bluuebunny/crossref_metadata_2025 huggingface dataset:
Actin and Microtubules in Cell Motility: Which One is in Control?
Authors: Etienne‐Manneville Sandrine
Published: June 2004

The cytoskeleton is composed of three distinct elements: actin microfilaments, microtubules and intermediate filaments. The actin cytoskeleton is thought to provide protrusive and contractile forces, and microtubules to form a polarized network allowing organelle and protein movement throughout the cell. Intermediate filaments are generally considered the most rigid component, responsible for the maintenance of the overall cell shape. Cytoskeletal elements must be coordinately regulated for the cell to fulfill complex cellular functions, as diverse as cell migration, cell adhesion and cell division. Coordination between cytoskeletal elements is achieved by signaling pathways, involving common regulators such as the Rho guanosine‐5′‐triphosphatases (GTPases). Furthermore, evidence is now accumulating that cytoskeletal elements participate in regulating each other. As a consequence, although their functions seem well defined, they are in fact overlapping, with actin playing a role in membrane trafficking and microtubules being involved in the control of protrusive and contractile forces. This cytoskeletal crosstalk is both direct and mediated by signaling molecules. Cell motility is a well‐studied example where the interplay between actin and microtubules appears bidirectional. This leads us to wonder which, if any, cytoskeletal element leads the way.
Regulating Actin Dynamics at Membranes: A Focus on Dynamin
Authors: Schafer Dorothy A.
Published: June 2004

Dynamin, the large guanosine triphosphatase, is generally considered to have a key role in deforming membranes to create tubules or vesicles. Dynamin, particularly dynamin2 isoforms, also are localized with actin filaments, often at locations where cellular membranes undergo remodeling. Perturbing dynamin function interferes with endocytic traffic and actin function. Thus, dynamin may regulate actin filaments coordinately with its activities that remodel membranes. This review will highlight recent observations that provide clues to mechanisms whereby dynamin might coordinate membrane remodeling and actin filament dynamics during endocytic traffic, cell morphogenesis and cell migration.
SYM1
Is the Stress-Induced
Saccharomyces cerevisiae
Ortholog of the Mammalian Kidney Disease Gene
Mpv17
and Is Required for Ethanol Metabolism and Tolerance during Heat Shock
Authors: Trott Amy , Morano Kevin A.
Published: June 2004

Organisms rapidly adapt to severe environmental stress by inducing the expression of a wide array of heat shock proteins as part of a larger cellular response program. We have used a genomics approach to identify novel heat shock-induced genes in
Saccharomyces cerevisiae
. The uncharacterized open reading frame (ORF)
YLR251W
was found to be required for both metabolism and tolerance of ethanol during heat shock.
YLR251W
has significant homology to the mammalian peroxisomal membrane protein Mpv17, and Mpv17
−/−
mice exhibit age-onset glomerulosclerosis, deafness, hypertension, and, ultimately, death by renal failure. Expression of Mpv17 in
ylr251w
Δ cells complements the 37°C ethanol growth defect, suggesting that these proteins are functional orthologs. We have therefore renamed ORF
YLR251W
as
SYM1
(for “stress-inducible yeast Mpv17”). In contrast to the peroxisomal localization of Mpv17, we find that Sym1 is an integral membrane protein of the inner mitochondrial membrane. In addition, transcriptional profiling of
sym1
Δ cells uncovered changes in gene expression, including dysregulation of a number of ethanol-repressed genes, exclusively at 37°C relative to wild-type results. Together, these data suggest an important metabolic role for Sym1 in mitochondrial function during heat shock. Furthermore, this study establishes Sym1 as a potential model for understanding the role of Mpv17 in kidney disease and cardiovascular biology.
Novel Chimeric Spermidine Synthase-Saccharopine Dehydrogenase Gene (
SPE3-LYS9
) in the Human Pathogen
Cryptococcus neoformans
Authors: Kingsbury Joanne M. , Yang Zhonghui , Ganous Tonya M. , Cox Gary M. , McCusker John H.
Published: June 2004

The
Cryptococcus neoformans LYS9
gene (encoding saccharopine dehydrogenase) was cloned and found to be part of an evolutionarily conserved chimera with
SPE3
(encoding spermidine synthase).
spe3-lys9
,
spe3-LYS9
, and
SPE3-lys9
mutants were constructed, and these were auxotrophic for lysine and spermidine, spermidine, and lysine, respectively. Thus,
SPE3-LYS9
encodes functional spermidine synthase and saccharopine dehydrogenase gene products. In contrast to
Saccharomyces cerevisiae spe3
mutants, the polyamine auxotrophy of
C. neoformans spe3-LYS9
mutants was not satisfied by spermine. In vitro phenotypes of
spe3-LYS9
mutants included reduced capsule and melanin production and growth rate, while
SPE3-lys9
mutants grew slowly at 30°C, were temperature sensitive in rich medium, and died upon lysine starvation. Consistent with the importance of saccharopine dehydrogenase and spermidine synthase in vitro,
spe3-lys9
mutants were avirulent and unable to survive in vivo and both functions individually contributed to virulence.
SPE3-LYS9
mRNA levels showed little evidence of being influenced by exogenous spermidine or lysine or starvation for spermidine or lysine; thus, any regulation is likely to be posttranscriptional. Expression in
S. cerevisiae
of the full-length
C. neoformans SPE3-LYS9
cDNA complemented a
lys9
mutant but not a
spe3
mutant. However, expression in
S. cerevisiae
of a truncated gene product, consisting of only
C. neoformans SPE3
, complemented a
spe3
mutant, suggesting possible modes of regulation. Therefore, we identified and describe a novel chimeric
SPE3-LYS9
gene, which may link spermidine and lysine biosynthesis in
C. neoformans
.
Biostratigraphic significance of lower Paleozoic microfaunas from eastern Canada
Authors: Asselin Esther , Achab Aïcha , Soufiane Azzedine
Published: June 2004

