bluuebunny/crossref_metadata_2025 huggingface dataset:
Seasonal variation in habitat use by marsh fishes
Authors: Jordan F. , Babbitt K. J. , Mclvor C. C.
Published: July 2006

Abstract—We used I‐m2throw traps to examine habitat use by smallsized fishes within a mosaic of wet prairies and sloughs in the headwaters of the St. Johns River, Florida between August 1992 and November 1995. Estimates of total fish density and biomass varied temporally, but did not differ significantly between habitats. Patterns of habitat use, however, differed among the five numerically dominant species. Bluefin killifish, mosquitofish, and golden topminnows were more abundant in sloughs than in wet prairies. In contrast, Everglades pygmy sunfish were more abundant in wet prairies than in sloughs. Finally, the abundance of least killifish did not differ between habitats. Fish densities were positively correlated with plant biomass (i. e., habitat complexity) and negatively correlated with water depth (i. e., hydrology). Species richness and composition were similar among habitats. However, consistent differences in the relative abundance of numerically dominant species between habitats indicated some degree of habitat‐specific assemblage structure. Most species were concentrated into deeper sloughs during drying events. This assemblage of small‐sized fishes appears to respond relatively rapidly to changes in habitat structure and hydrologic conditions. We therefore recommend that resource managers consider using fishes as indicator taxa to evaluate the efficacy of ongoing restoration and management efforts in wetland systems.
Are native brook charr and introduced rainbow trout differentially adapted to upstream and downstream reaches?
Authors: Magoulick D. D. , Wilzbach M. A.
Published: July 2006

Abstract— Due to species introductions, brook charr (Salvelinus fontinalis) and rainbow trout (Oncorhynchus mykiss) occur together in many North American streams and typically exhibit a pattern of distribution in which brook charr numerically dominate headwaters and rainbow trout dominate downstream reaches. It has been suggested that 1) the two species compete or 2) the two species do not compete because they are differentially adapted to environmental conditions found in upstream and downstream zones. We assessed whether there were differences in growth and macrohabitat (pool, run and riffle) selection of brook charr and rainbow trout in upper, middle and lower stream zones of a small Pennsylvania stream. Brook charr and rainbow trout placed in replicate paired enclosures set in upstream and downstream reaches showed no significant differences in growth and survival rates upstream, but brook charr had significantly greater growth rates than rainbow trout downstream. Enclosed fish and free‐ranging fish both had negative growth rates during the summer. Enclosed fish lost significantly less weight than free‐ranging fish. Instantaneous growth rates of free‐ranging adult brook charr and rainbow trout from May to August were negative for both species in all stream zones. Underwater observations of adult brook charr and rainbow trout showed both species occurred significantly more often in pool macrohabitats than expected on the basis of macrohabitat availability, except for rainbow trout in the upstream zone. The proportion of pool macrohabitat was not significantly different among stream zones. Brook charr do not appear to be better adapted to upstream environments in Powdermill Run based on growth, survival and macrohabitat selection during summer. Negative biotic interactions acting along with differential environmental adaptations may explain the pattern of distribution of brook charr and rainbow trout in streams, but long‐term transplant experiments with additional life stages will be necessary to examine this hypothesis.
Predator response to releases of American shad larvae in the Susquehanna River basin
Authors: Johnson J. H. , Ringler N. H.
Published: July 2006

Abstract— Predation on American shad (Alosa sapidissima) larvae within the first two hours of release was examined from 1989 to 1992 on 31 occasions at stocking sites in the Susquehanna River basin. Twenty‐two fish species consumed shad larvae; the dominant predators were spotfin shiner (Cyprinella spiloptera), mimic shiner (Notropis volucellus) and juvenile smallmouth bass (Micropterus dolomieu). The number of shad larvae found in predator stomachs ranged from 0 to 900. Mortality of shad larvae at the stocking site was usually less than 2%. The greatest mortality (9.6%) occurred at the highest stocking level (1.5 million larvae). Highly variable predation rates and release levels of shad insufficient to achieve predator satiation hindered the ability to determine a specific type of functional response of predators. Predator numbers increased with stocking density, indicating short‐term aggregation at the release site. Because of practical problems associated with releasing the large numbers of larvae that would be required to satiate predators, routine stocking at these levels is probably unreasonable. Releases of 400,000 to 700,000 larvae may reduce predation by offsetting depensatory mechanisms that operate on small releases and the effects of increased predation due to predator aggregation on large releases. Night stocking may reduce predation on larval shad at the release site.
Evaluation of ovum storage techniques for reproductive studies of fishes
Authors: Heins D. C. , Baker J. A.
Published: July 2006

Abstract– We compared dry masses of mature oocytes and ripe eggs from Etheostoma lynceum and Etheostoma caeruleum that were stored in varying concentrations of either formalin or isopropyl alcohol. In comparison to 10% formalin, alcohol significantly reduced the weights of both mature oocytes and ripe eggs, with 25% isopropyl alcohol resulting in much smaller reductions than 50% isopropanol. Three percent formalin resulted in smaller decreases in the masses of oocytes and eggs than the alcohol treatments, and not all comparisons with 10% formalin were significantly different. We recommend fixing specimens and storing them and gametic cells removed from them in 10% formalin. In cases where specimens or eggs in alcohol must be used in addition to material in formalin, correction factors (to formalin standard) should be developed, but the correction should not be made uncritically due to the varying effects alcohol may have among samples.
A test for competition between two Gobiomorphus species (Teleostei: Eleotridae) in artificial channels
Authors: Glova G. J.
Published: July 2006

