Raman spectroscopy of selected tsumcorite Pb(Zn,Fe3+)2(AsO4)2(OH,H2O) minerals –implications for arsenate accumulation

The presence of arsenic in the environment is a hazard. The accumulation of arsenate by a range of cations in the formation of minerals provides a mechanism for the accumulation of arsenate. The formation of the tsumcorite minerals is an example of a series of minerals which accumulate arsenate. There are about twelve examples in this mineral group. Raman spectroscopy offers a method for the analysis of these minerals. The structure of selected tsumcorite minerals with arsenate and sulphate anions were analysed by Raman spectroscopy. Isomorphic substitution of sulphate for arsenate is observed for gartrellite and thometzekite. A comparison is made with the sulphate bearing mineral natrochalcite. The position of the hydroxyl and water stretching vibrations are related to the strength of the hydrogen bond formed between the OH unit and the AsO43- anion. Characteristic Raman spectra of the minerals enable the assignment of the bands to specific vibrational modes.

Raman spectroscopy of the multianion mineral gartrellite-PbCu(Fe3+,Cu)(AsO4)2(OH,H2O)2

The multianion mineral gartrellite PbCu(Fe3+,Cu)(AsO4)2(OH,H2O)2 has been studied by a combination of Raman and infrared spectroscopy. The vibrational spectra of two gartrellite samples from Durango and Ashburton Downs were compared. Gartrellite is one of the tsumcorite mineral group based upon arsenate and sulphate anions. Crystal symmetry is either triclinic in the case of an ordered occupation of two cationic sites, triclinic due to ordering of the H bonds in the case of species with 2 water molecules per formula unit, or monoclinic in the other cases. Characteristic Raman spectra of the minerals enable the assignment of the bands to specific vibrational modes. These spectra are related to the structure of gartrellite. The position of the hydroxyl and water stretching vibrations are related to the strength of the hydrogen bond formed between the OH unit and the AsO4 anion.

A distributional analysis of the native-immigrant wage gap : the importance of employment discrimination

It is well documented that immigrants earn less than natives in the United States, and various attempts have been made to determine whether these earnings differentials reflect underlying differences in skill or ethnic discrimination in the labor market. The earnings of immigrants and ethnic minorities is an extensively studied area focusing on the economic integration of immigrants (e.g., Chiswick (1978), Lalonde and Topel (1993), Borjas (1995)). Yet, the role of occupational segregation as a mechanism for discrimination is yet to be addressed (to our knowledge). Discrimination can be effective at either of two stages in the earnings process – in the assignment of earnings to people within occupational groups (henceforth referred to as wage discrimination) or in the allocation of people to occupations (henceforth referred to as employment discrimination). While it would be premature to attribute the underlying cause to discriminatory hiring policies of employers, it would be of social-political and economic interest to investigate the possibility.

Assessment of the molecular structure of the borate mineral sakhaite Ca12Mg4(BO3)7(CO3)4Cl(OH)2·H2O using vibrational spectroscopy

The structure of the borate mineral sakhaite Ca12Mg4(BO3)7(CO3)4Cl(OH)2·H2O, a borate–carbonate of calcium and magnesium has been assessed using vibrational spectroscopy. Assignment of bands is undertaken by comparison with the data from other published results. Intense Raman band at 1134 cm−1 with a shoulder at 1123 cm−1 is assigned to the symmetric stretching mode. The Raman spectrum displays bands at 1479, 1524 and 1560 cm−1 which are assigned to the antisymmetric stretching vibrations. The observation of multiple carbonate stretching bands supports the concept that the carbonate units are non-equivalent. The Raman band at 968 cm−1 with a shoulder at 950 cm−1 is assigned to the symmetric stretching mode of trigonal boron. Raman bands at 627 and 651 cm−1 are assigned to the out-of-plane bending modes of trigonal and tetrahedral boron. Raman spectroscopy coupled with infrared spectroscopy enables the molecular structure of the mineral sakhaite to be assessed.

