bluuebunny/crossref_metadata_2025 huggingface dataset:
Convergence of Molecular, Modeling, and Systems Approaches for an Understanding of the
Escherichia coli
Heat Shock Response
Authors: Guisbert Eric , Yura Takashi , Rhodius Virgil A. , Gross Carol A.
Published: September 2008

The heat shock response (HSR) is a homeostatic response that maintains the proper protein-folding environment in the cell. This response is universal, and many of its components are well conserved from bacteria to humans. In this review, we focus on the regulation of one of the most well-characterized HSRs, that of
Escherichia coli
. We show that even for this simple model organism, we still do not fully understand the central component of heat shock regulation, a chaperone-mediated negative feedback loop. In addition, we review other components that contribute to the regulation of the HSR in
E. coli
and discuss how these additional components contribute to regulation. Finally, we discuss recent genomic experiments that reveal additional functional aspects of the HSR.
Progress in Metabolic Engineering of
Saccharomyces cerevisiae
Authors: Nevoigt Elke
Published: September 2008

The traditional use of the yeast
Saccharomyces cerevisiae
in alcoholic fermentation has, over time, resulted in substantial accumulated knowledge concerning genetics, physiology, and biochemistry as well as genetic engineering and fermentation technologies.
S. cerevisiae
has become a platform organism for developing metabolic engineering strategies, methods, and tools. The current review discusses the relevance of several engineering strategies, such as rational and inverse metabolic engineering, evolutionary engineering, and global transcription machinery engineering, in yeast strain improvement. It also summarizes existing tools for fine-tuning and regulating enzyme activities and thus metabolic pathways. Recent examples of yeast metabolic engineering for food, beverage, and industrial biotechnology (bioethanol and bulk and fine chemicals) follow.
S. cerevisiae
currently enjoys increasing popularity as a production organism in industrial (“white”) biotechnology due to its inherent tolerance of low pH values and high ethanol and inhibitor concentrations and its ability to grow anaerobically. Attention is paid to utilizing lignocellulosic biomass as a potential substrate.
Candida albicansCell Wall Proteins
Authors: Chaffin W. LaJean
Published: September 2008

The Candida albicans cell wall maintains the structural integrity of the organism in addtion to providing a physical contact interface with the environment. The major components of the cell wall are fibrillar polysaccharides and proteins. The proteins of the cell wall are the focus of this review. Three classes of proteins are present in the candidal cell wall. One group of proteins attach to the cell wall via a glycophosphatidylinositol remnant or by an alkali-labile linkage. A second group of proteins with N-terminal signal sequences but no covalent attachment sequences are secreted by the classical secretory pathway. These proteins may end up in the cell wall or in the extracellular space. The third group of proteins lack a secretory signal, and the pathway(s) by which they become associated with the surface is unknown. Potential constituents of the first two classes have been predicted from analysis of genome sequences. Experimental analyses have identified members of all three classes. Some members of each class selected for consideration of confirmed or proposed function, phenotypic analysis of a mutant, and regulation by growth conditions and transcription factors are discussed in more detail.
Fish Gill Structural Changes Induced by Toxicants and Other Irritants: A Statistical Review
Authors: Mallatt Jon
Published: September 2008

Here I quantitatively review the literature on how fish gill morphology is affected by chemical and physical irritants in the surrounding water (e.g. various toxicants, extremes of temperature or pH). I catalogued histopathological gill lesions that were reported, and used statistics to explore how such lesions relate to the irritant-exposure conditions under which they occurred (specifically, to dose and class of irritant, to temperature, and to salinity of the surrounding water). Frequently recorded histopathologic lesions include changes in gill epithelium (lifting, necrosis, hyperplasia, hypertrophy, rupture), bulbing or fusing of gill lamellae, hypersecretion and proliferation of mucocytes, and changes in chloride cells and gill vasculature. I conclude that these lesions are largely nonspecific in nature, as each was detected under many different exposure conditions. The lesions are not entirely independent of exposure conditions, however, as my statistical analysis discerns these trends: (1) Most gill lesion types have been reported more frequently after lethal than after sublethal exposure to irritants. (2) Some lesions were more frequently detected in studies employing heavy metals than in studies using organic toxicants or other irritants; such lesions include necrosis and hypertrophy of gill epithelial cells, plus mucous hypersecretion. (3) Lifting of the branchial epithelium, the most commonly reported lesion, was reported more often in freshwater than in marine fish, suggesting that osmolarity of the ambient water influences this lesion. Little relation was found between recorded lesion frequencies and temperature. Following my statistical analysis, the etiology of irritant-induced gill lesions is considered. The nonspecificity of branchial alterations suggests that they primarily represent stereotyped physiological reactions of gills to stress, and many of them are logically considered defense responses. Some branchial alterations have been considered inflammatory, but I conclude that the literature cannot support that hypothesis. Ultrastructural studies have detected irritant-induced disruptions of branchial epithelial cells, including cytoplasmic vacuolization, autophagosomes and inclusions, loss of microvilli, and abnormal mitochondria and nuclei.
Species Selective Predation on Juvenile Pink (Oncorhynchus gorbuscha) and Chum Salmon (O. keta) by Coho Salmon (O. kisutch)
Authors: Hargreaves N. Brent , Lebrasseur Robin J.
Published: September 2008

