New species and biostratigraphic significance of middle Palaeozoic brachiopod genus Linguopugnoides Havliček

Linguopugnoides Havli?ek 1960, originally based on 3 Early Devonian (Lochkovian‐Pragian) species from the Czech Republic, is now construed as embracing at least 25 species distributed over all northern hemisphere continents as well as Australia, and extending from late Llandovery to early Emsian. Species‐diversity peaked during the Lochkovian when the genus was widespread, with 15 species having been reported. Four species are described as new. L. praecarens sp.nov. from the latest Silurian (Pridoli) of the Turkestan Range (South Tien Shan) is considered to be ancestral to the numerous, mainly late Lochkovian‐Pragian forms that appeared during the great diversification of the genus during the early Devonian. Three new species are described from the Lochkovian of the Zeravshan Range, Uzbekistan: L. rectiplicatus, L. diversiplicatus as well as the previously figured but not described L. kimi Rzhonsnitskaya. Species of Linguopugnoides have biostratigraphic and biogeographic significance and have obvious value for inter‐regional correlation.     

Evolutionary History of Eukaryotic α-Glucosidases from the α-Amylase Family

Although some α-glucosidases from the α-amylase family (glycoside hydrolase family GH13) have been studied extensively, their exact number, organization on the chromosome, and orthology/paralogy relationship were unknown. This was true even for important disease vectors where gut α-glucosidase is known to be receptor for the Bin toxin used to control the population of some mosquito species. In some cases orthologs from related species were studied intensively, while potentially important paralogs were omitted. We have, therefore, used a bioinformatics approach to identify all family GH13 α-glucosidases from the selected species from Metazoa (including three mosquito species: Aedes aegypti, Anopheles gambiae, and Culex quinquefasciatus) as well as from Fungi in an effort to characterize their arrangement on the chromosome and evolutionary relationships among orthologs and among paralogs. We also searched for pseudogenes and genes coding for enzymatically inactive proteins with a possible new function. We have found GH13 α-glucosidases mostly in Arthropoda and Fungi where they form gene families, as a result of multiple lineage-specific gene duplications. In mosquito species we have identified 14 α-glucosidase (Aglu) genes of which only five have been biochemically characterized so far, two are putative pseudogenes and the rest remains uncharacterized. We also revealed quite a complex evolutionary history of the eukaryotic α-glucosidases probably involving multiple losses of genes or horizontal gene transfer from bacteria.     

Phylogenomic Analysis of the α Proteasome Gene Family from Early-Diverging Eukaryotes

We employed a phylogenomic approach to study the evolution of α subunits of the proteasome gene family from early diverging eukaryotes. BLAST similarity searches of the Giardia lamblia genome identified all seven α proteasome genes characteristic of eukaryotes from the crown group. In addition, a PCR strategy for the amplification of multiple α subunit sequences generated single α proteasome products for representatives of the Kinetoplastida (Leishmania major), the Parabasalia (Trichomonas vaginalis), and the Microsporidia (Vairimorpha sp., Nosema sp., Endoreticulata sp., and Spraguea lophii). The kinetoplastid Trypanosoma cruzi and the eukaryote crown group Acanthamoeba castellanii yielded two distinct α proteasome genes each. The presence of seven distinct α proteasome genes in G. lamblia, one of the earliest-diverging eukaryotes, indicates that the α proteasome gene family evolved rapidly from a minimum of one gene in Archaea to seven or more in Eukarya. Results from the phylogenomic analysis are consistent with the idea that the Diplomonida (as represented by G. lamblia), the Kinetoplastida, the Parabasalia, and the Microsporidia diverged after the duplication events that originated the α proteasome gene family. A model for the early origin and evolution of the proteasome gene family is presented. Received: 14 February 2000 / Accepted: 14 August 2000     

Bacterial communities in the 'petola' microbial mat from the Sečovlje salterns (Slovenia)

