Advances in Taxonomy, Ecology, and Biogeography of Dirivultidae (Copepoda) Associated with Chemosynthetic Environments in the Deep Sea

Background: Copepoda is one of the most prominent higher taxa with almost 80 described species at deep-sea hydrothermal vents. The unique copepod family Dirivultidae with currently 50 described species is the most species rich invertebrate family at hydrothermal vents. Methodology/Principal Findings: We reviewed the literature of Dirivultidae and provide a complete key to species, and map geographical and habitat specific distribution. In addition we discuss the ecology and origin of this family. Conclusions/Significance: Dirivultidae are only present at deep-sea hydrothermal vents and along the axial summit trough of midocean ridges, with the exception of Dirivultus dentaneus found associated with Lamellibrachia species at 1125 m depth off southern California. To our current knowledge Dirivultidae are unknown from shallow-water vents, seeps, whale falls, and wood falls. They are a prominent part of all communities at vents and in certain habitat types (like sulfide chimneys colonized by pompei worms) they are the most abundant animals. They are free-living on hard substrate, mostly found in aggregations of various foundation species (e. g. alvinellids, vestimentiferans, and bivalves). Most dirivultid species colonize more than one habitat type. Dirivultids have a world-wide distribution, but most genera and species are endemic to a single biogeographic region. Their origin is unclear yet, but immigration from other deep-sea chemosynthetic habitats (stepping stone hypothesis) or from the deep-sea sediments seems unlikely, since Dirivultidae are unknown from these environments. Dirivultidae is the most species rich family and thus can be considered the most successful taxon at deep-sea vents

A Plant Biologist’s Toolbox to Study Translation

Across a broad range of species and biological questions, more and more studies are incorporating translation data to better assess how gene regulation occurs at the level of protein synthesis. The inclusion of translation data improves upon, and has been shown to be more accurate than, transcriptional studies alone. However, there are many different techniques available to measure translation and it can be difficult, especially for young or aspiring scientists, to determine which methods are best applied in specific situations. We have assembled this review in order to enhance the understanding and promote the utilization of translational methods in plant biology. We cover a broad range of methods to measure changes in global translation (e.g., radiolabeling, polysome profiling, or puromycylation), translation of single genes (e.g., fluorescent reporter constructs, toeprinting, or ribosome density mapping), sequencing-based methods to uncover the entire translatome (e.g., Ribo-seq or translating ribosome affinity purification), and mass spectrometry-based methods to identify changes in the proteome (e.g., stable isotope labeling by amino acids in cell culture or bioorthogonal noncanonical amino acid tagging). The benefits and limitations of each method are discussed with a particular note of how applications from other model systems might be extended for use in plants. In order to make this burgeoning field more accessible to students and newer scientists, our review includes an extensive glossary to define key terms

Relevance of Translational Regulation on Plant Growth and Environmental Responses

The authors acknowledge funding by MINECO BIO2015-70483-R to AF, by CAM S2013/ABI-2734 and by ERC GA260468 to MMC, by the Deutsche Forschungsgemeinschaft (DFG, grant TRR175-C05) to DL, by NSF IOS 1444561 and NSF IOS PAPM-EAGER 1650139 to AS, and by Bio4Energy, a Strategic Research Environment appointed by the Swedish government to JH.Ferrando Monleón, AR.; Castellano, M.; Lisón, P.; Leister, D.; Stepanova, AN.; Hanson, J. (2017). Relevance of Translational Regulation on Plant Growth and Environmental Responses. Frontiers in Plant Science. 8:1-2. https://doi.org/10.3389/fpls.2017.02170S128Hummel, M., Cordewener, J. H. G., de Groot, J. C. M., Smeekens, S., America, A. H. P., & Hanson, J. (2012). Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MSE proteomics. PROTEOMICS, 12(7), 1024-1038. doi:10.1002/pmic.201100413Vermeulen, S. J., Campbell, B. M., & Ingram, J. S. I. (2012). Climate Change and Food Systems. Annual Review of Environment and Resources, 37(1), 195-222. doi:10.1146/annurev-environ-020411-130608Vogel, C., & Marcotte, E. M. (2012). Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Nature Reviews Genetics, 13(4), 227-232. doi:10.1038/nrg318

