Complete mitochondrial genome sequencing reveals novel haplotypes in a Polynesian population

The high risk of metabolic disease traits in Polynesians may be partly explained by elevated prevalence of genetic variants involved in energy metabolism. The genetics of Polynesian populations has been shaped by island hoping migration events which have possibly favoured thrifty genes. The aim of this study was to sequence the mitochondrial genome in a group of Maoris in an effort to characterise genome variation in this Polynesian population for use in future disease association studies. We sequenced the complete mitochondrial genomes of 20 non-admixed Maori subjects using Affymetrix technology. DNA diversity analyses showed the Maori group exhibited reduced mitochondrial genome diversity compared to other worldwide populations, which is consistent with historical bottleneck and founder effects. Global phylogenetic analysis positioned these Maori subjects specifically within mitochondrial haplogroup - B4a1a1. Interestingly, we identified several novel variants that collectively form new and unique Maori motifs – B4a1a1c, B4a1a1a3 and B4a1a1a5. Compared to ancestral populations we observed an increased frequency of non-synonymous coding variants of several mitochondrial genes in the Maori group, which may be a result of positive selection and/or genetic drift effects. In conclusion, this study reports the first complete mitochondrial genome sequence data for a Maori population. Overall, these new data reveal novel mitochondrial genome signatures in this Polynesian population and enhance the phylogenetic picture of maternal ancestry in Oceania. The increased frequency of several mitochondrial coding variants makes them good candidates for future studies aimed at assessment of metabolic disease risk in Polynesian populations.

Improving the statistical preparation for measuring soil N2O flux by closed chamber

Nitrous oxide emissions from soil are known to be spatially and temporally volatile. Reliable estimation of emissions over a given time and space depends on measuring with sufficient intensity but deciding on the number of measuring stations and the frequency of observation can be vexing. The question of low frequency manual observations providing comparable results to high frequency automated sampling also arises. Data collected from a replicated field experiment was intensively studied with the intention to give some statistically robust guidance on these issues. The experiment had nitrous oxide soil to air flux monitored within 10 m by 2.5 m plots by automated closed chambers under a 3 h average sampling interval and by manual static chambers under a three day average sampling interval over sixty days. Observed trends in flux over time by the static chambers were mostly within the auto chamber bounds of experimental error. Cumulated nitrous oxide emissions as measured by each system were also within error bounds. Under the temporal response pattern in this experiment, no significant loss of information was observed after culling the data to simulate results under various low frequency scenarios. Within the confines of this experiment observations from the manual chambers were not spatially correlated above distances of 1 m. Statistical power was therefore found to improve due to increased replicates per treatment or chambers per replicate. Careful after action review of experimental data can deliver savings for future work.

Influence of nitrogen fertiliser application and timing on greenhouse gas emissions from a lychee (Litchi chinensis) orchard in humid subtropical Australia

Nitrous oxide emissions from intensive, fertilised agricultural systems have been identified as significant contributors to both Australia's and the global greenhouse gas (GHG) budget. This is expected to increase as rates of agriculture intensification and land use change accelerate to support population growth and food production. Limited data exists on N2O trace gas fluxes from subtropical or tropical tree cropping soils critical for the development of effective mitigation strategies.This study aimed to quantify GHG emissions over two consecutive years (March 2007 to March 2009) from a 30 year (lychee) orchard in the humid subtropical region of Australia. GHG fluxes were measured using a combination of high temporal resolution automated sampling and manually sampled chambers. No fertiliser was added to the plots during the 2007 measurement season. A split application of nitrogen fertiliser (urea) was added at the rate of 265kgNha-1 during the autumn and spring of 2008. Emissions of N2O were influenced by rainfall events and seasonal temperatures during 2007 and the fertilisation events in 2008. Annual N2O emissions from the lychee canopy increased from 1.7kgN2O-Nha-1yr-1 for 2007, to 7.6kgN2O-Nha-1yr-1 following fertiliser application in 2008. This represented an emission factor of 1.56%, corrected for background emissions. The timing of the split application was found to be critical to N2O emissions, with over twice as much lost following an application in spring (2.44%) compared to autumn (EF: 1.10%). This research suggests that avoiding fertiliser application during the hot and moist spring/summer period can reduce N2O losses without compromising yields.

