Increased optical pathlength through aqueous media for the infrared microanalysis of live cells

The study of live cells using Fourier transform infrared spectroscopy (FTIR) and FTIR microspectroscopy (FT-IRMS) intrinsically yields more information about cell metabolism than comparable experiments using dried or chemically fixed samples. There are, however, a number of barriers to obtaining high-quality vibrational spectra of live cells, including correction for the significant contributions of water bands to the spectra, and the physical stresses placed upon cells by compression in short pathlength sample holders. In this study, we present a water correction method that is able to result in good-quality cell spectra from water layers of 10 and 12 μm and demonstrate that sufficient biological detail is retained to separate spectra of live cells based upon their exposure to different novel anti-cancer agents. The IR brilliance of a synchrotron radiation (SR) source overcomes the problem of the strong water absorption and provides cell spectra with good signal-to-noise ratio for further analysis. Supervised multivariate analysis (MVA) and investigation of average spectra have shown significant separation between control cells and cells treated with the DNA cross-linker PL63 on the basis of phosphate and DNA-related signatures. Meanwhile, the same control cells can be significantly distinguished from cells treated with the protein kinase inhibitor YA1 based on changes in the amide II region. Each of these separations can be linked directly to the known biochemical mode of action of each agent. Keywords: Synchrotron radiation (SR), Fourier transform infrared spectroscopy (FTIR), Infrared microspectroscopy (IRMS), Cancer, Single cell, Drug-cell interaction

A Direct Comparison between the use of Double Gray and Multiwavelength Radiative Transfer in a General Circulation Model with and without Radiatively Active Clouds

Inhomogeneous cloud formation and wavelength-dependent phenomena are expected to shape hot Jupiter atmospheres. We present a General Circulation Model (GCM) with multiwavelength "picket fence" radiative transfer and radiatively active, temperature dependent clouds, and compare the results to a double gray routine. The double gray method inherently fails to model polychromatic effects in hot Jupiter atmospheres, while picket fence captures these non-gray aspects and performs well compared to fully wavelength-dependent methods. We compare both methods with radiatively active clouds and cloud-free models, assessing the limitations of the double gray method. Although there are broad similarities, the picket fence models have larger day-night side temperature differences, non-isothermal upper atmospheres, and multiwavelength effects in the presence of radiatively active clouds. We model the well-known hot Jupiters HD 189733 b and HD 209458 b. For the hotter HD 209458 b, the picket fence method prevents clouds from thermostating dayside temperatures, resulting in hotter upper atmospheres and the dissipation of dayside clouds. Differences in the temperature structures are then associated with nuanced differences in the circulation patterns and clouds. Models of the cooler HD 189733 b have global cloud coverage, regardless of radiative transfer scheme, whereas there are larger differences in the models of HD 209458 b, particularly in the extent of the partial cloud coverage on its dayside. This results in minor changes to the thermal and reflected light phase curves of HD 189733 b, but more significant differences for the picket fence and double gray versions of HD 209458 b.Comment: Submitted to ApJ, 31 page

Effects of crystal size on methanol to hydrocarbon conversion over single crystals of ZSM-5 studied by synchrotron infrared microspectroscopy

IBM and PAW would like to thank the EPSRC and CRITICAT Centre for Doctoral Training for Financial Support [PhD studentship to IBM, and supplementary equipment grant EP/L016419/1]. The UK Catalysis Hub is thanked for resources and support provided via membership of the UK Catalysis Hub Consortium and funded by EPSRC (grants EP/I038748/1, EP/I019693/1, EP/K014706/1, EP/K014668/1, EP/K014854/1, EP/K014714/1 and EP/M013219/1). We thank the Diamond Light Source for provision of beam time and support facilities at the MIRIAM beamline B22 (Experiments SM13725-1, SM16257-1, SM18680-1, SM20906-1). IBM and PAW thank EPSRC and CRTICAT Centre for Doctoral Training for a PhD Studentship (grant EP/IO17008/1) and Supplementary Equipment Grant (EP/L016419/1). We thank Pit Losch and Hans J. Bongard, Max-Planck-Institut fur Kohlenforschung for cross-sectional SEM-EDX analysis, Daniel M. Dawson, University of St Andrews, for solid state NMR, and Juan M.Gonzalez-Carballo, University of St Andrews, for assistance with ammonia TPD. The research data supporting this publication can be accessed at https://doi.org/10.17630/306bd3c3-014b-466f-9538-b107628c847d.Peer reviewedPostprin

