Lead-tellurium oxysalts from Otto Mountain near Baker, California: IV. Markcooperite, Pb(UO_2)Te^(6+)O_6, the first natural uranyl tellurate

Markcooperite, Pb_2(UO_2)Te^(6+)O_6, is a new tellurate from Otto Mountain near Baker, California, named in honor of Mark A. Cooper of the University of Manitoba for his contributions to mineralogy. The new mineral occurs on fracture surfaces and in small vugs in brecciated quartz veins. Markcooperite is directly associated with bromian chlorargyrite, iodargyrite, khinite-4O, wulfenite, and four other new tellurates: housleyite, thorneite, ottoite, and timroseite. Various other secondary minerals occur in the veins, including two other new secondary tellurium minerals: paratimroseite and telluroperite. Markcooperite is monoclinic, space group P2_1/c, a = 5.722(2), b = 7.7478(2), c = 7.889(2) Å, β = 90.833(5)°, V = 349.7(2) Å^3, and Z = 2. It occurs as pseudotetragonal prisms to 0.2 mm with the forms {100} and {011} and as botryoidal intergrowths to 0.3 mm in diameter; no twinning was observed. Markcooperite is orange and transparent, with a light orange streak and adamantine luster, and is non-fluorescent. Mohs hardness is estimated at 3. The mineral is brittle, with an irregular fracture and perfect {100} cleavage. The calculated density is 8.496 g/cm3 based on the empirical formula. Markcooperite is biaxial (+), with indices of refraction α= 2.11, β = 2.12, γ= 2.29 calculated using the Gladstone-Dale relationship, measured α-β birefringence of 0.01 and measured 2V of 30(5)°. The optical orientation is X = c, Y = b, Z = a. The mineral is slightly pleochroic in shades of orange, with absorption: X > Y = Z. No dispersion was observed. Electron microprobe analysis provided PbO 50.07, TeO_3 22.64, UO_3 25.01, Cl 0.03, O≡Cl –0.01, total 97.74 wt%; the empirical formula (based on O+Cl = 8) is Pb_(2.05)U_(0.80)Te^(6+)_(1.18)O_(7.99)Cl_(0.01). The strongest powder X-ray diffraction lines are [d_(obs) in Å (hkl) I]: 3.235 (120, 102, 1[overbar]02) 100, 2.873 (200) 40, 2.985 (1[overbar]21, 112, 121) 37, 2.774 (022) 30, 3.501 (021, 012) 29, 2.220 (221, 2[overbar]21, 212) 23, 1.990 (222, 2[overbar]22) 21, and 1.715 (320) 22. The crystal structure (R_1 = 0.052) is based on sheets of corner-sharing uranyl square bipyramids and tellurate octahedra, with Pb atoms between the sheets. Markcooperite is the first compound to show Te^(6+) substitution for U^(6+) within the same crystallographic site. Markcooperite is structurally related to synthetic Pb(UO_2)O_2

CARMA: specifications and status

The Combined Array for Research in Millimeter-wave Astronomy (CARMA) is a 23-antenna heterogeneous millimeter array under construction in the White/Inyo Mountains of eastern California. CARMA will merge the existing Owens Valley and Berkeley-Illinois-Maryland Association arrays into a single instrument focusing on pure research, technology development and student training. A new high-altitude site will enable routine 205-265 GHz observing, and may allow observations in the 345 GHz window. Eight additional 3.5-m antennas from the University of Chicago will also be integrated into CARMA when not imaging the Sunyaev-Zel'dovich effect towards clusters of galaxies. At first light, the array will observe at 12, 3 and 1.3 mm using a mix of SIS and MMIC-based receivers. A new, highly flexible correlator incorporating reprogrammable FPGA technology will process configurable subsets of the antennas specified according to the science objectives. Leading-edge water vapor radiometers will be used to correct for atmospheric opacity and signal phase fluctuations. CARMA will be capable of both high resolution and wide-field imaging, covering a range of angular scales unmatched by any current or planned millimeter-wave instrument. The high sensitivity, sub-arcsecond angular resolution and excellent uv-coverage of CARMA will ensure major advances in studies of the universe. The array will provide high-fidelity resolved images of solar-system objects, protostars, protoplanetary disks, and galaxies both nearby and at high redshift - directly addressing many key research areas in astronomy and astrophysics

Lead-tellurium oxysalts from Otto Mountain near Baker, California: V. Timroseite, Pb_2Cu_5^(2+)(Te^(6+)O_6)_2(OH)_2, and paratimroseite, Pb_2Cu_4^(2+)(Te^(6+)O_6)_2(H_2O)_2, two new tellurates with Te-Cu polyhedral sheets

