bluuebunny/crossref_metadata_2025 huggingface dataset:
Vaccination Against Helicobacter pylori in Non‐Human Primate Models and Humans
Authors: Lee C. K.
Published: March 2003

Several vaccination studies have been performed in monkeys and humans testing the feasibility of prophylactic and therapeutic immunizations against Helicobacter pylori. The monkey studies showed that immune responses were induced by oral vaccination with the mucosal adjuvant LT (Escherichia coli heat‐labile enterotoxin), parenteral administration with a cationic lipid adjuvant, and by mucosal priming followed by parenteral boosts. Both prophylactic and therapeutic activities were demonstrated in monkeys, providing a strong impetus for human vaccine trials. Preliminary studies in humans were undertaken in order to identify a tolerable dose of LT adjuvant or to test the effectiveness of mutant atoxic LT adjuvants. The results from these preliminary studies suggest that native LT causes diarrhoea at doses required for adjuvanticity while a mutant LT does not. In one study in which infected human subjects were vaccinated with orally administered urease antigen with native LT, there was a modest reduction in the level of H. pylori gastric colonization. A second clinical study employing H. pylori whole cell antigen and a mutant LT in infected subjects showed immune responses and although the subjects remained infected, the study was not designed to measure reduction in H. pylori colonization. Recombinant Salmonella expressing urease and other H. pylori antigens have been effective in mice (see accompanying Frontlines Topic Review by John O. Nedrud [1]), but monkey studies are not possible because of host range restriction. Human trials of parenteral immunization, mucosal immunization with mutant LT and live Salmonella vectors are needed to fully assess the ability of vaccines to prevent or treat H. pylori infections.
Experimental Chronic Arthritis and Granulomatous Inflammation Induced byBifidobacteriumCell Walls
Authors: Zhang X. , Rimpiläinen M. , Hoffmann B. , Šimelyte E. , Aho H. , Toivanen P.
Published: March 2003

Effects of cell walls (CWs) from two almost identical strains ofBifidobacterium adolescentiswere studied in rats, using three different doses. A single i.p. injection of both CWs triggered a long‐lasting arthritis with CW degradation products present in the joint tissue. Histologically, the arthritis was characterized by inflammatory cells, synovial hyperplasia, pannus formation and bone erosion, closely resembling human rheumatoid arthritis (RA). In addition, CWs of the other strain induced a remarkable granuloma formation in the spleen and liver. Both CWs have the same peptidoglycan (PG) type A4α/β, but differ from each other in three aspects. CW of the granuloma inducing strain: firstly has more lysine and less ornithine in PG stem peptides; secondly is more resistant to lysozyme degradation, and thirdly is better retained in the spleen. All these in comparison to the other strain used. Such characteristics are associated with the capacity to induce chronic arthritis, but it remains open how crucial they are for the granuloma formation.
IL‐4‐Dependent Effector Phase in Autoimmune Exocrinopathy as Defined by the NOD.IL‐4‐Gene Knockout Mouse Model of Sjögren's Syndrome
Authors: Brayer J. B. , Cha S. , Nagashima H. , Yasunari U. , Lindberg A. , Diggs S. , Martinez J. , Goa J. , Humphreys‐Beher M. G. , Peck A. B.
Published: March 2003

NOD mice manifest many features of autoimmune exocrinopathy (Sjögren's syndrome), a disease generally characterized by a chronic, progressive immunological attack against the exocrine tissues of the salivary and lacrimal glands. Previous studies using the NOD congenic partner strain, NOD.Igμnull, defined an important role for B lymphocytes in the development of xerostomia, implicating autoantibodies reactive with the acetylcholine muscarinic receptor (M3R) as the possible effector mechanism. In the present study, we have examined the impact of the cytokine, interleukin (IL)‐4, on autoimmune exocrinopathy by using the IL‐4 gene knockout (KO) NOD mouse strain, NOD.IL‐4−/−. Despite manifesting the physiological aberrations and marked leukocytic infiltration of the salivary glands characteristic of autoimmune xerostomia in NOD mice, the NOD.IL‐4−/− mice do not develop xerostomia. However, NOD.IL‐4−/− mice that received adoptively transferred T lymphocytes derived from NOD.Igμ−/− mice progress to xerostomia, thereby reversing the defect. While progression or lack of progression to xerostomia correlated with the ability of the NOD.IL‐4−/− mice to express detectable anti‐M3R autoantibodies, the precise mechanism of how IL‐4 influences the development of autoimmune xerostomia remains speculative.
Ku Protein and DNA Strand Breaks in Lip Glands of Normal and Primary Sjögren's Syndrome Subjects: Lack of Correlation with Apoptosis
Authors: Larsson Å. , Henriksson G. , Manthorpe R. , Sallmyr A. , Bredberg A.
Published: March 2003

