bluuebunny/crossref_metadata_2025 huggingface dataset:
Transcriptional analysis of the pheromone gland of the turnip moth, Agrotis segetum (Noctuidae), reveals candidate genes involved in pheromone production
Authors: Strandh M. , Johansson T. , Ahrén D. , Löfstedt C.
Published: September 2010

Moths generally rely on pheromone communication for mate finding. The pheromone components of most moths are produced by a common pathway of fatty‐acid biosynthesis coupled with species‐specific modifications of the final products. Some genes involved in moth pheromone production have previously been described, whereas others remain to be characterized and thus the molecular mechanisms accounting for the production of species‐specific blends are far from understood. The turnip moth, Agrotis segetum, has a multicomponent pheromone, consisting of at least four components derived from palmitic and stearic acid. Different populations produce and respond to different pheromone blends, which makes this species an excellent model for research on genes and molecular mechanisms involved in moth pheromone production. For this purpose, we performed an expressed sequence tag (EST) analysis of two cDNA libraries, one representing the female pheromone gland and the other representing the remainder of the insect body. Among 2285 ESTs analysed altogether, we identified a unigene set of 707 putative gene representatives. The comparative distribution of those in the two libraries showed the transcriptomes of the tissues to be clearly different. One third of the gene representatives were exclusively found in the pheromone gland. From sequence homology to public database information we assigned putative functional roles for a majority of the unigenes and then compared functional profiles of the two tissues. In the set of ESTs more abundant in the pheromone gland library, we found homologues of an acyl‐CoA Δ11‐desaturase, a G‐protein subunit, a chemosensory protein as well as a juvenile hormone binding protein.
Membrane fluidity and lipid content of human spermatozoa selected by swim‐up method
Authors: Force A. , Grizard G. , Giraud M. N. , Motta C. , Sion B. , Boucher D.
Published: September 2010

In this work, we examined whether spermatozoa (spz) from normospermic fertile patients and selected by a swim‐up (S‐U) procedure had a particular membrane fluidity related to their maturity and their lipid content as compared with the sperm cells from the whole ejaculate (total sperm). Swim‐up selected sperm had a reduced cytoplasmic space as revealed by a lower creatine kinase (CK) activity compared with total sperm (2 ± 1 vs. 12 ± 5 mUI/107 spz, p < 0.05). The cholesterol (Chol) and total phospholipid (PL) contents were significantly lower in S‐U selected sperm than in total sperm (0.72 ± 0.08 vs. 1.20 ± 0.30 nmol/106 spz for Chol and 1.77 ± 0.17 vs. 2.78 ± 0.50 nmol/106 spz for PL, p < 0.05) and such a decrease was observed for the three major membrane PL: phosphatidylethanolamine (PE), phosphatidylcholine (PC) and sphingomyelin (SM). However, these decreases were not associated with a change in either Chol/PL or PC/(PC + PE) molar ratios. Membrane fluidity estimated by fluorescence polarization remained comparable between the S‐U sperm fraction and total sperm (fluorescence polarization anisotropy, r, which is inversely proportional to the fluidity: 0.235 ± 0.006 vs. 0.230 ± 0.005). The sperm membrane fluidity obtained in normospermic patients was compared with abnormospermic ones (oligoasthenoteratospermia). In abnormospermic patients, the membrane fluidity was decreased in migrated spermatozoa compared with total sperm (anisotropy: 0.210 ± 0.010 vs. 0.250 ± 0.013, p < 0.01). Our data suggest that the S‐U method selected a subpopulation of mature spermatozoa characterised by a low content of Chol and PL, likely related to a reduced membrane area. The fact that Chol/PL and PC/(PC + PE) molar ratios were unchanged shows a maintenance of the membrane quality. This was confirmed by the fluorescence anisotropy measurement showing no difference in plasma membrane fluidity between S‐U selected sperm and total sperm. In abnormal semen the migrated spermatozoa had a lower fluidity compared with total sperm suggesting a defective sperm function. These results bring new elements characterizing the S‐U selected spermatozoa.
Sperm washing method alters the ability of seminal plasma proteins to revert the cold‐shock damage on ram sperm membrane
Authors: Pérez‐Pé R. , Muiño‐Blanco T. , Cebrián‐Pérez J. A.
Published: September 2010

Prolonged exposure of spermatozoa to seminal plasma (SP) has been found to have adverse effects on sperm function. Therefore, the separation of mammalian spermatozoa from SP is a practice routinely used in the laboratory and in assisted reproductive technology application. We have previously shown that adsorption of seminal plasma proteins (SPP) to the sperm cell surface partially restores the functional characteristics of damaged spermatozoa, reproducing those of live cells. In the present report, we have compared the influence of two different semen washing methods, a dextran/swim‐up or a filtration procedure, on the SPP adsorption to the sperm surface, and on their ability to recover membrane integrity of cold‐shocked sperm.

