New genus and two new species of the family Ethmolaimidae (Nematoda: Chromadorida), found in two different cold-seep environments

This study describes a new genus Dystomanema gen. nov. with two new species, D. cadizensis sp. nov. and D. brandtae sp. nov. within the family Ethmolaimidae, subfamily Neotonchinae, based on specimens from two low-activity cold-seep environments at distant geographical locations. The new genus was first identified in samples from the Darwin mud volcano (1100 m depth) in the Gulf of Cadiz and later on also found in samples from a low-activity seep in the Larsen B embayment (820m depth) off the eastern Antarctic Peninsula. Until now, the family Ethmolaimidae contained nine genera: Ethmolaimus and Paraethmolaimus in the subfamily Ethmolaiminae, and Comesa, Filitonchoides, Filitonchus, Gomphionchus, Gomphionema, Nannolaimus, and Neothonchus in the subfamily Neotonchinae. The most important family characteristics are: an annulated cuticle bearing transverse rows of dots, cephalic sensilla arrangement of 6+6+4, a spiral amphid, an oesophagus with muscular posterior bulb, paired gonads and males with cup-shaped precloacal supplements. The new genus resembles Comesa and Neotonchus, but is typified by a ventrally displaced oral opening with three very small teeth that are easily overlooked. D. cadizensis gen. nov. sp. nov. is characterized by the 1401-2123 mu m long body; cuticle transversally striated with fine punctation; head conical; low lips; amphid spiralled 3 turns, oral opening ventrally displaced, male with outstretched testes; spicules of equal size; gubernaculum plate-like and ten to twelve conspicuous cup-shaped precloacal supplements with external longitudinal articulated flange. D. brandtae gen. nov. sp. nov. can be distinguished by the 2438-3280 mu m long body; cuticle transversally striated with fine punctuation; head conical; low lips; amphid spiraled 3+ turns; oral opening ventrally displaced; male with anterior testes outstretched and posterior one smaller and reflexed; spicules of equal size; gubernaculum plate-like and twenty conspicuous cup-shaped precloacal supplements with external longitudinal articulated flange. Notes on the ecology and habitat of the new genus are provided in light of its discovery in cold-seep environments.

Family-level AMBI is valid for use in the north-eastern Atlantic but not for assessing the health of microtidal Australian estuaries

Analysis of benthic macroinvertebrate samples at a higher taxonomic level than species, e.g. family, potentially provides a more cost-effective protocol for environmental impact assessments and monitoring as it requires less time, funds and taxonomic expertise. Using the AMBI database, species ecological group scores are shown to be coherent within families. Faunal data from a wide range of environmental impact scenarios in the north-eastern Atlantic demonstrate that AMBI, calculated from mean values for families, exhibits a strong linear relationship with species-level AMBI, the correlation improving by using square-root transformed rather than untransformed abundances. In many regions of the world, however, the sensitivity of benthic macroinvertebrates to environmental perturbations is unknown, precluding the use of AMBI for environmental assessments. Yet the families are essentially the same as in the AMBI database. The utility of family-level AMBI is tested using data for four south-western Australian estuaries previously subjected to environmental quality assessments, but where only 17 species of the 144 taxa are included in the AMBI database. Although family-level AMBI scores reflect differences in environmental quality spatially and temporally within an estuary, they do not follow variations in environmental quality among estuaries. Indeed, south-western Australia estuaries are numerically dominated by families with high AMBI scores, probably due to the detrimental effects of natural accumulations of organic material in estuaries with long residence times. As taxonomic distinctness follows trends in environmental quality among estuaries, as well as temporally and spatially within a system, it provides an appropriate substitute for assessing the 'heath' of microtidal estuaries.

The type I antifreeze protein gene family in Pleuronectidae

Antifreeze proteins (AFPs) protect marine teleosts from freezing in icy seawater by binding to nascent ice crystals and preventing their growth. It has been suggested that the gene dosage for AFPs in fish reflects the degree of exposure to harsh winter climates. The starry flounder, _Platichthys stellatus_, has been chosen to examine this relationship because it inhabits a range of the Pacific coast from California to the Arctic. This flatfish is presumed to produce type I AFP, which is an alanine-rich, amphipathic alpha-helix. Genomic DNA from four starry flounder was Southern blotted and probed with a cDNA of a winter flounder liver AFP. The hybridization signal was consistent with a gene family of approximately 40 copies. Blots of DNA from other starry flounder indicate that California fish have far fewer gene copies whereas Alaska fish have far more. This analysis is complicated by the fact that there are three different type I AFP isoforms. The first is expressed in the liver and secreted into circulation, the second is a larger hyperactive dimer also thought to be expressed in the liver, and the third is expressed in peripheral tissues. To evaluate the contribution of these latter two isoforms to the overall gene signal on Southern blots, hybridization probes for the three isoforms were isolated from starry flounder DNA by genomic cloning. Two clones revealed linkage of genes for different isoforms, and this was confirmed by genomic Southern blotting, where hybridization patterns indicated that the majority of genes were present in tandem repeats. The sequence and diversity of all three isoforms was sampled in the starry flounder genome by PCR. All coding sequences derived for the skin and liver isoforms were consistent with the proposed structure-function relationships for this AFP, where the flat hydrophobic side of the helix is conserved for ice binding. There was greater sequence diversity in the skin and hyperactive isoforms than in the liver isoform, suggesting that the latter evolved recently from one of the other two. The genomic PCR primers are currently being used to sample isoform diversity in related right-eyed flounders to test this hypothesis.

CAMP factor homologues in Propionibacterium acnes: a new protein family differentially expressed by types I and II

Analysis of the draft genome sequence of the opportunistic pathogen Propionibacterium acnes type strain NCTC 737 (=ATCC 6919) revealed five genes with sequence identity to the co-haemolytic Christie-Atkins-Munch-Peterson (CAMP) factor of Streptococcus agalactiae. The predicted molecular masses for the expressed proteins ranged from 28 to 30 kDa. The genes were present in each of the three recently identified recA-based phylogenetic groupings of P. acnes (IA, IB and 11), as assessed by PCR amplification. Conserved differences in CAMP factor gene sequences between these three groups were also consistent with their previous phylogenetic designations. All type IA, IB and 11 isolates were positive for the co-haemolytic; reaction on sheep blood agar. Immunoblotting and silver staining of SIDS-PAGE gels, however, revealed differential protein expression of CAMP factors amongst the different groups. Type IB and 11 isolates produced an abundance of CAMP factor 1, detectable by specific antibody labelling and silver staining of SDS-PAGE gels. In contrast, abundant CAMP factor production was lacking in type A isolates, although larger amounts of CAMP factor 2 were detectable by immunoblotting compared with type 11 isolates. While the potential role of the abundant CAMP factor 1 in host colonization or virulence remains to be determined, it should be noted that the type strain of P. acnes used in much of the published literature is a type A isolate and is, therefore, lacking in this attribute.