bluuebunny/crossref_metadata_2025 huggingface dataset:
Werner syndrome protein associates with γH2AX in a manner that depends upon Nbs1
Authors: Cheng Wen-Hsing , Sakamoto Shuichi , Fox Jennifer T. , Komatsu Kenshi , Carney James , Bohr Vilhelm A.
Published: January 2005

The WRN protein is mutated in the chromosomally unstable Werner syndrome (WS) and the Nbs1 protein is mutated in Nijmegen breakage syndrome (NBS). The Nbs1 protein is an integral component of the M/R/N complex. Although WRN is known to interact with this complex in response to γ‐irradiation, the mechanism of action is unclear. Here, we show that WRN co‐localizes and associates with γH2AX, a marker protein of DNA double strand breaks (DSBs), after cellular exposure to γ‐irradiation. While the DNA damage‐inducible Nbs1 foci formation is normal in WS cells, WRN focus formation is defective in NBS cells. Consistent with this, γH2AX colocalizes with Nbs1 in WS cells but not with WRN in NBS cells. The defective WRN‐γH2AX association in NBS cells can be complemented with wild‐type Nbs1, but not with an Nbs1 S343A point mutant that lacks an ATM phosphorylation site. WRN associates with H2AX in a manner dependent upon the M/R/N complex. Our results suggest a novel pathway in which Nbs1 may recruit WRN to the site of DNA DSBs in an ATM‐dependent manner.
Screening of genes expressed in developing mandibles during soldier differentiation in the termite Hodotermopsis sjostedti
Authors: Koshikawa Shigeyuki , Cornette Richard , Hojo Masaru , Maekawa Kiyoto , Matsumoto Tadao , Miura Toru
Published: January 2005

We investigated the morphological changes accompanying soldier differentiation in the damp‐wood termite Hodotermopsis sjostedti. Genes expressed in the developing mandibles, which undergo the most remarkable morphological changes during soldier differentiation, were screened using fluorescent differential display. Database searches for sequence similarities were conducted and the relative expression levels were then quantified by real‐time polymerase chain reaction. Among the identified candidate genes, 12 genes were upregulated during soldier differentiation. These included genes for cuticle proteins, nucleic acid binding proteins, ribosomal proteins and actin‐binding protein, which were inferred to be involved in caste‐specific morphogenesis in termites.
An alternative echo-integrating method
Authors: Aksland Magnar
Published: January 2005

An alternative method of estimating the number of individuals in marine populations by echo integration is presented. The method was published almost two decades ago by the same author and here it is reviewed and developed. The method is based on just two defined concepts, the Echo Abundance and the mean Echo-Value Constant, respectively. The ratio of these quantities is equal to the number of scattering individuals within a covered area. As the Echo Abundance is estimated by interpolating echo-integrator values over selected areas, the mean Echo-Value Constant can be estimated from representative resolved echoes and their detection angles from individuals in the population, as obtained by the split-beam echosounder system. Two types of estimators for the mean Echo-Value Constant are given and discussed theoretically with respect to their properties. The approach is described and discussed in relation to the conventional theory of abundance estimation by echo integration.
The consequences of different scenarios in the management of the gillnet and purse-seine fisheries targeting Pomatomus saltatrix and Cynoscion guatucupa in southern Brazil: a bio-economic approach
Authors: Lucena Flávia , O'Brien Carl M.
Published: January 2005

The bluefish Pomatomus saltatrix and the striped weakfish Cynoscion guatucupa are two of the most important commercially exploited species in southern Brazil. These species overlap spatially and temporally in southern Brazil and are exploited by a multi-purpose fleet. We analyse the consequences of different management options in terms of the bio-economy of the gillnet and purse-seine fisheries by considering P. saltatrix and C. guatucupa as the main targets. Development of the bio-economic model was based upon multi-fleet, single species models for P. saltatrix and C. guatucupa. The results are compared at the medium-term forecast level from stochastic simulations, and the technical interactions between the fleets that exploit the bluefish and striped weakfish are also addressed. The purse-seine fishery has a strong impact on the gillnet fishery. A management plan, which allocates moderate levels of effort for all co-existing fleets and interacting species, seems efficient, but effort should be controlled for P. saltatrix (for both fleets) and, for the gillnet fleet, relatively more trips should be allocated for C. guatucupa. For P. saltatrix, the best management relies upon the scenarios harvesting the oldest individuals.
Local influence diagnostics for the retrospective problem in sequential population analysis
Authors: Cadigan Noel G. , Farrell Patrick J.
Published: January 2005

The retrospective problem involves systematic differences in sequential population analysis (SPA) estimates of stock size or some other quantity in a reference year. The differences occur as successively more data are used for estimation, and they appear to be structural biases caused by a mis-specification of the SPA. In some cases the retrospective problem is so severe that the SPA is considered to be too unreliable for stock assessment purposes. There are many possible sources of retrospective patterns, and it is usually difficult in practice to determine which are more likely. We propose diagnostics to help determine the more likely causes. We use local influence diagnostics to investigate whether small changes or perturbations to SPA input components such as catches or natural mortalities can remove or reduce retrospective patterns. We show, for the fall-spawning herring stock in the southern Gulf of St. Lawrence SPA, that relatively small age- and year-specific changes to the SPA assumptions about the proportional relationship between an abundance index and stock size can result in greatly reduced retrospective patterns. We therefore conclude primafacie that these assumptions are a plausible source of the retrospective pattern. Larger changes to catches, natural mortality assumptions, or estimation weights are required to reduce the retrospective pattern. These other factors seem to be less plausible sources of the retrospective pattern, although this is best assessed by the herring stock experts who are more knowledgeable about the fishery and other scientific information for this stock.
Bone compaction enhances implant fixation in a canine gap model
Authors: Kold Søren , Rahbek Ole , Toft Marianne , Ding Ming , Overgaard Søren , Søballe Kjeld
Published: January 2005