Seminal plasma proteins were added to cold‐shocked sperm samples obtained by both washing procedures. Adsorption of proteins to the sperm membrane surface was assessed by centrifugal counter‐current distribution (CCCD) in an aqueous two‐phase system, as well as membrane integrity being determined by fluorescence markers. The percentage of reversion of cold‐shock effect in the sample containing plasma proteins with respect to the control sample was determined by assessing the percentage of membrane‐intact spermatozoa, i.e. propidium iodide‐negative. The addition of 700 μg of SPP to the swim‐up damaged samples caused a 32% reversion, whereas the reversal percentage found with the same amount of SPP on filtered damaged samples was 10% (p < 0.05). Likewise, the loss of heterogeneity and the decrease in viability after the cold‐shock revealed by CCCD analysis were greatly reversed by the addition of SPP to sperm samples obtained by swim‐up. However, this restorative effect was again much lower when SPP were added to the cold‐shocked filtered sample. These results strongly suggest that the washing method influences the ability of SPP to recover membrane integrity of cold‐shocked sperm. Separation of spermatozoa by swim‐up accounts for higher viability recovery than that obtained by filtration washing.
Towards a biogeographic regionalization of the European biota
Authors: Rueda Marta , Rodríguez Miguel Á. , Hawkins Bradford A.
Published: September 2010

Aim  To determine if it is possible to generate analytically derived regionalizations for multiple groups of European plants and animals and to explore potential influences on the regions for each taxonomic group.

Location  Europe.

Methods  We subjected range maps of trees, butterflies, reptiles, amphibians, birds and mammals to k‐means clustering followed by v‐fold cross‐validation to determine the pattern and number of regions (clusters). We then used the mean range sizes of species in each group as a correlate of the number of regions obtained for each taxon, and climate and species richness gradients as correlates of the spatial arrangement of the group‐specific regions. We also included the pattern of tree clusters as a predictor of animal clusters in order to test the ‘habitat templet’ concept as an explanation of animal distribution patterns.

Results  Spatially coherent clusters were found for all groups. The number of regions ranged from three to eight and was strongly associated with the mean range sizes of the species in each taxon. The cluster patterns of all groups were associated with various combinations of climate, underlying species richness gradients and, in the case of animals, the arrangement of tree clusters, although the rankings of the correlates differed among groups. In four of five groups the tree pattern was the strongest single predictor of the animal cluster patterns.

Main conclusions  Despite a long history of human disturbance and habitat modification, the European biota retains a discernable biogeographic structure. The primary driver appears to be aspects of climate related to water–energy balance, which also influence richness gradients. For many animals, the underlying habitat structure, as measured by tree distributions, appears to have a strong influence on their biogeographic structure, highlighting the need to preserve natural forest formations if we want to preserve the historical signal found in geographic distributions.
Consensus on interprofessional collaboration in hospitals: statistical agreement of ratings from ethnographic fieldwork and measurement scales
Authors: Kenaszchuk Chris , Conn Lesley Gotlib , Dainty Katie , McCarthy Colleen , Reeves Scott , Zwarenstein Merrick
Published: September 2010

Rationale  Few methods are available for analysing psychometric properties of combined qualitative and quantitative data. While conventional reliability of measures – meaning reproducibility or consistency – may not be meaningful in small‐N research, in some health services studies agreement on perceptions arising from data generated by fieldwork and quantitative measures can be examined to good effect.

Methods  We studied interprofessional collaboration (IPC) in seven hospitals. An ethnographer shadowed and conducted interviews with regulated health professionals in medicine wards. Concurrently, nurses completed the nurse–doctor relations subscale of the Nursing Work Index (NWI‐NDRS) and a new measurement scale for IPC with doctors in the domains of communication, accommodation, and isolation. After fieldwork, the ethnographer rank‐ordered hospital sites on IPC from 1 to 7 based on interpretation of the qualitative data. Mean‐scale scores were calculated for hospital sites and converted to ranks similarly. The Tinsley‐Weiss T‐index (Tinsley & Weiss, 1975) for agreement among rank orderings was calculated for dyadic combinations of fieldwork and measurement ranks.

Results  Perfect agreement was obtained for the most liberal agreement definitions considered – differences of two rank positions – involving qualitative data agreement with IPC subscales for accommodation and isolation. Defining agreement as a difference of 1 rank at most, the T‐index was 0.77 for agreement between fieldworker and IPC accommodation and the same for NWI‐NDRS and IPC isolation.

Conclusion  Qualitative data from fieldwork rankings were substantially in accord with the contemporary IPC scales, less so with the NWI‐NDRS. Qualitative data appear to be useful as an additional approach to confirming the validity of quantitative scale data in measuring a complex interpersonal relational construct.
Laboratory sample turnaround times: do they cause delays in the ED?
Authors: Gill Dipender , Galvin Sean , Ponsford Mark , Bruce David , Reicher John , Preston Laura , Bernard Stephani , Lafferty Jessica , Robertson Andrew , Rose‐Morris Anna , Stoneham Simon , Rieu Romelie , Pooley Sophie , Weetch Alison , McCann Lloyd
Published: September 2010

Objectives  Blood tests are requested for approximately 50% of patients attending the emergency department (ED). The time taken to obtain the results is perceived as a common reason for delay. The objective of this study was therefore to investigate the turnaround time (TAT) for blood results and whether this affects patient length of stay (LOS) and to identify potential areas for improvement.

Methods  A time‐in‐motion study was performed at the ED of the John Radcliffe Hospital (JRH), Oxford, UK. The duration of each of the stages leading up to receipt of 101 biochemistry and haematology results was recorded, along with the corresponding patient's LOS.