The Se?ovlje saltern is one of the few remaining solar salterns for traditional, seasonal salt production. The bottom of the crystallizer ponds is covered with a microbial mat, known as the 'petola', that has continuously been cultivated from medieval times. Outside the salt production season, the petola is fertilized with anoxic marine mud and covered with saline water; during the season, it is covered by brine. Here, we have applied culture-independent techniques and microelectrode-based activity measurements to study the bacterial communities in three different layers of the petola during the peak of the harvesting season. For reference, we used nonactive petola that had been abandoned for several years. The upper 2 mm of the petola were dominated by the cyanobacterial species Coleofasciculus chthonoplastes and the Phormidium/Lyngbya group, and Gammaproteobacteria (Acinetobacter sp.), while the third anoxic layer was dominated by as yet uncultured phyla. The nonactive petola showed a higher biodiversity. Oxygen and sulfide concentrations differed between the mats studied, in terms of the depth of oxygen penetration and diel changes. This study provides the first molecular insight into the microbiology of the petola, and it represents an important contribution towards understanding the geomicrobiological cycles of the traditional Se?ovlje saltern.     

A re-examination of the human fossil specimen from Bački Petrovac (Serbia)

A fragmented human calotte was discovered during the early 1950s near Ba?ki Petrovac (Serbia), in association with Palaeolithic stone tools. After its initial publication, the fossil specimen remained largely unknown outside of the Serbian academe and no detailed comparative study has ever been carried out. Since the whereabouts of the fossil itself are currently unknown, and given its potential significance for the Pleistocene human evolution, we re-examine the data published by 0255 and 0260. Using the original measurements, mostly taken on the frontal bone, and a wide comparative sample of 68 fossil specimens, the fossil was compared and analyzed by statistical multivariate methods. We also conducted a visual examination of the morphology based on the available photographic material. Our analysis reveals phenetic similarity with Middle Pleistocene archaic Homo from Africa and anatomically modern Homo sapiens. However, the absence of primitive cranial traits in Ba?ki Petrovac indicates a clear modern Homo sapiens designation. Although lost at the moment, there is a chance for the re-discovery of the fossil in the years to come. This would give us an opportunity to acquire absolute dates and to study the specimen in a more detailed manner.     

Revision of Cretaceous Radiolarians of the Family Hagiastridae from Lipman’s Collection

Based on the Lipman’s hagiastrid collection and original material, Late Cretaceous holotypes of the genera Histiastrum Ehrenberg, Hagiastrum Haeckel, and Tesserastrum Haeckel are revised. Histiastrum aster Lipman, H. cruciferum Lipman, H. membraniferum Lipman, H. latum Lipman, H. tetracanthum Lipman, H. tumeniense Lipman, Hagiastrum crux Lipman, and Tesserastrum quadratum Lipman are transferred to the genus Crucella Pessagno. A new species, Rhombastrum lipmanae sp. nov., is described. It is shown that Crucella lata (Lipman) and C. crux (Lipman) are Santonian–Campanian index species and C. crucifera (Lipman), C. tetracantha (Lipman), C. tumeniensis (Lipman), and Rhombastrum lipmanae sp. nov. are markers of the Campanian Boreal Realm.     

Age-influenced morphological changes inLeptestheria saetosa Marinček et Petrov, 1992 (Conchostraca,Crustacea)

Morphological changes during the process of ageing ofLeptestheria saetosa Marinek et Petrov, 1992 were observed. It was established thet the greatest number of analysed characteristics change intensively after sexual maturation. These changes continue throughout the entire life, although they are very slow in old specimens. Such a large number of changes brings about considerable morphological differences between adult specimens of different age.     

Galls on the <Emphasis Type="Italic">Compositiphyllum retinerve</Emphasis> (Herman) Herman et Kvaček leaves (angiosperms) from the Turonian of the Northwestern Kamchatka Peninsula,Russia

A new gall species, Paleogallus kamchaticus, from the Turonian of the Northwestern Kamchatka Peninsula (Russia), located on Compositiphyllum retinerve (Herman) Herman et Kva?ek leaves, is described. The gall-forming process and basic principles of fossil galls classification are discussed.     