Abstract– The occurrence of competition between common (Gobiomorphus cotidianus) and upland (G. breviceps) bullies was tested in summer in artificial channels. Although these species have different life histories, they are morphologically and ecologically similar, and frequently cooccur in New Zealand's fresh waters. Mortality during the test period averaged 11.3±2.4% and 17.7±1.9% for the common bully in triplicate control and experimental channels, respectively; in contrast, upland bully mortality was 2.3±1.9% in the control and zero in the experimental channels. Common bullies showed no significant differences in mean length, weight, condition, and specific growth between the control and experimental tests. For upland bullies, all of the above parameters were significantly less in the controls than the experimentals, an outcome that was indicative of intraspecific competition. Moreover, there was a significant linear trend in the distribution of upland bullies, with their numbers being highest at the upstream end of the channels in both the control and experimental tests. Common bullies showed no such trend, although significantly higher proportions of fish were present towards the central positions in the experimental channels, suggesting there was some displacement of them by upland bullies. It is concluded that interspecific competition is not of major importance between populations of these two eleotrids in small streams, although the abundance and upstream penetration of common bullies may be affected to some extent by interaction with upland bullies.
Sex ratio changes in the long‐term Windermere pike and perch sampling program
Authors: Paxton C. G. M. , Fletcher J. M. , Hewitt D. P. , Winfield I. J.
Published: July 2006

Abstract– Analysis of the Windermere (England), Perca fluviatilis (1965–1997) and Esox lucius (1943‐1997) fishery data indicates there have been substantial changes in sex ratios through time. In the case of perch, a 1976 perch disease outbreak substantially skewed the sex ratio in favor of females. It took over a decade for the fishery to recover to its pre‐1976 state. In the case of pike, both catch and year‐class data are female biased, but this bias has significantly weakened through time. This trend towards proportionately more males through time may reflect an effect of increasing spring temperatures or an evolutionary or phenotypic response to female‐biased fishing pressure.
Ecological genetics: introductory note
Authors: Utter F. M.
Published: July 2006

Abstract– The eight papers resulting from the Ecological Genetics session of the symposium Ecology of Stream Fish: State of the Art and Future Prospects (Luarca, Spain, April 1998) describe the use of molecular genetic markers to investigate questions of population distinctness, interbreeding, and adaptation in five salmonid species. Widely contrasting ecological distinctions described in four species indigenous to western North America [steelhead (rainbow) trout, sockeye salmon, pink salmon and bull trout] reflect past natural and human‐induced activities, serving to guide future management and conservation actions through optimizing adaptive opportunities, and preventing genetic losses through localized extinctions. Studies of brown trout contrast widespread introgressions from exogenous hatchery introductions that threaten the integrity of native Spanish populations with a reduced threat based on use of indigenous fish in Portuguese hatcheries. A 9‐year study of natural progeny of two genetically distinct Swedish brown trout populations introduced to a previously trout‐free area identifies apparent local adaptations as a model to guide other translocations.
Genetic population structure within streams: microsatellite analysis of bull trout populations
Authors: Spruell P. , Rieman B. E. , Knudsen K. L. , Utter F. M. , Allendorf F. W.
Published: July 2006

Abstract– We used six polymorphic microsatellite loci to investigate a potential metapopulation system in bull trout (Salvelinus confluentus) from five spawning localities in the Lightning Creek drainage, a tributary to Lake Pend Oreille, Idaho. The number of spawners as estimated by redd counts is low in all populations sampled. Analytic viability models indicate that local isolated populations of these sizes are unlikely to persist. We tested two hypotheses: (1) these are remnant populations that are vulnerable to local extinction, or (2) these populations are interconnected by migration and are being maintained at larger effective sizes than indicated by the redd counts (i. e. metapopulation dynamics). All populations within the Lightning Creek basin are significantly differentiated (P > 0.005), and the allele frequencies appear to be stable among temporally separated subsamples within locations. It is therefore unlikely that extensive dispersal has linked tributaries in a manner consistent with a metapopulation structure. The low number of spawning individuals combined with the degree of isolation indicated by the genetic data suggest that extinction of the tributary populations is probable if temporal variability and small size is prolonged. However, these populations contain amounts of genetic variation similar to populations throughout the range of bull trout. Therefore, if the apparent demographic trends are reversed, these populations may recover without suffering the detrimental effects of a severe bottleneck.
Allozyme and mitochondrial DNA variation describe ecologically important genetic structure of even‐year pink salmon inhabiting Prince William Sound, Alaska
Authors: Seeb J. E. , Habicht C. , Templin W. D. , Seeb L. W. , Shaklee J. B. , Utter F. M.
Published: July 2006

