bluuebunny/crossref_metadata_2025 huggingface dataset:
A Neoepitope‐Based Enzyme Immunoassay for Quantification of C1‐Inhibitor in Complex with C1r and C1s
Authors: FURE H. , NIELSEN E. W. , HACK C. E. , MOLLNES T. E.
Published: November 2003

Monoclonal antibodies (MoAb) recognizing neoepitopes exposed on activation products of complement proteins but hidden in the native components have been used for quantification of activated complement. A previously produced and characterized mouse MoAb, recognizing a neoepitope on the human plasma protein C1‐inhibitor complexed with its substrates, was used to design an enzyme immunoassay for detection of C1‐inhibitor complexed with C1r and C1s. These complexes are indicators of early classical complement pathway activation. The standard was serum activated with heat aggregated IgG defined to contain 1000 arbitrary units (AU)/ml. The lower detection limit was ≈0.05 AU/ml corresponding to 0.005% of fully activated serum. The reliability of the assay, including day‐to‐day variation, was tested. Intra‐assay variation coefficients were 12% for low plasma control and 13% for high plasma control (n = 12 for both). Inter‐assay variation coefficients were 12% for low control (n = 6), 19% for high control (n = 6) and 15% for the normal plasma control (n = 9). A 2.5–97.5 percentile reference range (normal blood donors) was 16–33 AU/ml. Two patients with systemic lupus erythematosus had considerably elevated plasma levels of the activation product (56 and 62 AU/ml), and six patients with hereditary angioedema had normal plasma levels despite considerably reduced C1‐inhibitor concentration. We conclude that the present method is sensitive and reliable for detection of early classical pathway activation and superior to previously published methods by utilizing neoepitope specificity and non‐radiolabelled reagents.
Cytokine mRNA Profile of Peripheral Blood Mononuclear Cells Isolated from Individuals with Trypanosoma cruzi Chronic Infection
Authors: DUTRA W. O. , GOLLOB K. J. , PINTO‐DIAS J. C. , GAZZINELLI G. , CORREA‐OLIVEIRA R. , COFFMAN R. L. , CARVALHO‐PARRA J. F.
Published: November 2003

Characterization of immunologic activities during chronic infection with Trypanosoma cruzi is critical for understanding the dynamics of human Chagas' disease. Since cytokine production is mainly regulated by transcription and mRNA stability, quantitative RT‐PCR analysis gives an accurate picture of the influences of disease on cytokine profile. Using RT‐PCR, the authors analysed the levels of message expression for several cytokines in peripheral blood mononuclear cells (PBMC) freshly isolated from chagasic patients (CP) and non‐infected individuals (NI), and in in vitro‐stimulated PBMC from CP. Ex vivo analysis showed that mean levels of expression of IL‐5, IL‐10, IL‐13 and IFNγ were dramatically increased in PBMC from CP, compared to NI. The levels of IL‐2 and IL‐4 were not significantly different between groups. Analysis of cytokine mRNA production after in vitro culture with parasite‐derived antigens (EPI or TRP) or anti‐epimastigote antibodies (Id) showed that these two classes of stimuli induced distinct cytokine responses. While EPI or TRP induced higher production of IFNγ specific message and low IL‐10, anti‐Id cells produced higher levels of IL‐10 and low IFNγ. The simultaneous presence of antigenic and antibody stimulation in the host during the chronic phase of Chagas' disease could explain the existence of both inflammatory and anti‐inflammatory cellular reactivity detected in most patients.
Smoking and Immunity: an Additional Player in the Mosaic of Autoimmunity
Authors: GEORGE J. , LEVY Y. , SHOENFELD Y.
Published: November 2003

Autoimmune diseases are associated with a variety of predisposing factors. However, the relative contribution of each remains to be established. The purpose of the paper is to focus on cigarette smoking, a common Western habit, as a possible environmental factor for the emergence of autoimmunity. This association is described in view of several recent studies documenting increased susceptibility to autoimmune diseases among smokers.
An Endogenous Superantigen in the Rat Gut Lumen as a Model to Study the Role of Human Protein‐Fv
Authors: GUIHARD A. I. , PIRES R. , BOUVET J.‐P.
Published: November 2003

Protein‐Fv (pFv) is a human B superantigen which can bind the variable domain (VH) of the heavy chain of immunoglobulins (Igs) and enhance the effector functions of secretory antibodies in the gut lumen. This study describes a rat molecule related to pFv by a similar specificity to the human VH3 domain. Investigation of the content of different gut segments shows that the rat pFv is usually hidden by its binding to local Igs to form macromolecular complexes similar to the immune fortresses described in normal humans. Furthermore, the pFv level generally increases from the jejunum to the colon in parallel with the decreasing water dilution, and finally a discontinuous presence can occur along the digestive tract. Detection of this molecule in the fetus proves its non‐microbial origin. Variations of the release of pFv, according to the breeding and to littermating, suggest the influence of external factors. This animal model allows the development of a study of the functions of pFv in vivo using a current laboratory species and has already provided evidence that the synthesis of this important molecule of the secretory immune system is regulated by environmental factors.
Selective Usage of VH Genes in Adult Human B Lymphocyte Repertoires
Authors: DAVIDKOVA G. , PETTERSSON S. , HOLMBERG D. , LUNDKVIST I.
Published: November 2003

