bluuebunny/crossref_metadata_2025 huggingface dataset:
Movement of flathead catfish in the Missouri River: examining opportunities for managing river segments for different fishery goals
Authors: Travnichek V. H.
Published: December 2004

The dispersal patterns of 2939 flathead catfish, Pylodictis olivaris (Rafinesque), were determined within a 90‐km section of the Missouri River, USA. Fish were captured by electric fishing and tagged in early June each year from 1999 through 2001. Dispersal was determined via angler tag returns between 1999 and 2001 or by subsequent recapture during sampling 1 or 2 years after initial tagging (June 2000 or 2001). Dispersal was localised for the majority of the 370 flathead catfish recaptured in the Missouri River. Over 80% of recaptures were within 5 km of tagging location, and 94% were within 20 km of tagging location. Maximum displacement was 160 km. To examine differences in movement patterns of various sized fish, flathead catfish were placed into one to three size groups (305–380, 381–507, or ≥508 mm). A significant difference (P < 0.001) was detected in dispersal patterns among the three size groups; the largest size group moved greater distances than either of the smaller size groups. Movements average 4.5, 5.6 and 12.6 km for small, medium, and large size classes, respectively. Dispersal movements of flathead catfish in the Missouri River appeared to be localised, suggesting that different sections of the Missouri River could be managed for different fishery goals for flathead catfish to accommodate a variety of angler types and desires.
Distribution and abundance of overwintering Calanus finmarchicus in the Faroe–Shetland Channel
Authors: Heath M.R. , Jónasdóttir S.H.
Published: December 2004

The distribution and abundance of overwintering Calanus finmarchicus in the Faroe–Shetland Channel was studied during December 1994 and January 1995. Maximum abundance of animals in the Channel was approximately 50 000 m−2, with a peak concentration of 627 m−3 at a depth of 930 m. Copepodite stages IV and V accounted for > 98% of the population. A clear association was found between the horizontal and vertical distribution of animals and the Arctic water masses in the bottom of the Faroe–Shetland Channel. The Wyville–Thomson Ridge formed a barrier to the southern distribution of Arctic waters and the abundance of overwintering C. finmarchicus was 25 times lower to the south of the Ridge than to the north. Spatial variability in lipid content and composition indicated that overwintering C. finmarchicus in the southern Norwegian Sea were in poorer condition with respect to wax ester content, and in a more advanced state of emergence from overwintering, than the animals within the Channel. The overwintering stock in the Channel probably originated from the Norwegian Sea or from north of the Faroe Islands. The Faroe–Shetland Channel is an important source of animals advected into the northern North Sea in the spring (March/April). The population abundance in the Faroe–Shetland Channel was estimated to be 4.5 × 1014 individuals, which is more than adequate to account for the mean concentration of adult stages observed in the northern North Sea in April.
The ascent migration of Calanus finmarchicus from overwintering depths in the Faroe–Shetland Channel
Authors: Heath M.R.
Published: December 2004

The Faroe–Shetland Channel is an important overwintering area for the copepod Calanus finmarchicus in the north‐east Atlantic. Stage V copepodites descend to depths of greater than 600 m, where they remain in an arrested development state (diapause) until the following spring. The ascent of the copepods back to the surface waters in the spring was investigated by six surveys in the Faroe–Shetland Channel between October 1993 and May 1995. In February, the first animals emerged from diapause and moulted to become stage VI males; these ascended to depths of 300–500 m. Females constituted a higher proportion of animals that emerged later in the season and these ascended through the layer of males, presumably mating on the way, and proceeded to the upper 100 m to begin spawning in March. Emergence was not synchronous in the population, and was estimated to occur over a 60–70 day period beginning around 10 February. The mean ascent rate of individuals was estimated to be 15–20 m day–1, so that for any individual the ascent from a mean overwintering depth of 800 m to a depth of 100 m took between 35 and 47 days. The ascent migration resulted in the mass transfer of the C. finmarchicus stock from its overwintering habitat in the cold southerly flowing Norwegian Sea Deep Water of Arctic origin to warm northerly flowing Atlantic water masses. The extent of asynchrony suggests that emergence is probably not triggered by environmental cues. An alternative hypothesis for regulation of the life cycle is proposed that involves reduced development rates during the winter.
Climate change and abundance of the Atlantic‐Iberian sardine (Sardina pilchardus)
Authors: Guisande C. , Vergara A. R. , Riveiro I. , Cabanas J. M.
Published: December 2004

Climatic warming is affecting oceanic circulation patterns in coastal upwelling areas, but the impact of this climatic change on pelagic fish populations remains unclear. From juvenile landings collected over 38 years, the thresholds of environmental factors were determined that limited the optimal environmental window (OEW) for sardine (Sardina pilchardus recruitment success in the northwestern Iberian peninsula. The environmental factors considered were: water column stability in February, offshore water transport in March–April (QxMA), upwelling intensity in the preceding year from May to August (QxMJJA), and the winter North Atlantic Oscillation (NAO) index. From 1875 to the mid‐1920s, the mean number of years within the OEW was relatively constant. However, since the mid‐1920s, there have been oscillations and alternating decades with high and low number of years within the OEW, which were related to oscillations in sardine landings. From 1906 to 2000, there were four record, low sardine catches in the 1920s, 1950s, 1970s and 1990s, related to a high number of successive years with prevailing conditions out of the OEW. From 1875 to the present, a high year‐to‐year variation of the NAO, QxMJJA and water stability in February was observed, although with mean values usually within the OEW. The collapse in the 1950s was related, partly, to successive years with low QxMJJA. Successive years with high NAO values may be related to the collapse of the sardine fishery in the 1990s. QxMA has been the most significant factor controlling SRS in this area, being the factor related to the low catches observed in the 1920s, 1950s and 1970s. Water stability was not responsible for any of the collapses observed, but since the 1920s, there has been a significant trend toward decreasing water column stability before the onset of the spring bloom.
Water quality assessment using diatom assemblages and advanced modelling techniques
Authors: Gevrey Muriel , Rimet Frédéric , Park Young Seuk , Giraudel Jean‐Luc , Ector Luc , Lek Sovan
Published: December 2004

