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.

A Robust Co-Localisation Measurement Utilising Z-Stack Image Intensity Similarities for Biological Studies

Background: Co-localisation is a widely used measurement in immunohistochemical analysis to determine if fluorescently labelled biological entities, such as cells, proteins or molecules share a same location. However the measurement of co-localisation is challenging due to the complex nature of such fluorescent images, especially when multiple focal planes are captured. The current state-of-art co-localisation measurements of 3-dimensional (3D) image stacks are biased by noise and cross-overs from non-consecutive planes.

Method: In this study, we have developed Co-localisation Intensity Coefficients (CICs) and Co-localisation Binary Coefficients (CBCs), which uses rich z-stack data from neighbouring focal planes to identify similarities between image intensities of two and potentially more fluorescently-labelled biological entities. This was developed using z-stack images from murine organotypic slice cultures from central nervous system tissue, and two sets of pseudo-data. A large amount of non-specific cross-over situations are excluded using this method. This proposed method is also proven to be robust in recognising co-localisations even when images are polluted with a range of noises.

Results: The proposed CBCs and CICs produce robust co-localisation measurements which are easy to interpret, resilient to noise and capable of removing a large amount of false positivity, such as non-specific cross-overs. Performance of this method of measurement is significantly more accurate than existing measurements, as determined statistically using pseudo datasets of known values. This method provides an important and reliable tool for fluorescent 3D neurobiological studies, and will benefit other biological studies which measure fluorescence co-localisation in 3D.

The application of gas liquid chromatography to the simultaneous analysis of sugars and sugar phosphates in biological samples /|nby David J. LeBlanc. -- 260 St. Catharines [Ont. : s. n.],

A study was undertaken' to determine the applicability of gas liquid chromatography to the simultaneous analysis of sugars and sugar phosphates from biological samples. A new method of silylation involving dimethylsulfoxide, hexamethyldisilazane, trimethylchlorosilane and cyclohexane (1:0.2:0.1:1) which rapidly silylated sugars and sugar phosphates was developed. Subsequent chromatography on a 5% SE-52 column gave good resolution of the sugar and sugar phosphate samples. Sugar phosphates decomposed during chromatography and were lost at the 7 x 10-3 ~mole level. Acidic ethanol extraction of yeast samples revealed background contamination from the yeast sample, the culture medium and the silylation reagents which would further limit the level of detection obtainable with the glc for sugars in biological samples to the 3 x 10-4 ~mole level.

Bacteriophages of Erwinia amylovora and their potential use in biological control

Forty-four bacteriophage isolates of Erwinia amy/ovora, the causal agent of fire blight, were collected from sites in and around the Niagara Region of Southern Ontario in the summer of 1998. Phages were isolated only from sites where fire blight was present. Thirty-seven of these phages were isolated from the soil surrounding infected trees, with the remainder isolated from aerial plant tissue samples. A mixture of six E. amy/ovora bacterial host strains was used to enrich field samples in order to avoid the selection bias of a single-host system. Molecular characterization of the phages with a combination of peR and restriction endonuclease digestions showed that six distinct phage types were isolated. Ten phage isolates related to the previously characterized E. amy/ovora phage PEa1 were isolated, with some divergence of molecular markers between phages isolated from different sites. The host ranges of the phages revealed that certain types were unable to efficiently lyse some E. amy/ovora strains, and that some types were able to lyse the epiphytic bacterium Pantoea agg/omerans. Biological control of E. amy/ovora by the bacteriophages was assessed in a bioassay using discs of immature pear fruit. Twenty-three phage isolates were able to significantly suppress the incidence of bacterial exudate on the pear disc surface. Quantification of the bacterial population remaining on the disc surface indicated that population reductions of up to 97% were obtainable by phage treatment, but that elimination of bacteria from the surface was not possible with this model system.

