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https://www.readbyqxmd.com/read/28830116/phylogenomic-resolution-of-the-phylogeny-of-laurasiatherian-mammals-exploring-phylogenetic-signals-within-coding-and-noncoding-sequences
#1
Meng-Yun Chen, Dan Liang, Peng Zhang
The interordinal relationships of Laurasiatherian mammals are currently one of the most controversial questions in mammalian phylogenetics. Previous studies mainly relied on coding sequences (CDS) and seldom used noncoding sequences. Here, by data mining public genome data, we compiled an intron data set of 3,638 genes (all introns from a protein-coding gene are considered as a gene) (19,055,073 bp) and a CDS data set of 10,259 genes (20,994,285 bp), covering all major lineages of Laurasiatheria (except Pholidota)...
August 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28830114/automated-assembly-of-species-metabolomes-through-data-submission-into-a-public-repository
#2
Reza M Salek, Pablo Conesa, Keeva Cochrane, Kenneth Haug, Mark Williams, Namrata Kale, Pablo Moreno, Kalai Vanii Jayaseelan, Jose Ramon Macias, Venkata Chandrasekhar Nainala, Robert D Hall, Laura K Reed, Mark R Viant, Claire O'Donovan, Christoph Steinbeck
Following similar global efforts to exchange genomic and other biomedical data, global databases in metabolomics have now been established. MetaboLights, the first general purpose, publically available, cross-species, cross-application database in metabolomics, has become the fastest growing data repository at the European Bioinformatics Institute in terms of data volume. Here we present the automated assembly of species metabolomes in MetaboLights, a crucial reference for chemical biology, which is growing through user submissions...
August 1, 2017: GigaScience
https://www.readbyqxmd.com/read/28830100/photosynthetic-limitations-in-two-antarctic-vascular-plants-importance-of-leaf-anatomical-traits-and-rubisco-kinetic-parameters
#3
Patricia L Sáez, León A Bravo, Lohengrin A Cavieres, Valentina Vallejos, Carolina Sanhueza, Marcel Font-Carrascosa, Eustaquio Gil-Pelegrín, José Javier Peguero-Pina, Jeroni Galmés
Particular physiological traits allow the vascular plants Deschampsia antarctica Desv. and Colobanthus quitensis (Kunth) Bartl. to inhabit Antarctica. The photosynthetic performance of these species was evaluated in situ, focusing on diffusive and biochemical constraints to CO2 assimilation. Leaf gas exchange, Chl a fluorescence, leaf ultrastructure, and Rubisco catalytic properties were examined in plants growing on King George and Lagotellerie islands. In spite of the species- and population-specific effects of the measurement temperature on the main photosynthetic parameters, CO2 assimilation was highly limited by CO2 diffusion...
May 17, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28830095/oenococcus-oeni-and-the-genomic-era
#4
Eveline J Bartowsky
Oenococcus oeni is the main lactic acid bacteria species associated with grapes and wine. It is a bacterium that has adapted itself to the harsh conditions of wine, and demonstrated its importance in the production of quality wines. It has a small genome (1.8 Mb); over 200 strains have had their genome sequenced. Genomic analyses have proposed that there are two major branches of O. oeni strains that might be linked to wine style (sparkling wine versus white and red) and metagenomic studies have suggested a possible influence of terroir...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830092/phase-variable-methylation-and-epigenetic-regulation-by-type-i-restriction-modification-systems
#5
Megan De Ste Croix, Irene Vacca, Min Jung Kwun, Joseph D Ralph, Stephen D Bentley, Richard Haigh, Nicholas J Croucher, Marco R Oggioni
Epigenetic modifications in bacteria, such as DNA methylation, have been shown to affect gene regulation, thereby generating cells that are isogenic but with distinctly different phenotypes. Restriction-modification (RM) systems contain prototypic methylases that are responsible for much of bacterial DNA methylation. This review focuses on a distinctive group of type I RM loci that , through phase variation, can modify their methylation target specificity and can thereby switch bacteria between alternative patterns of DNA methylation...