Abstract– Allozyme and mitochondrial DNA (mtDNA) data were obtained from pink salmon throughout Prince William Sound, Alaska, from two hatchery, five upstream, and 20 tidal locations distributed among five management regions collected during 1994. Screening for allozymes included 66 loci for 92 to 100 fish per sample. Thirty‐four loci had variant allele frequencies <0.01 in one or more collections and were used for population analyses. Eight haplotypes were detected after screening 40 fish per collection for variation at the ND5/ND6 region of mtDNA using six restriction enzymes. Significant and apparently stable differences detected by both data sets permit rejecting a null hypothesis of panmixia and support managing native populations in Prince William Sound at the regional level. Distinctions between upstream and tidal collections were detected within Lagoon Creek (allozymes) and Koppen Creek (mtDNA). Significant regional heterogeneity was detected within upstream (allozymes and mtDNA) and tidal (allozymes) collections; however, upstream collections were more divergent from each other than were tidal collections. The absence of distinction of Armin F. Koernig Hatchery from almost all regions was consistent with multiple origins of this stock. Conversely, Solomon Gulch Hatchery in the East Region was distinct from all regions but East, consistent with a more restricted origin and influence.
Genetic effects of introduced hatchery stocks on indigenous brown trout (Salmo trutta L.) populations in Spain
Authors: Cagigas M. E. , Vázquez E. , Blanco G. , Sãnchez J. A.
Published: July 2006

Abstract– To assess the levels of gene introgression from cultured to wild brown trout populations, four officially stocked locations and four nonstocked locations were sampled for one to three consecutive years and compared to the hatchery strain used for stocking. Allozyme analysis for 25 loci included those previously described as providing allelic markers distinguishing hatchery stocks and native populations. Different levels of hybridization and introgression with hatchery índividuals were detected in stocked drainages as well as in protected locations. These findings indicate that new policies for stocking and monitoring hatchery fish are needed if gene pools of wild Spanish brown trout populations are to be preserved.
Erosion of the native genetic resources of brown trout in Spain
Authors: García‐Marín J. L. , Sanz N. , Pla C.
Published: July 2006

Abstract– We analyzed the introduction of hatchery‐reared trout in the Riutort Creek, a small stream in the eastern Spanish Pyrennees. We used gene correlation matrices between individuals to analyze the fish coancestry in the Riutort Creek samples and in the hatchery stock. Hatchery fish disturbed the single ancestry in the native population of the creek, and were clearly detected with principal coordinate analysis of the gene correlation matrix. The amount of introgression produced by successful introductions was estimated from the principal coordinate analysis projections of the matrix of FST values between the putative native Riutort Creek population, the hatchery stock and the introgressed population. In only two years the amount of introgression rose to 10%, indicating that 5% of the native ancestry is lost each year as a result of the stocking program. Based on these results, we review the present understandings on the genetic impact of hatchery fish on indigenous Spanish brown trout populations. The stocking of these populations involves a non‐native broodstock widespread through the Spanish hatcheries, but successful stockings appear to be limited to wild populations subjected to occasional releases in protected or unfished areas. Surprisingly, extensive stocking in fished areas result in a more limited genetic impact on the recipient native population.
Microsatellite diversity in sympatric reproductive ecotypes of Pacific steelhead (Oncorhynchus mykiss) from the Middle Fork Eel River, California
Authors: Nielsen J. L. , Fountain M. C.
Published: July 2006

Abstract– Genetic differentiation between two reproductive ecotypes of anadromous steelhead found in the Middle Fork Eel River in northern California was tested using 16 microsatellite loci. Twelve of these loci showed significant differences in allelic frequency between the two Middle Fork Eel River steelhead populations (Fisher's exact P <0.05). Fisher's combined test for independence also supported significant genetic separation between the two reproductive ecotype (P < 0.001). Analysis of molecular variance indicated that only 1% of the overall microsatellite allelic variation contributed to differences between summer‐ and winter‐run steelhead in the Middle Fork Eel River. Variation found among individuals within the two runs equaled 18.2%. Analyses showed less genetic distance between the two populations of steelhead in the Middle Fork Eel River than in comparisons made with geographically proximate coastal winter‐run fish. Divergence time based on genetic distance for the two within‐basin reproductive ecotypes was estimated to be 16,000–28,000 years ago.
Spatial and temporal variation in habitat and fish community characteristics in a Kansas Flint Hills stream
Authors: Tripe J. A. , Guy C. S.
Published: July 2006

Abstract– Four locations (i. e., mouth, lower midreach, upper midreach, and headwater) were sampled bimonthly for two years in a Kansas, Flint Hills stream. Principal components 1 (PC1; depth, width, substrate) and 2 (PC2; velocity, water temperature, conductivity) accounted for 70% of the variation in habitat variables. Principal component 1 varied more spatially than temporally, and PC2 exhibited the opposite pattern. Species diversity varied spatially with the highest values at the upper midreach and mouth and lowest in the headwaters. Species diversity also varied temporally with highest values in summer months and lowest in late fall and carly spring. Catch per unit effort (C/f) varied temporally and spatially by trophic guilds and species. In general, C/f values were highest in late fall and early spring and were lowest in early and mid summer. Fixed spatial variation (i. e., spatial difference independent of temporal factors) was higher than ephemeral spatial variation (i. e., spatial variation that varies temporally) for species with specialized feeding habits. Conversely, ephemeral spatial variation was highest for fish species with generalized feeding habits. These data indicate that standardizing reaches and dates are important if habitat, species diversity, and C/f data will be used in managing stream ecosystems.
Predation relationships between introduced salmonids and the native fish fauna in lakes and reservoirs in northern Patagonia
Authors: Macchi P. J. , Cussac V. E. , Alonso M. F. , Denegri M. A.
Published: July 2006

