• Gadolinium-doped iron oxide nanoparticles induced magnetic field hyperthermia combined with radiotherapy increases tumour response by vascular disruption and improved oxygenation

      Jiang, P-S.; Tsai, H-Y.; Drake, Philip; Wang, F-N.; Chiang, C-S. (2017)
      The gadolinium-doped iron oxide nanoparticles (GdIONP) with greater specific power adsorption rate (SAR) than Fe3O4 was developed and its potential application in tumour therapy and particle tracking were demonstrated in transgenic adenocarcinoma of the mouse prostate C1 (TRAMP-C1) tumours. The GdIONPs accumulated in tumour region during the treatment could be clearly tracked and quantified by T2-weighted MR imaging. The therapeutic effects of GdIONP-mediated hyperthermia alone or in combination with radiotherapy (RT) were also evaluated. A significant increase in the tumour growth time was observed following the treatment of thermotherapy (TT) only group (2.5 days), radiation therapy only group (4.5 days), and the combined radio-thermotherapy group (10 days). Immunohistochemical staining revealed a reduced hypoxia region with vascular disruption and extensive tumour necrosis following the combined radio-thermotherapy. These results indicate that GdIONP-mediated hyperthermia can improve the efficacy of RT by its dual functions in high temperature (temperature greater than 45 °C)-mediated thermal ablation and mild-temperature hyperthermia (MTH) (temperature between 39 and 42 °C)-mediated reoxygenation.
    • Gait Alterations Negotiating A Raised Surface Induced by Monocular Blur

      Vale, Anna; Buckley, John G.; Elliott, David B. (2008-12-01)
      Falls in the elderly are a major cause of serious injury and mortality. Impaired and absent stereopsis may be a significant risk factor for falls or hip fracture, although data from epidemiological studies are not consistent. Previous laboratory based studies, however, do suggest that stereoacuity is an important factor in adaptive gait. The present study investigates how acute impairment of stereopsis, through monocular blur of differing levels, ranging from 0.50 diopter (D) to a monovision correction affected gait when negotiating a raised surface in elderly subjects. Eleven elderly subjects (73.3 3.6 years) walked up to and negotiated a raised surface under nine visual conditions, binocular vision, one eye occluded and 0.50 D, 1.00 D and monovision correction (mean 2.50 D 0.20 D) with blur and occlusion either over the dominant or non-dominant eye. Analysis focused on foot positioning and toe clearance parameters. There was no effect of ocular dominance on any parameters. Monocular blur impaired stereopsis (p 0.01), with more minor effects on high and low contrast acuity. Vertical and horizontal lead limb toe clearance both increased under all levels of monocular blur including the lowest level of 0.50 DBlur (p 0.03) and monovision correction led to toe clearance levels similar to that found with occlusion of one eye. Findings demonstrated that even small amounts of monocular blur can lead to a change in gait when negotiating a raised surface, suggesting acute monocular blur affected the ability to accurately judge the height of a step in the travel path. Further work is required to investigate if similar adaptations are used by patients with chronic monocular blur.
    • Gamma-irradiated human amniotic membrane decellularised with sodium dodecyl sulfate is a more efficient substrate for the ex vivo expansion of limbal stem cells

      Figueiredo, G.S.; Bojic, S.; Rooney, P.; Wilshaw, Stacy-Paul; Connon, C.J.; Gouveia, R.M.; Paterson, C.; Lepert, G.; Mudhar, H.S.; Figueiredo, F.C.; et al. (2017)
      The gold standard substrate for the ex vivo expansion of human limbal stem cells (LSCs) remains the human amniotic membrane (HAM) but this is not a defined substrate and is subject to biological variabil-ity and the potential to transmit disease. To better define HAM and mitigate the risk of disease transmis-sion, we sought to determine if decellularisation and/or c-irradiation have an adverse effect on culture growth and LSC phenotype. Ex vivo limbal explant cultures were set up on fresh HAM, HAM decellularised with 0.5 M NaOH, and 0.5% (w/v) sodium dodecyl sulfate (SDS) with or without c-irradiation. Explant growth rate was measured and LSC phenotype was characterised by histology, immunostaining and qRT-PCR (ABCG2, DNp63, Ki67, CK12, and CK13). Ƴ-irradiation marginally stiffened HAM, as measured by Brillouin spectromicroscopy. HAM stiffness and c-irradiation did not significantly affect the LSC phe-notype, however LSCs expanded significantly faster on Ƴ-irradiated SDS decellularised HAM (p < 0.05) which was also corroborated by the highest expression of Ki67 and putative LSC marker, ABCG2. Colony forming efficiency assays showed a greater yield and proportion of holoclones in cells cultured on Ƴ-irradiated SDS decellularised HAM. Together our data indicate that SDS decellularised HAM may be a more efficacious substrate for the expansion of LSCs and the use of a c-irradiated HAM allows the user to start the manufacturing process with a sterile substrate, potentially making it safer.
    • Gaps in Propolis Research: Challenges Posed to Commercialisation and the Need for an Holistic Approach

