bluuebunny/crossref_metadata_2025 huggingface dataset:
In situ examination of the behaviour of fish in response to demersal trawl nets in an Australian trawl fishery
Authors: Piasente M. , Knuckey I. A. , Eayrs S. , McShane P. E.
Published: December 2004

In situ examination of the behaviour of fish was undertaken with underwater cameras positioned on demersal trawl gear used by Australia’s South East Trawl Fishery. Blue grenadier (Macruronus novaezelandiae), pink ling (Genypterus blacodes) and whiptails (Coelorinchus spp.) swam in an anguilliform mode whereas other species displayed a carangiform swimming mode. Tiger flathead (Neoplatycephalus richardsoni) and ocean perch (Heliocolenus spp.) were active in response to the approaching trawl net compared with the generally passive activity of whiptails, New Zealand dory (Cyttus novaezelandiae), and jackass morwong (Nemadactylus macropterus). However, when in the body of the trawl, gemfish were active while ocean perch, whiptails and New Zealand dory were generally passive. Some blue grenadier, ocean perch and whiptails escaped capture by passing through open meshes in the trawl mouth, whereas tiger flathead passed under the ground gear. In the trawl body, small numbers of blue grenadier passed through open meshes in the top panel whereas numerous spotted warehou swam faster than the towing speed, presumably escaping capture by swimming forwards and out of the trawl. Interspecific behavioural variation in escape response could be utilised to design more efficient trawl gears.
DMS and DMSP in mucus ropes, coral mucus, surface films and sediment pore waters from coral reefs in the Great Barrier Reef
Authors: Broadbent Andrew D. , Jones Graham B.
Published: December 2004

Concentrations of dimethylsulphide (DMS) and its precursor compound dimethylsulphoniopropionate (DMSP), two sulphur compounds that are involved in the formation of clouds, were measured for mucus ropes, coral mucus, surface films and sediment pore waters collected from three coral reefs in the Great Barrier Reef, Australia. The concentrations of DMS (61–18 665 nm) and DMSP (1978–54 381 nm) measured in mucus rope samples are the highest yet reported in the marine environment. The values exceed concentrations of DMS and DMSP reported from highly productive polar waters and sea ice algal communities. Concentrations of DMSP in coral mucus ranged from 1226 to 25 443 nm, with mucus from Acropora formosa containing the highest levels of DMSP. Dimethylsulphide and DMSP in surface microlayer samples from three coral reefs were two to four times subsurface (0.5 m) concentrations. In coral-reef sediment pore waters, concentrations of DMS and DMSP were substantially higher than water-column concentrations, suggesting that coral sediments may be a significant source of these two compounds to reef waters. Overall, the results strongly suggest that coral reefs in the Great Barrier Reef are significant sources of these two sulphur substances.
Two perfectly conserved arginine residues are required for substrate binding in a high-affinity nitrate transporter
Authors: Unkles Shiela E. , Rouch Duncan A. , Wang Ye , Siddiqi M. Yaeesh , Glass Anthony D. M. , Kinghorn James R.
Published: December 2004

This study represents the first attempt to investigate the molecular mechanisms by which nitrate, an anion of significant ecological, agricultural, and medical importance, is transported into cells by high-affinity nitrate transporters. Two charged residues, R87 and R368, located within hydrophobic transmembrane domains 2 and 8, respectively, are conserved in all 52 high-affinity nitrate transporters sequenced thus far. Site-directed replacements of either of R87 or R368 residues by lysine were found to be tolerated, but such residue changes increased the
K
m
for nitrate influx from micromolar to millimolar values. Seven other amino acid substitutions of R87 or R368 all led to loss of function and lack of growth on nitrate. No evidence was obtained of R87 or R368 forming a salt-bridge with conserved acidic residues. Remarkably, the phenotype of loss-of-function mutant R87T was found to be alleviated by an alteration to lysine of N459, present in the second copy of the nitrate signature (transmembrane domain 11), suggesting a structural or functional interplay between residues R87 and N459 in the three-dimensional NrtA protein structure. Failure of the potential reciprocal second site suppressor N168K (in the first nitrate signature copy of transmembrane domain 5) to revert R368T was observed. Taken with recent structural studies of other major facilitator superfamily proteins, the results suggest that R87 and R368 are involved in substrate binding and probably located in a region of the protein close to N459.
Unexpected connections between Burnside groups and knot theory
Authors: Dabkowski Mieczyslaw K. , Przytycki Józef H.
Published: December 2004

In classical knot theory and the theory of quantum invariants substantial effort was directed toward the search for unknotting moves on links. We solve, in this article, several classical problems concerning unknotting moves. Our approach uses a concept, Burnside groups of links, that establishes an unexpected relationship between knot theory and group theory. Our method has the potential to be used in computational biology in the analysis of DNA via tangle embedding theory, as developed by D. W. Sumners [Sumners, D. W., ed. (1992)New Scientific Applications of Geometry and Topology(Am Math. Soc., Washington, DC) and Ernst, C. & Sumners, D. W. (1999)Math. Proc. Cambridge Philos. Soc.126, 23–36].
Differences in the folding transition state of ubiquitin indicated by φ and ψ analyses
Authors: Sosnick Tobin R. , Dothager Robin S. , Krantz Bryan A.
Published: December 2004