Predation on juvenile pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) by yearling coho (O. kisutch) was studied in marine enclosures in Masset Inlet, B.C. These experiments demonstrate that coho prey selectively upon pink salmon even when chums are both significantly smaller and more abundant than pink salmon. Reexamination of the results of similar experiments conducted in Burke Channel, B.C., also confirms that mortality was biased towards pink salmon. Prey species may be more important than prey size for coho that prey upon mixed populations of pink and chum salmon during early sea-life.
Distribution and Abundance of Belugas, Delphinapterus leucas, and Narwhals, Monodon monoceros, in the Canadian High Arctic
Authors: Smith T. G. , Hammsll M. O. , Burrage D. J. , Sleno G. A.
Published: September 2008

Opportunistic reconnaissance aerial surveys of Lancaster Sound, Barrow Strait, Peel Sound, and Prince Regent Inlet were conducted between 1974 and 1982 to determine the distribution and abundance of belugas, Delphinapterus leucas, and narwhals, Monodon monoceros. In 1981, two stratified strip-transect surveys were flown. From these we estimate that a total of 6300 – 18 600 belugas and approximately 13 200 –18 000 narwhals summer in Lancaster Sound and adjoining waterways. Improvement in the precision of these estimates would require a substantial increase in survey coverage and may not be justified considering the significant increase in costs. Our review of the results of surveys conducted since 1975 in the same study area, of which most of the information is not yet available in the scientific literature, shows much duplication of effort, little increase in information, and a lack of confidence limits for the estimated numbers.
Comparison of Spawning Areas and Times for Two Runs of Chinook Salmon (Oncorhynchus tshawytscha) in the Kenai River, Alaska
Authors: Burger Carl V. , Wilmot Richard L. , Wangaard David B.
Published: September 2008

From 1979 to 1982,188 chinook salmon (Oncorhynchus tshawytscha) were tagged with radio transmitters to locate spawning areas in the glacial Kenai River, southcentral Alaska. Results confirmed that an early run entered the river in May and June and spawned in tributaries, and a late run entered the river from late June through August and spawned in the main stem. Spawning peaked during August in tributaries influenced by lakes, but during July in other tributaries. Lakes may have increased fall and winter temperatures of downstream waters, enabling successful reproduction for later spawning fish within these tributaries. This hypothesis assumes that hatching and emergence can be completed in a shorter time in lake-influenced waters. The time of upstream migration and spawning (mid- to late August) of the late run is unique among chinook stocks in Cook Inlet. This behavior may have developed only because two large lakes (Kenai and Skilak) directly influence the main-stem Kenai River. If run timing is genetically controlled, and if the various components of the two runs are isolated stocks that have adapted to predictable stream temperatures, there are implications for stock transplantation programs and for any activities of man that alter stream temperatures.
Nickel Accumulation byScenedesmusand Daphnia: Food-Chain Transport and Geochemical Implications
Authors: Watras Carl J. , MacFarlane John , Morel François M. M.
Published: September 2008

The accumulation of Ni in two levels of a simple aquatic food chain was determined as a function of the concentration of the free metal ion. in NTA-buffered media, Scenedesmus obliquus accumulated Ni to concentrations 30–300 times above ambient. At pNi (= −log Ni2+concentration) below 8, algal growth rate declined, cellular Ni quota increased, but no change in the relative size of labile and nonlabile Ni pools was detected. In the same media, Daphnia magna also concentrated Ni but only to levels slightly above ambient. Both short-term (72-h) and long-term (13-d) incubations with D. magna indicated that direct uptake from solution rather than uptake from ingested algae was the primary accumulation vector. There was no biomagnification from the algae to the zooplankton. Ingested particulate Ni was concentrated presumably in fecal matter, which normally sinks to the sediment.
The Influence of pH, Water Hardness, and Alkalinity on the Acute Lethality of Zinc to Rainbow Trout (Salmo gairdneri)
Authors: Bradley R. W. , Sprague J. B.
Published: September 2008

The acute lethality of dissolved zinc to rainbow trout (Salmo gairdneri) was significantly increased at higher pH and lower hardness levels. Changes in pH from 5.5 to 7.0 increased zinc toxicity by factors of 2 to 5, depending on total hardness levels. A decrease in hardness from 386 to 31 mg CaCO3/L increased zinc toxicity by more than an order of magnitude at both pH levels. These effects of pH and hardness were not caused by changes in the chemical speciation of zinc. An increase in carbonate alkalinity from 8.4 to 24 mg CaCO3/L at pH 7.0 did not significantly alter zinc toxicity at either hardness level. Thus, carbonate alkalinity is not an important factor at or below pH 7.0. At low hardness, dissolved zinc was more than 10 times as toxic at pH 9.0 as at pH 5.5. Two competing mechanisms appear to operate: as the pH rises, dissolved zinc becomes increasingly toxic, but at higher pH levels it is increasingly replaced by zinc precipitate, which is of very low toxicity to fish.
Differences in Early Development Among Lake Trout (Salvelinus namaycush) Populations
Authors: Horns William H.
Published: September 2008

Genetic differences among surviving lake trout (Salvelinus namaycush) populations might be important for the reestablishment of self-sustaining populations in the Great Lakes, but little relevant information is available to guide stocking practices. I studied eggs and fry of four populations, two from Lake Superior, one from Trout Lake, and one (the Green Lake strain) derived in part from Lake Michigan. I found significant interpopulation differences in hatching and emergence times as well as in indices of morphological development rates. Interpopulation differences in morphological development at the times of emergence suggest that the Green Lake strain emerges at an earlier stage of morphological development than do the other populations. Between-lake differences are the most important sources of variability in my data; the Lake Superior populations were similar to one another, and variation among crosses within populations was small.
A Computer-Controlled Turbidostat for the Culture of Planktonic Algae
Authors: Hill S. H. , Abbott M. R. , Denman K. L.
Published: September 2008