A new bone preparation technique, compaction, has increased fixation of implants inserted with exact‐fit or press‐fit to bone. Furthermore, a demonstrated spring‐back effect of compacted bone might be of potential value in reducing the initial gaps that often exist between clinical inserted implants and bone. However, it is unknown whether the compression and breakage of trabeculae during the compaction procedure results in impaired gap‐healing of compacted bone. Therefore, we compared compaction with conventional drilling in a canine gap model. Grit‐blasted titanium implants (diameter 6 mm) were bilaterally inserted into cavities initially expanded to 8 mm diameters in the proximal humeri. Each dog served as its own control; thus, one humerus had the implant cavity prepared with compaction, the other with drilling. Eight dogs were euthanized after 2 weeks, and 7 dogs after 4 weeks. Humeri from additional 7 dogs represented time 0. At time 0 a spring‐back effect of compacted bone was demonstrated as cavities, initially expanded to 8 mm by compaction, were reduced to a median cavity diameter of 6.6 mm. In contrast, cavities initially expanded to 8 mm by drilling, had a median cavity diameter of 8.0 mm at time 0. Compaction significantly increased all pushout parameters at 2 weeks. Compaction significantly increased peri‐implant bone density at 0 and 2 weeks, and bone implant contact at 2 and 4 weeks. The faster mechanical and histological fixation with compaction indicates that the beneficial effect of reduced gap size, as compacted bone springs back, is not eliminated by an impaired gap‐healing of compacted bone. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
The influence of bone allograft processing on osteoblast attachment and function
Authors: Hofmann A. , Konrad L. , Hessmann M. H. , Küuchle R. , Korner J. , Rompe J. D. , Rommens P. M.
Published: January 2005

In order to assess the influence of eight different sterilisation and disinfection methods for bone allografts on adhesion, proliferation, and differentiation of human bone marrow stromal cells (BMSC), cells were grown in culture and then plated onto pieces of human bone allografts. Following processing methods were tested: autoclavation (AUT), low‐temperature‐plasma sterilisation of demineralised allografts (D‐LTP), ethylene oxide sterilisation (EtO), fresh frozen bone (FFB), 80°C‐thermodisinfection (80°C), γ‐irradiation (Gamma), chemical solvent disinfection (CSD), and Barrycidal®‐disinfection (BAR). The seeding efficiency was determined after one hour to detect the number of attached cells before mitosis started. The cell viability was determined after 3, 7, and 21 days. Tests to confirm the osteoblastic differentiation included histochemical alkaline phosphatase staining and RT‐PCR for osteocalcin.

Human BMSC showed greatest attachment affinities for D‐LTP‐, 80°C‐, and CSD‐allografts, whereas less cells were found attached to AUT‐, EtO‐, FFB‐, Gamma‐, and BAR‐probes. Cell viability assays at day 3 revealed highest proliferation rates within the FFB‐ and 80°C‐groups, whereas after 21 days most viable cells were found in D‐LTP‐, 80°C‐, CSD‐, and Gamma‐groups. BAR‐treatment showed a considerably toxic effect and therefore was excluded from all further experiments. Highest AP‐activity and gene expression of osteocalcin were detected in the D‐LTP‐group in comparison with all other groups.

In summary, our results demonstrate that cell adhesion, final population, and function of BMSC are influenced by different disinfection and sterilisation methods. Therefore, processing‐related alterations of BMSC‐function may be important for the success of bone grafting. The experimental setup used in the present work may be useful for further optimisation of bone allograft processing. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Optically stimulated luminescence dating of late Holocene raised strandplain sequences adjacent to Lakes Michigan and Superior, Upper Peninsula, Michigan, USA
Authors: Argyilan Erin P. , Forman Steven L. , Johnston John W. , Wilcox Douglas A.
Published: January 2005

This study evaluates the accuracy of optically stimulated luminescence to date well-preserved strandline sequences at Manistique/Thompson bay (Lake Michigan), and Tahquamenon and Grand Traverse Bays (Lake Superior) that span the past ∼4500 yr. The single aliquot regeneration (SAR) method is applied to produce absolute ages for littoral and eolian sediments. SAR ages are compared against AMS and conventional 14C ages on swale organics. Modern littoral and eolian sediments yield SAR ages <100 yr indicating near, if not complete, solar resetting of luminescence prior to deposition. Beach ridges that yield SAR ages <2000 yr show general agreement with corresponding 14C ages on swale organics. Significant variability in 14C ages >2000 cal yr B.P. complicates comparison to SAR ages at all sites. However, a SAR age of 4280 ± 390 yr (UIC913) on ridge77 at Tahquamenon Bay is consistent with regional regression from the high lake level of the Nipissing II phase ca. 4500 cal yr B.P. SAR ages indicate a decrease in ridge formation rate after ∼1500 yr ago, likely reflecting separation of Lake Superior from lakes Huron and Michigan. This study shows that SAR is a credible alternative to 14C methods for dating littoral and eolian landforms in Great Lakes and other coastal strandplains where 14C methods prove problematic.
The sedimentary record of drifting ice (early Wisconsin Sunnybrook deposit) in an ancestral ice-dammed Lake Ontario, Canada
Authors: Eyles Nicholas , Eyles Carolyn H. , Woodworth-Lynas Christopher , Randall Todd A.
Published: January 2005