We compare the folding transition state (TS) of ubiquitin previously identified by using ψ analysis to that determined by using φ analysis. Both methods attempt to identify interactions and their relative populations at the rate-limiting step for folding. The TS ensemble derived from ψ analysis has an extensive native-like chain topology, with a four-stranded β-sheet network and a portion of the major helix. According to φ analysis, however, the TS is much smaller and more polarized, with only a local helix/hairpin motif. We find that structured regions can have φ values far from unity, the canonical value for such sites, because of structural relaxation of the TS. Consequently, these sites may be incorrectly interpreted as contributing little to the structure of the TS. These results stress the need for caution when interpreting and drawing conclusions from φ analysis alone and highlight the need for more specific tools for examining the structure and energetics of the TS ensemble.
Direct demonstration of carbamoyl phosphate formation on the C‐terminal domain of carbamoyl phosphate synthetase
Authors: Kothe Michael , Purcarea Cristina , Guy Hedeel I. , Evans David R. , Powers‐Lee Susan G.
Published: December 2004

Carbamoyl phosphate synthetase synchronizes the utilization of two ATP molecules at duplicated ATP‐grasp folds to catalyze carbamoyl phosphate formation. To define the dedicated functional role played by each of the two ATP sites, we have carried out pulse/labeling studies using the synthetases from Aquifex aeolicus and Methanococcus jannaschii, hyperthermophilic organisms that encode the two ATP‐grasp folds on separate subunits. These studies allowed us to differentially label each active site with [γ‐32P]ATP and determine the fate of the labeled γ‐phosphate in the synthetase reaction. Our results provide the first direct demonstration that enzyme‐catalyzed transfer of phosphate from ATP to carbamate occurs on the more C‐terminal of the two ATP‐grasp folds. These findings rule out one mechanism proposed for carbamoyl phosphate synthetase, where one ATP acts as a molecular switch, and provide additional support for a sequential reaction mechanism where the γ‐phosphate groups of both ATP molecules are transferred to reactants. CP synthesis by subunit C in our single turnover pulse/chase assays did not require subunit N, but subunit N was required for detectable CP synthesis in the traditional continuous assay. These findings suggest that cross‐talk between domain N and C is required for product release from subunit C.
Contribution of the intrinsic disulfide to the assembly mechanism of islet amyloid
Authors: Koo Bon W. , Miranker Andrew D.
Published: December 2004

Amyloidogenesis from soluble protein requires conformational and oligomeric assembly steps. In systems where the precursor protein is natively unfolded, such as islet amyloid polypeptide (IAPP), forces and structural changes relevant to protein unfolding are not thought to participate in the assembly mechanism. Thus, fiber core structure elements should provide the dominant contributions to assembly kinetics. Here we show, however, that residues outside the amyloid core can influence the mechanism of IAPP fiber assembly. IAPP possesses an intramolecular disulfide bond between residues 2 and 7. This short‐range disulfide prohibits the N‐terminal region from adopting the β‐strand structure of an amyloid. We examined the role of this disulfide in fiber formation by generating a truncated construct (IAPP8–37) and a stable reduced form of the full‐length protein (IAPPCAM). The fiber structures and assembly kinetics of these variants were assessed via optical and mass spectroscopy. Our data confirm that the disulfide does not contribute to the amyloid fiber core structure. Remarkably, however, it plays a central role in the assembly mechanism. First, loss of the disulfide substantially reduces fiber formation by secondary nucleation, i.e., the ability of pre‐existing fibers to participate in the formation of new fibers. Second, the bypass of nucleation by seed addition is a two‐step process, termed activation. Loss of the disulfide eliminates this two‐step nature of seeded kinetics.
The structures of the unique sulfotransferase retinol dehydratase with product and inhibitors provide insight into enzyme mechanism and inhibition
Authors: Pakhomova Svetlana , Buck Jochen , Newcomer Marcia E.
Published: December 2004

The structure of retinol dehydratase (DHR) from Spodoptera frugiperda, a member of the sulfotransferase superfamily, in complexes with the inactive form of the cofactor PAP 3′‐phosphoadenosine 5′‐phosphate (PAP) and (1) the product of the reaction with retinol anhydroretinol (AR), (2) the retinoid inhibitor all‐trans‐4‐oxoretinol (OR), and (3) the potent steroid inhibitor androsterone (AND) have been determined and compared to the enzyme complex with PAP and retinol. The structures show that the geometry of the active‐site amino acids is largely preserved in the various complexes. However, the β‐ionone rings of the retinoids are oriented differently with respect to side chains that have been shown to be important for the enzymatic reaction. In addition, the DHR:PAP:AND complex reveals a novel mode for steroid binding that contrasts significantly with that for steroid binding in other sulfotransferases. The molecule is displaced and rotated ∼180° along its length so that there is no acceptor hydroxyl in close proximity to the site of sulfate transfer. This observation explains why steroids are potent inhibitors of retinol dehydratase activity, rather than substrates for sulfonation. Most of the steroid‐protein contacts are provided by the α‐helical cap that distinguishes this member of the superfamily. This observation suggests that in addition to providing a chemical environment that promotes the dehydration of a sulfonated intermediate, the cap may also serve to minimize a promiscuous sulfotransferases activity.
Identifying natural substrates for chaperonins using a sequence‐based approach
Authors: Stan George , Brooks Bernard R. , Lorimer George H. , Thirumalai D.
Published: December 2004