We designed, built, and tested a microprocessor-controlled turbidostat that maintains phytopSankton cells at nearly constant biomass concentrations without nutrient limitation of growth rates. There are fundamental limits placed on the achievable degree of constancy by physiological changes in the organisms being cultured. The sensor responds nearly linearly over a wide range of cell densities, extending well into high pigment concentrations (approx. 20 mg Chl a/m3). The microprocessor-based controller eliminates the need for time-consuming and delicate set-up and modification of operational variables and provides for simple implementation of virtually any logical feedback algorithm to control cell concentration. Although the result was not unexpected, we have shown that growth rates measured in the turbidostat are equivalent to corresponding measurements in a batch culture growing under identical conditions, until such time as the populations develop differing physiological and physical properties due to their different environments.
Effects of Low Environmental pH on the Survival, Growth, and ionic Composition of Postemergent Atlantic Salmon (Salmo salar)
Authors: Lacroix Gilles L. , Gordon D. James , Johnston Dana J.
Published: September 2008

Postemergent Atlantic salmon (Salmo salar) were reared during the early feeding phase in the soft, acidic water of the Westfield River (mean pH 5.0) in Nova Scotia. The fry were held in a flow-through system of tanks in situ and were fed a hatchery diet. Bioassays were also conducted in river water treated with limestone (mean pH 6.1) to provide a control. Cumulative mortality of fry after 30 d in the tanks was 70% at pH 5.0 and only 4% at pH 6.1. Fry in untreated river water were inactive, ingested little food, and lost weight (approximately 25%) during the first 15 d of exposure. Large increases in body [Ca2+] and [Na+] were observed in fry at both pH levels during that time, but the increase in [Ca2+] lagged and that in [Na+] was less in fry at low pH. Deaths occurred 15–30 d after swim-up and dead fry were all severely emaciated, indicating that deaths were probably from starvation. Although there were differences in ionic composition changes in fry held at pH 5.0 compared with control, no major depletion of body ionic reserves occurred relative to initial concentrations. Surviving fry at pH 5.0 developed a tolerance after 25 d and had growth rates, condition factors, and ionic concentrations similar to those of fry in treated water. The mortality of fry during the transition to exogenous feeding, in response to low pH stress in soft water, is probably responsible for reduced recruitment and the decline or loss of salmon stocks in this and other acidic rivers of Nova Scotia.
Nitrogen, Phosphorus, and Organic Carbon Cycling in an Arctic Lake
Authors: Whalen S. C. , Cornwell J. C.
Published: September 2008

Budgets for nitrogen, phosphorus, and organic carbon in Toolik Lake, Alaska, were assembled from data collected during 1977–81. The annual total organic carbon (TOC), total nitrogen (TN), and total phosphorus (TP) loads to the Sake were 8557, 290, and 4.64 mmol∙m−2. Inlet streams were the major source of nutrients to the lake, as direct precipitation provided only 1, 2, and 5%, respectively, of the annual TOC, TN, and TP loads to the lake. Up to 30% of the annual N and P inputs to the lake from riverine sources occurred during the first 10 d of stream flow following breakup when cold water temperatures and snow-covered ice limited primary production. Due to the short water renewal time (0.5 yr), efficiency of nutrient retention was poor and 90, 82, and 70% of the annual TOC, TN, and TP inputs to the lake were discharged at the outlet stream. Regeneration within the water column supplied 40–66% and 68–78% of the N and P necessary for measured primary production. Yearly accumulation rates for C, N, and P in the sediment were about 220, 21.0, and 1.75 mmol∙m−2. Phosphorus remineralized within the sediment was completely retained due to adsorption onto Fe oxide minerals in the oxidizing surface layer. Annual rates of release of C and N to the overlying water column were 110 and 11.5–22.2 mmol∙m2. Mass balance considerations showed no serious errors in estimates of any terms of the annual sediment and water column N, P, and organic C budgets.
Comparison of the Phosphorus–Chlorophyll Relationships in Mixed and Stratified Lakes
Authors: Riley E. T. , Prepas E. E.
Published: September 2008

Data from the literature were used to calculate separate regressions of summer chlorophyll a concentration ([Chl a]) on spring total phosphorus concentration ([TP]) for lakes that remain thermally stratified during the summer and lakes that mix intermittently during the summer. Significant differences were found in the spring [TP] – summer [Chl a] relationships for the two lake types (P < 0.05). The mean ratios of summer [TP] to spring [TP] were also significantly different in stratified and mixed lakes (P < 0.001); this difference is the explanation offered for why the spring [TP] – summer [Chl a] relationships were different in stratified and mixed lakes.
Fishery Resource Allocation: An Exploratory Essay
Authors: Regier H. A. , Grima A. P.
Published: September 2008

