Classification and nomenclature of endogenous retroviral sequences (ERVs): Problems and recommendations

The genomes of many species are crowded with repetitive mobile sequences. In the case of endogenous retroviruses (ERVs) there is, for various reasons, considerable confusion regarding names assigned to families/groups of ERVs as well as individual ERV loci. Human ERVs have been studied in greater detail, and naming of HERVs in the scientific literature is somewhat confusing not just to the outsider. Without guidelines, confusion for ERVs in other species will also probably increase if those ERVs are studied in greater detail. Based on previous experience, this review highlights some of the problems when naming and classifying ERVs, and provides some guidance for detecting and characterizing ERV sequences. Because of the close relationship between ERVs and exogenous retroviruses (XRVs) it is reasonable to reconcile their classification with that of XRVs. We here argue that classification should be based on a combination of similarity, structural features, (inferred) function, and previous nomenclature. Because the RepBase system is widely employed in genome annotation, RepBase designations should be considered in further taxonomic efforts. To lay a foundation for a phylogenetically based taxonomy, further analyses of ERVs in many hosts are needed. A dedicated, permanent, international consortium would best be suited to integrate and communicate our current and future knowledge on repetitive, mobile elements in general to the scientific community.     

The invertebrate fauna of High Arctic seabird nests: the microarthropod community inhabiting nests on Spitsbergen,Svalbard

The invertebrate fauna of the nests of three seabird species, black-legged kittiwakes (Rissa tridactyla), common eider (Somateria mollissima) and glaucous gull (Larus hyperboreus), were sampled in Kongsfjorden, Spitsbergen, Svalbard. The invertebrate community was species poor, consisting predominantly of the flea, Mioctenopsylla arctica arctica (Insecta: Siphonaptera), but with six species of oribatid mite (Acari: Oribatida), Diapterobates notatus, Oribatula tibialis, Ameronothrus lineatus, Hermannia reticulata, Trichoribates trimaculatus and Ceratoppia bipilis, plus an occasional mesostigmatid mite. No Collembola or ticks (Acari: Ixodidae) were observed. With the exception of M. arctica arctica, the fauna of seabird nests consisted of opportunistic microarthropod species rather than specialised nest-dwelling or bird parasitic species. Species diversity of soil oribatid mites was greater in nests of the common eider than compared to nests of the black-legged kittiwake, which may be related to the ground nesting behaviour of the common eiders. No rare or unusual microarthropod species for Svalbard were found in the seabird nests. The contentions that nests may facilitate microarthropod colonisation of High Arctic regions via bird phoresy by providing a high-quality habitat at the point of arrival, or that there might be a specialised microarthropod fauna exploiting this habitat, were not supported in this study. These are amongst the first data on the microarthropod community of seabird nests in the High Arctic.     

Response of calcareous nannofossil assemblages to paleoenvironmental changes through the mid-Pleistocene revolution at Site 1090 (Southern Ocean)

Quantitative study on calcareous nannofossil assemblages has been performed in high time resolution (2–3 kyr) at the Ocean Drilling Program Site 1090. The location of this site in the Southern Ocean is crucial for the comprehension of thermohaline circulation and frontal boundary dynamics, and for testing the employ of nannoflora as paleoceanographical tool. The chronologically well constrained investigated record spans between Marine Isotope Stage (MIS) 35 and 15, through an interval of global paleoclimate and paleoceanographical modification also known as mid-Pleistocene revolution (MPR). Measures of ecological (Shannon–Weaver diversity and paleoproductivity) and dissolution indices together with spectral and wavelet analyses carried out on the acquired time series provide valuable information for interpretation of data in terms of paleoecology and paleoceanography. Assemblages are mainly represented by dominant small Gephyrocapsa, common Calcidiscus leptoporus s.l., Coccolithus pelagicus s.l., Gephyrocapsa (4-5.5 μm), the extinct Pseudoemiliania lacunosa and Reticulofenestra spp. (R. asanoi and Reticulofenestra sp.). Morphotypes discriminated within Calcidiscus leptoporus s.l. and Coccolithus pelagicus s.l., reveal that they may have had different ecological preferences during Pleistocene with respect to the present. The composition and fluctuation in nannofossil assemblage and their comparison with the available Sea Surface Temperature (SST) and C-org curves suggest a primary ecological response to paleoenvironmental changes; relationships to different surface water features and boundary dynamics, as well as to different efficiencies and motions of the intermediate and deep water masses have been inferred. A more northward position of Subantarctic Front (SAF) during most of the Early Pleistocene record has been highlighted based on assemblage composition characterised by common Calcidiscus leptoporus s.l., Coccolithus pelagicus s.l., medium Gephyrocapsa (4–5.5 μm), and by the rarity or absence of Umbilicosphaera spp., Rhabdosphaera spp., Pontosphaera spp., Oolithotus fragilis. Exceptions are the more intense interglacials MIS 31, 17, and probably MIS 15, when a southward displacement of frontal system occurred, coincident with peaks in abundance of Helicosphaera spp. and Syracosphaera spp. Higher nutrient content and more dynamic conditions occurred between MIS 32 and MIS 25, in relation to shallower location of nutrient-rich Antarctic Intermediate Water (AAIW) core and to reduction of glacial–interglacial variability. A nannofossil barren interval is coincident with the known stagnation of South Atlantic deep water circulation during MIS 24, when North Atlantic Deep Water (NADW) was reduced or suppressed and an enhanced northward deep penetration of the more corrosive Circumpolar Deep Water (CPDW) took place. An event of strong instability in nutricline dynamics characterised the transition MIS 23–22 as suggested by sharp fluctuations in paleoproductivity proxies, linked to major changes in oceanographic circulation and to the first distinct increase of larger ice volumes at this time. From MIS 21 upward the nannofossil variations seem to be primarily controlled by glacial–interglacial cyclicity and temperature fluctuations. The cyclic fluctuation recognised in nannofossil abundance seems to be linked to orbitally-forced climatic variation, primarily to the obliquity periodicity recorded in the patterns of C. leptoporus intermediate (5–8 μm) and C. pelagicus pelagicus (6–10 μm); however no obvious and linear relations may be always observed between nannoflora fluctuation and Milankovitch parameters, suggesting more complex and unclear relationships between nannofossils and environmental change.     