1. Two types of artificial neural networks procedures were used to define and predict diatom assemblage structures in Luxembourg streams using environmental data.

2. Self‐organising maps (SOM) were used to classify samples according to their diatom composition, and multilayer perceptron with a backpropagation learning algorithm (BPN) was used to predict these assemblages using environmental characteristics of each sample as input and spatial coordinates (X and Y) of the cell centres of the SOM map identified as diatom assemblages as output. Classical methods (correspondence analysis and clustering analysis) were then used to identify the relations between diatom assemblages and the SOM cell number. A canonical correspondence analysis was also used to define the relationship between these assemblages and the environmental conditions.

3. The diatom‐SOM training set resulted in 12 representative assemblages (12 clusters) having different species compositions. Comparison of observed and estimated sample positions on the SOM map were used to evaluate the performance of the BPN (correlation coefficients were 0.93 for X and 0.94 for Y). Mean square errors of 12 cells varied from 0.47 to 1.77 and the proportion of well predicted samples ranged from 37.5 to 92.9%. This study showed the high predictability of diatom assemblages using physical and chemical parameters for a small number of river types within a restricted geographical area.
Hydrological variability, organic matter supply and denitrification in the Garonne River ecosystem
Authors: Baker Michelle A. , Vervier Philippe
Published: December 2004

1. Groundwater nitrate contamination has become a worldwide problem as increasing amounts of nitrogen fertilisers are used in agriculture. Alluvial groundwater is uniquely juxtaposed between soils and streams. Hydrological connections among these subsystems regulate nutrient cycling.

2. We measured denitrification using an in situ acetylene‐block assay in a nitrate‐contaminated portion of the Garonne River catchment along a gradient of surface water–ground water mixing during high (snowmelt) and low flow.

3. During high flow (mid‐April to early June) the water table rose an average of 35 cm and river water penetrated the subsurface to a great extent in monitoring wells. Denitrification rates averaged 5.40 μgN2O L−1 min−1 during the high flow period, nearly double the average rate (2.91 μgN2O L−1 min−1) measured during base flow. This was driven by a strong increase in denitrification in groundwater under native riparian vegetation. Nitrate concentrations were significantly lower during high flow compared with base flow. Riparian patches had higher dissolved organic carbon concentrations that were more aromatic compared with the gravel bar patch closest to the river.

4. Multiple linear regression showed that the rate of denitrification was best predicted by the concentration of low molecular weight organic acids. These molecules are probably derived from decomposition of soil organic matter and are an important energy source for anaerobic respiratory processes like denitrification. The second best predictor was per cent surface water, reflecting higher denitrification rates during spring when hydrological connection between surface water and ground water was greatest.

5. Our results indicate that, while denitrification rates in Garonne River alluvium were spatially and temporally variable, denitrification was a significant NO3 sink during transport from the NO3‐contaminated floodplain to the river. DOC availability and river–floodplain connectivity were important factors influencing observed spatial and temporal patterns.
The influence of scale and geography on relationships between stream community composition and landscape variables: description and prediction
Authors: Townsend Colin R. , Dolédec Sylvain , Norris Richard , Peacock Kathi , Arbuckle Chris
Published: December 2004

SUMMARY 1. We analysed an existing database of macroinvertebrates and fish in the context of a newly established geographical information system (GIS) of physical features to determine the relationships between stream community composition and physical factors measured at three landscape scales – catchment, reach and bedform. Both an exploratory (concordance analysis) and a predictive (ausrivas) approach were used.

2. The environmental variables that most successfully accounted for variation in macroinvertebrate assemblages were mainly ‘natural’ and at the catchment‐scale (relief ratio, basin diameter, etc.) but the human‐induced physical setting of percentage of pasture in the riparian zone was also influential. For fish, ‘natural’ variables were also dominant, but these were mostly at the bedform or reach scales and land use featured strongly.

3. Geographic location accounted for some of the variation in invertebrate assemblages, partly because geography and influential conditions/resources are correlated but also because different species may have evolved in different places and have not colonised every ‘ecologically appropriate’ location. Geographic location was not influential in accounting for variation in assemblages of strongly flying invertebrates, supporting the hypothesis that organisms having high dispersal potential can be expected to break down geographic barriers more readily than those with poor dispersal powers. In accord with what is known about the local evolution and restricted distributions of native and exotic species, history (reflected in geography) appeared to account for some variation in fish assemblages.