      Katekhaye, S.; Fearnley, H.; Fearnley, J.; Paradkar, Anant R. (2019)
      Both the season and region in which propolis is collected influence its chemical composition, resulting in variations in biological activity. Significant differences in composition and concentration of certain chemical compounds in propolis make standardisation and quality control challenging. In addition, the lack of uniformity in evaluation methodology and analytical techniques, make it extremely difficult to correlate data across the climatic zones. In this report, we focus on the gaps in propolis research and the challenges they pose for commercialisation, with suggestions as to how we might address them. We hope to stimulate further research which explores the holistic nature of propolis in order to derive a propolis bioactivity standard.
    • Gaps, traps, bridges and props: a mixed-methods study of resilience in the medicines management system for heart failure patients at hospital discharge

      Fylan, Beth; Marques, Iuri; Ismail, Hanif; Breen, Liz; Gardner, Peter H.; Armitage, Gerry R.; Blenkinsopp, Alison (2019-02)
      Poor medicines management places patients at risk, particularly during care transitions. For patients with heart failure (HF), optimal medicines management is crucial to control symptoms and prevent hospital readmission. This study explored the concept of resilience using HF as an example condition to understand how the system compensates for known and unknown weaknesses. We explored resilience using a mixed-methods approach in four healthcare economies in the north of England. Data from hospital site observations, healthcare staff and patient interviews, and documentary analysis were collected between June 2016 and March 2017. Data were synthesised and analysed using framework analysis. Interviews were conducted with 45 healthcare professionals, with 20 patients at three timepoints and 189 hours of observation were undertaken. We identified four primary inter-related themes concerning organisational resilience. These were named as gaps, traps, bridges and props. Gaps were discontinuities in processes that had the potential to result in poorly optimised medicines. Traps were features of the system that could produce errors or unintended adverse medication events. ‘Bridges’ were features of the medicines management system that promoted safety and continuity which ensured that, despite varying conditions, care could be delivered successfully. ‘Props’ were informal, temporary or impromptu actions taken by patients or healthcare staff to avoid potential adverse events. The numerous opportunities for HF patient safety to be compromised and sub-optimal medicines management during this common care transition are mitigated by system resilience. Cross-organisational bridges and temporary fixes or ‘props’ put in place by patients and carers, healthcare teams and organisations are critical for safe and optimal care to be delivered in the face of continued system pressures.
    • Gas chromatographic, mass spectrometric and stable carbon isotope investigations of organic residues in `slab-lined pits' from Arctic Norway

      Heron, Carl P.; Nilsen, G.; Stern, Ben; Craig, O.E.; Nordby, C.C. (2010)
      Gas chromatography-mass spectrometry (GC-MS) and bulk carbon isotope determinations have been performed on samples ('cemented organic residues', charcoal, sediment and fire-cracked rock) excavated from twelve slab-lined pits from various locations in Arctic Norway to test the premise that these archaeological features were used for the extraction of oil from the blubber of marine mammals, such as seal, whale and walrus. A wide range of lipid compound classes were detected especially in the cemented organic residues and in the charcoal samples. The presence of long-chain unsaturated and isoprenoid fatty acids together with oxidation and thermal alteration products of unsaturated acids such as dicarboxylic acids, dihydroxyfatty acids and ω-(o-alkylphenyl)alkanoic acids suggests that these features were used for marine oil extraction at elevated temperatures. Notably the location of the hydroxyl groups in the dihydroxyfatty acids provides a record of the positional isomer of the precursor fatty acid and allows confirmation that 11-docosenoic (cetoleic) acid, the most abundant C22:1 isomer in marine oil, was a major component of the original lipid. Further information was provided by the presence of long-chain fatty acyl moieties in surviving triacylglycerols and the presence of cholesterol. A fungal metabolite, mycose (trehalose), was found in all samples apart from a fire-cracked rock and points to microbiological activity in the pits. Bulk isotope analysis conducted on the 'cemented organic residues' is consistent with modern reference samples of blubber and oil from seal and whale. These data provide clear analytical evidence of the function of slab-lined pits in the archaeological record and suggest widespread exploitation of marine mammals for producing oil for heating, lighting and myriad other uses in the past.
    • Gene expression profiling identifies distinct molecular subgroups of leiomyosarcoma with clinical relevance