Kengyilia longiaristata———A New Species of the Family Gramineae from Qinghai,China

Kengyilia longiaristata , a new species of Gramineae from Qinghai Province , is described .     

The Tetramer Structure of the Glycoside Hydrolase Family 27 α-Galactosidase I from Umbelopsis vinacea

The crystal structure of Umbelopsis vinacea α-galactosidase I, which belongs to glycoside hydrolase family 27, was determined at 2.0 Å resolution. The monomer structure was well conserved with those of glycoside hydrolase family 27 enzymes. The biological tetramer structure of this enzyme was constructed by the crystallographic 4-fold symmetry, and tetramerization appeared to be caused by three inserted peptides that were involved in the tetramer interface. The quaternary structure indicated that the substrate specificity of this enzyme might be related to the tetramer formation. Three N-glycosylated sugar chains were observed, and their structures were found to be of the high-mannose type.     

Crystal Structure and Characterization of the Glycoside Hydrolase Family 62 α-l-Arabinofuranosidase from Streptomyces coelicolor

α-l-Arabinofuranosidase, which belongs to the glycoside hydrolase family 62 (GH62), hydrolyzes arabinoxylan but not arabinan or arabinogalactan. The crystal structures of several α-l-arabinofuranosidases have been determined, although the structures, catalytic mechanisms, and substrate specificities of GH62 enzymes remain unclear. To evaluate the substrate specificity of a GH62 enzyme, we determined the crystal structure of α-l-arabinofuranosidase, which comprises a carbohydrate-binding module family 13 domain at its N terminus and a catalytic domain at its C terminus, from Streptomyces coelicolor. The catalytic domain was a five-bladed β-propeller consisting of five radially oriented anti-parallel β-sheets. Sugar complex structures with l-arabinose, xylotriose, and xylohexaose revealed five subsites in the catalytic cleft and an l-arabinose-binding pocket at the bottom of the cleft. The entire structure of this GH62 family enzyme was very similar to that of glycoside hydrolase 43 family enzymes, and the catalytically important acidic residues found in family 43 enzymes were conserved in GH62. Mutagenesis studies revealed that Asp²⁰² and Glu³⁶¹ were catalytic residues, and Trp²⁷⁰, Tyr⁴⁶¹, and Asn⁴⁶² were involved in the substrate-binding site for discriminating the substrate structures. In particular, hydrogen bonding between Asn⁴⁶² and xylose at the nonreducing end subsite +2 was important for the higher activity of substituted arabinofuranosyl residues than that for terminal arabinofuranoses.     

Identifying a Folding Nucleus for the Lysozyme/α-Lactalbumin Family from Sequence Conservation Clusters

Four subfamilies of c-type lysozyme and one subfamily of α-lactalbumin are defined from 78 sequences, and their folding nucleus is identified with a method based on conserved residues and native structural contacts between pairs of conserved residues. One large cluster of 19 conserved residues is found which is mostly nonpolar, buried, and nonfunctional. It can be subdivided into three subclusters: (1) conserved residues in four helices; (2) conserved residues that stabilize the connector between the α and the β domains; and (3) a β-turn, sitting in the middle of a bowl of α-helix residues. It is proposed that this folding nucleus initiates four helices, A, B, C, and D, three β sheets, and the connector, which corresponds closely to the nucleation of the so-called fast folding track pathway. As the secondary structures propagate, nonconserved residues and functionally conserved residues would form additional contacts. The conserved residues are selected with a phylogenetic scheme in which single members of subfamilies are selected. Subfamilies are then equally weighted to obtain the consensus conservation. Received: 11 June 2001 / Accepted: 28 August 2001     

