bluuebunny/crossref_metadata_2025 huggingface dataset:
Macroarray‐based analysis of tail regeneration in Xenopus laevis larvae
Authors: Tazaki Akira , Kitayama Atsushi , Terasaka Chie , Watanabe Kenji , Ueno Naoto , Mochii Makoto
Published: June 2005

Xenopus larvae possess a remarkable ability to regenerate their tails after they have been severed. To gain an understanding of the molecular mechanisms underlying tail regeneration, we performed a cDNA macroarray‐based analysis of gene expression. A Xenopus cDNA macroarray representing 42,240 independent clones was differentially hybridized with probes synthesized from the total RNA of normal and regenerating tails. Temporal expression analysis revealed that the up‐regulated genes could be grouped into early or late responding genes. A comparative expression analysis revealed that most genes showed similar expression patterns between tail development and regeneration. However, some genes showed regeneration‐specific expression. Finally, we identified 48 up‐regulated genes that fell into several categories based on their putative functions. These categories reflect the various processes that take place during regeneration, such as inflammation response, wound healing, cell proliferation, cell differentiation, and control of cell structure. Thus, we have identified a panel of genes that appear to be involved in the process of regeneration. Developmental Dynamics 233:1394–1404, 2005. © 2005 Wiley‐Liss, Inc.
Cre‐mediated site‐specific recombination in zebrafish embryos
Authors: Thummel Ryan , Burket Christopher T. , Brewer Jeffrey L. , Sarras Michael P. , Li Li , Perry Martin , McDermott Jeffrey P. , Sauer Brian , Hyde David R. , Godwin Alan R.
Published: June 2005

Cre‐mediated site‐specific recombination has become an invaluable tool for manipulation of the murine genome. The ability to conditionally activate gene expression or to generate chromosomal alterations with this same tool would greatly enhance zebrafish genetics. This study demonstrates that the HSP70 promoter can be used to inducibly control expression of an enhanced green fluorescent protein (EGFP) –Cre fusion protein. The EGFP–Cre fusion protein is capable of promoting recombination betweenloxsites in injected plasmids or in stably inherited transgenes as early as 2 hr post–heat shock induction. Finally, the levels of Cre expression achieved in a transgenic fish line carrying the HSP70‐EGFP–cretransgene are compatible with viability and both male and female transgenic fish are fertile subsequent to induction of EGFP–Cre expression. Hence, our data suggests that Cre‐mediated recombination is a viable means of manipulating gene expression in zebrafish. Developmental Dynamics 233:1366–1377, 2005. © 2005 Wiley‐Liss, Inc.
Induction of initial cardiomyocyte α‐actin—smooth muscle α‐actin—in cultured avian pregastrula epiblast: A role for nodal and BMP antagonist
Authors: Matsui Hiroko , Ikeda Kazuo , Nakatani Kazuki , Sakabe Masahide , Yamagishi Toshiyuki , Nakanishi Toshio , Nakajima Yuji
Published: June 2005

During early cardiogenesis, endoderm‐derived bone morphogenetic protein (BMP) induces the expression of both heart‐specific transcription factors and sarcomeric proteins. However, BMP antagonists do not inhibit the expression of the “initial heart α‐actin”—smooth muscle α‐actin (SMA)—which is first expressed in the anterior lateral mesoderm and then recruited into the initial myofibrils (Nakajima et al. [2002] Dev. Biol. 245:291–303). Therefore, mechanisms that regulate the expression of SMA in the heart‐forming mesoderm are not well‐understood. Regional explantation experiments using chick blastoderm showed that the posterolateral region of the epiblast differentiated into cardiomyocytes. Posterior epiblast cultured with or without the associated hypoblast showed that interaction between the tissues of these two germ layers at the early pregastrula stage (stages X–XI) was a prerequisite for the expression of SMA. Posterior epiblast that is cultured without hypoblast could also be induced to express SMA if TGF‐β or activin was added to the culture medium. However, neither neutralizing antibodies against TGF‐βs nor follistatin perturbed the expression of SMA in cultured blastoderm. Adding BMP to the cultured blastoderm inhibited the expression of SMA, whereas BMP antagonists, such as chordin, were able to induce the expression of SMA in cultured posterior epiblast. Furthermore, adding lefty‐1, a nodal antagonist, to the blastoderm inhibited the expression of SMA, and nodal plus BMP antagonist up‐regulated the expression of SMA in cultured posterior epiblast. Results indicate that the interaction between the tissues of the posterior epiblast and hypoblast is necessary to initiate the expression of SMA during early cardiogenesis and that nodal and BMP antagonist may play an important role in the regulation of SMA expression. Developmental Dynamics 233:1419–1429, 2005. © 2005 Wiley‐Liss, Inc.
Isolation of arterial‐specific genes by subtractive hybridization reveals molecular heterogeneity among arterial endothelial cells
Authors: Shin Donghun , Anderson David J.
Published: June 2005

