS)-C-13 and of the 0(0) - 1(-1) E line of methanol (CH3OH) in an extragalactic source.

Acetylation of Rb by PCAF is required for nuclear localization and keratinocyte differentiation

Although the retinoblastoma protein (Rb) functions as a checkpoint in the cell cycle, it also regulates differentiation. It has recently been shown that Rb is acetylated during differentiation; however, the role of this modification has not been identified. Depletion of Rb levels with short hairpin RNA resulted in inhibition of human keratinocyte differentiation, delayed cell cycle exit and allowed cell cycle re-entry. Restoration of Rb levels rescued defects in differentiation and cell cycle exit and re-entry; however, re-expression of Rb with the major acetylation sites mutated did not. During keratinocyte differentiation, acetylation of Rb is mediated by PCAF and it is further shown that PCAF acetyltransferase activity is also required for normal differentiation. The major acetylation sites in Rb are located within the nuclear localization sequence and, although mutation did not alter Rb localization in cycling cells, the mutant is mislocalized to the cytoplasm during differentiation. Studies indicate that acetylation is a mechanism for controlling Rb localization in human keratinocytes, with either reduction of the PCAF or exogenous expression of the deacetylase SIRT1, resulting in mislocalization of Rb. These findings identify PCAF-mediated acetylation of Rb as an event required to retain Rb within the nucleus during keratinocyte differentiation.

Nuclear activation as a high dynamic range diagnostic of laser-plasma interactions

Proton imaging has become a common diagnostic technique for use in laser-plasma research experiments due to their ability to diagnose electric field effects and to resolve small density differences caused through shock effects. These interactions are highly dependent on the use of radiochromic film (RCF) as a detection system for the particle probe, and produces very high-resolution images. However, saturation effects, and in many cases, damage to the film limits the usefulness of this technique for high-flux particle probing. This paper outlines the use of a new technique using contact radiography of (p,n)-generated isotopes in activation samples to produce high dynamic range 2D images with high spatial resolution and extremely high dynamic range, whilst maintaining both energy resolution and absolute flux measurements. (C)007 Elsevier B.V. All rights reserved.

Congruence between nuclear and mitochondrial genes in Demospongiae: A new hypothesis for relationships within the G4 clade (Porifera: Demospongiae)

The current morphological classification of the Demospongiae G4 clade was tested using large subunit ribosomal RNA (LSU rRNA) sequences from 119 taxa. Fifty-three mitochondrial cytochrome oxidase 1 (CO1) barcoding sequences were also analysed to test whether the 28S phylogeny could be recovered using an independent gene. This is the largest and most comprehensive study of the Demospongiae G4 clade. The 28S and CO1 genetrees result in congruent clades but conflict with the current morphological classification. The results confirm the polyphyly of Halichondrida, Hadromerida, Dictyonellidae, Axinellidae and Poecilosclerida and show that several of the characters used in morphological classifications are homoplasious. Robust clades are clearly shown and a new hypothesis for relationships of taxa allocated to G4 is proposed. (C) 2011 Elsevier Inc. All rights reserved.

NUCLEAR STAINING IN ALGAL HERBARIUM MATERIAL - A REAPPRAISAL OF THE HOLOTYPE OF CALLITHAMNION-DECOMPOSITUM AGARDH,J. (RHODOPHYTA)

The taxonomic importance of uninucleate vs. multinucleate vegetative cells in the Ceramiaceae is emphasized. It has been possible to make visible nuclei in old material, including type specimens, using aceto-carmine and aceto-iron-haematoxylin stains. The holotypes of Ceramium roseum and Callithamnion fasciculatum (currently known as Callithamnion roseum and Pleonosporium borreri var. fasciculatum) have uninucleate cells and belong to Aglaothamnion. In contrast, the holotype of Callithamnion decompositum, a name that has been applied to collections of at least two uninucleate taxa, has multinucleate cells; its morphological and cytological details agree with those of specimens collected in France and Ireland that were previously thought to represent an undescribed species. Female reproductive morphology (described from a thallus with gametangia in addition to tetrasporangia), in conjunction with habit and vegetative features, indicates that this species belongs to Compsothamnion (Compsothamnieae), as a third species, being distinguished from C. thuyoides and C. gracillimum by its sessile, lateral tetrasporangia. The required new combinations under Aglaothamnion and Compsothamnion are made.

Nuclear factor-kappaB as a potential therapeutic target for the novel cytotoxic agent LC-1 in acute myeloid leukaemia

Nuclear factor-kappaB (NF-kappaB) has been implicated in a number of malignancies and has been suggested to be a potential molecular target in the treatment of leukaemia. This study demonstrated the constitutive activation of NF-kappaB in human myeloid blasts and a clear correlation between NF-kappaB expression and in vitro cytoprotection. High NF-kappaB expression was found in many of the poor prognostic acute myeloid leukaemia (AML) subtypes, such as French-American-British classification M0 and M7, and the poor cytogenetic risk group. The in vitro effects of LC-1, a novel dimethylamino-parthenolide analogue, were assessed in 62 primary untreated AML samples. LC-1 was found to be cytotoxic to AML cells in a dose-dependent manner, mediated through the induction of apoptosis. The median drug concentration necessary to kill 50% of the cells was 4.5 micromol/l for AML cells, compared with 12.8 micromol/l for normal marrow cells. LC-1 was shown to reduce the five individual human NF-kappaB Rel proteins in a dose-dependent manner. The subsequent inhibition of many NF-kappaB-regulated cytokines was also demonstrated. Importantly, sensitivity to LC-1 was correlated with the basal NF-kappaB activity. Consequently, LC-1 treatment provides a proof of principle for the use of NF-kappaB inhibitors in the treatment of AML.

Variable selection via RIVAL and its application in nuclear material detection

In many situations, the number of data points is fixed, and the asymptotic convergence results of popular model selection tools may not be useful. A new algorithm for model selection, RIVAL (removing irrelevant variables amidst Lasso iterations), is presented and shown to be particularly effective for a large but fixed number of data points. The algorithm is motivated by an application of nuclear material detection where all unknown parameters are to be non-negative. Thus, positive Lasso and its variants are analyzed. Then, RIVAL is proposed and is shown to have some desirable properties, namely the number of data points needed to have convergence is smaller than existing methods.