August 1, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28830085/temperature-induced-lipocalin-til-a-shield-against-stress-inducing-environmental-shocks-in-saccharomyces-cerevisiae
#6
Nadia Maria Berterame, Stefano Bertagnoli, Vera Codazzi, Danilo Porro, Paola Branduardi
The yeast Saccharomyces cerevisiae is a well-established workhorse, either for recombinant or natural products, thanks to its natural traits and easily editable metabolism. However, during a bio-based industrial process it meets multiple stresses generated by operative conditions such as non-optimal temperature, pH, oxygenation and product accumulation. The development of tolerant strains is therefore indispensable for the improvement of production, yield and productivity of fermentative processes. In this regard, plants as resilient organisms are a generous source for fishing genes and/or metabolites that can help the cell factory to counteract environmental constraints...
September 1, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28830073/platelet-activating-factor-increases-reactive-oxygen-species-mediated-microbicidal-activity-of-human-macrophages-infected-with-leishmania-viannia-braziliensis
#7
Arissa Felipe Borges, Camila Imai Morato, Rodrigo Saar Gomes, Miriam Leandro Dorta, Milton Adriano Pelli de Oliveira, Fátima Ribeiro-Dias
Platelet-activating factor (PAF) is produced by macrophages during inflammation and infections. We evaluated whether PAF is able to modulate the infection of human macrophages by Leishmania braziliensis, the main Leishmania sp. in Brazil. Monocyte-derived macrophages were incubated with promastigote forms in absence or presence of exogenous PAF. We observed that the treatment of macrophages with low concentrations of PAF prior to infection increased the phagocytosis of L. braziliensis. More importantly, exogenous PAF reduced the parasitism when it was added before, during or after infection...
September 29, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28830062/a-practical-strategy-for-the-characterization-of-ponicidin-metabolites-in-vivo-and-in-vitro-by-uhplc-q-tof-ms-based-on-nontargeted-swath-data-acquisition
#8
Weiwei Xie, Yiran Jin, Ludan Hou, Yinghua Ma, Huijun Xu, Kerong Zhang, Lantong Zhang, Yingfeng Du
Ponicidin is an active natural ent-kaurane diterpenoid ingredient originating from many Isondon herbs and is expected to become a new anticancer agent. In this study, a practical strategy was developed for the identification of ponicidin metabolites in vivo and in vitro utilizing ultra-high-performance liquid chromatography coupled with hybrid triple quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS). The analytical strategy was as follows: potential ponicidin metabolites were detected by a novel on-line data acquisition approach, i...
August 11, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28830051/ozone-affects-leaf-physiology-and-causes-injury-to-foliage-of-native-tree-species-from-the-tropical-atlantic-forest-of-southern-brazil
#9
Bárbara Baêsso Moura, Edenise Segala Alves, Mauro Alexandre Marabesi, Silvia Ribeiro de Souza, Marcus Schaub, Pierre Vollenweider
In southern Brazil, the recent increase in tropospheric ozone (O3) concentrations poses an additional threat to the biodiverse but endangered and fragmented remnants of the Atlantic Forest. Given the mostly unknown sensitivity of tropical species to oxidative stress, the principal objective of this study was to determine whether the current O3 levels in the Metropolitan Region of Campinas (MRC), downwind of São Paulo, affect the native vegetation of forest remnants. Foliar responses to O3 of three tree species typical of the MRC forests were investigated using indoor chamber exposure experiments under controlled conditions and a field survey...
August 19, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28830047/microbiological-and-environmental-significance-of-metal-dependent-anaerobic-oxidation-of-methane
#10
REVIEW
Zhanfei He, Qingying Zhang, Yudong Feng, Hongwei Luo, Xiangliang Pan, Geoffrey Michael Gadd
Anaerobic oxidation of methane (AOM) can be coupled to the reduction of sulfate, nitrate and nitrite, which effectively reduces methane emission into the atmosphere. Recently, metal-dependent AOM (metal-AOM, AOM coupled to metal reduction) was demonstrated to occur in both environmental samples and enrichment cultures. Anaerobic methanotrophs are capable of respiration using Fe(III) or Mn(IV), whether they are in the form of soluble metal species or insoluble minerals. Given the wide distribution of Fe(III)/Mn(IV)-bearing minerals in aquatic methane-rich environments, metal-AOM is considered to be globally important, although it has generally been overlooked in previous studies...
