Attard, MRG, Chamoli, U, Ferrara, TL, Rogers, TL & Wroe, S 2011, 'Skull mechanics and implications for feeding behaviour in a large marsupial carnivore guild: the thylacine, Tasmanian devil and spotted‐tailed quoll', Journal of Zoology, vol. 285, no. 4, pp. 292-300.
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AbstractExtinction risk varies across species and is influenced by key ecological parameters, such as diet specialization. For predictive conservation science to be effective, we need to understand extinction risk factors that may have implicated recent species extinctions. Diet and feeding behaviour of the large extinct marsupial carnivore Thylacinus cynocephalus or thylacine have long been debated. Improved understanding of the skull's biomechanical performance and its limitations in a comparative context may yield important insights. Here, we use three‐dimensional (3D) finite element analysis to assess aspects of biomechanical performance in the skull of T. cynocephalus relative to those of two extant marsupial carnivores with known diets that occurred sympatrically with T. cynocephalus: the Tasmanian devil, Sarcophilus harrisii, and spotted‐tailed quoll, Dasyurus maculatus. Together, these three species comprised the large mammalian carnivore guild in Tasmania at the time of European settlement. The bone‐cracking S. harrisii produced high bite forces for its size as expected, but the stresses induced were surprisingly high. A higher proportion of cancellous bone in the skull of this osteophage may act to absorb shock but decrease rigidity and hence raise stress. A relatively high bite force and rigid skull characterized D. maculatus, which may allow them to target prey of variable sizes. Compared with S. harrisii and D. maculatus, we found that the skull of T. cynocephalus was least well adapted to withstand forces driven solely by its jaw‐closing musculature, as well as to simulations of struggling prey. Our findings suggest that T. cynoc...
Bajan, S & Hutvagner, G 2011, 'Another “Loophole” in miRNA Processing', Molecular Cell, vol. 44, no. 3, pp. 345-347.
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In this issue of Molecular Cell, Suzuki et al. (2011) present the intriguing finding that an RNAse known to play an important role in immunity regulates miRNA processing in cancer and inflammation by cleaving the terminal loops of many miRNAs. © 2011 Elsevier Inc.
Beck, D, Ayers, S, Wen, J, Brandl, MB, Pham, TD, Webb, P, Chang, C-C & Zhou, X 2011, 'Integrative analysis of next generation sequencing for small non-coding RNAs and transcriptional regulation in Myelodysplastic Syndromes', BMC Medical Genomics, vol. 4, no. 1, pp. 1-16.
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Abstract Background Myelodysplastic Syndromes (MDSS) are pre-leukemic disorders with increasing incident rates worldwide, but very limited treatment options. Little is known about small regulatory RNAs and how they contribute to pathogenesis, progression and transcriptome changes in MDS. Methods Patients' primary marrow cells were screened for short RNAs (RNA-seq) using next generation sequencing. Exon arrays from the same cells were used to profile gene expression and additional measures on 98 patients obtained. Integrative bioinformatics algorithms were proposed, and pathway and ontology analysis performed. Results In low-grade MDS, observations implied extensive post-transcriptional regulation via microRNAs (miRNA) and the recently discovered Piwi interacting RNAs (piRNA). Large expression differences were found for MDS-associated and novel miRNAs, including 48 sequences matching to miRNA star (miRNA*) motifs. The detected species were predicted to regulate disease stage specific molecular functions and pathways, including apoptosis and response to DNA damage. In high-grade MDS, results suggested extensive post-translation editing via transfer RNAs (tRNAs), providing a potential link for reduced apoptosis, a hallmark for this disease stage. Bioinformatics analysis confirmed important regulatory roles for MDS linked miRNAs and TFs, and strengthened the biological significance of miRNA*. The 'RNA polymerase II promoters' were identified as the tightest controlled biological function. We suggest their control by a miRNA dominated feedback loop, which might be linked to the dramatically different miRNA amounts seen between low and high-gra...
Bjørnerem, Å, Ghasem-Zadeh, A, Bui, M, Wang, X, Rantzau, C, Nguyen, TV, Hopper, JL, Zebaze, R & Seeman, E 2011, 'Remodeling markers are associated with larger intracortical surface area but smaller trabecular surface area: A twin study', Bone, vol. 49, no. 6, pp. 1125-1130.
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Bridge, P, Pocock, NA, Nguyen, T, Munns, C, Cowell, CT, Forwood, N & Thompson, MW 2011, 'Validation of Longitudinal DXA Changes in Body Composition From Pre- to Mid-Adolescence Using MRI as Reference', Journal of Clinical Densitometry, vol. 14, no. 3, pp. 340-347.
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Cerezo-Guisado, MI, Reino, PD, Remy, G, Kuma, Y, Arthur, JSC, Gallego-Ortega, D & Cuenda, A 2011, 'Evidence of p38γ and p38δ involvement in cell transformation processes', Carcinogenesis, vol. 32, no. 7, pp. 1093-1099.
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Chamoli, U & Wroe, S 2011, 'Allometry in the distribution of material properties and geometry of the felid skull: Why larger species may need to change and how they may achieve it', Journal of Theoretical Biology, vol. 283, no. 1, pp. 217-226.