In Canada our approach to the management of fish resources and their habitats has been in turmoil for several decades, especially during the past decade. That many direct and indirect users of the aquatic ecosystems have been and are continuing to make improper use of them is widely recognized by the public and in formal government policies. Some of the improprieties have been reduced while others are intensifying. How to reduce all improprieties and how to foster meliorative husbandry are being addressed with respect to ecological, social, economic, and political aspects of the man–nature ecosystem. Reconsideration of all rights to the use of fish and their habitats, where the "rights" may be de jure and formally sanctioned, or de facto and informally accepted or imagined and illegal, is leading to proposals that legitimate rights be clarified and be allocated in more explicit and open ways. As allocative devices both the market system and processes of community-level negotiation are being developed further, and the centralized administrative (or bureaucratic) device is being reformed to accommodate the greater use of complementary devices. These issues are here explored with respect to intrajurisdictional problems and opportunities in Canada.
Characterization and chromosomal organization of satellite DNA sequences inPicea abies
Authors: Sarri V. , Minelli S. , Panara F. , Morgante M. , Jurman I. , Zuccolo A. , Cionini P. G.
Published: September 2008

Three clones containing satellite DNA sequences were selected from a randomly sheared genomic DNA library of Picea abies (clones PAF1, PAG004P22F (2F), and PAG004E03C (3C)). PAF1 contained 7 repeats that were 37–55 bp in length and had 68.9%–91.9% nucleotide sequence similarity. Two 2F repeats were 305–306 bp in length and had 83% sequence similarity. Two 3C repeats were 193–226 bp in length and had a sequence similarity of 78.6%. The copy number per 1C DNA of PAF1, 2F, and 3C repeats was 2.7 × 106, 2.9 × 105, and 2.9 × 104, respectively. In situ hybridization showed centromeric localization of these sequences in two chromosome pairs with PAF1, all pairs but one with 2F, and three pairs with 3C. Moreover, PAF1 sequences hybridized at secondary constrictions in six pairs, while 2F-related sequences were found at these chromosome regions only in four pairs. These hybridization patterns allow all chromosome pairs to be distinguished. PAF1-related repeats were contained in the intergenic spacer (IGS) of ribosomal cistrons in all six nucleolar organizers of the complement, while sequences related to 2F were found on only one side of the rDNA arrays in four pairs, showing structural diversity between rDNA regions of different chromosomes.
Allopolyploid speciation of the Mexican tetraploid potato species Solanum stoloniferum and S. hjertingii revealed by genomic in situ hybridization
Authors: Pendinen Galina , Gavrilenko Tatjana , Jiang Jiming , Spooner David M.
Published: September 2008

Thirty-six percent of the wild potato ( Solanum L. section Petota Dumort.) species are polyploid, and about half of the polyploids are tetraploid species (2n = 4x = 48). Determination of the type of polyploidy and development of the genome concept for members of section Petota traditionally has been based on the analysis of chromosome pairing in species and their hybrids and, most recently, DNA sequence phylogenetics. Based on these data, the genome designation AABB was proposed for Mexican tetraploid species of series Longipedicellata Buk. We investigated this hypothesis with genomic in situ hybridization (GISH) for both representatives of the series, S. stoloniferum Schltdl. and S. hjertingii Hawkes. GISH analysis supports an AABB genome constitution for these species, with S. verrucosum Schltdl. (or its progenitor) supported as the A genome donor and another North or Central American diploid species (S. cardiophyllum Lindl., S. ehrenbergii (Bitter) Rydb., or S. jamesii Torrey) as the B genome donor. GISH analysis of chromosome pairing of S. stoloniferum also confirms the strict allopolyploid nature of this species. In addition, fluorescence in situ hybridization data suggest that 45S rDNA regions of the two genomes of S. stoloniferum were changed during coevolution of A and B genomes of this allotetraploid species.
Do phosphorus requirements for RNA limit genome size in crustacean zooplankton?
Authors: Hessen Dag O. , Ventura Marc , Elser James J.
Published: September 2008

As for most other organisms, genome size in zooplankton differs widely. This may have a range of consequences for growth rate, development, and life history strategies, yet the causes of this pronounced variability are not settled. Here we propose that small genome size may be an evolutionary consequence of phosphorus (P) allocation from DNA to RNA under P deficiency. To test this hypothesis we have compared the two major groups of zooplankton, copepods and cladocerans, that have overlapping niches and body size. Relative to the cladocerans, copepods have a more complex life history and a lower mass-specific P content, while cladocerans tend to have higher P and RNA contents and higher specific growth rates and frequently experience P-limited growth, likely due to a shortage of P for ribosome synthesis. Cladocerans also generally have smaller genomes than copepods (1C = 0.17–0.63 pg DNA·cell–1vs. 1C = 0.10–10 pg DNA·cell–1). Furthermore, cladocerans have a higher slope of the relationship of body size with DNA content (1.5 vs. 0.28 in copepods) and present almost 15-fold higher RNA:DNA ratios (24.8 in cladocerans vs. 1.6 in copepods). Hence, small genome size in cladocerans could reflect an evolutionary pressure towards “efficient” genomes to conserve a key element needed to maximize growth rate. We do not claim that this is a universal cause of genome size variability, but propose that streamlining of genomes could be related to P conservation rather than energy conservation. This could be relevant for a range of organisms that may suffer P-limited growth rates.
Quantitative trait loci underlying domestication- and yield-related traits in anOryza sativa ×Oryza rufipogonadvanced backcross population
Authors: Tan Lubin , Zhang Peijiang , Liu Fengxia , Wang Guijuan , Ye Sheng , Zhu Zuofeng , Fu Yongcai , Cai Hongwei , Sun Chuanqing
Published: September 2008

