Micro-PIXE (Particle-Induced X-Ray Emission Analysis) Applications in Minerals Research

The versatility of the PIXE method with microbeams of protons as a non-destructive, in-situ probe for trace element analysis in the geosciences has been demonstrated in an ever increasing number of cases. While in most applications the method can be considered as derivative or as an extension of electron microprobe methodology, features unique to the proton microprobe enable new approaches to hitherto intractable problems of analysis. An appropriate niche has been established in igneous mineralogy and petrology, with important implications both in the basic geosciences as well as mineral industry applications, particularly in the diamond exploration industry. This paper reviews recent advances and discusses the advantages and limitations of current micro-PIXE applications in the geosciences in view of other competing and complimentary methods

Accretion and photodesorption of CO ice as a function of the incident angle of deposition

Non-thermal desorption of inter- and circum-stellar ice mantles on dust grains, in particular ultraviolet photon-induced desorption, has gained importance in recent years. These processes may account for the observed gas phase abundances of molecules like CO toward cold interstellar clouds. Ice mantle growth results from gas molecules impinging on the dust from all directions and incidence angles. Nevertheless, the effect of the incident angle for deposition on ice photo-desorption rate has not been studied. This work explores the impact on the accretion and photodesorption rates of the incidence angle of CO gas molecules with the cold surface during deposition of a CO ice layer. Infrared spectroscopy monitored CO ice upon deposition at different angles, ultraviolet-irradiation, and subsequent warm-up. Vacuum-ultraviolet spectroscopy and a Ni-mesh measured the emission of the ultraviolet lamp. Molecules ejected from the ice to the gas during irradiation or warm-up were characterized by a quadrupole mass spectrometer. The photodesorption rate of CO ice deposited at 11 K and different incident angles was rather stable between 0 and 45$^{\circ}$. A maximum in the CO photodesorption rate appeared around 70$^{\circ}$-incidence deposition angle. The same deposition angle leads to the maximum surface area of water ice. Although this study of the surface area could not be performed for CO ice, the similar angle dependence in the photodesorption and the ice surface area suggests that they are closely related. Further evidence for a dependence of CO ice morphology on deposition angle is provided by thermal desorption of CO ice experiments

Genotyping of Sarawak rice cultivars using microsatellite markers

Genetic diversity of 53 Sarawak rice cultivars, originating from Southern Sarawak, was assessed using 54 microsatellite markers. Initial polymorphism detection was conducted using 54 primer pairs distributed on 12 rice chromosomes. Polymorphic markers were chosen from the initial screening results in order to obtain microsatellite marker panels that can differentiate the rice cultivars undertaken in the study. The chosen microsatellite marker panel consisted of RM1, RM240, RM489, RM252, RM413, RM204, RM11, RM404, RM316, RM271, RM206, and RM19, with one representative from each chromosome. A total of 43 alleles were detected with an average of 3.58 alleles per locus. The polymorphism information content (PIC) values obtained from the microsatellite marker panels ranged from 0.306 to 0.730, with an average of 0.622. The Unweighted Pair Group Method with Arithmetic Mean (UPGMA) dendrogram (r = 0.789) revealed 2 major groups with 6 sub-clusters and the wide range of similarity values (0.24-1.0) obtained showed a high degree of diversity among the cultivars. The results suggest microsatellite markers as a useful tool for the estimation of genetic diversity and cultivar differentiation and present invaluable genetic information for future breeding and association mapping efforts

Measurement of Intrinsic Dirac Fermion Cooling on the Surface of the Topological Insulator Bi_2Se_3 Using Time-Resolved and Angle-Resolved Photoemission Spectroscopy

We perform time- and angle-resolved photoemission spectroscopy of a prototypical topological insulator (TI) Bi_2Se_3 to study the ultrafast dynamics of surface and bulk electrons after photoexcitation. By analyzing the evolution of surface states and bulk band spectra, we obtain their electronic temperature and chemical potential relaxation dynamics separately. These dynamics reveal strong phonon-assisted surface-bulk coupling at high lattice temperature and total suppression of inelastic scattering between the surface and the bulk at low lattice temperature. In this low temperature regime, the unique cooling of Dirac fermions in TI by acoustic phonons is manifested through a power law dependence of the surface temperature decay rate on carrier density

The need for allele mining: perspectives of the System-wide Genetic Resources Programme (SGRP)

The SGRP is a consortium of all CGIAR gene banks. These banks aim to (1) conserve diversity efficiently, including and especially rare alleles and genotypes; (2) ensure efficient use of collection by delivering appropriately selected subsets of germplasm to users, maximizing the chance of giving users the set of alleles or genotypes that they need; and (3) ensure that the entire collection remains available for use. The SGRP exists to ensure a consistent, integrated, system-wide approach to the efficient achievement of these goals

LINE-1 ORF2p expression is nearly imperceptible in human cancers

Background Long interspersed element-1 (LINE-1, L1) is the major driver of mobile DNA activity in modern humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. Many types of human cancers are characterized by L1 promoter hypomethylation, L1 transcription, L1 ORF1p protein expression, and somatic L1 retrotransposition. ORF2p encodes the endonuclease and reverse transcriptase activities required for L1 retrotransposition. Its expression is poorly characterized in human tissues and cell lines. Results We report mass spectrometry-based tumor proteome profiling studies wherein ORF2p eludes detection. To test whether ORF2p could be detected with specific reagents, we developed and validated five rabbit monoclonal antibodies with immunoreactivity for specific epitopes on the protein. These reagents readily detect ectopic ORF2p expressed from bicistronic L1 constructs. However, endogenous ORF2p is not detected in human tumor samples or cell lines by western blot, immunoprecipitation, or immunohistochemistry despite high levels of ORF1p expression. Moreover, we report endogenous ORF1p-associated interactomes, affinity isolated from colorectal cancers, wherein we similarly fail to detect ORF2p. These samples include primary tumors harboring hundreds of somatically acquired L1 insertions. The new data are available via ProteomeXchange with identifier PXD013743. Conclusions Although somatic retrotransposition provides unequivocal genetic evidence for the expression of ORF2p in human cancers, we are unable to directly measure its presence using several standard methods. Experimental systems have previously indicated an unequal stoichiometry between ORF1p and ORF2p, but in vivo, the expression of these two proteins may be more strikingly uncoupled. These findings are consistent with observations that ORF2p is not tolerable for cell growth

Linear dichroism and circular dichroism in photosynthesis research

The efficiency of photosynthetic light energy conversion depends largely on the molecular architecture of the photosynthetic membranes. Linear- and circular-dichroism (LD and CD) studies have contributed significantly to our knowledge of the molecular organization of pigment systems at different levels of complexity, in pigment–protein complexes, supercomplexes, and their macroassemblies, as well as in entire membranes and membrane systems. Many examples show that LD and CD data are in good agreement with structural data; hence, these spectroscopic tools serve as the basis for linking the structure of photosynthetic pigment–protein complexes to steady-state and time-resolved spectroscopy. They are also indispensable for identifying conformations and interactions in native environments, and for monitoring reorganizations during photosynthetic functions, and are important in characterizing reconstituted and artificially constructed systems. This educational review explains, in simple terms, the basic physical principles, and theory and practice of LD and CD spectroscopies and of some related quantities in the areas of differential polarization spectroscopy and microscopy