Results  The findings reveal that the mean time for haematology results to become available was 1 hour 6 minutes (95% CI: 29 minutes to 2 hours 13 minutes), while biochemistry samples took 1 hour 42 minutes (95% CI: 1 hour 1 minute to 4 hours 21 minutes), with some positive correlation noted with the patient LOS, but no significant variation between different days or shifts.

Conclusions  With the fastest 10% of samples being reported within 35 minutes (haematology) and 1 hour 5 minutes (biochemistry) of request, our study showed that delays can be attributable to laboratory TAT. Given the limited ability to further improve laboratory processes, the solutions to improving TAT need to come from a collaborative and integrated approach that includes strategies before samples reach the laboratory and downstream review of results.
Patterns of colonization, evolution and gene flow in species of the genusPatellain the Macaronesian Islands
Authors: SÁ‐PINTO ALEXANDRA , BRANCO MADALENA , SAYANDA DIOGO , ALEXANDRINO PAULO
Published: September 2010

The study of phylogeographical patterns may contribute to a better understanding of factors affecting the dispersal of organisms in ecological and historical times. For intertidal organisms, islands are particularly suitable models allowing the test of predictions related to the efficacy of pelagic larvae dispersal. Here, we study the phylogeographical patterns and gene flow within three groups of species of the genusPatellapresent in the Macaronesian Islands that have been previously shown to be monophyletic. The genetic variability of around 600 bp of the mitochondrial gene cytochromecoxidase subunit I was studied by single strand conformation polymorphism and/or sequencing for seven species of limpets. A total of 420 samples were analysed from the Macaronesian archipelagos, North Africa, and Atlantic and Mediterranean shores of the Iberian Peninsula. No clear geographical pattern or temporal congruence was found between the three groups of species, pointing to independent histories and colonization events. However, for the three groups, the split between the Macaronesian and the mainland forms most probably occurred before 3.9 million years ago, predating the establishment of the current circulation patterns. The presence of pelagic larvae in these species is shown to be insufficient to ensure gene flow between continental and Macaronesian populations and between the Macaronesian archipelagos. In the endangered Azorean populations ofPatella candei, there is restricted gene flow to Flores and Graciosa.
Evidence for widespread cryptic sexual generations in apparently purely asexual Andricus gallwasps
Authors: STONE GRAHAM N. , ATKINSON RACHEL J. , ROKAS ANTONIS , ALDREY JOSÉ‐LUIS NIEVES , MELIKA GEORGE , Ács ZOLTAN , CSÓKA GYÖRGY , HAYWARD ALEXANDER , BAILEY RICHARD , BUCKEE CAROLINE , McVEAN GILEAN A. T.
Published: September 2010

Oak gallwasps (Hymenoptera, Cynipidae, Cynipini) are one of seven major animal taxa that commonly reproduce by cyclical parthenogenesis (CP). A major question in research on CP taxa is the frequency with which lineages lose their sexual generations, and diversify as purely asexual radiations. Most oak gallwasp species are only known from an asexual generation, and secondary loss of sex has been conclusively demonstrated in several species, particularly members of the holarctic genus Andricus. This raises the possibility of widespread secondary loss of sex in the Cynipini, and of diversification within purely parthenogenetic lineages. We use two approaches based on analyses of allele frequency data to test for cryptic sexual generations in eight apparently asexual European species distributed through a major western palaearctic lineage of the gallwasp genus Andricus. All species showing adequate levels of polymorphism (7/8) showed signatures of sex compatible with cyclical parthenogenesis. We also use DNA sequence data to test the hypothesis that ignorance of these sexual generations (despite extensive study on this group) results from failure to discriminate among known but morphologically indistinguishable sexual generations. This hypothesis is supported: 35 sequences attributed by leading cynipid taxonomists to a single sexual adult morphospecies, Andricus burgundus, were found to represent the sexual generations of at least six Andricus species. We confirm cryptic sexual generations in a total of 11 Andricus species, suggesting that secondary loss of sex is rare in Andricus.
Phylogeography and postglacial expansion of Mus musculus domesticus inferred from mitochondrial DNA coalescent, from Iran to Europe
Authors: RAJABI‐MAHAM HASSAN , ORTH ANNIE , BONHOMME FRANÇOIS
Published: September 2010

Few genetic data document the postglacial history of the western house mouse, Mus musculus domesticus. We address this by studying a sample from the southeastern tip of the Fertile Crescent in the Iranian province of Ahvaz. Including other published and unpublished data from France, Germany, Italy, Bulgaria, Turkey and other places in Iran, altogether 321 mitochondrial D‐loop sequences are simultaneously analysed. The patterns of coalescence obtained corroborate the classical proposal according to which the Fertile Crescent is where commensalism with humans has started in the Western Hemisphere, and from where the subspecies has expanded further west. Our data also clearly show that despite multiple colonisations and long‐range transportation, there is still a rather high ΦST of 0.39. The original expansion signal is still recognisable, with two well‐separated derived clades, allowing us to propose a hypothetical scenario in which expansion toward Europe and Asia Minor took at least two routes, tentatively termed the Mediterranean and the Bosphorus/Black Sea routes. This scenario resembles that of another domesticated species, the goat, and fits with the known progression of Neolithic culture. Given the concomitance of both phenomena around 12 000 years ago, we propose a recalibration of the D‐loop mutation rate to a much faster tick of ~40% per site per million years (Myr). This value should be used for intrasubspecific polymorphism, while the interspecific rate in Mus is presently estimated at 6–10%/site/Myr. This is in keeping with the now well recognised fact that only a subfraction of segregating mutations go to fixation.
Ecological and biogeographical inferences on two sympatric and enigmatic Andean cat species using genetic identification of faecal samples
Authors: NAPOLITANO CONSTANZA , BENNETT MAGDALENA , JOHNSON WARREN E. , O’BRIEN STEPHEN J. , MARQUET PABLO A. , BARRÍA IVÁN , POULIN ELIE , IRIARTE AGUSTÍN
Published: September 2010

