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https://www.readbyqxmd.com/read/28108551/genotype-calling-from-population-genomic-sequencing-data
#1
Takahiro Maruki, Michael Lynch
Genotype calling plays important roles in population-genomic studies, which have been greatly accelerated by sequencing technologies. To take full advantage of the resultant information, we have developed maximum-likelihood (ML) methods for calling genotypes from high-throughput sequencing data. As the statistical uncertainties associated with sequencing data depend on depths of coverage, we have developed two types of genotype callers. One approach is appropriate for low-coverage sequencing data, and incorporates population-level information on genotype frequencies and error rates pre-estimated by an ML method...
January 20, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28107438/first-insights-into-the-subterranean-crustacean-bathynellacea-transcriptome-transcriptionally-reduced-opsin-repertoire-and-evidence-of-conserved-homeostasis-regulatory-mechanisms
#2
Bo-Mi Kim, Seunghyun Kang, Do-Hwan Ahn, Jin-Hyoung Kim, Inhye Ahn, Chi-Woo Lee, Joo-Lae Cho, Gi-Sik Min, Hyun Park
Bathynellacea (Crustacea, Syncarida, Parabathynellidae) are subterranean aquatic crustaceans that typically inhabit freshwater interstitial spaces (e.g., groundwater) and are occasionally found in caves and even hot springs. In this study, we sequenced the whole transcriptome of Allobathynella bangokensis using RNA-seq. De novo sequence assembly produced 74,866 contigs including 28,934 BLAST hits. Overall, the gene sequences were most similar to those of the waterflea Daphnia pulex. In the A. bangokensis transcriptome, no opsin or related sequences were identified, and no contig aligned to the crustacean visual opsins and non-visual opsins (i...
2017: PloS One
https://www.readbyqxmd.com/read/28095184/ecotoxicological-effects-of-larvicide-used-in-the-control-of-aedes-aegypti-on-nontarget-organisms-redefining-the-use-of-pyriproxyfen
#3
Vanessa Santana Vieira Santos, Evelyn Siqueira Caixeta, Edimar Olegário de Campos Júnior, Boscolli Barbosa Pereira
The continued widespread use of larvicides in Aedes aegypti control programs is still a necessary strategy, since there are no apparent efficient vaccines against arboviruses. However, chemical approaches may affect nontarget organisms and produce detrimental effects to environmental health. Therefore, the aim of this study was to conduct toxicity testing for pyriproxyfen at different concentrations using Daphnia magna and Artemia salina as model organisms to evaluate the ecotoxicological parameters. This study describes the toxicological effects of pyriproxyfen on both microcrustaceans, which are widely used in bioassays because of their sensitivity to changes in hydrosphere...
January 17, 2017: Journal of Toxicology and Environmental Health. Part A
https://www.readbyqxmd.com/read/28079143/lethal-sublethal-responses-of-daphnia-magna-to-acute-norfloxacin-contamination-and-changes-in-phytoplankton-zooplankton-interactions-induced-by-this-antibiotic
#4
Ying Pan, Shi-Wei Yan, Ruo-Zhu Li, Yi-Wen Hu, Xue-Xiu Chang
Although the well-known antibiotic norfloxacin (NOR) is recognized as an important environmental pollutant, little is known about its impacts on ecological processes, particularly on species interactions. In this paper, we quantified Daphnia magna (Crustacea, Cladocera) responses in mortality rate at lethal NOR concentrations (0, 25, 50, 100, 200, 300 and 400 mg L(-1)), and in heartbeat rate, swimming behavior and feeding rate (on the green alga Chlorella pyrenoidosa) at sublethal NOR concentrations (0, 25, 50 and 100 mg L(-1)) to determine the effects of this antibiotic in plankton systems...
January 12, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28079015/chemometrics-expertise-in-the-links-between-ecotoxicity-and-physicochemical-features-of-silver-nanoparticles-environmental-aspects
#5
Miroslava A Nedyalkova, Borjana V Donkova, Vasil D Simeonov
Studies of the ecotoxicological aspects of nanomaterials in aquatic environments are scarce. Given the growing varietyof nanoparticles (NPs), along with the diversity of aquatic species and environments, the key to promoting sound risk assessment in nanoecotoxicology is understanding the mechanisms that govern the fate of NPs in aquatic environments and their behavior at the NP-biota interface. In this paper, data collected from the literature on ecotoxicological effects observed in aquatic species is discussed and analyzed using multivariate statistics techniques...