Arteries are distinguished from veins by differences in gene expression, as well as in their anatomy and physiology. The characterization of arterial‐ and venous‐specific genes may improve our understanding of cardiovascular development and disease. Here we report the results of a subtractive hybridization screen for arterial‐specific genes, and describe in detail the expression of a novel arterial‐specific gene, Depp (decidual protein induced by progesterone), using a GFP‐Cre knock‐in that permits a comparison of both instantaneous and cumulative expression patterns in situ. Several features of Depp expression are noteworthy. First, Depp is expressed in endothelial cells of peripheral tissues, but not in atrial or ventricular endocardial cells of the heart. Very few genes have been reported to discriminate between these two cell types, and therefore this specificity may be useful in generating conditional mutations in other genes implicated in cardiovascular development. Second, Depp reveals an unexpected degree of molecular heterogeneity among arterial endothelial cells. Third, Depp is up‐regulated in subsets of endothelial cells, in settings of adult neo‐vascularization, including tumor angiogenesis. Taken together, these data reveal unanticipated temporal and spatial heterogeneity among arterial endothelial cells of various tissues and organs, raising new questions regarding the functional significance of this diversity. Developmental Dynamics 233:1589–1604, 2005. © 2005 Wiley‐Liss, Inc.
Zebrafish acvr2a and acvr2b exhibit distinct roles in craniofacial development
Authors: Albertson R. Craig , Payne‐Ferreira Tracie L. , Postlethwait John , Yelick Pamela C.
Published: June 2005

To examine the roles of activin type II receptor signaling in craniofacial development, full‐length zebrafish acvr2a and acvr2b clones were isolated. Although ubiquitously expressed as maternal mRNAs and in early embryogenesis, by 24 hr postfertilization (hpf), acvr2a and acvr2b exhibit restricted expression in neural, hindbrain, and neural crest cells (NCCs). A morpholino‐based targeted protein depletion approach was used to reveal discrete functions for each acvr2 gene product. The acvr2a morphants exhibited defects in the development of most cranial NCC‐derived cartilage, bone, and pharyngeal tooth structures, whereas acvr2b morphant defects were largely restricted to posterior arch structures and included the absence and/or aberrant migration of posterior NCC streams, defects in NCC‐derived posterior arch cartilages, and dysmorphic pharyngeal tooth development. These studies revealed previously uncharacterized roles for acvr2a and acvr2b in hindbrain and NCC patterning, in NCC derived pharyngeal arch cartilage and joint formation, and in tooth development. Developmental Dynamics 233:1405–1418, 2005. © 2005 Wiley‐Liss, Inc.
JAM‐A expression during embryonic development
Authors: Parris James J. , Cooke Vesselina G. , Skarnes William C. , Duncan Melinda K. , Naik Ulhas P.
Published: June 2005

Cell adhesion molecules of the immunoglobulin superfamily play an important role in embryonic development. We have shown recently that JAM‐A, a member of this family expressed at endothelial and epithelial tight junctions, is involved in platelet activation, leukocyte transmigration, and angiogenesis. Here, we determine the expression pattern of the JAM‐A gene during embryogenesis using transgenic mice expressing lacZ under the control of the endogenous JAM‐A promoter. Histochemical staining for β‐galactosidase in heterozygous mouse embryos was first seen in the inner cell mass and trophectoderm of the blastocyst. By 8.5 days post coitum (dpc), JAM‐A gene activity was detected in the endoderm and part of the surface ectoderm. At 9.5 dpc, JAM‐A expression began to localize to certain organ systems, most notably the developing inner ear and early vasculature. Localization of JAM‐A to embryonic vasculature was confirmed by double‐staining with antibodies against JAM‐A and platelet endothelial cell adhesion molecule‐1, a known endothelial cell marker. As organogenesis progressed, high levels of JAM‐A expression continued in the epithelial component of the inner ear as well as the epithelium of the developing skin, olfactory system, lungs, and kidneys. In addition, JAM‐A gene activity was found in the developing liver, choroid plexuses, and gut tubes. Immunofluorescent staining with a JAM‐A antibody was performed to confirm that expression of the JAM‐A–β‐galactosidase fusion protein accurately represented endogenous JAM‐A protein. Thus, JAM‐A is prominently expressed in embryonic vasculature and the epithelial components of several organ systems and may have an important role in their development. Developmental Dynamics 233:1517–1524, 2005. © 2005 Wiley‐Liss, Inc.
Embryonic expression of murine 5T4 oncofoetal antigen is associated with morphogenetic events at implantation and in developing epithelia
Authors: Barrow Katie M. , Ward Christopher M. , Rutter Jennifer , Ali Sumia , Stern Peter L.
Published: June 2005

Overexpression of 5T4 oncofoetal antigen, an early marker of ES cell differentiation, in vitro increases cellular motility and decreases adhesion, properties relevant to development and cancer. Embryonic expression of m5T4 antigen is first detected on trophectoderm at implantation and is restricted to extra‐embryonic tissues to embryonic day (E) 11.5. In the embryo, significant m5T4 expression is detected at E12.5 in hindbrain roofplate and in various epithelia derived from all germ layers. In keratin 14‐expressing epithelia, there is a congruent 5T4 expression pattern with many of these cells being Ki‐67 positive. In brain, expression is observed in roofplate, ependymal layers, choroid plexus, and subventricular zones of lateral ventricles at E14.5. By E17.5, expression is decreased in the subventricular zone with further restriction to choroid plexus in adult brain. Our data demonstrate a limited 5T4 expression profile during embryogenesis associated with actively cycling, undifferentiated epithelial progenitor cells that may contribute to their migration. Developmental Dynamics 233:1535–1545, 2005. © 2005 Wiley‐Liss, Inc.
Joint development in Xenopus laevis and induction of segmentations in regenerating froglet limb (spike)
Authors: Satoh Akira , Suzuki Makoto , Amano Takanori , Tamura Koji , Ide Hiroyuki
Published: June 2005