The carnivore community of the altiplano ecosystem of the high Andes, including the Andean mountain cat (Leopardus jacobita) and pampas cat (Leopardus colocolo), is one of the least studied in the world. We determined the origin of 186 carnivore samples (184 faeces and two skulls) collected above 3000 m above sea level in northern Chile, including 33 from the Andean mountain cat and 75 from the pampas cat using diagnostic molecular genetic sequence variation. We determined for the first time food habits, habitat and physiographic associations, and general patterns of molecular genetic variation of the Andean mountain cat and the pampas cat in Chile. Both species had narrow dietary niches dominated by small rodents and there was a wide overlap in diet composition (0.82), suggesting low levels of prey partitioning between species. The mountain viscacha (Lagidium viscacia) made up a large proportion of the biomass of the diet of both species, especially for the Andean mountain cat (93.9% vs. 74.8% for the pampas cat), underscoring the importance of further research and conservation focus on this vanishing prey species. Although the probability of finding Andean mountain cat scats increased with altitude and slope, there was substantial geographical overlap in distribution between species, revealing that the pampas cat distribution includes high‐altitude grassland habitats. The Andean mountain cat had relatively low levels of mitochondrial DNA (mtDNA) genetic variation (two mtDNA haplotypes) compared with the pampas cat (17 mtDNA haplotypes), suggestive of a distinct evolutionary history and relatively smaller historic populations. These insights will facilitate and provide tools and hypotheses for much‐needed research and conservation efforts on these species and this ecosystem.
Postglacial range expansion from northern refugia by the wood frog,Rana sylvatica
Authors: LEE‐YAW JULIE A. , IRWIN JASON T. , GREEN DAVID M.
Published: September 2010

Although the range dynamics of North American amphibians during the last glacial cycle are increasingly better understood, the recolonization history of the most northern regions and the impact of southern refugia on patterns of intraspecific genetic diversity and phenotypic variation in these regions are not well reconstructed. Here we present the phylogeographic history of a widespread and primarily northern frog,Rana sylvatica. We surveyed 551 individuals from 116 localities across the species’ range for a 650‐bp region of the NADH dehydrogenase subunit 2 and tRNATRPmitochondrial genes. Our phylogenetic analyses revealed two distinct clades corresponding to eastern and western populations, as well as a Maritime subclade within the eastern lineage. Patterns of genetic diversity support multiple refugia. However, high‐latitude refugia in the Appalachian highlands and modern‐day Wisconsin appear to have had the biggest impact on northern populations. Clustering analyses based on morphology further support a distinction between eastern and western wood frogs and suggest that postglacial migration has played an important role in generating broad‐scale patterns of phenotypic variation in this species.
Evolutionary genetics of a defensive facultative symbiont of insects: exchange of toxin‐encoding bacteriophage
Authors: DEGNAN PATRICK H. , MORAN NANCY A.
Published: September 2010

The facultative endosymbiont of aphids, Hamiltonella defensa, kills parasitoid wasp larvae, allowing aphid hosts to survive and reproduce. This protection may depend on toxins that are encoded by the genomes of H. defensa and of its bacteriophage (APSE). Strains of H. defensa vary in degree of protection conferred upon Acyrthosiphon pisum (pea aphid). Although H. defensa is known to undergo some horizontal transmission among aphid maternal lineages, divergence, recombination, and population structure in H. defensa and APSE have not been characterized. We performed a multilocus sequence analysis of 10 bacterial and five phage loci for strains isolated from A. pisum and other aphid species. The H. defensa chromosome was found to be largely clonal, allowing us to generate a well‐resolved H. defensa strain phylogeny. In contrast, APSE chromosomes undergo recombination and numerous H. defensa strains have probably lost the phage. Within a set of H. defensa strains that are indistinguishable on the basis of chromosomal genes or restriction digests of chromosomal fragments, loss of APSE is associated with decreased protection, strongly suggesting that APSE‐encoded genes contribute to the defensive phenotype. Thus, homologous recombination of APSE genes and sexual transmission of symbionts and phage are likely factors influencing the exchange of ecologically important genes among symbionts. Although H. defensa has been lost, transferred and gained within A. pisum, one subclade of H. defensa appears to be universal within a subclade of the aphid genus Uroleucon, suggesting a transition from facultative, horizontal transmission to strictly vertical inheritance.
Colonization genetics of an animal‐dispersed plant (Vaccinium membranaceum) at Mount St Helens, Washington
Authors: YANG S. , BISHOP J. G. , WEBSTER M. S.
Published: September 2010

