Advanced mass spectrometry-based multi-omics technologies for exploring the pathogenesis of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is one of the primary hepatic malignancies and is the third most common cause of cancer related death worldwide. Although a wealth of knowledge has been gained concerning the initiation and progression of HCC over the last half century, efforts to improve our understanding of its pathogenesis at a molecular level are still greatly needed, to enable clinicians to enhance the standards of the current diagnosis and treatment of HCC. In the post-genome era, advanced mass spectrometry driven multi-omics technologies (e.g., profiling of DNA damage adducts, RNA modification profiling, proteomics, and metabolomics) stand at the interface between chemistry and biology, and have yielded valuable outcomes from the study of a diversity of complicated diseases. Particularly, these technologies are being broadly used to dissect various biological aspects of HCC with the purpose of biomarker discovery, interrogating pathogenesis as well as for therapeutic discovery. This proof of knowledge-based critical review aims at exploring the selected applications of those defined omics technologies in the HCC niche with an emphasis on translational applications driven by advanced mass spectrometry, toward the specific clinical use for HCC patients. This approach will enable the biomedical community, through both basic research and the clinical sciences, to enhance the applicability of mass spectrometry-based omics technologies in dissecting the pathogenesis of HCC and could lead to novel therapeutic discoveries for HCC.

Gravity-induced coronal plane joint moments in the adolescent scoliotic spine

INTRODUCTION Calculating segmental (vertebral level-by-level) torso masses in Adolescent Idiopathic Scoliosis (AIS) patients allows the gravitational loading on the scoliotic spine during relaxed standing to be estimated. METHODS Existing low dose CT scans were used to calculate vertebral level-by-level torso masses and joint moments occurring in the spine for a group of female AIS patients with right-sided thoracic curves. Image processing software, ImageJ (v1.45 NIH USA) was used to reconstruct the torso segments and subsequently measure the torso volume and mass corresponding to each vertebral level. Body segment masses for the head, neck and arms were taken from published anthropometric data. Intervertebral joint moments at each vertebral level were found by summing each of the torso segment masses above the required joint and multiplying it by the perpendicular distance to the centre of the disc. RESULTS AND DISCUSSION Twenty patients were included in this study with a mean age of 15.0±2.7 years and a mean Cobb angle 52±5.9°. The mean total trunk mass, as a percentage of total body mass, was 27.8 (SD 0.5) %. Mean segmental torso mass increased inferiorly from 0.6kg at T1 to 1.5kg at L5. The coronal plane joint moments during relaxed standing were typically 5-7Nm at the apex of the curve (Figure 1), with the highest apex joint of 7Nm. CT scans were performed in the supine position and curve magnitudes are known to be 7-10° smaller than those measured in standing [1]. Therefore joint moments produced by gravity will be greater than those calculated here. CONCLUSIONS Coronal plane joint moments as high as 7Nm can occur during relaxed standing in scoliosis patients, which may help to explain the mechanics of AIS progression. The body mass distributions calculated in this study can be used to estimate joint moments derived using other imaging modalities such as MRI and subsequently determine if a relationship exists between joint moments and progressive vertebral deformity.

The importance of science fiction and other STEM-related mass media in young people’s decisions to enrol in university STEM courses

This paper presents Australian results from the Interests and Recruitment in Science (IRIS) study with respect to the influence of STEM-related mass media, including science fiction, on students’ decisions to enrol in university STEM courses. The study found that across the full cohort (N=2999), students tended to attribute far greater influence to science-related documentaries/channels such as Life on Earth and the Discovery Channel, etc. than to science-fiction movies or STEM-related TV dramas. Males were more inclined than females to consider science fiction/fantasy books and films and popular science books/magazines as having been important in their decisions. Students taking physics/astronomy tended to rate the importance of science fiction/fantasy books and films higher than students in other courses. The implications of these results for our understanding of influences on STEM enrolments are discussed.

Determinants and measurement of lean body mass in Indian adults

Indians tend to have lower lean body mass than other ethnic groups which increases the risk of chronic diseases. Three complementary studies included in this thesis advanced knowledge on determinants of lean body mass in Indians and the techniques to measure it. The first study examined the determinants of lean body mass in young Indian adults and highlighted the importance of diet and physical activity for development of lean body mass. This study has important implications for policy on prevention of chronic diseases in India. The other two studies helped refinement of the techniques of lean body mass measurement and are expected to facilitate future research in this area. The thesis is presented in the form of publications in high ranking journals.