The aim was to examine tissue expression of Ku protein in lower lip salivary gland (LSG) biopsies from cases of primary Sjögren's syndrome (SS) and from normal subjects. Methods: immunohistochemistry was used with antibodies to Ku70/86 and also Ki67, PCNA and p53. In addition, the Klenow method was applied in order to detect evidence of apoptosis. Sections of hyperplastic tonsil served as additional controls. Results: in normal controls, LSG acinar cells stained negatively whereas LSG excretory duct cell nuclei stained positively with Ku and Klenow and occasionally with PCNA but negatively with Ki67 and p53. In LSG focal sialadenitis of SS cases, some lymphocytic cells showed staining with Ku, Ki67, PCNA, Klenow and p53. In addition to duct cell Ku and Klenow as well as PCNA staining which was not much different from normals, a few ductal epithelial and also mononuclear cells stained with p53. In focal sialadenitis, some acinar cells showed staining with PCNA as well as with Klenow. Conclusions: our findings in LSG biopsies of SS cases added little to an increased understanding about the pathogenetic mechanisms in the development of focal sialadenitis in SS. However, in normal LSG, ductal epithelial but not acinar cells seem to express a constitutively specific Ku protein and Klenow profile, suggestive of DNA strand breaks but not clearly associated with ongoing apoptotic events. It may reflect an enhanced stress response, which may be pathogenetically important in the early events of focal sialadenitis development in primary Sjögren's syndrome.
Ocular Toxoplasmosis: More Than Just What Meets the Eye*
Authors: Vallochi A. L. , Nakamura M. V. , Schlesinger D. , Martins M. C. , Silveira C. , Belfort R. , Rizzo L. V.
Published: March 2003

Toxoplasma gondii is an intracellular parasite whose life cycle may include the man as an intermediate host. Close to a billion people are infected with this parasite worldwide. Ocular lesions may occur in up to 25% of those individuals infected. The infection may occur intra‐uterus, through the placenta when the mother is infected during pregnancy. The parasite may also infect adults after the ingestion of contaminated food products, most notably meats or water. We have shown that although congenital and post‐natal (acquired) infection results in similar ocular lesions, the immunological mechanisms behind the development of disease are different. On the other hand, contrary to published data obtained in mice, we were unable to find evidence that the T. gondii express superantigen activity for human lymphocytes. Our findings are important because they suggest that superantigen activity is not important as a pathological mechanism in human disease. Our data also suggest that, whereas the ocular lesion caused by infection after birth is the result of an excessive or dysfunctional immune response, the lesions caused by congenital infection may be due to a lack of an appropriate response to the parasite.
The Search for the Missing ‘Missing‐Self’ Receptor on Natural Killer Cells
Authors: Yokoyama W. M.
Published: March 2003

In this article, I outline the studies that led to the discovery of Ly49A as the first ‘missing‐self ’ receptor on natural killer cells. It is a more detailed and formal version of my acceptance speech at the Novartis Award ceremony at the International Congress of Immunology in Stockholm. Yet, it is impossible to mention my gratitude to all of my previous mentors and colleagues or to credit all the scientists and immunologists who preceded us by making contributions, large and small, to knowledge upon which our findings were based. It is therefore humbling to accept the 2001 Novartis Award for Basic Immunology along with Professors Klas Kärre and Lorenzo Moretta.
Costimulatory Molecule Requirement for Bovine WC1+γδ T Cells' Proliferative Response to Bacterial Superantigens
Authors: Fikri Y. , Pastoret P.‐P. , Nyabenda J.
Published: March 2003

We have previously shown that the proliferation of freshly isolated bovine WC1+γδ T cells to superantigens (SAgs) including staphylococcal enterotoxin A (SEA), and staphylococcal enterotoxin B (SEB) or toxic shock syndrome type‐1 (TSST‐1) required the presence of antigen‐presenting cells (APC) and the addition of exogenous interleukin (IL)‐2. The costimulatory activity provided by molecules expressed on professional APC for the proliferation of γδ T cells has not been addressed hitherto. In the present study, we investigated the ability of two selected APC populations, the dendritic cells (DCs) highly expressing CD80 and CD86 molecules (CD80highCD86high) and the monocytes expressing the same molecules at a rather low level (CD80lowCD86low), to stimulate the proliferation of purified bovine WC1+γδ T cells to SAgs. DCs were more efficient than monocytes in inducing γδ T‐cell proliferation, and this response was dependent on exogenous IL‐2 in both presentation modes. Stimulating γδ T cells with gradual doses of SAgs or concanavalin A (ConA) resulted in similar dose‐dependent reaction profiles suggesting a minimal role of the major histocompatibility complex (MHC). However, significant proliferation was already obtained with the starting doses in the presence of DC compared with monocytes, and higher proliferation was reached with DC at optimal doses. Finally, the addition of monoclonal antibody (MoAb) anti‐CD86 markedly inhibited SAgs‐ and ConA‐mediated proliferation, whereas MoAb anti‐CD80 had no effect. The combination of both anti‐CD80 and anti‐CD86, however, suppressed this response. These results suggest that bovine γδ T‐cell proliferation response requires indubitably CD86 costimulation. The role of CD80 molecule seems less clear.
Spontaneous Downregulation of Antibody/Autoantibody Synthesis in Susceptible Mice upon Chronic Exposure to Mercuric Chloride is not Owing to a General Immunosuppression
Authors: Roether S. , Rabbani H. , Mellstedt H. , Abedi‐Valugerdi M.
Published: March 2003