Outcrops of pebbly mud (diamict) at Scarborough in Southern Ontario, Canada (the so-called Sunnybrook ‘Till’) are associated with the earliest incursion of the Laurentide Ice Sheet (LIS) into mid-continent North America some 45,000 years ago. The Sunnybrook is a blanket-like deposit containing deepwater ostracodes and occurs conformably within a thick (100 m) succession of deltaic and glaciolacustrine facies that record water depth changes in a large proglacial lake. Contextual evidence (associated facies, sedimentary structures, deposit geometry and landforms) indicates a low energy depositional setting in an ice-dammed ancestral Lake Ontario in which scouring by floating ice masses was an important process. U-shaped, iceberg-cut scours (with lateral berms) up to 7 m deep, occur on the upper surface of the Sunnybrook and are underlain by ‘sub-scour’ structures that extend several meters below the scour base. Ice-rafted concentrations of clasts (‘clast layers’), grooved surfaces formed by floating ice glissading over a muddy lake floor (‘soft sediment striations’) and melanges of sand and mud mixed by grounding ice keels (‘ice keel turbates’) are present and are all well known from modern cold environments. The wider significance of this depositional model is that the LIS margin lay east of Scarborough and did not overrun Southern Ontario. This finding is in agreement with recent data from the Erie Basin of Canada, Ohio, and Indiana where deposits formerly correlated with the Sunnybrook (and thus implying an extensive early Wisconsin ice sheet) are now regarded as Illinoian. A speculative hypothesis is proposed that relates deposition of the Sunnybrook and two younger deposits of similar sedimentology, to surge-like instabilities of the southern LIS margin.
Comparison of meteor radar and Na Doppler lidar measurements of winds in the mesopause region above Maui, Hawaii
Authors: Franke S. J. , Chu X. , Liu A. Z. , Hocking W. K.
Published: January 2005

Simultaneous sodium (Na) Doppler lidar and meteor radar measurements of horizontal winds in the mesopause region over Maui, Hawaii, were collected in July 2002 and October/November 2003. The coincident measurements span 96 hours and altitudes between 80 and 100 km. Statistical comparisons are carried out on radar/lidar winds with 1 hour and 4 km time and height resolution, respectively. The RMS radar/lidar wind component differences observed in this study are in the range 12–17 m/s at altitudes below 96 km. This is smaller than the RMS differences observed in a previous Na lidar and meteor radar comparison. Lidar wind component variances exceed radar variances, and radar/lidar covariance, is nearly equal to the radar variance. Excess variance observed by the lidar is consistent with the fact that the meteor radar cannot resolve wind perturbations with horizontal scales smaller than ∼200 km, whereas the lidar will respond to all horizontal scales. Close correspondence between the radar wind variance and radar/lidar covariance suggests that measurement errors associated with the radar winds are swamped by geophysical variation. Furthermore, the excess lidar variance exceeds lidar estimation errors by a large factor, indicating that the lidar measurement errors are also insignificant relative to geophysical variations. Together these observations suggest that the observed radar/lidar differences are a consequence of the different horizontal wave number filters associated with the techniques, and hence the differences are determined by the strength and shape of the horizontal wave number spectrum for wind perturbations at scales smaller than ∼200 km.
Structure and mechanics of the San Andreas–San Gregorio fault junction, San Francisco, California
Authors: Parsons Tom , Bruns Terry R. , Sliter Ray
Published: January 2005

The right‐lateral San Gregorio and San Andreas faults meet west of the Golden Gate near San Francisco. Coincident seismic reflection and refraction profiling across the San Gregorio and San Andreas faults south of their junction shows the crust between them to have formed shallow extensional basins that are dissected by parallel strike‐slip faults. We employ a regional finite element model to investigate the long‐term consequences of the fault geometry. Over the course of 2–3 m.y. of slip on the San Andreas‐San Gregorio fault system, elongated extensional basins are predicted to form between the two faults. An additional consequence of the fault geometry is that the San Andreas fault is expected to have migrated eastward relative to the San Gregorio fault. We thus propose a model of eastward stepping right‐lateral fault formation to explain the observed multiple fault strands and depositional basins. The current manifestation of this process might be the observed transfer of slip from the San Andreas fault east to the Golden Gate fault.
Flow reorganizations in the Panama Seaway: A cause for the demise of Miocene corals?
Authors: von der Heydt Anna , Dijkstra Henk A.
Published: January 2005

A large number of coral species in the Caribbean Sea disappeared in the early Miocene. Based on climate model simulations, we propose that this regional extinction is related to a flow reorganization in the Panama Seaway. It is shown that large‐scale tectonic events, such as the opening of Drake Passage and the closing of the Tethys Seaway, reorganized the global ocean currents to induce a reversal of the volume transport between Atlantic and Pacific. This flow reversal, which is timed near the Oligocene‐Miocene boundary, allowed cool Pacific waters to enter the Caribbean Sea possibly affecting the habitat of warm water tolerant coral species.
Morphology of evening sector aurorae in λ557.7‐nm Doppler temperatures
Authors: Holmes J. M. , Conde M. , Deehr C. , Lummerzheim D.
Published: January 2005

