Lower Devonian reef structures in Russia: an example from the Urals

The Lower Devonian reefs of the Urals were formed in two different environmental settings: (1) the Novaya Zemlya-West-Uralian reefs were rigid organic structures that grew at a passive platform at the eastern margin of Baltica; (2) reefal limestones from the Eastern Urals developed in an island arc during a phase of volcanism. The reef belts can be traced for more than 2,500 km. The largest barrier reefs (up to 1,500 m thick) formed during the Pragian-Lower Emsian (West-Urals zone) and Emsian (East-Urals zone). They are characterized by rather uniform faunal and sedimentary features from the Arctic Ocean as south as near the Aral Lake. The Uralian reef facies was constructed mainly with algal and microbial communities (calcimicrobes and cyanobacteria) in association with low-diverse metazoan assemblages. In the Lower Devonian reefs of both regions, there are similar groups of organisms comprising some of the major taxa of reef-builders and reef-dwellers. The distinctive feature of the Lower Devonian reefs of both regions is the stromatolite-like framework structure. A clear palaeobiogeographic link is obvious between West-Uralian and East-Uralian environment settings during the Early Devonian.     

Succession of sessile organisms on experimental plates immersed in Nabeta Bay,Izu Peninsula,Japan V. An integrated consideration on the definition and prediction of succession

Successional changes of sessile organisms over about 3 years on concrete plates immersed at depths of 1.0, 2.5, 4.0 and 5.5 m in Nabeta Bay, Shimoda, Pacific coast of Japan, were investigated from their species composition, percentage cover, and the structure, metabolism, biomass and maturity of the community for the purpose of verifying the hypothesis of succession by Margalef (1968) and Odum (1969). The process of succession was divided into five stages from a cluster analysis based on Horn's (1966) similarity in community structure. The five stages were characterized from dominant, species and 18 community attributes in terms of structure, metabolism, biomass and maturity. With the advance of stages, two large-sized, long-lived species, the kelpEisenia bicyclis and the oysterCrassostrea nippona, dominated; 18 community attributes showed a directional succession ending in a constant community structure, low community metabolism, accumulation of community biomass except chlorophylla and an enhanced degree of community maturity. This directionality in succession of community attributes was valid for the prediction of Margalef and Odum, despite a tendency for estimated daily energy budget to be more heterotrophic in such an open system. From these results, it was suggested that the definition of succession by Odum (1969) should be interpreted as the regularity in shift of dominant species, not individual species, and as the control of system by feedback mechanism developing with succession rather than community-controlled mechanism.     

Quantification of high-frequency sea-level fluctuations in shallow-water carbonates: an example from the Berriasian–Valanginian (French Jura)

When quantifying sedimentary processes on shallow carbonate platforms, it is important to know the high-frequency accommodation changes through time. Accommodation changes in cyclic successions are often analysed by simply converting cycle thickness to Fischer plots. This approach is not satisfactory, because it does not account for differential compaction, possible erosion, sea-level fall below the depositional surface, or subtidal cycles. An attempt is made here to reconstruct a realistic, high-frequency accommodation and sea-level curve based on a detailed facies and cyclostratigraphical analysis of Middle Berriasian to Lower Valanginian sections in the French Jura Mountains. The general depositional environment was a shallow-marine carbonate platform on a passive margin. Our approach includes the following steps: (1) facies interpretation; (2) cyclostratigraphical analysis and identification of Milankovitch parameters in a well-constrained chronostratigraphic framework; (3) differential decompaction according to facies; (4) estimation of depth ranges of erosion and vadose zone; (5) estimation of water-depth ranges at sequence boundaries and maximum flooding intervals; (6) estimation of mean subsidence rate; (7) classification of depositional sequences according to types of facies evolution: ‘catch-up’, ‘catch-down’, ‘give-up’, or ‘keep-up’; (8) classification of depositional sequences according to long-term sea-level evolution: ‘rising’, ‘stable’, ‘falling’; (9) calculation of ‘eustatic’ sea-level change for each depositional sequence using the parameters inferred from these scenarios, assuming that sea-level cycles were essentially symmetrical (which is probable in Early Cretaceous greenhouse conditions); (10) calculation of a sea-level curve for each studied section; (11) comparison of these curves among each other to filter out differential subsidence; (12) construction of a ‘composite eustatic’ sea-level curve for the entire studied platform; (13) spectral analysis of the calculated sea-level curves. Limitations of the method are those common to every stratigraphic analysis. However, the method has the potential to improve the original cyclostratigraphical interpretations and to better constrain the high-frequency sea-level changes that control carbonate production and sediment fluxes.     