The Escherichia coli chaperonin machinery, GroEL, assists the folding of a number of proteins. We describe a sequence‐based approach to identify the natural substrate proteins (SPs) for GroEL. Our method is based on the hypothesis that natural SPs are those that contain patterns of residues similar to those found in either GroES mobile loop and/or strongly binding peptide in complex with GroEL. The method is validated by comparing the predicted results with experimentally determined natural SPs for GroEL. We have searched for such patterns in five genomes. In the E. coli genome, we identify 1422 (about one‐third) sequences that are putative natural SPs. In Saccharomyces cerevisiae, 2885 (32%) of sequences can be natural substrates for Hsp60, which is the analog of GroEL. The precise number of natural SPs is shown to be a function of the number of contacts an SP makes with the apical domain (NC) and the number of binding sites (NB) in the oligomer with which it interacts. For known SPs for GroEL, we find ∼4 < NC < 5 and 2 ≤ NB ≤ 4. A limited analysis of the predicted binding sequences shows that they do not adopt any preferred secondary structure. Our method also predicts the putative binding regions in the identified SPs. The results of our study show that a variety of SPs, associated with diverse functions, can interact with GroEL.
Hydrogen exchange and ligand binding: Ligand‐dependent and ligand‐independent protection in the Src SH3 domain
Authors: Wildes David , Marqusee Susan
Published: December 2004

Amide hydrogen‐deuterium exchange has proven to be a powerful tool for detecting and characterizing high‐energy conformations in protein ensembles. Since interactions with ligands can modulate these high‐energy conformations, hydrogen exchange appears to be an ideal experimental probe of the physical mechanisms underlying processes like allosteric regulation. The chemical mechanism of hydrogen exchange, however, can complicate such studies. Here, we examine hydrogen exchange rates in a simple model system, the c‐Src SH3 domain interacting with a short peptide ligand. Addition of ligand slows the rates of hydrogen exchange at nearly every amide for which we can obtain data. Careful analysis, however, reveals that this slowing is due primarily to a reduction in the population of free protein in the system, and not to any specific property of the complex. We present a method to separate the contributions of free and bound protein to the exchange kinetics that has allowed us to identify the subset of amides where exchange arises directly from the complex. These results demonstrate that the slowing of hydrogen exchange induced by ligand interactions should be interpreted with caution, and more extensive experiments are required to correlate changes in hydrogen exchange with changes in structure or internal dynamics.
Going It Alone? Strategic Entry under Mixed Electoral Rules
Authors: Ferrara Federico , Herron Erik S.
Published: December 2004

Recent studies on strategic voting and entry in elections that combine plurality or majority and proportional representation (PR) have found candidate placement in single‐member district (SMD) races to improve a party's PR performance. The primary implication of the existence of “contamination effects” is that parties have an incentive to nominate candidates in as many single‐member districts as possible. Pre‐electoral coordination in the majoritarian component of mixed electoral systems, however, is far from uncommon. In this article, we identify a number of institutional incentives that induce political parties to form pre‐electoral alliances in spite of contamination effects. By identifying institutions that favor and hamper coordination, we seek to advance the understanding of PR‐SMD interactions and to assess their implications for the design, classification, and empirical analysis of mixed electoral rules. Our statistical tests evaluate strategic entry in a diverse sample of countries.
Electoral Context and MP Constituency Focus in Australia, Canada, Ireland, New Zealand, and the United Kingdom
Authors: Heitshusen Valerie , Young Garry , Wood David M.
Published: December 2004

The job description for legislators in western democracies includes constituency‐focused activities such as casework and district visits. Unfortunately we have a limited theoretical and empirical understanding of the factors affecting legislators' constituency‐oriented activities, in large part because most studies focus on single nations; even studies that are comparative do not span a variety of electoral systems. In this article we examine the constituency focus of MPs in six chambers that do provide such variance: the Australian House and Senate, Canadian House, Irish Dáil, New Zealand House, and the British House of Commons. We find that electoral considerations and incentives provided by different electoral systems, as well as other factors, affect the priority that MPs place on constituency service.
The Corrective Effect of Ministerial Resignations on Government Popularity
Authors: Dewan Torun , Dowding Keith
Published: December 2004

Using data from the United Kingdom, we estimate the effects of ministerial resignation on government popularity. We test a counterfactual argument that resignations should have a corrective effect, that is, there is an increase in popularity following a resignation when taking into account the negative effect on popularity of the resignation issue. We get empirical estimates by using the age of ministers involved in resignation issues as an instrument. Our IV estimates provide empirical support for the corrective effect.
Misreading One's Sources: Charles Taylor's Rousseau
Authors: Marks Jonathan
Published: December 2004

This article challenges Taylor's defense of community by criticizing his reading of Jean‐Jacques Rousseau. Taylor, who adheres to the old charge that Rousseau is at bottom a totalitarian, neglects several points of resistance to the claims of the community that are present in Rousseau's political thought. Such points of resistance prove, on close examination, to be unavailable to Taylor. Taylor inadvertently offers a theoretical attack on individualism and a foundation for social tyranny more powerful than any to be found in Rousseau's thought.
Divisor Methods for Sequential Portfolio Allocation in Multi‐Party Executive Bodies: Evidence from Northern Ireland and Denmark
Authors: O'Leary Brendan , Grofman Bernard , Elklit Jørgen
Published: December 2004