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Deng, W, Jin, D, Drozdowicz‐Tomsia, K, Yuan, J, Wu, J & Goldys, EM 2011, 'Ultrabright Eu–Doped Plasmonic Ag@SiO2 Nanostructures: Time‐gated Bioprobes with Single Particle Sensitivity and Negligible Background', Advanced Materials, vol. 23, no. 40, pp. 4649-4654.
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Eu chelate-doped plasmonic silver-core-silica-shell nanocomposites show greatly increased fluorescence enhancement factors of up to 145 at high excitation intensities, due to significantly increased radiative rates in samples with metal cores. They offer exceptionally high signal intensity, sufficient for single particle detection and compatibility with time-gated imaging offering nearly background-free conditions. A bioassay application is also presented. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Deng, W, Sudheendra, L, Zhao, J, Fu, J, Jin, D, Kennedy, IM & Goldys, EM 2011, 'Upconversion in NaYF4:Yb, Er nanoparticles amplified by metal nanostructures', Nanotechnology, vol. 22, no. 32, pp. 325604-325604.
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Upconversion (UC) fluorescence in NaYF4:Yb, Er nanoparticles amplified by metal nanostructures was compared in two nanostructure geometries: gold nanoshells surrounding nanoparticles and silver nanostructures adjacent to the nanoparticles, both placed on a dielectric silica surface. Enhanced UC luminescence signals and modified lifetimes induced by these two metals were observed in our study. The UC luminescence intensities of green and red emissions were enhanced by Ag nanostructures by a factor of approximately 4.4 and 3.5, respectively. The corresponding UC lifetimes were reduced ∼ 1.7-fold and ∼ 2.4-fold. In NaYF4:Yb, Er nanoparticles encapsulated in gold nanoshells, higher luminescence enhancement factors were obtained (∼9.1-fold for the green emission and ∼ 6.7-fold for the red emission). However, the Au shell coating extended the red emission by a factor of 1.5 and did not obviously change the lifetime of green emission. The responsible mechanisms such as plasmonic enhancement and surface effects are discussed. © 2011 IOP Publishing Ltd.
Duncan, EL, Danoy, P, Kemp, JP, Leo, PJ, McCloskey, E, Nicholson, GC, Eastell, R, Prince, RL, Eisman, JA, Jones, G, Sambrook, PN, Reid, IR, Dennison, EM, Wark, J, Richards, JB, Uitterlinden, AG, Spector, TD, Esapa, C, Cox, RD, Brown, SDM, Thakker, RV, Addison, KA, Bradbury, LA, Center, JR, Cooper, C, Cremin, C, Estrada, K, Felsenberg, D, Glüer, C-C, Hadler, J, Henry, MJ, Hofman, A, Kotowicz, MA, Makovey, J, Nguyen, SC, Nguyen, TV, Pasco, JA, Pryce, K, Reid, DM, Rivadeneira, F, Roux, C, Stefansson, K, Styrkarsdottir, U, Thorleifsson, G, Tichawangana, R, Evans, DM & Brown, MA 2011, 'Genome-Wide Association Study Using Extreme Truncate Selection Identifies Novel Genes Affecting Bone Mineral Density and Fracture Risk', PLoS Genetics, vol. 7, no. 4, pp. e1001372-e1001372.
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Osteoporotic fracture is a major cause of morbidity and mortality worldwide. Low bone mineral density (BMD) is a major predisposing factor to fracture and is known to be highly heritable. Site-, gender-, and age-specific genetic effects on BMD are thought to be significant, but have largely not been considered in the design of genome-wide association studies (GWAS) of BMD to date. We report here a GWAS using a novel study design focusing on women of a specific age (postmenopausal women, age 55-85 years), with either extreme high or low hip BMD (age- and gender-adjusted BMD z-scores of +1.5 to +4.0, n = 1055, or -4.0 to -1.5, n = 900), with replication in cohorts of women drawn from the general population (n = 20,898). The study replicates 21 of 26 known BMD-associated genes. Additionally, we report suggestive association of a further six new genetic associations in or around the genes CLCN7, GALNT3, IBSP, LTBP3, RSPO3, and SOX4, with replication in two independent datasets. A novel mouse model with a loss-of-function mutation in GALNT3 is also reported, which has high bone mass, supporting the involvement of this gene in BMD determination. In addition to identifying further genes associated with BMD, this study confirms the efficiency of extreme-truncate selection designs for quantitative trait association studies. © 2011 Duncan et al.
Ebrahimi Warkiani, M, Lou, C-P & Gong, H-Q 2011, 'Fabrication of multi-layer polymeric micro-sieve having narrow slot pores with conventional ultraviolet-lithography and micro-fabrication techniques', Biomicrofluidics, vol. 5, no. 3, pp. 36504-365049.
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Fast detection of waterborne pathogens is important for securing the hygiene of drinking water. Detection of pathogens in water at low concentrations and minute quantities demands rapid and efficient enrichment methods in order to improve the signal-to-noise ratio of bio-sensors. We propose and demonstrate a low cost and rapid method to fabricate a multi-layer polymeric micro-sieve using conventional lithography techniques. The micro-fabricated micro-sieves are made of several layers of SU-8 photoresist using multiple coating and exposure steps and a single developing process. The obtained micro-sieves have good mechanical properties, smooth surfaces, high porosity (≈40%), and narrow pore size distribution (coefficient of variation < 3.33%). Sample loading and back-flushing using the multi-layer micro-sieve resulted in more than 90% recovery of pathogens, which showed improved performance than current commercial filters.