In Xenopus laevis, amputation of the adult limb results in the formation of a simple (hypomorphic) spike‐like structure without joints, although tadpole limb bud regenerates complete limb pattern. The expression of some joint marker genes was examined in limb development and regeneration. Bmp‐4 and gdf‐5 were expressed and sox‐9 expression was decreased in the joint region. Although developing cartilages were well‐organized and had bmp‐4 expressing perichondrocytes, the spike cartilage did not have such a structure, but only showed sparse bmp‐4 expression. Application of BMP4‐soaked beads to the spike led to the induction of a joint‐like structure. These results suggest that the lack of joints in the spike is due to the deficiency of the accumulation of the cells that express bmp‐4. Improvement of regeneration in the Xenopus adult limb that we report here for the first time will give us important insights into epimorphic regeneration. Developmental Dynamics 233:1444–1453, 2005. © 2005 Wiley‐Liss, Inc.
Conditional expression of a myocardium‐specific transgene in zebrafish transgenic lines
Authors: Huang Chiu‐Ju , Jou Tzuu‐Shuh , Ho Yi‐Lwun , Lee Wu‐Hsun , Jeng Yu‐Ting , Hsieh Fong‐Jou , Tsai Huai‐Jen
Published: June 2005

To develop the first heart‐specific tetracycline (Tet)‐On system in zebrafish, we constructed plasmids in which the cardiac myosin light chain 2 promoter of zebrafish was used to drive the reverse Tet‐controlled transactivator (rtTA) and the green fluorescent protein (GFP) reporter gene was preceded by an rtTA‐responsive element. In the zebrafish fibroblast cell‐line, rtTA‐M2, one of rtTA's derivatives, demonstrated the highest increase in luciferase activity upon doxycycline (Dox) induction. We then generated two germ lines of transgenic zebrafish: line T03 was derived from microinjection of a plasmid containing rtTA‐M2 and a plasmid containing a responsive reporter gene, whereas line T21 was derived from microinjection of a single dual plasmid. Results showed that line T21 was superior to line T03 in terms of greater GFP intensity after induction and with of minimal leakiness before induction. The photographic images of induced GFP in the heart of F2 larvae showed that the fluorescent level of GFP was dose‐responsive. The level of GFP expressed in the F3 3 days postfertilization larvae that were treated with Dox for 1 hr decreased gradually after the withdrawal of the inducer; and the fluorescent signal disappeared after 5 days. The GFP induction and reduction were also tightly controlled by Dox in the F3 adult fish from line T21. This Tet‐On system developed in zebrafish shows much promise for the study of the gene function in a specific tissue at the later developmental stage. Developmental Dynamics 233:1294–1303, 2005. © 2005 Wiley‐Liss, Inc.
Oligonucleotide‐based microarray analysis of retinoic acid target genes in the protochordate, Ciona intestinalis
Authors: Ishibashi Tomoko , Usami Takeshi , Fujie Manabu , Azumi Kaoru , Satoh Nori , Fujiwara Shigeki
Published: June 2005

Oligonucleotide‐based microarray analyses were carried out to identify retinoic acid target genes in embryos of the ascidian Ciona intestinalis. Of 21,938 spots, 50 (corresponding to 43 genes) showed over twofold up‐regulation in retinoic acid‐treated tail bud embryos. In situ hybridization verified retinoic acid‐induced up‐regulation of 23 genes. Many of them were expressed in the anterior tail region, where a retinaldehyde dehydrogenase homolog is expressed. Homologs of vertebrate genes involved in neurogenesis and/or neuronal functions (e.g., COUP‐TF, Ci‐Hox1, and SCO‐spondin) were expressed in the central nervous system of Ciona embryos, and activated by retinoic acid. Genes encoding transcription factors (e.g., Ci‐lmx1.2, vitamin D receptor, and Hox proteins) and apoptosis‐related proteins (e.g., transglutaminase and an apoptosis‐inducing factor homolog) were also activated by retinoic acid. Simultaneous treatment of embryos with retinoic acid and puromycin revealed a few direct targets, including genes encoding Ci‐Hox1, Ci‐Cyp26, and an Rnf126‐like ring finger protein. Developmental Dynamics 233:1571–1578, 2005. © 2005 Wiley‐Liss, Inc.
Experimental analyses of the function of the proepicardium using a new microsurgical procedure to induce loss‐of‐proepicardial‐function in chick embryos
Authors: Männer Jörg , Schlueter Jan , Brand Thomas
Published: June 2005