Chitinozoan studies recently carried out in the Appalachian Forelands and St. Lawrence Platform National Geoscience Mapping Program (NATMAP) project have confirmed the regional biostratigraphic value of a number of chitinozoan species and led to a better documentation of their stratigraphic and geographic distribution in eastern Canada. The typical Darriwilian microfaunas first described from the Table Head Group of western Newfoundland and containing Conochitina chydaea are now recognised in the Rivière Ouelle Formation at Les Méchins, Gaspé Peninsula. In the Upper Ordovician successions of the St. Lawrence Platform at Neuville and in the Charlevoix area, Quebec, Conochitina primitiva is indicative of the multidenspre-americanus graptolite zonal range, Hercochitina duplicitas of the americanus Zone, and Hercochitina spinetum and Acanthochitina cancellata characterize the ruedemanni  lower spiniferus zonal interval. The occurrence of Cyathochitina vaurealensis and Hercochitina crickmayi in turbidite deposits of the Grog Brook Group of northwestern New Brunswick confirms the minimal facies dependence of these two Richmondian index species. Eisenackitina dolioliformis, characteristic of the late Aeronian and Telychian successions of Arctic Canada, Gaspé Peninsula, and Anticosti Island, is now recognised in samples from the Upsalquitch Formation of northwestern New Brunswick and the Cabano Formation of the Rimouski area in Quebec. The palynological data from Devonian successions of the Matapedia Valley, the Rimouski area, and the Beauce  Eastern Townships region show that the succession of Lower Devonian chitinozoan assemblages of the Forillon Peninsula based on short-ranging species can be used in establishing regional correlations in the Gaspé Belt.
Paleogeography of the Matapédia basin in the Gaspé Appalachians: initiation of the Gaspé Belt successor basin
Authors: Malo Michel
Published: June 2004

The Matapédia basin consists of the uppermost Ordovician  lowermost Silurian deep-water, fine-grained carbonatesiliciclastic rocks of the Honorat (Garin Formation) and Matapédia groups (Pabos and White Head formations), the lower rock assemblage of the Gaspé Belt in the Gaspé Appalachians. Paleogeographic maps of eight time slices from the Caradocian to the Llandoverian are presented to better understand the tectonosedimentary evolution of the Matapédia basin. Deposition evolved from siliciclastic (Garin Fm.) to argillaceous limestones (Pabos Fm.), to limestones (White Head Fm.). The overall change from terrigenous (Garin Fm.) to limestone facies (White Head Fm.) reflects a change in the source area. Paleocurrent directions and composition of sandstones indicate an orogenic source area to the south for the Garin Formation, which is believed to be the inliers of the Humber and Dunnage zones in the southern Gaspé and New Brunswick Appalachians. Lime muds deposited by turbidity currents coming from the north suggest the Anticosti active carbonate platform as the source area for the White Head Formation. The Matapédia basin was filled from south to north. First deposits, the Garin Formation, occurred south of the Taconian thrust sheets (Humber Zone) and also south of the Grenville basement. This region was the domain of the Ordovician Iapetus Ocean (Dunnage Zone). The northern limit of the basin migrated northward during deposition of the Matapédia Group in AshgillianLlandoverian times and reached its actual northern limit at the very end of the Llandoverian (C6), when siliciclastic facies of the lower Chaleurs Group were deposited.
Stratigraphy and tectono-sedimentary evolution of the Late Ordovician to Middle Devonian Gaspé Belt in northern New Brunswick: evidence from the Restigouche area
Authors: Wilson Reginald A , Burden Elliott T , Bertrand Rudolf , Asselin Esther , McCracken Alexander D
Published: June 2004

The Gaspé Belt in the Restigouche area comprises three successions separated by a Late Silurian (Salinic) disconformity and an Early Devonian angular unconformity. The lower, Upper Ordovician to Lower Silurian sequence consists of siliciclastic turbidites of the Boland Brook and Whites Brook formations (Grog Brook Group), overlain by calcareous turbidites of the Pabos and White Head formations (Matapédia Group), and slope and shelf deposits of the Upsalquitch and Limestone Point formations (lower Chaleurs Group). Above the Salinic disconformity, the upper Chaleurs Group and the Dalhousie Group record a transgressiveregressive cycle. The former comprises Pridolian carbonate rocks of the West Point Formation and overlying Pridolian to Lochkovian sedimentary rocks of the Indian Point Formation. The Chaleurs Group is conformably overlain by Lochkovian to early Emsian subaerial volcanic rocks of the Dalhousie Group (Val d'Amour Formation), which is unconformably overlain by alluviallacustrine deposits of the late Emsian Campbellton Formation. Acadian orogenesis began during the Emsian and is characterized by open to closed folding, heterogenous cleavage development, and reverse and strike-slip faults. The Salinic orogeny is manifested in extensional block faulting, within-plate volcanism, and uplift and deep erosion of Early Silurian strata. Early Devonian high-level intrusion of the Matapédia Group, White Head clasts in Indian Point conglomerate, and thermal maturation data all indicate an extended period of Late Silurian  Early Devonian uplift in parts of the Restigouche area. Thermal maturities of West Point and Indian Point strata are within the oil and condensate windows and suggest potential for hydrocarbons in the study area.
Taconian and Acadian transpression between the internal Humber Zone and the Gaspé Belt in the Gaspé Peninsula: tectonic history of the Shickshock Sud fault zone
Authors: Sacks Paul E , Malo Michel , Trzcienski, Jr Walter E , Pincivy Alix , Gosselin Patrice
Published: June 2004