Frost, SA, Nguyen, ND, Black, DA, Eisman, JA & Nguyen, TV 2011, 'Risk factors for in-hospital post-hip fracture mortality', Bone, vol. 49, no. 3, pp. 553-558.
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Introduction: Approximately 10% of hip fracture patients die during hospitalization; however, it is not clear what risk factors contribute to the excess mortality. This study sought to examine risk factors of, and to develop prognostic model for, predicting in-hospital mortality among hip fracture patients. Methods: We studied outcomes among 410 men and 1094 women with a hip fracture who were admitted to a major-teaching-hospital in Sydney (Australia) between 1997 and 2007. Clinical data, including concomitant illnesses, were obtained from inpatient data. The primary outcome of the study was in-hospital mortality regardless of length of stay. A Log-binomial regression model was used to identify risk factors for in-hospital mortality. Using the identified risk factors, prognostic nomograms were developed for predicting short term risk of mortality for an individual. Results: The median duration of hospitalization was 9. days. During hospitalization, the risk of mortality was higher in men (9%) than in women (4%). After adjusting for multiple risk factors, increased risk of in-hospital mortality was associated with advancing age (rate ratio [RR] for each 10-year increase in age: 1.91 95% confidence interval [CI]: 1.47 to 2.49), in men (RR 2.13; 95% CI 1.41 to 3.22), and the presence of comorbid conditions on admission (RR for one or more comorbid conditions vs. none: 2.30; 95% CI 1.52 to 3.48). Specifically, the risk of mortality was increased in patients with a pre-existing congestive heart failure (RR 3.02; 95% CI: 1.65 to 5.54), and liver disease (RR 4.75; 95% CI: 1.87 to 12.1). These factors collectively accounted for 69% of the risk for in-hospital mortality. A nomogram was developed from these risk factors to individualize the risk of in-hospital death following a hip fracture. The area under the receiver operating characteristic curve of the final model containing age, sex and comorbid conditions was 0.76. Conclusion: These data suggest that among ...
Guo, F, Xu, XX, Sun, ZZ, Zhang, JX, Meng, ZX, Zheng, W, Zhou, HM, Wang, BL & Zheng, YF 2011, 'A novel amperometric hydrogen peroxide biosensor based on electrospun Hb–collagen composite', Colloids and Surfaces B: Biointerfaces, vol. 86, no. 1, pp. 140-145.
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Ho-Pham, LT, Nguyen, ND, Lai, TQ, Eisman, JA & Nguyen, TV 2011, 'Vitamin D status and parathyroid hormone in a urban population in Vietnam', Osteoporosis International, vol. 22, no. 1, pp. 241-248.
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Jannot, G, Bajan, S, Giguère, NJ, Bouasker, S, Banville, IH, Piquet, S, Hutvagner, G & Simard, MJ 2011, 'The ribosomal protein RACK1 is required for microRNA function in both C. elegans and humans', EMBO reports, vol. 12, no. 6, pp. 581-586.
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Despite the importance of microRNAs (miRNAs) in gene regulation, it is unclear how the miRNA–Argonaute complex—or miRNA‐induced silencing complex (miRISC)—can regulate the translation of their targets in such diverse ways. We demonstrate here a direct interaction between the miRISC and the ribosome by showing that a constituent of the eukaryotic 40S subunit, receptor for activated C‐kinase (RACK1), is important for miRNA‐mediated gene regulation in animals. In vivo studies demonstrate that RACK1 interacts with components of the miRISC in nematodes and mammals. In both systems, the alteration of RACK1 expression alters miRNA function and impairs the association of the miRNA complex with the translating ribosomes. Our data indicate that RACK1 can contribute to the recruitment of miRISC to the site of translation, and support a post‐initiation mode of miRNA‐mediated gene repression.
Johnston, M & Hutvagner, G 2011, 'Posttranslational modification of Argonautes and their role in small RNA-mediated gene regulation', Silence, vol. 2, no. 1, pp. 5-5.
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Shortly after their discovery, repertoires of miRNA were identified, together with proteins involved in their biogenesis and action. It is now obvious that miRNA-mediated gene regulation itself is regulated at multiple levels. Identifying the regulatory mechanisms that underpin small RNA homeostasis by modulation of their biogenesis and action has become a key issue, which can be partly resolved by identifying mediators of Argonautes turnover. An emerging theme in the control of Argonaute stability and activity is through posttranslational modifications, which are the focus of this review. © 2011 Johnston and Hutvagner; licensee BioMed Central Ltd.
Lee, HJ, Hinshelwood, RA, Bouras, T, Gallego-Ortega, D, Valdés-Mora, F, Blazek, K, Visvader, JE, Clark, SJ & Ormandy, CJ 2011, 'Lineage Specific Methylation of the Elf5 Promoter in Mammary Epithelial Cells', Stem Cells, vol. 29, no. 10, pp. 1611-1619.