Decisions,decisions, decisions: the host colony choices of a social parasite

Many factors contribute to the success of a socially parasitic strategy, especially the ability of the parasite to invade a host colony. However, little research has focused on the choices that may be made by an invading parasite, specifically whether parasites actively discriminate between different host colonies and if they have a preference for colonies of a particular size. When an allodapine social parasite, Inquilina schwarzi, was presented with colonies of their host species, Exoneura robusta, the parasites were found to invade the larger host colonies. However, it could not be ascertained from this study whether the parasites were making an active decision concerning which colony to invade, or whether they were simply more attracted to the larger colonies due to potentially stronger odour cues. Regardless of the cause, the larger host colonies are more at risk of being invaded by a social parasite, which would give parasites greater resources for exploitation and could also provide selection against the large host colony sizes.     

Predicting Biological Invasions

There are various approaches to explain the mechanisms of biological invasions. It is possible (1) to focus on the characteristics of invading species and (2) on those of the ecosystems invaded, (3) to investigate the relationship between these two factors (key–lock approach), or (4) to differentiate the invasion process in time. Each of these approaches may serve to improve the understanding of some aspects of biological invasions, and each of them is in some way suitable for the purpose of predicting invasions. We discuss the usefulness and the limitations of these approaches, focusing on case studies from central Europe. An example of the fourth approach, a model of steps and stages of plant invasions that describes the invasion process in greater detail, illustrates some general limitations in predicting biological invasions. This revised version was published online in July 2006 with corrections to the Cover Date.     

Forest fragmentation and rhinocryptid nest predation in central Chile

Fragmentation of forest landscapes can raise the intensity of nest predation by increasing the abundance and richness of generalist or introduced predators. Understory foraging birds, such as rhinocryptids, can be highly vulnerable to nest predation in fragmented landscapes because they often place their nests on the ground. Temperate deciduous forests in Chile have been intensively fragmented in the last centuries, causing changes in nest predator densities. We tested if predation of artificial nests, mimicking those of rhinocryptids, placed on and above ground was higher in the remnant fragments of central Chile due to an increase in predator abundance. The rate of nest predation in forest remnants was larger than in native continuous forest. Small mammals were the main nest predators. Despite high predation rates, the abundance of rhinocryptids is higher in forest remnants, suggesting that fragments might constitute ecological traps.     

三肽囊素(bursin)的鸡、鸭免疫器官组织学定位特征分析(简报)

三肽囊素(bursin)是法氏囊组织提取物中一种非常重要的活性因子,由Audhya T.等在1986年首次报道。近十几年,有关三肽囊素的研究取得了较大的进展,涉及对三肽囊素的生物学活性、组织学定位、功能机制及其应用前景。本研究分别探索了三肽囊素在鸡、鸭免疫器官中的定位,并对其特征进行分析,以期更深入理解三肽囊素的存在及其生物学意义。鸡用近交系(CB系),由12、14及20日龄胚、新生雏、1—9周龄鸡,采集法氏囊、法氏囊T细胞区、胸腺、哈德氏腺、脾脏及骨髓。鸭用北京鸭,由新生     