The Shickshock Sud fault has a history of Ordovician (Taconian), Silurian (Salinic), and Devonian (Acadian) movements. Taconian deformation involving ductile dextral oblique-slip faulting is recorded in Cambrian rocks in the footwall of the Shickshock Sud fault. Metabasalt and metaarkose at amphibolite grade are converted into phyllonite and mylonitic schist. Shear bands, asymmetric garnet porphyroclasts, CS fabrics, and mica-fish textures indicate dextral shearing. The regional sense of shear is top to west and southwest on generally southeast dipping shear zones. Hornblende of metabasalt yielded an 40Ar/39Ar age of 455.9 ± 2 Ma, and muscovite from the mylonitic schist yielded an 40Ar/39Ar age of 454.3 ± 0.9 Ma, which indicate metamorphism and deformation during the Taconian orogeny. Evidence for Silurian activity is indicated by the Salinic unconformity to the south related to normal block-faulting. Deformation features in the Ordovician and SilurianDevonian rocks in the hanging wall were predominantly brittle and involved dextral transpression. Kinematic indicators point to predominantly dextral strike-slip movement. Kinematic analysis of brittle fault-slip data indicates that the shortening axis direction during strike-slip deformation was northwestsoutheast and subhorizontal, which is essentially coaxial to the average pole of Acadian cleavage. Deformation in the hanging wall of the Shickshock Sud fault is Acadian-related. The irregular geometry of the Laurentian margin, including the Grenville basement, might be the cause for Taconian and Acadian transpression in the Gaspé Appalachians.
The Late Ordovician  Middle Devonian Gaspé Belt in eastern Canada  recent advances
Authors: Lavoie Denis , Malo Michel , Tremblay Alain
Published: June 2004

The Appalachian Forelands and Platform NATMAP (National Geoscience Mapping Program) project in eastern Canada is a multi-discipline and multi-organization research endeavour aimed at the understanding of the evolution and architecture of the ancient continental margin of Laurentia. This Canadian Journal of Earth Sciences Special Issue presents some recent research progress for our knowledge of the SilurianDevonian Gaspé Belt of that ancient margin.
Lack of long-term sublethal effects of reduced freshwater pH alone on Atlantic salmon (Salmo salar) smolts subsequently transferred to seawater
Authors: Fivelstad Sveinung , Olsen Anne Berit , Stefansson Sigurd , Handeland Sigurd , Waagbø Rune , Kroglund Frode , Colt John
Published: June 2004

Atlantic salmon (Salmo salar) smolts (mean start weight 42 g) in soft freshwater were exposed to three pH ranges (two replicates in each group) for 35 days: pH 6.56.8 (control group), pH 5.96.3 (medium-pH group), and pH 5.45.9 (low-pH group). All exposures had citrate added to remove labile, toxic Al from the water. On day 35, all groups were transferred to 34 seawater and kept there for 100 days. H+was the main stressor in the exposures because labile Al was <6 µg·L1and the gill Al was lower than 27 µg·g dry weight1(highest in the medium group). The exposure environments did not cause any significant changes to gill tissue structures, gill Na+,-K+-ATPase activity, mortality, and growth parameters during the freshwater period. However, haematocrit was significantly increased and mean plasma chloride was significantly reduced (p < 0.05) in the low-pH group compared with the control group. This study indicated that the H+concentrations in the pH range 5.45.9 in water containing no to little gill-reactive Al do not impact salmon growth and physiology during smoltification. However, the reduction in blood haematocrit in the low-pH group 3 months after seawater transfer may imply long-term effects of the treatment.
Effects of nonrandom mating schemes to delay the inbreeding accumulation in cultured populations of coho salmon (Oncorhynchus kisutch)
Authors: Gallardo José A , Lhorente Jean Paul , García Ximena , Neira Roberto
Published: June 2004

Chilean salmon culture is based on a high degree of artificial selection, which has had the tendency to increase the inbreeding (F). Three types of nonrandom mating were evaluated to control the inbreeding in two best linear unbiased prediction selected coho salmon (Oncorhynchus kisutch) populations (even and odd). These included compensatory mating on the basis of breeding values (C), modified compensatory mating (C1) based on the family mean of breeding values, and mating that minimized the mean co-ancestry of the group selected (MC scheme). In the odd population, the MC scheme (F = 2.0%) reduced the increase in inbreeding of the next generation by 50% and 46% when compared with random mating of selected individuals with sib mating restricted (F = 3.9%) and with C (F = 3.7%), respectively. In the even population, the MC scheme reduced the increase in inbreeding by 14% compared with C1 (9.7 versus 11.2). In both populations, the MC scheme also reduced variance in inbreeding (even, 59%; odd, 39%). Thus, the MC scheme was more efficient in reducing the increase and variance of inbreeding, thus limiting the expression of inbreeding depression. Although the MC scheme was more time consuming, we recommend this scheme to carry out crosses in each generation.
Preservation of genetic diversity in restocking of the sea cucumberHolothuria scabrainvestigated by allozyme electrophoresis
Authors: Uthicke Sven , Purcell Steven
Published: June 2004