A rapid and sensitive UPLC-ESI MS method for analysis of isofraxidin, a natural antistress compound, and its metabolites in rat plasma

Isofraxidin is one of the main bioactive constituents in the root of Acanthopanax senticosus, which has antifatigue, antistress, and immuno-accommondating effects. In this study, an ultraperformance LC (UPLC)-ESI MS method was developed for analyzing isofraxidin and its metabolites in rat plasma. The analysis was performed on a UPLC coupled with ESI MS (quadropole MS tandem TOF MS). The lower LOD (LLOD) for isofraxidin was 0.25 ng/mL, the intraday precision was less than 10%, the interday precision was less than 10%, and the extraction recovery was more than 80%. Isofraxidin and two metabolites (M1 and M2) were detected in rat plasma after oral administration of isofraxidin, and the molecular polarities of M1 and M2 were both increased compared to isofraxidin. The metabolites were identified as 5,6-dihydroxyl-7-methoxycoumarin and 5-hydroxyl-6,7-dimethoxycoumarin when subjected to parent ion spectra, product ion spectra, and extract mass and element composition analyses.

Quantifying alterations in cell migration : tracking fluorescently-tagged migrating cells by FACs and live-imaging

Cell migration is fundamental to many different physiological processes including embryonic development, inflammation and wound healing. Given the range and importance cell migration plays a number of assays have been developed to measure different aspects of cell migration. Here we describe two different methods to analyze cell migration. The first method analyzes the migration of fluorescently tagged cells using Boyden chambers and FACs and the second looks at migration properties using time-lapse microscopy.

Galectin-1 : a link between tumor hypoxia and tumor immune privilege

Purpose: To identify a 15-KDa novel hypoxia-induced secreted protein in head and neck squamous cell carcinomas (HNSCC) and to determine its role in malignant progression. Methods: We used surface-enhanced laser desorption ionization time-of-flight mass spectrometry (SELDI-TOF-MS) and tandem MS to identify a novel hypoxia-induced secreted protein in FaDu cells. We used immunoblots, real-time polymerase chain reaction (PCR), and enzyme-linked immunoabsorbent assay to confirm the hypoxic induction of this secreted protein as galectin-1 in cell lines and xenografts. We stained tumor tissues from 101 HNSCC patients for galectin-1, CA IX (carbonic anhydrase IX, a hypoxia marker) and CDS (a T-cell marker). Expression of these markers was correlated to each other and to treatment outcomes. Results: SELDI-TOF studies yielded a hypoxia-induced peak at 15 kDa that proved to be galectin-1 by MS analysis. Immunoblots and PCR studies confirmed increased galectin-1 expression by hypoxia in several cancer cell lines. Plasma levels of galectin-1 were higher in tumor-bearing severe combined immunodeficiency (SCID) mice breathing 10% O 2 compared with mice breathing room air. In HNSCC patients, there was a significant correlation between galectin-1 and CA IX staining (P = .01) and a strong inverse correlation between galectin-1 and CDS staining (P = .01). Expression of galectin-1 and CDS were significant predictors for overall survival on multivariate analysis. Conclusion: Galectin-1 is a novel hypoxia-regulated protein and a prognostic marker in HNSCC. This study presents a new mechanism on how hypoxia can affect the malignant progression and therapeutic response of solid tumors by regulating the secretion of proteins that modulate immune privilege. © 2005 by American Society of Clinical Oncology.