The proepicardium (PE) is a primarily extracardiac progenitor cell population that colonizes the embryonic heart and delivers the epicardium, the subepicardial and intramyocardial fibroblasts, and the coronary vessels. Recent data show that PE‐derived cells additionally play important regulatory roles in myocardial development and possibly in the normal morphogenesis of the heart. Developmental Dynamics 233, 2005. Research on the latter topics profits from the fact that loss‐of‐PE‐function can be experimentally induced in chick embryos. So far, two microsurgical techniques were used to produce such embryos: (1) blocking of PE cell transfer with pieces of the eggshell membrane, and (2) mechanical excision of PE. Both of these techniques, however, have their shortcomings. We have searched, therefore, for new techniques to eliminate the PE. Here, we show that loss‐of‐PE‐function can be induced by photoablation of the PE. Chick embryos were treated in ovo by means of a window in the eggshell at Hamburger and Hamilton (HH) stage 16 (iday 3). The pericardial coelom was opened, and the PE was externally stained with a 1% solution of Rose Bengal by means of a micropipette. Photoactivation of the dye was accomplished by illumination of the operation field with visible light. Examination on postoperative day 1 (iday 4, HH stages 19/20) disclosed complete removal of PE in every experimental embryo. On iday 9 (HH stages 33/34), the survival rate of experimental embryos was 35.7% (15 of 42). Development of the PE‐derivatives was compromised in the heart of every survivor. The abnormalities encompassed hydro‐ or hemopericardium, epicardium‐free areas with aneurysmatic outward bulging of the ventricular wall, thin myocardium, defects of the coronary vasculature, and abnormal tissue bridges between the ventricles and the pericardial wall. Our results show that photoablation of the PE is a powerful technique to induce long‐lasting loss‐of‐PE‐function in chick embryos. We have additionally obtained new data that suggest that the embryonic epicardium may make important contributions to the passive mechanics of the developing heart. Developmental Dynamics 233:1454–1463, 2005. © 2005 Wiley‐Liss, Inc.
Modal model identification of structures under unmeasured seismic excitations
Authors: Sepe Vincenzo , Capecchi Danilo , De Angelis Maurizio
Published: June 2005

Techniques developed for structural identification of a structural model are typically based on information regarding the response and the forcing actions. However, in some situations it can be necessary, or simply useful, to refer only to the measured responses. In this paper we describe a technique suitable for identifying the modal model of a spatial frame in the frequency domain when the seismic input is unknown both in time contents and direction. In some previous theoretical works we established that this identification problem has a unique solution when at least three time‐history responses are known. Here numerical techniques are developed which allow the evaluation of the modal quantities in practice. Numerical applications are carried out on plane and spatial framed structures by using a modal model which may be complete, including all the structure's modes, or incomplete, including only the lowest modes. In most cases the obtained results are satisfactory. Copyright © 2005 John Wiley & Sons, Ltd.
Rock albedo and monitoring of thermal conditions in respect of weathering: some expected and some unexpected results
Authors: Hall Kevin , Lindgren B. Staffan , Jackson Peter
Published: June 2005

Broadly speaking, there is, at least within geomorphic circles, a general acceptance that rocks with low albedos will warm both faster and to higher temperatures than rocks with high albedos, reflectivity influencing radiative warming. Upon this foundation are built notions of weathering in respect of the resulting thermal differences, both at the grain scale and at the scale of rock masses. Here, a series of paving bricks painted in 20 per cent reflectivity intervals from black through to white were used to monitor albedo‐influenced temperatures at a site in northern Canada in an attempt to test this premise. Temperatures were collected, for five months, for the rock surface and the base of the rock, the blocks being set within a mass of local sediment. Resulting thermal data did indeed show that the dark bricks were warmer than the white but only when their temperatures were equal to or cooler than the air temperature. As brick temperature exceeded that of the air, so the dark and light bricks moved to parity; indeed, the white bricks frequently became warmer than the dark. It is argued that this ‘negating’ of the albedo influence on heating is a result of the necessity of the bricks, both white and black, to convect heat away to the surrounding cooler air; the darker brick, being hotter, initially convects faster than the white as a product of the temperature difference between the two media. Thus, where the bricks become significantly hotter than the air, they lose energy to that air and so their respective temperatures become closer, the albedo influence being superceded by the requirement to equilibrate with the surrounding air. It is argued that this finding will have importance to our understanding of weathering in general and to our perceptions of weathering differences between different lithologies. Copyright © 2005 John Wiley & Sons, Ltd.
Logging effects on sediment flux observed in a pollen‐based record of overbank deposition in a northern California catchment
Authors: Constantine José A. , Pasternack Gregory B. , Johnson Michael L.
Published: June 2005

A palynological approach was used to estimate overbank deposition rates in a forested catchment affected by logging. The palynological approach uses downcore variations in total fossil pollen and fossil pollen assemblage to calculate rates of overbank deposition and has a distinct advantage over radioisotopic approaches in that it is not limited by radioactive decay. Using this approach, we determined that overbank deposition rates increased over 400 per cent within years of logging events and that the increased rates persisted for less than 4 years. After logging‐induced deposition peaked, overbank deposition decreased over 60 per cent relative to the pre‐logging background values. The decreased deposition rates persisted for over 40 years. The immediate effect of logging in this catchment was to induce mass‐wasting events in hollows that produced rapidly travelling sediment pulses. In the subsequent recovery period, reduced sediment loading occurred as a result of a reduction in the volume of sediment available for transport. The reduction in sediment load led to a reduction in overbank deposition rates until subsequent logging disturbances destabilized and emptied other hollows. Copyright © 2005 John Wiley & Sons, Ltd.
An automated salt‐tracing gauge for flow‐velocity measurement
Authors: Planchon Olivier , Silvera Norbert , Gimenez Raphael , Favis‐Mortlock David , Wainwright John , Bissonnais Yves Le , Govers Gerard
Published: June 2005

This article introduces the SVG (salt‐velocity gauge), a novel automated technique for measuring flow velocity by means of salt tracing. SVG allows a high measuring rate (up to one every 2 seconds), short control section length (down to 10 cm), high accuracy (+[sol ]−1·5 cm s−1), and unbiased calculation of the mean velocity in experimental conditions with turbulent, supercritical flow.

