bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping of early firing origins on a replication profile of budding yeast
Authors: Yabuki Nami , Terashima Hiromichi , Kitada Kunio
Published: March 2003

Background: Understanding of the firing time determination of replication origins in the entire genome will require a genome‐wide survey of replication origins and their mapping on chromosomes. A microarray technology was applied to obtain a genome‐wide profile of DNA replication and to classify early firing origins.

Results: A total of 260 potential replication origins (PROs) were identified in the entire budding yeast genome: 247 as defined peaks on the replication profile and 13 as regions located in the chromosomal termini. Based on the firing time, the 247 PROs were classified into 143 early PROs and 104 late PROs, that were not randomly distributed on chromosomes but formed separated clusters. Most of the early PROs were found to fire in the presence of hydroxyurea, indicating that they were free from the control of the intra‐S‐checkpoint mediated by Mec1 and Rad53.

Conclusions: The monitoring method of DNA replication and the analysis method of microarray data used in this study proved powerful for obtaining a genome‐wide view of the initiation and progression of DNA replication.
Clamp and clamp loader structures of the human checkpoint protein complexes, Rad9‐1‐1 and Rad17‐RFC
Authors: Shiomi Yasushi , Shinozaki Ayako , Nakada Daisuke , Sugimoto Katsunori , Usukura Jiro , Obuse Chikashi , Tsurimoto Toshiki
Published: March 2003

Background: We have reported that protein imaging by transmission electron microscope observation based on low‐angle platinum shadowing can reproduce characteristic ring structures of the replication clamp, proliferating cell nuclear antigen (PCNA), and the clamp loader protein, replication factor C (RFC). The checkpoint protein complexes, Rad9‐Hus1‐Rad1 (Rad9‐1‐1) and Rad17‐RFCs2‐5 (Rad17‐RFC), have been predicted to function as novel clamp and clamp loader proteins, respectively, due to their amino acid sequence similarities with PCNA and RFC.

Results: We reconstituted human Rad9‐1‐1 and Rad17‐RFC complexes in insect cells using a baculovirus expression system and showed purified Rad9‐1‐1 to be composed of equimolar amounts of Rad9, Hus1 and Rad1 proteins, exhibiting a native molecular mass of 100 kDa, in line with a trimeric complex. When Rad17 was co‐expressed with the four small subunits of RFC in insect cells, these proteins formed a complex of 240 kDa that displayed DNA binding, ATPase activity and binding to its predicted target protein, Rad9‐1‐1. Analyses of the molecular architecture of Rad9‐1‐1 and Rad17‐RFC using transmission electron microscopy, in comparison with PCNA and RFC, revealed the Rad9‐1‐1 complex to have a characteristic ring structure indistinguishable from that of PCNA in shape and size. In addition, the Rad17–RFC complex was found to be oval in structure and 26 × 22 nm in size with a cleft, reminiscent of the structure of RFC.

Conclusion: Our direct comparison of images from the two sets of clamp and clamp loader proteins indicated that Rad9‐1‐1 and Rad17‐RFC are, respectively, structural orthologs of PCNA and RFC, with presumed functions as novel clamp and clamp‐loader proteins in eukaryotes.
Cut1/separase C‐terminus affects spindle pole body positioning in interphase of fission yeast: pointed nuclear formation
Authors: Nakamura Takahiro , Nagao Koji , Nakaseko Yukinobu , Yanagida Mitsuhiro
Published: March 2003

Background: The separase‐securin complex is required for anaphase. Separase activated by securin destruction cleaves the cohesin subunit Scc1/Rad21 enriched in kinetochores. Fission yeast Cut1/separase resides in interphase cytoplasm and mobilizes to the spindle and the spindle pole bodies (SPBs) in mitosis, while Cut2/securin remains in the nucleus from interphase to metaphase, and temporarily locates at the short spindle.

Results: We here report a novel SPB‐led dynamic nuclear movement in fission yeast, when the Cut1 C‐terminal fragment is over‐expressed. The tip of the pointed nucleus contained both SPB and centromeric DNA, and rapidly moved along the bundled cytoplasmic microtubules. The same pointed nucleus was produced when the human separase C‐fragment was over‐expressed. The pointed nuclear formation did not require the protease site of separase, but required the conserved C‐terminus and a microtubule‐ and kinetochore‐binding protein Mtc1/Alp14, a homologue of frog XMAP215 and budding yeast Stu2. The movement‐inducing C‐fragment should be cytoplasmic, as the pointed nucleus was abolished when the fragment contained the NLS (nuclear localization signal).

Conclusions: Overproduced separase C‐fragment abolishes correct SPB‐positioning in interphase. Resulting pointed nuclear formation (alternatively called ‘pigtail movement’) requires cytoplasmic microtubules and Mtc1/Alp14.
lal‐1: a differentially expressed novel gene during proliferation in liver regeneration and in hepatoma cells
Authors: Della Fazia Maria Agnese , Piobbico Danilo , Bartoli Daniela , Castelli Marilena , Brancorsini Stefano , Viola Magni Mariapia , Servillo Giuseppe
Published: March 2003

Background: During liver regeneration, 95% of the resting hepatocytes enter in G1/S phase of the cell cycle. A number of hormones, growth factors and cytokines were identified that activate signal transduction pathways playing a primary role in hepatocyte proliferation. A wide and representative cDNA library containing 1.5 × 106 independent clones was constructed from regenerating liver in order to identify and characterize gene the products which play a crucial role in the first hours of the proliferative process of liver regeneration.