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Abstract Recent characterization of mammary stem and progenitor cells has improved our understanding of the transcriptional network that coordinates mammary development; however, little is known about the mechanisms that enforce lineage commitment and prevent transdifferentiation in the mammary gland. The E-twenty six transcription factor Elf5 forces the differentiation of mammary luminal progenitor cells to establish the milk producing alveolar lineage. Methylation of the Elf5 promoter has been proposed to act as a lineage gatekeeper during embryonic development. We used bisulphite sequencing to investigate in detail whether Elf5 promoter methylation plays a role in lineage commitment during mammary development. An increase in Elf5 expression was associated with decreasing Elf5 promoter methylation in differentiating HC11 mammary cells. Similarly, purified mammary epithelial cells from mice had increased Elf5 expression and decreased promoter methylation during pregnancy. Finally, analysis of epithelial subpopulations revealed that the Elf5 promoter is methylated and silenced in the basal, stem cell-containing population relative to luminal cells. These results demonstrate that Elf5 promoter methylation is lineage-specific and developmentally regulated in the mammary gland in vivo, and suggest that loss of Elf5 methylation specifies the mammary luminal lineage, while continued Elf5 methylation maintains the stem cell and myoepithelial lineages.
Lu, Y, Jin, D, Leif, RC, Deng, W, Piper, JA, Yuan, J, Duan, Y & Huo, Y 2011, 'Automated detection of rare‐event pathogens through time‐gated luminescence scanning microscopy', Cytometry Part A, vol. 79A, no. 5, pp. 349-355.
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AbstractMany microorganisms have a very low threshold (<10 cells) to trigger infectious diseases, and, in these cases, it is important to determine the absolute cell count in a low‐cost and speedy fashion. Fluorescent microscopy is a routine method; however, one fundamental problem has been associated with the existence in the sample of large numbers of nontarget particles, which are naturally autofluorescent, thereby obscuring the visibility of target organisms. This severely affects both direct visual inspection and the automated microscopy based on computer pattern recognition. We report a novel strategy of time‐gated luminescent scanning for accurate counting of rare‐event cells, which exploits the large difference in luminescence lifetimes between the lanthanide biolabels, >100 μs, and the autofluorescence backgrounds, <0.1 μs, to render background autofluorescence invisible to the detector. Rather than having to resort to sophisticated imaging analysis, the background‐free feature allows a single‐element photomultiplier to locate rare‐event cells, so that requirements for data storage and analysis are minimized to the level of image confirmation only at the final step. We have evaluated this concept in a prototype instrument using a 2D scanning stage and applied it to rare‐event Giardia detection labeled by a europium complex. For a slide area of 225 mm2, the time‐gated scanning method easily reduced the original 40,000 adjacent elements (0.075 mm × 0.075 mm) down to a few “elements of interest” containing the Giardia cysts. We achieved an averaged signal‐to‐background ratio of 41.2 (minimum ratio of 12.1). Such high contrasts ensured the accurate mapping of all the potential Giardia cysts free of false positives or negatives. This was confirmed by the automatic retrieving and time‐gated luminescence bioim...
Meng, ZX, Xu, XX, Zheng, W, Zhou, HM, Li, L, Zheng, YF & Lou, X 2011, 'Preparation and characterization of electrospun PLGA/gelatin nanofibers as a potential drug delivery system', Colloids and Surfaces B: Biointerfaces, vol. 84, no. 1, pp. 97-102.
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Moore, HC, Johnston, M, Nicol, SM, Bourdon, J-C, Thompson, AM, Hutvagner, G & Fuller-Pace, FV 2011, 'An evolutionarily conserved, alternatively spliced, intron in the p68/DDX5 DEAD-box RNA helicase gene encodes a novel miRNA', RNA, vol. 17, no. 4, pp. 555-562.
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The DEAD-box RNA helicase p68 (DDX5) plays important roles in several cellular processes, including transcription, pre-mRNA processing, and microRNA (miRNA) processing. p68 expression is growth and developmentally regulated, and alterations in p68 expression and/or function have been implicated in tumor development. The p68 gene encodes an evolutionarily conserved, alternatively spliced, intron the function of which has to date remained unclear. Although the intron-containing p68 RNA does not appear to yield an alternative p68 protein, it is differentially expressed in cell lines and tissues, indicating regulation of expression. Here we show that the p68 conserved intron encodes a novel putative miRNA, suggesting a previously unknown possible regulatory function for the p68 intron. We show that this miRNA (referred to as p68 miRNA) is processed from the intron via the canonical miRNA-processing pathway and that it associates with the Argonaute protein Ago2. Finally we show that the p68 miRNA suppresses an mRNA bearing complementary target sequences, suggesting that it is functional. These findings suggest a novel mechanism by which alterations in p68 expression may impact on the cell.
O'Dowd, BF, Ji, X, Alijaniaram, M, Nguyen, T & George, SR 2011, 'Separation and reformation of cell surface dopamine receptor oligomers visualized in cells', European Journal of Pharmacology, vol. 658, no. 2-3, pp. 74-83.