Timroseite, Pb_2Cu_5^(2+)(Te^(6+)O_6)_2(OH)_2, and paratimroseite, Pb_2Cu_4^(2+)(Te^(6+)O_6)_2(H_2O)_2, are two new tellurates from Otto Mountain near Baker, California. Timroseite is named in honor of Timothy (Tim) P. Rose and paratimroseite is named for its relationship to timroseite. Both new minerals occur on fracture surfaces and in small vugs in brecciated quartz veins. Timroseite is directly associated with acanthite, cerussite, bromine-rich chlorargyrite, chrysocolla, gold, housleyite, iodargyrite, khinite-4O, markcooperite, ottoite, paratimroseite, thorneite, vauquelinite, and wulfenite. Paratimroseite is directly associated with calcite, cerussite, housleyite, khinite-4O, markcooperite, and timroseite. Timroseite is orthorhombic, space group P2_1nm, a = 5.2000(2), b = 9.6225(4), c = 11.5340(5) Å, V = 577.13(4) Å^3, and Z = 2. Paratimroseite is orthorhombic, space group P2_12_12_1, a = 5.1943(4), b = 9.6198(10), c = 11.6746(11) Å, V = 583.35(9) Å^3, and Z = 2. Timroseite commonly occurs as olive to lime green, irregular, rounded masses and rarely in crystals as dark olive green, equant rhombs, and diamond-shaped plates in subparallel sheaf-like aggregates. It has a very pale yellowish green streak, dull to adamantine luster, a hardness of about 2 1/2 (Mohs), brittle tenacity, irregular fracture, no cleavage, and a calculated density of 6.981 g/cm^3. Paratimroseite occurs as vibrant "neon" green blades typically intergrown in irregular clusters and as lime green botryoids. It has a very pale green streak, dull to adamantine luster, a hardness of about 3 (Mohs), brittle tenacity, irregular fracture, good {001} cleavage, and a calculated density of 6.556 g/cm^3. Timroseite is biaxial (+) with a large 2V, indices of refraction > 2, orientation X = b, Y = a, Z = c and pleochroism: X = greenish yellow, Y = yellowish green, Z = dark green (Z > Y > X). Paratimroseite is biaxial (–) with a large 2V, indices of refraction > 2, orientation X = c, Y = b, Z = a and pleochroism: X = light green, Y = green, Z = green (Y = Z >> X). Electron microprobe analysis of timroseite provided PbO 35.85, CuO 29.57, TeO_3 27.75, Cl 0.04, H_2O 1.38 (structure), O≡Cl –0.01, total 94.58 wt%; the empirical formula (based on O+Cl = 14) is Pb_(2.07) Cu^(2+)_(4.80)Te^(6+)_(2.04)O_(12)(OH)_(1.98)Cl_(0.02). Electron microprobe analysis of paratimroseite provided PbO 36.11, CuO 26.27, TeO_3 29.80, Cl 0.04, H_2O 3.01 (structure), O≡Cl –0.01, total 95.22 wt%; the empirical formula (based on O+Cl = 14) is Pb_(1.94)Cu^(2+)_(3.96)Te^(6+)_(2.03)O_(12)(H_2O)_(1.99)Cl_(0.01). The strongest powder X-ray diffraction lines for timroseite are [d_(obs) in Å (hkl) I]: 3.693 (022) 43, 3.578 (112) 44, 3.008 (023) 84, 2.950 (113) 88, 2.732 (130) 100, 1.785 (multiple) 33, 1.475 (332) 36; and for paratimroseite 4.771 (101) 76, 4.463 (021) 32, 3.544 (120) 44, 3.029 (023,122) 100, 2.973 (113) 48, 2.665 (131) 41, 2.469 (114) 40, 2.246 (221) 34. The crystal structures of timroseite (R_1 = 0.029) and paratimroseite (R_1 = 0.039) are very closely related. The structures are based upon edge- and corner-sharing sheets of Te and Cu polyhedra parallel to (001) and the sheets in both structures are identical in topology and virtually identical in geometry. In timroseite, the sheets are joined to one another along c by sharing the apical O atoms of Cu octahedra, as well as by sharing edges and corners with an additional CuO_5 square pyramid located between the sheets. The sheets in paratimroseite are joined only via Pb-O and H bonds