4. Given their different mathematical bases, the fact that exploratory and predictive analyses yielded similar results provides added confidence to our conclusions.
Potassium dependence and phytoplankton ecology: an experimental study
Authors: Jaworski G. H. M. , Talling J. F. , Heaney S. I.
Published: December 2004

SUMMARY 1. Unialgal cultures of three species common in the freshwater phytoplankton were used to test limitation of specific growth rate and final yield in defined media of low K+ concentration (range <0.3–6 μmol L−1 or mmol m−3).

2. Growth rate of the diatom Asterionella formosa was independent of K+ concentration above 0.7 μmol L−1. Final yield was dependent on initial concentration when accompanied by K+ depletion below this concentration, but not by lesser depletion with more residual K+. Analyses of particulate K in the biomass indicated a mean final cell content of 2.8 μmol K 10−8 cells, approximately 1.0% of the organic dry weight.

3. Less detailed work with the diatom Diatoma elongatum showed no dependence of growth rate or final yield upon the initial K+ concentration in the range 0.8–3.2 μmol L−1. The phytoflagellate Plagioselmis nannoplanctica suffered net mortality in the lowest concentration tested, 0.8 μmol L−1.

4. Comparison with the range of K+ concentration in natural fresh waters, including a depletion induced by an aquatic macrophyte, suggests that K+ is unlikely to limit growth of phytoplankton. Nevertheless, there can be correlation of K+ with lake trophy.
Seasonal patterns of viruses, bacteria and dissolved organic carbon in a riverine wetland
Authors: Farnell‐Jackson E. A. , Ward A. K.
Published: December 2004

SUMMARY 1. Viral and bacterial abundances were studied in relation to environmental attributes over an annual period, for both planktonic and attached (sediment, aquatic macrophyte and submerged wood) habitats, in a riverine wetland.

2. Annual mean abundance of planktonic viruses ranged from 2.3 × 105−3.8 × 105 particles mL−1 and varied according to sampling site. Significant seasonal patterns in viral abundance were evident and appeared to be linked to variations in bacterial abundance, dissolved organic carbon and inorganic nutrients.

3. Annual mean abundance of viruses associated with surfaces ranged from 1.3 × 106 particles cm−2 on aquatic macrophytes to 1.1 × 107 particles cm−2 on wood and also showed seasonal patterns. The difference in viral dynamics among the different sites emphasizes the importance of considering habitat diversity within wetlands when examining microbial communities.
The annual cycle of growth rate and biomass change in Planktothrix spp. in Blelham Tarn, English Lake District
Authors: Davis P.A. , Dent M. , Parker J. , Reynolds C.S. , Walsby A.E.
Published: December 2004

SUMMARY 1. The changes in the vertical distributions of red coloured Planktothrix rubescens and green P. agardhii filaments in Blelham Tarn, English Lake District, were related to vertical profiles of temperature and light attenuation and to continuous records of the surface irradiance and windspeed, from August 1999 to October 2000.

2. The potential growth rate of each organism was calculated from the irradiance and temperature at 0.5 m depths and hourly intervals throughout the year, using algorithms determined from growth rates in culture. The analyses indicated that there was sufficient irradiance for growth, integrated over the 24‐h cycle, at depths down to the metalimnion where the Planktothrix populations stratified in summer. The compensation depth for growth by P. rubescens reached a maximum of 9.3 m in spring and midsummer, and fell to a minimum of 1.6 m in midwinter; the corresponding values for P. agardhii were 7.9 and 0.5 m.

3. The mixed depth (zm) exceeded the critical depth for growth (zb) by P. rubescens (the condition preventing population increase) on only 3 days of the year; for P. agardhii, however, zm exceeded zb on 31 days, contributing to its faster decline. The stratified population of P. rubescens was the major cause of light attenuation during the summer of 2000, and resulted in competitive exclusion of P. agardhii.

4. The calculated growth rates integrated over the depth of the water column in Blelham Tarn equalled, or exceeded, the measured changes of the populations during periods when they were increasing, during summer and autumn. Close agreement between the two values was found for much of the year when allowance was made for dilution of the lake population by rainfall over the watershed. During periods of rapid decline, of P. agardhii in September 1999, P. rubescens in December 1999 and both in July–August 2000, additional losses (e.g. by chytrid parasitism and grazing) are invoked.
Effects of hydrogeomorphic region, catchment storage and mature forest on baseflow and snowmelt stream water quality in second‐order Lake Superior Basin tributaries
Authors: Detenbeck Naomi E. , Elonen Colleen M. , Taylor Debra L. , Anderson Leroy E. , Jicha Terri M. , Batterman Sharon L.
Published: December 2004

1. In this study we predict stream sensitivity to non‐point source pollution based on the non‐linear responses of hydrological regimes and associated loadings of non‐point source pollutants to catchment properties. We assessed two hydrologically based thresholds of impairment, one for catchment storage (5–10%) and one for mature forest (<50% versus >60% of catchment in mature forest cover) across two different hydrogeomorphic regions within the Northern Lakes and Forest (NLF) ecoregion: the North Shore [predominantly within the North Shore Highlands Ecological Unit] and the South Shore (predominantly within the Lake Superior Clay Plain Ecological Unit). Water quality samples were collected and analysed during peak snowmelt and baseflow conditions from 24 second‐order streams grouped as follows: three in each region × catchment storage × mature forest class.

