bluuebunny/crossref_metadata_2025_split huggingface dataset:
Discovery of Mutations inSaccharomyces cerevisiaeby Pooled Linkage Analysis and Whole-Genome Sequencing
Authors: Birkeland Shanda R , Jin Natsuko , Ozdemir Alev Cagla , Lyons Robert H , Weisman Lois S , Wilson Thomas E 
Published: October 2010

AbstractMany novel and important mutations arise in model organisms and human patients that can be difficult or impossible to identify using standard genetic approaches, especially for complex traits. Working with a previously uncharacterized dominant Saccharomyces cerevisiae mutant with impaired vacuole inheritance, we developed a pooled linkage strategy based on next-generation DNA sequencing to specifically identify functional mutations from among a large excess of polymorphisms, incidental mutations, and sequencing errors. The VAC6-1 mutation was verified to correspond to PHO81-R701S, the highest priority candidate reported by VAMP, the new software platform developed for these studies. Sequence data further revealed the large extent of strain background polymorphisms and structural alterations present in the host strain, which occurred by several mechanisms including a novel Ty insertion. The results provide a snapshot of the ongoing genomic changes that ultimately result in strain divergence and evolution, as well as a general model for the discovery of functional mutations in many organisms.
The Rate of Fitness-Valley Crossing in Sexual Populations
Authors: Weissman Daniel B , Feldman Marcus W , Fisher Daniel S 
Published: October 2010

AbstractBiological traits result in part from interactions between different genetic loci. This can lead to sign epistasis, in which a beneficial adaptation involves a combination of individually deleterious or neutral mutations; in this case, a population must cross a “fitness valley” to adapt. Recombination can assist this process by combining mutations from different individuals or retard it by breaking up the adaptive combination. Here, we analyze the simplest fitness valley, in which an adaptation requires one mutation at each of two loci to provide a fitness benefit. We present a theoretical analysis of the effect of recombination on the valley-crossing process across the full spectrum of possible parameter regimes. We find that low recombination rates can speed up valley crossing relative to the asexual case, while higher recombination rates slow down valley crossing, with the transition between the two regimes occurring when the recombination rate between the loci is approximately equal to the selective advantage provided by the adaptation. In large populations, if the recombination rate is high and selection against single mutants is substantial, the time to cross the valley grows exponentially with population size, effectively meaning that the population cannot acquire the adaptation. Recombination at the optimal (low) rate can reduce the valley-crossing time by up to several orders of magnitude relative to that in an asexual population.
Maintenance of Neuronal Laterality in Caenorhabditis elegans Through MYST Histone Acetyltransferase Complex Components LSY-12, LSY-13 and LIN-49
Authors: O'Meara M Maggie , Zhang Feifan , Hobert Oliver 
Published: October 2010

Abstract
Left/right asymmetrically expressed genes permit an animal to perform distinct tasks with the right vs. left side of its brain. Once established during development, lateralized gene expression patterns need to be maintained during the life of the animal. We show here that a histone modifying complex, composed of the LSY-12 MYST-type histone acetyltransferase, the ING-family PHD domain protein LSY-13, and PHD/bromodomain protein LIN-49, is required to first initiate and then actively maintain lateralized gene expression in the gustatory system of the nematode Caenorhabditis elegans. Similar defects are observed upon postembryonic removal of two C2H2 zinc finger transcription factors, die-1 and che-1, demonstrating that a combination of transcription factors, which recognize DNA in a sequence-specific manner, and a histone modifying enzyme complex are responsible for inducing and maintaining neuronal laterality.
A Relaxed Implant Bed: Implants Placed After Two Weeks of Osteotomy With Immediate Loading: A One Year Clinical Trial
Authors: Bansal Jyoti , Kedige Suresh , Bansal Abhishek , Anand Samir 
Published: October 2010

A waiting period of 2 weeks after osteotomy increases the surrounding tissue activity to its maximum level as collagen formation and neoangiogenesis represent a relaxed and acceptable implant bed configuration. The aim of the present study was a clinical and radiologic evaluation of early osteotomy with implant placement delayed for 2 weeks with immediate loading in the anterior and premolar region with minimally invasive approach. Seven GS II implants (Osstem) were placed in 6 patients. Osteotomy was done followed by flap closure without placement of the implant. After waiting for approximately 2 weeks, implant placement was done, which was loaded immediately with provisional crown in implant protected occlusion. It was replaced by definitive restoration after 6–8 weeks, which was considered baseline. Implant stability and marginal bone levels were assessed with clinical and radiologic parameters at baseline, 6- and 12-month intervals. None of the implants were found mobile during the 1-year period. The average mean marginal bone loss was 0.4 mm over the 1-year follow-up period. In the present study, early osteotomy with delayed implant placement showed negligible crestal bone loss with no mobility.
Genetic Assessment of the Mating System and Patterns of Egg Cannibalism in Atka Mackerel
Authors: Canino M. F. , Spies I. B. , Guthridge J. L. , Hollowed M. M. 
Published: October 2010