Lead-tellurium oxysalts from Otto Mountain near Baker, California: VI. Telluroperite, Pb_3Te^(4+)O_4Cl_2, the Te analog of perite and nadorite

Telluroperite, Pb_3Te^(4+)O_4Cl_2, is a new tellurite from Otto Mountain near Baker, California. The new mineral occurs on fracture surfaces and in small vugs in brecciated quartz veins in direct association with acanthite, bromine-rich chlorargyrite, caledonite, cerussite, galena, goethite, and linarite. Various other secondary minerals occur in the veins, including six new tellurates, housleyite, markcooperite, paratimroseite, ottoite, thorneite, and timroseite. Telluroperite is orthorhombic, space group Bmmb, a = 5.5649(6), b = 5.5565(6), c = 12.4750(14) Å, V = 386.37(7) Å^3, and Z = 2. The new mineral occurs as rounded square tablets and flakes up to 0.25 mm on edge and 0.02 mm thick. The form {001} is prominent and is probably bounded by {100}, {010}, and {110}. It is bluish-green and transparent, with a pale bluish-green streak and adamantine luster. The mineral is non-fluorescent. Mohs hardness is estimated to be between 2 and 3. The mineral is brittle, with a curved fracture and perfect {001} cleavage. The calculated density based on the empirical formula is 7.323 g/cm^3. Telluroperite is biaxial (–), with very small 2V (~10°). The average index of refraction is 2.219 calculated by the Gladstone-Dale relationship. The optical orientation is X = c and the mineral exhibits moderate bluish-green pleochrosim; absorption: X < Y = Z. Electron microprobe analysis provided PbO 72.70, TeO_2 19.26, Cl 9.44, O≡Cl –2.31, total 99.27 wt%. The empirical formula (based on O+Cl = 6) is Pb_(2.79)Te_(1.03)^(4+)O_(3.72)Cl_(2.28). The six strongest powder X-ray diffraction lines are [d_(obs) in Å (hkl) I]: 3.750 (111) 58, 2.857 (113) 100, 2.781 (020, 200) 43, 2.075 (024, 204) 31, 1.966 (220) 30, and 1.620 (117, 313, 133) 52. The crystal structure (R_1 = 0.056) is based on the Sillén X_1 structure-type and consists of a three-dimensional structural topology with lead-oxide halide polyhedra linked to tellurium/lead oxide groups. The mineral is named for the relationship to perite and the dominance of Te (with Pb) in the Bi site of perite

Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura

BACKGROUND: A primary objective of comparative genomics is to identify genomic elements of functional significance that contribute to phenotypic diversity. Complex changes in genome structure (insertions, duplications, rearrangements, translocations) may be widespread, and have important effects on organismal diversity. Any survey of genomic variation is incomplete without an assessment of structural changes. RESULTS: We re-examine the genome sequences of the diverged species Drosophila melanogaster and D. pseudoobscura to identify fine-scale structural features that distinguish the genomes. We detect 95 large insertion/deletion events that occur within the introns of orthologous gene pairs, the majority of which represent insertion of transposable elements. We also identify 143 microinversions below 5 kb in size. These microinversions reside within introns or just upstream or downstream of genes, and invert conserved DNA sequence. The sequence conservation within microinversions suggests they may be enriched for functional genetic elements, and their position with respect to known genes implicates them in the regulation of gene expression. Although we found a distinct pattern of GC content across microinversions, this was indistinguishable from the pattern observed across blocks of conserved non-coding sequence. CONCLUSION: Drosophila has long been known as a genus harboring a variety of large inversions that disrupt chromosome colinearity. Here we demonstrate that microinversions, many of which are below 1 kb in length, located in/near genes may also be an important source of genetic variation in Drosophila. Further examination of other Drosophila genome sequences will likely identify an array of novel microinversion events

Discovery of malathion resistance QTL in Drosophila melanogaster using a bulked phenotyping approach