      Lee, Stephanie; Roe, T.; Mangham, D.C.; Fisher, C.; Grimer, R.J.; Judson, I. (2016)
      Background: Soft tissue sarcomas are heterogeneous and a major complication in their management is that the existing classification scheme is not definitive and is still evolving. Leiomyosarcomas, a major histologic category of soft tissue sarcomas, are malignant tumours displaying smooth muscle differentiation. Although defined as a single group, they exhibit a wide range of clinical behaviour. We aimed to carry out molecular classification to identify new molecular subgroups with clinical relevance. Methods: We used gene expression profiling on 20 extra-uterine leiomyosarcomas and cross-study analyses for molecular classification of leiomyosarcomas. Clinical significance of the subgroupings was investigated. Results: We have identified two distinct molecular subgroups of leiomyosarcomas. One group was characterised by high expression of 26 genes that included many genes from the sub-classification gene cluster proposed by Nielsen et al. These sub-classification genes include genes that have importance structurally, as well as in cell signalling. Notably, we found a statistically significant association of the subgroupings with tumour grade. Further refinement led to a group of 15 genes that could recapitulate the tumour subgroupings in our data set and in a second independent sarcoma set. Remarkably, cross-study analyses suggested that these molecular subgroups could be found in four independent data sets, providing strong support for their existence. Conclusions: Our study strongly supported the existence of distinct leiomyosarcoma molecular subgroups, which have clinical association with tumour grade. Our findings will aid in advancing the classification of leiomyosarcomas and lead to more individualised and better management of the disease.
    • Gene Regulation at a Distance: Higher-Order Chromatin Folding and the Coordinated Control of Gene Transcription at the Epidermal Differentiation Complex Locus

      Fessing, Michael Y. (2014)
      Chromatin structure and spatial interactions between proximal and distal gene regulatory elements, including gene core promoters and enhancers, are important in the control of gene transcription. In this issue, Oh et al. characterized an AP-1-dependent enhancer at the epidermal differentiation complex locus that establishes spatial interactions with numerous gene promoter regions at that locus.
    • Generalization of prior information for rapid Bayesian time estimation

      Roach, N.W.; McGraw, Paul V.; Whitaker, David J.; Heron, James (2017-01-10)
      To enable effective interaction with the environment, the brain combines noisy sensory information with expectations based on prior experience. There is ample evidence showing that humans can learn statistical regularities in sensory input and exploit this knowledge to improve perceptual decisions and actions. However, fundamental questions remain regarding how priors are learned and how they generalize to different sensory and behavioral contexts. In principle, maintaining a large set of highly specific priors may be inefficient and restrict the speed at which expectations can be formed and updated in response to changes in the environment. However, priors formed by generalizing across varying contexts may not be accurate. Here, we exploit rapidly induced contextual biases in duration reproduction to reveal how these competing demands are resolved during the early stages of prior acquisition. We show that observers initially form a single prior by generalizing across duration distributions coupled with distinct sensory signals. In contrast, they form multiple priors if distributions are coupled with distinct motor outputs. Together, our findings suggest that rapid prior acquisition is facilitated by generalization across experiences of different sensory inputs but organized according to how that sensory information is acted on.
    • Genetic basis and timing of a major mating system shift in Capsella