Astringency and other oral sensations : biological sources of individual variation and association with food and beverage behaviour

Orosensory perception strongly influences liking and consumption of foods and beverages. This thesis examines the influence of biological sources of individual variation on the perception of prototypical orosensory stimuli, food liking, self-reported alcohol liking and consumption, and indices of health. Two orosensory indices were examined: propylthiouracil (PROP) responsiveness, a genetically-mediated index of individual variation associated with enhanced responsiveness to orosensory stimuli often expressed as PROP taster status (PTS); and thermal taster status (TTS), a recently reported index of orosensory responsiveness. Taster status in PTS and/or TTS confers greater responsiveness to most orosensory stimuli. Gender, age, ethnicity, and fungiform papillae (FP) density were not associated with orosensory responsiveness to tastants, an astringent, and a flavour. Unlike PROP responsiveness, FP density was not associated with TTS. Both PROP responsiveness and TTS were associated with increased responsiveness to orosensory stimuli, including temperature and astringency. For PROP, this association did not hold when stimuli were presented at cold or warm temperatures, which are ecologically valid since most foods and beverages are not consumed at ambient temperature. Thermal tasters (TTs), who perceive 'phantom' taste sensations with lingual thermal stimulation, were more responsive to stimuli at both temperatures than thermal non-tasters (TnTs). While PTS, TIS, and gender affected self-reported liking and consumption of some alcoholic beverages, gender associated with the greatest number of beverage types and consumption parameters, with males generally liking and consuming alcoholic beverages more than females. Age and gender were the best predictors of alcoholic beverageAiking and consumption. As expected, .. liking of bitter and fatty foods and cream was inversely related to PROP responsiveness. TTS did not associate with body mass index or waist circumference, and contrary to previous studies, neither did PROP responsiveness. Taken together, TnTs' greater liking of cooked fruits and vegetables and high alcohol, and astringent alcoholic beverages than TTs suggests differences between TTS groups may be driven by perceived temperature and texture. Neither an interaction between PTS and TTS nor a TTS effect on PROP responsiveness was observed, suggesting these two indices of individual variation exert their influences on orosensory perception independently.

Biomedical Sciences Library tour

Audio recording of a tour of the Biomedical Sciences Library at the Boldrewood Campus for the academic session 2007-2008. Voices of 2 students from the School of Biological Sciences.

Búsqueda de selección en el polimorfismo 677C>T (c.665C>T) del gen de la metilentetrahidrofolato reductasa (MTHFR) en una población Colombiana

Se realizó un estudio genético – poblacional en dos grupos etarios de población colombiana con la finalidad de evaluar las diferencias genéticas relacionadas con el polimorfismo MTHFR 677CT en busca de eventos genéticos que soporten la persistencia de este polimorfismo en la especie humana debido que este ha sido asociado con múltiples enfermedades. De esta manera se genotipificaron los individuos, se analizaron los genotipos, frecuencias alélicas y se realizaron diferentes pruebas genéticas-poblacionales. Contrario a lo observado en poblaciones Colombianas revisadas se identificó la ausencia del Equilibrio Hardy-Weinberg en el grupo de los niños y estructuras poblacionales entre los adultos lo que sugiere diferentes historias demográficas y culturales entre estos dos grupos poblacionales al tiempo, lo que soporta la hipótesis de un evento de selección sobre el polimorfismo en nuestra población. De igual manera nuestros datos fueron analizados junto con estudios previos a nivel nacional y mundial lo cual sustenta que el posible evento selectivo es debido a que el aporte de ácido fólico se ha incrementado durante las últimas dos décadas como consecuencia de las campañas de fortificación de las harinas y suplementación a las embarazadas con ácido fólico, por lo tanto aquí se propone un modelo de selección que se ajusta a los datos encontrados en este trabajo se establece una relación entre los patrones nutricionales de la especie humana a través de la historia que explica las diferencias en frecuencias de este polimorfismo a nivel espacial y temporal.  