Combination therapy with gefitinib and rofecoxib in patients with platinum-pretreated relapsed non-small-cell lung cancer

Purpose: In non-small-cell lung cancer (NSCLC), the epidermal growth factor receptor (EGFR) and cyclooxygenase-2 (COX-2) play major roles in tumorigenesis. This phase I/II study evaluated combined therapy with the EGFR tyrosine kinase inhibitor (TKI) gefitinib and the COX-2 inhibitor rofecoxib in platinum-pretreated, relapsed, metastatic NSCLC (n = 45). Patients and Methods: Gefitinib 250 mg/d was combined with rofecoxib (dose escalated from 12.5 to 25 to 50 mg/d through three cohorts, each n = 6). Because the rofecoxib maximum-tolerated dose was not reached, the 50 mg/d cohort was expanded for efficacy evaluation (n = 33). Results: Among the 42 assessable patients, there was one complete response (CR) and two partial responses (PRs) and 12 patients with stable disease (SD); disease control rate was 35.7% (95% CI, 21.6% to 52.0%). Median time to tumor progression was 55 days (95% CI, 47 to 70 days), and median survival was 144 days (95% CI, 103 to 190 days). In a pilot study, matrix-assisted laser desorption/ionization (MALDI) proteomics analysis of baseline serum samples could distinguish patients with an objective response from those with SD or progressive disease (PD), and those with disease control (CR, PR, and SD) from those with PD. The regimen was generally well tolerated, with predictable toxicities including skin rash and diarrhea. Conclusion: Gefitinib combined with rofecoxib provided disease control equivalent to that expected with single-agent gefitinib and was generally well tolerated. Baseline serum proteomics may help identify those patients most likely to benefit from EGFR TKIs. © 2007 by American Society of Clinical Oncology.

Differentiation of isomeric N-glycan structures by normal-phase liquid chromatography-MALDI-TOF/TOF tandem mass spectrometry

The detailed characterization of protein N-glycosylation is very demanding given the many different glycoforms and structural isomers that can exist on glycoproteins. Here we report a fast and sensitive method for the extensive structure elucidation of reducing-end labeled N-glycan mixtures using a combination of capillary normal-phase HPLC coupled off-line to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and TOF/TOF-MS/MS. Using this method, isobaric N-glycans released from honey bee phospholipase A2 and Arabidopsis thaliana glycoproteins were separated by normal-phase chromatography and subsequently identified by key fragment ions in the MALDI-TOF/TOF tandem mass spectra. In addition, linkage and branching information were provided by abundant cross-ring and "elimination" fragment ions in the MALDI-CID spectra that gave extensive structural information. Furthermore, the fragmentation characteristics of N-glycans reductively aminated with 2-aminobenzoic acid and 2-aminobenzamide were compared. The identification of N-glycans containing 3-linked core fucose was facilitated by distinctive ions present only in the MALDI-CID spectra of 2-aminobenzoic acid-labeled oligosaccharides. To our knowledge, this is the first MS/MS-based technique that allows confident identification of N-glycans containing 3-linked core fucose, which is a major allergenic determinant on insect and plant glycoproteins.

Timing and source constraints on the relationship between mafic and felsic intrusions in the Emeiashan large igneous province