Some proportional representation (PR) rules can also be used to specify the sequence in which each party in a parliament or each member in a multiparty governing coalition is given its choice about (unique) desired resources, e.g., “indivisible goods” such as cabinet ministries or executive positions, thus providing an algorithmic method for determining “fair” allocations. Divisor rule sequencing using the d'Hondt method was recently used to determine the ten cabinet positions in the Northern Ireland Executive Committee created under the 1998 Belfast (“Good Friday”) Agreement; and such sequential allocation procedures have been used in some Danish municipal governments, and for determination of committee chairs in the European parliament. Here we examine in some detail the procedures used in Northern Ireland and Denmark, with a focus on special features such as the option in Denmark to form post‐election alliances.
Immunological Analysis in Paediatric HIV Patients at Different Stages of the Disease
Authors: Lian Y. C. , Della‐Negra M. , Rutz R. , Ferriani V. , De Moraes Vasconcelos D. , Da Silva Duarte A. J. , Kirschfink M. , Grumach A. S.
Published: December 2004

There are only few clinical studies on complement in well‐defined (or characterized) paediatric HIV patients. Aim of this study was to evaluate the complement system and immunoglobulins in HIV‐infected children and to correlate data to stage of disease. Blood samples of 127 HIV‐infected children (11–134 months; 62 male : 65 female) were collected in order to evaluate humoral immunity. The patients were classified according to CDC clinical (N‐asymptomatic; A‐mild symptoms such as common recurrent infections; B‐moderate symptoms such as Candidiasis and herpes infections, meningitis, sepsis and anaemia; C‐severe symptoms such as opportunistic infections and neoplasia) and with respect to immunological criteria (T CD4+ cell count). Analysis of complement system included the classical (CH50), alternative (APH50) pathway activities and plasma concentrations of mannan‐binding lectin (MBL), of the C4 allotypic variants C4A and C4B. (ELISA), and of the C3 split product C3d (rocket immunoeletrophoresis). Immunodiagnosis also included CD4+ and CD8+ lymphocyte count and immunoglobulin concentrations. Complement activation and consumption was observed in all patients correlating with disease activity. Activated classical and alternative pathways and elevated C3d were significantly correlated with immunologic category 3. C3d levels were also significantly correlated with immunologic category 1. Undetectable CH50 and APH50 were found in two (group C) and 10 patients (n = 2, A = 2, B = 2, C = 4), respectively. Low MBL values were found in 13/127 but without correlation to disease severity. Undetectable C4B levels were observed in three patients, favouring the diagnosis of a complete deficiency. Although not related to clinical symptomatology, a strong ongoing complement activation can be observed in all stages of HIV infection. In contrast to earlier reports MBL could not be considered as a risk factor for HIV.
Reduction of Soluble Complement Receptor 2/CD21 in Systemic Lupus Erythomatosus and Sjögren's Syndrome but not Juvenile Arthritis
Authors: Masilamani M. , Nowack R. , Witte T. , Schlesier M. , Warnatz K. , Glocker M. O. , Peter H. H. , Illges H.
Published: December 2004

A soluble form of the complement receptor CD21 (sCD21) is shed from the lymphocyte surface. The amount of sCD21 in serum may modulate immunity as sCD21 levels are correlated with several clinical conditions. We report here the serum levels of sCD21 in juvenile arthritis (JA), systemic lupus erythematosus (SLE) and Sjögren's syndrome (SS). Using enzyme‐linked immunosorbent assay, we determined sCD21 levels in SLE, SS and JA patients. Mann–Whitney test for nonparametric two‐tail P value was performed to obtain statistical significance. Cytometrical analysis of synovial fluid leucocytes of JA patients was done on a FACSsort. While sCD21 levels in SLE and SS are reduced to levels previously found in rheumatoid arthritis (RA), JA sCD21 levels were normal. sCD21 levels did not correlate with clinical parameters and immunophenotype of synovial cells. CD4 T cells in the synovium were almost all of the CD45RO memory type and 13 of 40 patients displayed synovial expansion of γδT cells. CD21 shedding in JA differs from RA/SS/SLE. JA sCD21 levels in synovial fluid are always lower compared to blood levels of the same patients. Analysis of JA synovial T cells indicates a T‐cell driven response.
Cortisol and Dehydroepiandrosterone Affect the Response of Peripheral Blood Mononuclear Cells to Mycobacterial Antigens during Tuberculosis
Authors: Mahuad C. , Bay M. L. , Farroni M. A. , Bozza V. , Del Rey A. , Besedovsky H. , Bottasso O. A.
Published: December 2004

The effect of cortisol and/or dehydroepiandrosterone (DHEA) on the immune response to antigens obtained from Mycobacterium tuberculosis was studied in vitro by using peripheral blood mononuclear cells obtained from patients at various stages of lung tuberculosis (TB) and from healthy control people (HCo). The results obtained show for the first time that addition of cortisol within concentrations of physiological range can inhibit the mycobacterial antigen‐driven proliferation of cells from HCo and TB patients and the production of interferon‐γ (IFN‐γ), indicating that endogenous levels of cortisol may contribute to the decreased lymphoid cell response to mycobacterium antigens observed in TB patients. DHEA did not affect lymphoid cell proliferation, IFN‐γ production and the cortisol‐mediated inhibitory effects. Interestingly, we found that DHEA, but not cortisol, suppressed the in vitro transforming growth factor‐β production by lymphoid cells from TB patients with an advanced disease, which is indicative of a selective direct effect of this hormone.
Poor In Vitro Maturation and Pro‐Inflammatory Cytokine Response of Dendritic Cells in Children at Genetic Risk of Type 1 Diabetes
Authors: Skarsvik S. , Tiittanen M. , Lindström A. , Casas R. , Ludvigsson J. , Vaarala O.
Published: December 2004