To understand the genetic characteristics of the traits related to differentiation between cultivated rice and its wild progenitor, genetic factors controlling domestication- and yield-related traits were identified using a BC3F2population derived from an accession of common wild rice (donor, Oryza rufipogon Griff.) collected from Yuanjiang, Yunnan province, China, and an indica cultivar, Teqing (recipient, Oryza sativa L.). A genetic linkage map consisting of 125 simple sequence repeat (SSR) markers was constructed. Based on the phenotypes of the 383 BC3F2families evaluated in two environments, two domestication-related morphological traits, panicle shape and growth habit, were found to be controlled by single Mendelian factors. This implies that the recessive mutations of single genes controlling some morphological traits could have been easily selected during early domestication. By single-point analysis and interval mapping, 59 putative quantitative trait loci (QTLs) that influence 11 quantitative traits were detected at two sites, and 37.5% of the QTL alleles originating from O. rufipogon had a beneficial effect for yield-related traits in the Teqing background. Regions with significant QTLs for domestication- and yield-related traits were detected on chromosomes 1, 4, 5, 7, 8, and 12. Fine mapping and cloning of these domestication-related genes and QTLs will be useful in elucidating the origin and differentiation of Asian cultivated rice in the future.
The Pic19 NBS-LRR gene family members are closely linked toScmv1, but not involved in maize resistance to sugarcane mosaic virus
Authors: Jiang Lu , Ingvardsen Christina Rønn , Lübberstedt Thomas , Xu Mingliang
Published: September 2008

Sugarcane mosaic virus (SCMV) is the causal pathogen for a severe mosaic virus disease of maize worldwide. In our previous research, the maize resistance gene analog (RGA) Pic19 and its three cognate BAC contigs were mapped to the same region as the SCMV resistance gene Scmv1. Here we report the isolation and characterization of the Pic19R gene family members from the inbred line FAP1360A, which shows complete resistance to SCMV. Two primer pairs were designed based on the conserved regions among the known Pic19 paralogs and used for rapid amplification of cDNA ends of FAP1360A. Six full-length cDNAs, corresponding to the Pic19R-1 to -6 paralogs, were obtained. Three of them (Pic19R-1 to -3) had uninterrupted coding sequences and were, therefore, regarded as candidates for the Scmv1 gene. A total of 18 positive BAC clones harboring the Pic19R-2 to -5 paralogs were obtained from the FAP1360A BAC library and assembled into two BAC contigs. Two markers, tagging Pic19R-2 and -3 and Pic19R-4, were developed and used to genotype a high-resolution mapping population segregating solely for the Scmv1 locus. Although closely linked, none of these three Pic19R paralogs co-segregated with the Scmv1 locus. Analysis of the Pic19R family indicated that the Pic19R-1 paralog is identical to the known Rxo1 gene conferring resistance to rice bacterial streak disease and none of the other Pic19R paralogs seems to be involved in resistance to SCMV.
Phylogenetic analysis of Carthamus species based on the nucleotide sequence of the nuclear SACPD gene and chloroplast trnL–trnF IGS region
Authors: Sasanuma Tsuneo , Sehgal Deepmala , Sasakuma Tetsuo , Raina Soom Nath
Published: September 2008

To clarify the phylogenetic relationships of Carthamus species, we performed sequence analysis of the nuclear stearoyl acyl carrier protein desaturase (SACPD) gene and the chloroplast intergenic spacer region between leucine and phenylalanine tRNA genes (trnL–trnF IGS) in 13 taxa of Carthamus. The previous division of the genus into 4 taxonomic sections and allocation of particular genomes to various taxa on the basis of morphological, cytogenetic, and biosystematic analyses is not supported by the present study. Our results provide evidence of the occurrence of 5 nuclear genomes (A, B, C, X, and Y) and 3 cytoplasm types (A, B, and C) in the genus Carthamus. The cultivated safflower, C. tinctorius (2n = 24), has the B genome and type B cytoplasm. Both of these are not present in the polyploid taxa. This contradicts the earlier view that one of the genomes involved in the origin of the polyploid taxa of Carthamus is the B genome. Comparison with an outgroup species ( Cirsium japonicum ) indicated that C. arborescens is the most primitive species in the genus. Carthamus palaestinus is genetically closest to the cultivated safflower.
Y-specific sequences and polymorphisms in rainbow trout and Chinook salmon
Authors: Brunelli Joseph P. , Wertzler Kelsey J. , Sundin Kyle , Thorgaard Gary H.
Published: September 2008

Improved methods for genetically sexing salmonids and for characterization of Y-chromosome homologies between species can contribute to understanding the evolution of sex chromosomes and sex-determining mechanisms. In this study we have explored 12.5 kb of Y-chromosome-specific sequence flanking the previously described OtY2 locus in Chinook salmon ( Oncorhynchus tshawytscha ) and 21 kb of homologous rainbow trout ( Oncorhynchus mykiss ) Y-chromosome-specific sequence. This is the first confirmed Y-specific sequence for rainbow trout. New Y-specific markers are described for Chinook salmon (OtY3) and rainbow trout (OmyY1), which are readily detected by PCR assays and are advantageous because they also produce autosomal control amplification products. Additionally, AFLP analysis of Chinook salmon yielded another potential Y-chromosome marker. These descriptions will facilitate genotypic sexing and should be useful for population studies of Y-chromosome polymorphisms and for future studies to characterize what appears to be a common sex-determining mechanism between these species.
Characterization and environmental evaluation of Atikokan coal fly ash for environmental applications
Authors: Yeheyis Muluken B. , Shang Julie Q. , Yanful Ernest K.
Published: September 2008