2. Water quality was affected by a combination of regional influences, catchment storage and mature forest. Regional differences were significant for suspended solids, phosphorus, nitrogen: phosphorus ratios, dissolved organic carbon (DOC) and alkalinity. Catchment storage was significantly correlated with dissolved silica during the early to mid‐growing season, and with DOC, specific conductance and alkalinity during all seasons. Total nitrogen and dissolved nitrogen were consistently less in low mature forest than in high mature forest catchments. Catchment storage interacted with the influence of mature forest for only two metrics: colour and the soluble inorganic nitrogen : phosphorus ratio.

3. Significant interaction terms (region by mature forest or region by storage) suggest differences in regional sensitivity for conductance, alkalinity, total organic carbon, and colour, as well as possible shifts in thresholds of impact across region or mature forest class.

4. Use of the NLF Ecoregion alone as a basis for setting regional water quality criteria would lead to the misinterpretation of reference condition and assessment of condition. There were pronounced differences in background water quality between the North and South Shore streams, particularly for parameters related to differences in soil parent material and glacial history. A stratified random sampling design for baseflow and snowmelt stream water quality based on both hydrogeomorphic region and catchment attributes improves assessments of both reference condition and differences in regional sensitivity.
The ciliate epibiont Epistylis pygmaeum: selection for zooplankton hosts, reproduction and effect on two rotifers
Authors: Gilbert J. J. , Schröder T.
Published: December 2004

1. A clonal culture of the peritrich Epistylis pygmaeum was used for all observations and experiments. Motile cells preferentially attached to the eggs of three species of Brachionus but also attached to the body of adult B. angularis. Zooids on the transitory egg substratum developed only short stalks, while those on the body often developed long stalks and branched colonies. Selection for the eggs positions the ciliate near the cloaca, and thus high concentrations of fine particulate material excreted by the host. Settlement on eggs occurred equally well in the light and dark, and on moving and stationary eggs.

2. Motile Epistylis cells attached to a wide variety of rotifer and crustacean zooplankton, but exhibited some pronounced selectivity. They readily settled on the eggs of other rotifers (Epiphanes, Polyarthra), on the carapace of several cladocerans (Ceriodaphnia, Daphnia, Diaphanosoma), and on the egg sacs of a copepod (Tropocyclops). They settled less readily on the bodies of the rotifers Asplanchna and Synchaeta, and rarely or never settled on the rotifer Keratella, the cladocerans Bosmina and Scapholeberis, and the body of the copepod.

3. Epistylis populations initiated with a single zooid on Brachionus increased exponentially and often contained several hundred attached zooids and motile cells after 3 days at 20 °C. Observations of a culture initiated from a single telotroch provided new information about peritrich life cycles: (1) motile cells reproduced themselves at a rapid rate (λ = 4.26 day−1); (2) telotrochs produced or transformed into swimming zooids and vice versa. Functions of the two types of motile cells remain to be clarified. Telotrochs likely are specialised for finding and attaching to hosts. Swimming zooids can feed and reproduce, producing both their own cell type and telotrochs. Together, they should enhance dispersal and population growth, especially when hosts are rare.

4. Life‐table experiments with two species of Brachionus showed that colonisation by Epistylis had no effect on adult survival but significantly decreased fecundity, by 29% in both cases. Zooids attached to eggs could be a weight burden, increase drag, and possibly inhibit egg development. Those on the body of B. angularis also could interfere with coronal cilia, inhibiting feeding and further slowing locomotion. The ability of E. pygmaeum to select and then interfere with its hosts indicates that this epibiont has the potential to influence the species structure of zooplankton communities.
Asymmetry, testis and sperm size in Yellow Dung Flies
Authors: Hosken D. J. , Garner T. W. J. , Blanckenhorn W. U.
Published: December 2004

Fluctuating asymmetry (FA), small random deviations from perfect bilateral symmetry, is a widely used measure of developmental stability, and has been linked to fitness measures including male primary reproductive traits such as sperm quality. However, there have been relatively few investigations of potential associations between these male traits and FA, and hence the current balance of evidence is equivocal.

There is also evidence that levels of FA vary across populations with, for example, organisms inhabiting marginal populations often displaying increased FA. Moreover, environmental variation may select for different levels of developmental buffering across populations that are only revealed in ‘common garden’ experiments.

Investigations of potential associations between male leg FA and testis and sperm size in Yellow Dung Flies are reported here. In addition, levels of FA in a mainland and two island populations were compared when flies were reared under common conditions.

No associations were found between any measure of FA and sperm size (or variation) or testis size. Additionally, no evidence was found that FA varied across the three populations when flies were reared under identical controlled conditions.
Within‐colony transmission and the cost of a mutualistic bacterium in the leaf‐cutting ant Acromyrmex octospinosus
Authors: Poulsen M. , Bot A. N. M. , Currie C. R. , Nielsen M. G. , Boomsma J. J.
Published: December 2004

Stable mutualistic interactions require the long‐term alignment of fitness interests of participating species. This condition is fulfilled when the benefits of the relationship exceed the costs for all partners.

One apparent stabilizing factor in mutualisms is the vertical (parent to offspring) transmission of symbionts, as this tends to reduce the expression of virulent traits and reproductive conflicts. This study examines the cost and mode of transmission of a mutualistic Streptomyces bacterium that grows on the cuticle of leaf‐cutting ants and produces antibiotics against a specialized fungal parasite of the ant fungus gardens.