Administration of mercuric chloride into susceptible rats and mice induces a systemic autoimmune disease, which is characterized by a T‐cell‐dependent polyclonal B‐cell activation, an increase in serum levels of immunoglobulin (Ig)G1 and IgE, production of antibodies of different specificities and development of renal IgG deposits. A peculiar feature of mercury‐induced autoimmunity is that the polyclonal B‐cell activation spontaneously disappears in spite of continuous injection of mercury. The exact mechanism(s) for autoregulation of mercury‐induced autoimmunity is not well understood. In the present study, we analysed the regulation of mercury‐induced immune/autoimmune responses in mice and tested whether spontaneous downregulation of these responses is owing to a general immunosuppression. Mercury‐susceptible [SJL (H‐2s)] and ‐resistant [DBA/2 (H‐2d)] mice were injected with mercury for 4, 10, 15 and 17 weeks. Immune/autoimmune responses were monitored in these mice. Thereafter, mercury‐injected mice for 17 weeks were further immunized with horse red blood cells (HRBC) to study whether the subsequent humoral immune response to a foreign antigen is suppressed. We found that except for IgG1 anti‐nucleolar antibody production and renal IgG1 deposition, other characteristics of mercury‐induced autoimmunity were downregulated in SJL (H‐2s) mice after chronic treatment with mercury. However, these mice did not show any reduction in the number of splenic antibody‐secreting cells and/or in serum titres of specific IgM, IgG1 and IgG2a anti‐HRBC antibodies in response to HRBC as compared with naïve mice. Similarly, in mercury‐resistant DBA/2 (H‐2d) mice, chronic treatment with mercury did not either suppress specific antibody responses against HRBC. Our findings show that the autoregulation of mercury‐induced immune/autoimmune responses observed after chronic treatment with mercury is not owing to a general immunosuppression.
Heme Oxygenase is Downregulated in Stress‐Triggered and Interleukin‐12‐Mediated Murine Abortion
Authors: Zenclussen A. C. , Joachim R. , Hagen E. , Peiser C. , Klapp B. F. , Arck P. C.
Published: March 2003

Heme oxygenases (HOs) are responsible for heme degradation. Besides their enzymatic activities, HOs are involved in tissue protection. Failing upregulation of HOs has been linked to increased necrosis in inflammatory tissues. Interestingly, previously published data indicated that mice exposed to sonic stress during early gestation show an augmented production of decidual inflammatory T‐helper 1 (Th1) cytokines, thus resulting in increased abortion rate. No data linked the Th1‐inducer interleukin (IL)‐12 with the event of abortion. As little is known about the role of HO in pregnancy maintenance, we evaluated the expression of decidual and placental HO‐1 and HO‐2 in the abortion‐prone murine mating combination CBA/J × DBA/2 J with (1) CBA/J female control mice, (2) CBA/J mice exposed to stress during early gestation and (3) CBA/J females injected with recombinant IL‐12. Decidual and placental HOs protein expression was analysed by immunohistochemistry and mRNA levels by real time polymerase chain reaction (PCR).

As expected, an increased abortion rate was present in mice exposed to stress compared with the control. IL‐12 injections also boosted the abortion rate compared with control mice, mimicking the effect of stress. HOs' proteins could be detected in placenta and decidua. Real time PCR revealed lower levels of HO‐1 and HO‐2 mRNA in stress‐triggered and IL‐12‐injected mice. We conclude that increased Th1‐cytokine levels during murine pregnancy may result in low expression of HO‐1 and HO‐2, thus leading to placental necrosis and foetal rejection.
IL‐12: The Role of p40 Versus p75
Authors: Abdi K.
Published: March 2003

Interleukin (IL)‐12p75 is a heterodimeric cytokine composed of the product of two different genes that specify p35 and p40 subunits. The prevailing view is that IL‐12 acts as a proinflammatory cytokine that bridges the innate and adaptive immune responses and skews T‐cell reactivity toward a TH1 cytokine pattern. Though the terms IL‐12 and IL‐12p40 are often used interchangeably, and measurements of the p40 chain are often interpreted as measurements of the intact p75 heterodimer, such interchangeable usage may be incorrect.

In the following discussion, I will delineate an alternative hypothesis for the roles of the p40 and p75 proteins, suggesting specifically, that: (1) in vivo, secretion of free p40 precedes that of p75 in response to pathogens; (2) induction of p40 is a T‐independent response by antigen presenting cells (APCs) to early host–pathogen interactions; and (3) IL‐12p75 is a late product, whose induction requires T‐dependent signals. It is made as a result, rather than as a cause, of TH1 differentiation. Thus, it is the p40 protein, either alone or paired with other polypeptides, rather than p75, that acts as an interface between the innate and adaptive immune responses.
Multiple Mycobacterium microti Derived Lipids Stimulate iNOS Gene Expression in the J774 Murine Macrophage Cell Line
Authors: Pacheco‐García U. , Legorreta‐HerrEra M. , Hernández‐Rodríguez C. , Sánchez‐García F. J.
Published: March 2003

The inducible nitrogen oxygen synthase (iNOS) and nitric oxide (NO) system acting in concert with superoxide radicals is recognized as a powerful macrophage microbicidal mechanism. However, experimentation with iNOS knockout mice has rendered contradictory results on the protective role of iNOS/NO in the course of mycobacterial infections. On the other hand, NO also plays an immunoregulatory role. Knowing the nature of the mycobacterial constituents that induce iNOS gene expression would help to better understand the host–parasite relationship.