January 12, 2017: Journal of AOAC International
https://www.readbyqxmd.com/read/28078368/time-dependent-toxicity-responses-in-daphnia-magna-exposed-to-cuo-and-zno-nanoparticles
#6
Soyoun Kim, Palas Samanta, Jisu Yoo, Woo-Keun Kim, Jinho Jung
Aggregation and dissolution of CuO and ZnO nanoparticles (NPs) increased with increasing exposure time (24, 48, and 72 h). Acute toxicity of CuO NPs to Daphnia magna also increased significantly with increasing exposure time (p < 0.05), whereas exposure time did not significantly affect acute toxicity of ZnO NPs. The dissolved Cu concentration of CuO NPs was much lower than the median effective concentration (EC50) value (44 μg L(-1) at 72 h), implying that the increase in acute toxicity was caused by particles rather than by dissolved ions...
January 11, 2017: Bulletin of Environmental Contamination and Toxicology
https://www.readbyqxmd.com/read/28077777/no-evidence-for-thermal-transgenerational-plasticity-in-metabolism-when-minimizing-the-potential-for-confounding-effects
#7
Ø N Kielland, C Bech, S Einum
Environmental change may cause phenotypic changes that are inherited across generations through transgenerational plasticity (TGP). If TGP is adaptive, offspring fitness increases with an increasing match between parent and offspring environment. Here we test for adaptive TGP in somatic growth and metabolic rate in response to temperature in the clonal zooplankton Daphnia pulex Animals of the first focal generation experienced thermal transgenerational 'mismatch' (parental and offspring temperatures differed), whereas conditions of the next two generations matched the (grand)maternal thermal conditions...
January 11, 2017: Proceedings. Biological Sciences
https://www.readbyqxmd.com/read/28076700/correlation-between-acute-toxicity-for-daphnia-magna-aliivibrio-fischeri-and-physicochemical-variables-of-the-leachate-produced-in-landfill-simulator-reactors
#8
José J Barrios Restrepo, Letícia Flohr, Silvia P Melegari, Cristina H da Costa, Cristiane F Fuzinatto, Armando B de Castilhos, William G Matias
Due to the diversified nature of municipal solid waste (MSW) and the different stages of its decomposition, the formed leachates result in a complex chemical mixture with toxic potential. These chemicals can cause environmental problems, such as the contamination of surface or groundwater, thus affecting the balance of aquatic ecosystems. The aim of our study was to evaluate the acute toxicity of leachates in Daphnia magna and Aliivibrio fischeri and to identify the main physicochemical variables that influence the toxicity of the landfill leachates produced in reactors within pilot simulations...
January 11, 2017: Environmental Technology
https://www.readbyqxmd.com/read/28074365/determination-of-cytostatic-drugs-in-bes%C3%A3-s-river-ne-spain-and-comparison-with-predicted-environmental-concentrations
#9
Helena Franquet-Griell, Deborah Cornadó, Josep Caixach, Francesc Ventura, Silvia Lacorte
The number of cytostatic drugs used in cancer treatments is wide and increases every year; therefore, tools have been developed to predict their concentration in the environment to prioritize those for monitoring studies. In the present study, the predicted environmental concentrations (PECs) were calculated according to consumption data in Catalonia (NE Spain) for 2014. According to PECs and to the most widely reported compounds, 19 cytostatics were monitored in two sampling campaigns performed along the Besòs River...
January 10, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28073528/use-of-cholinesterase-activity-as-an-ecotoxicological-marker-to-assess-anatoxin-a-s-exposure-responses-of-two-cladoceran-species-belonging-to-contrasting-geographical-regions
#10
Emanuela Cristina Freitas, Liane Biehl Printes, Odete Rocha
The specificity of cholinesterase (ChE) activity to detect the presence of anatoxin-a(s) and sublethal effects of a 7-day exposure to Anabaena spiroides extract containing anatoxin-a(s) were assessed in two freshwater cladoceran species. Activities of ChE of both Pseudosida ramosa and Daphnia magna can be used to indicate the presence of the neurotoxin anatoxin-a(s), but not for the hepatotoxic microcystin. Activity of ChE of P. ramosa, however, performed better as a biomarker of exposure to A. spiroides than that of D...
