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.     

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.     

Distal end of 105-125 loop - A putative reductase binding domain of phthalate dioxygenase

The phthalate dioxygenase system consists of the dioxygenase, PDO, which contains a Rieske [2Fe-2S] center and a Fe(II)-mononuclear center, and the reductase, PDR. Involvement of the distal end of the 105-125 loop of PDO in its interaction with PDR was tested by substituting charged residues in the loop with alanines and by replacing the conserved tryptophan-94. Compared to wild-type PDO, all variants had lower catalytic activity and the Rieske centers were reduced more slowly by reduced PDR. The rates of oxidation of the Rieske centers by oxygen, which represent electron transfer between the Rieske and mononuclear centers, were essentially unaffected. These results suggest that positively charged residues of the distal end of the 105-125 loop are collectively involved in PDR binding with the PDO. Contrary to expectations, Trp94 variants were not directly involved in electron transfer between PDR and PDO. The tryptophan appears to have mainly a structural role, apparently preserving the hydrophilic environment of the Rieske center.     

南京牛头岗遗址植硅体分析及环境考古意义

牛头岗遗址是江苏南京较大的古文化遗址,遗址文化层中植硅体组合揭示在新石器晚期（约3500Cal．aBP前）,南京地区气候偏暖偏湿;商代（约3500—3000Cal．aBP）,气候温暖湿润;西周早期（约3000Cal．aBP后）,气候又偏暖偏湿。明显的气候波动与全新世中晚期全球气候变化可以对比。相邻何颖遗址的文化内涵和哺乳动物遗存,与牛头岗植硅体组合反映的植被与生态比较一致。新石器晚期至西周时期的气候与环境适宜古代先民的繁衍与生存,南京及滁河流域古文化内涵丰富。     

Genetic variability, body characteristics and reproductive parameters of neighbouring rural and urban common kestrel (Falco tinnuculus) populations

We tested the genetic and ecological differences between neighbouring urban and rural populations of common kestrels (Falco tinnuculus) in southern Bohemia. The aims were to (1) assess the genetic variability of the studied kestrel populations using microsatellite markers, (2) check the genetic relatedness of individuals within the urbanization gradient, and (3) compare possible gradients of body characteristics and reproductive parameters on the urbanization gradient. The mean expected allelic polymorphism did not differ among the studied populations, which were not genetically separated (F _ST  = 0.0003, P = 0.781). Also, an individual assignment test did not show a separation of these populations. Urban kestrels that bred in the city centre were indicatively more related than others, and no relationship was found in the rural kestrel population. Kestrel females were heavier towards the city centre, but males did not show this relationship. Nest distance from the city centre had no significant effect on any of the tested reproductive parameters. Our results do not support the notion of genetic differentiation between rural and urban kestrels, but revealed trends in body characteristics and genetic relatedness along the urbanization gradient.     

甘肃徐家城旧石器遗址石制品拼合研究

徐家城遗址是甘肃省新发现的含丰富旧石器文化遗物的遗址,主要埋藏于水洛河二级阶地上覆的马兰黄土中,年代在距今4.3~2.3万年间。徐家城遗址的拼合分析显示,4B、4C层剥片与石器加工行为是石制品空间分布形成的主要原因,但可能存在遗址使用时古人类对石制品位置改变的行为;4A层石制品零散分布可能反映了此时遗址处于古人类活动的边缘地带。遗址剥片方法以硬锤锤击法为主,石核剥片序列主要以转向为主,古人类对石料进行单层或多层开发;同时部分石器破碎后古人类可能对其进行再利用。平面分布显示发掘区内可能存在两个相对集中的剥片区域,并且古人类在同一区域剥片和加工石器。然因遗址石制品原料性质、发掘面积等局限性,拼合分析的优势并未在此项研究中尽现。今后此类研究应结合其他研究方法,综合多方面信息解释遗址形成过程、石器技术及遗址空间利用方式。     

Initial soil amendments still affect plant community composition after nine years in succession on a heavy metal contaminated mountainside

Many efforts to restore disturbed landscapes seek to meet ecological goals over timescales from decades to centuries. It is thus crucial to know how different actions available to restoration practitioners may affect ecosystems in the long term, yet few such data exist. Here, we test the effects of seed and compost applications on plant community composition 9 years after their application, by taking advantage of a well‐controlled restoration experiment on a mountainside severely degraded by over 80 years of zinc smelting emissions. We asked whether plots have converged on similar plant communities regardless of initial seed and compost treatments, or if these initial treatments have given rise to lasting differences in whole plant communities or in the richness and abundance of native, exotic, and planted species. We found that compost types significantly affected plant communities 9 years later, but seed mix species composition did not. Observed differences in species richness and vegetative cover were negatively correlated, and both were related to the differences in plant communities associated with different compost types. These observed differences are due primarily to the number and abundance of species not in original seed mixes, of which notably many are native. Our results underscore the importance of soils in shaping the aboveground composition of ecosystems. Differences in soil characteristics can affect plant diversity and cover, which are both common restoration targets. Even in highly polluted and devegetated sites, compost and seed application can reinstate high vegetative cover and allow continued colonization of native species.     