The authors have compared the VH gene utilization patterns among small resting immunocompetent B cells and large naturally activated B lymphocytes of healthy human adults. They employed a non‐radioactive RNA in situ hybridization technique that allows detection of VH gene family expression at the single cell level. Pokeweed mitogen stimulated and unmanipulated mononuclear cells from peripheral blood and spleen of unrelated individuals were hybridized to digoxigenin‐labelled antisense RNA probes specific for human VH families 1–6 and for the constant region genes Cμ and Cγ. The observed VH gene family utilization patterns did not correlate with the genomic complexity of human VH genes. The VH3 gene family was most frequently used among resting B cells in both peripheral blood and spleen. Among naturally activated lymphocytes the VH6 gene was markedly over‐represented, while expression of the VH1 and VH3 gene families was decreased. The data show that V‐region mediated selection participates in shaping the peripheral antibody repertoire in healthy adults.
Expression of the Mouse Interleukin‐2 Receptor Gamma Chain in Insect Cells Using a Baculovirus Expression Vector—Comparison with the Human Common Gamma Chain
Authors: STENROOS K. , WEST A. , RAIVIO E. , LINDQVIST C.
Published: November 2003

The gene encoding the γ‐chain of the mouse Interleukin‐2 receptor was expressed in lepidopteran insect cells using the baculovirus expression vector system. The corresponding gene was inserted under the polyhedrin promoter of the Autographa californica nuclear polyhedrosis virus and expressed in the Spodoptera frugiperda insect cell line Sf9 during viral infection. The recombinant receptor protein was identified by immunoblotting in cell lysates prepared from insect cells infected with the produced recombinant virus VL1392‐mIL‐2Rγ. Kinetic analysis demonstrated that the corresponding protein could be detected as an ≈50 kDa protein already at 24 h post‐infection. Intrinsic labelling with [35S]‐methionine/cysteine and SDS‐PAGE analysis of the recombinant baculovirus infected insect cells verified the immunoblotting data. The expressed IL‐2Rγ protein could also be determined on the surface of infected insect cells by flow cytometric analysis. Comparison of the molecular weights between baculovirus expressed human and mouse IL‐2Rγ chains indicated differences in the glycosylation pattern despite similar numbers of N‐linked glycosylation sites.
Contrary Roles of IL‐4 and IL‐12 on IL‐10 Production and Proliferation of Human Tumour Reactive T Cells
Authors: HEIKE M. , SCHLAAK J. , HEYL S. , SCHULZE‐BERGKAMEN H. , SCHMITT U. , MEYER ZUM BU¨SCHENFELDE K.‐H.
Published: November 2003

The cytokine profile of tumour reactive T cells is likely to play a central role in their function. However, little is known about how cytokine patterns of tumour reactive T cells can be regulated. Here, the authors investigated the influence of exogenous regulatory cytokines in addition to interleukin‐2 (IL‐2) on cytokine patterns and the proliferation of T cells recognizing an autologous sarcoma cell line. In this system, IL‐4 and IL‐12 showed the most polarizing influences on tumour reactive T cells. Exogenous IL‐4 induced a predominant production of IL‐4 while decreasing the interferon‐γ (IFN‐γ) and IL‐10 production by tumour reactive T cells. It also stimulated the growth of tumour reactive CD4+ T cell clones. In contrast, IL‐12 substantially increased the production of IL‐10 and IFN‐γ. This was accompanied by a growth inhibition of tumour reactive T cells. The growth of CD4+ tumour reactive T cells was also suppressed by exogenous IL‐10. This study shows that cytokine patterns and proliferation tumour reactive T cells can be significantly influenced by exogenous cytokines and confirms the hypothesis of a negative feedback loop of IL‐12 by the induction of IL‐10 in the context of human tumour reactive T cells.
Reduced Expression of the Interferon‐Gamma Messenger RNA in IgG2 Deficiency
Authors: KONDO N. , INOUE R. , KASAHARA K. , FUKAO T. , KANEKO H. , TASHITA H. , TERAMOTO T.
Published: November 2003

The specific defect that causes IgG2 deficiency, which is one of the primary immunodeficiencies, is unknown. Recently, it was shown that interferon‐γ (IFN‐γ) induces synthesis of human germline Cγ2 transcripts. In the authors’ previous study and the present one, peripheral blood lymphocytes (PBLs) of all five tested patients with IgG2 deficiency failed to produce enough IFN‐γ when stimulated with phytohaemagglutinin or concanavalin A although they produced a sufficient amount of interleukin‐2 (IL‐2). The low level of IgG2 production in pokeweed mitogen‐stimulated PBLs of four tested patients was improved by the addition of recombinant IFN‐γ. In this study, the amount of IFN‐γ messenger RNA showed various degrees of reduction in all five tested patients. Sequence analysis of the IFN‐γ coding regions and flanking regions revealed neither a point mutation nor a deletion for any of the patients. Thus the results suggest that the reduced expression of IFN‐γ messenger RNA may play an important role in the IgG2 deficiency of these patients.
CD4 Dependence of Activation Threshold and TCR Signalling in Mouse T Lymphocytes
Authors: FEITO M. J. , BALLESTER S. , DıEZ‐OREJAS R. , OJEDA G. , CRIADO G. , PORTOLÉS P. , ROJO J. M.
Published: November 2003