Results: A novel gene expressed in liver regeneration was cloned by subtractive hybridization. The putative protein displays in the N′‐terminal a annexin‐like domain and an aminopeptidase domain. We named the novel gene Liver Annexin Like‐1 (lal‐1). The lal‐1 gene is modulated during liver regeneration, in hepatoma cells following physiological stimulation and after cAMP induction.

Conclusion: The results indicate that lal‐1 is involved in liver regeneration and that its expression is finely regulated during proliferative process. The isolation of lal‐1 paves the way for a further characterization helping to assess lal‐1 involvement in cell function and proliferation.
A comparative cDNA microarray analysis reveals a spectrum of genes regulated by Pax6 in mouse lens
Authors: Chauhan Bharesh K. , Reed Nathan A. , Yang Ying , Čermák Lukáš , Reneker Lixing , Duncan Melinda K. , Cvekl Aleš
Published: March 2003

Background: Pax6 is a transcription factor that is required for induction, growth, and maintenance of the lens; however, few direct target genes of Pax6 are known.

Results: In this report, we describe the results of a cDNA microarray analysis of lens transcripts from transgenic mice over‐expressing Pax6 in lens fibre cells in order to narrow the field of potential direct Pax6 target genes. This study revealed that the transcript levels were significantly altered for 508 of the 9700 genes analysed, including five genes encoding the cell adhesion molecules β1‐integrin, JAM1, L1 CAM, NCAM‐140 and neogenin. Notably, comparisons between the genes differentially expressed in Pax6 heterozygous and Pax6 over‐expressing lenses identified 13 common genes, including paralemmin, GDIβ, ATF1, Hrp12 and Brg1. Immunohistochemistry and Western blotting demonstrated that Brg1 is expressed in the embryonic and neonatal (2‐week‐old) but not in 14‐week adult lenses, and confirmed altered expression in transgenic lenses over‐expressing Pax6. Furthermore, EMSA demonstrated that the BRG1 promoter contains Pax6 binding sites, further supporting the proposition that it is directly regulated by Pax6.

Conclusions: These results provide a list of genes with possible roles in lens biology and cataracts that are directly or indirectly regulated by Pax6.
Mechanism of H‐8 inhibition of Cyclin‐dependent kinase 9: study using inhibitor‐immobilized matrices
Authors: Shima Daisuke , Yugami Masato , Tatsuno Michiko , Wada Tadashi , Yamaguchi Yuki , Handa Hiroshi
Published: March 2003

Background: Positive transcription elongation factor b (P‐TEFb), which phosphorylates the carboxyl‐terminal domain (CTD) of RNA polymerase II (RNAPII), is comprised of the catalytic subunit cyclin‐dependent kinase 9 (CDK9) and the regulatory subunit cyclin T. The kinase activity and transcriptional activation potential of P‐TEFb is sensitive to various compounds, including H‐8, 5,6‐dichloro‐1‐β‐d‐ribofuranosylbenzimidazole (DRB), and flavopiridol.

Results: We investigated the molecular mechanism of the H‐8 inhibition of CDK9 using matrices to which H‐9, an amino derivative of H‐8, was immobilized. CDK9 bound specifically to H‐9, and this interaction was competitively inhibited by ATP and DRB, but not by flavopiridol. Mutational analyses demonstrated that the central region of CDK9, which encompasses the T‐loop region, was important for its binding to H‐9.

Conclusions: H‐9‐immobilized latex beads are useful for trapping CDK9 and a subset of kinases from crude cell extracts. The flavopiridol‐binding region of CDK9 is most likely different from its H‐9‐binding region. These biochemical data support previously reported observations which were based on crystallographic data.
Matrix metalloproteinase‐12 gene expression in human vascular smooth muscle cells
Authors: Wu Lihua , Tanimoto Akihide , Murata Yoshitaka , Sasaguri Takakazu , Fan Jianglin , Sasaguri Yasuyuki , Watanabe Teruo
Published: March 2003

Background: Matrix metalloproteinases (MMPs) play an important role in smooth muscle cell (SMC) migration and proliferation during vascular remodelling. To investigate the expression of MMP‐12 by SMCs, we examined the protein secretion and mRNA expression of MMP‐12 by cultured medial SMCs and intimal SMCs derived from human aortic atherosclerotic lesions. To further elucidate the molecular mechanism for MMP‐12 expression in SMCs, we determined the sequence requirements for MMP‐12 gene transcriptional activity.

Results: Cultured medial SMCs and intimal SMCs showed substantial MMP‐12 expression at both the protein and mRNA levels. A series of 5′‐deletion and site‐directed mutants of the human MMP‐12 promoter demonstrated that an AP‐1 site spanning −81 to −75 bp was critical for the MMP‐12 promoter activity in SMCs. An electrophoretic mobility shift assay confirmed the AP‐1 binding activity in SMCs and showed that the protein bound to the AP‐1 site consisted predominantly of c‐Jun, JunD and Fra‐1. Two structurally different inhibitors of phosphatidylinositol 3‐kinase, wortmannin and LY294002, inhibited MMP‐12 transcriptional activity and AP‐1 binding.

