Phylogenetic analyses suggest that Psammomitra (Ciliophora,Urostylida) should represent an urostylid family,based on small subunit rRNA and alpha‐tubulin gene sequence information

The morphologically unique ciliate Psammomitra has long been considered as a systematically uncertain stichotrich. This is mainly because of its highly specialized morphology and a lack of either detailed information concerning its ontogenesis, or molecular data. Based on the small subunit rRNA (SSrRNA) gene and alpha‐tubulin gene sequences, we re‐evaluated the phylogenetic position of Psammomitra retractilis using multiple algorithms. Phylogenetic trees inferred from the SSrRNA gene sequences representing a total of 53 spirotrichs demonstrated the closest relationship of Psammomitra was with Holosticha‐like taxa, with strong support, which clearly suggested that Psammomitra should be placed into the order Urostylida although it branched at a rather deep level, and is likely to be closely related to Holostichidae. With consideration to molecular evidence and morphological characters, Psammomitra should be a clearly outlined taxon at about the rank of family, i.e. Psammomitridae stat. nov. , within the order Urostylida. The improved diagnosis for this family is as follows: Urostylida possessing extremely contractile, elongated body which consists of three parts: head, trunk, and slender tail; midventral complex composed of midventral pairs only and restricted to about anterior 1/3 of ventral surface; frontal, frontoterminal, and transverse cirri present; one left and one right marginal rows which commence near proximal end of adoral zone and extend to near rear body end.     

Molecular characterization of a fungal gene paralogue of the penicillin penDE gene of Penicillium chrysogenum

Background  

Penicillium chrysogenum converts isopenicillin N (IPN) into hydrophobic penicillins by means of the peroxisomal IPN acyltransferase (IAT), which is encoded by the penDE gene. In silico analysis of the P. chrysogenum genome revealed the presence of a gene, Pc13g09140, initially described as paralogue of the IAT-encoding penDE gene. We have termed this gene ial because it encodes a protein with high similarity to IAT (IAL for IAT-Like). We have conducted an investigation to characterize the ial gene and to determine the role of the IAL protein in the penicillin biosynthetic pathway.     

Phylogenetic tests of the hypothesis of block duplication of homologous genes on human chromosomes 6, 9, and 1

There are 10 gene families that have members on both human chromosome 6 (6p21.3, the location of the human major histocompatibility complex [MHC]) and human chromosome 9 (mostly 9q33-34). Six of these families also have members on mouse chromosome 17 (the mouse MHC chromosome) and mouse chromosome 2. In addition, four of these families have members on human chromosome 1 (1q21-25 and 1p13), and two of these have members on mouse chromosome 1. One hypothesis to explain these patterns is that members of the 10 gene families of human chromosomes 6 and 9 were duplicated simultaneously as a result of polyploidization or duplication of a chromosome segment ("block duplication"). A subsequent block duplication has been proposed to account for the presence of representatives of four of these families on human chromosome 1. Phylogenetic analyses of the 9 gene families for which data were available decisively rejected the hypothesis of block duplication as an overall explanation of these patterns. Three to five of the genes on human chromosomes 6 and 9 probably duplicated simultaneously early in vertebrate history, prior to the divergence of jawed and jawless vertebrates, and shortly after that, all four of the genes on chromosomes 1 and 9 probably duplicated as a block. However, the other genes duplicated at different times scattered over at least 1.6 billion years. Since the occurrence of these clusters of related genes cannot be explained by block duplication, one alternative explanation is that they cluster together because of shared functional characteristics relating to expression patterns.      