      Bachmann, J.A.; Tedder, Andrew; Laenen, B.; Fracassetti, M.; Désamoré, A.; Lafon-Placette, C.; Steige, K.A.; Callot, C.; Marande, W.; Neuffer, B.; et al. (2019-06)
      A crucial step in the transition from outcrossing to self-fertilization is the loss of genetic self-incompatibility (SI). In the Brassicaceae, SI involves the interaction of female and male speci-ficity components, encoded by the genesSRKandSCRat the self-incompatibility locus (S-lo-cus). Theory predicts thatS-linked mutations, and especially dominant mutations inSCR, arelikely to contribute to loss of SI. However, few studies have investigated the contribution ofdominant mutations to loss of SI in wild plant species. Here, we investigate the genetic basis of loss of SI in the self-fertilizing crucifer speciesCapsella orientalis, by combining genetic mapping, long-read sequencing of completeS-hap-lotypes, gene expression analyses and controlled crosses. We show that loss of SI inC. orientalisoccurred<2.6 Mya and maps as a dominant trait totheS-locus. We identify a fixed frameshift deletion in the male specificity geneSCRand con-firm loss of male SI specificity. We further identify anS-linked small RNA that is predicted tocause dominance of self-compatibility. Our results agree with predictions on the contribution of dominantS-linked mutations toloss of SI, and thus provide new insights into the molecular basis of mating system transitions.
    • Genetic characterisation of Escherichia coli RecN protein as a member of SMC family of proteins

      Youssef, M.M.; Al-Omair, M.A.; Picksley, Stephen M. (2014)
      The proteins of SMC family are characterised by having Walker A and B sites. The Escherichia coli RecN protein is a prokaryotic member of SMC family that involved in the induced excision of Tn10 and the repair of the DNA double strand breaks. In this work, the Walker A nucleotide binding site of the E. coli RecN protein was mutated by changing the highly conserved lysine residue 35 to the aspartic acid (D), designated as recN(K35D). Reverse genetics was utilized to delete the entire recN gene (Delta recN108) or introduce the recN(K35D) gene into the E. coli chromosomal DNA. The recN(K35D) cells showed decreasing in the frequency of excision of Tn10 from gal76
    • Genetic damage in oligozoospermic patients detected by fluorescence in-situ hybridization, inverse restriction site mutation assay, sperm chromatin structure assay and the Comet assay.

      Schmid, Thomas E.; Kamischke, A.; Bollwein, H.; Nieschlag, E.; Brinkworth, Martin H. (2003)
      BACKGROUND: The possibility that oligozoospermic men may have elevated levels of genetic damage in their sperm is of particular concern as they could transmit defects to their offspring. METHODS: Sperm samples were obtained from 12 infertile, oligozoospermic patients and 12 healthy normozoospermic volunteers. Fluorescence in-situ hybridization (FISH) was used to determine aneuploidy rates in sperm and inverse restriction site mutation (iRSM) assay to determine gene mutations; defective chromatin packaging was quantified by sperm chromatin structure assay (SCSA) and DNA strand breaks by the Comet assay. RESULTS: FISH analysis showed a significant increase in gonosomal X,Y,18 (P < 0.01) disomy and diploid sperm with X,Y,18,18 (P < 0.05) in the infertility patients compared with the controls. A significant increase (P < 0.01) in disturbed sperm chromatin was found in the infertility patients compared with the control group using the SCSA assay. In the Comet assay, a significant increase (P < 0.01) in the tail moment was found in the infertility patients compared with the control group, indicating significantly high levels of DNA strand breaks. There was no significant increase in point mutations detected by iRSM assay. CONCLUSIONS: The data indicate that infertile oligozoospermic men have an elevated level of XY aneuploidy and XY diploidy in the germ-line, as well as elevated levels of sperm chromatin disturbances and sperm DNA strand breaks. These data demonstrate that oligozoospermic infertility patients show several different types of genetic damage in their sperm. Thus, such men appear to have defects at a variety of levels of spermatogenesis and their infertility may not just be a result of the oligozoospermia.
    • Genetic inactivation of Kcnj16 identifies Kir5.1 as an important determinant of neuronal PCO2/pH sensitivity