Conclusion: These results indicated the expression of MMP‐12 in vascular SMCs and showed that the MMP‐12 gene expression was dependent on the AP‐1 binding activity. Phosphatidylinositol 3‐kinase signalling may be involved in MMP‐12 transcriptional activation through AP‐1 binding activity.
The ruby mines of Mogok
Authors: Waltham Tony
Published: March 2003

The world's finest rubies all come from the metamorphic rocks of Mogok, in Myanmar. Traditional methods of mining, with little mechanization, are still used; they work best in digging the gemstones out of narrow calcite veins and thin beds of buried placer gravel.
Flash flood at Sólheimajökull heralds the reawakening of an Icelandic subglacial volcano
Authors: Russell Andrew J. , Tweed Fiona S. , Knudsen Óskar
Published: March 2003

An unpredicted sudden outburst flood from Sólheimajökull, Southern Iceland, in July 1999 may herald a major subglacial volcanic eruption beneath Mýrdalsjökull ice cap.
Lincolnshire – gaps and more gaps
Authors: Straw Allan
Published: March 2003

The history of the possible flows of rivers through the Lincoln and Ancaster Gaps, and other gaps in Lincoln Edge and the Lincolnshire Wolds, is far from settled; puzzles remain. Quaternary geology influenced the geomorphological phenomena above.
Very high resolution 3D marine seismic data processing for geotechnical applications
Authors: Marsset  , Missiaen  , De Roeck  , Noble  , Versteeg  , Henriet
Published: March 2003

The processing of a small‐scale, very high resolution (VHR) shallow marine 3D data volume is described. The data were acquired over a small clay diapir, on the river Schelde, in 1990. Using an array of 12 dual‐channel microstreamers towed from a catamaran, a network of 1 m × 1 m bins could be produced over an area of 50 m × 180 m (< 100 m penetration). Positioning was performed with an auto‐tracking laser ranging system, assuring an absolute accuracy of a few decimetres.

Preliminary processing steps included tidal correction and multiple removal. An important step concerned the application of 3D prestack Kirchhoff depth migration. Indeed this processing allows easy handling of the exact positions of both source and receivers as the latter were not set out on a conventional regular grid due to navigation difficulties. Because of the restricted data volume and the more‐or‐less stratified medium, a 1D velocity model could be used. This allowed a considerable simplification of the migration algorithm, based on summation. Traveltimes were calculated only once, using a 2D time grid with 0.1 m intervals.

This migration method proved very efficient, greatly improving the seismic image, and involved only limited CPU time on a small computer (Sparc 10 workstation). It clearly demonstrates that advanced seismic processing can form a valuable and economically feasible tool for VHR shallow subsurface 3D seismics, as long as the velocity field is not too complex. This method should therefore no longer be restricted to large computers and hydrocarbon exploration, but should also become a routine for VHR 3D shallow seismic work.
Use of magnetotelluric signals from 50 Hz power lines for resistivity mapping of geothermal fields in New Zealand
Authors: Risk  , Caldwell  , Bibby
Published: March 2003

Electromagnetic (EM) fields radiated from the transmission lines of the New Zealand electricity grid have been digitally recorded at test sites near the Tokaanu geothermal field. Amplitudes and phases of the 50 Hz signals (and the odd harmonics up to 450 Hz) were determined using a software implementation of a phase‐locked filter. These data were then analysed to determine the components of the magnetotelluric impedance tensor and the corresponding apparent resistivities and phases. At most sites, there was sufficient variation in the elliptical polarization of the EM fields to enable the impedance tensors to be determined in full. Sites where the EM data had been affected by near‐source effects were identified by having large vertical magnetic field components and by being closer to a power line source than about 3–5 skin depths. With the test measurements, the north‐eastern part of the Tokaanu geothermal field was successfully delineated giving low resistivities (< 5 Ωm) on the inside and higher resistivities on the outside, in agreement with the Schlumberger array DC apparent resistivities. The small size of the 50 Hz magnetotelluric equipment and its portable nature make this method of resistivity measurement suitable for reconnaissance resistivity mapping in places with difficult access.
Short note on electrode charge‐up effects in DC resistivity data acquisition using multi‐electrode arrays
Authors: Dahlin Torleif
Published: March 2003

The measurement sequence used in DC resistivity data using multi‐electrode arrays should be carefully designed so as to minimize the effects of electrode charge‐up effects. These effects can be some orders of magnitude larger than the induced signal and remain at significant levels for tens of minutes. Even when using a plus‐minus‐plus type of measurement cycle, one should avoid making potential measurements with an electrode that has just been used to inject current, as the decay immediately after current turn‐off is clearly non‐linear.
Electrical resistivity tomography to investigate geological structures of the earth's upper crust
Authors: Storz  , Storz  , Jacobs
Published: March 2003

It is important to have detailed knowledge of the electrical properties of the earth's crust in order to recognize geological structures and to understand tectonic processes. In the area surrounding the German Continental Deep Drilling Project (KTB), we have used DC dipole–dipole soundings to investigate the electrical conductivity distribution down to a depth of several kilometres. We have adapted the electrical resistivity tomography (ERT) technique, a well‐established near‐surface method, to large‐scale experiments. Independent transmitting and receiving units were used to realize the concept of simultaneous multichannel registration of the scalar electrical potential at 44 dipoles. The measured data yielded apparent resistivities which were inverted to a 2D resistivity model ranging from the surface down to a depth of 4 km. Two highly conductive structures with steep inclination were detected. They are expected to be major fault zones embedded in a metamorphic body. The rather low resistivity (ρ < 10 Ωm) can be explained by the existence of graphitic minerals and/or electrolytic fluids.
Selection of the wavenumbers k using an optimization method for the inverse Fourier transform in 2.5D electrical modelling
Authors: Xu Shi‐zhe , Duan Ben‐chun , Zhang Da‐hai
Published: March 2003

An optimization method is used to select the wavenumbers k for the inverse Fourier transform in 2.5D electrical modelling. The model tests show that with the wavenumbers k selected in this way the inverse Fourier transform performs with satisfactory accuracy.
The effect of subsurface pipes on apparent‐resistivity measurements
Authors: Vickery Anna C. , Hobbs Bruce A.
Published: March 2003

Subsurface conducting pipes can be either a target or a noise source in geophysical surveying. Their effect as a noise source in resistivity imaging can be so severe as to render the geophysical data uninterpretable. A method is developed here for identifying, locating and removing the effects of subsurface conducting pipes from image data, thus revealing the background resistivity structure.