May 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073492/stress-responsive-expression-of-a-glutathione-s-transferase-delta-gene-in-waterflea-daphnia-magna-challenged-by-microcystin-producing-and-microcystin-free-microcystis-aeruginosa
#11
Kai Lyu, Lei Gu, Bangping Li, Yichun Lu, Changcan Wu, Haoyong Guan, Zhou Yang
Harmful cyanobacterial blooms resulting from eutrophication and global warming have emerged as a worldwide environmental concern. Some zooplankton populations, including Daphnia, have been shown to adapt locally to microcystin-producing Microcystis. Previous in vitro experiments indicate that glutathione-S-transferase (GST) may act as the first step of detoxification in Daphnia by conjugating microcystins (MCs) with glutathione. The GST family is categorized into many classes, and different classes present distinct responses to MC detoxification...
June 2016: Harmful Algae
https://www.readbyqxmd.com/read/28073472/the-interaction-between-cyanobacteria-and-zooplankton-in-a-more-eutrophic-world
#12
REVIEW
Kemal Ali Ger, Pablo Urrutia-Cordero, Paul C Frost, Lars-Anders Hansson, Orlando Sarnelle, Alan E Wilson, Miquel Lürling
As blooms of cyanobacteria expand and intensify in freshwater systems globally, there is increasing interest in their ecological effects. In addition to being public health hazards, cyanobacteria have long been considered a poor quality food for key zooplankton grazers that link phytoplankton to higher trophic levels. While past laboratory studies have found negative effects of nutritional constraints and defensive traits (i.e., toxicity and colonial or filamentous morphology) on the fitness of large generalist grazers (i...
April 2016: Harmful Algae
https://www.readbyqxmd.com/read/28069588/diet-quality-determines-lipase-gene-expression-and-lipase-esterase-activity-in-daphnia-pulex
#13
Apostolos-Manuel Koussoroplis, Anke Schwarzenberger, Alexander Wacker
We studied the short- (12 hours) and long-term (144h) response of Daphnia pulex lipases to quality shifts in diets consisting of different mixtures of the green alga Scenedesmus with the cyanobacterium Synechococcus, two species with contrasting lipid compositions. The lipase/esterase activity in both the gut and the body tissues responded fast to the diet shift and increased with higher dietary contributions of Synechococcus When screening the Daphnia genome for TAG lipases, we discovered a large gene-family expansion of these enzymes...
January 9, 2017: Biology Open
https://www.readbyqxmd.com/read/28065573/rapid-evolution-of-tolerance-to-road-salt-in-zooplankton
#14
Kayla D Coldsnow, Brian M Mattes, William D Hintz, Rick A Relyea
Organisms around the globe are experiencing novel environments created by human activities. One such disturbance of growing concern is the salinization of freshwater habitats from the application of road deicing salts, which creates salinity levels not experienced within the recent evolutionary history of most freshwater organisms. Moreover, salinization can induce trophic cascades and alter the structure of freshwater communities, but knowledge is still scarce about the ability of freshwater organisms to adapt to elevated salinity...
December 27, 2016: Environmental Pollution
https://www.readbyqxmd.com/read/28065232/establishment-of-an-alloxan-induced-diabetes-model-in-daphnia-pulex
#15
An-Min Hu, Tao Zhu, Ye Jiang, Li Dong, Hong Gao, Gui-Zhi DU
Objective To establish a Daphnia model of alloxan-induced diabetes. Methods Daphnia were exposed to three different concentrations of alloxan (3, 5, and 10 mmol/L) for 30 minutes. Blood glucose and survival rate were recorded for 72 hours after alloxan insult. Sequence analysis and phylogenetic inference for glucose transporters (GLUT) were clustered with the maximum-likelihood method. Using reverse transcription and quantitative polymerase chain reaction techniques, we investigated the transcriptional changes of GLUT at 12 hours after alloxan (5 mmol/L) exposure...