A few cubic centimetres of saturated salt solution (NaCl) are injected into the flow at regular time intervals using a programmable solenoid valve. The tracer successively passes two conductivity probes placed a short distance downstream. The transformation of the signal between the two probes is modelled as a one‐dimensional diffusion wave equation. Model calibration gives an estimation of the mean velocity and the diffusion for each salt plume.

Two implementations of the SVG technique are described. The first was an outdoors simulated rainfall experiment in Senegal (conductivity probes at 40 cm apart, 8 Hz measurement rate, salt injections at 10 second intervals). Mean velocity was estimated to range between 0·1 and 0·3 m s−1. The second was a laboratory‐based flume experiment (conductivity probes at 10 cm apart, 32 Hz, salt injections at 2 second intervals). Another SVG with probes at 34 cm apart was used for comparison. An acoustic Doppler velocimeter (ADV) was also used to give an independent assessment of velocity. Using the 10 cm salt gauge, estimated mean velocity ranged from 0·6 to 0·9 m s−1 with a standard deviation of 1·5 cm s−1. Comparisons between ADV, 10 cm SVG and 34 cm SVG were consistent and demonstrated that the salt‐tracing results were unbiased and independent of distance between probes. Most peaks were modelled with r2 > 90 per cent.

The SVG technology offers an alternative to the dye‐tracing technique, which has been severely criticized in the literature because of the wide interval of recommended values for the correction factor α to be applied to the timings. This article demonstrates that a fixed value of α is inappropriate, since the correction factor varies with velocity, diffusion and the length of the control section. Copyright © 2005 John Wiley & Sons, Ltd.
Understanding the temporal dynamics of the wandering Renous River, New Brunswick, Canada
Authors: Burge Leif M. , Lapointe Michel F.
Published: June 2005

Wandering rivers are composed of individual anabranches surrounding semi‐permanent islands, linked by single channel reaches. Wandering rivers are important because they provide habitat complexity for aquatic organisms, including salmonids. An anabranch cycle model was developed from previous literature and field observations to illustrate how anabranches within the wandering pattern change from single to multiple channels and vice versa over a number of decades. The model was used to investigate the temporal dynamics of a wandering river through historical case studies and channel characteristics from field data.

The wandering Renous River, New Brunswick, was mapped from aerial photographs (1945, 1965, 1983 and 1999) to determine river pattern statistics and for historical analysis of case studies. Five case studies consisting of a stable single channel, newly formed anabranches, anabranches gaining stability following creation, stable anabranches, and an abandoning anabranch were investigated in detail. Long profiles, hydraulic geometry, channel energy, grain size and sediment mobility variables were calculated for each channel.

Within the Renous study area, the frequency of channel formation and abandonment were similar over the 54 years of analysis, indicating that the wandering pattern is being maintained. Eight anabranches were formed through avulsions, five were formed through the emergence of islands from channel bars and 11 anabranches were abandoned. The stable anabranch pair displayed similar hydraulic geometry and channel energy characteristics, while unstable anabranch pairs did not. The anabranch pair that gained stability displayed more similar channel energy characteristics than the anabranch pair that was losing stability (abandoning). It appears that anabranch pairs with similar energy characteristics are more stable than anabranches where these characteristics are out of balance. This is consistent with the hypothesis that anabranch pairs of similar length will be more stable than those with dissimilar lengths. Copyright © 2005 John Wiley & Sons, Ltd.
The challenge of turbulence modelling in modern aeronautical design
Authors: Hutton A. G. , Ashworth R. M.
Published: June 2005

Modern aeronautical design is driven by a number of factors such as evolving operational requirements, the relentless drive to reduce costs and increasingly stringent environmental constraints. These have led to the requirement to treat a range of complex turbulent flow regimes. Designers demand a fine balance between simplicity of approach and competency, and thus research has inevitably focussed upon RANS‐based turbulence modelling. This paper reviews the considerable progress of recent years in improving model proficiency for aerodynamic applications. The limitations to what can be achieved are discussed and it is suggested that some important flow regimes are beyond the RANS approach. The opportunities for the development and adoption of more advanced strategies such as hybrid RANS/LES methods are briefly examined. Copyright © 2005 John Wiley & Sons, Ltd.
A high‐order TVD transport method for hybrid meshes on complex geological geometry
Authors: Matthäi S. K. , Mezentsev A. A. , Pain C. C. , Eaton M. D.
Published: June 2005