The effect of CD4 expression on the activation threshold of mouse T lymphocytes has been analysed. To do this, the authors studied the response to antigen and other T cell receptor (TCR) ligands in a series of CD4− mutants obtained from the SR.D10 clone. This non‐tumour clone spontaneously arose from the Th2 clone D10.G4.1, and characteristically shows a low threshold for antigen activation as well as reactivity to syngeneic antigen presenting cells (APC). Although SR.D10 CD4− mutant cells can be stimulated by antigen, they need higher antigen concentration or more APC than SR.D10 or CD4 transfectants to yield optimal antigen responses. Furthermore, CD4− clones are not activated by syngeneic APC or by clonotypic antibodies. These effects do not correlate with changes in the expression of cell surface molecules implicated in antigen recognition, like TCR/CD3, CD2, LFA‐1, or CD45, or with lower p56lck or p59fyn activity in the mutant cells. Since inhibition experiments using anti‐CD4 antibodies have previously shown that activation of the CD4+ T cell clone D10.G4.1 by antigen or alloantigens is largely dependent on CD4, our results indicate that activation by antigen‐plus self MHC may become CD4‐independent if the activation threshold is lowered enough, e.g. in cells like SR.D10. Expression of CD4 further lowers the activation threshold of the cells, allowing the detection of low‐affinity TCR reactivities like those directed at self MHC. Moreover, by using anti‐TCR/CD3 antibodies, the authors have confirmed the importance of CD4‐associated tyrosine kinase activity in early TCR/CD3 signalling in this Th2 cell line, as (1) upon TCR/CD3 ligation, tyrosine phosphorylation is detected only in those CD3 chains co‐precipitating with CD4; and (2) CD4 expression is needed for efficient early tyrosine phosphorylation and detectable p56lck‐TCR co‐precipitation.
Molecular Modelling of HLA‐DQ Suggests a Mechanism of Resistance in Type 1 Diabetes
Authors: HOOVER M. L. , MARTA R. T.
Published: November 2003

Genetic resistance and susceptibility to insulin‐dependent diabetes mellitus (IDDM) have been associated with the HLA class II region on chromosome 6. In many races, the DQB1*0602 allele has been observed at a decreased frequency in IDDM, suggesting a protective role. A DNA sequence analysis of five patients, previously typed as having allele DQB1*0602, revealed sequence variation: one is DQB1*0603 and four possess unique sequences related to DQB1*0602 (one patient) or DQB1*0603 (three patients). Samples from four unaffected controls possessed normal DQB1*0602 sequences, and all patients and controls have normal DQA1 sequences. Each of the four unique patient sequences yields predicted amino acid sequences differing from the more common DQB1 alleles by variation at codons 9, 38 (silent), 59, and/or 62. Molecular modelling of the predicted protein sequence of these permissive variants reveals an HLA‐DQ structure from diabetic patients that differs in the surface contour of the peptide‐binding groove from normal DQB1*0602 sequence. In all the models of permissive molecules, the surface area corresponding to the HLA‐DR pockets 6, 7 and 9 are modified. These pockets accommodate side chains of the bound peptide; thus modification of this region could alter peptide specificity. This ‘pocket change’ suggests that the normal allele could confer dominant protection against the development of IDDM by affecting peptide and/or T cell receptor (TCR) binding. This could regulate the deletion or suppression of T cell clones inappropriately recognizing the beta cells of the pancreas.
Polyreactive Binding of Antibodies Generated by Polyclonal B Cell Activation. I. Polyreactivity Could be Caused by Differential Glycosylation of Immunoglobulins
Authors: FERNÁNDEZ C. , ALARCÓN‐RIQUELME M. E. , ABEDI‐VALUGERDI M. , SVERREMARK E. , CORTES V.
Published: November 2003

The aim of this study was to gain knowledge of the pre‐immune repertoire with reactivity directed to the carbohydrate antigen dextran B512 (Dx). Polyclonal activation of spleen cells in mice has been estimated to be a method of revealing the available repertoire. Hybridoma cell lines derived from lipopolysaccharide‐(LPS)stimulated C57BL/6 spleen cells were screened for reactivity with Dx and with the non‐related protein bovine serum albumin (BSA). Despite the lack of structural similarity between Dx and BSA we observed that nearly all of the Dx positive monoclonal antibodies (MoAbs) cross‐reacted with BSA. The Dx and BSA cross‐reactive MoAbs were also found to bind to several foreign‐and auto‐antigens, and therefore we concluded that these MoAbs fulfilled the criteria of polyreactivity. The Dx and BSA cross‐reactive antibodies were produced in an apparently random fashion as judged by the use of κ and λ light chains and the use of VH J558 subfamily genes. There are two possible explanations for this type of polyreactivity: (1) LPS induces a randomly generated polyreactive and a randomly generated specific immunoglobulin (Ig) repertoire; (2) polyreactivity can be the result of post‐translational modifications. Since immunoglobulins are glycoproteins we considered the possibility that post‐translational modifications such as glycosylation could be responsible for the generation of the polyreactive pool. Dextran‐specific and Dx/BSA cross‐reactive MoAbs showed different degrees of sensitivity to inhibition of glycosylation performed by treatment with tunicamycin (Tm), an inhibitor of the formation of N‐glycosidic linkages. Other polyreactive, connective and specific MoAbs were also tested. The authors found that Tm treatment had a more profound effect in reducing the binding capacity of the polyreactive antibodies (Abs), suggesting that the polyreactive Abs may be more dependent than the specific Abs on the carbohydrate content of the molecule for binding to the antigens. The authors propose that lymphocytes may use differential glycosylation as a means to generate polyreactive or monospecific Abs.
Beneficial Effect of Glucocorticoids on the Course of Haematogenously Acquired Staphylococcus aureus Nephritis
Authors: VERBA V. , SAKINIENE E. , TARKOWSKI A.
Published: November 2003