Energy Expenditure in Kidney Failure: Implications for Management

Renal replacement therapy, in the form of dialysis or transplantation, is the cornerstone of management for end-stage renal disease. UK renal registry shows nearly half of those needing renal replacement therapy are treated by dialysis – predominantly by haemodialysis. Patients on renal replacement therapy have increased mortality risk compared to age matched general population. Moreover, some specific subgroups of patients on haemodialysis have increased risk of mortality than expected. The survival benefit seen in women in the general population is attenuated resulting in similar survival for men and women on haemodialysis therapy. In addition, obese individuals and those of non-Caucasian origin have better survival outcome. Though the underlying reason for these findings is not clear and is likely to be multi-factorial, it has been hypothesised that this paradox could be due to the current practice of normalising dialysis dose to total body water. A number of metabolic factors – body surface area, resting energy expenditure and total energy expenditure – have been proposed as alternative to total body water for scaling dialysis dose. There were two overarching aims of this work – one was to study the effect of declining renal function on resting and total energy expenditure and to study the influence of various energy expenditure measures on uraemic toxin generation. The second was to study the impact on survival outcome of using these alternate parameters for normalising dialysis dose and to derive dialysis dose adjustments based on these metabolic parameters. In order to study these aims, studies were designed to explore different aspects of energy expenditure measures along with a longitudinal study to examine the impact of these parameters on survival outcome. The relationship between energy metabolism, body composition and uraemic toxin generation was studied with a retrospective analysis of 166 haemodialysis patients in whom urea generation rate was used as surrogate marker of uraemic toxin generation. It was found that total energy expenditure and fat-free mass predicted uraemic toxin generation after adjustment for other relevant variables. This study provided the preliminary data which was useful in designing further studies for this work. The effect of renal function on resting and total energy expenditure was studied in 80 patients with varying stages of chronic kidney disease who were not on renal replacement therapy. Resting and total energy expenditures were measured directly using gold-standard methods. It was found that declining renal function did not have a significant influence on either of these measures. This supports the hypothesis that metabolic rate is the driving force for glomerular filtration rate and not vice-versa. The directly measured energy expenditure measures were also found to have a moderately strong relationship with urea generation rate in these patients not on renal replacement therapy. The impact of physical activity on uraemic toxin generation, and thereby dialysis requirement, was studied in a prospective cross-sectional study of 120 haemodialysis patients in whom the physical activity was measured by an accelerometer device. Results from the study showed physical activity level to be a significant predictor of uraemic toxin generation after adjustment for gender and body size differences. This study results stressed the importance of adjusting dialysis dose based on individual’s physical activity level. To study the impact of using metabolic factors as normalising parameter for scaling dialysis dose on survival outcome, a large-scale longitudinal study was conducted with 1500 maintenance haemodialysis patients recruited for the study. Dialysis dose-related parameters and survival outcomes were collected at baseline and at various time points during the follow-up period of 18 months. Study results were analysed in two parts - the theoretical basis for using these metabolic factors as scaling parameters was explored which showed that current minimum target dialysis dose risks under-dialysis in certain subgroups of patients and using these alternative parameters may provide a more equivalent dialysis dose across individuals of different body sizes and gender. With these results arguing for potential use of the alternative parameters, the impact on survival of using them were examined. It was found that all three parameters performed better than the current parameter (total body water) with regards to predicting mortality. Total energy expenditure was found to be the best parameter with the lowest hazard ratio for risk of death. The study data was also analysed to derive an algorithm for adjustment of minimum target dialysis dose based on body size and physical activity level. This newly derived minimum dose target was also shown to impact on survival with those underdialysed based on this criteria having poorer survival outcomes. To understand the impact of whole body protein turnover on resting energy expenditure and uraemic toxin generation, a cross-sectional study was conducted on 12 patients with advanced CKD – 6 each in pre-dialysis CKD and haemodialysis group. It was found that haemodialysis patients had higher rate of protein turnover compared to pre-dialysis patients. Whole body protein turnover was found to contribute significantly to resting energy expenditure and had a moderately strong relationship with urea generation rate. In the course of these studies, two questionnaire tools have been validated for use for clinical and research purposes – one is a self-report comorbidity questionnaire and the other, the Recent Physical Activity Questionnaire. The comorbidity questionnaire was developed as part of this work and was validated against Charlson Comorbidity Index. The Recent Physical Activity Questionnaire was validated for physical activity data collection and energy expenditure calculation against the gold-standard doubly labelled water method. In conclusion, it has been demonstrated that metabolic factors such as body surface area, resting energy expenditure and total energy expenditure are more closely related to uraemic toxin generation compared to total body water. It has also been demonstrated that physical activity contributes to metabolic waste production and may necessitate changes in dialysis requirement. It has been shown that these metabolic factors, when used as scaling parameter for dialysis dosing, may predict survival better than the current parameter in use. The algorithm for dialysis dose adjustment and the questionnaires validated in this work have provided novel tools for further research studies and clinical practice. The central hypothesis of this work is that some metabolic factors may be better markers of uraemic toxin generation compared to total body water. It is hypothesised that modifications in dialysis practice based on these factors may improve the quality of haemodialysis and favourably impact on survival outcome for patients with end-stage renal disease. The work presented here largely supports this hypothesis