Population founding and spatial spread may profoundly influence later population genetic structure, but their effects are difficult to quantify when population history is unknown. We examined the genetic effects of founder group formation in a recently founded population of the animal‐dispersed Vaccinium membranaceum (black huckleberry) on new volcanic deposits at Mount St Helens (Washington, USA) 24 years post‐eruption. Using amplified fragment length polymorphisms and assignment tests, we determined sources of the newly founded population and characterized genetic variation within new and source populations. Our analyses indicate that while founders were derived from many sources, about half originated from a small number of plants that survived the 1980 eruption in pockets of remnant soil embedded within primary successional areas. We found no evidence of a strong founder effect in the new population; indeed genetic diversity in the newly founded population tended to be higher than in some of the source regions. Similarly, formation of the new population did not increase among‐population genetic variance, and there was no evidence of kin‐structured dispersal in the new population. These results indicate that high gene flow among sources and long‐distance dispersal were important processes shaping the genetic diversity in this young V. membranaceum population. Other species with similar dispersal abilities may also be able to colonize new habitats without significant reduction in genetic diversity or increase in differentiation among populations.
Landscape characteristics influence morphological and genetic differentiation in a widespread raptor (Buteo jamaicensis)
Authors: HULL JOSHUA M. , HULL ANGUS C. , SACKS BENJAMIN N. , SMITH JEFF P. , ERNEST HOLLY B.
Published: September 2010

Landscape‐scale population genetic structure in vagile vertebrates was commonly considered to be a contradiction in terms whereas recent studies have demonstrated behaviour and habitat associated structure in several such species. We investigate whether landscape features influence morphological and genetic differentiation in a widespread, mobile raptor. To accurately describe genetic differentiation associated with regional landscape factors, we first investigated subspecies relationships at a continental scale. We used 17 microsatellite loci and five morphological measurements to investigate differentiation between eastern and western subspecies of red‐tailed hawks (Buteo jamaicensis) and to identify patterns between differentiation and habitat within western North America. Bayesian and frequency‐based analyses of microsatellite data revealed clear distinctions betweenB. j. borealis(eastern) andB. j. calurus(western) samples. Furthermore, hawks sampled in Texas were stouter than those collected from the Rocky Mountains and farther west. Among western samples, birds from the Great Basin, Rocky Mountains, and Washington were significantly different in morphology than those from Oregon and California. We identified a pattern of isolation by distance among western breeding sites around the Sierra Nevada. Given the long‐range dispersal capabilities of raptors, this pattern suggests that population‐specific habitat preferences, corresponding with habitat breaks between eastern and western slopes of the Sierra Nevada, and/or regionally variable population densities limit migration between the Mediterranean habitat of central California and the xeric habitats of southern California and interior west. We suggest habitat preferences and regionally disparate population densities may play a role in shaping genetic structure in vagile avian taxa.
On the origin of non‐tidal flaser bedding in point bar deposits of the river Ajay, Bihar and West Bengal, NE India
Authors: BHATTACHARYA ASOKKUMAR
Published: September 2010

Flaser bedding of non‐tidal origin has been described from point bar deposits of the Ajay river, NE India. Mud drapes are deposited during waning flood phases. The preferential accumulation of curled, desiccated mud laminae in ripple troughs during periods of exposure produces mud streaks resembling classical flaser bedding. This process of non‐tidal flaser formation is unlike the common tidal origin related to flood and ebb cycles, and the less common mechanism of formation in fluvial systems by deposition of mud in ripple troughs after floods.
Response of reef coral communities to sea‐level rise: a Holocene model from Mauritius (Western Indian Ocean)
Authors: MONTAGGIONI LUCIEN F. , FAURE GÉRARD
Published: September 2010

The fringing reef at Pointe‐au‐Sable (Mauritius, Indian Ocean) was used to examine the effects of Holocene sea‐level rise on coral growth. This reef is about 1000 m wide and comprises a forereef slope (30 m maximum depth), a narrow reef crest and a very shallow backreef (1·5 m maximum depth).

Four major coral communities were recognized, which developed within relatively narrow depth ranges: a Pachyseris/Oulophyllia community (deeper than 20 m), an Acropora‘tabulate’Faviid community (20–6 m); a robust branching Acropora community (less than 6 m) and a Pavona community (less than 10m). Three high‐recovery cores show the Holocene reef sequence is a maximum of 19·3 m thick and comprises four coral biofacies which are similar to counterparts identified in modern communities: robust branching, tabular‐branching, robust branching‐domal and foliaceous coral facies.