August 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28830046/fish-life-history-traits-are-affected-after-chronic-dietary-exposure-to-an-environmentally-realistic-marine-mixture-of-pcbs-and-pbdes
#11
Khaled Horri, Sébastien Alfonso, Xavier Cousin, Catherine Munschy, Véronique Loizeau, Salima Aroua, Marie-Laure Bégout, Bruno Ernande
Polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants that have been shown to affect fish life-history traits such as reproductive success, growth and survival. At the individual level, their toxicity and underlying mechanisms of action have been studied through experimental exposure. However, the number of experimental studies approaching marine environmental situations is scarce, i.e., in most cases, individuals are exposed to either single congeners, or single types of molecules, or high concentrations, so that results can hardly be transposed to natural populations...
August 18, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28830012/early-oxidative-stress-dna-damage-and-inflammation-resulting-from-subcutaneous-injection-of-sulfur-mustard-into-mice
#12
Xiaorui Zhang, Yizhou Mei, Tongxing Wang, Feng Liu, Ning Jiang, Wenxia Zhou, Yongxiang Zhang
Oxidative stress, DNA damage repair, and inflammation are three important reactions of sulfur mustard (SM) exposure. But molecular related chronological events in the earlier stage of SM exposure model are still unclear. In the research, reactive oxygen species (ROS) was measured by using flow cytometry. Cytokines were tested in Luminex method. Myeloperoxidase (MPO), inducible nitric oxide synthase (iNOS), 8-hydroxy-2-deoxyguanosine (8-OHdG) and glutathione (GSH) activity or levels in serum were determined by commercially available kits...
July 17, 2017: Environmental Toxicology and Pharmacology
https://www.readbyqxmd.com/read/28830010/contradictory-effects-of-silver-nanoparticles-on-activated-sludge-wastewater-treatment
#13
Zhiya Sheng, Joy D Van Nostrand, Jizhong Zhou, Yang Liu
Increased amount of nano-silver will be released into domestic and industrial waste streams due to its extensive application. However, great controversy still exists on the effects of silver nanoparticle (Ag-NP) on biological wastewater treatment processes and a toxicology model has not been built yet. Four sequencing batch reactors with activated sludge has been run for over three months with different silver species at a concentration of 1mg Ag/L in influent. Both freshly prepared Ag-NPs and aged Ag-NPs were tested with released silver ion as control...
August 2, 2017: Journal of Hazardous Materials
https://www.readbyqxmd.com/read/28830000/fate-and-abundance-of-classical-and-heteroatomic-naphthenic-acid-species-after-advanced-oxidation-processes-insights-and-indicators-of-transformation-and-degradation
#14
Mohamed N A Meshref, Pamela Chelme-Ayala, Mohamed Gamal El-Din
The toxicological effects from all components in oil sands process-affected water (OSPW) are not known. Alternatively, monitoring the variations and abundance of different classes and compounds after treatments might be a useful approach in OSPW remediation. In this study, the variations in the compositions of classical and heteroatomic naphthenic acids (NAs) after treatment using advanced oxidation processes (AOPs), mainly ozone and peroxone, and two different mass spectrometry methods; ultra-performance liquid chromatography time-of-flight (UPLC-TOFMS) and Fourier transform ion cyclotron resonance (FTICR-MS), were examined...
August 4, 2017: Water Research
https://www.readbyqxmd.com/read/28829956/adsorption-of-5f-electron-atoms-thcm-on-graphene-surface-an-all-electron-zora-dft-study
#15
Jiguang Du, Gang Jiang
All-electron calculations were performed to investigate the adsorption of 5f-electron atoms (An=ThCm) on graphene surface. The hollow site is energetically preferred for the An-graphene complexes studied. The interaction strengths between An and C decrease in the order of Th>Pa>U>Np>Pu>Cm>Am. The AnC interactions show predominately closed-shell characteristics, meanwhile ThC chemical bond formed through orbital overlaps of Th (6d) and C (2p) possesses partial covalent nature. The participation of 6d(5f)-electron into bonding orbitals are gradually weakened (enhanced) from Th to Pu because the 5f electrons are more and more diffuse...