Lipoarabinomannan (LAM) and a 19 KDa lipoprotein are the two known mycobacterial constituents that have shown to induce iNOS. By screening a set of methanol extracted lipids from Mycobacterium microti, here we provide evidence that multiple mycobacterial molecules of lipidic nature both of intermediate and of high polarity, with free amino groups or carbohydrates but no phosphate groups as part of their structure are capable of inducing iNOS gene expression in J774 cells, thus implying a complex relationship between mycobacteria and their host immune system in regard to iNOS gene expression.
IL‐15 Induces Unspecific Effector Functions in Human Peptide‐Specific CD8+ T‐Cell Cultures
Authors: Lyngstrand S. T. , Würtzen P. A. , Ødum N. , Nissen M. H. , Röpke C.
Published: March 2003

Antigen (Ag)‐specific CD8+ T cells are a major host defence against viral infections. In the present study, we generated human CD8+ T‐cell lines specific towards influenza matrix peptide (IMP)‐pulsed Ag‐presenting cells. We compared the effect of interleukin‐2 (IL‐2) and IL‐15 on the proliferation and cytotoxic activity of primary and secondary IMP‐specific cytotoxic T lymphocyte (CTL) culture. In primary CTL cultures, IL‐15‐induced cell expansion was considerably reduced as compared with IL‐2‐induced cell expansion, and IL‐15 favoured the outgrowth of CTLs without peptide specificity in these cultures.

Secondary IMP‐specific CD8+ T cells were generated by the addition of IL‐2 during two cycles of restimulation. From the third restimulation, identical CTL cultures were expanded with either IL‐2 or IL‐15 in parallel. Cell expansion as well as Ag specificity was considerably reduced after a 5 day culture period in the presence of IL‐15. No or low CD69 expression was observed in IL‐15‐cultured CTLs, whereas IL‐2‐cultured CTLs contained high fractions of CD69+ cells. Furthermore, a high fraction of these latter cells coexpressed the cytotoxic marker CD56. However, IL‐15‐cultured CTLs exhibited cytotoxic activity without detectable expression of CD56, suggesting that CD56 is not essential for cytotoxic activity. Thus, the results presented suggest that IL‐15 favours the outgrowth of unspecific cytotoxic effector T cells.
Anastomosing river sedimentation in the Channel Country of central Australia
Authors: GIBLING MARTIN R. , NANSON GERALD C. , MAROULIS JERRY C.
Published: March 2003

Anastomosing river plains of the Channel Country, central Australia, have aggraded slowly over the past 100 ka. Channel sediments accumulate mainly as accretionary benches of mud and sand, sandy channel‐base sheets and vegetation‐shadow deposits. The channels are laterally stable and the sediments have aggraded locally against erosional banks of tough floodplain muds. Channel sediments are profoundly affected by desiccation during dry periods and by bioturbation caused by within‐channel trees and burrowing invertebrates, especially crayfish. Excavations show that mud‐dominated channel bodies of low width:thickness ratio are generated by a combination of vertical and lateral accretion. Levees and braided surfaces, composed mainly of mud aggregates, border the channels and are activated during valley‐wide floods which lay down distal mud sheets. Floodplain muds are converted to vertisols with gilgai, deep desiccation cracks, and impregnations of carbonate and gypsum. A fixed‐channel facies model is applicable to the Channel Country river deposits. Anastomosis apparently results from the need for the system to move large volumes of water and moderate sediment loads across low‐gradient interior basins.

Channels distant from upland source areas receive an abundant supply of pedogenic, sand‐sized mud aggregates generated on adjacent floodplains and reworked into braid bars during valley‐wide floods. Some quartz sand is provided from excavation of subsurface Pleistocene sands in deep channels and waterholes and from aeolian dunes on the floodplains. Adjacent gibber plains supply some gravel to the system.
Porewater sulphur geochemistry and fossil preservation during phosphate diagenesis in a Lower Cretaceous shelf mudstone
Authors: POULTON  , BOTTRELL  , UNDERWOOD
Published: March 2003

Lower Cretaceous mudstones exposed at Speeton in North Yorkshire, UK, contain lobsters and burrows preserved in diagenetic phosphate concretions. Isotopic compositions of sulphur in both diagenetic sulphide and structural sulphate in diagenetic phosphate have been measured in an attempt to constrain diagenetic porewater chemistry. The occurrence of phosphatized and pyritized lobsters and similarly preserved burrows, allows a detailed comparison of these microenvironments with the host sediments. Host sediments are extensively bioturbated and characterized by very light sulphide isotopic compositions (mean sulphide δ34S = –48·3 ± 3‰ (1σ, n = 19)) and sulphate isotopic compositions that are lighter than Lower Cretaceous seawater sulphate (mean sulphate δ34S = +8·7 ± 3·2‰ (1σ, n = 19)). These isotopic values can be explained by the action of bioturbating macrofauna; the introduction of oxygen in ventilating seawater results in the oxidation of early formed isotopically light pyrite, resulting in porewater sulphate that is enriched in 32S. Subsequent pyrite formation via bacteriogenic reduction of isotopically light porewater sulphate leads to the formation of isotopically light pyrite, whilst residual porewater sulphate apparently remains relatively enriched in the 32S isotope. Sulphur isotopic values for the burrows are very different; sulphide isotopic compositions average –34·4 ± 0·4‰ (1σ, n = 3) and sulphate isotopic compositions average –14·4 ± 6·6‰ (1σ, n = 4). These isotopic compositions are the result of rapid development of closed system conditions in burrows, resulting in the build‐up of acidity necessary for phosphate precipitation and coprecipitation of isotopically light sulphate (formed by oxidation of isotopically light sulphide surrounding the burrows). Lobster shell isotopic compositions fall between these two groups. On the basis of their isotopic compositions, some lobsters appear to have died close to the sediment–water interface, whilst others appear to have been buried (in burrows) prior to death.
Rapid in situ silicification of microbes at Loburu hot springs, Lake Bogoria, Kenya Rift Valley
Authors: RENAUT R. W. , JONES B. , TIERCELIN J.‐J.
Published: March 2003

Microbial mats, located along the margins of hot‐spring pools and outflow channels at Lake Bogoria, Kenya, are commonly silicified forming friable laminated crusts. Columnar microstromatolites composed of silica and calcite are also forming at several springs in sites of oscillating water level or spray. Silicification of the microbes involves impregnation of organic tissue by very fine amorphous silica particles and encrustation by small (< 2 μm) silica spheroids. Rapid silicification of the microbes, which may begin while some are still alive, can preserve sheaths and in some examples, the filaments, capsules and cells. Although this provides evidence of their general morphology, the biological features that are required for taxonomic identifications are commonly poorly preserved.