First evidence of Late Carnian radiolarians from the Izmir-Ankara suture complex, central Sakarya, Turkey: implications for the opening age of the Izmir-Ankara branch of Neo-Tethys

Within the Late Cretaceous mélange complex of the Izmir-Ankara suture zone in central Sakarya area, north-western Turkey, a megablock with radiolarian cherts associated with basaltic pillow lavas has been dated by radiolarians. The studied radiolarian assemblage and conodonts yielded an early Late Carnian age. This age is the oldest obtained from the chert blocks all along the suture belt and has important implications for the rifting/opening age of the Izmir-Ankara branch of the Tethys ocean in north-western Turkey. Based on this new data, it is concluded that during the Late Triassic the Izmir-Ankara seaway was connected to the other Tethyan oceanic branches and deep enough to provide chert sedimentation and exchange radiolarians with the main open oceans. It is further suggested that the long-lasting misinterpretation of a Liassic rifting/opening of the Izmir-Ankara ocean should be revised.     

Oreoglanis infulatus, a new species of glyptosternine catfish (Siluriformes: Sisoridae) from central Vietnam

A new species of glyptosternine catfish, Oreoglanis infulatus , is described from the Lam River drainage in central Vietnam. The new species is distinguished from all its congeners by possessing the following combination of characters: a dark band running across the anal fin, a lunate and uniformly dark caudal fin, the lower lip lacking a medial notch and with a lobulate posterior margin, maxillary barbel with a rounded tip, length of caudal peduncle 19·0–22·6 % L _S, depth of caudal peduncle 2·6–3·2 % L _S, post-adipose distance 6·8–8·0 % L _S, eye diameter 10·5–12·1 % L _H, 12 principal caudal-fin rays.     

Outbreak of central nervous system disease associated with hand,foot, and mouth disease in Japan during the summer of 2000: detection and molecular epidemiology of enterovirus 71

Few outbreaks of the serious enterovirus 71 (EV71) infections, which affect the central nervous system (CNS), had been reported in Japan before 2000. During June through August 2000, a patient died of pulmonary edema caused by brainstem encephalitis accompanied by EV71-induced hand, foot, and mouth disease (HFMD), and many patients complicated by serious CNS disease, including paralysis, were hospitalized in a restricted area in Hyogo Prefecture, Japan (K-area). During the same period, endemics of HFMD were reported in other areas in Hyogo Prefecture, where EV71 was isolated from HFMD patients, but few patients developed aseptic meningitis. The isolations of EV71 from K-area patients were difficult with the use of Vero cells, so the strains were isolated by use of GL37 cells; Vero cells, however, could isolate EV71 strains from other areas in Hyogo Prefecture. We sequenced VP4 coding regions of these EV71 isolates and found that the isolates from K-area had the same sequence, which, except for one isolate, was different from the sequences of EV71 strains isolated from other areas of Hyogo Prefecture. Although these results were not enough to state that EV71 from K-area was a virulent strain, it seemed reasonable to conclude that serious CNS diseases in K-area were caused by EV71 because it was the only infectious agent detected in the inpatients of K-area.     

New era of optogenetics: from the central to peripheral nervous system

Abstract

Optogenetics has recently gained recognition as a biological technique to control the activity of cells using light stimulation. Many studies have applied optogenetics to cell lines in the central nervous system because it has the potential to elucidate neural circuits, treat neurological diseases and promote nerve regeneration. There have been fewer studies on the application of optogenetics in the peripheral nervous system. This review introduces the basic principles and approaches of optogenetics and summarizes the physiology and mechanism of opsins and how the technology enables bidirectional control of unique cell lines with superior spatial and temporal accuracy. Further, this review explores and discusses the therapeutic potential for the development of optogenetics and its capacity to revolutionize treatment for refractory epilepsy, depression, pain, and other nervous system disorders, with a focus on neural regeneration, especially in the peripheral nervous system. Additionally, this review synthesizes the latest preclinical research on optogenetic stimulation, including studies on non-human primates, summarizes the challenges, and highlights future perspectives. The potential of optogenetic stimulation to optimize therapy for peripheral nerve injuries (PNIs) is also highlighted. Optogenetic technology has already generated exciting, preliminary evidence, supporting its role in applications to several neurological diseases, including PNIs.     