Chemotherapeutic response to cisplatin-like drugs in human breast cancer cells probed by vibrational microspectroscopy

Studies of drug-cell interactions in cancer model systems are essential in the preclinical stage of rational drug design, which relies on a thorough understanding of the mechanisms underlying cytotoxic activity and biological effects, at a molecular level. This study aimed at applying complementary vibrational spectroscopy methods to evaluate the cellular impact of two Pt(ii) and Pd(ii) dinuclear chelates with spermine (Pt2Spm and Pd2Spm), using cisplatin (cis-Pt(NH3)2Cl2) as a reference compound. Their effects on cellular metabolism were monitored in a human triple-negative metastatic breast cancer cell line (MDA-MB-231) by Raman and synchrotron-radiation infrared microspectroscopies, for different drug concentrations (2-8 μM) at 48 h exposure. Multivariate data analysis was applied (unsupervised PCA), unveiling drug- and concentration-dependent effects: apart from discrimination between control and drug-treated cells, a clear separation was obtained for the different agents studied - mononuclear vs. polynuclear, and Pt(ii) vs. Pd(ii). Spectral biomarkers of drug action were identified, as well as the cellular response to the chemotherapeutic insult. The main effect of the tested compounds was found to be on DNA, lipids and proteins, the Pd(ii) agent having a more significant impact on proteins while its Pt(ii) homologue affected the cellular lipid content at lower concentrations, which suggests the occurrence of distinct and unconventional pathways of cytotoxicity for these dinuclear polyamine complexes. Raman and FTIR microspectroscopies were confirmed as powerful non-invasive techniques to obtain unique spectral signatures of the biochemical impact and physiological reaction of cells to anticancer agents

IFNβ Protects Neurons from Damage in a Murine Model of HIV-1 Associated Brain Injury.