Effect of CT electron density identification on Monte Carlo simulations of radiotherapeutic treatments

Introduction: The accurate identification of tissue electron densities is of great importance for Monte Carlo (MC) dose calculations. When converting patient CT data into a voxelised format suitable for MC simulations, however, it is common to simplify the assignment of electron densities so that the complex tissues existing in the human body are categorized into a few basic types. This study examines the effects that the assignment of tissue types and the calculation of densities can have on the results of MC simulations, for the particular case of a Siemen’s Sensation 4 CT scanner located in a radiotherapy centre where QA measurements are routinely made using 11 tissue types (plus air). Methods: DOSXYZnrc phantoms are generated from CT data, using the CTCREATE user code, with the relationship between Hounsfield units (HU) and density determined via linear interpolation between a series of specified points on the ‘CT-density ramp’ (see Figure 1(a)). Tissue types are assigned according to HU ranges. Each voxel in the DOSXYZnrc phantom therefore has an electron density (electrons/cm3) defined by the product of the mass density (from the HU conversion) and the intrinsic electron density (electrons /gram) (from the material assignment), in that voxel. In this study, we consider the problems of density conversion and material identification separately: the CT-density ramp is simplified by decreasing the number of points which define it from 12 down to 8, 3 and 2; and the material-type-assignment is varied by defining the materials which comprise our test phantom (a Supertech head) as two tissues and bone, two plastics and bone, water only and (as an extreme case) lead only. The effect of these parameters on radiological thickness maps derived from simulated portal images is investigated. Results & Discussion: Increasing the degree of simplification of the CT-density ramp results in an increasing effect on the resulting radiological thickness calculated for the Supertech head phantom. For instance, defining the CT-density ramp using 8 points, instead of 12, results in a maximum radiological thickness change of 0.2 cm, whereas defining the CT-density ramp using only 2 points results in a maximum radiological thickness change of 11.2 cm. Changing the definition of the materials comprising the phantom between water and plastic and tissue results in millimetre-scale changes to the resulting radiological thickness. When the entire phantom is defined as lead, this alteration changes the calculated radiological thickness by a maximum of 9.7 cm. Evidently, the simplification of the CT-density ramp has a greater effect on the resulting radiological thickness map than does the alteration of the assignment of tissue types. Conclusions: It is possible to alter the definitions of the tissue types comprising the phantom (or patient) without substantially altering the results of simulated portal images. However, these images are very sensitive to the accurate identification of the HU-density relationship. When converting data from a patient’s CT into a MC simulation phantom, therefore, all possible care should be taken to accurately reproduce the conversion between HU and mass density, for the specific CT scanner used. Acknowledgements: This work is funded by the NHMRC, through a project grant, and supported by the Queensland University of Technology (QUT) and the Royal Brisbane and Women's Hospital (RBWH), Brisbane, Australia. The authors are grateful to the staff of the RBWH, especially Darren Cassidy, for assistance in obtaining the phantom CT data used in this study. The authors also wish to thank Cathy Hargrave, of QUT, for assistance in formatting the CT data, using the Pinnacle TPS. Computational resources and services used in this work were provided by the HPC and Research Support Group, QUT, Brisbane, Australia.

Improved sub-cellular resolution via simultaneous analysis of organelle proteomics data across varied experimental conditions

Spatial organisation of proteins according to their function plays an important role in the specificity of their molecular interactions. Emerging proteomics methods seek to assign proteins to sub-cellular locations by partial separation of organelles and computational analysis of protein abundance distributions among partially separated fractions. Such methods permit simultaneous analysis of unpurified organelles and promise proteome-wide localisation in scenarios wherein perturbation may prompt dynamic re-distribution. Resolving organelles that display similar behavior during a protocol designed to provide partial enrichment represents a possible shortcoming. We employ the Localisation of Organelle Proteins by Isotope Tagging (LOPIT) organelle proteomics platform to demonstrate that combining information from distinct separations of the same material can improve organelle resolution and assignment of proteins to sub-cellular locations. Two previously published experiments, whose distinct gradients are alone unable to fully resolve six known protein-organelle groupings, are subjected to a rigorous analysis to assess protein-organelle association via a contemporary pattern recognition algorithm. Upon straightforward combination of single-gradient data, we observe significant improvement in protein-organelle association via both a non-linear support vector machine algorithm and partial least-squares discriminant analysis. The outcome yields suggestions for further improvements to present organelle proteomics platforms, and a robust analytical methodology via which to associate proteins with sub-cellular organelles.