The silica precipitation results mainly from evaporative concentration and rapid cooling of spring waters that have been drawn upward through the mats and microstromatolites by capillary processes. Almost all the silica at the Loburu springs nucleates on microbial substrates. This affinity of silica for functional groups on microbial surfaces contributes to the rapid silicification of the microbes and their preservation in modern and ancient cherts.
The Canary Debris Flow: source area morphology and failure mechanisms
Authors: Masson  , Canals  , Alonso  , Urgeles  , Huhnerbach
Published: March 2003

The morphology of the source area of the Canary Debris Flow has been mapped using both GLORIA reconnaissance and TOBI high‐resolution sidescan sonar systems. West of ≈19°W, the seafloor is characterized by a strongly lineated downslope‐trending fabric. This fabric can be interpreted as being caused by streams of debris separated by longitudinal shears. Multiple flow pulses are indicated by a series of asymmetrical lateral ridges which mark the northern boundary of the flow. East of ≈19°W, GLORIA data show only a weak fabric of irregular patches and alongslope lineaments. The TOBI data show the patches to be coherent sediment blocks up to 10 km across, surrounded by debris flow material. These are interpreted as in situ areas of seafloor sediment which have survived the slope failure and debris flow event rather than transported fragments of a failed sediment slab. TOBI data from the best developed area of alongslope lineaments show a series of small faults downstepping to the west. This area of seafloor is interpreted as one of partial sediment failure, where the failure process became ‘frozen’ before total mobilization of the seafloor sediments could occur. The overall morphology of the failure area indicates removal of a slab‐like body of sediment, although we cannot distinguish between retrogressive and slab‐slide failure mechanisms. If the latter mechanism is applicable, fragmentation of the failing ‘slab’ must have commenced concurrently with the onset of downslope transport. Immediately upslope from the debris flow source area, a seafloor of characteristic rough blocky texture is interpreted as the surface of a debris avalanche derived from the slopes of the island of El Hierro. The debris flow and avalanche appear to be simultaneous events, with failure of the slope sediments occurring while the avalanche deposits were still mobile enough to fill and disguise the topographic expression of the debris flow headwall. Loading of the slope sediments by the debris avalanche most probably triggered the Canary Debris Flow.
A quantitative approach to sedimentary surface structures contoured by the interplay of microbial colonization and physical dynamics
Authors: Noffke Nora , Krumbein Wolfgang E.
Published: March 2003

In the tidal flats of Mellum Island (southern North Sea), biofilms and microbial mats, generated largely by cyanobacteria, colonize the sedimentary surfaces. Biostabilization effects and biomass enrichment influence erosional and depositional dynamics resulting from tidal flushing and storm surges. The overlapping of both biological and physical forces causes the development of characteristic sedimentary structures. To obtain a quantitative expression of the degree of effectiveness of microbial colonization in the formation of structures in an extended tidal area, a modification index (MOD‐I) was developed based on the following values: (i) the proportion of mat‐covered area related to a defined investigation area (IA); (ii) the degree of steepness of slope angles of raised erosional remnants (IS); and (iii) the degree of microbial levelling of a rippled sedimentary surface (IN). The MOD‐I was calculated for several defined regions within the study area, and both winter and summer situations were considered. The MOD‐I values show, first, that the lower intertidal zone is characterized by index values approaching zero. This implies that microbially induced effects in this zone are negligible, even in summer. Second, the upper intertidal zone is characterized by lower index values in winter and relatively high values in summer. This implies a predominantly seasonal control on the biofilm development in this zone. Third, in the lower supratidal zone, the index values are almost identical during both winter and summer. This implies non‐seasonal biological effects in this zone. Concomitant empirical studies on the composition of microbial mats and films suggest that the dominant microbial type influences the MOD‐I value.
Behaviour of particle‐laden flows into the ocean: experimental simulation and geological implications
Authors: Mcleod Paul , Carey Steven , Sparks R. Stephen J.
Published: March 2003