A previously known analytic solution for the potential distribution produced by current injection in a uniform half‐space containing an infinitely long conducting cylinder is used to calculate apparent resistivities corresponding to electrode arrays on the surface of the half‐space. Most results concern the Wenner array and an examination is made of the effects produced by varying the electrode spacing and the depth, size and orientation of the pipe with respect to the array. A method is developed for locating pipes in resistivity image data by cross‐correlation of the analytic solution with the measured field data. Pipe effects are then removed by multiplying each datum point in the measurements by the reciprocal of the corresponding value in the analytic solution. The success of the method is demonstrated by applications to synthetic data sets involving one or two pipes embedded in non‐uniform half‐spaces.

In further examples, the method is applied to some measured resistivity images from an ex‐industrial site (a former oil distribution terminal), where an electromagnetic survey had previously revealed a labyrinth of underground pipes. The method is shown to be successful in removing the effects of the pipes to reveal the underlying geology.
A comparison of aeromagnetic levelling techniques with an introduction to median levelling
Authors: Mauring Eirik , Beard Les P. , Kihle Ola , Smethurst Mark A.
Published: March 2003

Aeromagnetic data collected in areas with severe diurnal magnetic variations (auroral zones) are difficult to level. This paper describes levelling of an aeromagnetic survey where such conditions prevail, and where sophisticated levelling techniques are needed. Corrections based on piecewise low‐order polynomial functions are often used to minimize mis‐ties in aeromagnetic data. We review this technique and describe similar mis‐tie fitting methods based on low‐pass filter levelling, tensioned B‐spline levelling and median levelling. It is demonstrated that polynomial levelling, low‐pass filter levelling and tensioned B‐spline levelling depend on the careful editing of outlying mis‐ties to avoid the introduction of false anomalies. These three techniques are equally efficient at removing level errors. Median levelling also removes level errors efficiently, but it is more robust in the sense that mis‐tie editing is not required. This is due to the inherent noise‐removal capabilities of the median filter. After mis‐tie editing, the total field anomalies of the other three techniques closely resemble the unedited median‐levelled total field anomaly.
Uncertainties in quantitative time‐lapse seismic analysis
Authors: Landrø Martin
Published: March 2003

Most seismic time‐lapse studies so far have been of a qualitative nature. Identification of areas with minor or no seismic changes has been used to plan new infill drilling targets. Increased accuracy in seismic acquisition methods, in both conventional streamer surveys and newer methods such as multicomponent sea‐bed seismic and permanent sensors, opens possibilities for the next step: quantitative time‐lapse analysis. Quantitative methods here mean the estimation of, for instance, a change in fluid saturation from 20% water to 90% water or the estimation of a pore pressure change of 5 MPa. Explicit expressions for the uncertainties associated with estimated changes in, for instance, reservoir pressure and fluid saturation are derived. These formulae can be used to compare relative uncertainties between estimated parameters as well as to identify the critical factors in various estimation techniques. The importance of accurate rock physics input, as well as that of highly repeatable time‐lapse seismic data, is emphasized. Furthermore, uncertainty analysis can be used to find optimal weight factors when the same parameter (e.g. saturation change) is estimated by two or three different techniques.
Deep structure of the northeastern margin of the Parnaiba Basin, Brazil, from magnetotelluric imaging
Authors: Mohamed Adel K. , Meju Maxwell A. , Fontes Sergio L.
Published: March 2003

The magnetotelluric (MT) method has been applied to the determination of the deep resistivity structure of the northeastern margin of the Parnaiba Basin. Transient electromagnetic (TEM) and MT data were collected in early 1999 along a 95 km long N–S line, extending from the coast across the projected subcrop position of a discontinuous fault found to the west of the study area that is believed to be a possible basin‐bounding fault. The MT data were processed to yield the TE‐ and TM‐mode responses and then corrected for static shift using central‐loop and single‐loop TEM data, respectively. Regularized 2D MT inversion was subsequently undertaken using a structured initial model with the near‐surface constrained by TEM inversion results. As a consistency check, we performed another set of 2D inversions using different smooth initial models. The various optimal 2D inversion models show clearly the presence of a major basement trough, over 2 km deep, located about 70 km from the coast. We interpret it as possibly marking the main basin margin and suggest that it may have implications for groundwater resource development in the area.
Wave velocities and attenuation of shaley sandstones as a function of pore pressure and partial saturation
Authors: Pham Nam H. , Carcione José M. , Helle Hans B. , Ursin Bjørn
Published: March 2003