Vibrational spectroscopy of the multianion mineral gartrellite from the Anticline Deposit, Ashburton Downs, Western Australia

The multianion mineral gartrellite PbCu(Fe3+,Cu)(AsO4)2(OH,H2O)2 has been studied by a combination of Raman and infrared spectroscopy. The molecular structure of gartrellite is assessed. Gartrellite is one of the tsumcorite mineral group based upon arsenate and/or sulphate anions. Crystal symmetry is either triclinic in the case of an ordered occupation of two cationic sites, triclinic due to ordering of the H bonds in the case of species with two water molecules per formula unit, or monoclinic in the other cases. Characteristic Raman spectra of the mineral gartrellite enable the assignment of the bands to specific vibrational modes. These spectra are related to the structure of gartrellite. The position of the hydroxyl and water stretching vibrations are related to the strength of the hydrogen bond formed between the OH unit and the AsO3/4 anion.

Ozone-induced dissociation : Elucidation of double bond position within mass-selected lipid ions

Ions formed from lipids during electrospray ionization of crude lipid extracts have been mass-selected within a quadrupole linear ion trap mass spectrometer and allowed to react with ozone vapor. Gas-phase ion-molecule reactions between unsaturated lipid ions and ozone are found to yield two primary product ions for each carbon-carbon double bond within the molecule. The mass-to-charge ratios of these chemically induced fragments are diagnostic of the position of unsaturation within the precursor ion. This novel analytical technique, dubbed ozone-induced dissociation (OzID), can be applied both in series and in parallel with conventional collision-induced dissociation (CID) to provide near-complete structural assignment of unknown lipids within complex mixtures without prior fractionation or derivatization. In this study, OzID is applied to a suite of complex lipid extracts from sources including human lens, bovine kidney, and commercial olive oil, thus demonstrating the technique to be applicable to a broad range of lipid classes including both neutral and acidic glycerophospholipids, sphingomyelins, and triacylglycerols. Gas-phase ozonolysis reactions are also observed with different types of precursor ions including \[M + H](+), \[M + Li](+), \[M + Na](+), and \[M H](-): in each case yielding fragmentation data that allow double bond position to be unambiguously assigned. Within the human lens lipid extract, three sphingomyelin regioisomers, namely SM(d18:0/15Z-24:1), SM(d18:0/17Z-24:1), and SM(d18:0/19Z-24:1), and a novel phosphatidylethanolamine alkyl ether, GPEtn(11Z-18:1e/9Z18:1), are identified using a combination of CID and OzID. These discoveries demonstrate that lipid identification based on CID alone belies the natural structural diversity in lipid biochemistry and illustrate the potential of OzID as a complementary approach within automated, high-throughput lipid analysis protocols.

The genome of woodland strawberry (Fragaria vesca)

The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria Ã- ananassa) and other economically important rosaceous plants. Here we report the draft F. vesca genome, which was sequenced to ×-39 coverage using second-generation technology, assembled de novo and then anchored to the genetic linkage map into seven pseudochromosomes. This diploid strawberry sequence lacks the large genome duplications seen in other rosids. Gene prediction modeling identified 34,809 genes, with most being supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time were identified. Macrosyntenic relationships between Fragaria and Prunus predict a hypothetical ancestral Rosaceae genome that had nine chromosomes. New phylogenetic analysis of 154 protein-coding genes suggests that assignment of Populus to Malvidae, rather than Fabidae, is warranted.

Time to face the fats : What can mass spectrometry reveal about the structure of lipids and their interactions with proteins?