Abstract
The mating system and patterns of gender-specific egg cannibalism in Atka mackerel Pleurogrammus monopterygius were examined through genetic parentage analysis of embryos in egg clutches produced in captive and wild populations. Like other hexagrammid fishes, Atka mackerel exhibit polygynandry, which is characterized by serial matings by both genders within a breeding season. Most matings in captivity were pairings of females with nest-attendant males, although parentage analysis of clutches produced in a small tank with limited nesting substrate revealed that 31% contained contributions by non—nest-guarding males. In contrast, all egg clutches produced in a large exhibit tank were sired by guardian males. Multiple parentage, sometimes involving both genders, was detected in 35% of egg clutches collected in the field or retrieved from the guts of adult male and female cannibals. Half-sib and unrelated full-sib embryos were found in several putative clutches, indicating that the reproductive output from multiple males and females may be combined sequentially and fused into a single clutch. These results suggested that nest takeovers, combined with alloparental care of existing broods, represent common reproductive tactics in males. Egg cannibalism is a significant seasonal factor in the diets of male and female Atka mackerel. Analysis of loose eggs and partial egg clutches ingested by 4 female and 15 male cannibals showed that nearly all conspecific predation represented heterocannibalism. One instance of partial filial cannibalism was documented in a male that was one of multiple sires for the clutch.
Highly Discordant Nuclear and Mitochondrial DNA Diversities in Atka Mackerel
Authors: Canino M. F. , Spies I. B. , Lowe S. A. , Grant W. S. 
Published: October 2010

Abstract
Levels of neutral genetic diversity largely reflect effective population size (Ne), which is influenced by physical and biological environmental variables. While large populations of marine fishes generally harbor higher diversities than freshwater species, historical demography or the effects of natural selection may significantly reduce Ne and differentially affect genomic diversities. Here, we surveyed levels of genetic diversity and examined genetic structure among populations of the Atka mackerel Pleurogrammus monopterygius across most of its geographic range by screening variation at nine nuclear microsatellite DNA markers (n = 745) and in a 468-base-pair segment of the mitochondrial DNA (mtDNA) control region (n = 119). Samples from Japan to the western Gulf of Alaska were collected between 2004 and 2006 at six locations, including temporal replicates at two sites. Microsatellite allele frequency homogeneity across the North Pacific indicated an apparent lack of genetic population substructure. While levels of polymorphism at microsatellite loci were typical for marine fishes (haplotype diversity h = 0.34–0.96), mtDNA control region diversity was extremely low (nucleotide diversity = 0.00007; h = 0.033). Only three mtDNA haplotypes, two occurring as singletons, were detected among 119 individuals. The strong contrast between microsatellite and mtDNA diversities appears to be due to the smaller Ne for mtDNA, perhaps resulting from population bottlenecks during postglacial colonizations of the central North Pacific or the effects of natural selection on mtDNA.
Annual Intrabasin Movement and Mortality of Adult Bonneville Cutthroat Trout among Complementary Riverine Habitats
Authors: Carlson Andrew J. , Rahel Frank J. 
Published: October 2010

AbstractWe evaluated annual movement and mortality patterns of native Bonneville cutthroat troutOncorhynchus clarkii utahin the Smiths Fork–Bear River watershed, which is part of the Great Basin in the western USA. Our objectives were to identify complementary habitats within the watershed, identify sources of mortality for Bonneville cutthroat trout during seasonal movements, and determine whether anthropogenic structures disrupt movement of adult Bonneville cutthroat trout within this system. Bonneville cutthroat trout migrated upstream during spring runoff (median distance = 37.1 km) and experienced a seasonal mortality rate of 43% during this period. After spawning in the headwater streams, fish moved downstream during the summer–autumn period (median distance = 11.6 km) and experienced a seasonal mortality rate of 16%. Whereas upstream movement in the spring was fast and highly directed, downstream movement during summer–autumn was slower and less directed. During winter, fish remained generally sedentary (median movement upstream = 0.1 km) and the seasonal mortality rate was 11%. No anthropogenic structures blocked fish movement throughout the watershed. However, an irrigation canal entrained 9% of the fish that moved past its headgate, suggesting that the canal may act as an ecological trap. Our results provide empirical support for conceptual models that emphasize the importance of habitat complementarity as the basis for annual long‐distance movement patterns in riverine fishes. Managing migratory species such as the Bonneville cutthroat trout will require maintaining river connectivity and minimizing ecological traps so that fish can move among widely separated habitats to meet their life history requirements.
The Effects of the Stronach Dam Removal on Fish in the Pine River, Manistee County, Michigan
Authors: Burroughs Bryan A. , Hayes Daniel B. , Klomp Kristi D. , Hansen Jonathan F. , Mistak Jessica 
Published: October 2010

