bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative Susceptibility of Deschutes River, Oregon, Tubifex tubifex Populations to Myxobolus cerebralis
Authors: Zielinski Christopher M. , Lorz Harriet V. , Hallett Sascha L. , Xue Lan , Bartholomew Jerri L. 
Published: December 2011

Abstract
Dams along the Deschutes River (DR) in central Oregon have blocked fish migration for over 40 years. Reestablishment of anadromous fish runs above the dams as part of a fish passage plan may introduce fish pathogens, such as Myxobolus cerebralis, the myxozoan parasite that causes salmonid whirling disease. This parasite is carried by adult salmon that stray into the DR system during their return to enzootic areas of the upper Columbia River basin, and it is now known to be established in at least one lower DR tributary. The life cycle of M. cerebralis involves two obligate hosts: a salmonid and the oligochaete worm Tubifex tubifex. To determine the likelihood of parasite establishment above the DR dams, we conducted benthic sediment surveys between 1999 and 2007 and found that T. tubifex had a patchy distribution and low relative abundance. Mitochondrial 16S ribosomal DNA gene analysis indicated that two lineages of T. tubifex (III and VI) were present both above and below the dams. Laboratory susceptibility studies to characterize differences in infection prevalence and parasite production between nine T. tubifex populations revealed that production varied considerably among exposed groups and was proportional to the number of lineage III worms present. Our results suggest that M. cerebralis could become established above the dams if infected fish are allowed passage into the upper DR system, but not all areas of the DR basin can be classified as having the same likelihood for parasite establishment, and the potential impact will be location dependent.
Received July 2, 2010; accepted October 24, 2010
An Evaluation of the Influence of Stock Origin and Out-migration History on the Disease Susceptibility and Survival of Juvenile Chinook Salmon
Authors: Dietrich Joseph P. , Boylen Deborah A. , Thompson Donald E. , Loboschefsky Erik J. , Bravo Claudia F. , Spangenberg Dina K. , Ylitalo Gina M. , Collier Tracy K. , Fryer Derek S. , Arkoosh Mary R. , Loge Frank J. 
Published: December 2011

Abstract
Various methods have been developed to mitigate the adverse effects of the Federal Columbia River Power System on juvenile Pacific salmon out-migrating through the Columbia River basin. In this study, we found that hatchery-reared spring Chinook salmon Oncorhynchus tshawytscha in the river are in varying degrees of health, which may affect delayed mortality and the assessment of the effectiveness of management actions to recover listed stocks (e.g., barging fish downstream versus leaving fish in the river). A laboratory disease challenge with Listonella anguillarum was completed on fish from Rapid River Hatchery and Dworshak National Fish Hatchery (NFH) with different out-migration histories: (1) transported by barge, (2) removed from the river before barging, or (3) left to travel in-river. Barged fish from Rapid River Hatchery experienced less mortality than fish from Dworshak NFH. No statistical differences were found between the hatcheries with fish that had in-river out-migration histories. We suggest that the stressors and low survival associated with out-migration through the hydropower system eliminated any differences that could have been present. However, 18–25% of the fish that were barged or collected before barging died in the laboratory before the disease challenge, compared with less than 2% of those that traveled in-river. Owing to disproportionate prechallenge mortality, the disease-challenged populations may have been biased; thus, they were also considered together with the prechallenge mortalities. The synthesis of prechallenge and disease-challenged mortalities and health characteristics evaluated during out-migration indicated that the benefit of barging was not consistent between the hatcheries. This finding agrees with adult survival and delayed mortality estimates for the individual hatcheries determined from adult returns. The results suggest that the health status of fish and their history before entering the hydropower system (hatchery of origin and out-migration path) are critical variables affecting the conclusions drawn from studies that evaluate mitigation strategies.
Received November 18, 2009; accepted January 6, 2011
Uptake of Metronidazole in Artemia at Different Developmental Life Stages
Authors: Rodriguez Loretta , Livengood Elisa J. , Miles Richard D. , Chapman Frank A. 
Published: December 2011