Type 1 diabetes (T1D) has been associated with an aberrant maturation of dendritic cells (DC). We studied the maturation of monocyte‐derived DC in children with newly diagnosed T1D and in healthy children with genetic risk for T1D. Peripheral blood monocytes from children with newly diagnosed T1D (n = 12; mean age 13.2 years), children with human leukocyte antigen (HLA)‐risk genotype of T1D (n = 7; mean age 12.7 years) and healthy children (n = 14; mean age 11.2 years) were in vitro differentiated into DC. Expression of HLA‐DR, CD80/86 and CD11c and secretion of interleukin (IL)‐12, tumor necrosis factor (TNF)‐α, IL‐6 and IL‐10 were measured using flow cytometry. Lower percentage of DC expressed CD11c and HLA‐DR, and decreased production of TNF‐α was found in children with newly diagnosed T1D and in children at genetic risk when compared to healthy children. Children with risk genotype also had decreased IL‐12 production by DC. Children with T1D and children at genetic risk of T1D appear to have similar aberrancies in the maturation of DC, which may predispose to β‐cell autoimmunity.
Interleukin‐15, as Interferon‐gamma, Induces the Killing of Leishmania infantum in Phorbol‐Myristate‐Acetate‐Activated Macrophages Increasing Interleukin‐12
Authors: D'Agostino P. , Milano S. , Arcoleo F. , Di Bella G. , La Rosa M. , Ferlazzo V. , Caruso R. , Chifari N. , Vitale G. , Mansueto S. , Cillari E.
Published: December 2004

The potential leishmanicidal activity of interleukin‐15 (IL‐15) was examined while priming with the cytokine phorbol‐myristate‐acetate (PMA)‐activated macrophages and infecting them with Leishmania infantum parasites. The activation of macrophage cultures with IL‐15 determined a significant anti‐leishmanial activity, comparable with that induced by interferon‐gamma (IFN‐γ). The killing of Leishmania in macrophages primed with IL‐15, as well as with IFN‐γ, was followed by an increase in the IL‐12 synthesis. The neutralization of IL‐15 or IFN‐γ, by specific monoclonal antibodies (MoAb) caused a significant reduction in leishmanicidal activity. Furthermore, in PMA‐activated macrophages, the neutralization of IL‐12 production by a specific anti‐IL‐12 MoAb reduced leishmanicidal activity induced by IL‐15 and IFN‐γ. Data indicate that IL‐15 could have a role as an activator of leishmanicidal activity, directly or indirectly, by inducing IL‐12 production.
The use of a double subgenomic Sindbis virus expression system to study mosquito gene function: effects of antisense nucleotide number and duration of viral infection on gene silencing efficiency
Authors: Tamang D. , Tseng S. M. , Huang C. Y. , Tsao I. Y. , Chou S. Z. , Higgs S. , Christensen B. M. , Chen C. C.
Published: December 2004

Recently we established a simple, effective antisense strategy using a double subgenomic Sindbis (dsSIN) virus expression system to study gene function in mosquitoes. In this study, we further elucidate the effects of antisense nucleotide number and duration of viral infection on mosquito gene silencing efficiency by the dsSIN virus expression system. Over 15 days post virus infection, the degree of parasite melanization was progressively reduced by more than 95%, 75% and 55% in the mosquito Armigeres subalbatus transduced with 600, 147 or 36 bases antisense RNA, targeted to the highly conserved copper binding region of the Ar. subalbatus prophenoloxidase I gene (As‐pro‐POI), respectively. As the duration of viral infection increased from day 3–15, the degree of parasite melanization progressively decreased in all mosquitoes transduced with antisense RNA, irrespective of the lengths of antisense RNA. Progressive loss of parasite melanization function was found to correlate with down regulation of As‐pro‐PO expression at both the mRNA and protein activity levels, and reductions in virus titres in mosquitoes transduced with antisense RNA. A small pro‐PO RNA (c. twenty‐five nucleotides) was identified in mosquitoes transduced with antisense RNA. These data suggest that As‐pro‐POI gene expression is knocked down by degrading the As‐pro‐POI mRNA through the RNAi pathway. In conclusion, our study demonstrates that even a short antisense RNA (thirty‐six bases) can cause silencing of the As‐pro‐POI gene, and the effects of endogenous gene silencing by dsSIN expression system on mosquito gene functions can be accumulative.
Allogenic forcing of the late Quaternary Rhine–Meuse fluvial record: the interplay of sea‐level change, climate change and crustal movements
Authors: Wallinga Jakob , Törnqvist Torbjörn E. , Busschers Freek S. , Weerts Henk J. T.
Published: December 2004