This study presents the results of physical, chemical, and mineralogical characterization of fresh and landfilled coal fly ash from Atikokan Thermal Generating Station, Ontario. The acid neutralization capacity, heavy metal sorption capacity, and possible environmental impact under different environmental conditions during utilization of the coal fly ash were also evaluated. The results show significant variations in morphology, mineralogy, and chemical composition between fresh and landfilled fly ashes attributed largely to weathering of the coal fly ash during landfilling. The formation of secondary minerals (predominantly calcite) in landfilled fly ash samples is confirmed by X-ray diffraction, thermal analysis, and Chittick tests. Chemical analysis of the generalized acid neutralization leaching test indicated that the heavy metals from both fresh and landfilled fly ash samples were below the leachate criteria set by the Ontario Government. Despite variations in acid neutralization capacity and physical and geochemical behaviors between fresh and landfilled coal fly ash materials, the overall results of this study suggest both materials have favorable engineering and environmental properties that make them suitable for various environmental applications.
Quantitative microbial risk assessment of a drinking water – wastewater cross-connection simulation
Authors: Mena Kristina D. , Mota Linda C. , Meckes Mark C. , Green Christopher F. , Hurd William W. , Gibbs Shawn G.
Published: September 2008

Quantitative microbial risk assessment is a useful way to predict the incidence of infection and illness within a community following exposure to pathogens. We used this risk assessment technique to determine the expected number of Salmonella infections and illnesses resulting from a drinking water – wastewater cross-connection incident using data generated from a distribution system simulator study and compared our results to a reported cross-contamination event that occurred in Pineville, Louisiana in 2000. Probabilities of infection and illness were estimated for different exposure scenarios representing different Salmonella concentrations and the characteristic varied attack rates for waterborne Salmonella. Risks of Salmonella infection range from 10% after a 1 day exposure (assuming the lower bound Salmonella concentration) to a 1-log greater risk of infection for all other scenarios, with risks of infection approximately 99% for 30 and 90 day exposure durations.
Décontamination de sols pollués par les hydrocarbures aromatiques polycycliques par biodégradation en présence de substrats organiques supplémentaires
Authors: Siméon Nathalie , Mercier Guy , Blais Jean-François , Ouvrard Stéphanie , Cébron Aurélie , Leyval Corinne , Goergen Jean-Louis , Guedon Emmanuel
Published: September 2008

Les hydrocarbures aromatiques polycycliques (HAP) sont connus pour être cancérigènes et mutagènes. Cette étude a porté sur la biodégradation de HAP (les 16 HAP de la liste prioritaire établie par l’Agence américaine de protection de l’environnement) présents dans un sol industriel en ajoutant des substrats organiques comme du lisier de porc, du compost de crevettes ou des boues d’épuration. Les boues municipales et le lisier de porc ont été utilisés comme inoculum pour améliorer la biodégradation des HAP. Les résultats ont montré une biodégradation de 60 % de la somme des 16 HAP en 16 semaines à 30 °C. Cette dégradation a été obtenue dans le cas d’une biopile composée de 75 % de sol pollué, 10 % d’inoculum (boues acclimatées), 10 % de boues brutes et 3 % de paille (pour améliorer le niveau d’aération). Pour cette condition, le ratio sol–amendements était de 1,0:0,3 et le rapport C/N de 30. Lors de cet essai, le GC-MS montre un taux de 68 % ± 16 % de dégradation des HAP de cinq à six cycles. La quantification de la HAP-dioxygénase par « polymerase chain reaction » en temps réel montre que la majorité des bactéries dégradantes provenant du sol contaminé et de l’inoculum sont des Gram+, alors que l’inoculum fait à partir des boues favorise le développement des bactéries dégradantes Gram–.
Stimulation of respiratory immunity by oral administration ofLactococcus lactis
Authors: Villena Julio , Medina Marcela , Vintiñi Elisa , Alvarez Susana
Published: September 2008

This work demostrates that nonrecombinant Lactococcus lactis NZ, administered by the oral route at the proper dose, is able to improve resistance against pneumococcal infection. Lactococcus lactis NZ oral administration was able to improve pathogen lung clearance, increased survival of infected mice, and reduced lung injuries. This effect was related to an upregulation of the respiratory innate and specific immune responses. Administration of L. lactis NZ improved production of bronchoalveolar lavage (BAL) fluid TNF-α, enhanced recruitment of neutrophils into the alveolar spaces, and induced a higher activation of BAL phagocytes compared with the control group. Lactococcus lactis NZ administered orally stimulated the IgA cycle, increased IgA+ cells in intestine and bronchus, and improved production of BAL IL-4 and IL-10 during infection. Moreover, mice treated with L. lactis NZ showed higher levels of BAL anti-pneumococcal IgA and IgG. Taking into consideration that orally administered L. lactis NZ stimulates both the innate and the specific immune responses in the respiratory tract and that bacterial and viral antigens have been efficiently produced in this strain, L. lactis NZ is an excellent candidate for the development of an effective pneumococcal oral vaccine.
B subunit ofEscherichia coliheat-labile enterotoxin as adjuvant of humoral immune response in recombinant BCG vaccination
Authors: da Silva Ramos Rocha Andréa , Conceição Fabricio Rochedo , Grassmann André Alex , Lagranha Valeska Lizzi , Dellagostin Odir Antônio
Published: September 2008