AbstractAlthough dam removal has been increasingly used as an option in dam management and as a river restoration tool, there are few studies providing detailed quantitative assessment of the response of fish populations to dam removal. In this study, we document the response of the fish community in the Pine River, Michigan, to the gradual removal of Stronach Dam. Ten sites were sampled annually during the course of the removal (1997–2003) and for 4 years following removal (2004–2007). Before the removal of Stronach Dam, 11 fish species were found only downstream of the dam, 1 species was found only upstream of the dam, and 19 species were captured both above and below the dam. Following removal, 8 species formerly found only below the dam utilized newly available portions of the river above the dam. Most fish species (18 of the 25 evaluated) showed an increase in abundance following removal, strongly supporting the idea that dam removal reduces multiple factors limiting riverine fishes. Brown trout Salmo trutta and rainbow trout Oncorhynchus mykiss were the primary sport fishes present in the river, and the abundance of both species increased by more than twofold over the course of the study. The abundance of white suckers Catostomus commersonii also increased significantly due to increased reproductive success. The results of this study illustrate how dam removal is a useful tool for restoration of habitat connectivity and habitat conditions and how the fish community in a coldwater stream responded to the removal.
Abundance and Recruitment of Juvenile Atlantic Sturgeon in the Altamaha River, Georgia
Authors: Schueller Paul , Peterson Douglas L. 
Published: October 2010

AbstractJuvenile Atlantic sturgeon Acipenser oxyrinchus remain in natal rivers for several years prior to out‐migrating to marine environments during later portions of their life history. Data regarding river‐resident juvenile population dynamics are unknown. During the summers of 2004–2007, we performed mark–recapture of juvenile Atlantic sturgeon in the Altamaha River to assess age‐specific abundance, apparent survival, per capita recruitment, and factors influencing recruitment. Estimates indicated that juvenile abundance ranged from 1,072 to 2,033 individuals, and age‐1 and age‐2 individuals comprised greater than 87% of the juvenile population, while age‐3 or older individuals constituted less than 13% of the population. Estimates of apparent survival and per capita recruitment from Pradel models indicated that the juvenile population experienced high annual turnover: apparent survival rates were low (<33%), and per capita recruitment was high (0.82–1.38). Fall discharge, which had a positive relationship with recruitment, was the only factor assessed that significantly explained time variation in per capita recruitment. The findings of this study suggest that juvenile populations at the southern extreme of the Atlantic sturgeon's range may remain in natal rivers for less time than northern counterparts. This is further evidence of life history differences between northern and southern populations of Atlantic sturgeon. Potential findings of density dependence could have major implications for both population recovery and management of this species.
Persistence of Colorado River Cutthroat Trout Populations in Isolated Headwater Streams of Wyoming
Authors: Cook Nathan , Rahel Frank J. , Hubert Wayne A. 
Published: October 2010

AbstractFor populations of cutthroat trout Oncorhynchus clarkii, isolation in headwater streams may provide protection from invasion by nonnative species but also may enhance a population's vulnerability to extirpation. We assessed the risk of extirpation for eight Colorado River cutthroat trout O. clarkii pleuriticus populations isolated above water diversion structures in the North Fork Little Snake River drainage, Wyoming. The populations had been isolated for 25–44 years, occupied headwater streams that ranged from 850 to 6,100 m in length, and had adult populations that were estimated to range from 12 to 506 fish. Adult population sizes were compared with published occurrence models to identify populations that may be at risk of extirpation. One population had experienced an 11% annual rate of decline in abundance over the past 29 years, but there was no evidence of declines among the other populations. There was evidence of recruitment failure for age‐1 fish in two of the smaller populations. Abundance estimates and published logistic regression models consistently identified the largest tributary in the drainage as being the most likely to support a Colorado River cutthroat trout population in the future and the smallest tributary as being the least likely to support a population in the future. The analyses indicated that isolated populations may persist for decades, but small effective population sizes can make populations vulnerable to eventual loss of genetic variability and to extirpation.
Streamflow Reductions and Habitat Drying Affect Growth, Survival, and Recruitment of Brassy Minnow across a Great Plains Riverscape
Authors: Falke Jeffrey A. , Bestgen Kevin R. , Fausch Kurt D. 
Published: October 2010