The behaviour of subaerial particle‐laden gravity currents (e.g. pyroclastic flows, lahars, debris flows, sediment‐bearing floods and jökulhlaups) flowing into the sea has been simulated with analogue experiments. Flows of either saline solution, simple suspensions of silicon carbide (SiC) in water or complex suspensions of SiC and plastic particles in methanol were released down a slope into a tank of water. The excess momentum between subaerial and subaqueous flow is dissipated by a surface wave. At relatively low density contrasts between the tank water and the saline or simple suspensions, the flow mixture enters the water and forms a turbulent cloud involving extensive entrainment of water. The cloud then collapses gravitationally to form an underwater gravity current, which progresses along the tank floor. At higher density contrasts, the subaerial flow develops directly into a subaqueous flow. The flow slows and thickens in response to the reduced density contrast, which is driving motion, and then continues in the typical gravity current manner. Complex suspensions become dense flows along the tank floor or buoyant flows along the water surface, if the mixtures are sufficiently denser or lighter than water respectively. Flows of initially intermediate density are strongly influenced by the internal stratification of the subaerial flow. Material from the particulate‐depleted upper sections of the subaerial flow becomes a buoyant gravity current along the water surface, whereas material from the particulate‐enriched lower sections forms a dense flow along the tank floor. Sedimentation from the dense flow results in a reduction in bulk density until the mixture attains buoyancy, lifts off and becomes a secondary buoyant flow along the water surface. Jökulhlaups, lahars and debris flows are typically much denser than seawater and, thus, will usually form dense flows along the seabed. After sufficient sedimentation, the freshwater particulate mixture can lift off to form a buoyant flow at the sea surface, leading to a decoupling of the fine and coarse particles. Flood waters with low particulate concentrations (<2%) may form buoyant flows immediately upon entering the ocean. Subaerial pyroclastic flows develop a pronounced internal stratification during subaerial run‐out and, thus, a flow‐splitting behaviour is probable, which agrees with evidence for sea surface and underwater flows from historic eruptions of Krakatau and Mont Pelée. A pyroclastic flow with a bulk density closer to that of sea water may form a turbulent cloud, resulting in the deposition of much of the pyroclasts close to the shore. Dense subaqueous pyroclastic flows will eventually lift off and form secondary buoyant flows, either before or after the transformation to a water‐supported nature.
Crevasse splays from the rapidly aggrading, sand‐bed, braided Niobrara River, Nebraska: effect of base‐level rise
Authors: Bristow  , Skelly  , Ethridge
Published: March 2003

Base‐level rise of ≈2·35 m on the Niobrara River has resulted in aggradation of the channel belt and a recent avulsion. Overbank areas have become flooded by rising groundwaters, and more than eight crevasse splays have formed between 1993 and 1997. Two crevasse splays, situated on the west and east sides of the Niobrara, have been studied using ground‐penetrating radar (GPR), shallow boreholes and topographic surveys. The vibracores and GPR profiles provide a nearly three‐dimensional view of the architecture of crevasse splay deposits. The east splay was initiated in the winter of 1993/94 and has expanded to cover an area ≈200 m by 1000 m, with sediment up to 2·5 m thick. The west splay, which was initiated by the opening of a crevasse channel through a levee in the autumn of 1995, covers an area ≈150 m by 250 m, with up to 1·2 m of sand deposited in a single year. The Niobrara splays are sand dominated and characterized by bedload deposition within channels, 5–30 m wide and 0·5–2 m deep, with the development of slipfaces where splays prograde into standing bodies of water. Sedimentary structures in cores include horizontal lamination, ripple lamination and sets of cross‐stratification. There is a slight tendency for splays to coarsen up, but individual beds within the splays often fine up. The abundance of crevasse splays on the Niobrara River contrasts with other braided river floodplains. In the Niobrara, crevasse splay formation followed aggradation within the channel belt, which occurred in response to base‐level rise. The link between crevasse splays, channel aggradation and base‐level rise has important implications for the interpretation of ancient braided river and floodplain sequences. It is suggested that crevasse splay deposits should be an important component of aggrading fluvial sediments and, hence, should be preserved within the rock record. In this case, the aggradation and crevassing have been tied to a rise in base‐level elevation, and it is suggested that similar deposits should be preserved where braided rivers are affected by base‐level rise, for instance during transgression and filling of palaeovalleys.
The morphodynamics of fluvial sand dunes in the River Rhine, near Mainz, Germany. II. Hydrodynamics and sediment transport
Authors: Carling  , Williams  , Gölz  , Kelsey
Published: March 2003

The dynamics of large isolated sand dunes moving across a gravel lag layer were studied in a supply‐limited reach of the River Rhine. During daylong surveys, suspended sediment concentration, bedload transport rate, water depth, flow velocity, turbulence intensity, near‐bed shear stress and water temperature were recorded over individual isolated dunes. This paper considers the hydrodynamic environment and sediment transport over the dunes. A companion paper details the sedimentology and morphology of the dunes. Flow over the flat gravel lag upstream of large dunes is more uniform than that over dunes, and gravels are rarely entrained by in‐bank discharges. Unsteady and non‐logarithmic velocity profiles are common within the boundary layer above the stoss side of large dunes, and the near‐bed flow demonstrates evidence of large‐scale, coherent low‐frequency flow structures; these may reflect stacked sequences of separated boundary layers generated by secondary dunes. However, the low‐amplitude morphology of large dunes does not affect the statistical properties of turbulence production over the stoss sides. Bed roughness and near‐bed shear stress commonly increase steadily over the stoss of dunes, but may decrease near the crest, especially where a crestal platform exists that is devoid of secondary bedforms. Bed roughness scales with the physical size of bed roughness elements. However, variability in roughness lengths is large, owing to the composite nature of bed roughness. Bedload transport over stoss slopes is spatially variable, but often shows an increase with increasing bed shear stress over the stoss. Well‐formed wakes only develop downstream of lee slopes, which are close to the angle of repose; otherwise, separation is weak, and suspension and settling of fine sediments is of little consequence to dune evolution. Wake flow is characterized by turbulence production one order of magnitude greater than over the stoss side, which may be related to vortex shedding from the dune. However, wake current speeds are extremely low and variable in direction; reverse flow is not sustained, and no retrogressive bedforms occur in the lee of large dunes. Near‐bed shear stress and bed roughness are usually low within the wake, reflecting low current speeds. Weak wake‐flow reattachment occurs at a variable distance downstream, up to several times the duneform height. A two‐dimensional numerical model for flow over dune topography, calibrated using average parameter values, provided a reasonable description of the flow upstream, and over the backs of large dunes as far as the crestal region. Wake flow could not be modelled. However, the temporal and spatial complexity of natural three‐dimensional flow over the dunes resulted in variance in parameter estimates; this variance precluded modelling of flow and bedload transport. Consequently, it was not possible to model dune evolution in a deterministic sense.
Rock‐magnetic characterization of early, redoxomorphic diagenesis in turbiditic sediments from the Madeira Abyssal Plain
Authors: Robinson Simon G. , Sahota John T. S.
Published: March 2003