Population genetics analyses should be considered when releasing hatchery-produced juveniles of the sea cucumber Holothuria scabra when spawners from nonlocal populations are used. In New Caledonia, within-region genetic heterogeneity of H. scabra populations (examined through allozyme electrophoresis of 258 animals) indicated high gene flow between nine sites and FSTvalues did not deviate significantly from zero. However, exact tests indicated that populations at two sites with limited water exchange in the southern location were significantly different from populations at three other locations on the west coast. Inclusion of H. scabra sampled in Bali (n = 90) and Knocker Bay, Australia (n = 47), and comparisons with existing data from the west Pacific (Torres Strait, Solomon Islands, Upstart Bay, Hervey Bay) showed that populations were significantly different (using exact tests) and samples partitioned distinctly using unweighted pair group method with arithmetic mean clustering. Rogers' genetic distance values between populations were significantly related to geographic distances, showing a pattern of isolation by distance. The rapid increase in genetic distance over the first few hundred kilometres supports the view that the spatial extent of any translocation needs to be carefully considered on the basis of knowledge of variation in allele frequencies within the target area.
Macroinvertebrate response to logging in coastal headwater streams of Washington, U.S.A.
Authors: Haggerty S M , Batzer D P , Jackson C R
Published: June 2004

We examined the effects of logging on macroinvertebrate assemblages in first-order streams of four coniferous watersheds in Washington's Coastal Mountain ranges. Each watershed contained three to four first-order streams that were placed into one of three treatment types: clear-cut logging, operational buffer-strip (2.521 m) logging, or uncut reference streams. Prelogging baseline data on macroinvertebrate assemblages, channel morphology, sediment composition, sediment accretion rates, and water temperatures were collected from each stream in summer 1998. Logging operations were conducted the next winter and spring. Streams were resampled in summer 1999, within 1 year of logging, and summer 2000, 1+ years after logging. Preexisting treatment differences did not exist in 1998, indicating that postharvest treatment differences could be attributed to logging operations. In 1999, densities of macroinvertebrate collectors, densities and biomass of macroinvertebrate shredders, and accretion rates of organic sediments were greater in clear-cut and buffered streams than uncut references. These differences diminished by 2000. An increase in collecting and shredding macroinvertebrate is not a typical response to logging and may reflect the fact that logged streams became buried under slash, increasing detrital food supplies for these organisms. The narrow buffers used for this study did not prevent macroinvertebrate community changes associated with logging.
Impacts of sediment dewatering and rehydration on sediment nitrogen concentration and macrophyte growth
Authors: James William F , Barko John W , Eakin Harry L
Published: June 2004

River sediments were experimentally dewatered via exposure to air from an initial moisture content of 75% to 61% (~20% dewatered), 32% (~60% dewatered), and 4% (~95% dewatered). Sediments dewatered by 20% and 60% and rehydrated exhibited a lower exchangeable ammonium-N (NH4-N) concentration and a lower rate of nitrate/nitrite-N and NH4-N release from sediments compared with controls. In contrast, sediments dewatered by 95% and rehydrated exhibited a marked increase in exchangeable sediment NH4-N and a much higher rate of nitrate/nitrite-N (under oxic conditions) and NH4-N (under oxic and anoxic conditions) release from sediments. Sediment dewatered by 60% and 95% and rehydrated lost total N (18%), suggesting denitrification. Growth of Potamogeton pectinatus responded to changes in the exchangeable sediment NH4-N concentration; it was lower on partially dewatered and rehydrated sediments that exhibited lower exchangeable sediment NH4-N and elevated on sediment that was dewatered by 95%. Our results suggest that sediment N may be altered via sediment dewatering and rehydration to affect macrophyte growth.
Differences in juvenile phenotypes and survival between hatchery stocks and a natural population provide evidence for modified selection due to captive breeding
Authors: Kostow Kathryn E
Published: June 2004

Juvenile phenotypes and fitness as indicated by survival were compared for naturally produced steelhead (Oncorhynchus mykiss), a new local hatchery stock, and an old nonlocal hatchery stock on the Hood River, Oregon, U.S.A. Although the new hatchery stock and the naturally produced fish came from the same parent gene pool, they differed significantly at every phenotype measured except saltwater age. The characteristics of the new hatchery stock were similar to those of the old hatchery stock. Most of the phenotypic differences were probably environmentally caused. Although such character changes would not be inherited, they may influence the relative fitness of the hatchery and natural fish when they are in the same environment, as selection responds to phenotypic distributions. A difference in fitness between the new hatchery stock and naturally produced fish was indicated by significant survival differences. Acclimation of the new hatchery stock in a seminatural pond before release was associated with a further decrease in relative smolt-to-adult survival with little increase in phenotypic similarity between the natural and hatchery fish. These results suggest that modified selection begins immediately in the first generation of a new hatchery stock and may provide a mechanism for genetic change.
Definitive identification of fatty acid constituents in marine mammal tissues
Authors: Wetzel D L , Reynolds III J E
Published: June 2004