Abstract
The purpose of this study was to examine the capacity of live brine shrimp Artemia spp. to accumulate metronidazole at different developmental life stages. Metronidazole is used in fish as an antiparasitic medication. An effective drug delivery method is to enrich the Artemia with metronidazole and offer them as live feed to the infected fish, usually ornamental species and other small fishes. Artemia cysts were hatched and then soaked in a metronidazole solution (0.05%) at instars 1–3 of larval development. Our findings indicated that Artemia were able to accumulate metronidazole at levels considered therapeutic to other animals and humans (25–100 mg/kg). However, the levels varied depending on the stage of larval development. Artemia accumulated the highest levels of metronidazole (137–143 mg/kg) when they started filter feeding (instar 2), whereas newly hatched Artemia (instar 1) contained the lowest level (85 mg/kg). Based on this study and a review of the literature, a new protocol recommended for enriching Artemia with metronidazole consists of soaking the Artemia in a 0.05% metronidazole solution for 3 h at room temperature. Because metronidazole is relatively insoluble in water, it must first be dissolved in warm water with continuous stirring.
Received December 5, 2010; accepted January 30, 2011
A Real-Time Polymerase Chain Reaction Assay for Quantification of Edwardsiella ictaluri in Catfish Pond Water and Genetic Homogeneity of Diagnostic Case Isolates from Mississippi
Authors: Griffin Matt J. , Mauel Michael J. , Greenway Terrence E. , Khoo Lester H. , Wise David J. 
Published: December 2011

Abstract
A quantitative polymerase chain reaction (qPCR) assay was developed for the detection and quantification of Edwardsiella ictaluri in channel catfish Ictalurus punctatus pond water using modifications to a published E. ictaluri–specific qPCR assay and previously established protocols for the molecular detection of myxozoan parasites in catfish ponds. Genomic DNA equivalents indicative of the number of bacteria in a sample were determined and standard curves correlating to bacterial numbers were established. The assay was found to be highly repeatable and reproducible, with a linear dynamic range of five orders of magnitude. There was no interference of the assay from the presence of large quantities of nontarget DNA. Known quantities of bacteria were added to sample volumes of 40 or 500 mL of pond water collected from several different ponds. The minimum level of detection was approximately 100 cell equivalents (CE) in 40 (2.5 CE/mL) or 500 mL of pond water (0.2 CE/mL). Sample volumes of 40 mL yielded the most consistent results, which were not significantly different from those obtained from broth culture alone. Cell equivalents determined by qPCR in 40-mL pond water samples spiked with known quantities of bacteria were within one order of magnitude of the actual number of cells added. Repetitive element-based polymerase chain reaction analysis of archived isolates demonstrated the genetic homogeneity of E. ictaluri, and consistent amplification of these isolates by qPCR analysis demonstrated the stability of the PCR target. The assay described here provides a reliable method for the detection and quantification of E. ictaluri in pond water and will be an invaluable tool in epidemiological studies. Additionally, the assay provides a way to evaluate the effects that vaccination, antibiotic treatments, and restricted feeding practices have on E. ictaluri populations during an outbreak. Information obtained with these tools will aid in optimizing disease management practices designed to maximize productivity while minimizing losses.
Received October 20, 2010; accepted June 13, 2011
RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing
Authors: Xi Yuanxin , Bock Christoph , Müller Fabian , Sun Deqiang , Meissner Alexander , Li Wei 
Published: December 2011

Abstract
Summary: Reduced representation bisulfite sequencing (RRBS) is a powerful yet cost-efficient method for studying DNA methylation on a genomic scale. RRBS involves restriction-enzyme digestion, bisulfite conversion and size selection, resulting in DNA sequencing data that require special bioinformatic handling. Here, we describe RRBSMAP, a short-read alignment tool that is designed for handling RRBS data in a user-friendly and scalable way. RRBSMAP uses wildcard alignment, and avoids the need for any preprocessing or post-processing steps. We benchmarked RRBSMAP against a well-validated MAQ-based pipeline for RRBS read alignment and observed similar accuracy but much improved runtime performance, easier handling and better scaling to large sample sets. In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS.
Availability: http://rrbsmap.computational-epigenetics.org/ http://code.google.com/p/bsmap/
Contact: wl1@bcm.tmc.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
LPIN1 rs13412852 Polymorphism in Pediatric Nonalcoholic Fatty Liver Disease
Authors: Valenti Luca , Motta Benedetta Maria , Alisi Anna , Sartorelli Rita , Buonaiuto Giulia , Dongiovanni Paola , Rametta Raffaela , Pelusi Serena , Fargion Silvia , Nobili Valerio 
Published: December 2011