Several I- and A-type granite, syenite plutons and spatially associated, giant Fe–Ti–V deposit-bearing mafic ultramafic layered intrusions occur in the Pan–Xi(Panzhihua–Xichang) area within the inner zone of the Emeishan large igneous province (ELIP). These complexes are interpreted to be related to the Emeishan mantle plume. We present LA-ICP-MS and SIMS zircon U–Pb ages and Hf–Nd isotopic compositions for the gabbros, syenites and granites from these complexes. The dating shows that the age of the felsic intrusive magmatism (256.2 ± 3.0–259.8 ± 1.6 Ma) is indistinguishable from that of the mafic intrusive magmatism (255.4 ± 3.1–259.5 ± 2.7 Ma) and represents the final phase of a continuous magmatic episode that lasted no more than 10 Myr. The upper gabbros in the mafic–ultramafic intrusions are generally more isotopically enriched (lower eNd and eHf) than the middle and lower gabbros, suggesting that the upper gabbros have experienced a higher level of crustal contamination than the lower gabbros. The significantly positive eHf(t) values of the A-type granites and syenites (+4.9 to +10.8) are higher than those of the upper gabbros of the associated mafic intrusion, which shows that they cannot be derived by fractional crystallization of these bodies. They are however identical to those of the mafic enclaves (+7.0 to +11.4) and middle and lower gabbros, implying that they are cogenetic. We suggest that they were generated by fractionation of large-volume, plume-related basaltic magmas that ponded deep in the crust. The deep-seated magma chamber erupted in two stages: the first near a density minimum in the basaltic fractionation trend and the second during the final stage of fractionation when the magma was a low density Fe-poor, Si-rich felsic magma. The basaltic magmas emplaced in the shallowlevel magma chambers differentiated to form mafic–ultramafic layered intrusions accompanied by a small amount of crustal assimilation through roof melting. Evolved A-type granites (synenites and syenodiorites) were produced dominantly by crystallization in the deep crustal magma chamber. In contrast, the I-type granites have negative eNd(t) [-6.3 to -7.5] and eHf(t) [-1.3 to -6.7] values, with the Nd model ages (T Nd DM2) of 1.63-1.67 Ga and Hf model ages (T Hf DM2) of 1.56-1.58 Ga, suggesting that they were mainly derived from partial melting of Mesoproterozoic crust. In combination with previous studies, this study also shows that plume activity not only gave rise to reworking of ancient crust, but also significant growth of juvenile crust in the center of the ELIP.

The effect of nitroxides on swarming motility and biofilms, multicellular behaviors in Pseudomonas aeruginosa

The ability of NO to induce biofilm dispersion has been well established. Here we investigated the effect of nitroxides (sterically hindered nitric oxide analogues) on biofilm formation and swarming motility in Pseudomonas aeruginosa. A transposon mutant unable to produce nitric oxide endogenously (nirS) was deficient in swarming motility relative to wild type and the complemented strain. Moreover, expression of the nirS gene was up-regulated by 9.65-fold in wild type swarming cells when compared to planktonic cells. Wild type swarming levels were substantially restored upon exogenous addition of nitroxide containing compounds, consistent with the hypothesis that NO is necessary for swarming motility. Here, we showed that nitroxides not only mimicked the dispersal activity of NO, but also prevented biofilms from forming in flow cell chambers. In addition, a nirS transposon mutant was deficient in biofilm formation relative to wild type and the complemented strain, thus implicating NO in the formation of biofilms. Intriguingly despite its stand alone action in inhibiting biofilm formation and promoting dispersal, a nitroxide partially restored the ability of a nirS mutant to form biofilms.

Spatial prediction of N2O emissions in pasture : a Bayesian model averaging analysis

Nitrous oxide (N2O) is one of the greenhouse gases that can contribute to global warming. Spatial variability of N2O can lead to large uncertainties in prediction. However, previous studies have often ignored the spatial dependency to quantify the N2O - environmental factors relationships. Few researches have examined the impacts of various spatial correlation structures (e.g. independence, distance-based and neighbourhood based) on spatial prediction of N2O emissions. This study aimed to assess the impact of three spatial correlation structures on spatial predictions and calibrate the spatial prediction using Bayesian model averaging (BMA) based on replicated, irregular point-referenced data. The data were measured in 17 chambers randomly placed across a 271 m(2) field between October 2007 and September 2008 in the southeast of Australia. We used a Bayesian geostatistical model and a Bayesian spatial conditional autoregressive (CAR) model to investigate and accommodate spatial dependency, and to estimate the effects of environmental variables on N2O emissions across the study site. We compared these with a Bayesian regression model with independent errors. The three approaches resulted in different derived maps of spatial prediction of N2O emissions. We found that incorporating spatial dependency in the model not only substantially improved predictions of N2O emission from soil, but also better quantified uncertainties of soil parameters in the study. The hybrid model structure obtained by BMA improved the accuracy of spatial prediction of N2O emissions across this study region.