The B subunit of Escherichia coli heat-labile enterotoxin (LTB), a nontoxic molecule with potent biological properties, is a powerful mucosal and parenteral adjuvant that induces a strong immune response against co-administered or coupled antigens. In this paper, the effect of LTB on the humoral immune response to recombinant BCG (rBCG) vaccination was evaluated. Isogenic mice were immunized with rBCG expressing the R1 repeat region of the P97 adhesin of Mycoplasma hyopneumoniae alone (rBCG/R1) or fused to LTB (rBCG/LTBR1). Anti-R1 systemic antibody levels (IgG1, IgG2a, IgG2b, IgG3, IgM, and IgA) were measured by ELISA using recombinant R1 as antigen. With the exception of IgM, LTB doubled the anti-R1 antibody levels in rBCG vaccination. The IgG1/IgG2a mean ratio showed that both rBCG/LTBR1 and rBCG/R1 induced a mixed Th1/Th2 immune response. Interestingly, anti-R1 serum IgA was induced only by rBCG/LTBR1. These results demonstrate that LTB has an adjuvant effect on the humoral immune response to recombinant antigens expressed in BCG.
Differences in nitric oxide steady states between arginine, hypoxanthine, uracil auxotrophs (AHU) and non-AHU strains ofNeisseria gonorrhoeaeduring anaerobic respiration in the presence of nitrite
Authors: Barth Kenneth , Clark Virginia L.
Published: September 2008

Neisseria gonorrhoeae can grow by anaerobic respiration using nitrite as an alternative electron acceptor. Under these growth conditions, N. gonorrhoeae produces and degrades nitric oxide (NO), an important host defense molecule. Laboratory strain F62 has been shown to establish and maintain a NO steady-state level that is a function of the nitrite reductase/NO reductase ratio and is independent of cell number. The nitrite reductase activities (122–197 nmol NO2reduced·min–1·OD600–1) and NO reductase activities (88–155 nmol NO reduced·min–1·OD600–1) in a variety of gonococcal clinical isolates were similar to the specific activities seen in F62 (241 nmol NO2reduced·min–1·OD600–1and 88 nmol NO reduced·min–1·OD600–1, respectively). In seven gonococcal strains, the NO steady-state levels established in the presence of nitrite were similar to that of F62 (801–2121 nmol·L–1NO), while six of the strains, identified as arginine, hypoxanthine, and uracil auxotrophs (AHU), that cause asymptomatic infection in men had either two- to threefold (373–579 nmol·L–1NO) or about 100-fold (13–24 nmol·L–1NO) lower NO steady-state concentrations. All tested strains in the presence of a NO donor, 2,2′-(hydroxynitrosohydrazono)bis-ethanimine/NO, quickly lowered and maintained NO levels in the noninflammatory range of NO (<300 nmol·L–1). The generation of a NO steady-state concentration was directly affected by alterations in respiratory control in both F62 and an AHU strain, although differences in membrane function are suspected to be responsible for NO steady-state level differences in AHU strains.
Phenotypic and genotypic analysis of Flavobacterium psychrophilum isolates from Ontario salmonids with bacterial coldwater disease
Authors: Hesami Shohreh , Allen Katie J. , Metcalf Devon , Ostland Vaughn E. , MacInnes Janet I. , Lumsden John S.
Published: September 2008

Flavobacterium psychrophilum is the causative agent of bacterial coldwater disease (BCWD) and rainbow trout fry syndrome. BCWD has a considerable economic impact on aquaculture operations in Ontario, Canada, and our limited understanding of the population structure and epidemiology of F. psychrophilum isolates is an impediment to the development of improved management strategies. Seventy-five 16S rRNA gene and gyr polymerase chain reaction positive isolates of F. psychrophilum that had been collected over a 16-year period from farmed salmonids with tail rot, necrotic myositis, and osteochondrosis were characterized morphologically, biochemically, and genotypically. Although the isolates were homogeneous by preliminary biochemical and phenotypic characterization, two distinct biovars were found by API ZYM testing. As well, four restriction pattern types were detected by 16S rRNA polymerase chain reaction – restriction fragment length polymorphism analysis and there was a significant (P < 0.001) correlation between biovar I and digestion with MaeIII and between biovar II and digestion with MnlI or no site (P < 0.05). Further heterogenity was detected by sequence analysis of a 194 bp stem loop 3 region of rRNA. Nine sequence types were identified; 40/46 biovar I isolates were sequence type “a”, while 21/32 biovar II isolates belonged to either sequence type “c” or “d”. More than one biovar and genotype was identified among the strains recovered from separate fish sampled from three groups of rainbow trout ( Oncorhynchus mykiss ) experiencing BCWD mortality events. No association was found between genotype or biovar and type of disease. Taken together, these data suggest that F. psychrophilum from Ontario can be grouped into two major lineages based on biovar and 16S rRNA polymorphisms, and although three major strain types were most frequently isolated in this study, it appears that the population of F. psychrophilum with pathogenic potential is quite heterogeneous.
Prevalence of rectal carriage of extended-spectrum β-lactamase-producingEscherichia coliamong elderly people in community settings in China
Authors: Tian Su Fei , Chen Bai Yi , Chu Yun Zhuo , Wang Shuang
Published: September 2008