An all‐sky scanning Fabry‐Pérot spectrometer was used to observe temperatures of auroral OI (557.7‐nm) emissions over Poker Flat, Alaska (65.12N, 147.43W). The sudden temporal and spatial changes in Doppler temperatures observed are likely owing to the emission height changing as a response to variations in the characteristic energy of the precipitating electron population. Three cases were analyzed: (1) A Doppler temperature drop (∼200 K) over the entire sky occurred immediately after an auroral brightening; the temperature remained lower after the auroral intensity had resumed its quiescent levels. (2) A local increase of Doppler temperature, colocated with a weak auroral arc, occurred 25 minutes before a westward propagating substorm onset. When the auroral luminosity suddenly increased the Doppler temperature had a sharp decrease. (3) The region inside a loop‐like auroral arc showed elevated Doppler temperature relative to that of the arc itself. Auroral fading prior to onset was accompanied by increased temperatures.
An auroral source of hot oxygen in the geocorona
Authors: Shematovich V. I. , Bisikalo D. V. , Gérard J.‐C.
Published: January 2005

The high‐energy proton‐hydrogen (H+/H) beam associated with proton auroral precipitation transfers momentum in elastic and inelastic collisions with ambient thermal atomic oxygen in the high latitude thermosphere. This process provides a localized novel source of hot oxygen atoms in addition to exothermic photochemistry, charge exchange and momentum transfer from O+ ion precipitation and charge exchange with accelerated ionospheric O+ ions. We suggest that this source contributes to the population of the hot oxygen geocorona and to the flux of escaping oxygen atoms. For an incident proton energy flux of 1 mW m−2 and a mean energy Emean ≈ 5 keV, we calculate a density of hot oxygen atoms with energy above 1 eV of 2.0 × 103 cm−3 and a mean kinetic energy of about 3.5 eV at 700 km. The total upward flux of hot oxygen atoms with energies higher 1 eV is estimated as 3.5 × 108 cm−2 s−1.
Loess record of the aerodynamic environment in the east Asia monsoon area since 60,000 years before present
Authors: Qin Xiaoguang , Cai Binggui , Liu Tungsheng
Published: January 2005

The multimodal distribution of grains in loess and dust storm deposits has been widely reported in recent years. Our analysis demonstrates that the interaction of wind, atmospheric turbulence, and dust grain gravity along the dust transportation path results in a multimodal grain size distribution for suspended dust. Changes in the median sizes of the coarse and medium modes are related to variation in aerodynamic forcing (lift force related to vertical wind and turbulence) during dust entrainment in the source area and turbulence intensity in the depositional area. On the basis of the numeric characteristics of the three modes of suspended particles, a tentative model has been constructed, which is used to study fluctuations of paleoaerodynamic environments. From a time series of paleoatmospheric environmental changes of the loess plateau for the past 60,000 years, we find that there are three patterns of aerodynamic environments in the dust source area (stronger, strong, weak) and 13 strong turbulence events since 60,000 years B.P. Climatic variability in the dust depositional area is stronger than in the source area. During the last glacial period the aerodynamic environment changed synchronously in the dust source and depositional areas over the entire trend. However, after 8000 years B.P. the aerodynamic force is strong in the dust source area, while the turbulence intensity is weak in the dust depositional area, differing from that of the last glacial period. The strong turbulence periods correspond to the cooling events such as the Heinrich events and the Younger Dryas cold event and may not be related to factors forcing the alternation between glacial and interglacial periods. Since 60,000 years B.P. the three patterns of aerodynamic environments are mainly controlled by the environmental changes in the dust source area and may be related to fluctuations of the winter monsoon. In each pattern, fluctuations of the turbulence intensity in the dust depositional area and the distance from dust source to dust depositional area are the major changes of the environment. The summer monsoon, recorded by magnetic susceptibility, may vary prior to the winter monsoon since 50,000 years B.P. Changes in the intensity of the summer monsoon may force changes in the advance‐retreat cycles of dust source areas in each winter monsoon pattern.
Thermal response of sediment with vertical fluid flow to periodic temperature variation at the surface
Authors: Goto Shusaku , Yamano Makoto , Kinoshita Masataka
Published: January 2005

Characteristics of thermal responses of sediment with vertical fluid movement to periodic temperature variation at the surface were examined using a one‐dimensional analytical solution. The amplitude of the thermal response decays exponentially, and the phase is delayed linearly with increasing depth, but they depend on the direction and velocity of vertical fluid flow, thermal diffusivity of fluid‐saturated sediment, and period of surface temperature variation. To examine general characteristics of the thermal response, we defined two nondimensional parameters related to thermal diffusivity of fluid‐saturated sediment, vertical fluid flow velocity, period of the surface temperature variation, and specific penetration depth at which the amplitude of the thermal response decays to e−1 of that at the surface. Analysis using these nondimensional parameters shows that there are three heat transport regimes for downward flow: (1) heat transport strongly governed by advection, (2) heat transport strongly governed by conduction, and (3) transition between these regimes. For upward flow, there are also three heat transport regimes: (1) balance of heat transports by advection and conduction, (2) heat transport strongly governed by conduction, and (3) transition between these regimes. The analytical solution is used to estimate the downward fluid velocity and thermal diffusivity of sediment from temperatures measured by long‐term temperature monitoring at a site of seafloor hydrothermal circulation.
Evaluation of three probing techniques in a three‐dimensional air quality model
Authors: Zhang Yang , Vijayaraghavan Krish , Seigneur Christian
Published: January 2005