      D'Adamo, M.C.; Shang, Lijun; Imbrici, P.; Brown, S.D.M.; Pessia, M.; Tucker, S.J. (2011)
      The molecular identity of ion channels which confer PCO(2)/pH sensitivity in the brain is unclear. Heteromeric Kir4.1/Kir5.1 channels are highly sensitive to inhibition by intracellular pH and are widely expressed in several brainstem nuclei involved in cardiorespiratory control, including the locus coeruleus. This has therefore led to a proposed role for these channels in neuronal CO(2) chemosensitivity. To examine this, we generated mutant mice lacking the Kir5.1 (Kcnj16) gene. We show that although locus coeruleus neurons from Kcnj16((+/+)) mice rapidly respond to cytoplasmic alkalinization and acidification, those from Kcnj16((-/-)) mice display a dramatically reduced and delayed response. These results identify Kir5.1 as an important determinant of PCO(2)/pH sensitivity in locus coeruleus neurons and suggest that Kir5.1 may be involved in the response to hypercapnic acidosis.
    • Genetic prediction of myopia: prospects and challenges

      Guggenheim, J.A.; Ghorbani Mojarrad, Neema; Williams, C.; Flitcroft, D.I. (2017-09)
      Appeals have been made for eye care professionals to start prescribing anti-myopia therapies as part of their routine management of myopic children. 1–3 These calls are fuelled by two key considerations. Firstly, that interventions to slow myopia progression have shown success in randomized controlled trials (RCTs) 4–7, and secondly, appreciation that the risk of sight-threatening complications rises dose-dependently with the level of myopia. 8,9 Notwithstanding existing gaps in knowledge regarding the efficacy of current treatments (see below), these considerations argue that myopia control interventions should be widely adopted, and that they should be instigated at an early age – especially in children most at risk – in order to reduce the final level of myopia. Therefore in managing a child with myopia, an eye care professional would have to decide not only which therapy to recommend, but at what age to start treatment. In this review we discuss the future role of genetic prediction in helping clinicians treat myopia.
    • A genetic risk score and number of myopic parents independently predict myopia

      Ghorbani Mojarrad, Neema; Williams, C.; Guggenheim, J.A. (2018-09)
      Purpose: To investigate whether a genetic risk score (GRS) improved performance of predicting refractive error compared to knowing a child’s number of myopic parents (NMP) alone. Methods: This was a retrospective analysis of data from the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort study. Refractive error was assessed longitudinally between age 7–15 using non-cycloplegic autorefraction. Genetic variants (n=149) associated with refractive error from a Consortium for Refractive Error And Myopia (CREAM) genome-wide association study were used to calculate a GRS for each child. Using refractive error at ages 7 and 15 years as the outcome variable, coefficient of determination (R2) values were calculated via linear regression models for the predictors: NMP, GRS and a combined model. Results: Number of myopic parents was weakly predictive of refractive error in children aged 7 years, R2=3.0% (95% CI 1.8–4.1%,p<0.0001) and aged 15 years, R2=4.8% (3.1–6.5%,p<0.0001). The GRS was also weakly predictive;age 7 years, R2=1.1% (0.4–1.9%,p<0.0001) and 15 years R2=2.6% (1.3–3.9%,p<0.0001). Combining the 2 variables gave larger R2 values at age 7, R2=3.7%(2.5–5.0%,p<0.0001) and 15, R2=7.0% (5.0–9.0%,p<0.0001). The combined model improved performance at both ages (both p<0.0001). Conclusion: A GRS improved the ability to detect children at risk of myopia independently of knowing the NMP. We speculate this may be because NMP captures information concerning environmental risk factors for myopia. Nevertheless, further gains are required to make such predictive tests worthwhile in the clinical environment.
    • Genetics of type 5 M protein of Streptococcus pyogenes

      Kehoe, M.A.; Miller, L.; Poirier, T.P.; Beachey, E.H.; Lee, M.; Harrington, Dean J. (1987)
    • Genome organizing function of SATB1 in tumor progression.