The effect of combined antibiotic and corticosteroid treatment on the course of haematogenously acquired Staphylococcus aureus nephritis was studied. Mice were given a single injection of S. aureus producing toxic shock syndrome toxin‐1 in a dose capable of inducing a high frequency of inflammatory kidney lesions and divided into three groups according to a treatment regimen. In all untreated animals inflammatory infiltrates were seen in kidney cortex and medulla with high frequencies of glomerular (90%) and tubular damage (50%) as well as fibrotic changes (50%). The treatment with antibiotics alone reduced significantly only the occurrence of focal inflammatory infiltrates. In contrast, the mice treated with a combination of antibiotics and corticosteroids displayed in 64% of cases normal histological kidney appearance and a significant decrease in occurrence of glomerular (P<0.01) and tubular (P<0.05) lesions. Immunohistochemically, the combined treatment resulted in a more pronounced decrease in numbers of CD4, IL‐2R (four to fivefold) and CD8 positive cells in kidney inflammatory lesions compared to antibiotics only treated group. Thus, glucocorticoids in association with antibiotics are shown to improve the outcome of septic murine nephritis, possibly due to suppression of kidney infiltrating T cells.
Instability of Natural Antibody Repertoires in Systemic Lupus Erythematosus Patients, Revealed by Multiparametric Analysis of Serum Antibody Reactivities
Authors: FERREIRA C. , MOUTHON L. , NOBREGA A. , HAURY M. , KAZATCHKINE M. D. , FERREIRA E. , PADUA F. , COUTINHO A. , SUNDBLAD A.
Published: November 2003

Recent views on autoimmune diseases invoke generalized but specific perturbations in antibody repertoires, rather than the clonally restricted or non‐specific polyclonal alterations proposed thus far. The present experiments analyse serum antibody reactivities in 24 systemic lupus erythematosus (SLE) patients and 17 healthy controls, using a method that quantitatively scores a large number of antibody reactivities and allows for multiparametric statistical analyses. The results show global but relatively specific perturbations in SLE antibody repertoires, and identify novel disease‐associated reactivity patterns. Furthermore, a time series analysis of serum antibodies over 3 months demonstrates instability of natural antibody repertoires in individual SLE patients, contrasting with their remarkable conservation in healthy donors. Moreover, the method used clusters controls and patients independently, and might prove of diagnostic value, once large data bases are established.
Characterization of Chlamydia pneumoniae Antigens Using Human T Cell Clones
Authors: HALME S. , SAIKKU P. , SURCEL H.‐M.
Published: November 2003

Chlamydia pneumoniae infection is followed by the development of antigen‐specific cell‐mediated immunity (CMI), which is detectable as a positive lymphocyte proliferation (LP) response to C. pneumoniae elementary body (EB) antigen, but the proteins inducing the T cell activation are not known. In the present work the authors used human T lymphocyte clones (TLC) raised against C. pneumoniae EB antigen to characterize C. pneumoniae proteins as T cell‐stimulating antigens. A total of 55% of the TLC established recognized antigenic determinants only on C. pneumoniae species, while the rest of the TLC proliferated to both C. pneumoniae and C. trachomatis EB. The antigen specificity of the TLC was further analysed by stimulating with SDS‐PAGE fractionated C. pneumoniae EB proteins. Chlamydia pneumoniae species‐specific antigens were found in the molecular weight ranges 92–98, 51–55, 43–46 and 31.5–33 kDa and genus‐specific antigens in the ranges 12, 26 and 65–70 kDa. The 46.5–49.5 and 55–61 kDa regions contained both species‐specific and genus‐specific antigens. Human leucocyte antigen (HLA) restriction analysis for the TLC isolated from an HLA DR4, 15(2) heterozygous person showed the majority (81.3%) to be restricted to the HLA DR4 molecule, the rest being DR15(2)‐restricted. An interesting preliminary finding was that the expression of interferon‐gamma (IFN‐γ) mRNA by the TLC was predominantly associated with antigen recognition in the context of the HLA DR4 molecule, while interleukin‐4 (IL‐4) production was linked to antigen recognition in the context of the HLA DR15(2) molecule.
Distinguishable Patterns of Connectivity in Serum Immunoglobulins from SLE Patients and Healthy Individuals
Authors: AYOUBA A. , FERREIRA C. , COUTINHO A.
Published: November 2003

Given that normal individuals maintain significant levels of serum autoantibodies that share many characteristics with those found in association with autoimmune diseases (AID), it has been proposed that disease could result from defects in supraclonal regulation, namely deviations of normal patterns of immunoglobulin (Ig) connectivity. Using conventional methods, together with a recently developed technique to quantitatively score a variety of V‐region‐dependent serum IgG interactions, the authors have now compared serum Ig connectivity in a group of patients with systemic lupus erythematosus (SLE) to healthy controls. The results demonstrate the existence of V‐region interactions of serum IgG and IgM in SLE patients and healthy donors, with comparable connectivity titres, diversity and average affinities (μm range), but a wider individual variation and a tendency for higher F(ab′)2 directed reactivities in the group of SLE patients. Multivariate statistics analysis of the data derived from reactivity patterns on F(ab′)2 subsets, however, distinguished the two groups of donors, and demonstrated a larger dispersion and wider time‐dependent variations in the patient population, as compared to healthy controls. The authors conclude that SLE is associated with circulating antibody repertoires that deviate from the patterns and levels of V‐region connectivity characteristic of healthy individuals. These findings may shed light on the mechanisms of disease maintenance, and on the basis for the therapeutic effects of normal polyclonal Igs at high doses.
IFN‐γ Regulates Murine Interferon‐Inducible T Cell Alpha Chemokine (I‐TAC) Expression in Dendritic Cell Lines and during Experimental Autoimmune Encephalomyelitis (EAE)
Authors: Hamilton N. H. R. , Banyer J. L. , Hapel A. J. , Mahalingam S. , Ramsay A. J. , Ramshaw I. A. , Thomson S. A.
Published: November 2003