August 7, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28829948/contribution-of-attendant-anions-on-cadmium-toxicity-to-soil-enzymes
#16
Haixia Tian, Long Kong, Mallavarapu Megharaj, Wenxiang He
Sorption and desorption are critical processes to control the mobility and biotoxicity of cadmium (Cd) in soils. It is known that attendant anion species of heavy metals could affect metal adsorption on soils and might further alter their biotoxicity. However, for Cd, the influence of attendant anions on its sorption in soils and subsequent toxicity on soil enzymes are still unknown. In this work, four Cd compounds with different salt anions (SO4(2-), NO3(-), Cl(-), and Ac(-)) were selected to investigate their impact of on the sorption, soil dehydrogenase activity (DHA) and alkaline phosphatase activity (ALP)...
August 17, 2017: Chemosphere
https://www.readbyqxmd.com/read/28829943/hbl1-is-a-human-long-noncoding-rna-that-modulates-cardiomyocyte-development-from-pluripotent-stem-cells-by-counteracting-mir1
#17
Juli Liu, Yang Li, Bo Lin, Yi Sheng, Lei Yang
Cardiogenesis processes in human and animals have differential dynamics, suggesting the existence of species-specific regulators during heart development. However, it remains a challenge to discover the human-specific cardiac regulatory genes, given that most coding genes are conserved. Here, we report the identification of a human-specific long noncoding RNA, Heart Brake LncRNA 1 (HBL1), which regulates cardiomyocyte development from human induced pluripotent stem cells (hiPSCs). Overexpression of HBL1 repressed, whereas knockdown and knockout of HBL1 increased, cardiomyocyte differentiation from hiPSCs...
August 21, 2017: Developmental Cell
https://www.readbyqxmd.com/read/28829928/green-tree-frog-hyla-cinerea-and-ground-squirrel-xerospermophilus-spilosoma-mortality-attributed-to-inland-brevetoxin-transportation-at-padre-island-national-seashore-texas-2015
#18
Danielle E Buttke, Alicia Walker, I-Shuo Huang, Leanne Flewelling, Julia Lankton, Anne E Ballmann, Travis Clapp, James Lindsay, Paul V Zimba
On 16 September 2015, a red tide (Karenia brevis) bloom impacted coastal areas of Padre Island National Seashore Park. Two days later and about 0.9 km inland, 30-40 adult green tree frogs (Hyla cinerea) were found dead after displaying tremors, weakness, labored breathing, and other signs of neurologic impairment. A rainstorm, accompanied by high winds, rough surf, and high tides, which could have aerosolized brevetoxin, occurred on the morning of the mortality event. Frog carcasses were healthy but contained significant brevetoxin in tissues...
August 22, 2017: Journal of Wildlife Diseases
https://www.readbyqxmd.com/read/28829908/assessment-of-genetic-diversity-of-a-native-population-of-eplingiella-fruticosa-a-plant-with-therapeutic-potential
#19
D C Silva, L E C Diniz, A F Blank, D A C Nizio, J A O Pinto, K L G Pereira, M F Arrigoni-Blank
Eplingiella fruticosa (Salzm. ex Benth.) Harley & J.F.B. Pastore, ex Hyptis fruticosa Salzm. ex Benth. is an aromatic and medicinal plant of the family Lamiaceae, found mainly in regions with intense anthropic activity. Information on the genetic diversity of this species is scarce. However, it can be assessed using molecular markers that identify the level of diversity among phenotypically identical individuals. The present study aimed to characterize the genetic diversity of a native population of E. fruticosa from the State of Sergipe using ISSR molecular markers...
August 17, 2017: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28829901/morphological-diversity-of-cassava-accessions-of-the-south-central-mesoregion-of-the-state-of-mato-grosso-brazil
#20
B W Zago, M A A Barelli, E S S Hoogerheide, C L Corrêa, G I S Delforno, C J da Silva
Genetic variability of cassava (Manihot esculenta Crantz) in Brazil is wide, being this the result of natural and cultural selection during pre- and post-domestication of the species in different environments. Given the number of species of the genus found in the region (38 of a total of 98 species), the central region of Brazil was defined as the primary center of cassava diversity. Therefore, genetic diversity characterization of cassava accessions is fundamental, both for farmers and for plant breeders, because it allows the organization of genetic resources and better utilization of available genetic diversity...
August 17, 2017: Genetics and Molecular Research: GMR
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