ABSTRACTObjectives:The aim of the present study was to evaluate whether the lipin1 rs13412852 C>T polymorphism is associated with nonalcoholic steatohepatitis and fibrosis in pediatric Italian patients with nonalcoholic fatty liver disease (NAFLD).Methods:A total of 142 untreated, consecutive children and 115 adults with biopsy‐proven NAFLD and 337 healthy controls without steatosis were studied. Liver histology was assessed by the NAFLD activity score and the rs13412852 polymorphism by a 5′ nuclease Taqman assay.Results:Homozygosity for the rs13412852 T allele was underrepresented in pediatric, but not adult, patients with NAFLD compared with healthy controls (7% vs 14%; odds ratio [OR] 0.58, 95% confidence interval [CI] 0.35–0.91), and it was associated with lower triglycerides both in pediatric patients and healthy controls (P ≤ 0.01). Affected children carrying the rs13412852 TT genotype had a trend for a lower prevalence of nonalcoholic steatohepatitis, and significantly less severe liver damage, as indicated by NAFLD activity score severity (P = 0.026) and a lower prevalence of liver fibrosis (P = 0.012). The negative association between rs13412852 TT genotype and fibrosis was independent of Patatin‐like phospholipase domain‐containing‐3 genotype and other clinical risk factors, including age, waist circumference, the presence of hyperglycemia, and alanine transaminase levels (OR 0.29; 95% CI 0.11–0.66), and it was confirmed at multivariate analysis in adults (OR 0.15; 95% CI 0.02–0.67).Conclusions:Lipin1 rs13412852 single nucleotide polymorphism is associated with the severity of liver damage and fibrosis progression in pediatric patients with histological NAFLD.
Characterization of a PDK1 Homologue from the Moss Physcomitrella patens
Authors: Dittrich Anna C. Nelson , Devarenne Timothy P. 
Published: December 2011

Abstract
The serine/threonine protein kinase 3-phosphoinositide-dependent protein kinase 1 (PDK1) is a highly conserved eukaryotic kinase that is a central regulator of many AGC kinase subfamily members. Through its regulation of AGC kinases, PDK1 controls many basic cellular processes, from translation to cell survival. While many of these PDK1-regulated processes are conserved across kingdoms, it is not well understood how PDK1 may have evolved within kingdoms. In order to better understand PDK1 evolution within plants, we have isolated and characterized the PDK1 gene from the moss Physcomitrella patens (PpPDK1), a nonvascular representative of early land plants. PpPDK1 is similar to other plant PDK1s in that it can functionally complement a yeast PDK1 knockout line. However, unlike PDK1 from other plants, the P. patens PDK1 protein does not bind phospholipids due to a lack of the lipid-binding pleckstrin homology domain, which is used for lipid-mediated regulation of PDK1 activity. Sequence analysis of several PDK1 proteins suggests that lipid regulation of PDK1 may not commonly occur in algae and nonvascular land plants. PpPDK1 can phosphorylate AGC kinase substrates from tomato (Solanum lycopersicum) and P. patens at the predicted PDK1 phosphorylation site, indicating that the PpPDK1 substrate phosphorylation site is conserved with higher plants. We have also identified residues within the PpPDK1 kinase domain that affect kinase activity and show that a mutant with highly reduced kinase activity can still confer cell viability in both yeast and P. patens. These studies lay the foundation for further analysis of the evolution of PDK1 within plants.
Male fecundity and pollen dispersal in hill dipterocarps: significance of mass synchronized flowering and implications for conservation
Authors: Tani Naoki , Tsumura Yoshihiko , Fukasawa Keita , Kado Tomoyuki , Taguchi Yuriko , Lee S. L. , Lee C. T. , Muhammad Norwati , Niiyama Kaoru , Otani Tatsuya , Yagihashi Tsutomu , Ripin Azizi , Kassim Abdul Rahman 
Published: December 2011

