Whispering-gallery mode (WGM) sensors: review of established and WGM-based techniques to study protein conformational dynamics

This is the final version. Available on open access from Elsevier via the DOI in this recordMonitoring the conformational dynamics of proteins is crucial for a better understanding of their biological functions. To observe the structural dynamics of proteins, it is often necessary to study each molecule individually. To this end, single-molecule techniques have been developed such as Förster resonance energy transfer and optical tweezers. However, although powerful, these techniques do have their limitations, for example, limited temporal resolution, or necessity for fluorescent labelling, and they can often only access a limited set of all protein motions. Here, within the context of established structural biology techniques, we review a new class of highly sensitive optical devices based on WGM, which characterise protein dynamics on previously inaccessible timescales, visualise motions throughout a protein, and track movements of single atoms.Engineering and Physical Sciences Research Council (EPSRC

Validation of a method for the determination of the sensible-heat flux with Sodar data in free convection cases

A simple method to determine the value of the ground sensible-heat flux using Sodar data is presented and validated. The measurement of the variance of the wind velocity components gives us an estimate of the intensity of the atmospheric turbulence; the local value of variance of the vertical wind velocity s2w depends on the efficiency of thermal and mechanical turbulence production. The portion of the atmospheric boundary layer, where turbulent kinetic energy is prevalently produced by buoyancy forces, is characterised by profiles of s3w Oz and of (sensible-) heat flux which decrease linearly with height. The extrapolation to the ground of the former profile gives an estimate of the value of sensible-heat flux at the surface. The validation of the results is performed by comparison of the energy involved in the development of convective episodes calculated, over the same time interval, from sensible-heat flux at the surface with that derived from potential temperature profiles relative to two successive radio soundings. When perturbative processes like, for example, rise up of breezes, are absent, the estimates of energies are in excellent agreement, being the angular coefficient of regression line 1.01 and the linear correlation coefficient 0.93

Expanding exploration of dynamic microplastic surface characteristics and interactions

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this recordMicroplastics have been found in all marine ecosystems, raising concern about their potential environmental impacts. Yet relatively little research has focused on surface characteristics, compared to polymer type. The aim of this review is to discuss the importance of microplastic surface properties and how expanded characterisation and more detailed quantification can aid in assessing their behaviours in aquatic environments. Concepts including surface roughness, formation of surface ecocoronae and sorptive behaviours of microplastic surfaces are discussed. To address these concepts, three exemplary methods are introduced and their application to the study of microplastic surfaces discussed with the following recommendations; atomic force microscopy should be explored for conducting physical surface characterisation and to examine surface roughness; double-shot Pyrolysis-Gas Chromatography–Mass Spectroscopy should be considered for examining microplastic sorption behaviours in multi-solute media; and finally, Whispering Gallery Mode nanosensing techniques should be explored as a potential means to generate data on microplastic sorption kinetics.University of ExeterUniversity of QueenslandNatural Environment Research Council (NERC

The Culture Environment Influences Both Gene Regulation and Phenotypic Heterogeneity in Escherichia coli

This is the final version of the article. Available from Frontiers Media via the DOI in this record.Microorganisms shape the composition of the medium they are growing in, which in turn has profound consequences on the reprogramming of the population gene-expression profile. In this paper, we investigate the progressive changes in pH and sugar availability in the medium of a growing Escherichia coli (E. coli) culture. We show how these changes have an effect on both the cellular heterogeneity within the microbial community and the gene-expression profile of the microbial population. We measure the changes in gene-expression as E. coli moves from lag, to exponential, and finally into stationary phase. We found that pathways linked to the changes in the medium composition such as ribosomal, tricarboxylic acid cycle (TCA), transport, and metabolism pathways are strongly regulated during the different growth phases. In order to quantify the corresponding temporal changes in the population heterogeneity, we measure the fraction of E. coli persisters surviving different antibiotic treatments during the various phases of growth. We show that the composition of the medium in which β-lactams or quinolones, but not aminoglycosides, are dissolved strongly affects the measured phenotypic heterogeneity within the culture. Our findings contribute to a better understanding on how the composition of the culture medium influences both the reprogramming in the population gene-expression and the emergence of phenotypic variants.This work was supported by a Royal Society Research Grant (RG140203), a Wellcome Trust Strategic Seed Corn Fund (WT097835/Z/11/Z), and a start up Grant from the University of Exeter awarded to SP. AS acknowledges support from the BBSRC through a SWBio-DTP studentship (BB/M009122/1). KP, KM, and PO would like to acknowledge support from the following awards: Wellcome Trust Institutional Strategic Support Fund (WT097835MF), Wellcome Trust Multi User Equipment Award (WT101650MA), and Medical Research Council Clinical Infrastructure Funding (MR/M008924/1). This work was partly supported by BBSRC award BB/1024631/1 to RT