Analyse des artefacts lithiques du site de Longgupo

Excavation has enabled recovery of 854 artifacts within 30 archaeological levels in the south sector and 11 in the north (chapter 3). These levels are quite probably contemporaneous, or even the same. The quantitative disparity in the number of strata between the two sectors is simply due to the fact that only the lower half of the northern zone was completely investigated. Similarly, the number of artifacts recovered by level varies according to the surface area excavated, although is some cases the density of material is significant despite the small area excavated, for example stratum C IV 5 which contains 174 lithic artifacts in 2 m². Before undertaking the technological analysis of the artifacts, given the preceding polemics provoked by the great age of this site and its implications for the spread of the first populations out of Africa, it was deemed important to carry out a plurifactorial analysis combining all of the data related to: the stratigraphy, taphonomic processes (post-depositional disturbance), analysis of natural processes that may have produced eoliths, experimentation and techno-functional analysis of the material. The stratigraphy shows clear interstratifications of fine and coarse fluviatile levels with often very clear particle size sorting of the coarse fraction. The archaeological material is typically found at the interface of these strata, either at the base of a clayey matrix, overlying a preceding coarse level, or in the superficial part of a sandy-clay deposit underlying coarse deposits. Post-depositional disturbance revealed during the new excavations in 2003–2006 cannot alone be the cause of eoliths. Excavation of a 6 m² zone in the modern river bed, located below the site, has demonstrated that the technological traits of eoliths recovered cannot in any way be confused with the technological traits of the artifacts recovered at the site itself. Similarly, viewed quantitatively, the 6 m² zone excavated in the river bed yielded around 20 eoliths while the 30 m² zone excavated at the site yielded 854 artifacts, one stratum alone yielding 184 artifacts in a 3 m² zone. During the experimental phase, adopting the same conditions of procuring raw material, from the same river bed, we very quickly realized the rarity of types of adequate volume that had been generally used at the site and the need to use certain operational processes to create such a form. In addition, the hardness and presence of several natural fracture planes in the Triassic limestone explain the choice of different operational processes and the very high number of knapping accidents, including those occurring during bipolar percussion. Although 90% of the raw material used was cobbles or broken blocks of local Triassic limestone, 10% of the tools were made on exogenous raw materials – siliceous or gravelly limestone, quartzitic sandstone, chert, volcanic rock – that are absent from the immediate environment of the site. These raw materials were brought to the site in the form of tools: worked cobbles, large retouched flakes, backed double-truncated flakes, a plaquette with a lateral bifacial edge, etc. The 854 artifacts have been classified into six object classes: worked cobbles with transversal edge (39%), worked cobbles with lateral edge (2%), unipolar flakes (27%), bipolar objects (half-blocks, half-cobbles including some flat “split” cobbles, “orange slices”, flakes and diverse fragments) (17%) and fragments resulting from knapping of blocks or cobbles (13%), hammerstone (2%). When the frequencies of these classes are calculated for each of the sectors, percentages are similar, indicating a high degree of homogeneity in the archaeological assemblages at the site. The situation is somewhat different when assemblages are compared within a single sector. Slight differences appear in the percentages of bipolar pieces and unipolar flakes. These differences seem to be random, like the frequency rate of knapping accidents in bipolar reduction, or economic, such as the choice of operational schemes to create worked cobbles based on the availability of suitable raw materials. The technological affinity between each of the archaeological assemblages tends to demonstrate great stability in technological knowledge through time. The class of worked cobbles is by far the most important and, apart from a few flakes produced intentionally, it appears to group all of the tools. To avoid placing these tools in a restrictive, semantically meaningless, class, we prefer the concept of matrix to the term worked cobble. A matrix is a structured arrangement of a series of technological traits, in a form as close as possible to that of the future tool. The matrix phase leads to the tool production phase, which may be unnecessary if the matrix phase includes fictionalization. In other words, the concept of matrix enables separating the phase of preparing a predetermined volume, such as a blade, Levallois flake or bifacial piece, from the tool production phase, consisting in creating the type of transformative edge intended, if necessary. The tool is thus an artifact of a specific form with an integrated edge and an operational scheme both specific to the function attributed to it and means of use associated with the form. Observed variability relates to: the size of the volume ranging from to 20, morphology, the form of the line formed by the edge which can in frontal view be curved, linear, sinuous or denticulated, and in transversal view curved, linear, sinuous or saw-toothed, and the length of the edge ranging from 1 to 10. Matrices with a simple bevel are distinguished from double bevels. In the framework of the technological analysis of production schemes to produce matrices with a simple bevel, a broad range of variability in production schemes can be observed, divided arbitrarily into two stages. The first stage consists in creating as closely as possibly the technological traits of the future matrix due to five general schemes. The first scheme (A) consists in selecting a cobble or block naturally possessing at least some of the technological traits needed. The missing traits are added by various preparations, including bipolar percussion 3 times out of 5. The second scheme (B) consists in knapping a flake from the block with some of the technological traits required for the matrix present on one of its surfaces. The third scheme (C) consists in the choice of a plaquette from which a bipolar shock creates the main traits of the matrix. The fourth scheme (D) consists in choosing a volume very similar to the intended matrix. The fifth and final scheme (E) consists in knapping a flake with technological traits very different from those intended. Depending on the distance between intention and realization, a second stage may be necessary. In general, this second stage perfects or creates the intended active edge, which is rarely obtained in the first stage. To produce a matrix with a double bevel, it is sometimes necessary to add an intermediate stage in order to prepare the second bevel. The first stage remains the same, with the use of the five operational schemes. By contrast, a clear difference exists in the percentages for the use of these schemes. For a matrix with a simple bevel, scheme A is dominant, followed by scheme D, while the situation is reversed for a matrix with a double bevel, where scheme D is dominant. Unipolar flakes, representing 27% of the assemblage, are produced in three different ways. The most important is flakes resulting from matrix production. The two others are flakes produced during different knapping schemes, some flakes in relation to the few cores present, other flakes in exogenous raw materials produced elsewhere and generally much larger. The other classes are dominated by bipolar products resulting essentially from knapping accidents. To summarize, these assemblages are characterized by: the search for tools differentiated by form and active edges; more than 90% of the tools made on two kinds of supports: a matrix with a simple bevel or a double bevel; matrices obtained using different operational schemes successively associating if necessary a knapping stage and a shaping stage. While the Triassic limestone is hard and thus imposes a strong constraint on knapping, the range of operational schemes appears to have been a “cultural” response diversified to this constraint and the presence of tools on exogenous raw materials. At the scale of China, comparison of this industry is impossible since it is the only site of this age and to contain so much material. The site of Majuangou, the only site of similar caliber, is younger by several hundred thousand years and is located several thousand kilometers to the north, making comparisons meaningless. We note only that most of the tool supports at Majuangou are knapped flakes. On an inter-continental scale, the comparison of sites of equal age is more promising. But lithic analyses are based on different methods, preventing comparison of similar data. However, if we make a simple summary of the data available, we can first say that in Africa, during these periods, different development technological stages were present and stages that are considered more evolved are manifestly less common using our approach. While these stages are more or less contemporaneous, which counters the idea of uniqueness, they would more surely be evidence of populations that were not in direct contact and had separate lines of development. In Asia, the Longgupo industry evidences a different technological option than that of contemporaneous populations in Africa. By contrast, when we take into account its developmental stage, we realize that this is an “evolved” stage in which the form of the support of the future tool is predominant. If we compare Africa and Asia in terms of stages, we are a priori at the same stage with different options being selected.     