Abstract– A few native and exotic fish species are caught frequently in Andean lakes and reservoirs of northwestern Patagonia. Puyen (Galaxias maculatus) prey on zooplankton and benthos. Percichthys trucha has a wide range of prey, mainly benthos, while P. colhuapiensis become piscivorous when grown. Pejerrey (Odonthestes hatcheri) is omnivorous and large size individuals can be piscivorous. A siluroid, Diplomystes viedmensis, preys on benthos, insects, and fishes. Introduced salmonids are potential piscivorous. The puyen is the major prey category among fishes. Salmonids and perchichtids seem to partially overlap their diets but predation on Diplomystes appears to be restricted to salmonids. Present abundance of puyen, pejerrey and Percichthys spp. does not indicate a strong salmonid effect. However, the low abundance of D. viedmensis does. We studied present predation relationships among native and introduced fishes and postulated possible effects upon native fish fauna.
Influence of agriculture on in‐stream habitat and fish community structure in Piedmont watersheds of the Chattahoochee River System
Authors: Walser C. A. , Bart H. L.
Published: July 2006

Abstract– Historical and contemporary fish collections were used to examine the influence of agricultural land use on fish communities in the central Chattahoochee River, USA. In‐stream habitat data were also collected to examine the relationship between agricultural land use and stream habitat structure. We found a significant positive relationship between agricultural land use and in‐stream sediment (r2=0.43, P=0.01). Stream depth heterogeneity decreased significantly with increased sediment (r2=0.39, P=0.02). Mainstream reaches draining agricultural lands had significantly lower levels of fish diversity than forested reaches (r2=0.47, P < 0.01). Agriculture also explained significant variation in mainstream species abundances but was not a significant predictor of species diversity or species abundances in headwater reaches. Most pool species that use coarse substrates decreased in relative abundance with increasing agriculture in the watershed. Our results suggest that mainstream environments and their associated communities are more susceptible than headwater reaches to the effects of agriculture. This finding has important consequences for conservation, since mainstream reaches are reported to function as species refugia during pulse disturbance events (e. g., floods, droughts).
Abnormal Predicted Diffusion Capacities in Healthy Asians: An Inequality with a Solution
Authors: Pesola Gene R. , Huggins Gladstone , Sherpa Tsering Y.
Published: July 2006

Background: Asian lung volumes are 10–15% less than those of Caucasians. Objectives: To test the hypothesis that healthy Asians might be labeled as abnormal using three commonly used Caucasian-derived prediction equation estimates (PEE) of DLCO currently used. In addition, a Chinese-derived PEE of DLCO was tested to determine its validity in non-Chinese Asians. Methods: Forty-one healthy Asians underwent DLCO testing. Controls consisted of the PEE and 12 healthy Caucasians. Measured DLCO was compared with the Miller, Knudson, Crapo and one Chinese PEE. Abnormal was defined as a DLCO <80% predicted. Gas dilution and plethysmography estimated alveolar volume. Proportions in parentheses in the results below are DLCO adjusted for alveolar volume. Results: The average Asian DLCO was 25.75 ± 5.55 ml/min/mm Hg, no different than the predicted DLCO of 25.29 ± 5.53 seen with Chinese PEE. This was different (p < 0.01) than the predicted DLCO of 27.82 ± 5.09, 33.66 ± 6.29, and 31.64 ± 5.33 for the Miller, Knudson, and Crapo equations, respectively. This resulted in 4/41 (0/41), 27/39 (2/39), 21/41 (3/41) and 1/41 (0/41) DLCO measurements being defined as abnormal using Miller, Knudson, Crapo and Chinese PEE, respectively. In Caucasians, the measured DLCO was similar to the Miller but significantly lower than the Knudson and Crapo PEE. Measured lung volumes were significantly smaller compared to predicted for the three Caucasian PEE in Asians, with no difference in Caucasians. There was no difference in measured lung volumes and Chinese PEE. Conclusions: Current Caucasian PEE for DLCO when used in healthy Asians result in an abnormal reading that is incorrect from 10 to 50% of the time. This PEE failure is related to a reduction in lung volume not accounted for. The Chinese PEE for DLCO works for non-Chinese Asians and should replace Caucasian PEE in the US in all Asians.
Long-Term Oxygen Therapy in Chronic Obstructive Pulmonary Disease: The Use of Concentrators and Liquid Oxygen Systems in North-Western Greece
Authors: Katsenos Stamatis , Charisis Alexandros , Daskalopoulos Georgios , Constantopoulos Stavros H. , Vassiliou Miltiadis P.
Published: July 2006