Analyses of fatty acid constituents in a sample of bowhead whale (Balaena mysticetus) blubber were conducted using a method that has not been applied before to studies of lipids in marine mammals. It involves creation and analysis of nitrogen (picolinyl) ester derivatives of the fatty acids followed by combined gas chromatography  mass spectrometry for verification of structures. Use of this approach allowed the structural confirmation of 45 different fatty acids in the blubber sample. The traditional method of methyl ester derivatization of fatty acids followed by gas chromatography  mass spectrometry analyses provides more component characterization than analyses by gas chromatography  flame ionization detection, but not enough to effectively differentiate double bond isomers or branched compounds. Although the novel approach is time intensive, we recommend that it be employed for studies where the precise identification and confirmation of fatty acids is important.
Landscape controls on boulder-rich, winter habitat availability and their effects on Atlantic salmon (Salmo salar) parr abundance in two fifth-order mountain streams
Authors: Coulombe-Pontbriand M , Lapointe Michel
Published: June 2004

We test the effect at river reach and segment scales of landscape controls on the distribution of Atlantic salmon (Salmo salar) parr densities, as well as associated variations in boulder (diameter ≥ 256 mm) abundance and potential overwintering habitat. This study encompasses data from 45 km of fifth-order mainstem channels along two neighbouring river catchments in the Gaspé region, Québec. At both scales, winter habitat availability was correlated with boulder availability. At the river segment scale (15 km), parr densities significantly correlated (P < 0.05) with boulder availability along the Bonaventure River, which presented significant intersegment variations in boulder abundances. In contrast, segment-scale boulder and parr abundances were uniformly low along the Petite Cascapédia River. At the reach scale (600 m), positive but less strongly significant boulder  parr abundance correlations were observed in both the Bonaventure and Petite Cascapédia rivers. Spatial variations in boulder abundances in these systems reflected variations in the degree of channel to valley walls coupling and imposed channel formative shear stresses. In similarly boulder-poor segments with comparable fry abundances, parr abundances were significantly greater along the Bonaventure than the Petite Cascapédia River, possibly because of the presence in the former system of nearby boulder-rich refugia segments.
Consequences of potential density-dependent mechanisms on recovery of ocean-type chinook salmon (Oncorhynchus tshawytscha)
Authors: Greene Correigh M , Beechie Timothy J
Published: June 2004

Restoring salmon populations depends on our ability to predict the consequences of improving aquatic habitats used by salmon. Using a Leslie matrix model for chinook salmon (Oncorhynchus tshawytscha) that specifies transitions among spawning nests (redds), streams, tidal deltas, nearshore habitats, and the ocean, we compared the relative importance of different habitats under three density-dependent scenarios: juvenile density independence, density-dependent mortality within streams, delta, and nearshore, and density-dependent migration among streams, delta, and nearshore. Each scenario assumed density dependence during spawning. We examined how these scenarios influenced priorities for habitat restoration using a set of hypothetical watersheds whose habitat areas could be systematically varied, as well as the Duwamish and Skagit rivers. In all watersheds, the three scenarios shared high sensitivity to changes in in nearshore and ocean mortality and produced similar responses to changes in other parameters controlling mortality (i.e., habitat quality). However, the three scenarios exhibited striking variation in population response to changes in habitat area (i.e., capacity). These findings indicate that nearshore habitat relationships may play significant roles for salmon populations and that the relative importance of restoring habitat area will depend on the mechanism of density dependence influencing salmon stocks.
Shift in wetland plant composition and biomass following low-level episodes in the St. Lawrence River: looking into the future
Authors: Hudon Christiane
Published: June 2004

The effects of a 1-m drop in average water levels in 1999 on species composition and biomass were documented for a St. Lawrence River wetland and compared with a similar episode in 1931. These observations highlight the manifold effects of past and future water level fluctuations on St. Lawrence River wetlands and faunal habitats, resulting from natural hydrologic variability, climate change, and (or) human intervention. In 1931 and 1999, waters were 23 °C warmer than the previous 10-year average. Low water levels markedly altered wetland vegetation: various Graminea (including Phalaris arundinacea and Phragmites australis) and facultative annual species invaded previously marshy areas. Submerged species previously found in shallow waters were replaced on dry ground by annual terrestrial plants; Alisma gramineum colonized emergent waterlogged mudflats. The low water levels of 1999 induced a spatially discontinuous plant biomass that was richer in terrestrial material than in previous years (19931994). In comparison with the 1930s, recent surveys indicate a decline of assemblages dominated by Equisetum spp. and Najas flexilis and a rise of those dominated by Lythrum salicaria, Potamogeton spp., and filamentous algae. These shifts reveal the additional effects of nutrient enrichment, alien species, and shoreline alteration accompanying a change from a mostly agricultural to a mostly urbanized and industrialized landscape.
Diminished social status affects ionoregulation at the gills and kidney in rainbow trout (Oncorhynchus mykiss)
Authors: Sloman Katherine A , Scott Graham R , McDonald D Gordon , Wood Chris M
Published: June 2004