      Kohwi-Shigematsu, T.; Poterlowicz, Krzysztof; Ordinario, E.; Han, H.J.; Botchkarev, Vladimir A.; Kohwi, Y. (2013)
      When cells change functions or activities (such as during differentiation, response to extracellular stimuli, or migration), gene expression undergoes large-scale reprogramming, in cell type- and function-specific manners. Large changes in gene regulation require changes in chromatin architecture, which involve recruitment of chromatin remodeling enzymes and epigenomic modification enzymes to specific genomic loci. Transcription factors must also be accurately assembled at these loci. SATB1 is a genome organizer protein that facilitates these processes, providing a nuclear architectural platform that anchors hundreds of genes, through its interaction with specific genomic sequences; this activity allows expression of all these genes to be regulated in parallel, and enables cells to thereby alter their function. We review and describe future perspectives on SATB1 function in higher-order chromatin structure and gene regulation, and its role in metastasis of breast cancer and other tumor types.
    • Genome sequence analysis reveals evidence of quorum-sensing genes present in Aeromonas hydrophila strain M062, isolated from freshwater

      Chan, K.; Tan, W.; Chang, Chien-Yi; Yin, W.; Mumahad Yunos, N.Y. (2015-03)
      Aeromonas hydrophila has emerged worldwide as a human pathogen. Here, we report the draft whole-genome sequence of a freshwater isolate from Malaysia, A. hydrophila strain M062, and its N-acylhomoserine lactone genes are also reported here.
    • A genome-based species taxonomy of the Lactobacillus genus complex

      Wittouck, S.; Wuyts, S.; Meehan, Conor J.; van Noort, V.; Lebeer, S. (2019-09)
      There are more than 200 published species within the Lactobacillus genus complex (LGC), the majority of which have sequenced type strain genomes available. Although genome-based species delimitation cutoffs are accepted as the gold standard by the community, these are seldom actually checked for new or already published species. In addition, the availability of genome data is revealing inconsistencies in the species-level classification of many strains. We constructed a de novo species taxonomy for the LGC based on 2,459 publicly available genomes, using a 94% core nucleotide identity cutoff. We reconciled these de novo species with published species and subspecies names by (i) identifying genomes of type strains and (ii) comparing 16S rRNA genes of the genomes with 16S rRNA genes of type strains. We found that genomes within the LGC could be divided into 239 de novo species that were discontinuous and exclusive. Comparison of these de novo species to published species led to the identification of nine sets of published species that can be merged and one species that can be split. Further, we found at least eight de novo species that constitute new, unpublished species. Finally, we reclassified 74 genomes on the species level and identified for the first time the species of 98 genomes. Overall, the current state of LGC species taxonomy is largely consistent with genome-based species delimitation cutoffs. There are, however, exceptions that should be resolved to evolve toward a taxonomy where species share a consistent diversity in terms of sequence divergence.
    • Genome-based taxonomic revision detects a number of synonymous taxa in the genus Mycobacterium

      Tortoli, E.; Meehan, Conor J.; Grottola, A.; Fregni Serpini, J.; Fabio, A.; Trovato, A.; Pecorari, M.; Cirillo, D.M. (2019-11)
      The aim of this study was to clarify the taxonomic status of named species within the genus Mycobacterium. The analysis of genomes belonging to 174 taxa (species or subspecies) of the genus Mycobacterium was conducted using both the Average Nucleotide Identity and the Genome to Genome Distance. A number of synonymous taxa were detected. The list of synonyms includes: two subspecies of M. chelonae (M. chelonae subsp. bovis and M. chelonae subsp. gwanakae), two subspecies of M. fortuitum (M. fortuitum subsp. fortuitum and M. fortuitum subsp. acetamidolyticum), four subspecies of M. avium (M. avium subsp. avium, M. avium subsp. silvaticum, M. avium subsp. paratuberculosis and “M. avium subsp. hominissuis”), two couples of subspecies of M. intracellulare (M. intracellulare subsp. intracellulare/M. intracellulare subsp. paraintracellulare and M. intracellulare subsp. chimaera/M. intracellulare subsp. yongonense), the species M. austroafricanum and M. vanbaalenii, the species M. senegalense and M. conceptionense, the species M. talmoniae and M. eburneum and the species M. marinum, M. ulcerans and M. pseudoshottsii. Furthermore one species were reclassified as subspecies of another mycobacterium: M. lepraemurium was reclassified as a subspecies of M. avium (M. avium subsp. lepraemurium). The updates to nomenclature are proposed basing on the priority of names according the Code of nomenclature of prokaryotes. For two species (M. bouchedurhonense and M. marseillense) the loss of standing in nomenclature is proposed because of unavailability of respective type strains in culture collections.