Drosophila melanogaster has proved an effective system with which to understand the evolutionary genetics and molecular mechanisms of insecticide resistance. Insecticide use has left signatures of selection in the fly genome, and both functional and quantitative genetic studies in the system have identified genes and variants associated with resistance. Here, we use D. melanogaster and leverage a bulk phenotyping and pooled sequencing “extreme quantitative trait loci” approach to genetically dissect variation in resistance to malathion, an organophosphate insecticide. We resolve 2 quantitative trait loci, one of which implicates allelic variation at the cytochrome P450 gene Cyp6g1, a strong candidate based on previous work. The second shows no overlap with hits from a previous genome-wide association study for malathion resistance, recapitulating other studies showing that different strategies for complex trait dissection in flies can yield apparently different architectures. Notably, we see no genetic signal at the Ace gene. Ace encodes the target of organophosphate insecticide inhibition, and genome-wide association studies have identified strong Ace-linked associations with resistance in flies. The absence of quantitative trait locus implicating Ace here is most likely because our mapping population does not segregate for several of the known functional polymorphisms impacting resistance at Ace, perhaps because our population is derived from flies collected prior to the widespread use of organophosphate insecticides. Our fundamental approach can be an efficient, powerful strategy to dissect genetic variation in resistance traits. Nonetheless, studies seeking to interrogate contemporary insecticide resistance variation may benefit from deriving mapping populations from more recently collected strains

Control of globally invasive common carp: a 10 year commercial trial of the Williams\u27 carp separation cage in a Murray River fishway

Common carp Cyprinus carpio, are a highly migratory pest fish in Australia, North America, New Zealand and parts of Europe. Fishways built to facilitate native fish passage also benefit invasive carp. The Williams’ cage was developed to separate carp from native fish as they pass through fishways by exploiting their unique jumping behaviour. We report on a 10-year commercial application in a fishway on the lower Murray River (SE Australia) where a high biomass of carp resides. Between November 2007 and April 2017, the automated Williams’ cage was installed and operated at Lock 1 by a collaborative team of river managers, weir keepers, commercial fishers and researchers. To date, over 700 tonnes of adult carp, (approx. 350,000 fish) have been removed at a maximum rate of 5 tonnes per day. The income generated from the sale of the fish has far exceeded set up costs. Catches and separation efficiencies were highest in spring (Austral) when fish were migrating to spawn. During the cage design phase, refinements helped reduce bycatch of non-target native fish to practically zero (0.03%) and informed future designs, application and operation. The Williams’ cage has now successfully moved from an experimental idea to full commercial viability and could play a key role in controlling the dispersal and abundance of carp where high abundances preside and collaborative management alliances can be formed

Dissecting Complex Traits Using the Drosophila Synthetic Population Resource

For most complex traits we have a poor understanding of the positions, phenotypic effects, and population frequencies of the underlying genetic variants contributing to their variation. Recently, several groups have developed multi-parent advanced intercross mapping panels in different model organisms in an attempt to improve our ability to characterize causative genetic variants. These panels are powerful and are particularly well suited to the dissection of phenotypic variation generated by rare alleles and loci segregating multiple functional alleles. We describe studies using one such panel, the Drosophila Synthetic Population Resource, and the implications for our understanding of the genetic basis of complex traits. In particular, we note that many loci of large effect appear to be multiallelic. If multiallelism is a general rule, analytical approaches designed to identify multiallelic variants should be a priority for both genome wide association studies and multi-parental panels

IUPHAR-DB: An Expert-Curated, Peer-Reviewed Database of Receptors and Ion Channels

The International Union of Basic and Clinical Pharmacology database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 non-sensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of about a third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry. Individual gene pages provide a comprehensive description of the genes and their functions, with information on protein structure, ligands, expression patterns, signaling mechanisms, functional assays and biologically important receptor variants (e.g. single nucleotide polymorphisms and splice variants). The phenotypes resulting from altered gene expression (e.g. in genetically altered animals) and genetic mutations are described. Links are provided to bioinformatics resources such as NCBI RefSeq, OMIM, PubChem, human, rat and mouse genome databases. Recent developments include the addition of ligand-centered pages summarising information about unique ligand molecules in IUPHAR-DB. IUPHAR-DB represents a novel approach to biocuration because most data are provided through manual curation of published literature by a network of over 60 expert subcommittees coordinated by NC-IUPHAR. Data are referenced to the primary literature and linked to PubMed. The data are checked to ensure accuracy and consistency by the curators, added to the production server using custom-built submission tools and peer-reviewed by NC-IUPHAR, before being transferred to the public database. Data are reviewed and updated regularly (at least biennially). Other website features include comprehensive database search tools, online and downloadable gene lists and links to recent publications of interest to the field, such as reports on receptor-ligand pairings. The database is freely available at &#x22;http://www.iuphar-db.org&#x22;:http://www.iuphar-db.org. Curators can be reached at curators [at] iuphar-db.org. We thank British Pharmacological Society, UNESCO (through the ICSU Grants Programme), Incyte, GlaxoSmithKline, Novartis, Servier and Wyeth for their support

Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources

Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster. The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that “burden tests” that test for the effect of TEs as a class may be more fruitful