Competition for social status can result in physiological differences between individuals, including differences in ionoregulatory ability. Subordinate rainbow trout (Oncorhynchus mykiss) had two-fold higher uptake rates of sodium across the gill and two-fold higher whole-body sodium efflux rates than the dominant fish with which they were paired. Sodium efflux was then divided into branchial and renal components, both of which were higher in subordinates. Branchial sodium efflux accounted for 95%98% of sodium loss. Plasma sodium concentrations were more variable, although not significantly different, in subordinate fish, suggesting that the increased loss of sodium in these trout is compensated for by an increase in uptake rates. Urine flow rates and plasma cortisol concentrations were higher in subordinate fish, but there was no difference in glomerular filtration rate between dominants and subordinates. Renal sodium reabsorption was significantly reduced in subordinates. In summary, the ionoregulation of subordinate individuals was altered, most likely occurring as a result of stress-induced changes in gill permeability, resulting in a higher throughput of water and increased branchial sodium efflux. These changes in ionoregulatory ability have many physiological implications, including the increased susceptibility of subordinates to ionoregulatory challenges and an increased metabolic cost of ionoregulation.
Evaluation of a chinook salmon (Oncorhynchus tshawytscha) bioenergetics model
Authors: Madenjian Charles P , O'Connor Daniel V , Chernyak Sergei M , Rediske Richard R , O'Keefe James P
Published: June 2004

We evaluated the Wisconsin bioenergetics model for chinook salmon (Oncorhynchus tshawytscha) in both the laboratory and the field. Chinook salmon in laboratory tanks were fed alewife (Alosa pseudoharengus), the predominant food of chinook salmon in Lake Michigan. Food consumption and growth by chinook salmon during the experiment were measured. To estimate the efficiency with which chinook salmon retain polychlorinated biphenyls (PCBs) from their food in the laboratory, PCB concentrations of the alewife and of the chinook salmon at both the beginning and end of the experiment were determined. Based on our laboratory evaluation, the bioenergetics model was furnishing unbiased estimates of food consumption by chinook salmon. Additionally, from the laboratory experiment, we calculated that chinook salmon retained 75% of the PCBs contained within their food. In an earlier study, assimilation rate of PCBs to chinook salmon from their food in Lake Michigan was estimated at 53%, thereby suggesting that the model was substantially overestimating food consumption by chinook salmon in Lake Michigan. However, we concluded that field performance of the model could not be accurately assessed because PCB assimilation efficiency is dependent on feeding rate, and feeding rate of chinook salmon was likely much lower in our laboratory tanks than in Lake Michigan.
Survey gear calibration independent of spatial fish distribution
Authors: Lewy Peter , Nielsen J Rasmus , Hovgård Holger
Published: June 2004

Trawl surveys provide important information for evaluation of relative stock abundance fluctuations over time. Therefore, when survey gears or vessels are changed, it is important to compare the efficiency and selectivity of old and new gears and vessels. A method for estimation of conversion factors is developed based on a survey design where paired hauls are taken in the same trawl track line. The method explicitly accounts for changes in fish density caused by trawling disturbance. A generalized linear model for paired hauls catches is analytically derived and the gear conversion and disturbance parameters with their precision are obtained using standard software. Simulation studies carried out additionally showed that the estimated conversion factors were practically unbiased. Because of the independence of the spatial fish distribution, the new method is preferable to the traditional paired hauls design for which it is generally not possible to obtain the statistical properties of the estimated conversion factors. The paper is concluded with suggestions on how to optimize survey design. The method was used to estimate conversion factors for Atlantic cod (Gadus morhua) from Danish gear calibration experiments in the Baltic Sea.
Early life history studies of preypredator interactions: quantifying the stochastic individual responses to environmental variability
Authors: Pepin Pierre
Published: June 2004

Laboratory evidence shows that growth and survival of larval fish are strongly affected by variations in prey and predators; field evidence, in general, does not. This discrepancy may be partly due to the mismatch of scales at which manipulative and observational studies are conducted, or perhaps field studies are somehow not detecting the variable component of the larvae or their environment. I discuss potentially important variable features of fish larvae and their environment and show how mean values can be misleading. Using data from several field studies dealing with the growth and mortality of radiated shanny (Ulvaria subbifurcata) larvae, I illustrate how observational programs can miss important variation. I show evidence of how differences among individuals may lead to varying responses to fluctuations in prey availability. I also discuss issues concerning the level of variability in environmental conditions that may be described by standard survey methods used in the study of larval fish. The examples are intended to serve as illustration of the need to better describe the underlying stochastic structure of environmental conditions to understand early life dynamics.
Transition to an alternate state in a continental shelf ecosystem
Authors: Choi Jae S , Frank Kenneth T , Leggett William C , Drinkwater Ken
Published: June 2004

The collapse of Atlantic cod (Gadus morhua) stocks in the northwest Atlantic Ocean ranks among the most dramatic and widely known ecological changes of the 20th century. Less widely known are the systemic changes that occurred within these areas prior to and coincident with the cod collapse. Our analysis of a fishery-independent, long-term, standardized database collected on the eastern Scotian Shelf off Nova Scotia revealed that during the past four decades, coherent, community-level reductions in body size, biomass, and physiological condition have occurred in the resident demersal fish species. The changes occurred over large spatial (>104km2) and short temporal (<10 years) scales, suggesting a progressive decline in the nature and extent of the energy flow through the benthic system. The unexpected and persistent poor condition of a variety of morphologically and functionally dissimilar demersal fish species, living in an environment of reduced intra- and inter-specific competition, suggests a decoupling of the benthic pelagic systems. This decoupling appears to be attributable to a cascading series of processes involving the cumulative removal of biomass resulting from commercial fishing, compensatory and self-stabilizing increases in pelagic fish biomass, and a decline in groundfish productivity exacerbated by decadal scale variability in water temperature and stratification.
Heterogeneity of ITS1 sequences in the biting midge Culicoides impunctatus (Goetghebuer) suggests a population in Argyll, Scotland, may be genetically distinct
Authors: Ritchie Allyson , Blackwell Alison , Malloch Gaynor , Fenton Brian
Published: June 2004