The importance of community-acquired infections due to extended-spectrum β-lactamase-producing (ESBL) Escherichia coli has been increasingly recognized in recent years. No comprehensive data are available on the prevalence, risk factors, and genotypes of ESBL production in community residents in China. Rectal samples from 270 elderly people were collected in four communities in Shenyang (China). Colonies were screened by double-disk synergy test for ESBL production and then, ESBLs were characterized by PCR and sequencing. The clonal relatedness of all ESBL-producing isolates was determined by pulsed-field gel electrophoresis. Potential risk factors for rectal carriage of ESBL producers were examined by multivariate analysis. The prevalence of rectal carriage of ESBL-producing E. coli was 7.0%. All 19 ESBL-producing isolates produced CTX-M-type ESBLs, including CTX-M-14 (11 strains), CTX-M-22 (3 strains), CTX-M-79 (3 strains), CTX-M-24 (1 strain), and CTX-M-24 and CTX-M-79 together (1 strain). CTX-M-79 ESBL was first detected worldwide. ESBL-producing strains were clonally unrelated. Appearance of ESBL producers is strongly associated with the use of antibiotics in the past 3 months (odds ratio 3.2, 95% CI 1.1–9.0, P = 0.03). Our results show the importance of the intestinal tract as a reservoir for ESBL-producing isolates in community settings in China and that the use of antibiotics in the past 3 months is clearly linked to rectal carriage of ESBL producers.
Construction ofBacillus thuringiensiswild-type S76 and Cry–derivatives expressing a green fluorescent protein: two potential marker organisms to study bacteria–plant interactions
Authors: Parente Ana Flávia , Silva-Pereira Ildinete , Baldani José Ivo , Tibúrcio Victor Hugo da Silva , Báo Sônia Nair , De-Souza Marlene T.
Published: September 2008

Collectively, the species Bacillus thuringiensis , Bacillus cereus , and Bacillus anthracis represent microorganisms of high economic, medical, and biodefense importance. Although the genetic correlation and pathogenic characteristics have been extensively dissected, the ecological properties of these three species in their natural environments remain poorly understood. Thus, a tractable marker for detecting these bacteria under specific environmental and physiological conditions is a valuable tool. With this purpose, a plasmid (pAD43-25) carrying a functional gfp gene sequence (gfpmut3A) was introduced into the wild-type strain Bacillus thuringiensis subsp. kurstaki S76, which bears approximately 11 plasmids, allowing constitutive synthesis of green fluorescent protein (GFP) during vegetative growth (strain S76GFP+). Additionally, this vector was transferred to a plasmid-cured (Cry–) B. thuringiensis host. Bright green cells were detected by fluorescence microscopy in both recombinants by 2 h after inoculation in liquid medium and could be seen throughout the remaining cultivation time until complete sporulation was accomplished. For strain S76GFP+protein profile and plasmid DNA analyses indicate, respectively, that this recombinant maintained Cry proteins expression and resident plasmid outline. Thus, in addition to the potential of strain S76GFP+as a marker organism in bacteria–plant interaction studies, the production and stability of active GFPmut3a make this unique expression system a useful experimental model to study adaptive changes of host–plasmid as well as plasmid–plasmid relationships in a population of cells stressed by the production of a recombinant protein.
An intracellular symbiont and other microbiota associated with field-collected populations of sawflies (Hymenoptera: Symphyta)
Authors: Graham Robert I. , Zahner Viviane , Lucarotti Christopher J.
Published: September 2008

Six species of sawfly (Hymenoptera: Symphyta) from four taxonomic families (Agridae, Diprionidae, Pamphiliidae, and Tenthredinidae) were collected from locations across Canada and surveyed for their associated microbiota. Total DNA was extracted from individual insects, and polymerase chain reaction (PCR) was used to amplify the conserved 16S rRNA gene from microbiota. Denaturing gradient gel electrophoresis (DGGE) and restriction fragment length polymorphism (RFLP) were undertaken to separate bacterial clones associated with the host insect. Sequencing of the PCR–DGGE and PCR–RFLP products revealed a dominance of α- and γ-Proteobacteria, with most sequences showing high similarity to bacteria previously identified from other insect species and environmental samples. Additionally, a strain of the bacterial endosymbiont Wolbachia and a Wolbachia bacteriophage were identified from the mountain ash sawfly ( Pristiphora geniculata ).
Infection of rabbit kidney cells (RK13) by enteropathogenicEscherichia colias a model to study the dynamics of actin cytoskeleton
Authors: Oliver-Gonzalez Rubén , García-Tovar Carlos , Juárez-Mosqueda Lourdes , Navarro-Garcia Fernando
Published: September 2008

Enteropathogenic Escherichia coli (EPEC) colonizes the intestinal mucosa and causes a cell lesion known as attachment and effacement (A/E) lesion. The molecular mechanisms for A/E lesions include injection of Tir, which is a receptor for an adhesin named intimin. The Tir–intimin interaction causes rearrangement of the cytoskeleton forming actin-rich structures called pedestals. Unfortunately, the formation of the A/E lesions and the dynamics of the actin cytoskeleton during this rearrangement induced by EPEC cannot be studied in the natural host. However, there are EPEC strains that infect rabbit (REPEC) that are genetically and pathologically similar to EPEC. Here, we used REPEC for the infection of rabbit kidney epithelial cells, line RK13, as a model to understand the actin cytoskeleton dynamics during pedestal formation. Actin-rich pedestal formation during the infection of RK13 cells by REPEC was analyzed by electron and confocal microscopy. The kinetics of infection along with the use of antibiotics for eliminating the bacteria, as well as reinfection, evidenced the plasticity of the actin cytoskeleton during pedestal formation. Thus, this model is a helpful tool for studying the dynamics of actin cytoskeleton and for correlating the data with those observed in in vivo models in rabbits experimentally infected with REPEC.