Isolation of human lymphatic malformation endothelial cells, their in vitro characterization and in vivo survival in a mouse xenograft model

Human lymphatic vascular malformations (LMs), also known as cystic hygromas or lymphangioma, consist of multiple lymphatic endothelial cell-lined lymph-containing cysts. No animal model of this disease exists. To develop a mouse xenograft model of human LM, CD34NegCD31Pos LM lymphatic endothelial cells (LM-LEC) were isolated from surgical specimens and compared to foreskin CD34NegCD31Pos lymphatic endothelial cells (LECs). Cells were implanted into a mouse tissue engineering model for 1, 2 and 4 weeks. In vitro LM-LECs showed increased proliferation and survival under starvation conditions (P < 0.0005 at 48 h, two-way ANOVA), increased migration (P < 0.001, two-way ANOVA) and formed fewer (P = 0.029, independent samples t test), shorter tubes (P = 0.029, independent samples t test) than foreskin LECs. In vivo LM-LECs implanted into a Matrigel™-containing mouse chamber model assembled to develop vessels with dilated cystic lumens lined with flat endothelium, morphology similar to that of clinical LMs. Human foreskin LECs failed to survive implantation. In LM-LEC implanted chambers the percent volume of podoplaninPos vessels was 1.18 ± 2.24 % at 1 week, 6.34 ± 2.68 % at 2 weeks and increasing to 7.67 ± 3.60 % at 4 weeks. In conclusion, the significantly increased proliferation, migration, resistance to apoptosis and decreased tubulogenesis of LM-LECs observed in vitro is likely to account for their survival and assembly into stable LM-like structures when implanted into a mouse vascularised chamber model. This in vivo xenograft model will provide the basis of future studies of LM biology and testing of potential pharmacological interventions for patients with lymphatic malformations.

In vitro assessment of migratory behavior of two cell populations in a simple multichannel microdevice

Recent literature suggests that mesenchymal stem/stromal cells (MSC) could be used as Trojan Horses to deliver “death-signals” to cancer cells. Herein, we describe the development of a novel multichannel cell migration device, and use it to investigate the relative migration rates of bone marrow-derived MSC and breast cancer cells (MCF-7) towards each other. Confluent monolayers of MSC and MCF-7 were established in adjacent chambers separated by an array of 14 microchannels. Initially, culture chambers were isolated by air bubbles (air-valves) contained within each microchannel, and then bubbles were displaced to initiate the assay. The MCF-7 cells migrated preferentially towards MSC, whilst the MSC did not migrate preferentially towards the MCF-7 cells. Our results corroborate previous literature that suggests MSC migration towards cancer cells in vivo is in response to the associated inflammation rather than directly to signals secreted by the cancer cells themselves.

Advances in mass spectrometry for lipidomics

Recent expansion in research in the field of lipidomics has been driven by the development of new mass spectrometric tools and protocols for the identification and quantification of molecular lipids in complex matrices. Although there are similarities between the field of lipidomics and the allied field of mass spectrometry (e.g., proteomics), lipids present some unique advantages and challenges for mass spectrometric analysis. The application of electrospray ionization to crude lipid extracts without prior fractionation-the so-called shotgun approach-is one such example, as it has perhaps been more successfully applied in lipidomics than in any other discipline. Conversely, the diverse molecular structure of lipids means that collision-induced dissociation alone may be limited in providing unique descriptions of complex lipid structures, and the development of additional, complementary tools for ion activation and analysis is required to overcome these challenges. In this article, we discuss the state of the art in lipid mass spectrometry and highlight several areas in which current approaches are deficient and further innovation is required.