Background: Long-term oxygen therapy (LTOT) is the cornerstone mode of treatment in patients with chronic obstructive pulmonary disease (COPD). Objectives: The present study aims to investigate the effect of two oxygen sources (concentrator and liquid oxygen) on quality of life, exercise tolerance and compliance to LTOT in patients with COPD. Methods: The survey included 104 patients with COPD (31 on concentrator treatment and 73 on liquid oxygen). Patients were subjected to pulse oximetry, basic spirometry, measurement of health-related quality of life by the St. George’s Hospital respiratory questionnaire instrument and assessment of dyspnoea severity by the modified Borg category scale. Exercise tolerance was evaluated by the SaO2 value after 3 min of walking. SaO2 was measured before and after treatment with each device. Compliance with therapy was defined by the daily duration of oxygen use. Results: The two LTOT groups did not differ significantly concerning pulmonary function tests (p = 0.49 for FEV1, 0.98 for FVC, 0.15 for FEV1/FVC% and 0.38 for FEF50%), SaO2 before (p = 0.28) and after (p = 0.80) O2 treatment and after the 3-min walking trial (p = 0.47), and St. George’s Hospital respiratory questionnaire score (p = 0.45). The liquid oxygen group was less dyspnoeic before treatment (p = 0.02), but this difference disappeared after treatment (p = 0.95). A highly significant difference (p < 0.001) was noted concerning the daily oxygen use. Complete compliance to LTOT (≧15 h/day) was observed in 12.9 and 42.5%, respectively (p < 0.005). Noise disturbance was noted only in the concentrator group (80%). Conclusions: We conclude that stationary liquid oxygen seems to be a satisfactory alternative mode for LTOT treatment in COPD patients, with higher patient compliance to therapy in comparison with concentrators.
Cathodic Electrodeposition of Ordered Porous Titania Films by Polystyrene Colloidal Crystal Templating
Authors: Yan Hongwei , Yang Yingling , Fu Zhengping , Yang Beifang , Xia Linsheng , Xu Yuandong , Fu Shengquan , Li Fanqing
Published: July 2006

The fabrication of ordered porous titania films using polystyrene colloidal crystal templates by cathodic electrodeposition is reported. A new strategy using Ti(SO4)2 as Ti source for the potentiostatic electrodeposition of titania has been developed. An improved post-treatment of the electrodeposited samples was executed to obtain long-range ordered porous films.
No Accelerated Rate of Protein Evolution in Male-Biased Drosophila pseudoobscura Genes
Authors: Metta Muralidhar , Gudavalli Rambabu , Gibert Jean-Michel , Schlötterer Christian
Published: July 2006

Sexually dimorphic traits are often subject to diversifying selection. Genes with a male-biased gene expression also are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex-biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex-related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in the rate of evolution for genes with a male-biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male-biased genes, our data imply a radically different selection regime in D. pseudoobscura.
Introns Regulate RNA and Protein Abundance in Yeast
Authors: Juneau Kara , Miranda Molly , Hillenmeyer Maureen E , Nislow Corey , Davis Ronald W
Published: July 2006

The purpose of introns in the architecturally simple genome of Saccharomyces cerevisiae is not well understood. To assay the functional relevance of introns, a series of computational analyses and several detailed deletion studies were completed on the intronic genes of S. cerevisiae. Mining existing data from genomewide studies on yeast revealed that intron-containing genes produce more RNA and more protein and are more likely to be haplo-insufficient than nonintronic genes. These observations for all intronic genes held true for distinct subsets of genes including ribosomal, nonribosomal, duplicated, and nonduplicated. Corroborating the result of computational analyses, deletion of introns from three essential genes decreased cellular RNA levels and caused measurable growth defects. These data provide evidence that introns improve transcriptional and translational yield and are required for competitive growth of yeast.
Accumulation of Recessive Lethal Mutations in Saccharomyces cerevisiae mlh1 Mismatch Repair Mutants Is Not Associated With Gross Chromosomal Rearrangements
Authors: Heck Julie Akiko , Gresham David , Botstein David , Alani Eric
Published: July 2006

We examined mismatch repair (MMR)-defective diploid strains of budding yeast grown for ∼160 generations to determine whether decreases in spore viability due to the uncovering of recessive lethal mutations correlated with an increase in gross chromosomal rearrangements (GCRs). No GCRs were detected despite dramatic decreases in spore viability, suggesting that frameshift and/or other unrepaired DNA replication lesions play a greater role than chromosomal instability in decreasing viability in MMR-defective strains.
Novel Role for Checkpoint Rad53 Protein Kinase in the Initiation of Chromosomal DNA Replication inSaccharomyces cerevisiae
Authors: Dohrmann Paul R , Sclafani Robert A
Published: July 2006