AbstractFlow alterations caused by reservoir storage, groundwater pumping, diversions, and drought are widespread in North American Great Plains streams and have altered and fragmented habitats and reduced native fish biodiversity. Early life stages of fish are particularly sensitive to altered flow regimes, and reduced growth and survival may negatively affect the persistence of native species and assemblages. We investigated how growth and survival of brassy minnow Hybognathus hankinsoni larvae in the Arikaree River, Colorado, varied among three 6.4‐km river segments that differed in hydrology and how climate influenced drying rates of spawning and rearing habitats in these segments over 3 years. We found that brassy minnow spawned in backwater habitats within a discrete period from mid‐April to late May, based on otolith increment analysis. The timing of spawning and growth of larvae were influenced by climate and the hydrologic context of the river segment. Brassy minnow spawned 2 weeks earlier under warm, dry conditions in 1 year, and both growth rates and survival were significantly lower than during two wetter years (growth: 0.25 mm/d versus 0.30 and 0.41 mm/d; survival: 0.8391/d versus 0.894 and 0.897/d). For cohorts of larvae in individual backwaters, survival was higher in spawning habitats that were larger and that dried more slowly, and among cohorts that hatched in the middle of the spawning period under a moderate thermal regime. Overall, we found that brassy minnow spawning and recruitment were strongly influenced by habitat drying driven by interactions among stream geomorphology, groundwater pumping, and climate across multiple spatial scales. We suggest that conservation efforts explicitly consider the adaptations of this fish to harsh environments and focus on providing flows to maintain the spawning, rearing, and refuge habitats that are critical to brassy minnow population persistence.
Smolt Transformation in Two California Steelhead Populations: Effects of Temporal Variability in Growth
Authors: Beakes Michael P. , Satterthwaite William H. , Collins Erin M. , Swank David R. , Merz Joseph E. , Titus Robert G. , Sogard Susan M. , Mangel Marc 
Published: October 2010

AbstractWe tested the effect of temporal patterns in food supply on life history decisions in coastal steelhead Oncorhynchus mykiss irideus from a Central California coastal (CCC) population (Scott Creek) and a Northern California Central Valley (NCCV) population (upper Sacramento River basin). We manipulated growth through feeding experiments conducted from May to the following March using warm (2006 cohort) and cool (2007 cohort) temperature regimes. Survival in seawater challenges just before the time of typical juvenile emigration provided an index of steelhead smolt versus nonsmolt life history pathways. Survival varied significantly with fish size (with larger fish being more likely to survive than smaller fish) and by source population (with CCC steelhead being more likely to survive than NCCV steelhead of the same size). The timing of increased food supply (treatment group) did not significantly affect seawater survival rates in either NCCV or CCC steelhead. For both strains, the eventual survivors of seawater challenges (putative smolts) diverged from the eventual mortalities (putative nonsmolts) in both size and growth rate by June in both years, suggesting that the initial growth advantages were maintained throughout the experiments. A significant divergence in condition factor between smolts and nonsmolts by December matched the expected morphological transition of smolts, which showed faster growth in length than weight compared with nonsmolts. The apparent timing of the decision window, several months before the typical period of smolt emigration, matches the patterns observed for other salmonids. In coastal California, this decision must occur before fish have had the opportunity to take advantage of improved winter–early spring feeding conditions. These results support the role of early growth opportunity in life history decisions and provide insight into the applicability of life history models for managing California steelhead.
Introduced Lake Trout Produced a Four‐Level Trophic Cascade in Yellowstone Lake
Authors: Tronstad Lusha M. , Hall Robert O. , Koel Todd M. , Gerow Ken G. 
Published: October 2010

AbstractIntroduction of lake trout Salvelinus namaycush into a system can add a trophic level, potentially affecting organisms at lower trophic levels. Similar to many lakes and reservoirs in the western United States, lake trout were introduced into Yellowstone Lake, Wyoming. Previous studies showed that lake trout reduced the population and altered the size structure of native Yellowstone cutthroat trout Oncorhynchus clarkii bouvieri in Yellowstone Lake, but we sought to determine the degree to which lake trout predation changed lower trophic levels. We predicted that the structure of lower trophic levels would change in conformance with trophic cascade theory because Yellowstone cutthroat trout consume zooplankton. We compared zooplankton and phytoplankton assemblages between the period when Yellowstone cutthroat trout were abundant and the period after they declined. As predicted by trophic cascade theory, zooplankton biomass shifted from being dominated by copepods before lake trout introduction to being dominated by cladocerans after lake trout introduction, with zooplankton body lengths 17% longer after introduction. Vertical water clarity increased by 1.6 m because of a twofold decrease in chlorophyll a and a three‐ to sevenfold decrease in phytoplankton biovolume. Thus, the introduction of lake trout and subsequent decline of Yellowstone cutthroat trout likely altered lower trophic levels in Yellowstone Lake. Trophic cascades may be common in western U.S. lakes and reservoirs where native salmonids are present and where lake trout have been introduced.