December 20, 2016: Zhongguo Yi Xue Ke Xue Yuan Xue Bao. Acta Academiae Medicinae Sinicae
https://www.readbyqxmd.com/read/28064394/sacrificial-photocatalysis-removal-of-nitrate-and-hydrogen-production-by-nano-copper-loaded-p25-titania-a-kinetic-and-ecotoxicological-assessment
#16
Roberta Lucchetti, Antonietta Siciliano, Laura Clarizia, Danilo Russo, Ilaria Di Somma, Francesco Di Natale, Marco Guida, Roberto Andreozzi, Raffaele Marotta
The photocatalytic removal of nitrate with simultaneous hydrogen generation was demonstrated using zero-valent nano-copper-modified titania (P25) as photocatalyst in the presence of UV-A-Vis radiation. Glycerol, a by-product in biodiesel production, was chosen as a hole scavenger. Under the adopted experimental conditions, a nitrate removal efficiency up to 100% and a simultaneous hydrogen production up to 14 μmol/L of H2 were achieved (catalyst load = 150 mg/L, initial concentration of nitrate = 50 mg/L, initial concentration of glycerol = 0...
January 7, 2017: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/28064074/effect-of-humic-acid-on-the-toxicity-of-bare-and-capped-zno-nanoparticles-on-bacteria-algal-and-crustacean-systems
#17
K Akhil, S Sudheer Khan
Zinc oxide nanoparticles are one of the most extensively used nanoparticles in various commercial products. Depending on the purpose, the particles are coated with various agents including poly vinyl pyrrolidone, poly vinyl alcohol, ethylene glycol etc. As the particles are heavily used, the chance of the particles to get run off into the environment is very high. The study explains the difference in toxicity of bare and capped zinc oxide nanoparticles under various environmental conditions including humic acid and visible light against bacterial, algal and crustacean system...
December 19, 2016: Journal of Photochemistry and Photobiology. B, Biology
https://www.readbyqxmd.com/read/28061414/the-daphnia-magna-role-to-predict-the-cadmium-toxicity-of-sediment-bioaccumlation-and-biomarker-response
#18
Xiaomin Li, Weihua Peng, Yanyan Jiang, Yong Duan, Jinqian Ren, Yingying Liu, Wenhong Fan
To evaluate Daphnia magna role to predict the Cd toxicity in contaminated sediment, the Cd accumulation, metallothionein (MT), and mortality of D. magna exposed to overlying water system or water-sediment coexistence system were measured. The mortality, Cd accumulation, and MT in D. magna increased with the increasing Cd content in sediment. The Cd accumulation and MT in D. magna exposed to the coexistence system were significantly higher than those exposed to the overlying water system because of the ingestion of Cd-containing sediments by D...
January 3, 2017: Ecotoxicology and Environmental Safety
https://www.readbyqxmd.com/read/28057730/insertion-polymorphisms-of-mobile-genetic-elements-in-sexual-and-asexual-populations-of-daphnia-pulex
#19
Xiaoqian Jiang, Haixu Tang, Zhiqiang Ye, Michael Lynch
Transposable elements (TEs) constitute a substantial portion of many eukaryotic genomes, and can in principle contribute to evolutionary innovation as well as genomic deterioration. Daphnia pulex serves as a useful model for studying TE dynamics as a potential cause and/or consequence of asexuality. We analyzed insertion polymorphisms of TEs in 20 sexual and 20 asexual isolates of D. pulex across North American from their available whole-genome sequencing data. Our results show that the total fraction of the derived sequences of TEs is not substantially different between asexual and sexual D...
January 4, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28049073/variations-in-toxicity-of-semi-coking-wastewater-treatment-processes-and-their-toxicity-prediction
#20
Xiaoyan Ma, Xiaochang Wang, Yongjun Liu, Jian Gao, Yongkun Wang
Chemical analyses and bioassays using Vibrio fischeri and Daphnia magna were conducted to evaluate comprehensively the variation of biotoxicity caused by contaminants in wastewater from a semi-coking wastewater treatment plant (WWTP). Pretreatment units (including an oil-water separator, a phenols extraction tower, an ammonia stripping tower, and a regulation tank) followed by treatment units (including anaerobic-oxic treatment units, coagulation-sedimentation treatment units, and an active carbon adsorption column) were employed in the semi-coking WWTP...
December 31, 2016: Ecotoxicology and Environmental Safety
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