Murine interferon‐inducible T cell alpha chemokine (I‐TAC) is a potent non‐ELR Cys‐X‐Cys (CXC) chemokine that predominantly attracts activated T lymphocytes and binds to the receptor CXCR3. Using semiquantitative reverse transcription–polymerase chain reaction (RT–PCR) we analysed murine I‐TAC expression in two different progenitor dendritic cell (DC) lines, MTHC‐D2 and JAWS II which were exposed to various cytokines, and Con A‐activated splenocytes from a panel of knockout mice. Analysis of the progenitor DC lines and Con A cultures demonstrated that murine I‐TAC is primarily regulated by interferon (IFN)‐γ via interferon regulatory factor (IRF)‐1. It has been proposed that I‐TAC may have a role in autoimmune diseases such as multiple sclerosis (MS). Because I‐TAC appears to be secreted from antigen‐presenting cells (APCs) and attracts activated T cells, we examined the level of murine I‐TAC mRNA in the central nervous system (CNS) of wild‐type and IFN‐γ‐receptor knockout (IFN‐γR−/−) mice with myelin oligodendrocyte glycoprotein (MOG)35–55 peptide‐induced experimental autoimmune encephalomyelitis (EAE). Peak I‐TAC expression was detected in wild‐type mice on day 14 when the mice begin to recover, whereas very low levels of I‐TAC were detected in the CNS of IFN‐γR−/− mice which develop severe EAE and die. The expression characteristics of murine I‐TAC suggest an important mediator of immune cell communication that could augment vaccines and autoimmune therapies.
Uptake of Apoptotic K562 Leukaemia Cells by Immature Dendritic Cells is Greatly Facilitated by Serum
Authors: Dalgaard J. , Beckstrøm K. J. , Brinchmann J. E.
Published: November 2003

Dendritic cells (DCs) are potent antigen‐presenting cells and play an important role in T‐cell‐mediated immunity. DCs have been shown to induce strong antitumour immune responses both in vitro and in vivo. One way of providing the DCs with all relevant tumour antigens would be to incubate the DCs with material from dead tumour cells. We have examined the uptake of apoptotic and necrotic K562 leukaemia cells by DCs under different culture conditions. Results from coincubation experiments strongly suggested that uptake of apoptotic K562 cells was dependent upon the addition of autologous serum (AS). Under these conditions, 47–79% of all DCs were shown to ingest apoptotic material. AS also seemed to be important for the expression of functionally important markers, most notably HLA class I, CD86, CCR7 and CD83. The vast majority of DCs were shown to ingest necrotic material from K562 cells, with no additional effect of AS. The results suggest that incubation of DCs with apoptotic material for cell therapeutic purposes may best be performed in the presence of AS.
Authigenic mineralogy, depositional environments and evolution of fault‐bounded lakes of the Yunnan Plateau, south‐western China
Authors: XIOUZHU ZHANG , YUNFEI WANG , HUAIYAN LEI
Published: November 2003

The Dianchi, Erhai and Fuxian lakes lie in faulted basins in a subtropical humid region of the Yunnan Plateau, China. Three groups of authigenic minerals have been recognized in their recent sediments ‐ carbonate minerals, Fe‐bearing minerals and silica minerals. The main authigenic minerals are goethite, calcite, aragonite, siderite and quartzine. Goethite is chemically precipitated from a colloidal suspension. Calcite is a widespread chemical precipitate that is present in deep parts of the lakes and in shallow areas associated with aquatic macrophytes. Aragonite is mainly biochemical in origin, and commonly associated with shallow benthos. Siderite forms in reducing environments, associated with pore waters with a high PCO2 that resulted from microbial degradation of organic matter. It forms mainly in deep‐water environments. Quartzine, which occurs mainly in delta front and prodeltaic sites, forms from diatom dissolution and dissolved silica introduced by streams.

Six authigenic mineral associations are recognized, each of which can be related to depositional setting within the lake and the stage of lake development. The same associations can also be recognized in a 480‐m‐long core recovered from Dianchi Lake. Strong reducing environments and migrating pore fluids with high PCO2 have led to the early diagenetic alteration of some of the initial authigenic minerals. Using the mineral associations from the modern lakes, the Pliocene to Recent history of Dianchi Lake has been interpreted, and is in general agreement with palaeoenvironmental reconstructions based upon palaeontological and other evidence.
Petrogenesis of sediments in the absence of chemical weathering: effects of abrasion and sorting on bulk composition and mineralogy
Authors: NESBITT H. WAYNE , YOUNG GRANT M.
Published: November 2003