Summary1. To understand pollinator–plant symbioses and to conserve forest resources effectively, we need an understanding of pollen dispersal patterns and the heterogeneity (spatial and temporal) of male fecundity.2. We investigated pollen dispersal patterns of the hill dipterocarp species Shorea curtisii using a modified Neighbourhood model. Seeds were collected following a sporadic general flowering (GF) event in 2002 and two mass GF events in 1998 and 2005. Seed paternity was then determined to investigate pollen dispersal patterns and the heterogeneity of male fecundity.3. Pollen dispersal distances were longer, and the effective number of males lower, in the sporadic GF of 2002, than in the mass GF events of 1998 and 2005.4. There was high between‐individual variation in male fecundity, and small trees contributed less than large trees to the analysed seed pool. The results indicate that selective logging may adversely affect the reproduction of such species due to the removal of large trees from the reproductive population.5. Synthesis. The large number of effective male individuals during the mass GF events provides evidence of Allee effects, suggesting that the mass GF events are of evolutionary significance and may contribute to the maintenance of genetic diversity. Future forestry practice needs to take into account variation in male fecundity, pollen dispersal and the mating system to ensure sustainable regeneration.
Application of artificial neural networks for feature recognition in image registration
Authors: ONTMAN A.Y.M. , SHIFLET G.J. 
Published: December 2011

SummaryImage registration is a process of aligning two or more images taken at different times or using different sensors by transforming the same area into one coordinate system. Imaging conditions, image and area deteriorations from repeated sectioning, are serious impediments to successful image registration. The application of artificial neural networks for feature recognition is introduced to the field of metallurgy to assist in an automated approach to image registration of metallurgical microstructures. Low susceptibility to feature deterioration, often occurring during serial sectioning, is demonstrated and assessed. The process of image registration using an artificial neural network to aid in feature segmentation is performed using computer generated shapes and a metallurgical microstructure.
Knockdown of MYB305 disrupts nectary starch metabolism and floral nectar production
Authors: Liu Guangyu , Thornburg Robert W. 
Published: December 2011

SummaryMYB transcription factors have important roles during floral organ development. In this study, we generated myb305 RNAi knockdown tobacco plants and studied the role of MYB305 in the growth of the floral nectary. We have previously shown the MYB305 regulates the expression of flavonoid metabolic genes as well as of nectar proteins (nectarins); however, the myb305 plants showed other floral phenotypes that we investigate in these studies. The nectaries of myb305 plants show juvenile character at late stages of development and secrete reduced levels of nectar. Because starch metabolism is intimately involved in nectar secretion and is strongly regulated during normal nectary development, we examined the accumulation of starch in the nectaries of the myb305 plants. The myb305 plants accumulated lower levels of starch in their nectaries than did wild‐type plants. The reduced starch correlated with the reduced expression of the ATP‐glucose pyrophosphorylase (small subunit) gene in nectaries of the myb305 plants during the starch biosynthetic phase. Expression of genes encoding several starch‐degrading enzymes including β‐amylase, isoamylase 3, and α‐amylase was also reduced in the myb305 plants. In addition to regulating nectarin and flavonoid metabolic gene expression, these results suggest that MYB305 may also function in the tobacco nectary maturation program by controlling the expression of starch metabolic genes.
Third‐party mesenchymal stromal cell infusion is associated with a decrease in thrombotic microangiopathy symptoms observed post‐hematopoietic stem cell transplantation
Authors: Ansari Marc , Strunk Dirk , Schallmoser Katharina , Delcò Cristina , Rougemont Anne‐Laure , Moll Solange , Villard Jean , Gumy‐Pause Fabienne , Chalandon Yves , Parvex Paloma , Passweg Jakob , Ozsahin Hulya , Kindler Vincent 
Published: December 2011