Digital technology and public apology : responses by Indigenous Australians to a government saying sorry

Australia has had two recent public apologies, one to the ‘ Stolen Generation’ of Aboriginal and Torres Strait Islander Australians and the second to the ‘Forgotten Australians' – people who had been removed from their parents as children and institutionalized. Both acts occurred in time when there was no Internet and peoples’ stories took years to collect and decades for their weight to carry the public momentum required to gain a public apology. Now, in a digital age, the reports and the testimonies held within them are available for all to read on the Internet. We all now know what happened and formal public apologies ensued. Both public apologies also draw attention to an emerging intersection between digital technologies, personal historical stories and public apology. Research has identified the potential of digital narrative, such as digital storytelling3 and videoed oral histories to assist in the production of digital narratives that can help to present the multiple voices and viewpoints of those affected by these subjects co-creatively (Burgess et al, pp.152-153). Not all Australians however have access or the skills to use digital tools so as to benefit from these technologies ⎯ especially Indigenous Australians. While the Federal Government is committed to helping Australians enjoy digital confidence and digital media literacy skills, experience inclusive digital participation and benefit through online engagement (Department of Broadband, communications and the Digital Economy, 2009) there are many initiatives that can also be undertaken locally by State funded institutions, such as libraries to assist. This paper highlights the outcomes of recent empirical projects undertaken at the State Library of Queensland (SLQ) in particular focusing on digital initiatives in Family History practices by Indigenous users, and a digital story project in response to the public apology to the Stolen Generation instigated by SLQ.

Analysis of the extreme diversity of salivary alpha-amylase isoforms generated by physiological proteolysis using liquid chromatography-tandem mass spectrometry

Saliva is a crucial biofluid for oral health and is also of increasing importance as a non-invasive source of disease biomarkers. Salivary alpha-amylase is an abundant protein in saliva, and changes in amylase expression have been previously associated with a variety of diseases and conditions. Salivary alpha-amylase is subject to a high diversity of post-translational modifications, including physiological proteolysis in the oral cavity. Here we developed methodology for rapid sample preparation and non-targeted LC-ESI-MS/MS analysis of saliva from healthy subjects and observed an extreme diversity of alpha-amylase proteolytic isoforms. Our results emphasize the importance of consideration of post-translational events such as proteolysis in proteomic studies, biomarker discovery and validation, particularly in saliva. (C) 2012 Elsevier B.V. All rights reserved.

Collection and determination of nucleotide metabolites in neonatal and adult saliva by high performance liquid chromatography with tandem mass spectrometry

Saliva contains a number of biochemical components which may be useful for diagnosis/monitoring of metabolic disorders, and as markers of cancer or heart disease. Saliva collection is attractive as a non-invasive sampling method for infants and elderly patients. We present a method suitable for saliva collection from neonates. We have applied this technique for the determination of salivary nucleotide metabolites. Saliva was collected from 10 healthy neonates using washed cotton swabs, and directly from 10 adults. Two methods for saliva extraction from oral swabs were evaluated. The analytes were then separated using high performance liquid chromatography (HPLC) with tandem mass spectrometry (MS/MS). The limits of detection for 14 purine/pyrimidine metabolites were variable, ranging from 0.01 to 1.0 mu M. Recovery of hydrophobic purine/pyrimidine metabolites from cotton tips was consistently high using water/acetonitrile extraction (92.7-111%) compared with water extraction alone. The concentrations of these metabolites were significantly higher in neonatal saliva than in adults. Preliminary ranges for nucleotide metabolites in neonatal and adult saliva are reported. Hypoxanthine and xanthine were grossly raised in neonates (49.3 +/- 25.4; 30.9 +/- 19.5 mu M respectively) compared to adults (4.3 +/- 3.3; 4.6 +/- 4.5 mu M); nucleosides were also markedly raised in neonates. This study focuses on three essential details: contamination of oral swabs during manufacturing and how to overcome this; weighing swabs to accurately measure small saliva volumes; and methods for extracting saliva metabolites of interest from cotton swabs. A method is described for determining nucleotide metabolites using HPLC with photo-diode array or MS/MS. The advantages of utilising saliva are highlighted. Nucleotide metabolites were not simply in equilibrium with plasma, but may be actively secreted into saliva, and this process is more active in neonates than adults. (C) 2013 Elsevier B.V. All rights reserved.