Ribosomal DNA (rDNA) internal transcribed spacer 1 (ITS1) is a useful genomic region for understanding evolutionary and genetic relationships. In the current study, variation in ITS1 from eight Culicoides species was analysed by PCR, DNA restriction analysis, cloning, and sequencing. ITS1 variants were essentially homogenized within a species, as sequences were identical or closely related. However, Culicoides impunctatus ITS1 sequences derived from one (Argyll) of five populations contained considerable genomic diversity. The secondary structure of each ITS1 was computed. The structure aided the production of an accurate alignment and the identification of a large indel. A phylogenetic analysis was performed. Some of the sequences from the diverse Argyll C. impunctatus population were more related to Culicoides imicola, a vector of animal pathogens in the Old World, than they were to the other C. impunctatus sequences. Thus, the rDNA ITS1 regions of individuals in the Argyll C. impunctatus population were not conforming to the general theory of rDNA homogenization through molecular drive.Key words: Culicoides, ITS1, phylogeny, rDNA, secondary structure.
Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.)
Authors: Park Young Hoon , West Marilyn A.L , St. Clair Dina A
Published: June 2004

Cultivated tomato (L. esculentum L.) germplasm exhibits limited genetic variation compared with wild Lycopersicon species. Amplified fragment length polymorphism (AFLP) markers were used to evaluate genetic variation among 74 cultivars, primarily from California, and to fingerprint germplasm to determine if cultivar-specific patterns could be obtained. All 74 cultivars were genotyped using 26 AFLP primer combinations; of the 1092 bands scored, 102 AFLP bands (9.3%) were polymorphic. Pair-wise genetic similarity coefficients (Jaccard and Nei–Li) were calculated. Jaccard coefficients varied from 0.16 to 0.98 among cultivar pairs, and 72% of pair-wise comparisons exceeded 0.5. UPGMA (unweighted pair-group method with arithmetic averaging) clustering and principle component analysis revealed four main clusters, I–IV; most modern hybrid cultivars grouped in II, whereas most vintage cultivars grouped in I. Clusters III and IV contained three and two cultivars, respectively. Some groups of cultivars closely related by pedigree exhibited high bootstrap values, but lower values (<50%) were obtained for cluster II and its four subgroups. Unique fingerprints for all 74 cultivars were obtained by a minimum of seven AFLP primer pairs, despite inclusion of some closely related cultivars. This study demonstrated that AFLP markers are effective for obtaining unique fingerprints of, and assessing genetic diversity among, tomato cultivars.Key words: Lycopersicon esculentum, AFLPs, DNA fingerprinting, genetic diversity, phenetic relationships.
Phylogeny and expression of paralogous and orthologous sulphate transporter genes in diploid and hexaploid wheats
Authors: Buchner Peter , Prosser Ian M , Hawkesford Malcolm J
Published: June 2004

Twelve genes encoding two closely related subtypes (ST1.1a and ST1.1b) of a sulphate transporter have been identified in the diploid wheats Aegilops tauschii, Triticum urartu, and Aegilops speltoides, as well as the hexaploid Triticum aestivum. Based on phylogenetic comparisons with other plant sulphate transporters, the ST1.1a and 1.1b subtypes aligned with group 1 of the plant sulphate transporter gene family. The exon–intron structure was conserved within the ST1.1a or ST1.1b genes; however, substantial variability in intron sequences existed between the two types. The high overall sequence similarity indicated that ST1.1b represented a duplication of the ST1.1a gene, which must have occurred before the evolution of the ancestral diploid wheat progenitor. In contrast with the close relationship of the T. urartu and Ae. tauschii sequences to the corresponding A and D genome sequences of T. aestivum, the divergence between the Ae. speltoides sequences and the B genome sequences suggested that the B genome ST1.1a gene has been modified by recombination. Transcript analysis revealed predominant expression of the ST1.1a type and an influence of sulphur availability on the level of expression.Key words: genome, phylogeny, progenitor, sulphate transport, wheat.
An analysis of mismatched duplex DNA unzipping through a bacterial nanopore
Authors: Sutherland Todd C , Dinsmore Michael J , Kraatz Heinz-Bernhard , Lee Jeremy S
Published: June 2004

A 50-base Guide strand was synthesized that consisted of a central 10-base probe sequence flanked by two tracts of 20 adenine residues. Target sequences of 10 bases containing up to three mismatches were prepared and hybridized to the Guide strand in 1 M KCl. The transport of these constructs through single α-hemolysin pores was analysed by measuring the current blockade as a function of time. Complementary dsDNA takes significantly longer (840 ± 60 µs) to pass through the pore than a sequence of the same length containing a single (590 ± 45 µs) and a double (270 ± 50 µs) mismatch. Constructs involving three mismatches were indistinguishable from Guide ssDNA transport (120 ± 30 µs). The results suggest that dsDNA must unzip as it is transported through the nanopore. Duplexes containing mismatches unzip more quickly and can be distinguished from those with perfect complementarity.Key words: DNA unzipping, bacterial nanopores, DNA transport, single-molecule detection, DNA mismatch.
Characterization of glycineN-methyltransferase from rabbit liver
Authors: Kloor Doris , Karnahl Katrin , Kömpf Jost
Published: June 2004