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Pongchaiyakul, C, Kotruchin, P, Wanothayaroj, E & Nguyen, TV 2011, 'An innovative prognostic model for predicting diabetes risk in the Thai population', Diabetes Research and Clinical Practice, vol. 94, no. 2, pp. 193-198.
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Objective: To estimate the prevalence and type 2 diabetes, and to develop a prognostic model for identifying individuals at high risk of undiagnosed type 2 diabetes. Research design and methods: The study was designed as a cross-sectional investigation with 4314 participants of Thai background, aged between 15 and 85 years (mean age: 48). Fasting plasma glucose was initially measured, and repeated if the first measurement was more than 126 mg/dl. Type 2 diabetes was diagnosed using the World Health Organizations criteria. Logistic regression model was used to develop prognostic models for men and women separately. The prognostic performance of the model was assessed by the area under the receiver operating characteristic curve (AUC) and a nomogram was constructed from the logistic regression model. Results: The overall prevalence of type 2 diabetes was 7.4% (n = 125/1693) in men and 3.4% (n = 98/2621) in women. In either gender, the prevalence increased with age and body mass index (BMI). Gender, age, BMI and systolic blood pressure (SBP) were independently associated with type 2 diabetes risk. Based on the estimated parameters of model, a nomogram was constructed for predicting diabetes separated by gender. The AUC for the model with 3 factors was 0.75. Conclusions: These data suggest that the combination of age, BMI and systolic blood pressure could help identify Thai individuals at high risk of undiagnosed diabetes.
Sambrook, PN, Flahive, J, Hooven, FH, Boonen, S, Chapurlat, R, Lindsay, R, Nguyen, TV, Díez-Perez, A, Pfeilschifter, J, Greenspan, SL, Hosmer, D, Netelenbos, JC, Adachi, JD, Watts, NB, Cooper, C, Roux, C, Rossini, M, Siris, ES, Silverman, S, Saag, KG, Compston, JE, LaCroix, A & Gehlbach, S 2011, 'Predicting fractures in an international cohort using risk factor algorithms without BMD', Journal of Bone and Mineral Research, vol. 26, no. 11, pp. 2770-2777.
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Abstract Clinical risk factors are associated with increased probability of fracture in postmenopausal women. We sought to compare prediction models using self-reported clinical risk factors, excluding BMD, to predict incident fracture among postmenopausal women. The GLOW study enrolled women aged 55 years or older from 723 primary-care practices in 10 countries. The population comprised 19,586 women aged 60 years or older who were not receiving antiosteoporosis medication and were followed annually for 2 years. Self-administered questionnaires were used to collect data on characteristics, fracture risk factors, previous fractures, and health status. The main outcome measure compares the C index for models using the WHO Fracture Risk (FRAX), the Garvan Fracture Risk Calculator (FRC), and a simple model using age and prior fracture. Over 2 years, 880 women reported incident fractures including 69 hip fractures, 468 “major fractures” (as defined by FRAX), and 583 “osteoporotic fractures” (as defined by FRC). Using baseline clinical risk factors, both FRAX and FRC showed a moderate ability to correctly order hip fracture times (C index for hip fracture 0.78 and 0.76, respectively). C indices for “major” and “osteoporotic” fractures showed lower values, at 0.61 and 0.64. Neither algorithm was better than the model based on age + fracture history alone (C index for hip fracture 0.78). In conclusion, estimation of fracture risk in an international primary-care population of postmenopausal women can be made using clinical risk factors alone without BMD. However, more sophisticated models incorporating multiple clinical risk factors including falls were not superior to more parsimonious models in predicting future fracture in this population. © 2011 American Society for Bone and Mineral Research
Sandhu, SK, Nguyen, ND, Center, JR, Pocock, NA, Eisman, JA & Nguyen, TV 2011, 'Prognosis of fracture: evaluation of predictive accuracy of the FRAX algorithm and Garvan nomogram: rejoinder to comments by Pluskiewicz and Drozdzowska', Osteoporosis International, vol. 22, no. 9, pp. 2563-2563.
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Sobala, A & Hutvagner, G 2011, 'Transfer RNA‐derived fragments: origins, processing, and functions', WIREs RNA, vol. 2, no. 6, pp. 853-862.
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AbstractDeep sequencing approaches have revealed multiple types of small RNAs with known and unknown functions. In this review we focus on a recently identified group of small RNAs that are derived from transfer RNAs (tRNAs), tRNA fragments (tRFs). We review the mechanism of their processing and their functions in mammalian cells, and highlight points of possible cross‐talk between tRFs and the canonical small RNA pathway characterized by small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi‐interacting RNAs (piRNAs). We also propose a nomenclature that is based on their processing characteristics. WIREs RNA 2011 2 853–862 DOI: 10.1002/wrna.96This article is categorized under:RNA Processing > tRNA ProcessingRegulatory RNAs/RNAi/Riboswitches > Regulatory RNAs
Sreenivasan, VKA, Ivukina, EA, Deng, W, Kelf, TA, Zdobnova, TA, Lukash, SV, Veryugin, BV, Stremovskiy, OA, Zvyagin, AV & Deyev, SM 2011, 'Barstar:barnase — a versatile platform for colloidal diamond bioconjugation', J. Mater. Chem., vol. 21, no. 1, pp. 65-68.