The Rhine–Meuse system in the west‐central Netherlands is a continental‐scale fluvial system bordered by an extremely wide continental shelf. Consequently, late Quaternary eustatic sea‐level changes have resulted in dramatic shoreline displacements, by as much as 800 km. In addition, changes in climate have been severe, given the latitudinal and palaeogeographic setting of the Rhine–Meuse system. We investigated the relative importance of these allogenic controls on fluvial aggradation and incision during the last two glacial–interglacial cycles. We used optical dating of quartz from ∼30 samples in a cross‐section perpendicular to the palaeoflow direction, allowing us to correlate periods of aggradation and incision with independent records of sea‐level change, climate change and glacio‐isostatic crustal movements. We found the long‐term aggradation rate to be ∼8 cm kyr−1, a value similar to previous estimates of tectonic subsidence rates in the study area. Several excursions from this long‐term aggradation trend could be identified for the last glacial–interglacial cycle. Dry climatic conditions with relatively high sediment supply induced aggradation during oxygen‐isotope stages (OIS) 4 and 3. Build‐up of a glacio‐isostatic forebulge during OIS 2 is a likely cause of incision around the Last Glacial Maximum, followed by an aggradation phase during forebulge collapse. Sea‐level highstands during OIS 5 have likely resulted in the aggradation of coastal prisms, but only minor, basal estuarine deposits have been preserved because these coastal prisms were prone to erosion during ensuing sea‐level falls. Overall, the sedimentary record is dominated by strata formed during time intervals when the study area was completely unaffected by sea‐level control, and our evidence shows that the falling‐stage systems tract has the highest preservation potential. Our study highlights the importance of considering the complex interplay of both upstream and downstream controls to obtain a comprehensive understanding of the evolution of basin‐margin successions.
Late Cretaceous and Cenozoic sea‐level estimates: backstripping analysis of borehole data, onshore New Jersey
Authors: Van Sickel William A. , Kominz Michelle A. , Miller Kenneth G. , Browning James V.
Published: December 2004

Backstripping analysis of the Bass River and Ancora boreholes from the New Jersey coastal plain (Ocean Drilling Project Leg 174AX) provides new Late Cretaceous sea‐level estimates and corroborates previously published Cenozoic sea‐level estimates. Compaction histories of all coastal plain boreholes were updated using porosity–depth relationships estimated from New Jersey coastal plain electric logs. The new porosity estimates are considerably lower than those previously calculated at the offshore Cost B‐2 well. Amplitudes and durations of sea‐level variations are comparable in sequences that are represented at multiple boreholes, suggesting that the resultant curves are an approximation of regional sea level. Both the amplitudes and durations of third‐order (0.5–5 Myr) cycles tend to decrease from the Late Cretaceous to the late Miocene. Third‐order sea‐level amplitudes in excess of 60 m are not observed. Long‐term (108–107years) sea level was approximately constant at 30–80 m in the Late Cretaceous, rose to a maximum early Eocene value of approximately 100–140 m, and then fell through the Eocene and Oligocene.
Contribution of a three‐dimensional regional scale basin model to the study of the past fluid flow evolution and the present hydrology of the Paris basin, France
Authors: Gonçalvès J. , Violette S. , Guillocheau F. , Robin C. , Pagel M. , Bruel D. , De Marsily G. , Ledoux E.
Published: December 2004

A basin model was built to simulate in three dimensions the 248 Myr geological history of the Paris basin, France, i.e. sedimentation, erosion, compaction heat and fluid flow. This multidisciplinary study was based on a detailed stratigraphic database of more than 1100 well logs together with a hydrodynamic database of 1000 data (heads and permeabilities). The region covers a maximum surface area of 700 000 km2. The NEWBAS code of the Ecole des Mines de Paris was used in order to simulate compaction and heat and fluid flow. Three examples of the use of this model are given to illustrate different features of the geological functioning of the basin.

(i) By modelling processes such as sedimentation, compaction, fluid and heat flow, the model provides estimates of the hydraulic conductivity fields within one order of magnitude from observations at the regional scale. This permeability field can reproduce the present‐day observed pressures and fluxes in the basin.

(ii) Observed excess pressures in the main aquitards are considered as possible consequences of the geological history of the basin. The calculated excess pressures are small and stay within the range of the measured values, between 0 and 2.75 MPa, close to the pressures in the aquifers. However, the weak excess pressures measured in the Callovo–Oxfordian sequence in the eastern part of the basin are not reproduced by the model. Mechanisms other than compaction disequilibrium must be invoked.

(iii) This model also calculates regional‐scale palaeofluid flow whose value is currently arbitrarily assumed by geochemists when studying diagenetic processes. Hence, it provides a hydrologic background for diagenetic models. The cementation in the western Keuper reservoirs was investigated. Topographically driven flow during tectonic inversion periods, e.g. the Lower Cretaceous and Early Tertiary, is shown to be a plausible cause of brine migrations. This brine displacement would then explain the high salinities recorded in the fluid inclusions trapped in the Keuper cements. The conditions for the migration would have been most favourable at the time of the maximum burial, i.e. the Early Tertiary and not the Early Cretaceous as previously suggested.
Tectono‐thermal modelling of sedimentary basins with episodic extension and inversion, a case history of the Jiyang Basin, North China
Authors: He Lijuan , Wang Jiyang
Published: December 2004