The paper presents a new implicit pressure–implicit saturation higher‐order accurate in space and second‐order accurate in time advection–dispersion scheme for the hyperbolic transport equations in porous media with discrete three‐dimensional representation of material interfaces. We develop adaptive time differencing methods to use time steps greater than the mesh Courant number (Courant–Friedrich–Levy condition, CFL). The paper pays special attention to hybrid discretization of subsurface geometry, placing emphasis on the multiphase flow in fractured petroleum reservoirs. We also introduce numerical iso‐parametric double mapping integration method for node‐centred hybrid meshes and use it in our transport scheme. Copyright © 2005 John Wiley & Sons, Ltd.
Detection of regime switches between stationary and nonstationary processes and economic forecasting
Authors: Fukuda Kosei
Published: June 2005

It often occurs that no model may be exactly right, and that different portions of the data may favour different models. The purpose of this paper is to propose a new procedure for the detection of regime switches between stationary and nonstationary processes in economic time series and to show its usefulness in economic forecasting. In the proposed procedure, time series observations are divided into several segments, and a stationary or nonstationary autoregressive model is fitted to each segment. The goodness of fit of the global model composed of these local models is evaluated using the corresponding information criterion, and the division which minimizes the information criterion defines the best model. Simulation and forecasting results show the efficacy and limitations of the proposed procedure. Copyright © 2005 John Wiley & Sons, Ltd.
Cisplatin activates Akt in small cell lung cancer cells and attenuates apoptosis by survivin upregulation
Authors: Belyanskaya Larisa L. , Hopkins‐Donaldson Sally , Kurtz Stefanie , Simões‐Wüst Ana Paula , Yousefi Shida , Simon Hans‐Uwe , Stahel Rolf , Zangemeister‐Wittke Uwe
Published: June 2005

The inhibitor of apoptosis protein (IAP) survivin is overexpressed in many tumors but is absent in most normal adult tissues. We report high levels of survivin expression in small cell lung cancer (SCLC), and describe the role of the phosphatidylinositol 3‐kinase (PI3K)/Akt pathway in survivin upregulation. Moreover, the cytoprotective function of survivin in response to the anti‐cancer agent cisplatin (CDDP) was investigated. Negative modulation of PI3K/Akt using pharmacological inhibitors or dominant negative Akt (DN‐Akt) decreased Akt kinase activity and resulted in decreased survivin expression and phosphorylation on Thr34, whereas transfection of constitutively active Akt (CA‐Akt) increased survivin expression and phosphorylation. Interestingly, we found that treatment of SCLC cells with CDDP further increased survivin expression in a cell cycle independent manner by activation of Akt. CA‐Akt or lentiviral survivin also inhibited apoptosis induced by CDDP, whereas DN‐Akt or survivin‐specific RNA interference sensitized cells to CDDP. We identified survivin as an anti‐apoptotic protein in SCLC cells that is regulated by Akt, and demonstrate that treatment with the DNA damaging agent CDDP activates the PI3K/Akt/survivin pathway that in part protects cells from drug‐induced apoptosis. © 2005 Wiley‐Liss, Inc.
Monocyte/lymphocyte interactions and the foreign body response: In vitro effects of biomaterial surface chemistry
Authors: MacEwan Matthew R. , Brodbeck William G. , Matsuda Takehisa , Anderson James M.
Published: June 2005

To determine the effect of biomaterial surface chemistry on leukocyte interaction and activity at the material/tissue interface, human peripheral blood monocytes and lymphocytes were cultured on a series of poly(ethylene terephthalate) (PET)‐based biomaterials. Both monocytes and lymphocytes were isolated from whole human blood and separated by a nonadherent density centrifugation method before being plated on PET disks, surface modified by photograft copolymerization to yield hydrophobic, hydrophilic, anionic, and cationic surface properties. Monocytes and lymphocytes were cultured separately, to elicit baseline levels of activity, in direct coculture, to promote direct cell surface interactions, or in an indirect coculture system with both cell types separated by a 0.02‐μm Transwell apparatus, to promote indirect paracrine interactions. Monocyte adhesion, macrophage fusion, and lymphocyte proliferation were measured on days 3, 7, 10, and 14 of culture. Results demonstrated that the presence of monocytes increased the activity of cocultured lymphocytes at the biomaterial/tissue interface, while the corresponding presence of lymphocytes increased the activation and fusion of indirectly cocultured monocytes. Biomaterial surface chemistry was also found to have a significant effect on monocyte adhesion and activation, and lymphocyte activity. Hydrophilic surfaces significantly inhibited both initial and long‐term monocyte adhesion, and inhibited lymphocyte proliferation at longer time points. Anionic and cationic surfaces both exhibited mild inhibition of monocyte adhesion at prolonged time points, yet evoked different responses in lymphocyte populations. Anionic surfaces increased lymphocyte proliferation at longer time points and increased levels of macrophage fusion, while cationic surfaces decreased levels of lymphocyte proliferation and inhibited monocyte activity. These results elucidate the complex role of juxtacrine and paracrine interactions between monocytes and lymphocytes in the foreign body response, as well as promote the consideration of hydrophilic surfaces in future designs of implantable biomedical devices and prostheses. © 2005 Wiley Periodicals, Inc. J Biomed Mater Res, 2005
Effects of 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin (TCDD) and leptin on hypothalamic mRNA expression of factors participating in food intake regulation in a TCDD‐sensitive and a TCDD‐resistant rat strain
Authors: Lindén Jere , Korkalainen Merja , Lensu Sanna , Tuomisto Jouko , Pohjanvirta Raimo
Published: June 2005