Temporal settlement patterns of larvae of the broadcast spawning reef coral Favites chinensis and the broadcast spawning and brooding reef coral Goniastrea aspera from Okinawa, Japan

The faviid corals, Favites chinensis and Goniastrea aspera are widely distributed in the Indo-Pacific region. Both corals are hermaphroditic broadcast spawners, but G. aspera is also known to brood planula larvae in Okinawa. This study investigated the temporal settlement patterns of planula larvae of the scleractinian corals F. chinensis and G. aspera that developed from spawned gametes, and planula release and settlement of brooded larvae of G. aspera from Okinawa, Japan. Some of the broadcast-spawned larvae of F. chinensis and G. aspera had very short pre-competency periods of 1–2 and 2–3 days after spawning, and relatively long maximum settlement-competency periods of 56–63 and 63–70 days after spawning, respectively. These pre-competency periods are among the shortest reported for larvae of broadcast spawning coral species, and appear to be negatively correlated with seawater temperature. F. chinensis larvae tended to settle rapidly with 34–39% of larvae settling in the first week after spawning, while broadcast-spawned G. aspera larvae had a slower settlement pattern with 11–15% of larvae settling in the first week after spawning. Brooded larvae of G. aspera settled more rapidly, with settlement rates of 27–31% within the first 24 h and 45–65% within the first week after the start of the experiment. The production of planula larvae with rapid settlement capabilities may enable F. chinensis and G. aspera to establish and maintain populations in shallow reef sites at Okinawa. The release of the brooded planulae for up to 2 months may explain why G. aspera is locally more dominant on shallow reefs in Okinawa than F. chinensis. On a broader scale, the longer settlement competency periods of some of the broadcast-spawned larvae of these species increase their potential for longer-distance dispersal and may partly explain the wide biogeographic distribution of these species in the Indo-Pacific region.     

Notes on the boletes of Japan 1. Four new species of the genus Boletus from central Honshu,Japan

Four new species of Boletus are fully described and illustrated from central Honshu, Japan: (1) B. panniformis (Section Calopodes) produces a typically felted and scabrous pileus, bitter flesh, a finely reticulate, red stipe, and occurs in subalpine, coniferous forests; (2) B. ventricosus (Section Appendiculati) forms a usually ventricose or subbulbous stipe, yellow to greyish orange, extremely short tubes, often pluriseptate, broadly clavate to doliform caulocystidia, and occurs in lowland, mixed forests; (3) B. cepaeodoratus (Section Appendiculati) possesses a pinkish red pileus, a usually finely reticulate stipe, relatively short tubes, and occurs in lowland, mixed forest; (4) B. viscidipellis (Section Luridi) yields a hairy, viscid pileus, intensely cyanescent flesh, and occurs in lowland, mixed forests.     

Estimation of photosynthesis and calcification rates at a fringing reef by accounting for diurnal variations and the zonation of coral reef communities on reef flat and slope: a case study for the Shiraho reef, Ishigaki Island, southwest Japan

Seven coral reef communities were defined on Shiraho fringing reef, Ishigaki Island, Japan. Net photosynthesis and calcification rates were measured by in situ incubations at 10 sites that included six of the defined communities, and which occupied most of the area on the reef flat and slope. Net photosynthesis on the reef flat was positive overall, but the reef flat acts as a source for atmospheric CO₂, because the measured calcification/photosynthesis ratio of 2.5 is greater than the critical ratio of 1.67. Net photosynthesis on the reef slope was negative. Almost all excess organic production from the reef flat is expected to be effused to the outer reef and consumed by the communities there. Therefore, the total net organic production of the whole reef system is probably almost zero and the whole reef system also acts as a source for atmospheric CO₂. Net calcification rates of the reef slope corals were much lower than those of the branching corals. The accumulation rate of the former was approximately 0.5 m kyr⁻¹ and of the latter was ~0.7–5 m kyr⁻¹. Consequently, reef slope corals could not grow fast enough to keep up with or catch up to rising sea levels during the Holocene. On the other hand, the branching corals grow fast enough to keep up with this rising sea level. Therefore, a transition between early Holocene and present-day reef communities is expected. Branching coral communities would have dominated while reef growth kept pace with sea level rise, and the reef was constructed with a branching coral framework. Then, the outside of this framework was covered and built up by reef slope corals and present-day reefs were constructed.     