We obtain the wave velocities and quality factors of clay‐bearing sandstones as a function of pore pressure, frequency and partial saturation. The model is based on a Biot‐type three‐phase theory that considers the coexistence of two solids (sand grains and clay particles) and a fluid mixture. Additional attenuation is described with the constant‐Q model and viscodynamic functions to model the high‐frequency behaviour. We apply a uniform gas/fluid mixing law that satisfies the Wood and Voigt averages at low and high frequencies, respectively. Pressure effects are accounted for by using an effective stress law. By fitting a permeability model of the Kozeny– Carman type to core data, the model is able to predict wave velocity and attenuation from seismic to ultrasonic frequencies, including the effects of partial saturation. Testing of the model with laboratory data shows good agreement between predictions and measurements.
Organic matter accumulation following fires in a moorland soil chronosequence
Authors: Haslam S. F. I. , Chudek J. A. , Goldspink C. R. , Hopkins D. W.
Published: March 2003

Severe fires in 1957 and 1976 removed the vegetation and soil organic matter from the litter layers and organic horizons of soils at two adjacent moorland sites leaving exposed the uppermost mineral horizon of the soil. In the period since, plant recolonization and soil organic matter reaccumulation have occurred to give a chronosequence. Assuming no major changes in the carbon and nitrogen content of the unburned soil since 1957, the rates of accumulation of soil C and N were estimated to be 0.035 kg C m–2 y–1 and 0.001 kg N m–2 y–1 over the first 19 years, and 0.50 kg C m–2 y–1 and 0.023 kg N m–2 y–1 over the period from 19 to 38 years after burning. Solid‐state 13C NMR (cross‐polarization, magic angle spinning 13C nuclear magnetic resonance spectroscopy) showed that the ratio of alkyl‐ and methyl‐C‐to‐O‐alkyl‐C increased with stage of decomposition and in the unburned soil with decreasing particle‐size. For the organic matter that had reaccumulated in the 1957‐burned soil, the alkyl‐C‐to‐O‐alkyl‐C ratio of the > 2000 μm and 2000–250 μm particle‐size fractions were greater than those of the corresponding size fractions from the unburned soil, indicating that the reaccumulated soil organic matter was subject to decomposition but limited fragmentation or comminution.
Biomass and compositional changes occur in chalk grassland turves exposed to elevated CO2 for two seasons in FACE
Authors: Warwick Kevin Robert , Taylor Gail , Blum Herbert
Published: March 2003

Artificial turves composed of 7 chalk grassland species (Festuca ovina L.; Briza media L.; Bromopsis erecta (Hudson) Fourr.; Plantago media L.; Sanguisorba minor Scop.; Anthyllis vulneraria L. and Lotus corniculatus L.) were grown from seed and exposed to two seasons of elevated (600 μmol mol–1) and ambient (340 μmol mol–1) CO2 concentrations in free air CO2 enrichment (ETH‐FACE, Zurich). The turves were clipped regularly to a height of 5 cm and assessed for above ground biomass production and relative abundance based on accumulated clipped dry biomass as well as by point quadrat recording. Below ground biomass production was assessed with root in‐growth bags during the second season of growth.

Increases in total biomass (> 30%) were noted in elevated CO2, but the differences did not become significant until the second season of growth. Individual species’ biomass varied in response to elevated CO2, with significant increases in biomass in elevated CO2 turves for both legume species, and no significant CO2 effect on S. minor or P. media. An initial positive CO2 effect on biomass of combined grass species was reversed by the end of the experiment with less biomass and a significantly smaller proportion of total biomass present in elevated CO2, which was attributed primarily to changes in proportion of F. ovina.

Species relative abundance was significantly affected by elevated CO2 in the final 4 of the 6 clip events, with the legume species increasing in proportion at the expense of the other species, particularly the grasses. Root length and dry weight were both significantly increased in elevated CO2 (77% and 89%, respectively), and these increases were greater than increases in shoot biomass (36%) from the same period.

Species responses to elevated CO2, within the model community, were not consistent with predictions made from data on individual species, leading to the conclusion that responses to elevated CO2, at the community level, and species within the community level, are the result of direct physiological effects and indirect competitive effects. These conclusions are discussed with respect to the ecological responses of natural communities, and the chalk grassland community in particular, to elevated CO2.
Recent Juniperus occidentalis (Western Juniper) expansion on a protected site in central Oregon
Authors: Knapp PauL. A. , Soulé Peter T.
Published: March 2003

The expansion of Juniperus occidentalis (western juniper) has been extensive in the last century, and increases in density and cover have been linked with the indirect effects of domestic livestock grazing (i.e. cessation of periodic fires, increases of nurse‐plant sites), and more favourable climatic conditions. In this study, we document changes in vegetation (including J. occidentalis) in central Oregon over a 23‐year period and relate these changes to their probable causes. In June 1995 we returned to the Horse Ridge Research Natural Area (HRRNA), a site that has a history of minimal anthropogenic impacts, to replicate a 1972 vegetation survey. Using the canopy‐intercept method, line intercept method, and aerial photography analysis to measure herbaceous cover, shrub cover and tree cover, respectively, we found significant changes had occurred in the 23‐year period between studies. Relative changes of tree, shrub, and perennial herbaceous cover were 59%, 7%, and – 38%, respectively. Relative increases in J. occidentalis density, as measured by the number of clumps and the number of stems, were 37% and 53%, respectively. Mean maximum height of J. occidentalis had increased by 10%. We examined the role of potentially confounding influences (e.g. fire, grazing, pathogens, climatic variability) and found that none of the traditional mechanisms implicated in J. occidentalis expansion adequately explained the observed changes. We suggest that the role of biological inertia of both anthropogenic and natural means may have had a profound effect on the J. occidentalis ecology of HRRNA.
Effects of soil warming during spring on photosynthetic recovery in boreal Norway spruce stands
Authors: Bergh Johan , Linder SunE.
Published: March 2003