LOPHOSTEUS SUPERBUS PANDER: ZÄHNE, ZAHNKNOCHEN UND BESONDERE SCHUPPENFORMEN

Morphological and histological studies of numerous remains of Lophosteus superbus Pander from erratic boulders of Beyrichia Limestone prove that the peculiar teeth recently brought to notice by Gross (1969) belong to Lophosteus and are not of acanthodian origin. The structure of these teeth as well as that of some tooth-bearing bones and scales is described. The investigation was extended to cover the teeth of smaller Devonian actinopterygians and cross-opterygians to establish whether Lophosteus is an actinopterygian, a crossopterygian, or even a member of a hitherto unknown group of Osteichthyes. Results unfortunately proved negative, as the very small teeth of various species offer too few distinct and symptomatic histological characteristics. A solution of this question must await the discovery of determinable skull and lower jaw bones of the genus Lophosteus.
Die morphologische und histologische LTntersuchung zahlreicher in nordwest-deutschen Geschieben des Beyrichienkalkes gefundener Reste von Lophosteus superbus Pander beweist, daß die kürzlich von Gross (1969) erwähnten, eigenartigen und nicht von Acanthodiern stammenden Zähne zu Lophosteus gehören. Der Bau der Zähne und einiger Zahnknochen und Schuppen wird beschrieben. Um die Fragen zu klaren, ob Lophosteus zu den Actinopterygiern oder zu den Crossopterygiern gehört oder gar zu einer bisher unbekannten Gruppe der Osteichthyes, wurde die Untersuchung auch auf die Zähne kleiner devonischer Actinopterygier und Crossopterygier ausgedehnt. Das Ergebnis war leider negativ: die sehr kleinen Zähne der verschiedenen untersuchten Arten bieten zu wenig kennzeichnende und unterscheidende histologische Merkmale. Nur von der Entdeckung bestimmbarer Schädel- und Unterkiefer-Knochen der Gattung Lophosteus kann die Entscheidung dieser Frage erhofft werden.     

Carotenoid Distribution in Bleached Substrains of Euglena gracilis

SYNOPSIS. Several substrains of Euglena gracilis var. bacillaris made chlorotic by treatment with pyribenzamine or streptomycin, or by growth at high temperature (35–36°C.), have been examined for their carotenoid content. They differ from the normal green strain both qualitatively and quantitatively. Some strains produce no detectable carotenoids while the carotenoid concentration in the strains producing most is at best only one-fifth that of the normal strain. In all substrains producing carotenoids, the carotene fraction consists of β-carotene accompanied by some members of the phytofluene series. In only two of these substrains, HB-G and PBZ-G3, are xanthophylls produced in significant amounts. In HB-G, the main pigment is echinenone, and in PBZ-G3 it is zeaxanthin. The significance of these findings is briefly discussed.     

Über das Gebiss der Acanthodier und Placodermen

In their dentition, acanthodians and placoderms differ from other fishes by the ontogenetie development and replacement of their teeth and by the histology of the functional elements (teeth, cutting edges of the jaws). In some cases special diets are indicated. In general, however, their dentition seems to have been less effective than that of elasmobranchs and teleostomes. This fact may partly account for their early extinction.
Die Eigenart des Gebisses der Aoanthodier und Placodermen inbezug auf die Zahnbildung (Ontogenese), den Zahnersatz und den histologischen Bau der funktionalen Elemente (Zähne, Schneidekanten des Kieferknochens) wird dargestellt. Aus dem Bau des Gebisses läßt sich die Nahrung dieser Tiere teilweise erschließen. Das eigenartige Gebiß verursaehte vermutlich eine Konkurrenzunterlegenheit beim Nahrungserwerb gegenüber den Elasmobranchiern und Teleostomen, vielleicht einer der Gründe, der zum frühen Aussterben der Acanthodier und Placodermen führte.     

Inferring mechanisms of copy number change from haplotype structures at the human DEFA1A3 locus

Background

The determination of structural haplotypes at copy number variable regions can indicate the mechanisms responsible for changes in copy number, as well as explain the relationship between gene copy number and expression. However, obtaining spatial information at regions displaying extensive copy number variation, such as the DEFA1A3 locus, is complex, because of the difficulty in the phasing and assembly of these regions. The DEFA1A3 locus is intriguing in that it falls within a region of high linkage disequilibrium, despite its high variability in copy number (n = 3–16); hence, the mechanisms responsible for changes in copy number at this locus are unclear.

Results

In this study, a region flanking the DEFA1A3 locus was sequenced across 120 independent haplotypes with European ancestry, identifying five common classes of DEFA1A3 haplotype. Assigning DEFA1A3 class to haplotypes within the 1000 Genomes project highlights a significant difference in DEFA1A3 class frequencies between populations with different ancestry. The features of each DEFA1A3 class, for example, the associated DEFA1A3 copy numbers, were initially assessed in a European cohort (n = 599) and replicated in the 1000 Genomes samples, showing within-class similarity, but between-class and between-population differences in the features of the DEFA1A3 locus. Emulsion haplotype fusion-PCR was used to generate 61 structural haplotypes at the DEFA1A3 locus, showing a high within-class similarity in structure.

Conclusions

Structural haplotypes across the DEFA1A3 locus indicate that intra-allelic rearrangement is the predominant mechanism responsible for changes in DEFA1A3 copy number, explaining the conservation of linkage disequilibrium across the locus. The identification of common structural haplotypes at the DEFA1A3 locus could aid studies into how DEFA1A3 copy number influences expression, which is currently unclear.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-614) contains supplementary material, which is available to authorized users.