Probing techniques are useful to provide diagnostic evaluations of air quality models and to indicate the responses of model predictions to changes in emissions. Three probing tools are available in a three‐dimensional air quality model, CAMx: the Decoupled Direct Method (DDM), the Ozone Source Attribution Technology (OSAT), and Process Analysis (PA). These tools are evaluated in terms of consistency, complementarity, accuracy and robustness, and computational requirements using the 7–15 July 1995 O3 episode over the eastern United States. The NOx‐ versus VOC‐sensitivity of O3 chemistry and relative role of chemistry and transport predicted by the three tools are qualitatively consistent, except that OSAT predicts an NOx‐limited O3 chemistry at a few locations where both DDM and PA predict a VOC‐sensitive O3 chemistry. DDM and OSAT agree well on the top 10 contributors to O3 formation, but they predict different rankings, with greater importance given to biogenic VOC emissions by DDM and greater importance given to surface anthropogenic NOx emissions by OSAT. The major difference in the DDM and OSAT predictions on the relative impact of sources is that DDM predicts both positive and negative sensitivities whereas OSAT always predicts positive contributions. Compared to the single‐perturbation method (brute force method), DDM predicts accurate model responses under the 25% VOC or NOx emission reduction scenarios but inaccurate results under the 75% NOx emission reduction scenario. OSAT predicts accurate model responses under the 25% VOC emission reduction scenario, but inaccurate responses under the 25% and 75% NOx emission reduction scenarios. While these tools provide valuable and complementary information regarding O3 formation, each of them has limitations in terms of its design and application for the design of emission control strategies. DDM is suitable for such an application for small‐to‐moderate emission reductions of <40%. OSAT leads to incorrect results for VOC‐limited areas because it does not account for the titration/inhibition effect of NOx and/or VOC. PA provides an in‐depth understanding of the processes involved in controlling O3 formation locally. It can be used to understand some of the differences between the results of OSAT and DDM.
Surface water acidification responses and critical loads of sulfur and nitrogen deposition in Loch Vale watershed, Colorado
Authors: Sullivan T. J. , Cosby B. J. , Tonnessen K. A. , Clow D. W.
Published: January 2005

We evaluated the sensitivity of The Loch, a subalpine lake in Rocky Mountain National Park in Colorado, to acidification in response to increased atmospheric loading of sulfur (S) and nitrogen (N) using the Model of Acidification of Groundwater in Catchments (MAGIC). Lake water acid‐base chemistry was moderately sensitive to changes in both S and N deposition. However, the loads of S deposition that would drive chronic lake water acid neutralizing capacity (ANC) to below 0 or 20 μeq L−1 were estimated to be 11 and 8 kg S ha−1 yr−1, respectively, assuming constant future N deposition at current levels. Comparable loads for N deposition, assuming constant future S deposition, were estimated to be 21 and 12 kg N ha−1 yr−1, respectively. Modeling results for Andrews Creek, an alpine tributary to The Loch, suggested critical loads for surface water acidification that averaged about one third lower. Surface water ANC = 50 μeq L−1 was projected to occur in 50 years in The Loch if S or N deposition increased by a moderate amount (<40%) but could not be achieved in Andrews Creek by reducing either S or N deposition to zero. On the basis of the results of synoptic surveys of lake water chemistry, about one fifth of the wilderness lakes in the Colorado Front Range are more acid‐sensitive than The Loch. This modeling exercise suggests the need for a regional analysis of critical loads for the larger population of acid‐sensitive aquatic resources in order to provide part of the scientific foundation for federally mandated land management decisions.
Trend‐oriented sampling strategy and estimation of soluble reactive phosphorus loads in streams
Authors: Moosmann Lorenz , Müller Beat , Gächter René , Wüest Alfred , Butscher Ernst , Herzog Peter
Published: January 2005

Nutrient transfer from soils to surface waters is associated with large, hydrologically induced fluctuations. Consequently, stream‐based estimation of long‐term changes in nutrient leaching is masked by variations of stream discharge. Using high‐resolution discharge and soluble reactive phosphorus (SRP) data from three small catchments (up to 42 km2), SRP loads are calculated by applying two different rating curves. Monte Carlo simulations are carried out to determine monitoring strategies for optimizing the number of water samples, their distribution between periods of low and high discharge, and the duration of composite sample collection. Trends in SRP load are isolated from natural variations by applying the discharge time series of 1 year each to annually changing rating curves. By applying this approach to various monitoring data sets, collected over the past 15 years, downward trends in SRP leaching of up to −3% yr−1 are detected. We describe how to determine the number of annual samples required to detect trends in nutrient load, depending on monitoring duration, available resources, and the magnitude of the expected trend.
Algebraic geometry realization of quantum Hall soliton
Authors: Abounasr R. , Ait Ben Haddou M. , El Rhalami A. , Saidi E. H.
Published: January 2005