Barogali et l’Oued Doure. Deux gisements représentatifs du Paléolithique ancien en République de Djibouti

In the Republic of Djibouti, surveys and excavations, carried out from 1985 to 1992, confirmed the presence of the pre-Acheulean (Oldowan) and Acheulean sites in the country. Three seasons of excavations (1985-1987 in the Gobaad Basin, have unearthed in a hardened compact clay strata of an ancient marshland dating to the Lower Pleistocene, the fossilized skeletal remains of an Elephas recki ileretensis. Numerous stone tools have been gathered with the bones. The E.S.R. dating the elephant’s lower third molar gave a date between 1,.6 and 1,.3 MY that would confirm its paleontological grouping and the membership of this butchery site to the Oldowan period. The animal appeared to have been lying on its left side. The cranial roof had been separated from the calvarium, perhaps to get at the brain; but the skull remains in anatomic connection with the tusks. The jaw (mandible) seems to have been broken to extract the tongue. Hominids, perhaps Homo ergaster, knapped tools from a nearly outcrop of poor quality lava. The tools were specifically adapted to their needs, such as scraping, chopping and scattering the bones. The site has yielded 569 artifacts: utilized material and hammerstones (121); pebble tools (32); cores (14); “debitage” products (366); retouched flakes (36). Artifacts are rarely retouched and often broken. Five different types of choppers have been classified. The polyedrons and one bola make up 22% of the pebble tools. The cores are divided into unipolar, centripetal and polyhedrical types. In another site, Haïdalo, an almost complete skeleton of an Elephas recki recki in anatomical connection and without any sign of predation, has been found at eight kilometers from Barogali. During surveys in the Ali Sabîh region (1990-1992) seven sectors have been discovered and prospected in the Oued Doure Basin. On the surface area and also in situ into some little pits, 345 rhiolitic Acheulean artifacts have been found, near rhyolitic outcrop. These artifacts are generally large. The choppers (18) can be dividended into 2 sets : side choppers (55%) and end choppers (27%), often with a bifacial cutting edge. There is only one polyedron, but we have found eight heavy scrapers. The Acheulean group is important (43 tools). The bifaces are varied and there are also a few cleavers and picks. Cores are numerous (92) and Levallois cores are preponderant (45%). We find also centripetal cores (27%) and so unipolar, bipolar and polyhedral cores. Tools made of flakes (118) are numerous: scrapers are typologically diversified. Some of them have a double utilization. Notch tools, denticulate tools are presents but also end scrapers, burin, borer, back knifes and scantily retouched flakes. The characters of this lithic material, large cores and big flakes, large bifaces of various types, cleavers and retouched flakes, indicates that they are Acheulean products. So, the Doure Site can be placed in the Middle / Upper Acheulean transition.     

Determination of the lysosomal hydrolase activity in blood collected on filter paper,an alternative to screen high risk populations

This study aimed to determine the enzymatic activity in dried blood samples collected on filter paper (DBS) for the diagnosis of the following diseases: Fabry, Pompe, Mucopolysaccharidosis type I (MPS I) and Mucopolysaccharosis type VI (MPS VI). DBS was used for high risk patientscreening, according to clinical suspicion. Plasma, leukocytes and cultured fibroblasts were used to confirm the diagnosis when necessary. Among the 529 DBS samples sent to the laboratory, 164 had abnormal results. Confirmatory materials of 73 individuals were rerouted. The frequency of diagnosis for lysosomal storage disorders was 5.9%. DBS is an alternative screening technique used in high risk populations, which should lead to earlier diagnosis for lysosomal storage disorders (LSDs), help patients get treatment sooner and improve the outcome of the disease.     

影响侧脑室脑膜瘤手术疗效的多因素分析

目的：探讨影响侧脑室脑膜瘤手术疗效的因素,从而更好的促进侧脑室脑膜瘤的手术治疗。方法：回顾性分析侧脑室脑膜瘤显微手术30例的临床病理特征与顸后情况,其中KPS〉70分表示为预后良好,KP懿70分表示为预后不良。对各性别、年龄、部位、肿瘤大小、病理分型及术后有无并发症因素与预后进行χ^2检验与用Logistic回归分析其影响因素。结果：单因素分析表明肿瘤部位、病理分型及术后有无并发症对侧脑室脑膜瘤的预后有明显影响,P〈0．05,差异有统计学意义。经Logistic回归分析,最终进入模型的影响因素有2个,它们分别是肿瘤部位和术后有无并发症,其P值均小于0．05。结论：在显微手术下,侧脑室脑膜瘤大部分可以全切并取得了较好的远期疗效。肿瘤部位和术后有无并发症是影响预后的一个重要因素,及时处理并发症能显著地改善预后。