Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi

Thermogravimetric analysis and hot-stage Raman spectroscopy of cubic indium hydroxide

The transition of cubic indium hydroxide to cubic indium oxide has been studied by thermogravimetric analysis complimented with hot stage Raman spectroscopy. Thermal analysis shows the transition of In(OH)3 to In2O3 occurs at 219°C. The structure and morphology of In(OH)3 synthesised using a soft chemical route at low temperatures was confirmed by X-ray diffraction and scanning electron microscopy. A topotactical relationship exists between the micro/nano-cubes of In(OH)3 and In2O3. The Raman spectrum of In(OH)3 is characterised by an intense sharp band at 309 cm-1 attributed to ν1 In-O symmetric stretching mode, bands at 1137 and 1155 cm-1 attributed to In-OH δ deformation modes, bands at 3083, 3215, 3123 and 3262 cm-1 assigned to the OH stretching vibrations. Upon thermal treatment of In(OH)3 new Raman bands are observed at 125, 295, 488 and 615 cm-1 attributed to In2O3. Changes in the structure of In(OH)3 with thermal treatment is readily followed by hot stage Raman spectroscopy

Thermal stability of the 'cave' mineral ardealite Ca2(HPO4)(SO4).4H2O

Thermogravimetry combined with evolved gas mass spectrometry has been used to characterise the mineral ardealite and to ascertain the thermal stability of this ‘cave’ mineral. The mineral ardealite Ca2(HPO4)(SO4)•4H2O is formed through the reaction of calcite with bat guano. The mineral shows disorder and the composition varies depending on the origin of the mineral. Thermal analysis shows that the mineral starts to decompose over the temperature range 100 to 150°C with some loss of water. The critical temperature for water loss is around 215°C and above this temperature the mineral structure is altered. It is concluded that the mineral starts to decompose at 125°C, with all waters of hydration being lost after 226°C. Some loss of sulphate occurs over a broad temperature range centred upon 565°C. The final decomposition temperature is 823°C with loss of the sulphate and phosphate anions

Synthesis and thermal analysis of indium-based hydrotalcites of formula Mg6In2(CO3)(OH)16.4H2O

Insight into the unique structure of layered double hydroxides has been obtained using a combination of X-ray diffraction and thermal analysis. Indium containing hydrotalcites of formula Mg4In2(CO3)(OH)12•4H2O (2:1 In-LDH) through to Mg8In2(CO3)(OH)18•4H2O (4:1 In-LDH) with variation in the Mg:In ratio have been successfully synthesised. The d(003) spacing varied from 7.83 Å for the 2:1 LDH to 8.15 Å for the 3:1 indium containing layered double hydroxide. Distinct mass loss steps attributed to dehydration, dehydroxylation and decarbonation are observed for the indium containing hydrotalcite. Dehydration occurs over the temperature range ambient to 205 °C. Dehydroxylation takes place in a series of steps over the 238 to 277 °C temperature range. Decarbonation occurs between 763 and 795 °C. The dehydroxylation and decarbonation steps depend upon the Mg:In ratio. The formation of indium containing hydrotalcites and their thermal activation provides a method for the synthesis of indium oxide based catalysts

Synthesis and thermal stability of hydrotalcites based upon gallium

Hydrotalcites based upon gallium as a replacement for aluminium in hydrotalcite over a Mg/Al ratio of 2:1 to 4:1 were synthesised. The d(003) spacing varied from 7.83 A ° for the 2:1 hydrotalcite to 8.15 A ° for the 3:1 gallium containing hydrotalcite. A comparison is made with the Mg Al hydrotalcite in which the d(003) spacing for the Mg/Al hydrotalcite varied from 7.62 A ° for the 2:1Mg hydrotalcite to 7.98 A ° for the 4:1 hydrotalcite. The thermal stability of the gallium containing hydrotalcite was determined using thermogravimetric analysis. Four mass loss steps at 77, 263–280,485 and 828 degrees C with mass losses of 10.23, 21.55, 5.20 and 7.58% are attributed to dehydration, dehydroxylation and decarbonation. The thermal stability of the galliumcontaining hydrotalcite is slightly less than the aluminium hydrotalcite

Thermoanalytical studies of natural potassium, sodium and ammonium alunites

Dynamic and controlled rate thermal analysis (CRTA) has been used to characterise alunites of formula [M(Al)3(SO4)2(OH)6 ] where M+ is the cations K+, Na+ or NH4+. Thermal decomposition occurs in a series of steps. (a) dehydration, (b) well defined dehydroxylation and (c) desulphation. CRTA offers a better resolution and a more detailed interpretation of water formation processes via approaching equilibrium conditions of decomposition through the elimination of the slow transfer of heat to the sample as a controlling parameter on the process of decomposition. Constant-rate decomposition processes of water formation reveal the subtle nature of dehydration and dehydroxylation

Synthesis and characterization of cobalt hydroxide, cobalt oxyhydroxide, and cobalt oxide nanodiscs

Cobalt hydroxide, cobalt oxyhydroxide and cobalt oxide nanomaterials were synthesized through simple soft chemistry. The cobalt hydroxide displays hexagonal morphology with clear edges 20 nm long. This morphology and nanosize is retained through to cobalt oxide Co3O4 through a topotactical relationship. Cobalt oxyhydroxide and cobalt oxide nanomaterials were synthesized through oxidation and low temperature calcination from the as-prepared cobalt hydroxide. Characterisation of these cobalt-based nanomaterials were fully developed, including X-ray diffraction, transmission electron microscopy combined with selected area electron diffraction, scanning electron microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, and thermal gravimetric analysis. Bonding of the divalent cobalt hydroxide from the oxyhydroxide and oxides by studying their high resolution XPS spectra for Co 2p3/2 and O 1s. Raman spectroscopy of the as-prepared Co(OH)2, CoO(OH) and Co3O4 nanomaterials characterised each material. The thermal stability of the materials Co(OH)2 and CoO(OH) were established. This research has developed methodology for the synthesis of cobalt oxide and cobalt oxyhydroxide nanodiscs at low temperatures