An acutely toxic dose of 2,3,7,8‐tetrachlorodibenzo‐p‐dioxin (TCDD) leads to a drastically and permanently reduced feed intake and wasting by an unknown mechanism. We focused on the possible interference of TCDD with hypothalamic factors known to take part in the regulation of eating and metabolism, utilizing the over 1000‐fold TCDD‐sensitivity difference between Long‐Evans (Turku/AB; L‐E) and Han/Wistar (Kuopio) rats. The mRNA expression of 18 hypothalamic factors (including NPY, AgRP, and CART) was measured by quantitative RT‐PCR at 6, 24 and 96 h after TCDD administration. The effects of TCDD were compared with those of leptin and with feed restriction employing a TCDD dose that elicited a severe reduction of feed intake in L‐E rats. TCDD mainly modified expression of orexigenic factors causing an initial suppression followed by reversal to enhanced expression by 96 h. The latter was also seen in feed‐restricted controls. In contrast, leptin altered both orexigenic and anorexigenic factor mRNAs in a more even manner and its effects were clustered at 6 h. The transient nature of feeding‐promoting factor suppression does not strongly support a key role for this phenomenon in TCDD‐induced wasting syndrome. However, the fact that TCDD mainly affected orexigenic factors and the temporal differences in response found between the rat strains warrant further research. © 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:139–148, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20065
Effect of silybin and its glycosides on the expression of cytochromes P450 1A2 and 3A4 in primary cultures of human hepatocytes
Authors: Kosina Pavel , Maurel Patrick , Ulrichová Jitka , Dvořák Zdeněk
Published: June 2005

Four β‐glycosides of flavonoligan silybin, i.e. silybin β‐galactoside, silybin β‐glucoside, silybin β‐maltoside, silybin β‐lactoside were synthesized in order to improve silybin water solubility and bioavailability (Křen et al., J Chem Soc, Perkin Trans 1, 2467–2474, 1997). The presented paper deals with the effect of silybin and its synthetic β‐glycosides on the expression of two major cytochrome P450 isoforms, CYP1A2 and CYP3A4. Primary cultures of human hepatocytes were the model of choice. mRNAs were analyzed using Northern blot and P‐radiolabelled probes. CYP protein content was determined by immunoblotting using specific antibodies. Silybin and its β‐glycosides do not induce expression of CYP1A2 and CYP3A4. Tested compounds did not affect inducible expression of CYP1A2 and CYP3A4 by dioxin and rifampicin, respectively, as evaluated at the level of mRNAs and proteins. Silybin and its β‐glycosides do not interfere with the expression of CYP1A2 and CYP3A4, are not likely to produce drug–drug interactions in terms of the inducibility of two important cytochromes P450. © 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:149–153, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20066
Endogenous antioxidant defence system in rat liver following mercury chloride oral intoxication
Authors: Bando Inmaculada , Reus María Isabel Sánchez , Andrés David , Cascales María
Published: June 2005

Mercury is a highly toxic metal which induces oxidative stress. Superoxide dismutases, catalase, and glutathion peroxidase are proteins involved in the endogenous antioxidant defence system. In the present study rats were administered orally, by gavage, a single daily dose of HgCl2 for three consecutive days. In order to find a relation between the proteins involved in the antioxidant defence and mercury intoxication, parameters of liver injury, redox state of the cells, as well as intracellular protein levels and enzyme activities of Mn‐dependent superoxide dismutase (MnSOD), Cu‐Zn‐dependent superoxide dismutase (CuZnSOD), catalase, and glutathione peroxidase (GPx) were assayed both in blood and in liver homogenates.

HgCl2 at the doses of 0.1 mg/kg produced liver damage which that was detected by a slight increase in serum alanine aminotransferase and gamma glutamyl transferase. Hepatic GSH/GSSG ratio was assayed as a parameter of oxidative stress and a significant decrease was detected, as well as significant increases in enzyme activities and protein levels of hepatic antioxidant defence systems. Changes in both MnSOD and CuZnSOD were parallel to those of liver injury and oxidative stress, while the changes detected in catalase and GPx activities were progressively increased along with the mercury intoxication. Other enzyme activities related to the glutathione redox cycle, such as glutathione reductase (GR) and glucose‐6‐phosphate dehydrogenase (G6PDH), also increased progressively.

We conclude that against low doses of mercury that produce a slight oxidative stress and liver injury, the response of the liver was to induce the synthesis and activity of the enzymes involved in the endogenous antioxidant system. The activities of all the enzymes assayed showed a rapidly induced coordinated response. © 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:154–161, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20067
Effect of subchronic acrylamide exposure on the expression of neuronal and inducible nitric oxide synthase in rat brain
Authors: Kim Kisok
Published: June 2005