A novel role for Rad53 in the initiation of DNA replication that is independent of checkpoint or deoxynucleotide regulation is proposed. Rad53 kinase is part of a signal transduction pathway involved in the DNA damage and replication checkpoints, while Cdc7-Dbf4 kinase (DDK) is important for the initiation of DNA replication. In addition to the known cdc7-rad53 synthetic lethality, rad53 mutations suppress mcm5-bob1, a mutation in the replicative MCM helicase that bypasses DDK's essential role. Rad53 kinase activity but neither checkpoint FHA domain is required. Conversely, Rad53 kinase can be activated without DDK. Rad53's role in replication is independent of both DNA and mitotic checkpoints because mutations in other checkpoint genes that act upstream or downstream of RAD53 or in the mitotic checkpoint do not exhibit these phenotypes. Because Rad53 binds an origin of replication mainly through its kinase domain and rad53 null mutants display a minichromosome loss phenotype, Rad53 is important in the initiation of DNA replication, as are DDK and Mcm2–7 proteins. This unique requirement for Rad53 can be suppressed by the deletion of the major histone H3/H4 gene pair, indicating that Rad53 may be regulating initiation by controlling histone protein levels and/or by affecting origin chromatin structure.
Nonlinear Tests for Genomewide Association Studies
Authors: Zhao Jinying , Jin Li , Xiong Momiao
Published: July 2006

As millions of single-nucleotide polymorphisms (SNPs) have been identified and high-throughput genotyping technologies have been rapidly developed, large-scale genomewide association studies are soon within reach. However, since a genomewide association study involves a large number of SNPs it is therefore nearly impossible to ensure a genomewide significance level of 0.05 using the available statistics, although the multiple-test problems can be alleviated, but not sufficiently, by the use of tagging SNPs. One strategy to circumvent the multiple-test problem associated with genome-wide association tests is to develop novel test statistics with high power. In this report, we introduce several nonlinear tests, which are based on nonlinear transformation of allele or haplotype frequencies. We investigate the power of the nonlinear test statistics and demonstrate that under certain conditions, some nonlinear test statistics have much higher power than the standard $\batchmode \documentclass[fleqn,10pt,legalpaper]{article} \usepackage{amssymb} \usepackage{amsfonts} \usepackage{amsmath} \pagestyle{empty} \begin{document} \(\mathrm{{\chi}}^{2}\) \end{document}$-test statistic. Type I error rates of the nonlinear tests are validated using simulation studies. We also show that a class of similarity measure-based test statistics is based on the quadratic function of allele or haplotype frequencies, and thus they belong to nonlinear tests. To evaluate their performance, the nonlinear test statistics are also applied to three real data sets. Our study shows that nonlinear test statistics have great potential in association studies of complex diseases.
A Genomewide Screen for Suppressors of par-2 Uncovers Potential Regulators of PAR Protein-Dependent Cell Polarity in Caenorhabditis elegans
Authors: Labbé Jean-Claude , Pacquelet Anne , Marty Thomas , Gotta Monica
Published: July 2006

The PAR proteins play an essential role in establishing and maintaining cell polarity. While their function is conserved across species, little is known about their regulators and effectors. Here we report the identification of 13 potential components of the C. elegans PAR polarity pathway, identified in an RNAi-based, systematic screen to find suppressors of par-2(it5ts) lethality. Most of these genes are conserved in other species. Phenotypic analysis of double-mutant animals revealed that some of the suppressors can suppress lethality associated with the strong loss-of-function allele par-2(lw32), indicating that they might impinge on the PAR pathway independently of the PAR-2 protein. One of these is the gene nos-3, which encodes a homolog of Drosophila Nanos. We find that nos-3 suppresses most of the phenotypes associated with loss of par-2 function, including early cell division defects and maternal-effect sterility. Strikingly, while PAR-1 activity was essential in nos-3; par-2 double mutants, its asymmetric localization at the posterior cortex was not restored, suggesting that the function of PAR-1 is independent of its cortical localization. Taken together, our results identify conserved components that regulate PAR protein function and also suggest a role for NOS-3 in PAR protein-dependent cell polarity.
Genomewide Evolutionary Rates in Laboratory and Wild Yeast
Authors: Ronald James , Tang Hua , Brem Rachel B
Published: July 2006

As wild organisms adapt to the laboratory environment, they become less relevant as biological models. It has been suggested that a commonly used S. cerevisiae strain has rapidly accumulated mutations in the lab. We report a low-to-intermediate rate of protein evolution in this strain relative to wild isolates.
Antagonism of Chk1 Signaling in the G2 DNA Damage Checkpoint by Dominant Alleles of Cdr1
Authors: Calonge Teresa M , O'Connell Matthew J
Published: July 2006

Activation of the Chk1 protein kinase by DNA damage enforces a checkpoint that maintains Cdc2 in its inactive, tyrosine-15 (Y15) phosphorylated state. Chk1 downregulates the Cdc25 phosphatases and concomitantly upregulates the Wee1 kinases that control the phosphorylation of Cdc2. Overproduction of Chk1 causes G2 arrest/delay independently of DNA damage and upstream checkpoint genes. We utilized this to screen fission yeast for mutations that alter sensitivity to Chk1 signaling. We describe three dominant-negative alleles of cdr1, which render cells supersensitive to Chk1 levels, and suppress the checkpoint defects of chk1Δ cells. Cdr1 encodes a protein kinase previously identified as a negative regulator of Wee1 activity in response to limited nutrition, but Cdr1 has not previously been linked to checkpoint signaling. Overproduction of Cdr1 promotes checkpoint defects and exacerbates the defective response to DNA damage of cells lacking Chk1. We conclude that regulation of Wee1 by Cdr1 and possibly by related kinases is an important antagonist of Chk1 signaling and represents a novel negative regulation of cell cycle arrest promoted by this checkpoint.
The Mechanism of Secondary Nondisjunction inDrosophila melanogasterFemales
Authors: Xiang Youbin , Hawley R Scott
Published: July 2006