A minimum sea‐level curve for the past 7500 years was constructed. Using distribution patterns of coral biofacies and radiocarbon dates from corals, reconstruction of reef growth history indicates that both offshore and onshore reef zones were developing coevally, aggrading at rates of 4·3 mm year−1 from 6900 years B.P. The reef caught up with sea‐level only after sea‐level stabilized. Changes in coral community and reef growth rates were driven principally by increasing water agitation due to the decrease in accommodation space. Based on the composition of the successive coral assemblages, the reef appears to have grown through successive equilibrium stages.
Flow parameters of turbidity currents in a low‐sinuosity giant deep‐sea channel
Authors: KLAUCKE INGO , HESSE R. , RYAN W. B. F.
Published: September 2010

Flow parameters (velocity and density) for turbidity currents in the Northwest Atlantic Mid‐Ocean Channel (NAMOC) have been determined based on two different approaches, channel geometry and grain‐size distributions of turbidites. Channel geometry has been obtained by a quantitative morphological analysis of the NAMOC which shows three genetically different segments in the upper 2000 km: (1) an upper 350 km‐long ‘equilibrium channel’, (2) a middle 700 km‐long ‘modified equilibrium channel’and (3) a lower ‘basement‐controlled channel’which is more than 1000 km‐long. In contrast to other meandering submarine channels the NAMOC has very low sinuosities and gradients. A consistently higher right‐hand levee limits mean flow velocities to 3ms−1 and channel geometry indicates mean flow velocities of 0·86 m s−1 that decrease within the equilibrium channel to 0·05 m s−1. Grain‐size distributions on the levees and in the channel suggest strong vertical velocity and density gradients for bank‐full flows with velocities of up to 8 m s−1 and excess densities up to 87 kg m−3 at the base, and 0·45 m s−1 and 4 kg m−3 at the top. The internal shear produced by these strong vertical gradients results in a decoupling of the current head and body. Channel geometry appears to be mainly the result of the slowly moving dilute body of the current.
Sedimentology, stratigraphy and landscape evolution of a Holocene coastal dune system, Lodbjerg, NW Jutland, Denmark
Authors: Clemmensen Lars B. , Pye Kenneth , Murray Andrew , Heinemeier Jan
Published: September 2010

The stratigraphy and landscape evolution of the Lodbjerg coastal dune system record the interplay of environmental and cultural changes since the Late Neolithic. The modern dunefield forms part of a 40 km long belt of dunes and aeolian sand‐plains that stretches along the west coast of Thy, NW Jutland. The dunefield, which is now stabilized, forms the upper part of a 15–30 m thick aeolian succession. The aeolian deposits drape a glacial landscape or Middle Holocene lake sediments. The aeolian deposits were studied in coastal cliff exposures and their large‐scale stratigraphy was examined by ground‐penetrating radar mapping. The contact between the aeolian and underlying sediments is a well‐developed peaty palaeosol, the top of which yields dates between 2300 BC and 600 BC. Four main aeolian units are distinguished, but there is some lateral stratigraphic variation in relation to underlying topography. The three lower aeolian units are separated by peaty palaeosols and primarily developed as 1–4 m thick sand‐plain deposits; these are interpreted as trailing edge deposits of parabolic dunes that moved inland episodically. Local occurrence of large‐scale cross‐stratification may record the head section of a migrating parabolic dune. The upper unit is dominated by large‐scale cross‐stratification of various types and records cliff‐top dune deposition. The nature of the aeolian succession indicates that the aeolian landscape was characterized by alternating phases of activity and stabilization. Most sand transported inland was apparently preserved. Combined evidence from luminescence dating of aeolian sand and radiocarbon dating of palaeosols indicates that phases of aeolian sand movement were initiated at about 2200 BC, 700 BC and AD 1100. Episodes of inland sand movement were apparently initiated during marked climate shifts towards cooler, wetter and more stormy conditions; these episodes are thought to record increased coastal erosion and strong‐wind reworking of beach and foredune sediments. The intensity, duration and areal importance of these sand‐drift events increased with time, probably reflecting the increasing anthropogenic pressure on the landscape. The formation of the cliff‐top dunes after AD 1800 records the modern retreat of the coastal cliffs.
Long‐distance correlation between tectonic‐controlled, isolated carbonate platforms by cyclostratigraphy and sequence stratigraphy in the Devonian of South China
Authors: Chen Daizhao , Tucker Maurice E. , Jiang Maosheng , Zhu Jingquan
Published: September 2010

During the early Middle Devonian in South China, an extensive carbonate platform was broken up through extension to create a complex pattern of platforms, and interplatform basins. In Givetian and Frasnian carbonate successions, five depositional facies, including peritidal, restricted shallow subtidal, semi‐restricted subtidal, intermediate subtidal and deep subtidal facies, and 18 lithofacies units are recognized from measured sections on three isolated platforms. These deposits are arranged into metre‐scale, upward‐shallowing peritidal and subtidal cycles. Nine third‐order sequences are identified from changes in cycle stacking patterns, vertical facies changes and the stratigraphic distribution of subaerial exposure indicators. These sequences mostly consist of a lower transgressive part and an upper regressive part. Transgressive packages are dominated by thicker‐than‐average subtidal cycles, and regressive packages by thinner‐than‐average peritidal cycles. Sequence boundaries are transitional zones composed of stacked, high‐frequency, thinner‐than‐average cycles with upward‐increasing intensity of subaerial exposure, rather than individual, laterally traceable surfaces. These sequences can be further grouped into catch‐up and keep‐up sequence sets from the long‐term (second‐order) changes in accommodation and vertical facies changes. Catch‐up sequences are characterized by relatively thick cycle packages with a high percentage of intermediate to shallow subtidal facies, and even deep subtidal facies locally within some individual sequences, recording long‐term accommodation gain. Keep‐up sequences are characterized by relatively thin cycle packages with a high percentage of peritidal facies within sequences, recording long‐term accommodation loss. Correlation of long‐term accommodation changes expressed by Fischer plots reveals that during the late Givetian to early Frasnian increased accommodation loss on platforms coincided with increased accommodation gain in interplatform basins. This suggests that movement on faults resulted in the relative uplift of platforms and subsidence of interplatform basins. In the early Frasnian, extensive siliceous deposits in most interplatform basins and megabreccias at basin margins correspond to exposure disconformities on platforms.
Facies analysis and correlation of high‐order sequences in middle–outer ramp successions: variations in exported carbonate on basin‐wide δ13Ccarb (Kimmeridgian, NE Spain)
Authors: BÁDENAS BEATRIZ , AURELL MARC , GRÖCKE DARREN R.
Published: September 2010