A two‐dimensional kinematic model is presented for superimposed basins. It is based on a finite‐element algorithm in the Lagrangian system, which incorporates different stages of lithosphere stretching and shortening to simulate alternating extension and inversion. The Jiyang Basin, developed in the North China, is a superimposed basin comprising four proto‐type basins separated by several unconformities. Four‐phase extension and two‐phase inversion have developed in this basin since the Late Mesozoic era. The thermal history of the basin is modelled based on a seismic cross‐section across the basin. Tectonic subsidence (or uplift) histories from backstripping serve as the objective functions, and crustal thickness, as well as heat flow, provides additional constraints. Effects of different Mesozoic erosion on the thermal history are discussed. Modelling results show that the thermal history of the Jiyang Basin since the Late Mesozoic can be divided into six stages, including four phases of heating accompanied by following thermal attenuation, and two phases of cooling with following thermal recovery. The model also implies a variant pattern of thermal regime in the basin. In the deepest centres of the depressions, the maximum heat flow occurred during the Late Mesozoic, but in the slopes of the depressions, the maximum heat flow appeared in the Cenozoic era.
The Neoproterozoic Fiq glaciation and its aftermath, Huqf supergroup of Oman
Authors: Allen Philip A. , Leather Jonathan , Brasier Martin D.
Published: December 2004

The <1.5‐km thick Fiq Member of the Ghadir Manqil Formation, Huqf Supergroup, Oman, contains a succession of Marinoan‐age glacially and non‐glacially influenced deposits overlain by a transgressive, 13C‐depleted, deep‐water dolostone (Hadash Formation) that deepens up into the marine shales and siltstones of the Masirah Bay Formation. The Fiq Member and Hadash–Masirah Bay Formations are well exposed in the core of the Jebel Akhdar of northern Oman and provide a valuable insight into the processes operating during a Neoproterozoic glacial epoch and its aftermath.

The Fiq Member comprises seven stratigraphic units (F1–F7) of proximal and distal glacimarine, non‐glacial sediment gravity flow, and non‐glacial shallow marine facies associations. These units can be correlated over almost the entire Neoproterozoic outcrop belt (ca. 80 km) of the Jebel Akhdar. Four units contain glacimarine rainout diamictites, commonly at the top of cycles beneath strong lithofacies dislocations suggesting flooding. The units are thought to have been generated by combined glacio‐isostatic and glacio‐eustatic forcing caused by changing volumes of terrestrial glacier ice. The lateral persistence and thickness of massive diamictite units increase upwards in the stratigraphy, the youngest (F7) diamictite being abruptly overlain by the Hadash Formation. Correlation of lithofacies associations across the rift basin and palaeocurrents indicate that siliciclastic sediment and glacially entrained debris were derived from both basin margins. Open‐water conditions existed during interglacials, attested to by the presence of wave‐rippled sandstones in the western part of the basin. The Hadash carbonate also exhibits variations between east and west, showing that despite an overall deep‐water depositional setting, rift margin and intrabasinal structure continued to exert a control on facies development during the post‐glacial aftermath. Onlap of basin margins continued through the deposition of the Masirah Bay Formation.

The sedimentology and stratigraphy of the Fiq Member and Hadash–Masirah Bay Formations have a number of implications for the Snowball Earth hypothesis. The overall stratigraphic evolution of the Fiq Member suggests a dynamic, temperate/polythermal style of glaciation, perhaps nucleated on uplifted continental or rift margin topography, with marine‐terminating glaciers. Some transgressions coupled to deglaciations within the Fiq glacial epoch were accompanied by minor deposition of carbonate. However, final deglaciation triggered the deposition of a <8‐m thick, deep‐water dolomite contaminated with siliciclastics, with a lithofacies assemblage still reflecting the underlying bathymetric template, followed by relatively deep marine shales and siltstones. The preservation of relatively deep marine Masirah Bay sediments above the Fiq basin margin suggests either tectonic collapse of the rift shoulder or, more likely, rapid eustatic rise accompanying deglaciation.
A new less‐invasive and more informative low‐dose ACTH test: salivary steroids in response to intramuscular corticotrophin
Authors: Contreras Liliana N. , Arregger Alejandro L. , Persi Gabriel G. , Gonzalez Natalia S. , Cardoso Estela M.
Published: December 2004

objective  The intravenous low‐dose ACTH test has been proposed as a sensitive tool to assess adrenal function through circulating steroids. The aims of this study were to: (a) find the minimal intramuscular ACTH dose that induced serum and salivary cortisol and aldosterone responses equivalent to those obtained after a pharmacological dose of ACTH; and (b) define the minimum normal salivary cortisol and aldosterone responses in healthy subjects to that dose of ACTH. We also compared the performances of the standard‐ and low‐dose ACTH intramuscular tests to screen patients with known hypothalamo–pituitary–adrenal impairments.

design  Rapid ACTH tests were performed in individuals using various intramuscular doses (12·5, 25 and 250 µg) at 2‐week intervals.

subjects  Twenty‐one healthy volunteers and 19 patients with primary (nine cases) and secondary (10 cases) adrenal insufficiency.

measurement  Serum and salivary cortisol and aldosterone concentrations were measured at baseline and after ACTH. Serum cortisol ≥ 552·0 nmol/l and aldosterone ≥ 555·0 pmol/l concentrations at 30 min after 250 µg of ACTH were defined as normal responses.