Quantification of physical and biological uncertainty in the simulation of the yield of a tropical crop using present-day and doubled CO2 climates

The impacts of climate change on crop productivity are often assessed using simulations from a numerical climate model as an input to a crop simulation model. The precision of these predictions reflects the uncertainty in both models. We examined how uncertainty in a climate (HadAM3) and crop General Large-Area Model (GLAM) for annual crops model affects the mean and standard deviation of crop yield simulations in present and doubled carbon dioxide (CO2) climates by perturbation of parameters in each model. The climate sensitivity parameter (lambda, the equilibrium response of global mean surface temperature to doubled CO2) was used to define the control climate. Observed 1966-1989 mean yields of groundnut (Arachis hypogaea L.) in India were simulated well by the crop model using the control climate and climates with values of lambda near the control value. The simulations were used to measure the contribution to uncertainty of key crop and climate model parameters. The standard deviation of yield was more affected by perturbation of climate parameters than crop model parameters in both the present-day and doubled CO2 climates. Climate uncertainty was higher in the doubled CO2 climate than in the present-day climate. Crop transpiration efficiency was key to crop model uncertainty in both present-day and doubled CO2 climates. The response of crop development to mean temperature contributed little uncertainty in the present-day simulations but was among the largest contributors under doubled CO2. The ensemble methods used here to quantify physical and biological uncertainty offer a method to improve model estimates of the impacts of climate change.

Mathematics as a tool in the Life Sciences

Teaching mathematics to students in the biological sciences is often fraught with difficulty. Students often discover mathematics to be a very 'dry' subject in which it is difficult to see the motivation of learning it given its often abstract application. In this paper I advocate the use of mathematical modelling as a method for engaging students in understanding the use of mathematics in helping to solve problems in the Biological Sciences. The concept of mathematics as a laboratory tool is introduced and the importance of presenting students with relevant, real-world examples of applying mathematics in the Biological Sciences is discussed.

The prospect of applying chemical elicitors and plant strengtheners to enhance the biological control of crop pests

An imminent food crisis reinforces the need for novel strategies to increase crop yields worldwide. Effective control of pest insects should be part of such strategies, preferentially with reduced negative impact on the environment and optimal protection and utilization of existing biodiversity. Enhancing the presence and efficacy of native biological control agents could be one such strategy. Plant strengthener is a generic term for several commercially available compounds or mixtures of compounds that can be applied to cultivated plants in order to ‘boost their vigour, resilience and performance’. Studies into the consequences of boosting plant resistance against pests and diseases on plant volatiles have found a surprising and dramatic increase in the plants' attractiveness to parasitic wasps. Here, we summarize the results from these studies and present new results from assays that illustrate the great potential of two commercially available resistance elicitors. We argue that plant strengtheners may currently be the best option to enhance the attractiveness of cultivated plants to biological control agents. Other options, such as the genetic manipulation of the release of specific volatiles may offer future solutions, but in most systems, we still miss fundamental knowledge on which key attractants should be targeted for this approach.

Alanine is helix-stabilizing in both template-nucleated and standard peptide helices

Alanine-based peptides of defined sequence and length show measurable helix contents, allowing them to be used as a model system both for analyzing the mechanism of helix formation and for investigating the contributions of side-chain interactions to protein stability. Extensive characterization of many peptide sequences with varying amino acid contents indicates that the favorable helicity of alanine-based peptides can be attributed to the large helix-stabilizing propensity of alanine. Based on their analysis of alanine-rich sequences N-terminally linked to a synthetic helix-inducing template, Kemp and coworkers [Kemp, D. S., Boyd, J. G. & Muendel, C. C. (1991) Nature (London) 352, 451–454; Kemp, D. S., Oslick, S. L. & Allen, T. J. (1996) J. Am. Chem. Soc. 118, 4249–4255] argue that alanine is helix-indifferent, however, and that the favorable helix contents of alanine-based peptides must have some other explanation. Here, we show that the helix contents of template-nucleated sequences are influenced strongly by properties of the template–helix junction. A model in which the helix propensities of residues at the template–peptide junction are treated separately brings the results from alanine-based peptides and template-nucleated helices into agreement. The resulting model provides a physically plausible resolution of the discrepancies between the two systems and allows the helix contents of both template-nucleated and standard peptide helices to be predicted by using a single set of helix propensities. Helix formation in both standard peptides and template–peptide conjugates can be attributed to the large intrinsic helix-forming tendency of alanine.