Le gisement acheuléen de plein air de La Garde (Loire). Remarques sur une série lithique acheuléenne entre Rhône et Loire

The lithic assemblage of La Garde offers the opportunity to observe a Final Acheulean series located in the Loire department (south-east France). The site was probably a multi-activity place asking large tools and flakes, according to the strategies used by humans. Three main categories of large bifacial tools mainly made of flint can be described, with a triangular or oval shape and with a transversal cutting edge. These tools are more bifacial-tools than bifaces through the kind of shaping and the retouches on the cutting edges. The Levallois flaking is associated to various other types of knapping. The site, located along a small valley, suggests a human circulating between the Saône-Rhône corridor and the interior basins of the Massif Central Mountains. The Rhodanian corridor yielded little evidence of Acheulean settlements while in the Centre of France, they are numerous. La Garde proves that systematic prospecting in this area will permit in future to complete the map of the Acheulean occupations in south-east France.     

CST-II’s recognition domain for acceptor substrates in α-(2→8)-sialylations

CST-II is a bacterial sialyltransferase known for its ability to perform α-(2→8)-sialylations using GM₃ related trisaccharide substrates. Previously, we probed the enzyme’s substrate specificity and developed an efficient synthesis for α-(2→8)-oligosialosides, and we suggested that CST-II could have a very small substrate recognition domain. Here we report our full studies on CST-II’s recognition feature for acceptor substrates. The current study further demonstrates the versatility of CST-II in preparing complex oligosaccharides that contain α-(2→8)-oligosialyl moieties.