Molecular ion trap-depletion spectroscopy of BaCl+^+

We demonstrate a simple technique for molecular ion spectroscopy. BaCl$^+$ molecular ions are trapped in a linear Paul trap in the presence of a room-temperature He buffer gas and photodissociated by driving an electronic transition from the ground X$^1\Sigma^+$ state to the repulsive wall of the A$^1\Pi$ state. The photodissociation spectrum is recorded by monitoring the induced trap loss of BaCl$^+$ ions as a function of excitation wavelength. Accurate molecular potentials and spectroscopic constants are determined. Comparison of the theoretical photodissociation cross-sections with the measurement shows excellent agreement. This study represents the first spectroscopic data for BaCl$^+$ and an important step towards the production of ultracold ground-state molecular ions.Comment: 5 pages, 5 figure

Permeability of Noble Gases through Kapton, Butyl, Nylon, and "Silver Shield"

Noble gas permeabilities and diffusivities of Kapton, butyl, nylon, and "Silver Shield" are measured at temperatures between 22C and 115C. The breakthrough times and solubilities at 22C are also determined. The relationship of the room temperature permeabilities to the noble gas atomic radii is used to estimate radon permeability for each material studied. For the noble gases tested, Kapton and Silver Shield have the lowest permeabilities and diffusivities, followed by nylon and butyl, respectively.Comment: 14 pages, 7 figure

A simple procedure for directly obtaining haplotype sequences of diploid genomes

Background Almost all genome sequencing projects neglect the fact that diploid organisms contain two genome copies and consequently what is published is a composite of the two. This means that the relationship between alternate alleles at two or more linked loci is lost. We have developed a simplified method of directly obtaining the haploid sequences of each genome copy from an individual organism. Results The diploid sequences of three groups of cattle samples were obtained using a simple sample preparation procedure requiring only a microscope and a haemocytometer. Samples were: 1) lymphocytes from a single Angus steer; 2) sperm cells from an Angus bull; 3) lymphocytes from East African Zebu (EAZ) cattle collected and processed in a field laboratory in Eastern Kenya. Haploid sequence from a fosmid library prepared from lymphocytes of an EAZ cow was used for comparison. Cells were serially diluted to a concentration of one cell per microlitre by counting with a haemocytometer at each dilution. One microlitre samples, each potentially containing a single cell, were lysed and divided into six aliquots (except for the sperm samples which were not divided into aliquots). Each aliquot was amplified with phi29 polymerase and sequenced. Contigs were obtained by mapping to the bovine UMD3.1 reference genome assembly and scaffolds were assembled by joining adjacent contigs that were within a threshold distance of each other. Scaffolds that appeared to contain artefacts of CNV or repeats were filtered out leaving scaffolds with an N50 length of 27–133 kb and a 88–98 % genome coverage. SNP haplotypes were assembled with the Single Individual Haplotyper program to generate an N50 size of 97–201 kb but only ~27–68 % genome coverage. This method can be used in any laboratory with no special equipment at only slightly higher costs than conventional diploid genome sequencing. A substantial body of software for analysis and workflow management was written and is available as supplementary data. Conclusions We have developed a set of laboratory protocols and software tools that will enable any laboratory to obtain haplotype sequences at only modestly greater cost than traditional mixed diploid sequences

Effects of manipulated herbivore inputs on nutrient flux and decomposition in a tropical rainforest in Puerto Rico

Forest canopy herbivores are known to increase rates of nutrient fluxes to the forest floor in a number of temperate and boreal forests, but few studies have measured effects of herbivore-enhanced nutrient fluxes in tropical forests. We simulated herbivore-induced fluxes in a tropical rainforest in Puerto Rico by augmenting greenfall (fresh foliage fragments), frassfall (insect feces), and throughfall (precipitation enriched with foliar leachates) in replicated experimental plots on the forest floor. Background rates of greenfall and frassfall were measured monthly using litterfall collectors and augmented by adding 10× greenfall or 10× frassfall to designated plots. Throughfall fluxes of NH4, NO3 and PO4 (but not water) were doubled in treatment plots, based on published rates of fluxes of these nutrients in throughfall. Control plots received only background flux rates for these compounds but the same minimum amount of distilled water. We evaluated treatment effects as changes in flux rates for NO3, NH4 and PO4, measured as decomposition rate of leaf litter in litterbags and as adsorption in ion-exchange resin bags at the litter–soil interface. Frass addition significantly increased NO3 and NH4 fluxes, and frass and throughfall additions significantly reduced decay rate, compared to controls. Reduced decay rate suggests that nitrogen flux was sufficient to inhibit microbial decomposition activity. Our treatments represented fluxes expected from low–moderate herbivore outbreaks and demonstrated that herbivores, at these outbreak levels, increase ecosystem-level N and P fluxes by >30% in this tropical rainforest