It is shown that ant respiration rates are elevated by 10–20% when the bacterium is present on their cuticle. This increase is due to direct respiration of the bacterium and possible excess respiration by the ants. Although these two factors cannot be separated, it is clear that the total increase gives a reasonable quantification of the metabolic costs incurred by the Streptomyces symbiont.

Ants that actively maintain Streptomyces cultures on their cuticle tend to consume more of their mutualistic fungus garden than controls and this excess consumption increases with the amount of Streptomyces bacteria present.

Scanning electron microscopy showed that the mutualistic bacterium is not present on major workers immediately following eclosion, indicating that the bacterium is not transferred to callow workers until later.

The results of an experiment simulating within‐colony transmission to callow workers suggest that the bacterium is predominantly transmitted from older to newly eclosed major workers, but that transmission may also occur via the fungus garden. The presence of Streptomyces bacteria in the fungus garden implies that rare events of horizontal transmission of the fungal cultivar of attine ants may also imply horizontal transmission of strains of the mutualistic bacterium.
The consequences of crown traits for the growth and survival of tree saplings in a Mexican lowland rainforest
Authors: Sterck F. , Martinéz‐Ramos M. , Dyer‐Leal G. , Rodríguez‐Velazquez J. , Poorter L.
Published: December 2004

Many studies discuss the adaptive value of plant architecture, but few have actually measured architectural effects on plant growth and survival. In this study, sapling growth and survival are related to crown traits for two tree species, Trophis mexicana (Liebm.) Bur. and Pseudolmedia oxyphyllaria Donn. Sm., in the Los Tuxtlas lowland rainforest of Mexico. The traits investigated were crown width, crown depth, number of leaves, number of leaves per unit crown area (horizontal self‐shading), and number of leaves per unit silhouette area (vertical self‐shading).

Self‐shading indices decreased with crown size, but were unaffected by the number of leaves per tree. Larger crowns thus had more diffuse foliage, with less self‐shading.

The number of leaves had positive effects on growth and survival, while self‐shading indices had no effect. This indicates that shaded leaves do not necessarily have negative carbon balances.

Negative effects of crown width on horizontal crown growth, and positive effects on vertical crown growth, suggest that saplings tend to grow towards a shape intermediate between the narrow and wide crown extremes.

Survival was positively correlated with crown width in Pseudolmedia, and with the number of leaves in Trophis. Apparently, dependence of survival on crown traits differed among species.

Crown traits affected plant growth and survival, but the hypothesis emerging from light‐limited carbon acquisition was confounded by other factors, such as tree size and the inherent branching patterns.

Crown traits are good and rather simple predictors of future sapling growth and survival, and may help foresters to select potential crop trees.
Carbon dioxide assimilation by a wetland sedge canopy exposed to ambient and elevated CO2: measurements and model analysis
Authors: Rasse D. P. , Li J.‐H. , Drake B. G.
Published: December 2004

The wetland sedge Scirpus olneyi Gray displays fast rates of CO2 assimilation and responds positively to increased atmospheric CO2 concentration. The present study was aimed at identifying the ecophysiological traits specific to S. olneyi that drive these CO2‐assimilation patterns under ambient and elevated CO2 conditions.

The net ecosystem exchange (NEE) of CO2 between S. olneyi communities and the atmosphere was measured in open‐top chambers.

We developed a new mechanistic model for S. olneyi communities based on published ecophysiological data and additional measurements of photosynthetic parameters.

Our NEE measurements confirmed that S. olneyi communities have a high rate of summertime CO2 assimilation, with noontime peaks reaching 40 µmol CO2 m−2 ground s−1 on productive summer days, and that elevated CO2 increased S. olneyi CO2 assimilation by c. 35–40%.

Using S. olneyi‐specific ecophysiological parameters, comparison with measured NEE showed that the model accurately simulated these high rates of CO2 uptake under ambient or elevated CO2.

The model pointed to the Rubisco capacity of Scirpus leaves associated with their high total nitrogen content as the primary explanation for the high rates of CO2 assimilation, and indicated that the vertical‐leaf canopy structure of S. olneyi had comparatively little influence on CO2 assimilation.
Structure–function analysis of human Spt4: evidence that hSpt4 and hSpt5 exert their roles in transcriptional elongation as parts of the DSIF complex
Authors: Kim Dong‐ki , Inukai Naoto , Yamada Tomoko , Furuya Akiko , Sato Hiroe , Yamaguchi Yuki , Wada Tadashi , Handa Hiroshi
Published: December 2004

Background:The human Spt4/Spt5 complex, termed DRB‐sensitivity inducing factor (DSIF) is a dual regulator of transcription that stimulates, or, when cooperating with negative elongation factor (NELF), represses RNA polymerase II (RNAPII) elongation. Spt4 and Spt5 are also thought to be involved in mRNA capping, homologous DNA recombination, and transcription‐coupled DNA repair. As a first step to understanding how these proteins regulate diverse cellular processes, we investigated the structure and function of hSpt4in vitro.

Results:Immunodepletion of hSpt5 from HeLa nuclear extracts resulted in the efficient co‐depletion of hSpt4. Using DSIF‐depleted nuclear extracts and a series of Spt4 mutants, we examined the amino acid sequence of hSpt4 which was important for hSpt5 binding and for transcriptional repression and activation by DSIF. Unexpectedly, the zinc finger of hSpt4, which is critical for the yeast counterpart to functionin vivo, was dispensable for hSpt5 binding and for transcriptional regulationin vitro.

