ALBERT

Description: Pseudokinases lack conserved motifs typically required for kinase activity. Nearly half of pseudokinases bind ATP, but only few retain phosphotransfer activity, leaving the functional role of nucleotide binding in most cases unknown. Janus kinases (JAKs) are nonreceptor tyrosine kinases with a tandem pseudokinase–kinase domain configuration, where the pseudokinase domain (JAK homology 2, JH2) has important regulatory functions and harbors mutations underlying hematological and immunological diseases. JH2 of JAK1, JAK2, and TYK2 all bind ATP, but the significance of this is unclear. We characterize the role of nucleotide binding in normal and pathogenic JAK signaling using comprehensive structure-based mutagenesis. Disruption of JH2 ATP binding in wild-type JAK2 has only minor effects, and in the presence of type I cytokine receptors, the mutations do not affect JAK2 activation. However, JH2 mutants devoid of ATP binding ameliorate the hyperactivation of JAK2 V617F. Disrupting ATP binding in JH2 also inhibits the hyperactivity of other pathogenic JAK2 mutants, as well as of JAK1 V658F, and prevents induction of erythrocytosis in a JAK2 V617F myeloproliferative neoplasm mouse model. Molecular dynamic simulations and thermal-shift analysis indicate that ATP binding stabilizes JH2, with a pronounced effect on the C helix region, which plays a critical role in pathogenic activation of JAK2. Taken together, our results suggest that ATP binding to JH2 serves a structural role in JAKs, which is required for aberrant activity of pathogenic JAK mutants. The inhibitory effect of abrogating JH2 ATP binding in pathogenic JAK mutants may warrant novel therapeutic approaches.

Description: In adults, human hematopoietic stem and progenitor cells (HSPCs) reside in the bone marrow (BM) microenvironment. Our understanding of human hematopoiesis and the associated niche biology remains limited, due to human material accessibility and limits of existing in vitro culture models. The establishment of an in vitro BM system would offer an experimentally accessible and tunable platform to study human hematopoiesis. Here, we develop a 3D engineered human BM analog by recapitulating some of the hematopoietic niche elements. This includes a bone-like scaffold, functionalized by human stromal and osteoblastic cells and by the extracellular matrix they deposited during perfusion culture in bioreactors. The resulting tissue exhibited compositional and structural features of human BM while supporting the maintenance of HSPCs. This was associated with a compartmentalization of phenotypes in the bioreactor system, where committed blood cells are released into the liquid phase and HSPCs preferentially reside within the engineered BM tissue, establishing physical interactions with the stromal compartment. Finally, we demonstrate the possibility to perturb HSPCs’ behavior within our 3D niches by molecular customization or injury simulation. The developed system enables the design of advanced, tunable in vitro BM proxies for the study of human hematopoiesis.

Description: Sejkoraite-(Y), the triclinic (Y1.98Dy0.24){sum}2.22H0.34+ [(UO2)8O88O7OH(SO4)4](OH)(H2O)26, is a new member of the zippeite group from the [C]ervena vein, Jachymov (Street Joachimsthal) ore district, Western Bohemia, Czech Republic. It grows on altered surface of relics of primary minerals: uraninite, chalcopyrite, and tennantite, and is associated with pseudojohannite, rabejacite, uranopilite, zippeite, and gypsum. Sejkoraite-(Y) forms crystalline aggregates consisting of yellow-orange to orange crystals, rarely up to 1 mm in diameter. The crystals have a strong vitreous luster and a pale yellow-to-yellow streak. The crystals are very brittle with perfect {100} cleavage and uneven fracture. The Mohs hardness is about 2. The mineral is not fluorescent either in short- or long-wavelength UV radiation. Sejkoraite-(Y) is yellow, with no visible pleochroism, biaxial negative with {alpha}' = 1.62(2), {beta}' = 1.662(3), {gamma}' = 1.73(1), 2Vcalc = 79{degrees}. The empirical chemical formula (mean of 8 electron microprobe point analyses) was calculated on the basis of 12 (S + U) atoms: (Y1.49Dy0.17Gd0.11Er0.07Yb0.05Sm0.02){sum}1.90H0.54 + [(UO2)8.19O7OH(SO4)3.81](H2O)26.00. Sejkoraite-(Y) is triclinic, space group P[IMG]f1.gif" ALT="Formula" BORDER="0"〉, a = 14.0743(6), b = 17.4174(7), c = 17.7062(8) A, {alpha} = 75.933(4), {beta} = 128.001(5), {gamma} = 74.419(4){degrees}, V = 2777.00(19) A3, Z = 2, Dcalc = 4.04 g/cm3. The seven strongest reflections in the X-ray powder diffraction pattern are [dobs in A (I) (hkl)]: 9.28 (100) (100), 4.64 (39) (200), 3.631 (6) ([IMG]f1.gif" ALT="Formula" BORDER="0"〉42), 3.451 (13) ([IMG]f1.gif" ALT="Formula" BORDER="0"〉44), 3.385 (10) ([IMG]f2.gif" ALT="Formula" BORDER="0"〉[IMG]f3.gif" ALT="Formula" BORDER="0"〉2), 3.292 (9) (044), 3.904(7) (300), 2.984 (10) ([IMG]f1.gif" ALT="Formula" BORDER="0"〉[IMG]f3.gif" ALT="Formula" BORDER="0"〉2). The crystal structure of sejkoraite-(Y) has been solved by the charge flipping method from single-crystal X-ray diffraction data and refined to Robs = 0.060 with GOFobs = 2.38, based on 6511 observed reflections. The crystal structure consists of uranyl sulfate sheets of zippeite anion topology, which alternate with an interlayer containing Y3+(H2O)n polyhedra and uncoordinated H2O groups. Two yttrium atoms are linked to the sheet directly via uranyl oxygen atom, and the remaining one is bonded by hydrogen bonds only. In the Raman and infrared spectrum of sejkoraite-(Y) there are dominating stretching vibrations of SO4 tetrahedra (~1200-1100 cm-1), UO22+ stretching vibrations (~900-800 cm-1), and O-H stretching (~3500-3200 cm-1) and H-O-H bending modes (~1640 cm-1). The new mineral is named to honor Ji[r]i Sejkora, a Czech mineralogist of the National Museum in Prague.