Carbonate mud that accumulated in the deep parts of a late Kimmeridgian carbonate ramp (Iberian Basin, NE Spain) was partly derived by resedimentation from shallow water production areas. High‐frequency sea‐level changes, probably driven by climatic changes in tune with precession and short‐eccentricity cycles, affected carbonate production and the amount of exported sediment. Facies analysis and correlation of three outcrops located in middle and outer ramp settings allows a comparison of high‐order sequences (bundles of beds and sets of bundles) across a ramp transect and an assessment of the carbonate factory. Analysis of the storm deposits found in middle ramp settings identifies deepening to shallowing high‐frequency cycles based on the level of exported carbonate. In outer ramp areas, many of the bundles exhibit a thinning trend, indicating a progressive decrease of carbonate production and hence, carbonate export during periods of high‐frequency sea‐level rise. δ13Ccarb values show a gradual increase through the studied long‐term transgressive interval ranging from 1·5‰ to 2·8‰. Within this long‐term evolutionary trend, short‐term δ13Ccarb fluctuations occur that correspond with some of the high‐order cycles defined from sedimentary facies analysis. These short‐term δ13Ccarb shifts are interpreted as shifts in carbonate export from shallow reef regions to the outer ramp. A consequence of this study is that variation in δ13Ccarb can be used for correlation in outer ramp successions, at least on a basin‐wide scale.
Climatic control on Quaternary fluvial sedimentology of a Fenland Basin river, England
Authors: BRIANT REBECCA M. , BATEMAN MARK D. , RUSSELL COOPE G. , GIBBARD PHILIP L.
Published: September 2010

Understanding and interpreting climate response from ancient fluvial deposits requires a combined approach of detailed sedimentological description and interpretation, local climate proxies, and the accurate comparison of these sequences with further independent climate records. Application of these multiple lines of evidence is particularly effective in the Quaternary Period, where higher resolution and more detailed palaeoenvironmental reconstruction are possible. This paper presents results from a Devensian (Weichselian) age sequence in northern Fenland, England, that integrates these approaches. Detailed sedimentological description has identified three fluvial facies associations overlain by a period of ice‐wedge cast formation. Fossil plant and coleopteran material within these sediments have been studied to provide palaeoenvironmental reconstructions for the local landscape, including quantitative temperature estimates using the mutual climatic range method on fossil Coleoptera. In addition, joint application of radiocarbon and optically stimulated luminescence (OSL) dating allows this sequence to be compared with the stacked marine isotope record, although dates do not agree well at the limit of the radiocarbon technique. Sedimentological interpretations, palaeoenvironments and global ice‐volume variations (a proxy for climatic severity) are all in agreement and show clearly how the River Nene responded to subtle changes in climate and vegetation cover during the Devensian (Weichselian) Stage. The level of detail possible in this reconstruction shows the importance of this approach in understanding fluvial response to past climate changes.
Molar tooth structures of the Neoarchean Monteville Formation, Transvaal Supergroup, South Africa. I: Constraints on microcrystalline CaCO3 precipitation
Authors: BISHOP JAMES W. , SUMNER DAWN Y.
Published: September 2010

Molar tooth (MT) structures are enigmatic, contorted millimetre‐ to decimetre‐long veins and spheroids of microcrystalline calcite that formed during very early diagenesis in Precambrian sediments. MT structures in the ca 2·6 Ga Monteville Formation are 600–800 Myr older than previously reported occurrences and establish that conditions necessary for MT genesis were met locally throughout much of the Precambrian. In the Monteville Formation, MT structures were formed shallow subtidally, extending to depths near storm wave base, in shale host sediments intercalated with storm‐generated carbonate sand lenses. They are filled with microcrystalline calcite and rare pyrite. Microcrystalline calcite identical to that in MT structures fills other pore space, including porosity between grains in carbonate sand lenses, moldic porosity in sand grains, sheet cracks in columnar stromatolites, and shallow cracks on sandy bedding planes. Relationships in the Monteville Formation demonstrate that microcrystalline CaCO3 precipitated in fluid‐filled cracks and pores; microcrystalline calcite characteristics, as well as the paucity of carbonate mud in host rocks, are inconsistent with injection of lime mud as the origin of MT structures. Locally, MT cracks were filled by detrital sediment before or during precipitation. Precipitation occurred in stages, and MT CaCO3 evolved from granular cores to a rigid mass of cores with overgrowths – allowing both plastic and brittle deformation of MT structures, as well as reworking of eroded MT structures as rigid clasts and lime mud. Crystal size distributions and morphology suggest that cores precipitated through nucleation, Ostwald ripening and size‐dependent crystal growth, whereas overgrowths formed during size‐independent crystal growth.
The effect of subaerial exposure on the morphology and microstructure of stromatolites in the Cretaceous Sinyangdong Formation, Gyeongsang Supergroup, Korea1
Authors: NEHZA O. , WOO K. S.
Published: September 2010