Comminution in the glaciers that debouch into Guys Bight Basin, followed by selective sorting in the fluvial system, has had little effect on the bulk composition, or on the mineralogy, of the basin sands and muds. Most striking are the feldspar contents, and the feldspar‐quartz ratios in sands and muds, both of which remain similar to those of average bedrock. The feldspar contents of sands and muds range from 48 to 52% feldspar whereas average bedrock contains 51·7% feldspar. Feldspar‐quartz ratios average 1·58:1 in bedrock and 1·54:1, 1·66:1 and 1·69:1 in the medium to coarse sands, fine sands and muds, respectively, indicating minimal feldspar enrichment in the fine‐grained sediments. In the absence of appreciable chemical weathering, extreme abrasion followed by hydraulic sorting has not produced mature sediments such as quartz arenites and clay‐mineral‐rich muds. There is, however, some chemical differentiation. Preferential accumulation of mafic minerals in fine sands and muds is reflected in bulk compositions by higher abundances of MgO, FeO and TiO2, and in the mineralogy by enrichment of biotite in the fine grades. Bulk compositional studies focused solely on muds and mudstones will result in an overestimate of the mafic contribution from source rocks. This work shows that bulk compositional studies of sediments and sedimentary rocks should include all available granulometric grades.
Toward a model for airflow on the lee side of aeolian dunes
Authors: FRANK ANDREW , KOCUREK GARY
Published: November 2003

The interaction between dunes and the primary wind results in a complex pattern of secondary airflow on the lee side of dunes. From 15 dunes studied during transverse flow conditions at Padre Island in Texas, White Sands in New Mexico, and the Algodones in California, distinct flow regions can generally be recognized, with the overall flow structure comparing favourably to that proposed for subaqueous bedforms. Downwind of dunes with flow separation is a back‐flow eddy that extends about four dune‐brink heights downwind from the brink of the dune. Beyond the separation cell, the velocity profiles can be divided into regions based upon segments separated by ‘kinks’ in the velocity profiles. The interior is an area above the dunes of relative high wind speed but low velocity gradient. Beneath the interior is the wake, which consists of two layers. The upper wake exhibits an uppermost portion where the flow decelerates while the remainder exhibits accelerating flow, so that the overall velocity gradient decreases downwind. The lower wake exhibits low velocity gradients and wind speeds that accelerate downwind at all heights, but primarily near the top of the layer, thereby causing the velocity gradient to increase downwind. At about eight dune heights downwind, the upper and lower wakes equilibrate to a single profile with the kink between them no longer apparent. The lowest recognizable region is the internal boundary layer. It is recognized by a relatively steep velocity gradient below the wake, and never exceeds a few tens of centimetres in height for our data set. Because of acceleration and increasing shear stress within this layer, interdune flats are at least potentially erosional. Overall, the wake and internal boundary layer show a downward transfer of momentum from upper regions so that the flow recovers. Where flow separation does not occur, simple flow expansion down the lee‐face causes flow deceleration.
Flow dynamics and geomorphology of a trough blowout
Authors: HESP PATRICK A. , HYDE ROBERT
Published: November 2003

The dynamics and geomorphological development of a trough blowout located at Fiona Beach in the Myall Lakes National Park in NSW, Australia, are examined. Wind speeds, velocities and flow structure were measured utilizing an array of miniature Rimco cup anemometers, Gill bivane and UVW instruments, and wind vanes. Flow measurements indicate that when the wind approaches the trough blowout parallel to the throat orientation, jets occur both in the deflation basin and along the erosional walls, relative flow deceleration and expansion occurs up the depositional lobe, jets are formed over the depositional lobe crest accompanied by downwind flow separation on the leeward side of the lobe, and flow separation and the formation of corkscrew vortices occur over the crests of the erosional walls. Maximum erosion and transport occurs up the deflation basin and onto the depositional lobe. Trough blowout morphologies are explained as a function of these flow patterns.

When the wind approaches the blowout obliquely, the flow is steered considerably within the blowout, and the degree and complexity of topographic steering is dependent on the blowout topography. The flow is usually extremely turbulent and large corkscrew vortices are common. The local topography of a blowout can be very important in determining overall sand transport and blowout evolutionary conditions and paths.

Estimates of potential sand transport within the blowout may be up to two orders of magnitude lower than actual rates if remotely sensed wind data are used.
Hydraulic characteristics of bioclastic deposits: new possibilities for environmental interpretation using settling velocity fractions
Authors: KENCH PAUL S. , McLEAN ROGER F.
Published: November 2003

This paper examines the hydraulic behaviour of heterogeneous bioclastic sediments using settling velocity fractions. Bioclastic deposits are divided into fractions by splitting hydraulically sorted samples. Compositional analysis of fractions shows that grains exhibit marked variation in composition, shape, size and density which control the hydraulic behaviour of bioclastic deposits. Despite the heterogeneous grain properties of fractions (analogous to sieve fractions) sedimentation analysis shows that they possess a narrow range of settling velocity values. Flume experiments also show that the settling velocity fractions possess a narrow range of threshold velocity values. A threshold relationship is identified in which the velocity required to entrain mixed settling fractions increases from 20.5 to 65‐0cm s −1 for settling fractions with mean settling values of 5.5 chi (2‐2 cm s −1) to 1.4 chi (36.0 cm s −1), respectively. Heterogeneous settling fractions, due to intergrain effects, were found to possess larger threshold velocities than individual components showing that the composition of bioclastic deposits controls hydraulic behaviour. Thus, caution must be exercised in using the threshold relationship for homogeneous sediments or deposits of markedly different composition.

As settling velocity fractions reflect narrow hydraulic (settling and threshold) properties of sediments the mean settling velocity of fractions is considered a good indicator with which to interpret transport and depositional processes.