The effect of soil thawing and soil temperature on postwinter recovery of photosynthetic capacity was studied, during late spring and early summer, in Norway spruce stands in northern Sweden. Soil temperature was manipulated by means of buried heating cables. The warming treatment was applied to stands with low (natural) and high (fertilized) availability of nutrients. Soil thawing, expressed as water availability, was followed by means of sapflow in stems, and shoot water potentials. The recovery of photosynthetic capacity was assessed by measuring the rate of light‐saturated photosynthesis (Amax), and maximum photochemical efficiency of photosystem II in detached shoots, and chlorophyll a fluorescence. Accumulation of starch reserves in the needles was followed as an independent indicator of photosynthetic performance in situ. Snowmelt and soil thawing occurred more than one month earlier in heated than in unheated plots. This was expressed both as sapflow and as differences in shoot water potential between treatments. During May, the rates of Amax were significantly higher on heated than on control plots. The effect of soil warming on Amax was, however, not reflected in chlorophyll fluorescence or needle starch content. The time course of the recovery of photosynthetic capacity was mainly controlled by mean air temperature and by the frequency of severe night frosts, and to a lesser extent by earlier soil thawing and higher soil temperatures.
A test of the effect of supplemental UV‐B radiation on the common frog, Rana temporaria L., during embryonic development
Authors: Cummins Clive P. , Greenslade Peter D. , Mcleod Andrew R.
Published: March 2003

The release of certain man‐made chemicals has led to recurrent, seasonal destruction of ozone in the upper atmosphere, allowing more solar radiation in the UV‐B waveband to reach the Earth. Consequently, many amphibians may suffer increased exposure to UV‐B at various stages in their lives. Embryonic stages of species which spawn in the spring, in shallow, open water, are at high risk of increased exposure. We exposed newly fertilized eggs of one such species, Rana temporaria L., to sunlight with and without supplemental UV‐B. We used outdoor arrays of lamps to simulate the increase in UV‐B which might result from previously documented ozone depletion. From immediately after fertilization to when hatchlings began feeding, ambient solar UV‐B, weighted for DNA‐damaging potential, was supplemented by ≈ 81% in 1995 and 113% in 1996. These levels of supplementation approximated the increase in solar UV‐B expected to result from losses of 21% and 25%, respectively, of the total amount of ozone in the atmospheric column, relative to pre‐ozone‐depletion values. We found no evidence that these additions of UV‐B radiation increased the incidence of mortality or overt developmental abnormality among embryos. We stress the need for appropriate dosimetry in studies of effects of UV‐B on organisms.
Acclimation of respiration to temperature and CO2 in seedlings of boreal tree species in relation to plant size and relative growth rate
Authors: Tjoelker MarK. G. , Oleksyn Jacek , Reich Peter B.
Published: March 2003

The role of acclimation of dark respiration to temperature and CO2 concentration and its relationship to growth are critical in determining plant response to predicted global change. We explored temperature acclimation of respiration in seedlings of tree species of the North American boreal forest. Populus tremuloides, Betula papyrifera, Larix laricina, Pinus banksiana, and Picea mariana plants were grown from seed in controlled‐environments at current and elevated concentrations of CO2 (370 and 580 μmol mol–1) in combination with three temperature treatments of 18/12, 24/18, and 30/24 °C (light/dark period). Specific respiration rates of roots and shoots acclimated to temperature, damping increases in rates across growth‐temperature environments compared to short‐term temperature responses. Compared at a standard temperature, root and shoot respiration rates were, on average, 40% lower in plants grown at the highest compared to lowest growth temperature. Broad‐leaved species had a lower degree of temperature acclimation of respiration than did the conifers. Among species and treatment combinations, rates of respiration were linearly related to size and relative growth rate, and relationships were comparable among growth environments. Specific respiration rates and whole‐plant respiratory CO2 efflux as a proportion of daily net CO2 uptake increased at higher growth temperatures, but were minimally affected by CO2 concentration. Whole‐plant specific respiration rates were two to three times higher in broad‐leaved than coniferous species. However, compared to faster‐growing broad‐leaved species, slower‐growing conifers lost a larger proportion of net daily CO2 uptake as respiratory CO2 efflux, especially in roots. Interspecific variation in acclimation responses of dark respiration to temperature is more important than acclimation of respiration to CO2 enrichment in modifying tree seedling growth responses to projected increases in CO2 concentration and temperature.
Interactions of tropospheric CO2 and O3 enrichments and moisture variations on microbial biomass and respiration in soil
Authors: Islam K. R. , Mulchi C. L. , Ali A. A.
Published: March 2003

