ALBERT

Description: Ecological succession reveals potential signatures of marine–terrestrial transition in salt marsh fungal communities The ISME Journal 10, 1984 (August 2016). doi:10.1038/ismej.2015.254 Authors: Francisco Dini-Andreote, Victor Satler Pylro, Petr Baldrian, Jan Dirk van Elsas & Joana Falcão Salles

Description: Increasing evidence suggests that overlapping genes are much more common in eukaryotic genomes than previously thought. These different-strand overlapping genes are potential sense–antisense (SAS) pairs, which might have regulatory effects on each other. In the present study, we identified the SAS loci in the equine genome using previously generated stranded, paired-end RNA sequencing data from the equine chorioallantois. We identified a total of 1261 overlapping loci. The ratio of the number of overlapping regions to chromosomal length was numerically higher on chromosome 11 followed by chromosomes 13 and 12. These results show that overlapping transcription is distributed throughout the equine genome, but that distributions differ for each chromosome. Next, we evaluated the expression patterns of SAS pairs during the course of gestation. The sense and antisense genes showed an overall positive correlation between the sense and antisense pairs. We further provide a list of SAS pairs with both positive and negative correlation in their expression patterns throughout gestation. This study characterizes the landscape of sense and antisense gene expression in the placenta for the first time and provides a resource that will enable researchers to elucidate the mechanisms of sense/antisense regulation during pregnancy.

Description: Tapiaite (IMA2014-024), Ca 5 Al 2 (AsO 4 ) 4 (OH) 4 ·12H 2 O, is a new mineral from the Jote mine, Tierra Amarilla, Copiapó Province, Atacama, Chile. The mineral is a late-stage, low-temperature, secondary mineral occurring with conichalcite, joteite, mansfieldite, pharmacoalumite, pharmacosiderite and scorodite in narrow seams and vughs in the oxidized upper portion of a hydrothermal sulfide vein hosted by volcanoclastic rocks. Crystals occur as colourless blades, flattened on {101I} and elongated and striated along [010], up to ~0.5 mm long, and exhibiting the forms {101I}, {101} and {111}. The blades are commonly intergrown in subparallel bundles and less commonly in sprays. The mineral is transparent and has a white streak and vitreous lustre. The Mohs hardness is estimated to be between 2 and 3, the tenacity is brittle, and the fracture is splintery. It has two perfect cleavages on {101} and {101I}. The calculated density based on the empirical formula is 2.681 g cm –3 . It is optically biaxial (+) with α = 1.579(1), β = 1.588(1), = 1.610(1) (white light), 2V meas = 66(2)° and 2V calc = 66°. The mineral exhibits no dispersion. The optical orientation is X [101I]; Y = b, Z [101]. The electron-microprobe analyses (average of five) provided: Na 2 O 0.09, CaO 24.96, CuO 0.73, Al 2 O 3 10.08, Fe 2 O 3 0.19, As 2 O 5 40.98, Sb 2 O 5 0.09, H 2 O 23.46 (structure), total 100.58 wt.%. In terms of the structure, the empirical formula (based on 32 O a.p.f.u.) is (Ca 4.83 $${\mathrm{Cu}}_{0.10}^{2+}$$ Na 0.03 ) 4.96 (Al 2.14 $${\mathrm{Fe}}_{0.03}^{3+}$$ ) 2.17 [( $${\mathrm{As}}_{3.87}^{5+}$$ $${\mathrm{Sb}}_{0.01}^{5+}$$ ) 3.88 O 16 ][(OH) 3.76 (H 2 O) 0.24 ] 4 (H 2 O) 10 ·2H 2 O. The mineral is easily soluble in RT dilute HCl. Tapiaite is monoclinic, P 2 1 / n , with unit-cell parameters a = 16.016(1), b = 5.7781(3), c = 16.341(1) Å, β = 116.704(8)°, V = 1350.9(2) Å 3 and Z = 2. The eight strongest lines in the powder X-ray diffraction pattern are [ d obs Å ( I )( hkl )]: 13.91(100)(1I01), 7.23(17)(200,002), 5.39(22)(110,011), 4.64(33)(1I12,2I11,3I03), 3.952(42)(1I13,3I11,2I13), 3.290(35)(2I14,4I12,1I14,4I11), 2.823(39)(303,3I15) and 2.753(15)(5I13,1I15,121,5I11). The structure of tapiaite ( R 1 = 5.37% for 1733 F o 〉 4 F ) contains Al(AsO 4 )(OH) 2 chains of octahedra and tetrahedra that are topologically identical to the chain in the structure of linarite. CaO 8 polyhedra condense to the chains, forming columns, which are decorated with additional peripheral AsO 4 tetrahedra. The CaO 8 polyhedra in adjacent columns link to one another by corner-sharing to form thick layers parallel to {101I} and the peripheral AsO 4 tetrahedra link to CaO 6 octahedra in the interlayer region, resulting in a framework structure.