Comparison of settling and sieve‐size distributions shows that size distributions do not reflect the hydraulic behaviour of bioclastic deposits and should not be used to interpret environmental processes. The study indicates that examination of settling velocity fractions (for which hydraulic settling and threshold properties are known) coupled with compositional analysis of these fractions will allow much greater environmental interpretation of deposit‐forming and energy processes in reef environments.
Wind tunnel and field testing of a simple sand catcher for sampling inhomogeneously saltating sand in desertified environments
Authors: MOHAMMED A. E. , VEER O. D. VAN DE , OLDENZIEL H. J. , STIGTER C. J.
Published: November 2003

Problems of vertical alignment and vibrations of disposable coffee cups used in a modified version of the De Ploey saltating sand catcher were solved. The new version was tested in a sediment wind tunnel. Its catches appeared linearly related to amounts of eroded sand, largely independent of wind speed and wind direction, and depended logarithmically on height. The catch efficiency may therefore be taken to be approximately independent of wind speed and direction. The instrument performed well under conditions of inhomogeneously saltating sand in a strongly desertified environment in Central Sudan. Use and results show the improved simple catcher to be easy to assemble, reproducible and cheap, suitable for multipoint use to cover all inhomogeneities in outdoor saltating sand fields.
Facies architecture of alluvial floodbasin deposits: three‐dimensional data from the Upper Triassic Callide Coal Measures of east‐central Queensland, Australia
Authors: JORGENSEN P. J. , FIELDING C. R.
Published: November 2003

A detailed investigation of floodbasin facies architecture was undertaken in the Upper Triassic (Carnian‐Rhaetian) Callide Coal Measures in east‐central Queensland, Australia, using extensive highwall and exploration borehole data from ongoing mining activities. The composite Callide Seam Member varies up to 23 m in thickness and is locally split by a number of clastic partings up to several metres thick, ranging from claystone to coarse sandstone. A subset of the nine lithofacies recognized in surface exposures was identified from geologists' logs of cored and uncored drillholes through the Callide Seam Member. Facies mapping of each clastic parting (split) was then undertaken using all available highwall and drilling data. Sequential maps of facies and interval thickness for each coal body and clastic parting over the mine area (6000 × 2500 m) record sediment accumulation in alluvial channel and floodbasin environments (including levees, splays and splay complexes, and mires). The maps indicate that the numerous splays have dominantly elongate plan geometry (up to 4 km long), with lesser irregular and rare lobate shapes. Small, elongate splays were evidently formed during single flood events, whereas larger, elongate bodies and more irregularly shaped complexes were the product of longer‐term splay construction over several flood cycles. Quantitative summaries of splay dimensions indicate a wide variety of shape and size. The distribution of splay orientations is similar to the palaeocurrent distribution in major alluvial channel deposits as established from cross‐bedding. Alluvial channels that sourced the splays and other clastic sediments within seam splits were of low sinuosity, braided planform, constructed sediment bodies up to 2800 m wide and were dominantly loaded rather than incised into underlying peat‐rich substrates.
Grain‐size characteristics of fine‐grained unflocculated sediments II:‘multi‐round’ distributions
Authors: KRANCK KATE , SMITH P. C. , MILLIGAN T. G.
Published: November 2003

The grain‐size spectrum of sediment deposited by settling of a suspension with a ‘one‐round’ grain size distribution is described by a power law in which the integer exponent characterizing the fine‐grained limb is increased by one over that of the suspension. If this better‐sorted sediment, in turn, is resuspended and settles, further sorting and steepening of the limb occurs. Each resuspension event or‘round’changes the distribution by a predictable amount. Equations describing this sorting process, based on the derivation of the one‐round equation, are fitted to grain‐size analyses of well‐sorted sediment from a variety of locations to verify the model. A suite of sandy bottom sediment samples from the Bay of Fundy shows that the steepness of the fine‐grained limbs of the sand fraction indeed increases in integral steps.
Sedimentary model and high‐frequency cyclicity in a Mediterranean, shallow‐shelf, temperate‐carbonate environment (uppermost Miocene, Agua Amarga Basin, Southern Spain)
Authors: MARTÍN JOSÉ M. , BRAGA JUAN C. , BETZLER CHRISTIAN , BRACHERT THOMAS
Published: November 2003

Uppermost Tortonian to lower Messinian temperate carbonates crop out in the Agua Amarga Basin (SE Spain). They consist of four units. The lower three units can be tentatively assigned to the lowstand systems tract of a fourth‐order sequence, constituting in turn the lowstand (‘megatrough unit’), transgressive (‘breccia unit’) and highstand (‘bedded unit’) stages of a higher‐order cycle. All these materials were deposited in a small pull‐apart basin related to the sinistral Carboneras strike‐slip fault system. The best represented is the bedded unit (up to 25 m thick), which consists of bioclastic, bryozoan/bivalve‐dominated calcarenites/calcirudites with abundant fragments of echinoids, barnacles, benthic foraminifers, coralline algae, brachiopods and solitary corals. Facies trends within this unit are roughly arranged in an E‐W direction, with the coastline to the north of the basin. The depositional model is that of a gentle ramp with prograding beaches and shoals in its higher parts. Seaward of the shoals was the ‘factory area’, where most organisms lived and maximum carbonate production took place. From this area some of the skeletons were washed landwards by waves and/or currents during storms and incorporated into the shoals and beaches, and others moved downslope along the ramp as mass‐flows, accumulating to form the ‘fan‐bedded zone’.

The factory‐area and fan‐bedded sediments intercalate five well‐defined, thick beds of calcarenites/fine‐grained calcirudites. They show bar morphologies (single or amalgamated), or make up sand‐waves with very consistent tabular cross‐bedding pointing landwards. These beds formed in a very shallow, wave/current‐influenced, coastal environment. The bars and sand waves in the fan‐bedded zone developed during lowstands, while those located higher up in the ramp interbedded with the factory facies are related to transgressive stages. Prograding beaches, shoals, factory facies and fan‐bedded layers developed during the highstands. Net skeletal production occurred mainly during the highstands.