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Tran, BNH, Nguyen, ND, Nguyen, VX, Center, JR, Eisman, JA & Nguyen, TV 2011, 'Genetic profiling and individualized prognosis of fracture', Journal of Bone and Mineral Research, vol. 26, no. 2, pp. 414-419.
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Abstract Fragility fracture is a serious public health problem in the world. The risk of fracture is determined by genetic and nongenetic clinical risk factors. This study sought to quantify the contribution of genetic profiling to fracture prognosis. The study was built on the ongoing Dubbo Osteoporosis Epidemiology Study, in which fracture and risk factors of 858 men and 1358 women had been monitored continuously from 1989 and 2008. Fragility fracture was ascertained by radiologic reports. Bone mineral density at the femoral neck was measured by dual-energy X-ray absorptiometry (DXA). Fifty independent genes with allele frequencies ranging from 0.01 to 0.60 and relative risks (RRs) ranging from 1.01 to 3.0 were simulated. Three predictive models were fitted to the data in which fracture was a function of (1) clinical risk factors only, (2) genes only, and (3) clinical risk factors and 50 genes. The area under the curve (AUC) for model 1 was 0.77, which was lower than that of model II (AUC = 0.82). Adding genes into the clinical risk factors model (model 3) increased the AUC to 0.88 and improved the accuracy of fracture classification by 45%, with most (41%) improvement in specificity. In the presence of clinical risk factors, the number of genes required to achieve an AUC of 0.85 was around 25. These results suggest that genetic profiling could enhance the predictive accuracy of fracture prognosis and help to identify high-risk individuals for appropriate management of osteoporosis or intervention. © 2011 American Society for Bone and Mineral Research.
Warkiani, ME, Chen, L, Lou, C-P, Liu, H-B, Zhang, R & Gong, H-Q 2011, 'Capturing and recovering of Cryptosporidium parvum oocysts with polymeric micro-fabricated filter', Journal of Membrane Science, vol. 369, no. 1-2, pp. 560-568.
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Warkiani, ME, Lou, C-P & Gong, H-Q 2011, 'Fabrication and characterization of a microporous polymeric micro-filter for isolation ofCryptosporidium parvumoocysts', Journal of Micromechanics and Microengineering, vol. 21, no. 3, pp. 035002-035002.
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Xu, X, Yang, H, Liu, Y, Zheng, Y, Li, L, Ji, Y & Han, X 2011, 'Formation mechanism of novel two-dimensional single crystalline dendritic copper plates in an aqueous environment', Acta Materialia, vol. 59, no. 19, pp. 7177-7188.
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Xu, XX, Zhang, JX, Guo, F, Zheng, W, Zhou, HM, Wang, BL, Zheng, YF, Wang, YB, Cheng, Y, Lou, X & Jang, BZ 2011, 'A novel amperometric hydrogen peroxide biosensor based on immobilized Hb in Pluronic P123-nanographene platelets composite', Colloids and Surfaces B: Biointerfaces, vol. 84, no. 2, pp. 427-432.
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Yang, N, Schindeler, A, McDonald, MM, Seto, JT, Houweling, PJ, Lek, M, Hogarth, M, Morse, AR, Raftery, JM, Balasuriya, D, MacArthur, DG, Berman, Y, Quinlan, KGR, Eisman, JA, Nguyen, TV, Center, JR, Prince, RL, Wilson, SG, Zhu, K, Little, DG & North, KN 2011, 'alpha-Actinin-3 deficiency is associated with reduced bone mass in human and mouse', BONE, vol. 49, no. 4, pp. 790-798.
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Bone mineral density (BMD) is a complex trait that is the single best predictor of the risk of osteoporotic fractures. Candidate gene and genome-wide association studies have identified genetic variations in approximately 30 genetic loci associated with BMD variation in humans. alpha-Actinin-3 (ACTN3) is highly expressed in fast skeletal muscle fibres. There is a common null-polymorphism R577X in human ACTN3 that results in complete deficiency of the alpha-actinin-3 protein in approximately 20% of Eurasians. Absence of alpha-actinin-3 does not cause any disease phenotypes in muscle because of compensation by alpha-actinin-2. However, alpha-actinin-3 deficiency has been shown to be detrimental to athletic sprint/power performance. In this report we reveal additional functions for alpha-actinin-3 in bone. alpha-Actinin-3 but not alpha-actinin-2 is expressed in osteoblasts. The Actn3(-/-) mouse displays significantly reduced bone mass, with reduced cortical bone volume (-14%) and trabecular number (-61%) seen by microCT. Dynamic histomorphometry indicated this was due to a reduction in bone formation. In a cohort of postmenopausal Australian women, ACTN3 577XX genotype was associated with lower BMD in an additive genetic model, with the R577X genotype contributing 1.1% of the variance in BMD. Microarray analysis of cultured osteoprogenitors from Actn3(-/-) mice showed alterations in expression of several genes regulating bone mass and osteoblast/osteoclast activity, including Enpp1, Opg and Wnt7b. Our studies suggest that ACTN3 likely contributes to the regulation of bone mass through alterations in bone turnover. Given the high frequency of R577X in the general population, the potential role of ACTN3 R577X as a factor influencing variations in BMD in elderly humans warrants further study.