Bridges (1916) observed that X chromosome nondisjunction was much more frequent in XXY females than it was in genetically normal XX females. In addition, virtually all cases of X nondisjunction in XXY females were due to XX ↔ Y segregational events in oocytes in which the two X chromosomes had failed to undergo crossing over. He referred to these XX ↔ Y segregation events as “secondary nondisjunction.” Cooper (1948) proposed that secondary nondisjunction results from the formation of an X-Y-X trivalent, such that the Y chromosome directs the segregation of two achiasmate X chromosomes to opposite poles on the first meiotic spindle. Using in situ hybridization to X and YL chromosomal satellite sequences, we demonstrate that XX ↔ Y segregations are indeed presaged by physical associations of the X and Y chromosomal heterochromatin. The physical colocalization of the three sex chromosomes is observed in virtually all oocytes in early prophase and maintained at high frequency until midprophase in all genotypes examined. Although these XXY associations are usually dissolved by late prophase in oocytes that undergo X chromosomal crossing over, they are maintained throughout prophase in oocytes with nonexchange X chromosomes. The persistence of such XXY associations in the absence of exchange presumably facilitates the segregation of the two X chromosomes and the Y chromosome to opposite poles on the developing meiotic spindle. Moreover, the observation that XXY pairings are dissolved at the end of pachytene in oocytes that do undergo X chromosomal crossing over demonstrates that exchanges can alter heterochromatic (and thus presumably centromeric) associations during meiotic prophase.
Ubiquitin-Like Protein 5 Positively Regulates Chaperone Gene Expression in the Mitochondrial Unfolded Protein Response
Authors: Benedetti Cristina , Haynes Cole M , Yang Yun , Harding Heather P , Ron David
Published: July 2006

Perturbation of the protein-folding environment in the mitochondrial matrix selectively upregulates the expression of nuclear genes encoding mitochondrial chaperones. To identify components of the signal transduction pathway(s) mediating this mitochondrial unfolded protein response (UPRmt), we first isolated a temperature-sensitive mutation (zc32) that conditionally activates the UPRmt in C. elegans and subsequently searched for suppressors by systematic inactivation of genes. RNAi of ubl-5, a gene encoding a ubiquitin-like protein, suppresses activation of the UPRmt markers hsp-60∷gfp and hsp-6∷gfp by the zc32 mutation and by other manipulations that promote mitochondrial protein misfolding. ubl-5 (RNAi) inhibits the induction of endogenous mitochondrial chaperone encoding genes hsp-60 and hsp-6 and compromises the ability of animals to cope with mitochondrial stress. Mitochondrial morphology and assembly of multi-subunit mitochondrial complexes of biotinylated proteins are also perturbed in ubl-5(RNAi) worms, indicating that UBL-5 also counteracts physiological levels of mitochondrial stress. Induction of mitochondrial stress promotes accumulation of GFP-tagged UBL-5 in nuclei of transgenic worms, suggesting that UBL-5 effects a nuclear step required for mounting a response to the threat of mitochondrial protein misfolding.
Symptoms of Cognitive Impairment Among Children With Atopic Dermatitis
Authors: Ma Emily Z. , Chang Hannah R. , Radtke Sarah , Wan Joy
Published: March 2024

Importance

Previous studies suggest that atopic dermatitis (AD) is associated with cognitive impairment in children, but these studies have relied primarily on neurodevelopmental diagnoses (rather than symptoms) as proxy measures of cognitive function. It remains unknown if certain subpopulations of children with AD are at greater risk of cognitive impairment.

Objective

To examine the association of AD with symptoms of cognitive impairment (difficulty in learning or memory) among US children and whether this association varies according to the presence or absence of neurodevelopmental comorbidities (attention-deficit/hyperactivity disorder [ADHD], developmental delay, or learning disability).

Design, Setting, and Participants

This cross-sectional study used 2021 data from the US National Health Interview Survey collected on children aged 17 years or younger without intellectual disability or autism. The presence of AD was based on a parent or adult caregiver’s report indicating either a current diagnosis of AD or a previous medical confirmation of AD by a health care professional.

Main Outcomes and Measures

Difficulty with learning or memory as reported by the child’s caregiver.