Rock‐magnetic measurements of two sediment cores from the Madeira Abyssal Plain (MAP), north Atlantic, are used to investigate post‐depositional changes in the concentration, grain size and composition of magnetic minerals in the sediments that have occurred within organic‐rich turbidite horizons. The changes are associated with an initial stage of suboxic (reductive) diagenesis, following depletion of porewater O2, and a later stage of oxidative diagenesis associated with the slow descent of an oxidation front through the sediment, as a result of diffusion of O2 from the overlying sea water. The turbidites are of late Quaternary age (δ18O stages 1–3) and derive both from different sites on the NW African continental margin, and from the flanks of the Canary Islands. Thus, the turbidites are variable compositionally, especially in terms of carbonate, detrital magnetic mineral and organic carbon content. Diagenetic changes in these sediments have been identified using solid‐phase geochemical data (U, Mn, Corg and CaCO3) reported previously in more than one study. Rock‐magnetic parameters of the sediments, when expressed on a carbonate‐free basis, reveal that significant depletion of detrital ferrimagnetic iron (Fe2+/Fe3+) oxide grains has occurred within organic‐rich turbidites during redoxomorphic diagenesis. Normalized quotients of magnetic parameters also show that reductive diagenesis is a ferrimagnetic grain size‐selective process, but it has a minimal effect on the canted‐antiferromagnetic Fe3+ oxides in the sediment. Such components, if present, therefore become relatively enriched in magnetic assemblages as the ferrimagnetic grains are dissolved progressively, and bulk magnetic concentration is thus depleted. There is clear evidence in both cores for the existence of ultrafine ferrimagnetic grains at depth within the suboxic zone of the organic‐rich turbidites, beneath both active and fossil oxidation fronts. These grains are most probably associated with populations of live magnetotactic bacteria, which commonly inhabit such organic‐rich horizons and play a part in the chain of bacterially mediated reactions normally associated with suboxic diagenesis. These results show that simple and rapid rock‐magnetic techniques can be used to characterize early diagenetic processes involving iron phases in deep‐sea sediments, at least as effectively as more laborious, time‐consuming and sample‐destructive geochemical measurements.
Morphological evolution and dynamics of a large, sand braid‐bar, Jamuna River, Bangladesh
Authors: Ashworth Philip J. , Best James L. , Roden Julie E. , Bristow Charles S. , Klaassen Gerrit J.
Published: March 2003

The initiation and evolution of a kilometre‐scale, sand braid‐bar was monitored during a 28‐month survey period from 1993 to 1996 in one of the world’s largest braided rivers, the Jamuna River, Bangladesh. Repeated bathymetric surveys through two monsoon flood seasons, combined with bar‐top surveys during exposure of the bar at low flow, provide the most detailed chronology of braid‐bar growth yet compiled for a large sand‐bed river. During rising and peak flow of the 1994 monsoon flood, a 1·5‐km‐long, 0·5‐km‐wide, 12‐m‐high, symmetrical mid‐channel bar was deposited in the centre of a major channel downstream of a zone of flow convergence and significant bank erosion. Initial deposition and growth of the bar core were probably caused by amalgamation of dunes that are present in the Jamuna channels at all flow stages. Bar‐top aggradation continued through downstream migration of an ‘accretionary dune front’, a 3‐m‐high, angle‐of‐repose slipface that was composed of amalgamated, 0·5‐ to 1‐m‐high dunes. At waning and low flow, the mid‐channel bar widened by up to 1 km through the lateral accretion of dunes onto the margins of the initial bar core. A low‐velocity zone in the sheltered wake region of the bar‐tail led to the accumulation of substantial volumes of silts and clays. During the rising and peak flows of the next monsoon flood, the mid‐channel bar extended its bar‐tail by up to 1·5 km, as one of the anabranches became dominant, and flow was deflected across the bar‐tail. Accretion at the bar‐tail generated a lobate, transverse bar‐front with a 10‐m‐high, angle‐of‐repose avalanche face. Emergence of several smaller bars along this depositional front produced an overall reach morphology that more closely resembled an alternate bar rather than several mid‐channel bars. The conversion of a mid‐channel bar to an alternate bar is contrary to many previous descriptions of the braiding process.
Three‐dimensional modelling of a Holocene tufa system in the Lathkill Valley, north Derbyshire, using ground‐penetrating radar
Authors: Pedley  , Hill  , Denton  , Brasington
Published: March 2003