Using the Iqbal–Netzike–Vafa dictionary giving the correspondence between the H2 homology of del Pezzo surfaces and p-branes, we develop a way to approach the system of brane bounds in M-theory on S1. We first review the structure of 10-dimensional quantum Hall soliton (QHS) from the view of M-theory on S1. Then, we show how the D0 dissolution in D2-brane is realized in M-theory language and derive the p-brane constraint equations used to define appropriately the QHS. Finally, we build an algebraic geometry realization of the QHS in type IIA superstring and show how to get its type IIB dual. Other aspects are also discussed.
Maurer–Cartan equations for Lie symmetry pseudogroups of differential equations
Authors: Cheh Jeongoo , Olver Peter J. , Pohjanpelto Juha
Published: January 2005

A new method of constructing structure equations of Lie symmetry pseudogroups of differential equations, dispensing with explicit solutions of the (infinitesimal) determining systems of the pseudogroups, is presented, and illustrated by the examples of the Kadomtsev–Petviashvili and Korteweg–de Vries equations.
Path description of conserved quantities of generalized periodic box-ball systems
Authors: Mada Jun , Idzumi Makoto , Tokihiro Tetsuji
Published: January 2005

We investigate conserved quantities of periodic box-ball systems (PBBS) with arbitrary kinds of balls and box capacity greater than or equal to 1. We introduce the notion of nonintersecting paths on the two dimensional array of boxes, and give a combinatorial formula for the conserved quantities of the generalized PBBS using these paths.
Helix and Drugs: Snails for Western Health Care From Antiquity to the Present
Authors: Bonnemain Bruno
Published: January 2005

The land helix, or snail, has been used in medicine since antiquity and prepared according to several formulations. This historical report traces the understanding of their properties from the time of Hippocrates, who proposed the use of snail mucus against protoccle and Pliny who thought that the snail increased the speed of delivery and was “a sovereign remedy to treat pain related to burns, abscesses and other wounds”, Galien recommended snails against hydrops foetails. In the 18th century, various snail “preparations” were also recommended for external use with dermatological disorders and internally for symptoms associated with tuberculosis and nephritis. Surprisingly, the 19th century saw a renewed interest in the pharmaceutical and medical use of snails with numerous indications for snail preparations. This interest in snails did not stop at the end of the 19th century. The 1945 edition of Dorvault devotes an entire paragraph to snails, indicating that the therapeutic usage of snails was still alive at that time. Recently the FDA has also shown an interest in snails. Ziconotide (SNXIII), a synthetic peptide coming from snail venom, has been under FDA review since 1999. Pre‐clinical and clinical studies of this new drug are promising.
The Drosophila ortholog of vertebrate TRPA1 regulates thermotaxis
Authors: Rosenzweig Mark , Brennan Karen M. , Tayler Timothy D. , Phelps Paul O. , Patapoutian Ardem , Garrity Paul A.
Published: January 2005

Thermotaxis is important for animal survival, but the molecular identities of temperature sensors controlling this behavior have not been determined. We demonstrate dTRPA1, a heat-activated Transient Receptor Potential (TRP) family ion channel, is essential for thermotaxis in Drosophila. dTrpA1 knockdown eliminates avoidance of elevated temperatures along a thermal gradient. We observe dTRPA1 expression in cells without previously ascribed roles in thermosensation and implicate dTRPA1-expressing neurons in mediating thermotaxis. Our data suggest that thermotaxis relies upon neurons and molecules distinct from those required for high-temperature nociception. We propose dTRPA1 may control thermotaxis by sensing environmental temperature.
An Auxin Transport Independent Pathway Is Involved in Phosphate Stress-Induced Root Architectural Alterations in Arabidopsis. Identification of BIG as a Mediator of Auxin in Pericycle Cell Activation
Authors: López-Bucio José , Hernández-Abreu Esmeralda , Sánchez-Calderón Lenin , Pérez-Torres Anahí , Rampey Rebekah A. , Bartel Bonnie , Herrera-Estrella Luis
Published: January 2005

Arabidopsis (Arabidopsis thaliana) plants display a number of root developmental responses to low phosphate availability, including primary root growth inhibition, greater formation of lateral roots, and increased root hair elongation. To gain insight into the regulatory mechanisms by which phosphorus (P) availability alters postembryonic root development, we performed a mutant screen to identify genetic determinants involved in the response to P deprivation. Three low phosphate-resistant root lines (lpr1-1 to lpr1-3) were isolated because of their reduced lateral root formation in low P conditions. Genetic and molecular analyses revealed that all lpr1 mutants were allelic to BIG, which is required for normal auxin transport in Arabidopsis. Detailed characterization of lateral root primordia (LRP) development in wild-type and lpr1 mutants revealed that BIG is required for pericycle cell activation to form LRP in both high (1 mm) and low (1 μ  m) P conditions, but not for the low P-induced alterations in primary root growth, lateral root emergence, and root hair elongation. Exogenously supplied auxin restored normal lateral root formation in lpr1 mutants in the two P treatments. Treatment of wild-type Arabidopsis seedlings with brefeldin A, a fungal metabolite that blocks auxin transport, phenocopies the root developmental alterations observed in lpr1 mutants in both high and low P conditions, suggesting that BIG participates in vesicular targeting of auxin transporters. Taken together, our results show that auxin transport and BIG function have fundamental roles in pericycle cell activation to form LRP and promote root hair elongation. The mechanism that activates root system architectural alterations in response to P deprivation, however, seems to be independent of auxin transport and BIG.
Cyanidioschyzon merolae Genome. A Tool for Facilitating Comparable Studies on Organelle Biogenesis in Photosynthetic Eukaryotes
Authors: Misumi Osami , Matsuzaki Motomichi , Nozaki Hisayoshi , Miyagishima Shin-ya , Mori Toshiyuki , Nishida Keiji , Yagisawa Fumi , Yoshida Yamato , Kuroiwa Haruko , Kuroiwa Tsuneyoshi
Published: January 2005