Conclusion:These and other results suggest: (i) that the central region of hSpt4 is necessary and sufficient for its functionin vitroand (ii) that there is no free hSpt4 or hSpt5 in cells. We propose that hSpt4 and hSpt5 exert their roles in transcriptional regulation, and possibly in other nuclear processes, as parts of the DSIF complex.
Enforced cytokinesis without complete nuclear division in embryonic cells depleting the activity of DNA topoisomerase IIα
Authors: Akimitsu Nobuyoshi , Adachi Noritaka , Hirai Hiroshi , Hossain Muktadir S. , Hamamoto Hiroshi , Kobayashi Masao , Aratani Yasuaki , Koyama Hideki , Sekimizu Kazuhisa
Published: December 2004

Background: There are two distinct DNA topoisomerase II (topo II) isoforms, designated topo IIα and topo IIβ, in mammalian cells. The function of topo IIα in the development of mammalian cells has not been elucidated because of a lack of topo IIα mutants.

Results: We generated mice with a targeted disruption of the topo IIα gene. The development of topo IIα−/– embryos was terminated at the 4‐ or 8‐cell stage. When wild‐type embryos at the 2‐ or 4‐cell stage were treated with ICRF‐193, a catalytic inhibitor of topo II, nuclear division occurred followed by cytokinesis to form 4 or 8 cells, respectively, then development was terminated. Microscope analysis of 4,6‐diamidino‐2‐phenylindole (DAPI)‐stained nuclei of both topo IIα−/– and ICFR‐193‐treated embryonic cells revealed a droplet‐like structure connecting the terminals of two adjacent nuclei forming a bridge‐like structure. Phosphorylated histone H3, a marker for the M phases, disappeared from the nuclei of the topo IIα‐depleted embryonic cells. Laser scanning cytometry of the topo IIα‐depleted cells revealed the presence of 2N DNA cells.

Conclusions: Our results indicate that topo IIα has an essential role in the early stages of mouse development and that depletion of topo IIα from the embryonic cells causes incomplete nuclear division followed by enforced cytokinesis.
Cell cycle regulation of chromatin binding and nuclear localization of human Cdc7‐ASK kinase complex
Authors: Sato Noriko , Sato Megumi , Nakayama Masahito , Saitoh Rika , Arai Ken‐ichi , Masai Hisao
Published: December 2004

Background: During the course of DNA replication, regulation of cellular localization and chromatin binding of involved factors plays critical roles. Cdc7 kinase is required for DNA replication and its kinase activity is cell cycle‐regulated by its activation subunit Dbf4/ASK. In mammals, it is not known at which time point during the cell cycle Cdc7 and Dbf4/ASK proteins are imported into nuclei and loaded on to chromatin.

Results: We have constructed a series of truncation and deletion derivatives of ASK and expressed them as fusion proteins with GFP in mammalian cells. Both Dbf4‐motif‐M and ‐C conserved in Dbf4/ASK protein family are required for huCdc7 kinase activation. Two stretches of amino acid sequences, NLS1 (P346KKKRIK) and NLS2 (K201RVGSGAQKTRTGRLKK), are important for ASK nuclear localization. In stable transformants expressing GFP‐fused full‐length ASK under the tetracycline inducible promoter, GFP‐ASK protein accumulates in nuclei at the telophase, but its binding to chromatin does not reach a maximum until late G1, whereas huCdc7 is imported into nuclei and binds to chromatin at early G1. An important substrate of Cdc7‐ASK at the G1/S transition is likely to be MCM. Indeed, over‐expression of both huCdc7 and ASK results in the elevated phosphorylation of endogenous MCM2 protein, as manifested by appearance of the mobility‐shifted form on SDS‐PAGE, but does not cause any significant effects on cell cycle progression.

Conclusions: Nuclear localization and chromatin binding of endogenous huCdc7 and GFP‐ASK expressed during the post‐mitotic phase are independently regulated. Although GFP‐ASK is presumably imported into nuclei through its two nuclear localization signals at telophase, it may require additional signals for chromatin binding, the level of which increases at late G1 phase.

Cell cycle regulation of cellular localization and chromatin binding of Cdc7 and ASK proteins. See text for details.

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AKRL1 and AKRL2 activate the JNK pathway
Authors: Harada Takeshi , Matsuzaki Osamu , Hayashi Hideko , Sugano Sumio , Matsuda Akio , Nishida Eisuke
Published: December 2004

Background: c‐Jun N‐terminal kinase (JNK), a member of the mitogen‐activated protein kinase (MAPK) family, is activated by specific cytokines and various environmental stresses. MKK4 and MKK7 are shown to be direct activators of JNK. Although several upstream components of the JNK pathway, including members of the MAPKKK family have been described, the components lying between the receptors or sensors and JNK have not been fully characterized.