Soil microbial biomass C (Cmic) is a sensitive indicator of trends in organic matter dynamics in terrestrial ecosystems. This study was conducted to determine the effects of tropospheric CO2 or O3 enrichments and moisture variations on total soil organic C (Corg), mineralizable C fraction (CMin), Cmic, maintenance respiratory (qCO2) or Cmic death (qD) quotients, and their relationship with basal respiration (BR) rates and field respiration (FR) fluxes in wheat‐soybean agroecosystems. Wheat (Triticum aestivum L.) and soybean (Glycine max. L. Merr) plants were grown to maturity in 3‐m dia open‐top field chambers and exposed to charcoal‐filtered (CF) air at 350 μL CO2 L−1; CF air + 150 μL CO2 L−1; nonfiltered (NF) air + 35 nL O3 L−1; and NF air + 35 nL O3 L−1 + 150 μL CO2 L−1 at optimum (− 0.05 MPa) and restricted soil moisture (− 1.0 ± 0.05 MPa) regimes. The + 150 μL CO2 L−1 additions were 18 h d−1 and the + 35 nL O3 L−1 treatments were 7 h d−1 from April until late October. While Corg did not vary consistently, CMin, Cmic and Cmic
fractions increased in soils under tropospheric CO2 enrichment (500 μL CO2 L−1) and decreased under high O3 exposures (55 ± 6 nL O3 L−1 for wheat; 60 ± 5 nL O3 L−1 for soybean) compared to the CF treatments (25 ± 5 nL O3 L−1). The qCO2 or qD quotients of Cmic were also significantly decreased in soils under high CO2 but increased under high O3 exposures compared to the CF control. The BR rates did not vary consistently but they were higher in well‐watered soils. The FR fluxes were lower under high O3 exposures compared to soils under the CF control. An increase in Cmic or Cmic
fractions and decrease in qCO2 or qD observed under high CO2 treatment suggest that these soils were acting as C sinks whereas, reductions in Cmic or Cmic
fractions and increase in qCO2 or qD in soils under elevated tropospheric O3 exposures suggest the soils were serving as a source of CO2.
Yield response of Lolium perenne swards to free air CO2 enrichment increased over six years in a high N input system on fertile soil
Authors: Daepp Markus , Suter Daniel , Almeida José P. F. , Isopp Hubert , Hartwig Ueli A. , Frehner Marco , Blum Herbert , Nösberger Josef , Lüscher Andreas
Published: March 2003

After a step increase in the atmospheric partial pressure of CO2 (pCO2), the availability of mineral N may be insufficient to meet the plant's increased demand for N. Over time, however, the ecosystem may adapt to the new conditions, and a new equilibrium may be established in the fluxes of C and N. This would result in a higher dry mass (DM) yield response of the plants to elevated pCO2.

The effect of elevated atmospheric pCO2 (60 Pa pCO2) was studied in Lolium perenne L. swards with two N fertilization treatments (14 and 56 g m−2 y−1) in a six‐year FACE (Free Air Carbon dioxide Enrichment) experiment. In the high N treatment, the input of N with fertilizer considerably exceeded the export of N with the harvested plant material in both CO2 treatments leading to an apparent net input of N into the ecosystem. Accordingly, the proportion of harvested N derived from 15N labelled fertilizer N, applied throughout the experiment (< 6 years), increased over the years. Under these high N conditions, the annual DM yield response of the Lolium perenne sward to elevated pCO2 increased (from 7% in 1993 to 25% in 1998). In parallel, the response of N yield to elevated pCO2 increased, and the initially negative effect of elevated pCO2 on specific leaf area (SLA) disappeared. The high N input system seemed to overcome in part an initially limiting effect of N on the yield response to elevated pCO2 within a few years. In contrast, there was no apparent net input of N into the ecosystem in the low N treatment, because N fertilization just compensated the export of N with the harvested plant material. Accordingly, the proportion of harvested N yield, derived from fertilizer N, which was applied throughout the experiment, remained low. At low N, the availability of mineral N strongly limited plant growth and yield production in both CO2 treatments; the low yields of DM and N, the low concentration of N in the plant material, and the low SLA reflected this. Although the plants grew under the same environmental conditions and the same management treatment as plants in the high N treatment, the response of DM yields to elevated pCO2 in the low N treatment remained weak throughout the experiment (5% in 1993 and 9% in 1998). The results are discussed in the context of the sizes of the different N pools in the soil, the allocation of N within the plant and the possible effects on temporal immobilization, and the availability of mineral N for yield production as affected by elevated pCO2 and N fertilization.
The energy and water balance of high‐latitude wetlands: controls and extrapolation
Authors: Rouse Wayne R.
Published: March 2003

This paper examines, with examples, controls on the energy and water balance of northern wetlands. Most wetlands have organic soils and are thus peatlands. High‐latitude wetlands are underlain by ice‐rich permafrost, which helps maintain wetland systems and also imparts special characteristics to their energy and water balances. In North America, components of the radiation balance decrease linearly poleward, whereas the poleward rate of decrease of temperature and precipitation lessens. During the four‐month summer of a high subarctic wetland, net radiation is large and the latent heat flux dominates the energy cycle. The ground heat flux is substantial, especially in early summer, when the ice‐rich ground is rapidly thawing. Winter begins in October and heat loss from the ground approximately balances negative net radiation. The summer energy and water balance differs among terrain units. Large shallow lakes exhibit larger net radiation and potential evaporation rates than surrounding wetland surfaces which, in turn, exhibit substantially larger magnitudes than dryland terrain. There is a variable withdrawal rate of soil moisture depending on soil types and plant rooting characteristics, which influences the actual evaporation from the surface. Synoptic weather systems play a major role in day‐to‐day energy and water responses to climate forcing. Long‐term modelling of the water balance of a wetland shows year‐to‐year persistence in climatic patterns. Although net radiation, temperature and precipitation all influence the magnitudes of water deficit, the precipitation inputs are of paramount importance. Our ability to fully understand, model and extrapolate, in space and time, the major controls on the surface climate of wetlands, is evaluated. Spatial extrapolation is seen to be more readily achieved than temporal extrapolation.
Integrated models of livestock systems for climate change studies. 1. Grazing systems
Authors: Parsons D. J. , Armstrong A. C. , Turnpenny J. R. , Matthews A. M. , Cooper K. , Clark J. A.
Published: March 2003