Zhang, Y, He, J, Zhu, Y, Chen, H & Ma, H 2011, 'Directly observed Au–S bond breakage due to swelling of the anchored polyelectrolyte', Chem. Commun., vol. 47, no. 4, pp. 1190-1192.
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Zhu, Y, Lv, B, Zhang, P & Ma, H 2011, 'Swelling induced Au–S bond breakage is determined by the molecular composition of surface tethered copolymers—carboxylated poly(OEGMA-r-HEMA)', Chemical Communications, vol. 47, no. 35, pp. 9855-9855.
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Beck, D, Brandl, M, Pham, TD, Chang, C-C, Zhou, X, Pham, TD, Zhou, X, Tanaka, H, Oyama-Higa, M, Jiang, X, Sun, C, Kowalski, J & Jia, X 1970, 'In-Silico Identification Of Micro-Loops In Myelodysplastic Syndromes', AIP Conference Proceedings, 2011 INTERNATIONAL SYMPOSIUM ON COMPUTATIONAL MODELS FOR LIFE SCIENCES (CMLS-11), AIP, pp. 263-271.
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Micro-loops are regulatory network motifs that leverage transcriptional and posttranscriptional control to effectively regulate the transcriptome. In this paper a regulatory network for Myelodysplastic Syndromes (MDSs) was constructed from the literature and publicly available data sources. The network was filtered using data from deep-sequencing of small RNAs, exon and microarrays. Motif discovery showed that micro-loops might exist in MDS. We further used the identified micro-loops and performed basic network analysis to identify the known disease gene RUNX1/AML, as well as miRNA family hsa-mir-181. This suggested that the concept of micro-loops can be applied to enhance disease gene identification and biomarker discovery. © 2011 American Institute of Physics.
Brandl, MB, Beck, D, Pham, TD, Pham, TD, Zhou, X, Tanaka, H, Oyama-Higa, M, Jiang, X, Sun, C, Kowalski, J & Jia, X 1970, 'Application of Fuzzy c-Means and Joint-Feature-Clustering to Detect Redundancies of Image-Features in Drug Combinations Studies of Breast Cancer', AIP Conference Proceedings, 2011 INTERNATIONAL SYMPOSIUM ON COMPUTATIONAL MODELS FOR LIFE SCIENCES (CMLS-11), AIP, pp. 65-72.
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The high dimensionality of image-based dataset can be a drawback for classification accuracy. In this study, we propose the application of fuzzy c-means clustering, cluster validity indices and the notation of a joint-feature-clustering matrix to find redundancies of image-features. The introduced matrix indicates how frequently features are grouped in a mutual cluster. The resulting information can be used to find data-derived feature prototypes with a common biological meaning, reduce data storage as well as computation times and improve the classification accuracy. © 2011 American Institute of Physics.
Deng, W, Jin, D, Drozdowicz-Tomsia, K, Yuan, J, Wu, J & Goldys, EM 1970, 'Plasmonic Ag/SiO 2 composite nanoparticles doped with europium chelate and their metal enhanced fluorescence', SPIE Proceedings, SPIE BiOS, SPIE, USA.
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We report silver nanostructure-enhanced fluorescence of a europium (Eu) chelate, BHHCT-Eu-DPBT, which was covalently bound in Ag/SiO2 nanocomposites. This design enhances the europium signal intensity by more than one order of magnitude, and accelerates the decay time from 0.3 ms down to 60 microseconds, at low excitation conditions. These nanocomposites were bright enough to be observed in time-gated fluorescence microscopy under 365 nm LED excitation. The increased brightness and reduced lifetime of such fluorescent core-shell nanocomposites will enhance their applicability for ultrasensitive bioassays and bioimaging, especially with time-gating. © 2011 SPIE.
Elson, KM, Tipper, JL, Kirkham, J, Hall, RM & Ingham, E 1970, 'In situ cell monitoring in organ culture', European Cells and Materials, p. 58.
Gallego-Ortega, D, Gómez del Pulgar, T, Valdés-Mora, F, Cebrián, A & Lacal, JC 1970, 'Involvement of human choline kinase alpha and beta in carcinogenesis: A different role in lipid metabolism and biological functions', Advances in Enzyme Regulation, 51st International Symposium on Regulations of Enzyme Activity and Synthesis in Normal and Neoplastic Tissues, Elsevier BV, Univ Bologna, Bologna, ITALY, pp. 183-194.
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Goldys, EM, Deng, W, Calander, NP, Drozdowicz-Tomsia, K & Jin, D 1970, 'Nanoscale plasmonic resonators with high Purcell factor: spontaneous and stimulated emission', SPIE Proceedings, SPIE BiOS, SPIE, USA.