Neuroligin Trafficking Deficiencies Arising from Mutations in the α/β-Hydrolase Fold Protein Family

Despite great functional diversity, characterization of the α/β-hydrolase fold proteins that encompass a superfamily of hydrolases, heterophilic adhesion proteins, and chaperone domains reveals a common structural motif. By incorporating the R451C mutation found in neuroligin (NLGN) and associated with autism and the thyroglobulin G2320R (G221R in NLGN) mutation responsible for congenital hypothyroidism into NLGN3, we show that mutations in the α/β-hydrolase fold domain influence folding and biosynthetic processing of neuroligin3 as determined by in vitro susceptibility to proteases, glycosylation processing, turnover, and processing rates. We also show altered interactions of the mutant proteins with chaperones in the endoplasmic reticulum and arrest of transport along the secretory pathway with diversion to the proteasome. Time-controlled expression of a fluorescently tagged neuroligin in hippocampal neurons shows that these mutations compromise neuronal trafficking of the protein, with the R451C mutation reducing and the G221R mutation virtually abolishing the export of NLGN3 from the soma to the dendritic spines. Although the R451C mutation causes a local folding defect, the G221R mutation appears responsible for more global misfolding of the protein, reflecting their sequence positions in the structure of the protein. Our results suggest that disease-related mutations in the α/β-hydrolase fold domain share common trafficking deficiencies yet lead to discrete congenital disorders of differing severity in the endocrine and nervous systems.     

Domain Evolution in the α-Amylase Family

The available amino acid sequences of the α-amylase family (glycosyl hydrolase family 13) were searched to identify their domain B, a distinct domain that protrudes from the regular catalytic (β/α)₈-barrel between the strand β3 and the helix α3. The isolated domain B sequences were inspected visually and also analyzed by Hydrophobic Cluster Analysis (HCA) to find common features. Sequence analyses and inspection of the few available three-dimensional structures suggest that the secondary structure of domain B varies with the enzyme specificity. Domain B in these different forms, however, may still have evolved from a common ancestor. The largest number of different specificities was found in the group with structural similarity to domain B from Bacillus cereus oligo-1,6-glucosidase that contains an α-helix succeeded by a three-stranded antiparallel β-sheet. These enzymes are α-glucosidase, cyclomaltodextrinase, dextran glucosidase, trehalose-6-phosphate hydrolase, neopullulanase, and a few α-amylases. Domain B of this type was observed also in some mammalian proteins involved in the transport of amino acids. These proteins show remarkable similarity with (β/α)₈-barrel elements throughout the entire sequence of enzymes from the oligo-1,6-glucosidase group. The transport proteins, in turn, resemble the animal 4F2 heavy-chain cell surface antigens, for which the sequences either lack domain B or contain only parts thereof. The similarities are compiled to indicate a possible route of domain evolution in the α-amylase family. Received: 4 December 1996 / Accepted: 13 March 1997     

Family Dibrachicystidae (Echinodermata: Rhombifera) from the “Middle” Cambrian of the Barrandian area,Czech Republic

A slightly crushed but otherwise nearly complete specimen of the recently described rhombiferan echinoderm genus Vizcainoia Zamora and Smith, 2012 is documented from the “Middle” Cambrian Jince Formation of the P?íbram–Jince Basin of the Czech Republic. Isolated thecal plates, earlier determined as calyx plates of the eocrinoid Acanthocystites briareus Barrande, 1887 and/or as eocrinoid sp., occurring in diverse levels of the Jince Formation are reassigned to Dibrachicystidae gen. et sp. indet. Similarly, isolated thecal plates collected from the Buchava Formation of the Skryje–Tý?ovice Basin could be classified as Dibrachicystidae gen. et sp. indet. Specimens from the Barrandian area are the first records of the family Dibrachicystidae outside of southwestern Europe, of the family otherwise known only from the Languedocian of Montagne Noire of France and from the Caesaraugustian and Languedocian of Iberian Chains of northern Spain.