Since the 1950s, X-ray crystallography has been the mainstay of structural biology, providing detailed atomic-level structures that continue to revolutionize our understanding of protein function. From recent advances in this discipline, a picture has emerged of intimate and specific interactions between lipids and proteins that has driven renewed interest in the structure of lipids themselves and raised intriguing questions as to the specificity and stoichiometry in lipid-protein complexes. Herein we demonstrate some of the limitations of crystallography in resolving critical structural features of ligated lipids and thus determining how these motifs impact protein binding. As a consequence, mass spectrometry must play an important and complementary role in unraveling the complexities of lipid-protein interactions. We evaluate recent advances and highlight ongoing challenges towards the twin goals of (1) complete structure elucidation of low, abundant, and structurally diverse lipids by mass spectrometry alone, and (2) assignment of stoichiometry and specificity of lipid interactions within protein complexes.

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.

Insertions in the OCL1 locus of Acinetobacter baumannii lead to shortened lipooligosaccharides

Genomes of 82 Acinetobacter baumannii global clones 1 (GC1) and 2 (GC2) isolates were sequenced and different forms of the locus predicted to direct synthesis of the outer core (OC) of the lipooligosaccharide were identified. OCL1 was in all GC2 genomes, whereas GC1 isolates carried OCL1, OCL3 or a new locus, OCL5. Three mutants in which an insertion sequence (ISAba1 or ISAba23) interrupted OCL1 were identified. Isolates with OCL1 intact produced only lipooligosaccharide, while the mutants produced lipooligosaccharide of reduced molecular weight. Thus, the assignment of the OC locus as that responsible for the synthesis of the OC is correct.

A Bayesian model of source monitoring

The Source Monitoring Framework is a promising model of constructive memory, yet fails because it is connectionist and does not allow content tagging. The Dual-Process Signal Detection Model is an improvement because it reduces mnemic qualia to a single memory signal (or degree of belief), but still commits itself to non-discrete representation. By supposing that ‘tagging’ means the assignment of propositional attitudes to aggregates of anemic characteristics informed inductively, then a discrete model becomes plausible. A Bayesian model of source monitoring accounts for the continuous variation of inputs and assignment of prior probabilities to memory content. A modified version of the High-Threshold Dual-Process model is recommended to further source monitoring research.

Does size matter? An assessment of quota market evolution and performance in the Great Barrier Reef fin-fish fishery

In fisheries managed using individual transferable quotas (ITQs) it is generally assumed that quota markets are well-functioning, allowing quota to flow on either a temporary or permanent basis to those able to make best use of it. However, despite an increasing number of fisheries being managed under ITQs, empirical assessments of the quota markets that have actually evolved in these fisheries remain scarce. The Queensland Coral Reef Fin-Fish Fishery (CRFFF) on the Great Barrier Reef has been managed under a system of ITQs since 2004. Data on individual quota holdings and trades for the period 2004-2012 were used to assess the CRFFF quota market and its evolution through time. Network analysis was applied to assess market structure and the nature of lease-trading relationships. An assessment of market participants’ abilities to balance their quota accounts, i.e., gap analysis, provided insights into market functionality and how this may have changed in the period observed. Trends in ownership and trade were determined, and market participants were identified as belonging to one out of a set of seven generalized types. The emergence of groups such as investors and lease-dependent fishers is clear. In 2011-2012, 41% of coral trout quota was owned by participants that did not fish it, and 64% of total coral trout landings were made by fishers that owned only 10% of the quota. Quota brokers emerged whose influence on the market varied with the bioeconomic conditions of the fishery. Throughout the study period some quota was found to remain inactive, implying potential market inefficiencies. Contribution to this inactivity appeared asymmetrical, with most residing in the hands of smaller quota holders. The importance of transaction costs in the operation of the quota market and the inequalities that may result are discussed in light of these findings

The ownership question of plant gene and genome intellectual properties

The restructuring of the crop agriculture industry over the past two decades has enabled patent holders to exclude, prevent and deter others from using certain research tools and delay or block further follow-on inventions