The enzymatic properties of glycine N-methyltransferase from rabbit liver and the effects of endogenous adenosine nucleosides, nucleotides and methyltransferase inhibitors were investigated using a photometrical assay to detect sarcosine with o-dianisidine as a dye. After isolation and purification the denatured enzyme showed a two-banded pattern by SDS–PAGE. The enzyme was highly specific for its substrates with a pH-optimum at pH 8.6. Glycine N-methyltransferase exhibits Michaelis-Menten kinetics for its substrates, S-adenosylmethionine and glycine, respectively. The apparent Kmand Vmaxvalues were determined for both the substrates, the other substrate being present at saturating concentrations. The enzyme was strongly inhibited in the presence of S-adenosylhomocysteine, 3-deazaadenosine, and 5′-S-isobutylthio-5′-deoxyadenosine. All other inhibitors investigated, adenosine, 2′-deoxyadenosine, aciclovir, and 5′-N-ethylcarboxamidoadenosine were poor inhibitors of the methylation rection. Adenine nucleotides and vidarabin were without effect on the enzymatic activity. Based on the kinetic data glycine N-methyltransferase from rabbit liver exhibits appreciable activity at physiological S-adenosylmethionine and S-adenosylhomocysteine levels.Key words: glycine N-methyltransferase, S-adenosylhomocysteine, S-adenosylmethionine, sarcosine oxidase, peroxidase.
Expression of iNOS gene in macrophages stimulated with 17β-estradiol is regulated by free intracellular Ca2+
Authors: Azenabor A A , Yang S , Job G , Adedokun O O
Published: June 2004

17β-Estradiol has potent Ca2+ ionophore capability and its signaling in macrophages is mediated through binding to surface and genomic receptors, resulting in transient nitric oxide (NO) elaboration. We decided to examine if the transient release of NO is due to Ca2+ influx pattern or the quenching effect of superoxide (·O2–) through peroxynitrite formation. Differential chelation of intracellular Ca2+ ([Ca2+]i) showed that NO generation was favored by [Ca2+]i concentration of 237 nM. Application of an estrogen receptor antagonist ICI 182 780 resulted in attenuation of estradiol mediated NO release. Studies directed at identifying the possible role of ·O2– in the attenuation of NO showed no supportive evidence. Inhibition of extracellular Ca2+ channel or extracellular and intracellular Ca2+ channels showed data consistent with a case for optimum Ca2+ influx signal favoring iNOS gene expression, accompanied by an elevation in iNOS protein. These data show that Ca2+ influx pattern determines macrophage NO elaboration.Key words: optimum Ca2+ signals, activation of iNOS gene, estradiol signaling.
Bioenergetic remodeling during cellular differentiation: changes in cytochromecoxidase regulation do not affect the metabolic phenotype
Authors: Lyons Carrie N , Leary Scot C , Moyes Christopher D
Published: June 2004

Myogenesis induces mitochondrial proliferation, a decrease in reactive oxygen species (ROS) production, and an increased reliance upon oxidative phosphorylation. While muscles typically possess 20%–40% excess capacity of cytochrome c oxidase (COX), undifferentiated myoblasts have only 5%–20% of the mitochondrial content of myotubes and muscles. We used two muscle lines (C2C12, Sol8) and 3T3-L1 pre-adipocytes to examine if changes in COX regulation or activity with differentiation cause a shift in metabolic phenotype (i.e., more oxidative, less glycolytic, less ROS). COX activity in vivo can be suppressed by its inhibitor, nitric oxide, or sub-optimal substrate (cytochrome c) concentrations. Inhibition of nitric oxide synthase via L-NAME had no effect on the respiration of adherent undifferentiated cells, although it did stimulate respiration of myoblasts in suspension. While cytochrome c content increased during differentiation, there was no correlation with respiratory rate or reliance on oxidative metabolism. There was no correlation between COX specific activity and oxidative metabolism between cell type or in relation to differentiation. These studies show that, despite the very low activities of COX, undifferentiated myoblasts and pre-adipocytes possess a reserve of COX capacity and changes in COX with differentiation do not trigger the shift in metabolic phenotype.Key words: oxidative phosphorylation, myogenesis, nitric oxide, reactive oxygen species, cytochrome c oxidase.
Retinoic acid-inducible gene-I is induced by interferon-γ and regulates the expression of interferon-γ stimulated gene 15 in MCF-7 cells
Authors: Cui Xue-Fan , Imaizumi Tadaatsu , Yoshida Hidemi , Borden Ernest C , Satoh Kei
Published: June 2004

Retinoic acid-inducible gene-І (RIG-І) is a member of the DExH box family proteins, which have diverse roles in regulation of gene expression and cellular functions. We found RIG-I mRNA and protein were expressed in MCF-7 human breast cancer cells stimulated with interferon-γ (IFN-γ). This effect of IFN-γ was observed in concentration- and time-dependent manners, and IFN-γ also induced promoter activity of RIG-I. Transfection of GFP-RIG-I cDNA into MCF-7 cells resulted in the expression of RIG-I protein in cytoplasm. Overexpression of RIG-I induced the upregulation of IFN-γ stimulated gene 15, which has the potential to amplify the immunomodulatory effects. We conclude that IFN-γ induces the expression of RIG-I, which may play a role in the immunological effects of IFN-γ.Key words: retinoic acid-inducible gene-I, interferon-γ, interferon-γ stimulated gene 15.