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Plasmonic nanoparticles with silver cores and silica shells containing Eu fluorophores near the surface have been produced by wet chemistry method and their spontaneous emission properties characterized. Fluorescence amplification and decreased lifetime is interpreted within the Purcell framework which highlights the role of surface plasmon polariton modes of the nanoparticle. These behave as energy-storing resonators, with values of the Q factor between 50 and 170 at the fluorophore wavelength of 615 nm, and very small mode volumes, in the order of 104 nm3, producing high Purcell factors of over 4000. Comparison of experiment with theoretical calculations by using the Mie theory shows that the values of cavity Q factors are moderated by the nonradiative rate of fluorophore molecules close to metal. The criteria for laser action in such composite nanoparticles are also presented, including lasing frequencies and threshold gain. © 2011 SPIE.
Gough, CS, Wajayathunga, VN, Tipper, JL, Wilcox, RK, Hall, RM & Ingham, E 1970, 'The biology of the ovine functional spinal unit', European Cells and Materials, p. 67.
Jin, D, Lu, Y, Zhao, J, Deng, W, Lu, J & Piper, JA 1970, 'Advances in lanthanide bioprobes and high-throughput background-free biophotonics sensing', 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim incorporating the Australasian Conference on Optics, Lasers and Spectroscopy and the Australian Conference on Optical Fibre Technology, 2011 International Quantum Electronics Conference (IQEC) and Conference on Lasers and Electro-Optics (CLEO) Pacific Rim, IEEE, Sydney, NSW, Australia, pp. 80-82.
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We report time-domain techniques of biophotonics sensing. Our bioprobes have been engineered to emit tunable luminescence across multiple sharp spectra and microsecond-long lifetimes. This offers high-throughput opportunities for cellular-level disease diagnosis at low cost. © 2011 IEEE.
Mao, Y, Cui, K, Lulu, W, Zhao, H, Nie, F, Brandl, M, Beck, D, Gao, L & Wong, S 1970, 'An in-silico approach for drug repositioning to tumour anti-migration using an integrated genomic strategy', 2011 IEEE/NIH Life Science Systems and Applications Workshop (LiSSA), 2011 IEEE/NIH 5th Life Science Systems and Applications Workshop (LiSSA), IEEE, Bethesda, MD, USA, pp. 88-91.
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Cell migration is a key step for deterioration of many in situ or metastasis malignant tumours. Tumour anti-migration is a promising strategy to treat cancer, but corresponding drugs developed under such a strategy are still in dire poverty, partly due to the lengthly process of drug trials and approval required by the US Food and Drug Administration (FDA). Given there are thousands of FDA approved drugs in the market, we believe that drug repositioning may provide a fast and cost-effective way to identify potential anti-migration drugs. In this paper, an in-silico drug screening method using a genomic strategy is proposed for the goal, in which genomic signature identification combined with support vector machine modelling is adopted to estimate drug efficacy. And a high-throughput, sensitive, 3-dimensional invasion assay by quantitative bioluminescence imaging proved the performance of proposed method on in vitro disease models. © 2011 IEEE.
Tran, TS, Nguyen, ND, Center, JR, Seibel, MJ, Eisman, JA & Nguyen, TV 1970, 'SERUM TESTOSTERONE AND FRACTURE RISK INMEN: A COMPARISON OF RADIOIMMUNOASSAY VERSUS LIQUID CHROMATOGRAPHY TANDEM MASS SPECTROMETRY', OSTEOPOROSIS INTERNATIONAL, IOF Regionals 2nd Asia-Pacific Osteoporosis and Bone Meeting / ANZBMS Annual Scientific Meeting held with the JSBMR, SPRINGER LONDON LTD, Gold Coast, AUSTRALIA, pp. S589-S590.
Warkiani, ME, Gong, HQ, Fane, AG & Wicaksana, F 1970, 'Effects of Membrane Pore Morphology on Fouling Behavior of Polymeric Micro-fabricated Membrane During Crossflow Micro-filtration', CLEAN TECHNOLOGY 2011: BIOENERGY, RENEWABLES, STORAGE, GRID, WASTE AND SUSTAINABILITY, CTSI Clean Technology and Sustainable Industries Conference and Expo, Clean Technology 2011, CRC PRESS-TAYLOR & FRANCIS GROUP, Boston, MA, pp. 220-223.
Warkiani, ME, Gong, HQ, Fane, AG & Wicaksana, F 1970, 'Effects of membrane pore morphology on fouling behavior of polymeric microfabricated membrane during crossflow micro-filtration', Technical Proceedings of the 2011 NSTI Nanotechnology Conference and Expo, NSTI-Nanotech 2011, NSTI Nanotechnology Conference and Expo, CRC PRESS-TAYLOR & FRANCIS GROUP, Boston, MA, pp. 569-572.
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The effects of the membrane pore geometry on the fouling mechanism of high-flux polymeric micro-fabricated membranes were studied using latex particles with different sizes and concentrations. The micro-fabricated membranes are made of a thin layer SU-8 photoresist with smooth surface and well defined slotted (or circular) pores using dissolving mold technique. For particles larger than the membrane pore size, the fouling mechanism was pore blockage followed by cake filtration while pore narrowing was the dominant mechanism when the particles were smaller than the membrane pore size. Filtration with slotted membrane offers some interesting advantages over conventional filtration with circular pores. The initial rate of flux decline was slower for the membrane with slotted pores compared to the membrane with circular pores since the initial particle deposition only covered a small fraction of the slits. The flow resistance is also much lower for the slotted membrane compare to the circular membrane.