Sediment‐accretion values of these sediments are similar to those of present and ancient shallow‐marine, temperate carbonates considering that the whole bedded unit was deposited in a 100 000‐year interval (equivalent to the short eccentricity cycle). The five cycles inside the bedded unit would therefore correspond to the c. 20 000‐year precession cycles of the Milankovitch band.
Experimental soft‐sediment deformation: structures formed by the liquefaction of unconsolidated sands and some ancient examples
Authors: OWEN GERAINT
Published: November 2003

The effects of liquefaction in saturated sand bodies under a variety of driving forces are described from shaking table experiments, and structures from the geological record are presented which are analogous to the experimental structures. The collapse of sloping heaps of cross‐bedded sand under a gravitational body force generates low‐angle, essentially uncontorted stratification. A basal zone of shearing may be present, with steepened and folded foresets. Stretching of foresets may be accommodated on normal faults, and bottomsets may be contorted into inclined folds. In natural systems the substrate may also liquefy, causing deformation driven by an unevenly distributed confining load. Stratification in the surface bedform is flattened, and stratification in the substratum contorted. Experiments failed to produce relative displacement at the interface between stacked sand bodies. Liquefaction of gravitationally unstable systems in sands generates load structures comparable to those from sand‐mud systems. Recumbent‐folded deformed cross‐bedding is formed by current shear over a liquefied bed, as has been inferred from field and theoretical analyses. Shear of nonliquefied sand forms angular folds. Other deformation mechanisms, such as fluidization or seepage, may generate structures similar to all of these. Local water‐escape structures driven by fluidization occur in the upper parts of some liquefied sand bodies. They include cusps, sand volcanoes and clastic dykes. Transient cavities formed in some experiments and seemed to be preserved as breached cusps. Although the experiments tried to isolate individual driving forces, driving forces may operate together, and there may be a continuum between deformation driven by water escape and deformation driven by loading. Different structures from those described here may form where liquefaction develops in a buried layer as opposed to at the sediment surface.
Deep‐sea avulsion and morphosedimentary evolution of the Rhône Fan Valley and Neofan during the Late Quaternary (north‐western Mediterranean Sea)
Authors: TORRES J. , DROZ L. , SAVOYE B. , TERENTIEVA E. , COCHONAT P. , KENYON N. H. , CANALS M.
Published: November 2003

The Petit‐Rhône Fan Valley (north‐western Mediterranean) is a broad, sinuous, filled valley that is deeply incised by a narrow, sinuous thalweg. The valley fill is differentiated into three seismic subunits on high‐resolution seismic‐reflection profiles. The lower chaotic subunit probably consists of channel lag deposits that seem to be in lateral continuity with high‐amplitude reflections representing levee facies. The intermediate transparent subunit, which has an erosional base and clearly truncates levee deposits, is interpreted to be mass‐flow deposits resulting from the disintegration of the fan‐valley flanks. The upper bedded subunit shows an overall lens‐shaped geometry and the seismic reflections onlap either onto the top of the underlying transparent subunit or onto the Rhône levees. Piston core data show that the upper few meters of this upper subunit consist of thin turbidites, probably deposited by overflow processes. The few available 14C ages suggest that the upper stratified subunit filled the Petit‐Rhône Fan Valley between 21 and 11 kyr BP.

The upper bedded subunit is deposited within the Petit‐Rhône Fan Valley downslope of a major decrease in slope gradient. This upper subunit and the thalweg are genetically related and represent a small channel/levee system confined within the fan valley. Previous studies interpreted this thalweg to be an erosional feature resulting from a recent avulsion of the major channel course. Our interpretation implies that the thalweg is not a purely erosional feature but a depositional/erosional channel. This small channel/levee system is superimposed on a large muddy channel/levee system after the sediment supply changed from thick muddy flows during the main phase of aggradation of the Rhône Fan levees, to thin, mixed (sand and mud) flows at the end of Isotope Stage 2 (∼16–18 ka BP). The pre‐existing morphology of the Petit‐Rhône Fan Valley played a determinant role in the sediment dispersal leading to the creation of this small and confined channel/levee system. These mixed flows have undergone flow stripping resulting from the changes in the slope gradient along the thalweg course. The finer sediment overflowed from the thalweg and were deposited in the Petit‐Rhône Fan Valley. Coarser channelled sediment remaining in the thalweg were deposited as a ‘sandy’lobe (Neofan). As indicated by 14C dating, sedimentation on this lobe continued until very recently, suggesting a further evolution of the turbidity flows from small mixed flows to small sandy flows. the deposition of this study lobe and the sedimentary fill of the Petit‐Rhône Fan Valley may be related to widespread shelf edge and canyon wall failures with a resulting downslope evolution of failed sediment into turbidity currents.
A method for the disaggregation of mudstones
Authors: YANG YUNLAI , APLIN ANDREW C.
Published: November 2003

We describe a method which effectively and gently disaggregates muds and mudstones by combining a saturation‐freeze‐thaw technique with treatment by ultrasonic probe. The method works well for samples containing <5% TOC and which have been buried to depths less than about 3500 m. It does not work for samples strongly cemented with carbonates or silicates. Scanning electron micrographs of size fractions and the strong mineralogical segregation between size fractions are offered as evidence of complete disaggregation.