Description: Allanite-(Nd), ideally CaNdAl2Fe2+(SiO4)(Si2O7)O(OH), the Nd-analog of allanite-(Ce), occurs in the Åskagen pegmatite, central Sweden. It forms fine-grained aggregates within altered thalénite-(Y). The other associated minerals include: iimoriite-(Y), keiviite-(Y), allanite-(Y), and tengerite-(Y). Allanite-(Nd) is biaxial (−); with refractive indices α = 1.723(5), β = 1.754(7), γ = 1.772(5), and measured 2V = 82°(±3°). Larger fragments of allanite-(Nd) are moderately pleochroic (α = pale grayish-brown, γ = grayish-brown); small fragments are colorless. Allanite-(Nd) is monoclinic, space group P21/m, with the following unit-cell parameters: a = 8.8897(5), b = 5.7308(2), c = 10.1010(6) Å, β = 115.166(7)°, V = 465.75(4) Å3, Z = 2. The strongest five peaks from the X-ray powder diffraction patterns [d (Å)(I)(hkl)] are: 3.51(46)(2̄11), 2.89(100)(1̄13), 2.87(45)(020), 2.70(60)(120), 2.61(60)(3̄11). Allanite-(Nd) has a density of 3.98 g/cm3, vitreous luster, grayish-brown streak, and the Mohs hardness is ca. 6. It is brittle, with imperfect cleavage, and conchoidal fracture. The Mössbauer spectroscopy revealed Fe3+/Fetot ratio of 0.27 in the type sample. The refined empirical formula of the crystal used for the structure determination is: The allanite-(Nd) was approved by CNMNC (IMA 2010-060).

Description: The infrared (IR) spectra of gem-quality xenotime crystals containing considerable amounts of rare earth elements (REEs), are characterized by sharp and strongly pleochroic absorption bands in the 3650-3350 cm-1 region. In contrast, the spectra of partially metamict samples are dominated by a broad band centered at around 3450 cm-1. Xenotime presents the interesting case of a nominally anhydrous mineral, where the OH stretching frequency region of weakly hydrogen-bonded OH groups is overlapped by absorption bands due to low-energetic f-f electron transitions of REEs, especially of dysprosium. In polarized spectra measured parallel to the c-axis, Dy shows a prominent sharp band at 3519 cm-1. The assignment of the REE bands is based on the polarized IR spectra of REE doped xenotime single crystals, which have been synthesized by the flux method. A single band at 3480 cm-1, strongly polarized perpendicular to the c-axis, is assigned to the stretching vibration of an OH group. Deuteration experiments performed at 950 {degrees}C prove the assignment of this band and the presence of additional structural OH groups, appearing at annealing temperatures above 500 {degrees}C. Models of the OH point defect incorporation into the crystal structure of xenotime can be derived on the basis of fully occupied cation sites and under the assumption of Y- and P-site vacancies. The water content of the gem-quality samples ranges from 5 to 10 wt ppm and for the partially metamict samples from 370 wt ppm to 1.7 wt% H2O.

Description: The crystal structure of natural zippeite, K1.85H+0.15[(UO2)4O2(SO4)2OH2](H2O)4, from Jachymov, Czech Republic, has been determined by single-crystal X-ray diffraction and refined to R1 = 0.0367. Zippeite is monoclinic, space group C2/m, with a 8.7802(6), b 13.9903(12), c 8.8630(6) A, {beta} 104.524(7){degrees}, V 1053.92(12) A3 and Z = 2. The structure consists of structural sheets of the zippeite uranyl anion topology and an interlayer, in which split K+ atoms and disordered O atoms (of the H2O groups) are located. The structure unit [(UO2)4O2(SO4)2OH2]2- is novel for both natural and synthetic compounds, but generally consistent with the known zippeite-type structures. The structural formula is in agreement with bond-valence analysis and the results of an electron-microprobe study. The composition of the zippeite specimen studied is assessed from the point of view of the bond-valence approach. Further, we comment on morphology of zippeite, its optical properties, and its relationship to the crystal structure.