Description: Bariopharmacoalumite, ideally Ba0.5Al4(AsO4)3(OH)4{middle dot}4H2O, is a new mineral from Cap Garonne, France. It occurs in several places within the mine as colourless to pale yellow interpenetrating cubes up to 0.5 mm across. Bariopharmacoalumite is transparent to translucent, with a white streak, has an adamantine lustre and imperfect cleavage on {001}. The Vickers hardness is 234.35 and the Mohs harness is 3.5. Bariopharmacoalumite is isotropic, with n = 1.573 (upper estimate) [calculated from reflectance values at 589 nm using Fresnel Equations]. The empirical formula, based on 20 oxygen atoms, is: (Ba0.54Cu0.03K0.01){Sigma}0.58(Al3.99Fe0.02){Sigma}4.01(AsO4)3.00(OH)3.85O0.15{middle dot}4H2O and the calculated density (on the basis of the empirical formula and single-crystal unit cell) is 2.580 g/cm3. The four strongest lines in the X-ray powder diffraction pattern are [dobs(A), Iobs,(hkl)]: 7.759, 100, (001); 5.485, 27, (011); 3.878, 27, (002); 4.454, 18, (011). Bariopharmacoalumite from Cap Garonne is cubic, space group P[IMG]f1.gif" ALT="Formula" BORDER="0"〉3m with a = 7.742(4) A, V = 464.2(4) A3 and Z = 1. The crystal structure was solved by direct methods and refined to R1 = 0.0705 for 215 reflections with I 〉 4{sigma}(I) and is consistent with members of the pharmacosiderite supergroup. Data are also presented from zoned bariopharmacoalumite-bariopharmacosiderite crystals found at the Mina Grande mine, Chile.

Description: High blood urea nitrogen (BUN) decreases fertility of several mammals; however, the mechanisms have not been investigated in mares. We developed an experimental model to elevate BUN, with urea and control treatments (7 mares/treatment), in a crossover design. Urea-treatment consisted of a loading dose of urea (0.03 g/kg of body weight (BW)) and urea injections over 6 hours (0.03 g/kg of BW/h). Control mares received the same volume of saline solution. Blood samples were collected to measure BUN. Uterine and vaginal pH were evaluated after the last intravenous infusion, then endometrial biopsies were collected for RNA-sequencing with a HiSeq 4000. Cuffdiff (2.2.1) was used to identify the differentially expressed genes (DEG) between urea and control groups (false discovery rate-adjusted p-value 〈 0.1). There was a significant increase in BUN and a decrease of uterine pH in the urea group compared to the control group. A total of 193 genes were DEG between the urea and control groups, with five genes identified as upstream regulators (ETV4, EGF, EHF, IRS2, and SGK1). The DEG were predicted to be related to cell pH, ion homeostasis, changes in epithelial tissue, and solute carriers. Changes in gene expression reveal alterations in endometrial function that could be associated with adverse effects on fertility of mares.

Description: The different generations of calc-silicate assemblages formed during sequential metasomatic events make the Campiglia Marittima magmatic–hydrothermal system a prominent case study to investigate the mobility of rare earth element (REE) and other trace elements. These mineralogical assemblages also provide information about the nature and source of metasomatizing fluids. Petrographic and geochemical investigations of granite, endoskarn, and exoskarn bodies provide evidence for the contribution of metasomatizing fluids from an external source. The granitic pluton underwent intense metasomatism during post-magmatic fluid–rock interaction processes. The system was initially affected by a metasomatic event characterized by circulation of K-rich and Ca(-Mg)-rich fluids. A potassic metasomatic event led to the complete replacement of magmatic biotite, plagioclase, and ilmenite, promoting major element mobilization and crystallization of K-feldspar, phlogopite, chlorite, titanite, and rutile. The process resulted in significant gain of K, Rb, Ba, and Sr, accompanied by loss of Fe and Na, with metals such as Cu, Zn, Sn, W, and Tl showing significant mobility. Concurrently, the increasing fluid acidity, due to interaction with Ca-rich fluids, resulted in a diffuse Ca-metasomatism. During this stage, a wide variety of calc-silicates formed (diopside, titanite, vesuvianite, garnet, and allanite), throughout the granite body, along granite joints, and at the carbonate–granite contact. In the following stage, Ca-F-rich fluids triggered the acidic metasomatism of accessory minerals and the mobilization of high-field-strength elements (HFSE) and REE. This stage is characterized by the exchange of major elements (Ti, Ca, Fe, Al) with HFSE and REE in the forming metasomatic minerals (i.e., titanite, vesuvianite) and the crystallization of HFSE-REE minerals. Moreover, the observed textural disequilibrium of newly formed minerals (pseudomorphs, patchy zoning, dissolution/reprecipitation textures) suggests the evolution of metasomatizing fluids towards more acidic conditions at lower temperatures. In summary, the selective mobilization of chemical components was related to a shift in fluid composition, pH, and temperature. This study emphasizes the importance of relating field studies and petrographic observations to detailed mineral compositions, leading to the construction of litho-geochemical models for element mobilization in crustal magmatic-hydrothermal settings.