Effects of climate on the radial growth of tree species in the upper and lower distribution limits of an altitudinal ecotone on Mount Norikura,central Japan

Tree-ring width chronologies were developed for Abies veitchii, Betula ermanii and Betula platyphylla var. japonica in their altitudinal ecotone (approximately 1600m a.s.l.) on Mount Norikura, central Japan, to determine what climatic conditions affect the growth of tree species in the upper and lower distribution limits of an altitudinal ecotone. This altitude was the lower distribution limit for A.veitchii and B.ermanii in the subalpine zone, and was the upper distribution limit for B.platyphylla var. japonica in the montane zone on Mount Norikura. Tree-ring widths of the two Betula species and A.veitchii were positively correlated with the August precipitation of the current and previous years, respectively. Precipitation in August (the hottest month) was reduced compared with other months during summer. Tree-ring width of B.platyphylla var. japonica showed no correlation with temperatures in any month in its upper distribution limit. In contrast, tree-ring widths of B.ermanii and A.veitchii were negatively correlated with the August temperatures of the current and previous years, respectively, at the lower distribution limit of these species. Therefore, the two Betula species and A.veitchii responded to climatic conditions of the current and previous years, respectively. The present study also suggests that a water deficit in August reduces growth of these three species in this altitudinal ecotone, irrespective of the upper or lower distribution limits, and that a high August temperature is more detrimental to the growth of A.veitchii and B.ermanii in their lower distribution limits. Thus, the three species with different altitudinal distributions examined in the present study responded differently to climatic conditions in this altitudinal ecotone on Mount Norikura.     

Two new species of the interstitial genus Parvocythere (Crustacea, Ostracoda, Cytheroidea) from Japan: an example of morphological variation

Two new species of the interstitial ostracod genus Parvocythere, Parvocythere gottwaldisp. n. and Parvocythere gracilissp. n., are herein described. Although these two new species are clearly distinguishable by certain morphological differences in elements of the male copulatory organ, and the carapace, they share the following simplified characters of the appendages and male copulatory organ: antennular fourth podomere with no suture; reduced claws on the distal end of antenna; and asymmetric male copulatory organ. The morphological differences among known and new Parvocythere species suggest that the species of this genus can be classified into two groups by the presence/absence of the suture on the antennular fourth podomere. The "Group S" is characterised by the presence of the antennular suture, and all species of this group have a two-clawed antenna and symmetric male copulatory organ, characters which are generally seen in cytheroid ostracods. The species belonging to "Group N" are characterised by the absence of the suture, regarded as a pedomorphic character, show the following characters: two clawed or one clawed antenna, and symmetric or asymmetric male copulatory organ. The morphological variation within Group N includes reductive characters regarded as an adaptation to the narrow spaces of the interstitial environment of a sandy beach. These intrageneric morphological variations of the exclusively interstitial genus Parvocythere suggest the possibilities that Group N might be derived from Group S, and that some adaptive characters to an interstitial environment could have developed after the colonisation of these environments.     

New cockroaches from the Upper Carboniferous of Siberia (Insecta: Dictyoptera,Mylacridina)

Cockroaches (Dictyoptera, Mylacridina) from the Chunya locality (Upper Carboniferous of the Central Siberian Plateau) are considered. New representatives of the family Phyloblattidae Schneider, 1983 (Phyloblatta majuscula sp. nov., P. chunyensis sp. nov., Hesperoblatta vishniakovae sp. nov., and H. secunda sp. nov.) are described.     

Climatic changes during the past 1300 years as deduced from the sediments of Lake Nakatsuna, central Japan

Limnological features and sediment characteristics were studied in Lake Nakatsuna, a mesotrophic lake in central Japan. The lake is dimictic, and is anoxic in the hypolimnion during thermal stratification from May to September. In an attempt to reconstruct paleoclimatic changes around the lake, a sediment core taken from the lake center spanning the past 1300 years was analyzed for its organic and inorganic contents. Climatic influences were examined on the variation of total organic carbon (TOC), total nitrogen (TN), and sand contents. Short- and long-term fluctuations in TOC, TN, and sand contents are evident, and variation in atmospheric temperature appears to be important for their long-term variability. The sediment record from AD 900 to 1200 indicates hot summers and warm winters with less snow accumulation, whereas the record from AD 1200 to 1950 is characterized by high variation of temperature, with three cool phases from AD 1300 to 1470, 1700 to 1760, and 1850 to 1950. The warm period from AD 900 to 1200 corresponds well to the Medieval Warm Period, and the second and third cool phases are related to the Little Ice Age. Received: February 16, 2001 / Accepted: June 7, 2001     