Unlithified and partly lithified carbonate sequences are ideally suited to the application of ground‐penetrating radar (GPR), augmented by percussion augering and shallow seismic techniques, all tied to present‐day topography using global positioning system (GPS) methods. This methodology provides the first clear information on the distribution and geometry of lithofacies within buried tufa complexes. The approach has been applied to a thick succession of Holocene tufas filling a gorge site along a 3·5‐km length of the River Lathkill, north Derbyshire. Earlier studies have demonstrated the presence of up to 16 m of tufas and sapropels associated with two transverse tufa dams (barrages). These strata have been accumulating throughout the Holocene, although tufa developments at present are of minor extent. Internal tufa morphologies are recorded by GPR as ‘bright’, laterally continuous reflections for lithified, concretionary and lithoclast‐rich horizons. The ‘brightest’ reflectors occur within well‐cemented barrages and delineate core areas and prograding buttress zones. In contrast, unlithified lime muds and sapropels produce low‐contrast reflections. Lithostratigraphic control and depth calibration of the GPR profiles was provided by percussion augering at selected sites. Six distinct lithofacies and four secondary barrages are identified in the study. Constructional and destructional events can be identified and correlated within the GPR profile network, and the internal growth morphologies of the barrages are apparent. GPR profiles also clearly define the evolution of the facies geometries. Three phases of tufa development can be recognized within the GPR data and greatly extend our understanding of Holocene tufa‐forming processes in valley sites: (a) Early Holocene barrage build‐ups but with limited paludal deposition; (b) Middle Holocene ponding and sapropel accumulation under ‘warm’ conditions; and (c) Late Holocene barrage termination and valley levelling, probably coincidental with anthropogenic activity. This type of multidisciplinary approach should be considered as an essential prerequisite to all biostratigraphic and geochemical studies of Holocene freshwater carbonate sites.
Morphology and curvature of delta slopes in Swiss lakes: lessons for the interpretation of clinoforms in seismic data
Authors: Adams Erwin W. , Schlager Wolfgang , Anselmetti Flavio S.
Published: March 2003

Seismic surveys were conducted and bathymetric data obtained from four alpine lakes in Switzerland. The curvature of the delta slopes was analysed with mathematical equations. Linear or exponential profiles are observed, representing planar or concave morphologies respectively. Planar profiles are interpreted to represent sediment that rests at the angle‐of‐repose. The slope angle of these profiles shows a correlation with sediment calibre. Exponential profiles do not show a clear correlation between sediment calibre and slope angle; they do not rest at the angle‐of‐repose, and different kinds of sediment can rest at the same slope angle. At the transition from lower slope to toe‐ of‐slope, the exponential equation fails to predict the present‐day morphology. The toe‐of‐slope lies above the predicted trend. This is attributed to a drastic increase in turbidite deposition that provides additional sediment and raises the basin‐floor profile above the predicted trend. The breaks between delta plain and slope are sharp, reflecting an abrupt change from transport by river flow and waves to gravity‐driven transport. In these lakes, the base‐level fluctuations relative to supply are small and insufficient to alter this sharp topographic break. The absence of sigmoidal profiles on the Swiss deltas is attributed to the high rate of progradation coupled with small fluctuations in base level.
The Mackenzie Delta: sedimentary processes and facies of a high‐latitude, fine‐grained delta
Authors: Hill Philip R. , Lewis C. Peter , Desmarais Simon , Kauppaymuthoo Vassen , Rais Hasna
Published: March 2003

The Mackenzie Delta is a large fine‐grained delta deposited in a cold arctic setting. The delta has been constructed upon a flooding surface developed on a previous shelf‐phase delta. There are three principal depositional zones: the subaerial delta plain, the distributary channel mouth region and the subaqeous delta. The subaerial delta plain is characterized by an anastomosing system of high‐sinuosity channels and extensive thermokarst lake development. This region is greatly influenced by the annual cycle of seasonal processes including winter freezing of sediments and channels, ice‐jamming and flooding in the early spring and declining river stage during the summer and autumn. Deposition occurs on channel levees and in thermokarst lakes during flood events and is commonly rhythmic in nature with discrete annual beds being distinguishable. In the channel mouth environment, deposition is dominated by landward accretion and aggradation of mouth bars during river‐ and storm surge‐induced flood events. The subaqeous delta is characterized by a shallow water platform and a gentle offshore slope. Sediment bypassing of the shallow‐water platform is efficient as a result of the presence of incised submarine channels and the predominance of suspension transport of fine‐grained sediments. Facies of the shallow platform include silty sand with climbing ripple lamination. Offshore facies are dominated by seaward‐fining fine sand to silt tempestites. Sea‐ice scouring and sediment deformation are common beyond 10 m water depth where bioturbated muds are the predominant facies. The low angle profile of the shallow‐water platform is interpreted to be the combined response of a fine‐grained delta to (1) storm sediment dispersal; (2) autoretreat as a result of the increasing subaerial and subaqeous area of deposition as the delta progrades out of its glacial valley; (3) limited water depth above the underlying flooding surface; and (4) efficient nearshore bypassing of sediment through subice channels at the peak of spring discharge. Several indicators of the cold climate can be used as criteria for the interpretation of ancient successions, including thermokarst lake development, submarine channel scours, freeze–thaw deformation and ice‐scour deformation structures. Permafrost inhibits compaction subsidence and, together with the shallow‐water setting, also limits autocyclic lobe switching. The cold climate can thus influence stratal architecture by favouring the development of regional‐scale clinoform sets rather than multiple, smaller scale lobes separated by autocyclic flooding surfaces.