Manipulation of the membrane binding site of vitamin K-dependent proteins: Enhanced biological function of human factor VII

Recent studies suggested that modification of the membrane contact site of vitamin K-dependent proteins may enhance the membrane affinity and function of members of this protein family. The properties of a factor VII mutant, factor VII-Q10E32, relative to wild-type factor VII (VII, containing P10K32), have been compared. Membrane affinity of VII-Q10E32 was about 20-fold higher than that of wild-type factor VII. The rate of autoactivation VII-Q10E32 with soluble tissue factor was 100-fold faster than wild-type VII and its rate of activation by factor Xa was 30 times greater than that of wild-type factor VII. When combined with soluble tissue factor and phospholipid, activated factor VII-Q10E32 displayed increased activation of factor X. Its coagulant activity was enhanced in all types of plasma and with all sources of tissue factor tested. This difference in activity (maximum 50-fold) was greatest when coagulation conditions were minimal, such as limiting levels of tissue factor and/or phospholipid. Because of its enhanced activity, factor VII-Q10E32 and its derivatives may provide important reagents for research and may be more effective in treatment of bleeding and/or clotting disorders.

The design, computer modeling, solution structure, and biological evaluation of synthetic analogs of bryostatin 1

The bryostatins are a unique family of emerging cancer chemotherapeutic candidates isolated from marine bryozoa. Although the biochemical basis for their therapeutic activity is not known, these macrolactones exhibit high affinities for protein kinase C (PKC) isozymes, compete for the phorbol ester binding site on PKC, and stimulate kinase activity in vitro and in vivo. Unlike the phorbol esters, they are not first-stage tumor promoters. The design, computer modeling, NMR solution structure, PKC binding, and functional assays of a unique class of synthetic bryostatin analogs are described. These analogs (7b, 7c, and 8) retain the putative recognition domain of the bryostatins but are simplified through deletions and modifications in the C4-C14 spacer domain. Computer modeling of an analog prototype (7a) indicates that it exists preferentially in two distinct conformational classes, one in close agreement with the crystal structure of bryostatin 1. The solution structure of synthetic analog 7c was determined by NMR spectroscopy and found to be very similar to the previously reported structures of bryostatins 1 and 10. Analogs 7b, 7c, and 8 bound strongly to PKC isozymes with Ki = 297, 3.4, and 8.3 nM, respectively. Control 7d, like the corresponding bryostatin derivative, exhibited weak PKC affinity, as did the derivative, 9, lacking the spacer domain. Like bryostatin, acetal 7c exhibited significant levels of in vitro growth inhibitory activity (1.8–170 ng/ml) against several human cancer cell lines, providing an important step toward the development of simplified, synthetically accessible analogs of the bryostatins.

Highly sensitive biological and chemical sensors based on reversible fluorescence quenching in a conjugated polymer

The fluorescence of a polyanionic conjugated polymer can be quenched by extremely low concentrations of cationic electron acceptors in aqueous solutions. We report a greater than million-fold amplification of the sensitivity to fluorescence quenching compared with corresponding “molecular excited states.” Using a combination of steady-state and ultrafast spectroscopy, we have established that the dramatic quenching results from weak complex formation [polymer(−)/quencher(+)], followed by ultrafast electron transfer from excitations on the entire polymer chain to the quencher, with a time constant of 650 fs. Because of the weak complex formation, the quenching can be selectively reversed by using a quencher-recognition diad. We have constructed such a diad and demonstrate that the fluorescence is fully recovered on binding between the recognition site and a specific analyte protein. In both solutions and thin films, this reversible fluorescence quenching provides the basis for a new class of highly sensitive biological and chemical sensors.

The role of automated feedback in training and retaining biological recorders for citizen science

© 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology. This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. Acknowledgments The authors thank H. H. Nguyen for his early development work on the BeeWatch interface; E. O'Mahony, I. Pearce, and R. Comont for identifying numerous photographed bumblebees; B. Darvill, D. Ewing, and G. Perkins for enabling our partnership with the Bumblebee Conservation Trust; and S. Blake for his investments in developing the NLG feedback. The study was part of the Digital Conservation project of dot.rural, the University of Aberdeen's Digital Economy Research Hub, funded by RCUK (grant reference EP/G066051/1).