Results: We have identified AKRL1 and AKRL2 (Akr1p‐like 1 and 2) as novel activators of the JNK pathway. AKRL1 and AKRL2 proteins have a considerable sequence similarity to Akr1p, a protein essential for endocytosis in Saccharomyces cerevisiae. Expression of AKRL1 or AKRL2 activates JNK and its activators MKK4 and MKK7. This AKRL1/2‐induced JNK activation is significantly suppressed by the expression of a kinase‐negative mutant of TAK1, a member of the MAPKKK family. AKRL1 and AKRL2 localize to the Golgi. Both the N‐terminal half and the C‐terminal transmembrane domain of AKRL1/2 are required for the JNK activation. The C‐terminal transmembrane domain of AKRL1/2 is required for localization to the Golgi.

Conclusion: AKRL1 and AKRL2 are localized to Golgi and the novel activators of the JNK pathway.
VDE‐initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination‐like manner
Authors: Fukuda Tomoyuki , Nogami Satoru , Ohya Yoshikazu
Published: December 2004

Background: Inteins and group I introns found in prokaryotic and eukaryotic organisms occasionally behave as mobile genetic elements. During meiosis of the yeast Saccharomyces cerevisiae, the site‐specific endonuclease encoded by VMA1 intein, VDE, triggers a single double‐strand break (DSB) at an inteinless allele, leading to VMA1 intein homing. Besides the accumulating information on the in vitro activity of VDE, very little has been known about the molecular mechanism of intein homing in yeast nucleus.

Results: We developed an assay to detect the product of VMA1 intein homing in yeast genome. We analysed mutant phenotypes of RecA homologs, Rad51p and Dmc1p, and their interacting proteins, Rad54p and Tid1p, and found that they all play critical roles in intein inheritance. The absence of DSB end processing proteins, Sae2p and those in the Mre11‐Rad50‐Xrs2 complex, also causes partial reduction in homing efficiency. As with meiotic recombination, crossover events are frequently observed during intein homing. We also observed that the absence of premeiotic DNA replication caused by hydroxyurea (HU) or clb5Δ clb6Δ mutation reduces VDE‐mediated DSBs.

Conclusion: The repairing system working in intein homing shares molecular machinery with meiotic recombination induced by Spo11p. Moreover, like Spo11p‐induced DNA cleavage, premeiotic DNA replication is a prerequisite for a VDE‐induced DSB. VMA1 intein thus utilizes several host factors involved in meiotic and recombinational processes to spread its genetic information and guarantee its progeny through establishment of a parasitic relationship with the organism.
[PHI+], a novel Sup35‐prion variant propagated with non‐Gln/Asn oligopeptide repeats in the absence of the chaperone protein Hsp104
Authors: Crist Colin G. , Nakayashiki Toru , Kurahashi Hiroshi , Nakamura Yoshikazu
Published: December 2004

Background: The [PSI+] element of the budding yeast is an aggregated form of the translation release factor Sup35 that is propagated and transmitted cytoplasmically in a manner analogous to that of mammalian prions. The N‐terminal of Sup35, necessary for [PSI+], contains oligopeptide repeats and multiple Gln/Asn residues.

Results: We replaced the Gln/Asn‐rich prion repeats of Sup35 with non‐Gln/Asn repeats from heterologous yeast strains. These non‐Gln/Asn repeat Sup35s propagated a novel [PSI+] variant, [PHI+], that appeared de novo 103 times more frequent than [PSI+]. [PHI+] was stably inherited in a non‐Mendelian fashion, but not eliminated upon the inactivation of Hsp104, unlike known [PSI+] elements. In vitro, non‐Gln/Asn repeat domains formed amyloid fibres that were shorter and grew more slowly than did Gln/Asn‐rich prion domains, while [PHI+] aggregates were smaller than [PSI+] aggregates in vivo.

Conclusions: These findings suggest the existence of an alternative, Hsp104‐independent pathway to replicate non‐Gln/Asn variant Sup35 prion seeds.
Consequences of wildfire on ecosystem CO2 and water vapour fluxes in the Great Basin
Authors: OBRIST DANIEL , DELUCIA EVAN H. , ARNONE JOHN A.
Published: December 2004

Increased fire frequency in the Great Basin of North America's intermountain West has led to large‐scale conversion of native sagebrush (Artemisia tridentata Nutt.) communities to postfire successional communities dominated by native and non‐native annual species during the last century. The consequences of this conversion for basic ecosystem functions, however, are poorly understood. We measured net ecosystem CO2 exchange (NEE) and evapotranspiration (ET) during the first two dry years after wildfire using a 4‐m diameter (16.4 m3) translucent static chamber (dome), and found that both NEE and ET were higher in a postfire successional ecosystem (−0.9–2.6 µmol CO2 m−2 s−1 and 0.0–1.0 mmol H2O m−2 s−2, respectively) than in an adjacent intact sagebrush ecosystem (−1.2–2.3 µmol CO2 m−2 s−1 and −0.1–0.8 mmol H2O m−2 s−2, respectively) during relatively moist periods. Higher NEE in the postfire ecosystem appears to be due to lower rates of above‐ground plant respiration while higher ET appears to be caused by higher surface soil temperatures and increased soil water recharge after rains. These patterns disappeared or were reversed, however, when the conditions were drier. Daily net ecosystem productivity (NEP; g C m−2 d−1), derived from multiple linear regressions of measured fluxes with continuously measured climate variables, was very small (close to zero) throughout most of the year. The wintertime was an exception in the intact sagebrush ecosystem with C losses exceeding C gains leading to negative NEP while C balance of the postfire ecosystem remained near zero. Taken together, our results indicate that wildfire‐induced conversion of native sagebrush steppe to ecosystems dominated by herbaceous annual species may have little effect on C balance during relatively dry years (except in winter months) but may stimulate water loss immediately following fires.
Climate change and sea turtles: a 150‐year reconstruction of incubation temperatures at a major marine turtle rookery
Authors: HAYS GRAEME C. , BRODERICK ANNETTE C. , GLEN FIONA , GODLEY BRENDAN J.
Published: December 2004