Description: Tourmalines (dravite - schorl - uvite - povondraite) from intragranitic pegmatites of the T[r]ebi[c] Pluton (porphyritic, amphibole-biotite melasyenite to quartz melasyenite - melagranite), in the Czech Republic, were examined using an electron microprobe, Mossbauer spectroscopy and LA-ICP-MS analyses. Pegmatites with the common assemblage Kfs + qtz + pl (An0-13) + Fe-rich phlogopite (0.49 〈 XMg 〈 0.70) and accessory allanite-(Ce), ilmenite, tourmaline and titanite, were divided into three types generally related to the NYF (REL-REE) pegmatites: allanite-type, euxenite-type (+ euxenite, aeschynite, pyrochlore, beryl, niobian rutile, zircon), and the most evolved euxenite-type pegmatite, Klu[c]ov I (with annite, XMg 0.09), cassiterite, herzenbergite, and abundant graphic intergrowths of quartz + feldspars and quartz + tourmaline). Black tourmaline occurs in several distinct morphological, paragenetic and textural types with very high variability in zoning; however, the morphological types of tourmaline do not differ chemically. They generally show two distinct trends: Fetot/(Fetot + Mg) = 0.243-0.882, 0.657-0.978; Altot = 5.039-6.464, 5.040-7.030 apfu; Ca [≤]0.508, [≤]0.174 apfu; Mn [≤]0.079, [≤]0.445, respectively. High concentrations of Ti [≤]0.490, [≤]0.361 apfu are typical, as well as low F, [≤]0.288, 0.046-0.508 apfu, and low vacancy at the X site, 0.152, 0.348 pfu, respectively. Mossbauer spectroscopy revealed ~21% of the Fe as Fe3+ for allanite-type, 17 to 26% for euxenite-type, and 22% for tourmaline from the pegmatite Klu[c]ov I, respectively, values that are high relative to ordinary granitic pegmatites. Our LA-ICP-MS study revealed highly variable concentrations of the individual trace elements within single grains and within the individual types of pegmatites. Explicit compositional evolution from less to highly evolved pegmatites was revealed only rarely, e.g., increase in Ni, Co, Zn, Ga, Sc and Ce from less to more evolved pegmatites. Two distinct sets of substitutions are dominant: R3+O R2+ -1(OH) -1 and {square}R3+ Na-1R2+ -1. In addition, there are minor substitutions, CaR2+ Na-1Al-1, Fe2+ Mg-1 and MnF Fe2+ -1(OH) -1, the latter exclusively at Klu[c]ov I. They are similar to those from ordinary Li-poor to slightly Li-enriched granitic pegmatites. Tourmalines from allanite-type and euxenite-type pegmatites exhibit less convincing plots, with the dominant substitutions CaR2+ 3O2 Na-1R3+ -3(OH)-2 and Fe2+ Mg-1, and minor Al Fe3+ -1. High contents of Ti4+ imply the presence of the component XCa2+ YR2+ 1.5 YTi1.5 ZR3+ 5 ZMg2+ Si6O18 (BO3)3O3(OH). These substitutions are different from those normally encountered in granitic pegmatites, but show some features of non-pegmatitic Fe3+-enriched tourmalines. Textural relations suggest very late solidus to early subsolidus origin of the tourmaline. Discussions of a tourmaline's stability in moderately aluminous granitic systems is shifted to the role of tourmaline composition along with the melt's composition.

Description: The previously published structure determination of weeksite from the Anderson mine, Arizona, U.S.A., suggested that it is orthorhombic, Cmmb, with a = 14.209(2), b = 14.248(2), c = 35.869(4) Å, and V = 7262(2) Å3, and an ideal chemical formula (K,Ba)1–2(UO2)2(Si5O13)·H2O. Using single-crystal X-ray diffraction, electron microprobe analysis, and thermal analysis, we reexamined weeksite from the same locality. Our results demonstrate that weeksite is monoclinic, with the space group C2/m and unit-cell parameters a = 14.1957(4), b = 14.2291(5), c = 9.6305(3) Å, ß = 111.578(3)°, V = 1808.96(10) Å3, and an ideal formula K2(UO2)2(Si5O13)·4H2O. The previously reported orthorhombic unit cell is shown to result from twinning of the monoclinic cell. The structure refinement yielded R1 = 2.84% for 1632 observed reflections [Iobs 〉 3s(I)] and 5.42% for all 2379 reflections. The total H2O content derived from the structure refinement agrees well with that from the thermal analysis. Although the general topology of our structure resembles that reported previously, all Si sites in our structure are fully occupied, in contrast to the previous structure determination, which includes four partially occupied SiO4 tetrahedra. From our structure data on weeksite, it appears evident that the orthorhombic cell of the newly discovered weeksite-type mineral coutinhoite, ThxB1-2x(UO2)2Si5O13·3H2O, needs to be reevaluated.