Description: Climate change affects key nitrogen-fixing bacterial populations on coral reefs The ISME Journal 8, 2272 (November 2014). doi:10.1038/ismej.2014.70 Authors: Henrique F Santos, Flávia L Carmo, Gustavo Duarte, Francisco Dini-Andreote, Clovis B Castro, Alexandre S Rosado, Jan Dirk van Elsas & Raquel S Peixoto

Description: The new mineral canutite (IMA2013-070), NaMn 3 [AsO 4 ][AsO 3 (OH)] 2 , was found at two different locations at the Torrecillas mine, Salar Grande, Iquique Province, Chile, where it occurs as a secondary alteration phase in association with anhydrite, halite, lavendulan, magnesiokoritnigite, pyrite, quartz and scorodite. Canutite is reddish brown in colour. It forms as prisms elongated on [201I] and exhibiting the forms {010}, {100}, {102}, {201} and {102I}, or as tablets flattened on {102} and exhibiting the forms {102} and {110}. Crystals are transparent with a vitreous lustre. The mineral has a pale tan streak, Mohs hardness of 21/2, brittle tenacity, splintery fracture and two perfect cleavages, on {010} and {101}. The calculated density is 4.112 g cm –3 . Optically, canutite is biaxial (+) with α = 1.712(3), β = 1.725(3) and = 1.756(3) (measured in white light). The measured 2V is 65.6(4)°, the dispersion is r 〈 v (slight), the optical orientation is Z = b ; X ^ a = 18° in obtuse β and pleochroism is imperceptible. The mineral is slowly soluble in cold, dilute HCl. The empirical formula (for tabular crystals from near the mine shaft), determined from electron-microprobe analyses, is (Na 1.05 Mn 2.64 Mg 0.34 Cu 0.14 Co 0.03 ) 4.20 As 3 O 12 H 1.62 . Canutite is monoclinic, C 2/ c , a = 12.3282(4), b = 12.6039(5), c = 6.8814(5) Å, β = 113.480(8)°, V = 980.72(10) Å 3 and Z = 4. The eight strongest X-ray powder diffraction lines are [ d obs Å( I )( hkl )]: 6.33(34)(020), 4.12(26)(2I21), 3.608(29)(310,1I31), 3.296(57)(1I12), 3.150(28)(002,131), 2.819(42)(400,041,330), 2.740(100)(240,4I02,112) and 1.5364(31)(multiple). The structure, refined to R 1 = 2.33% for 1089 F o 〉 4 F reflections, shows canutite to be isostructural with protonated members of the alluaudite group.

Description: Type specimens of the molybdoarsenates betpakdalite, natrobetpakdalite and obradovicite and the molybdophosphates mendozavilite, paramendozavilite and melkovite, and similar material from other sources, have been examined in an effort to elucidate the relations among these phases, which we designate as the heteropolymolybdate family of minerals. Using electron microprobe analysis, X-ray powder diffraction and single-crystal X-ray diffraction with crystal structure determination where possible, it was found that natrobetpakdalite, mendozavilite and melkovite are isostructural with betpakdalite and that obradovicite has a closely related structure.The betpakdalite and obradovicite structure types are based on frameworks containing four-member clusters of edge-sharing MoO6 octahedra that link by sharing corners with other clusters, with Fe3+O6 octahedra and with PO4 or AsO4 tetrahedra (T). The structures differ in the linkages through the Fe3+O6 octahedra, which produce different but closely related framework configurations. The structures contain two types of non-framework cation sites, which are designated A and B. In general, there are two or more A sites partially occupied by disordered, generally larger cations that are coordinated to O atoms in the framework and to H2O molecules. The B site is occupied by a smaller cation that is octahedrally coordinated to H2O molecules. The general formula for minerals with either the betpakdalite or the obradovicite structure is: [A2(H2O)nB(H2O)6][Mo8T2 O30+7(OH)7–x], where x is the total charge of the cations in the A and B sites (+3 to +7) and n is variable, ideally 17 for arsenates and 15 for phosphates. The ideal total number of A cations is defined as 2 in the general formula, but varies from 1 to 3.8 in analysed samples. Dominant cations at the A site include K, Na and Ca and at the B site Na, Ca, Mg, Cu and Fe. The combinations that have been identified in this study define six new heteropolymolybdate species.A suffix-based nomenclature scheme is established for minerals of the betpakdalite, mendozavilite and obradovicite groups, with the following root names based on the structure types and the T-site cations: betpakdalite (T = As), mendozavilite (T = P) and obradovicite (T = As). Two suffixes of the form -AB, corresponding to the dominant cations in the two different types of non-framework cation sites complete the species name. The historical name melkovite is retained rather than introducing mendozavilite-CaCa.Our investigation of the paramendozavilite type specimen revealed no paramendozavilite, but an apparently closely related new mineral; however, another sample of paramendozavilite analysed had K 〉 Na.