The ultrasmall unicellular red alga Cyanidioschyzon merolae lives in the extreme environment of acidic hot springs and is thought to retain primitive features of cellular and genome organization. We determined the 16.5-Mb nuclear genome sequence of C. merolae 10D as the first complete algal genome. BLASTs and annotation results showed that C. merolae has a mixed gene repertoire of plants and animals, also implying a relationship with prokaryotes, although its photosynthetic components were comparable to other phototrophs. The unicellular green alga Chlamydomonas reinhardtii has been used as a model system for molecular biology research on, for example, photosynthesis, motility, and sexual reproduction. Though both algae are unicellular, the genome size, number of organelles, and surface structures are remarkably different. Here, we report the characteristics of double membrane- and single membrane-bound organelles and their related genes in C. merolae and conduct comparative analyses of predicted protein sequences encoded by the genomes of C. merolae and C. reinhardtii. We examine the predicted proteins of both algae by reciprocal BLASTP analysis, KOG assignment, and gene annotation. The results suggest that most core biological functions are carried out by orthologous proteins that occur in comparable numbers. Although the fundamental gene organizations resembled each other, the genes for organization of chromatin, cytoskeletal components, and flagellar movement remarkably increased in C. reinhardtii. Molecular phylogenetic analyses suggested that the tubulin is close to plant tubulin rather than that of animals and fungi. These results reflect the increase in genome size, the acquisition of complicated cellular structures, and kinematic devices in C. reinhardtii.
Nitric Oxide Mediates Gravitropic Bending in Soybean Roots
Authors: Hu Xiangyang , Neill Steven J. , Tang Zhangcheng , Cai Weiming
Published: January 2005

Plant roots are gravitropic, detecting and responding to changes in orientation via differential growth that results in bending and reestablishment of downward growth. Recent data support the basics of the Cholodny-Went hypothesis, indicating that differential growth is due to redistribution of auxin to the lower sides of gravistimulated roots, but little is known regarding the molecular details of such effects. Here, we investigate auxin and gravity signal transduction by demonstrating that the endogenous signaling molecules nitric oxide (NO) and cGMP mediate responses to gravistimulation in primary roots of soybean (Glycine max). Horizontal orientation of soybean roots caused the accumulation of both NO and cGMP in the primary root tip. Fluorescence confocal microcopy revealed that the accumulation of NO was asymmetric, with NO concentrating in the lower side of the root. Removal of NO with an NO scavenger or inhibition of NO synthesis via NO synthase inhibitors or an inhibitor of nitrate reductase reduced both NO accumulation and gravitropic bending, indicating that NO synthesis was required for the gravitropic responses and that both NO synthase and nitrate reductase may contribute to the synthesis of the NO required. Auxin induced NO accumulation in root protoplasts and asymmetric NO accumulation in root tips. Gravistimulation, NO, and auxin also induced the accumulation of cGMP, a response inhibited by removal of NO or by inhibitors of guanylyl cyclase, compounds that also reduced gravitropic bending. Asymmetric NO accumulation and gravitropic bending were both inhibited by an auxin transport inhibitor, and the inhibition of bending was overcome by treatment with NO or 8-bromo-cGMP, a cell-permeable analog of cGMP. These data indicate that auxin-induced NO and cGMP mediate gravitropic curvature in soybean roots.
Phylogenetic Analyses Identify 10 Classes of the Protein Disulfide Isomerase Family in Plants, Including Single-Domain Protein Disulfide Isomerase-Related Proteins
Authors: Houston Norma L. , Fan Chuanzhu , Xiang (Jenny) Qiu-Yun , Schulze Jan-Michael , Jung Rudolf , Boston Rebecca S.
Published: January 2005

Protein disulfide isomerases (PDIs) are molecular chaperones that contain thioredoxin (TRX) domains and aid in the formation of proper disulfide bonds during protein folding. To identify plant PDI-like (PDIL) proteins, a genome-wide search of Arabidopsis (Arabidopsis thaliana) was carried out to produce a comprehensive list of 104 genes encoding proteins with TRX domains. Phylogenetic analysis was conducted for these sequences using Bayesian and maximum-likelihood methods. The resulting phylogenetic tree showed that evolutionary relationships of TRX domains alone were correlated with conserved enzymatic activities. From this tree, we identified a set of 22 PDIL proteins that constitute a well-supported clade containing orthologs of known PDIs. Using the Arabidopsis PDIL sequences in iterative BLAST searches of public and proprietary sequence databases, we further identified orthologous sets of 19 PDIL sequences in rice (Oryza sativa) and 22 PDIL sequences in maize (Zea mays), and resolved the PDIL phylogeny into 10 groups. Five groups (I–V) had two TRX domains and showed structural similarities to the PDIL proteins in other higher eukaryotes. The remaining five groups had a single TRX domain. Two of these (quiescin-sulfhydryl oxidase-like and adenosine 5′-phosphosulfate reductase-like) had putative nonisomerase enzymatic activities encoded by an additional domain. Two others (VI and VIII) resembled small single-domain PDIs from Giardia lamblia, a basal eukaryote, and from yeast. Mining of maize expressed sequence tag and RNA-profiling databases indicated that members of all of the single-domain PDIL groups were expressed throughout the plant. The group VI maize PDIL ZmPDIL5-1 accumulated during endoplasmic reticulum stress but was not found within the intracellular membrane fractions and may represent a new member of the molecular chaperone complement in the cell.
Functional and Developmental Impact of Cytosolic Protein N-Terminal Methionine Excision in Arabidopsis
Authors: Ross Simon , Giglione Carmela , Pierre Michèle , Espagne Christelle , Meinnel Thierry
Published: January 2005