Ansari M, Strunk D, Schallmoser K, Delcò C, Rougemont A‐L, Moll S, Villard J, Gumy‐Pause F, Chalandon Y, Parvex P, Passweg J, Ozsahin H, Kindler V. Third‐party mesenchymal stromal cell infusion is associated with a decrease in thrombotic microangiopathy symptoms observed post‐hematopoietic stem cell transplantation. Pediatr Transplantation 2012: 16: 131–136. © 2011 John Wiley & Sons A/S.Abstract:  TA‐TMA is a pathology that occurs after allogenic HSC transplantation with an incidence of 4–13%, and represents one of the most severe vascular damage related with this therapy. We report here the case of a nine‐yr‐old girl suffering from a severe refractory aplastic anemia who received an unrelated, 9/10 HLA‐matched HSC. Soon after transplantation, the patient developed a graft‐versus‐host disease (GvHD), a TA‐TMA, and renal insufficiency. These pathologies remained refractory to the various treatments undertaken and required several hospitalizations in the intensive care unit. On day 106 post‐HSC transfusion, after several episodes of intensive care, the patient was infused with mismatched, third‐party MSCs. Schizocyte levels rapidly decreased after MSC infusion, and two wk later, most biological parameters returned to normal. Erythrocyte and thrombocyte transfusions were discontinued, and the patient remained stable for 10 wk. Thereafter, TA‐TMA symptoms, viral reactivation, pleural and cardiac effusions reappeared and lead to the death of the patient. Our observations suggest that allogenic MSC infusion may decrease the symptoms of TA‐TMA, but further investigation is required to determine how and when MSC should be infused to develop a long‐lasting protective effect.
The comparative biology of diving in two genera of European Dytiscidae (Coleoptera)
Authors: CALOSI P. , BILTON D. T. , SPICER J. I. , VERBERK W. C. E. P. , ATFIELD A. , GARLAND T. 
Published: December 2011

AbstractSurfacing behaviour is fundamental in the ecology of aquatic air‐breathing organisms; however, it is only in vertebrates that the evolutionary ecology of diving has been well characterized. Here, we explore the diving behaviour of dytiscid beetles, a key group of surface‐exchanging freshwater invertebrates, by comparing the dive responses of 25 taxa (Deronectes and Ilybius spp.) acclimated at two temperatures. The allometric slopes of dive responses in these dytiscids appear similar to those of vertebrate ectotherms, supporting the notion that metabolic mode shapes the evolution of diving performance. In both genera, beetles spend more time submerged than on the surface, and surface time does not vary with the temperature of acclimation. However, presumably in order to meet increased oxygen demand at higher temperatures, Deronectes species increase surfacing frequency, whereas Ilybius species decrease dive time, an example of ‘multiple solutions.’ Finally, widespread northern species appear to possess higher diving performances than their geographically restricted southern relatives, something which may have contributed to their range expansion ability.
Eggs Ultrastructure and Early Development of Franciscodoras marmoratus (Pisces: Doradidae)
Authors: Alberto Weber A. , Sato Y. , Enemir Santos J. , Rizzo E. , Bazzoli N. 
Published: December 2011

SummaryThis study presents, for the first time, information on the eggs and early development of Franciscodoras marmoratus, fish of São Francisco river, Brazil. To analyse the egg ultrastructure and morphological events of embryogenesis, a total of 36 F. marmoratus specimens (18 males and 18 females) were captured and subjected to spawning induction. Gametes were collected by manual extrusion, and fertilization was conducted using the dry method. After fertilization, eggs were kept in incubators with water temperature of 24°C. The embryonic development was monitored using a stereomicroscope until hatching. There was a 67% positive response to hypophysation by the females and the fertilization rate was 73.8 ± 6.2%. The oocytes are discoid, yellow, adhesive and covered by a thick jelly coat. Under the electron scanning microscope, the oocytes presented a surface with pore canals and funnel‐shaped micropyle with a smooth vestibule. Recently extruded oocytes had a mean diameter of 1.27 ± 0.4 mm and after hydration was 1.91 ± 0.05 mm. The jelly coat was 0.34 ± 0.03 mm thickness, and the perivitelline space was 0.19 ± 0.04 mm. Eight phases of the embryonic development were identified, and embryogenesis was completed at 47 h after fertilization, at 24°C water temperature. The recently hatched larvae had 2.76 ± 0.57 mm of total length. These results provide useful information for the successful breeding and reproductive strategies of fishes.