Acrylamide (ACR) is a known industrial neurotoxic chemical. Evidence suggests that ACR neurotoxic effect is related to brain neurotransmission disturbances. Since nitric oxide (NO) acts as a neurotransmission modulator and is produced by nitric oxide synthase (NOS), the neuronal NOS (nNOS) and inducible NOS (iNOS) expression pattern were determined in rat cerebral cortex and striatum after subchronic exposure to ACR. Using immunocytochemistry, the neuronal count of nNOS or optical density of iNOS from sections at three coronal levels, bregma 1.0, −0.4, and −2.3 mm, were compared between ACR‐treated and control rats. At all three levels, nNOS expressions were uniformly decreased in most of the neocortical subregions following the treatment of ACR. At bregma level 1.0 mm, total numbers of nNOS expressing neurons were significantly decreased to 58.7% and 64.7% of the control in the cortex and striatum of ACR‐treated rats, respectively. However, at the bregma level −2.3 mm, ACR treatment did not produce a significant difference in the numbers of nNOS expressing neurons both in the cortex and striatum. Contrary to nNOS, iNOS expressions were consistently increased to approximately 32% in the neocortex and 25% in the striatum, following the subchronic ACR treatment. These data suggest that subchronic ACR exposure involves compensatory mechanism on nNOS and iNOS expression to maintain the homeostasis of NO at the rostral part of the neocortex and the striatum. However, in the caudal brain, increased iNOS expression did not suppress nNOS expression. Therefore, the present study is consistent with the hypothesis that ACR toxicity is mediated through the disturbance to the NO signaling pathway and exhibits a rostrocaudal difference through the differential expressions of nNOS and iNOS in the neocortex and the striatum. © 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:162–168, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20069
The agricultural health study biomarker workshop on cancer etiology
Authors: Bonner Matthew R. , Alavanja Michael C. R.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:169–171, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20070
A study on immunological responses to exposures encountered in corn farming
Authors: Vermeulen R. , Roos A. J. De , Bakke B. , Blair A. , Hildesheim A. , Pinto L. , Gillette P. P. , Lynch C. F. , Allen R. H. , Alavanja M. C.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:172, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20071
Generation of reactive intermediates
Authors: Guengerich F. Peter
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:173–174, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20072
Biomarkers of thyroid function, genotoxicity and agricultural fungicide use
Authors: Garry Vincent F.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:175, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20073
Identification of biomarkers of arsenic exposure and metabolism in urine using SELDI technology
Authors: Moore L. E. , Pfeiffer R. , Warner M. , Clark M. , Skibola C. , Steinmous C. , Alguacil J. , Rothman N. , Smith M. T. , Smith A. H.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:176–176, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20074
Biomarkers of effects: The immune system
Authors: Selgrade MaryJane K.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:177–179, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20075
Toxicology of AHS important chemicals
Authors: Hodgson Ernest , Rose Randy L.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:180–181, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20076
The modulatory effects of ellagic acid and vitamin e succinate on TCDD‐induced oxidative stress in different brain regions of rats after subchronic exposure
Authors: Hassoun Ezdihar A. , Vodhanel Jennifer , Abushaban Ahmed
Published: June 2005

The original article to which this Erratum was published online 27 November 2004 in Wiley InterScience
Paraoxonase 1 (PON1) status and risk of insecticide exposure
Authors: Furlong Clement E. , Cole Toby B. , Walter Betsy J. , Shih Diana M. , Tward Aaron , Lusis Aldons J. , Timchalk Charles , Richter Rebecca J. , Costa Lucio G.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:182–183, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20079
Role of host susceptibility to toxicity and cancer caused by pesticides: Cytochromes P450
Authors: Nebert Daniel W.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:184–186, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20080
Glutathione S‐transferases as putative host susceptibility genes for cancer risk in agricultural workers
Authors: Eaton David L.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:187–189, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20081
DNA replication and repair reactions relevant to the AHS
Authors: Kunkel Thomas A.
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:190–191, 2005; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20082
Discussion and conclusions
Authors: Alavanja Michael C. R. , Bonner Matthew R. , Furlong Clement E. , Allen Ruth , Hodgson Ernest
Published: June 2005

© 2005 Wiley Periodicals, Inc. J Biochem Mol Toxicol 19:192–193, 2003; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20083
Introduction: is it possible to create pro‐poor agriculture‐related biotechnology?
Authors: Chataway Joanna
Published: June 2005

Biotechnology represents hope for those who believe that new technology can contribute to overcoming a range of pressing productivity and environmental constraints facing poor farmers. Pouring money into the science and technology however without recognizing institutional and systemic complexities associated with creating ‘pro‐poor’ technologies is unlikely to deliver much for those farmers. Moreover, there are a range of economic and political contextual factors which further complicate efforts to put the technology to use for poorer farmers. This article outlines some of the issues and possible new approaches which are discussed in more detail in later articles in this special issue. Copyright © 2005 John Wiley & Sons, Ltd.
Capacity development for agricultural biotechnology in developing countries: an innovation systems view of what it is and how to develop it
Authors: Hall Andy
Published: June 2005

There are divergent views on what capacity development might mean in relation to agricultural biotechnology. The core of this debate is whether this should involve the development of human capital and research infrastructure, or whether it should encompass a wider range of activities which also include developing the capacity to use knowledge productively. This paper uses the innovation systems concept to shed light on this discussion, arguing that it is innovation capacity rather than science and technology capacity that has to be developed. It then presents six examples of different capacity development approaches. It concludes by suggesting that policy needs to take a multidimensional approach to capacity development in line with innovation systems perspective. But it also argues that policy needs to recognise the need to develop the capacity of diversity of innovation systems and that a key part of the capacity development task is to bring about the integration of these different systems at strategic points in time. Copyright © 2005 John Wiley & Sons, Ltd.