Stromatolite morphology is usually controlled by a number of biological and environmental factors. In the south‐eastern part of the Korean Peninsula, three stromatolite units of the Cretaceous Sinyangdong Formation have been studied with regard to the effect of diagenesis on their morphology. Here, it is proposed that subaerial exposure and meteoric diagenesis are the most significant factors in shaping the stromatolites of the Cretaceous Sinyangdong Formation. Most previous palaeontological and sedimentological studies on stromatolites have concentrated on the environmental and biogenic controls on stromatolite morphology. These include extrinsic factors such as sedimentation rates or current velocities. The main controlling factor on the morphology of the stromatolites in the Sinyangdong Formation is apparently transient subaerial exposure and related meteoric diagenesis. Textural examination of stromatolite samples from three stratigraphic horizons shows a characteristic repetitive pattern of cycles with gradual transition from fibrous calcite to micrite layers, reflecting changes in the hydrological cycle of the lake in which the stromatolites grew. Stromatolite growth was terminated by corroded surfaces indicative of subaerial exposure related to a fall in lake level. The growth pattern of the stromatolites was mostly determined by the morphology of the corroded substrates during subaerial exposure. Furthermore, the internal stromatolite structure was strongly modified by the process of leaching. As a result, growth forms mostly changed from stratiform to columnar mesostructure. This study strongly implies that diagenesis could make a very significant influence on the morphogenesis of lacustrine stromatolites in the geological past.
A unified criterion for initiation of sediment motion and inception of sheet flow under water waves
Authors: YOU ZAI‐JIN , YIN BAOSHU
Published: September 2010

A unified criterion is developed for initiation of non‐cohesive sediment motion and inception of sheet flow under water waves over a horizontal bed of sediment based on presently available experimental data. The unified threshold criterion is of the single form, Uo = 2πC[1 + 5(TR/T)2]−1/4, where Uo is the onset velocity of sediment motion or sheet flow, T is wave period, and C and TR are the coefficients. It is found that for a given sediment, Uo initially increases sharply with wave period, then gradually approaches the maximum onset velocity Uo = 2πC and becomes independent of T when T is larger. The unified criterion can also be extended to define sediment initial motion and sheet flow under irregular waves provided the significant wave orbital velocity and period of irregular waves are introduced in this unified criterion.
Identifying redox‐sensitive extra‐chloroplastic enzymes by homology modeling
Authors: Anderson Louise E. , Li Alex Dong , Muslin Elizabeth H. , Schiffer Marianne , Stevens Fred J.
Published: September 2010

Homology modeling has been used to identify extra‐chloroplastic enzymes that contain potential disulfide bonds. All of the higher plant fructose bisphosphatases and mitochondrial citrate synthases that have been tested to date, two glyceraldehyde‐3‐P dehydrogenases, two enolases and one lactate dehydrogenase, are redox‐sensitive and may then be redox‐regulated in vivo. Apparently, redox‐sensitivity is not limited to the chloroplast.
Investigating the role of the thiol‐regulated enzyme sedoheptulose‐1,7‐bisphosphatase in the control of photosynthesis
Authors: Raines Christine A. , Harrison Elizabeth P. , Ölçer Hülya , Lloyd Julie C.
Published: September 2010

Sedoheptulose‐1,7‐bisphosphatase (SBPase; EC 3.1.3.37) catalyses the dephosphorylation of sedoheptulose‐1,7‐bisphosphate in the regenerative phase of the Calvin cycle. Antisense plants with reduced levels of SBPase have decreased photosynthetic capacity and altered carbohydrate status, leading to modifications in growth and development. The catalytic activity of SBPase is regulated by light via the ferredoxin/thioredoxin system. Recently, the amino acids within the SBPase protein involved in this regulatory mechanism have been identified and a deregulated, permanently active form of the enzyme has been produced using site‐directed mutagenesis. This paper explores how transgenic Nicotiana tabacum cv. Samsun plants, containing the deregulated form of the SBPase enzyme, may lead to a better understanding of the in vivo role of light activation of this important Calvin cycle enzyme.
Oxidation‐reduction properties of thioredoxins and thioredoxin‐regulated enzymes
Authors: Knaff David B.
Published: September 2010

Oxidation‐reduction midpoint potentials have been measured for the two chloroplast thioredoxins, thioredoxin f and m, for ferredoxin:thioredoxin reductase (FTR) and for the thioredoxin‐regulated enzymes fructose‐1,6‐bisphosphatase (FBPase), phosphoribulokinase and NADP‐malate dehydrogenase. The effects of pH on the midpoint potentials of these chloroplast proteins have been measured so that the effect of the light‐induced increase in chloroplast stromal pH on the redox properties of the proteins can be calculated. Spectroscopic measurements on FTR and on an N‐ethylmaleimide‐modified derivative of the enzyme have been used to elucidate the role of the [4Fe‐4S] cluster of FTR during the reduction of the enzyme's active‐site disulfide by ferredoxin.