Sensing Enzyme Activation Heat Capacity at the Single-Molecule Level Using Gold-Nanorod-Based Optical Whispering Gallery Modes

This is the final version. Available on open access from the American Chemical Society via the DOI in this recordHere, we report a label-free gold nanoparticle-based single-molecule optical platform to study the immobilization, activity, and thermodynamics of single enzymes. The sensor uses plasmonic gold nanoparticles coupled to optical whispering gallery modes (WGMs) to probe enzyme conformational dynamics during turnover at a microsecond time resolution. Using a glucosidase enzyme as the model system, we explore the temperature dependence of the enzyme turnover at the single-molecule (SM) level. A recent physical model for understanding enzyme temperature dependencies (macromolecular rate theory; MMRT) has emerged as a powerful tool to study the relationship between enzyme turnover and thermodynamics. Using WGMs, SM enzyme measurements enable us to accurately track turnover as a function of conformational changes and therefore to quantitatively probe the key feature of the MMRT model, the activation heat capacity, at the ultimate level of SM. Our data shows that WGMs are extraordinarily sensitive to protein conformational change and can discern both multiple steps with turnover as well as microscopic conformational substates within those steps. The temperature dependence studies show that the MMRT model can be applied to a range of steps within turnover at the SM scale that is associated with conformational change. Our study validates the notion that MMRT captures differences in dynamics between states. The WGM sensors provide a platform for the quantitative analysis of SM activation heat capacity, applying MMRT to the label-free sensing of microsecond substates of active enzymes.Engineering and Physical Sciences Research Council (EPSRC)Biotechnology and Biological Sciences Research Council (BBSRC)New Zealand Marsden Fun

Myocarditis following COVID-19 vaccine: incidence, presentation, diagnosis, pathophysiology, therapy, and outcomes put into perspective. A clinical consensus document supported by the Heart Failure Association of the European Society of Cardiology (ESC) and the ESC Working Group on Myocardial and Pericardial Diseases

Over 10 million doses of COVID-19 vaccines based on RNA technology, viral vectors, recombinant protein, and inactivated virus have been administered worldwide. Although generally very safe, post-vaccine myocarditis can result from adaptive humoral and cellular, cardiac-specific inflammation within days and weeks of vaccination. Rates of vaccine-associated myocarditis vary by age and sex with the highest rates in males between 12 and 39 years. The clinical course is generally mild with rare cases of left ventricular dysfunction, heart failure and arrhythmias. Mild cases are likely underdiagnosed as cardiac magnetic resonance imaging (CMR) is not commonly performed even in suspected cases and not at all in asymptomatic and mildly symptomatic patients. Hospitalization of symptomatic patients with electrocardiographic changes and increased plasma troponin levels is considered necessary in the acute phase to monitor for arrhythmias and potential decline in left ventricular function. In addition to evaluation for symptoms, electrocardiographic changes and elevated troponin levels, CMR is the best non-invasive diagnostic tool with endomyocardial biopsy being restricted to severe cases with heart failure and/or arrhythmias. The management beyond. guideline-directed treatment of heart failure and arrhythmias includes non-specific measures to control pain. Anti-inflammatory drugs such as non-steroidal anti-inflammatory drugs, and corticosteroids have been used in more severe cases, with only anecdotal evidence for their effectiveness. In all age groups studied, the overall risks of SARS-CoV-2 infection-related hospitalization and death are hugely greater than the risks from post-vaccine myocarditis. This consensus statement serves as a practical resource for physicians in their clinical practice, to understand, diagnose, and manage affected patients. Furthermore, it is intended to stimulate research in this area