Infection with human immunodeficiency virus-1 (HIV-1) causes brain injury. Type I interferons (IFNα/β) are critical mediators of any anti-viral immune response and IFNβ has been implicated in the temporary control of lentiviral infection in the brain. Here we show that transgenic mice expressing HIV-1 envelope glycoprotein 120 in their central nervous system (HIVgp120tg) mount a transient IFNβ response and provide evidence that IFNβ confers neuronal protection against HIVgp120 toxicity. In cerebrocortical cell cultures, neuroprotection by IFNβ against gp120 toxicity is dependent on IFNα receptor 1 (IFNAR1) and the β-chemokine CCL4, as IFNAR1 deficiency and neutralizing antibodies against CCL4, respectively, abolish the neuroprotective effects. We find in vivo that IFNβ mRNA is significantly increased in HIVgp120tg brains at 1.5, but not 3 or 6 months of age. However, a four-week intranasal IFNβ treatment of HIVgp120tg mice starting at 3.5 months of age increases expression of CCL4 and concomitantly protects neuronal dendrites and pre-synaptic terminals in cortex and hippocampus from gp120-induced damage. Moreover, in vivo and in vitro data suggests astrocytes are a major source of IFNβ-induced CCL4. Altogether, our results suggest exogenous IFNβ as a neuroprotective factor that has potential to ameliorate in vivo HIVgp120-induced brain injury

The role of morphological markedness in the processing of number and gender agreement in Spanish: an event-related potential investigation

Current morphological theory assumes that feature values, such as masculine and feminine or singular and plural, are asymmetrically represented. That is, one member of the opposition (e.g. feminine for gender, plural for number) is assumed to be marked, and the other one, unmarked. The present study examines how these asymmetries impact agreement resolution in Spanish. Agreement was manipulated between a noun acting as head of a relative clause and an adjective located inside the relative clause (e.g. catedral que parecía inmensa “cathedral that looked huge”). Half of the nouns were feminine (marked) and the other half, masculine (unmarked). Half of the nouns were used in the plural (marked) and the other half, in the singular (unmarked). Twenty-seven Spanish native speakers read 240 sentences while their brain activity was recorded with EEG and performed a grammaticality judgment. Results showed that both number and gender violations elicited a central-posterior P600, a component associated with syntactic repair, and a late anterior negativity, argued to reflect working memory costs. Only the P600 was affected by markedness. It started earlier for violations where the mismatching feature was marked. Moreover, it was larger for errors where the mismatching feature was marked, although this amplitude modulation only emerged for number, possibly due to differences in how number and gender cues were realized (i.e. both masculine and feminine showed overt inflection, but singular was uninflected relative to plural). These results suggest that the parser is sensitive to markedness asymmetries in the course of online processing

Rapid recognition of drug-resistance/sensitivity in leukemic cells by Fourier transform infrared microspectroscopy and unsupervised hierarchical cluster analysis.

We tested the ability of Fourier Transform (FT) InfraRed (IR) microspectroscopy (microFTIR) in combination with unsupervised Hierarchical Cluster Analysis (HCA) in identifying drug-resistance/sensitivity in leukemic cells exposed to tyrosine kinase inhibitors (TKIs). Experiments were carried out in a well-established mouse model of human Chronic Myelogenous Leukemia (CML). Mouse-derived pro-B Ba/F3 cells transfected with and stably expressing the human p210(BCR-ABL) drug-sensitive wild-type BCR-ABL or the V299L or T315I p210(BCR-ABL) drug-resistant BCR-ABL mutants were exposed to imatinib-mesylate (IMA) or dasatinib (DAS). MicroFTIR was carried out at the Diamond IR beamline MIRIAM where the mid-IR absorbance spectra of individual Ba/F3 cells were acquired using the high brilliance IR synchrotron radiation (SR) via aperture of 15 7 15 \u3bcm(2) in sizes. A conventional IR source (globar) was used to compare average spectra over 15 cells or more. IR signatures of drug actions were identified by supervised analyses in the spectra of TKI-sensitive cells. Unsupervised HCA applied to selected intervals of wavenumber allowed us to classify the IR patterns of viable (drug-resistant) and apoptotic (drug-sensitive) cells with an accuracy of >95%. The results from microFTIR + HCA analysis were cross-validated with those obtained via immunochemical methods, i.e. immunoblotting and flow cytometry (FC) that resulted directly and significantly correlated. We conclude that this combined microFTIR + HCA method potentially represents a rapid, convenient and robust screening approach to study the impact of drugs in leukemic cells as well as in peripheral blasts from patients in clinical trials with new anti-leukemic drugs