Results

Among the weighted total of 69 732 807 participants, 9 223 013 (13.2%) had AD. Compared with children without AD, children with AD were more likely to experience difficulties with learning (10.8% [95% CI, 7.8%-15.8%] vs 5.9% [95% CI, 5.1%-6.9%]; P < .001) and difficulties with memory (11.1% [95% CI, 8.0%-15.9%] vs 5.8% [95% CI, 4.9%-6.9%]; P < .001). In multivariable logistic regression models adjusted for sociodemographic factors, asthma, food allergies, and seasonal allergies or hay fever, AD was associated with increased odds of difficulties in learning (adjusted odds ratio [AOR], 1.77; 95% CI, 1.28-2.45) and memory (AOR, 1.69; 95% CI, 1.19-2.41). In analyses stratified by neurodevelopmental comorbidities, AD was associated with 2- to 3-fold greater odds of memory difficulties among children with any neurodevelopmental disorder (AOR, 2.26; 95% CI, 1.43-3.57), including ADHD (AOR, 2.90; 95% CI, 1.60-5.24) or learning disabilities (AOR, 2.04; 95% CI, 1.04-4.00). However, AD was not associated with learning or memory difficulties among children without neurodevelopmental conditions.

Conclusions and Relevance

Results of this cross-sectional study suggest that pediatric AD was generally associated with greater odds of reported difficulties in learning and memory. However, this association was primarily limited to children with neurodevelopmental comorbidities, such as ADHD or learning disabilities. These findings may improve the risk stratification of children with AD for cognitive impairments and suggest that evaluation for cognitive difficulties should be prioritized among children with AD and neurodevelopmental disorders.
Performance in Irish Selection and Future Performance in Surgical Training
Authors: Toale Conor , Morris Marie , Gross Sara , O’Keeffe Dara A. , Ryan Donncha M. , Boland Fiona , Doherty Eva M. , Traynor Oscar J. , Kavanagh Dara O.
Published: March 2024

Importance

Selection processes for surgical training should aim to identify candidates who will become competent independent practitioners and should aspire to high standards of reliability and validity.

Objective

To determine the association between measured candidate factors at the time of an Irish selection and assessment outcomes in surgical training, examined via rate of progression to Higher Specialist Training (HST), attrition rates, and performance as assessed through a multimodal framework of workplace-based and simulation-based assessments.

Design, Setting, and Participants

This retrospective observational cohort study included data from all successful applicants to the Royal College of Surgeons in Ireland (RCSI) national Core Surgical Training (CST) program. Participants included all trainees recruited to dedicated postgraduate surgical training from 2016 to 2020. These data were analyzed from July 11, 2016, through July 10, 2022.

Exposures

Selection decisions were based on a composite score that was derived from technical aptitude assessments, undergraduate academic performance, and a 4-station multiple mini-interview.

Main outcomes and measures

Assessment data, attrition rates, and rates of progression to HST were recorded for each trainee. CST performance was assessed using workplace-based and simulation-based technical and nontechnical skill assessments. Potential associations between selection and assessment measures were explored using Pearson correlation, logistic regression, and multiple linear-regression analyses.

Results

Data were available for 303 trainees. Composite scores were positively associated with progression to HST (odds ratio [OR], 1.09; 95% CI, 1.05-1.13). There was a weak positive correlation, ranging from 0.23 to 0.34, between scores and performance across all CST assessments. Multivariable linear regression analysis showed technical aptitude scores at application were associated with future operative performance assessment scores, both in the workplace (β = 0.31; 95% CI, 0.14-0.48) and simulated environments (β = 0.57; 95% CI, 0.33-0.81). There was evidence that the interpersonal skills interview station was associated with future performance in simulated communication skill assessments (β = 0.55; 95% CI, 0.22-0.87).

Conclusions and Relevance

In this study, performance at the time of Irish national selection, measured across technical and nontechnical domains in a multimodal fashion, was associated with future performance in the workplace and in simulated environments. Future studies will be required to explore the consequential validity of selection, including potential unintended effects of selection and ranking on candidate performance.
Active management is required to regenerate the Caledonian forest: Alladale as a case study
Authors: Williams Jake , Sandom Christopher J. , Pettorelli Nathalie
Published: March 2024

Passive approaches to nature recovery have been hailed as a low‐cost approach to boosting biodiversity in ecologically degraded sites. But there remains little evidence of whether this generalises to all climatic and ecological contexts.

To address this knowledge gap, we used satellite remote sensing to examine vegetation change in Alladale Wilderness Reserve, a remote rewilding site in Scotland where active and passive approaches have simultaneously taken place for the past decades.

In contrast to enclosures and tree planting, more passive approaches did not help regenerate the native Caledonian forest, failing to lead to structural or functional change within Alladale, relative to the wider landscape. Observed changes under both approaches were moreover much less dramatic than those reported for the Knepp Estate, another established rewilding site in Southern England.

Our results suggest that passive rewilding is unlikely to promote significant biodiversity change in areas where recent human forcing of ecological processes has been limited, even if past human pressures have intensively reshaped the ecosystem—as seen in Alladale. In such situations, active interventions are likely to be required to shift the system onto a new ecological trajectory.

Altogether, our study illustrates how freely available satellite data can (1) help contrast the impacts of environmental management approaches on ecosystem structure and functioning, in ways that complement existing ground‐based studies; and (2) help distinguish areas likely to benefit from passive nature recovery approaches from those where specific active interventions are needed.