Protein N-terminal methionine (Met) excision (NME) is carried out by two types of Met aminopeptidases (MAPs), MAP1 and MAP2, in eukaryotes. Three enzymes, MAP1A, MAP2A, and MAP2B, have been identified in the cytoplasm of Arabidopsis (Arabidopsis thaliana). MAP transcript quantification revealed a predominance of MAP2B and developmental and organ-specific regulation of both MAP1A and MAP2s. By combining reverse genetics and reverse chemogenomics in transgenic plant lines, we have devised specific and reversible switches for the investigation of the role of cytoplasmic NME in Arabidopsis and of the respective contributions of the two types of cytoplasmic MAPs throughout development. dsRNA interference and knockout (KO) plant lines targeting either MAP1A alone or both MAP2s simultaneously were constructed and shown to display wild-type phenotypes. In the MAP1A KO context, modulating MAP2 activity by treatment with various concentrations of the specific drug fumagillin impaired plant development, with particularly strong effects on the root system. Reciprocally, complete MAP2 inhibition in various MAP1A knocked-down genetic backgrounds also generated a gradient of developmentally abnormal plants, but the effects on the root system were milder than in the KO context. In the absence of MAP2 activity, the severity of the phenotype in the MAP1A knocked-down lines was correlated to the extent of MAP1A mRNA accumulation. Complete cytoplasmic NME inactivation blocked development after plant germination. Thus, in plants, (1) cytoplasmic NME is essential; (2) MAP1A and MAP2s are functionally interchangeable, which is not the case in fungi and animals, as a complete block of either MAP-type activity does not cause any visible molecular or phenotypic effect; and (3) a minimal level of cytoplasmic MAP is required for normal development.
A distinct subset of chemokines dominates the mucosal chemokine response in inflammatory bowel disease
Authors: Puleston J. , Cooper M. , Murch S. , Bid K. , Makh S. , Ashwood P. , Bingham A. H. , Green H. , Moss P. , Dhillon A. , Morris R. , Strobel S. , Gelinas R. , Pounder R. E. , Platt A.
Published: January 2005

Background : Inflammatory bowel disease (IBD) is characterised by intense mucosal recruitment of activated leukocytes. Chemokines determine inflammatory leukocyte recruitment and retention.

Aim : To compare expression of the entire chemokine family within colonic mucosa from IBD patients and uninflamed controls.

Methods : A microarray of cDNAs, representing every member of this superfamily and their cognate receptors, was hybridised with probes derived from colonoscopic biopsies.

Results : A distinct subset of chemokines, consisting of CXCLs 1–3 and 8 and CCL20, was upregulated in active colonic IBD, compared with uninflamed areas or tissue from controls. Increased expression of their cognate receptors, CXCR1, CXCR2 and CCR6, was confirmed by quantitative PCR and immunohistochemistry. An identical chemokine response was induced in Caco‐2 cells by stimulation with interleukin (IL)‐1β, but not tumour necrosis factor‐alpha (TNF‐α). By contrast, IL‐1β and TNF‐α were synergistic in an HT29 cell line and primary keratinocytes.

Conclusions : IL‐1β and TNF‐α appear to be the pivotal mediators of a previously unidentified coordinated epithelial chemokine response that dominates the mucosal chemokine environment in inflamed IBD tissue.
Rebound acid hypersecretion after long‐term inhibition of gastric acid secretion
Authors: Fossmark R. , Johnsen G. , Johanessen E. , Waldum H. L.
Published: January 2005

Background : Rebound acid hypersecretion develops after the use of acid inhibitors.

Aim : To estimate the duration of hypersecretion and to elucidate the role of the enterochromaffin‐like (ECL) cell in rebound acid hypersecretion.

Methods : Patients waiting for anti‐reflux surgery who had used a proton pump inhibitor daily > 1 year were included. All patients discontinued taking acid inhibiting drugs after the operation. Basal and pentagastrin stimulated acid output was measured at 4, 8, 16 and 26 weeks postoperatively. Oxyntic mucosal biopsies were collected before and 26 weeks after the operation for counting of histidine decarboxylase (HDC) immunoreactive cells. Serum chromogranin A (CgA) and gastrin were measured before and at 4, 8, 16 and 26 weeks after the operation.

Results : Pentagastrin stimulated acid secretion was higher at 4 and 8 weeks than at 26 weeks after the operation. Gastrin and CgA were significantly reduced at 4 and 8 weeks, respectively. The number of HDC immunoreactive cells was reduced by 60% at 26 weeks postoperative.

Discussion : Rebound acid hypersecretion lasts more than 8 weeks, but less than 26 weeks after long‐term proton pump inhibition.

Conclusion : The findings indicate that not only the parietal cell mass, but also ECL cell mass and activity are involved in the mechanism of acid hypersecretion.