Identification of salivary N-glycoproteins and measurement of glycosylation site occupancy by boronate glycoprotein enrichment and liquid chromatography/electrospray ionization tandem mass spectrometry

RATIONALE Diseases including cancer and congenital disorders of glycosylation have been associated with changes in the site-specific extent of protein glycosylation. Saliva can be non-invasively sampled and is rich in glycoproteins, giving it the potential to be a useful biofluid for the discovery and detection of disease biomarkers associated with changes in glycosylation. METHODS Saliva was collected from healthy individuals and glycoproteins were enriched using phenylboronic acid based glycoprotein enrichment resin. Proteins were deglycosylated with peptide-N-glycosidase F and digested with AspN or trypsin. Desalted peptides and deglycosylated peptides were separated by reversed-phase liquid chromatography and detected with on-line electrospray ionization quadrupole-time-of-flight mass spectrometry using a 5600 TripleTof instrument. Site-specific glycosylation occupancy was semi-quantitatively determined from the abundance of deglycosylated and nonglycosylated versions of each given peptide. RESULTS Glycoprotein enrichment identified 67 independent glycosylation sites from 24 unique proteins, a 3.9-fold increase in the number of glycosylation sites identified. Enrichment of glycoproteins rather than glycopeptides allowed detection of both deglycosylated and nonglycosylated versions of each peptide, and thereby robust measurement of site-specific occupancy at 21 asparagines. Healthy individuals showed limited biological variability in occupancy, with partially modified sites having characteristics consistent with inefficient glycosylation by oligosaccharyltransferase. Inclusion of negative controls without enzymatic deglycosylation controlled for spontaneous chemical deamidation, and identified asparagines previously incorrectly annotated as glycosylated. CONCLUSIONS We developed a sample preparation and mass spectrometry detection strategy for rapid and efficient measurement of site-specific glycosylation occupancy on diverse salivary glycoproteins suitable for biomarker discovery and detection of changes in glycosylation occupancy in human disease.

Multiphase porous media model for heat and mass transfer during drying of agricultural products

Modelling of food processing is complex because it involves sophisticated material and transport phenomena. Most of the agricultural products such fruits and vegetables are hygroscopic porous media containing free water, bound water, gas and solid matrix. Considering all phase in modelling is still not developed. In this article, a comprehensive porous media model for drying has been developed considering bound water, free water separately, as well as water vapour and air. Free water transport was considered as diffusion, pressure driven and evaporation. Bound water assumed to be converted to free water due to concentration difference and also can diffuse. Binary diffusion between water vapour and air was considered. Since, the model is fundamental physics based it can be applied to any drying applications and other food processing where heat and mass transfer takes place in porous media with significant evaporation and other phase change.

Characterization of acyl chain position in unsaturated phosphatidylcholines using differential mobility-mass spectrometry

Glycerophospholipids (GPs) that differ in the relative position of the two fatty acyl chains on the glycerol backbone (i.e., sn-positional isomers) can have distinct physicochemical properties. The unambiguous assignment of acyl chain position to an individual GP represents a significant analytical challenge. Here we describe a workflow where phosphatidylcholines (PCs) are subjected to ESI for characterization by a combination of differential mobility spectrometry and MS (DMS-MS). When infused as a mixture, ions formed from silver adduction of each phospholipid isomer {e.g., [PC (16:0/18:1) + Ag]+ and [PC (18:1/16:0) + Ag]+} are transmitted through the DMS device at discrete compensation voltages. Varying their relative amounts allows facile and unambiguous assignment of the sn-positions of the fatty acyl chains for each isomer. Integration of the well-resolved ion populations provides a rapid method (< 3 min) for relative quantification of these lipid isomers. The DMS-MS results show excellent agreement with established, but time-consuming, enzymatic approaches and also provide superior accuracy to methods that rely on MS alone. The advantages of this DMS-MS method in identification and quantification of GP isomer populations is demonstrated by direct analysis of complex biological extracts without any prior fractionation.