Monophasic synovial sarcoma of the pharynx: a case report

Synovial sarcomas are a rare form of soft tissue sarcomas. We present a case of a 62 year-old male presenting with a left thyroid lump initially though to be a thyroid adenoma but subsequently diagnosed as a monophasic synovial sarcoma of the pharynx. We discuss the diagnosis and treatment of this case

Tailoring Optical Complex Field with Spiral Blade Plasmonic Vortex Lens

Optical complex fields have attracted increasing interests because of the novel effects and phenomena arising from the spatially inhomogeneous state of polarizations and optical singularities of the light beam. In this work, we propose a spiral blade plasmonic vortex lens (SBPVL) that offers unique opportunities to manipulate these novel fields. The strong interaction between the SBPVL and the optical complex fields enable the synthesis of highly tunable plasmonic vortex. Through theoretical derivations and numerical simulations we demonstrated that the characteristics of the plasmonic vortex are determined by the angular momentum (AM) of the light, and the geometrical topological charge of the SBPVL, which is govern by the nonlinear superposition of the pitch and the number of blade element. In addition, it is also shown that by adjusting the geometric parameters, SBPVL can be utilized to focus and manipulate optical complex field with fractional AM. This miniature plasmonic device may find potential applications in optical trapping, optical data storage and many other related fields

Prelamin A mediates myocardial inflammation in dilated and HIV-Associated cardiomyopathies

Cardiomyopathies are complex heart muscle diseases that can be inherited or acquired. Dilated cardiomyopathy can result from mutations in LMNA, encoding the nuclear intermediate filament proteins lamin A/C. Some LMNA mutations lead to accumulation of the lamin A precursor, prelamin A, which is disease causing in a number of tissues, yet its impact upon the heart is unknown. Here, we discovered myocardial prelamin A accumulation occurred in a case of dilated cardiomyopathy, and we show that a potentially novel mouse model of cardiac-specific prelamin A accumulation exhibited a phenotype consistent with inflammatory cardiomyopathy, which we observed to be similar to HIV-associated cardiomyopathy, an acquired disease state. Numerous HIV protease therapies are known to inhibit ZMPSTE24, the enzyme responsible for prelamin A processing, and we confirmed that accumulation of prelamin A occurred in HIV' patient cardiac biopsies. These findings (a) confirm a unifying pathological role for prelamin A common to genetic and acquired cardiomyopathies; (b) have implications for the management of HIV patients with cardiac disease, suggesting protease inhibitors should be replaced with alternative therapies (i.e., nonnucleoside reverse transcriptase inhibitors); and (c) suggest that targeting inflammation may be a useful treatment strategy for certain forms of inherited cardiomyopathy

Four year experience of sarcoma of soft tissues and bones in a tertiary care hospital and review of literature

<p>Abstract</p> <p>Background</p> <p>Sarcoma encompasses an uncommon group of cancer and the data is insufficient from Pakistan. We report our four years experience of Sarcoma of soft tissues and bones.</p> <p>Methods</p> <p>This cross sectional study was carried out at Aga Khan University Hospital from 2004 to 2008. The patients were divided into two groups from the outset i.e. initially diagnosed and relapsed group and separate sub group analysis was conducted.</p> <p>Results</p> <p>Out of 93 newly diagnosed patients, 58 belonged to bone sarcoma and 35 to soft tissue sarcoma group. While for relapsed patients, 5 had soft tissue sarcoma and 9 had bone sarcoma. Mean age was 32.5 years. At presentation, approximately two third patients had localised disease while remaining one third had metastatic disease. The Kaplan Meier estimate of median recurrence free survival was 25 months, 35 months, and 44 months for Osteogenic sarcoma, Ewing's sarcoma and Chondrosarcoma respectively. For Leiomyosarcoma and Synovial sarcoma, it was 20 and 19 months respectively. The grade of the tumour (p = 0.02) and surgical margin status (p = 0.001) were statistically significant for determination of relapse of disease.</p> <p>Conclusion</p> <p>The median recurrence free survival of patients in our study was comparable to the reported literature but with significant lost to follow rate. Further large-scale, multi centre studies are needed to have a more comprehensive understanding of this heterogeneous disease in our population.</p