四川江油渔洞子下三叠统飞仙关组巨鲕灰岩中疑似蓝细菌及早三叠世疑似蓝细菌的双幕式爆发

二叠纪末海洋生态环境的恶化导致海洋底栖生物的大灭绝及早三叠世蓝细菌的爆发,有关这一时期我国华南蓝细菌化石的报道主要来自早三叠世早期的微生物岩。四川江油渔洞子剖面下三叠统飞仙关组下部巨鲕灰岩中首次发现有丰富的疑似蓝细菌,在种类和结构上与以往所报道的蓝细菌有着明显区别。疑似蓝细菌在巨鲕内和围岩中的富集,表明巨鲕灰岩的成因与疑似蓝细菌的活动有关,与飞仙关组底部微生物岩在成因上有着密切联系,显示早三叠世早期在这一地区发生了疑似蓝细菌的双幕式爆发,同时,暗示着这一地区二叠纪-三叠纪之交至少发生了两次海洋环境恶化及动物灭绝事件。疑似蓝细菌的爆发性生长,对于海洋生态环境的修复和海洋含氧条件的改善,进而为早三叠世末、中三叠世的生物全面复苏、辐射有着重要意义。     

Sedimentary facies from Upper Triassic reefal limestone of the Sambosan accretionary complex in Japan: mid-ocean patch reef development in the Panthalassa Ocean

Microfacies of the Early to Middle Norian reefal limestone of the Sambosan Accretionary Complex (SAC) at Kamase locality, southwest Japan, are classified into seven major facies types in stratigraphic order: peloidal grainstone-packstone, unfossiliferous lime-mudstone, tubular problematica-rich wackestone, sponge-coral floatstone, sponge bafflestone, coral rudstone, and peloidal-bioclastic packstone-grainstone. The SAC records patch reef development on a mid-oceanic seamount in the Panthalassa Ocean. Because most examples of Triassic reefs come from the former Tethys, counterparts such as those from the SAC are pivotal in resolving paleogeographic issues as well as clarifying the depositional patterns between the eastern Tethys and adjacent western Pacific (Panthalassa). We also reveal that the primary stratigraphy of the reefal limestone was disrupted by submarine landslides of the seamount in an open-ocean realm during the late Middle to Late Jurassic time.     

The plant landscape as inferred from a basket of the Roman town of Privernum (Latium,central Italy)

Abstract

Privernum was a rich Roman colony located 70 km southwest of Rome (southern Latium, central Italy). The archaeobotanical investigations focused on the garden and related structures of the luxury domus della Soglia nilotica. They are archaeologically and radiocarbon dated to the second half of the 1st century AD. The remains of a charred basket were found in the filling of the euripus, an ornamental water basin of the garden. The weaving was made with twisted strands of the leaves of Ampelodesmos mauritanicus (Poir.) T. Durand and Schinz; for the bottom and the handle/s of the basket, wood of evergreen oaks and ash and/or elm, respectively were probably used. The basket contained Pinus pinea seeds and cone scales, and Prunus persica endocarps, which were probably burnt in summer. The sediment in the drainage system and in the kitchen was processed for macro- and microremains. The results indicate the presence of spontaneous ruderal and weed flora elements, typical of human settlement areas, and crops.     

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny,physiology and stable isotope fractionation

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH₃) to nitrite (NO₂⁻). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (¹⁵ɛ_NH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal ¹⁵ɛ_NH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by ¹⁵ɛ_NH3 is similar.     

On the prosthetic groups of the NiFe sulfhydrogenase from Pyrococcus furiosus: topology, structure, and temperature-dependent redox chemistry

 The sulfhydrogenase complex of Pyrococcus furiosus is an αβγδ heterotetramer with both hydrogenase activity (borne by the αδ subunits) and sulfur reductase activity (carried by the βγ subunits). The β-subunit contains at least two [4Fe-4S] cubanes and the γ-subunit contains one [2Fe-2S] cluster and one FAD molecule. The δ-subunit contains three [4Fe-4S] cubanes and the α-subunit carries the NiFe dinuclear center. Only three Fe/S signals are observed in EPR-monitored reduction by dithionite, NADPH, or internal substrate upon heating. All other clusters presumably have reduction potentials well below that of the H⁺/H₂ couple. Heat-induced reduction by internal substrate allows, for the first time, EPR monitoring of the NiFe center in a hyperthermophilic hydrogenase, which passes through a number of states, some of which are similar to states previously defined for mesophilic hydrogenases. The complexity of the observed transitions reflects a combination of temperature-dependent activation and temperature-dependent reduction potentials. Received: 10 December 1998 / Accepted: 16 February 1999