The potential impact of climate change by the year 2050 on British grazing livestock systems is assessed through the use of simulation models of farming systems. The submodels, consisting of grass production, livestock feeding, livestock thermal balance, the thermal balance of naturally ventilated buildings and a stochastic weather generator, are described. These are integrated to form system models for sheep, beef calves and dairy cows. They are applied to scenarios representing eastern (dry) lowlands, western (wet) lowlands and uplands. The results show that such systems should be able to adapt to the expected climatic changes. There is likely to be a small increase in grass production, possibly allowing an increase in total productivity in some cases.
Modelling respiration of vegetation: evidence for a general temperature‐dependent Q10
Authors: Tjoelker Mark G. , Oleksyn Jacek , Reich Peter B.
Published: March 2003

Temperature responses of rates of respiratory CO2 efflux from plants, soils, and ecosystems are frequently modelled using exponential functions with a constant Q10 near 2.0 (fractional change in rate with a 10 °C increase in temperature). However, we present evidence that Q10 declines with short‐term increases in temperature in a predictable manner across diverse plant taxa. Thus, models using a constant Q10 are biased, and use of a temperature‐corrected Q10 may improve the accuracy of modelled respiratory CO2 efflux in plants and ecosystems in response to temperature and predicted global climate changes.
Integrated models of livestock systems for climate change studies. 2. Intensive systems
Authors: Turnpenny J. R. , Parsons D. J. , Armstrong A. C. , Clark J. A. , Cooper K. , Matthews A. M.
Published: March 2003

The potential impact of climate change by the year 2050 on intensive livestock systems in Britain is assessed through the use of simulation models of farming systems. The submodels comprise livestock feeding, livestock thermal balance and the thermal balance of controlled environment buildings and a stochastic weather generator. These are integrated to form system models for growing pigs and broiler chickens. They are applied to scenarios typical of SE England, which is the warmest region of the country and represents the worst case. For both species the frequency of severe heat stress is substantially increased, with a consequent risk of mortality. To offset this, it would be necessary to reduce stocking densities considerably, or to invest in improved ventilation or cooling equipment. Other effects on production are likely to be small.
Elevated carbon dioxide and irrigation effects on water stable aggregates in a Sorghum field: a possible role for arbuscular mycorrhizal fungi
Authors: Rillig Matthias C. , Wright Sara F. , Kimball Bruce A. , Pinter Paul J. , Wall Gary W. , Ottman Michael J. , Leavitt Steve W.
Published: March 2003

While soil biota and processes are becoming increasingly appreciated as important parameters for consideration in global change studies, the fundamental characteristic of soil structure is a neglected area of research. In a sorghum [Sorghum bicolor (L.) Moench] field experiment in which CO2[supplied using free‐air CO2 enrichment (FACE) technology] was crossed factorially with an irrigation treatment, soil aggregate (1–2 mm) water stability increased in response to elevated CO2. Aggregate water stability was increased by 40% and 20% in response to CO2, at ample and limited water supply treatments, respectively. Soil hyphal lengths of arbuscular mycorrhizal fungi (AMF) increased strongly (with a threefold increase in the dry treatment) in response to CO2, and the concentrations of one fraction (easily extractable glomalin, EEG) of the AMF‐produced protein glomalin were also increased. Two fractions of glomalin, and AMF hyphal lengths were all positively correlated with soil aggregate water stability. The present results further support the hypothesis that AMF can become important in global change scenarios. Although in this field study a causal relationship between hyphal length, glomalin and aggregate stability cannot be demonstrated, the present data do suggest that AMF could mediate changes in soil structure under elevated CO2. This could be of great importance in agricultural systems threatened by erosional soil loss.
Species‐specific responses of plant communities to altered carbon and nutrient availability
Authors: Joel Geeske , Chapin F. Stuart , Chiariello Nona R. , Thayer Susan S. , Field Christopher B.
Published: March 2003

In a field microcosm experiment, species‐specific responses of aboveground biomass of two California annual grassland communities to elevated CO2 and nutrient availability were investigated. One community grows on shallow, nutrient‐poor serpentine‐derived soil whereas the other occurs on deeper, modestly fertile sandstone/greenstone‐derived substrate. In most species, CO2 effects did not appear until late in the growing season, probably because the elevated CO2 increased water‐use‐efficiency easing, the onset of the summer drought. Responses of aboveground biomass to elevated CO2 differed depending on nutrient availability. Similarly, biomass responses to nutrient treatments differed depending on the CO2 status. For the majority of the species, production increased most under elevated CO2 with added nutrients (N,P,K, and micro nutrients). Some species were losers under conditions that increased overall community production, including Bromus hordeaceus in the serpentine community (negative biomass response under elevated CO2) and Lotus wrangelianus in both communities (negative biomass response with added nitrogen). Treatment and competitive effects on species‐specific biomass varied in both magnitude and direction, especially in the serpentine community, significantly affecting community structure. Individual resource environments are likely to be affected by neighbouring plants, and these competitive interactions complicate predictions of species' responses to elevated CO2.