Sea turtles show temperature dependent sex determination. Using an empirical relationship between sand and air temperature, we reconstructed the nest temperatures since 1855 at Ascension Island, a major green turtle (Chelonia mydas) rookery. Our results show that inter‐beach thermal variations, previously ascribed to the albedo of the sand, which varies hugely from one beach to another, have persisted for the last century. Reconstructed nest temperatures varied by only 0.5 °C on individual beaches over the course of the nesting season, while the temperature difference between two key nesting beaches was always around 3 °C. Hence inter‐beach thermal variations are the main factor causing a large range of incubation temperatures at this rookery. There was a general warming trend for nests, with a mean increase in reconstructed nest temperatures for different months of between 0.36 and 0.49 °C for the last 100 years.
Changes in carbon storage and fluxes in a chronosequence of ponderosa pine
Authors: LAW B. E. , SUN O. J. , CAMPBELL J. , VAN TUYL S. , THORNTON P. E.
Published: December 2004

Forest development following stand‐replacing disturbance influences a variety of ecosystem processes including carbon exchange with the atmosphere. On a series of ponderosa pine (Pinius ponderosa var. Laws.) stands ranging from 9 to> 300 years in central Oregon, USA, we used biological measurements to estimate carbon storage in vegetation and soil pools, net primary productivity (NPP) and net ecosystem productivity (NEP) to examine variation with stand age. Measurements were made on plots representing four age classes with three replications: initiation (I, 9–23 years), young (Y, 56–89 years), mature (M, 95–106 years), and old (O, 190–316 years) stands typical of the forest type in the region. Net ecosystem productivity was lowest in the I stands (−124 g C m−2 yr−1), moderate in Y stands (118 g C m−2 yr−1), highest in M stands (170 g C m−2 yr−1), and low in the O stands (35 g C m−2 yr−1). Net primary productivity followed similar trends, but did not decline as much in the O stands. The ratio of fine root to foliage carbon was highest in the I stands, which is likely necessary for establishment in the semiarid environment, where forests are subject to drought during the growing season (300–800 mm precipitation per year). Carbon storage in live mass was the highest in the O stands (mean 17.6 kg C m−2). Total ecosystem carbon storage and the fraction of ecosystem carbon in aboveground wood mass increased rapidly until 150–200 years, and did not decline in older stands. Forest inventory data on 950 ponderosa pine plots in Oregon show that the greatest proportion of plots exist in stands ∼ 100 years old, indicating that a majority of stands are approaching maximum carbon storage and net carbon uptake. Our data suggests that NEP averages ∼ 70 g C m−2 year−1 for ponderosa pine forests in Oregon. About 85% of the total carbon storage in biomass on the survey plots exists in stands greater than 100 years, which has implications for managing forests for carbon sequestration. To investigate variation in carbon storage and fluxes with disturbance, simulation with process models requires a dynamic parameterization for biomass allocation that depends on stand age, and should include a representation of competition between multiple plant functional types for space, water, and nutrients.
A reciprocal transplant experiment within a climatic gradient in a semiarid shrub‐steppe ecosystem: effects on bunchgrass growth and reproduction, soil carbon, and soil nitrogen
Authors: LINK STEVEN O. , SMITH JEFFREY L. , HALVORSON JONATHAN J. , BOLTON HARVEY
Published: December 2004

We investigated the effect of climate change on Poa secunda Presl. and soils in a shrub‐steppe ecosystem in south‐eastern Washington. Intact soil cores containing P. secunda were reciprocally transplanted between two elevations. Plants and soils were examined, respectively, 4.5 and 5 years later. The lower elevation (310 m) site is warmer (28.5 °C air average monthly maximum) and drier (224 mm yr−1) than the upper elevation (844 m) site (23.5 °C air average monthly maximum, 272 mm yr−1). Observations were also made on undisturbed plants at both sites. There was no effect of climate change on plant density, shoot biomass, or carbon isotope discrimination in either transplanted plant population. The cooler, wetter environment significantly reduced percent cover and leaf length, while the warmer, drier environment had no effect. Warming and drying reduced percent shoot nitrogen, while the cooler, wetter environment had no effect. Culm density was zero for the lower elevation plants transplanted to the upper site and was 10.3 culms m−2 at the lower site. There was no effect of warming and drying on the culm density of the upper elevation plants. Culm density of in situ lower elevation plants was greater than that of the in situ upper elevation plants. Warming and drying reduced total soil carbon 32% and total soil nitrogen 40%. The cooler, wetter environment had no effect on total soil C or N. Of the C and N that was lost over time, 64% of both came from the particulate organic matter fraction (POM, > 53 µm). There was no effect of warming and drying on the upper population of P. secunda while exposing the lower population to the cooler, wetter environment reduced reproductive effort and percent cover. With the warmer and drier conditions that may develop with climate change, total C and N of semiarid soils may decrease with the active fraction of soil C also rapidly decreasing, which may alter ecosystem diversity and function.