results  In healthy volunteers cortisol and aldosterone responded to ACTH in a dose‐dependent manner. The time to peak in saliva for each steroid was delayed as the dose of ACTH increased. The minimum ACTH dose that produced equivalent steroid responses at 30 min to 250 µg of ACTH (standard‐dose test; SDT) was 25 µg (low‐dose test; LDT). Saliva collection 30 min after LDT and SDT showed cortisol and aldosterone concentrations of at least 20·0 nmol/l and 100·0 pmol/l, respectively. These values were defined as normal steroid responses. Blunted salivary steroid responses to LDT and SDT were found in all patients with primary adrenal insufficiency. Subnormal salivary cortisol levels in response to LDT and SDT were found in all patients with secondary adrenal insufficiency. In five patients full recovery of adrenal function was demonstrated by both tests after steroid withdrawal. In the follow‐up of four patients studied during the recovery period, subnormal SAF response after LDT and normal after SDT was demonstrated. Preservation of the adrenal glomerulosa was found in all the patients with secondary adrenal insufficiency through the normal rise in salivary aldosterone after both LDT and SDT.

conclusions  Adrenal function can be accurately investigated with simultaneous measurements of salivary cortisol and aldosterone in response to 25 µg of corticotrophin injected into the deltoid muscle. Our data suggest that this may become a useful and relatively noninvasive clinical tool to detect subclinical hypoadrenal states.
Genomic structure of the human gene for protein kinase A regulatory subunit R1‐beta (PRKAR1B) on 7p22: no evidence for mutations in familial hyperaldosteronism type II in a large affected kindred
Authors: Elphinstone Martin S. , Gordon Richard D. , So Albertina , Jeske Yvette W. A. , Stratakis Constantine A. , Stowasser Michael
Published: December 2004

objective  Familial hyperaldosteronism type II (FH‐II) is characterized by inheritance of primary aldosteronism (PAL) but, unlike FH‐I, is not glucocorticoid remediable and not associated with the hybrid CYP11B1/CYP11B2 gene mutation. Analysis of two pedigrees previously demonstrated linkage of FH‐II with a locus at chromosome 7p22. We sought to determine whether mutations in the exons or intron/exon boundaries in PRKAR1B (encoding protein kinase A regulatory subunit R1‐beta), which resides within the linked locus, are associated with FH‐II.

methods  Primers enabling sequencing of all exons and intron/exon boundaries were designed by BLAT search using known mRNA sequence, and comparison with an orthologous mouse gene. Sequences from four affected and two unaffected subjects from an Australian family with FH‐II demonstrating linkage at 7p22 were compared with published sequences.

results  A probable two‐nucleotide GenBank sequence error, resulting in an amino acid change, was detected. Two of seven single nucleotide polymorphisms (SNPs) identified were in exons and five in introns. Neither exon‐localized SNP resulted in an amino acid change. All intron‐localized SNPs were at least 16 nucleotides from the closest intron/exon boundary and therefore unlikely to interfere with gene splicing. Importantly, none of the identified SNPs was exclusively associated with affectation status.

conclusions  Mutations in the exons or intron/exon boundaries of PRKAR1B do not appear to be responsible for FH‐II in this family, but a mutation in the promoter or remaining intronic or 5′ or 3′ untranslated regions could be. Alternatively, a mutation within another gene residing at the 7p22 locus may be responsible.
Insulin sensitivity and coronary vasoreactivity: insulin sensitivity relates to adenosine‐stimulated coronary flow response in human subjects
Authors: Dagres N. , Saller B. , Haude M. , Hüsing J. , Von Birgelen C. , Schmermund A. , Sack S. , Baumgart D. , Mann K. , Erbel R.
Published: December 2004

objective  Diabetes is associated with coronary microvasculature abnormalities and impaired coronary flow reserve (CFR). CFR is the ratio of coronary flow under maximal vasodilation to basal flow and is a measure for coronary vasoreactivity. Insulin resistance is the central defect in the development of type 2 diabetes, preceding its onset by 10–20 years. Thus, the relationship between insulin sensitivity and CFR in nondiabetic subjects is particularly interesting. The aim of the study was to investigate this relationship.

design  Cross‐sectional study.

patients  The study population consisted of 18 nondiabetic subjects without coronary artery stenosis on coronary angiography. We excluded patients with structural heart disease or with conditions affecting CFR or insulin sensitivity such as low density lipoprotein (LDL)‐cholesterol ≥ 4·14 mmol/l, smoking, hypertension or obesity with a body mass index (BMI) > 28 kg/m2.

measurements and results  CFR was 3·1 ± 0·8 (range 1·7–4·8), as assessed by intracoronary Doppler measurements in the left anterior descending coronary arteries after adenosine stimulation. Intravascular ultrasound revealed zero to moderate coronary atherosclerotic changes. Whole‐body insulin sensitivity (M‐value) was 7·5 ± 2·9 mg/kg/min (range 2·2–12·6), as assessed by the hyperinsulinaemic–euglycaemic clamp test. Subjects with low CFR (< 3·0) had a significantly lower M‐value than subjects with normal CFR (> 3·0) (6·0 ± 2·5 vs. 9·0 ± 2·5 mg/kg/min, P = 0·021). Univariate linear regression demonstrated a strong correlation between CFR and M‐value (r = 0·76, P < 0·001). In multiple regression analysis, the significant association of CFR with M‐value was independent of potential confounders (sex, age, BMI, LDL‐cholesterol and plaque burden on intravascular ultrasound). Bootstrap analysis corroborated this finding.

conclusions  Whole‐body insulin sensitivity relates to coronary vasoreactivity. Across a wide range of both insulin sensitivity and coronary flow reserve from markedly abnormal to normal values, an increase in insulin sensitivity appears to be associated with an increase in coronary flow reserve. Insulin resistance is therefore associated with coronary microvasculature abnormalities in nondiabetics.