A new look at acid catalyzed deacetylation of carbohydrates : A regioselective synthesis and reactivity of 2-O-acetyl aryl glycopyranosides

Abstract In the present work we report that acetyl groups of per – acetylated aryl glycosides have different reactivity during the acidic deacetylation using HCl/EtOH in CHCl3, which leads to preferential deacetylation at O-3, O-4 and O-6. Thereby, the one-step preparation of 2-O-acetyl aryl glycosides with simple aglycon was accomplished for the first time. It was proved that the found reagent is to be general and unique for the preparation of series of 2-О-acetyl aryl glycosides. We have determined the influence of both carbohydrate moiety and the aglycon on the selectivity of deacetylation reaction by kinetic experiments. Using DFT/B3LYP/6-31G(d,p) and semi-empirical АМ1 methods we have found that the highest activation barrier is for 2-О-acetyl group. This completely explains the least reactivity of 2-О-acetyl group.Peer reviewe

Gene-Specific Translation Regulation Mediated by the Hormone-Signaling Molecule EIN2

SummaryThe central role of translation in modulating gene activity has long been recognized, yet the systematic exploration of quantitative changes in translation at a genome-wide scale in response to a specific stimulus has only recently become technically feasible. Using the well-characterized signaling pathway of the phytohormone ethylene and plant-optimized genome-wide ribosome footprinting, we have uncovered a molecular mechanism linking this hormone’s perception to the activation of a gene-specific translational control mechanism. Characterization of one of the targets of this translation regulatory machinery, the ethylene signaling component EBF2, indicates that the signaling molecule EIN2 and the nonsense-mediated decay proteins UPFs play a central role in this ethylene-induced translational response. Furthermore, the 3′UTR of EBF2 is sufficient to confer translational regulation and required for the proper activation of ethylene responses. These findings represent a mechanistic paradigm of gene-specific regulation of translation in response to a key growth regulator

Efficiency of Transarterial Chemoembolization with Drug-Eluting Microspheres in the Treatment of Metastatic and Primary Liver Tumors

Background: Transarterial chemoembolization (TACE) is coming into use in the treatment of liver tumors, with drug-eluting microspheres as one of the technique variations. However, at the moment there are no systematic studies that would answer the questions: what is the role of the method in the treatment regimen for patients with primary and metastatic liver tumor and at what stage should it be used? Aim: to evaluate the effectiveness of transarterial chemoembolization with drug-eluting microspheres for the treatment of metastatic and primary malignant liver tumors at different stages of the disease. Methods: We performed а retrospective observational uncontrolled study of 65 patients with liver metastases (Group 1), and 10 patients with primary malignant liver tumors (Group 2), who underwent 102 operations of transarterial chemoembolization with drug-eluting microspheres. To plan transarterial chemoembolization and evaluate its effectiveness, computed tomography and magnetic resonance imaging were used every 89 weeks during the treatment. Results: After two transarterial chemoembolization controls, Group 1 included 51 responders (79%) and 14 non-responders (21%). Among the responders by the 16th week there was a decrease in the volume of the tumor mass in the liver from 12.4 [4.7; 24.6] to 5.2 cm3 [2; 15.5] for colorectal cancer, from 26 [18; 35] to 19 cm3 [13; 25] for neuroendocrine cancer, from 12 [4; 20] to 4 cm3 [0.6; 9] for adenocarcinomas of different localizations. There was no progression in Group 2, while, by week 16, there was a decrease in the tumor volume from 142 [51; 206] to 68 cm3 [23; 185] for hepatocellular carcinoma, from 465 [330; 600] to 187 cm3 [137;237] for intrahepatic cholangiocarcinoma. With repeated transarterial chemoembolization, a decrease in the volume of the tumor mass was also noted, while the time without progression decreased from 303 [170; 369] to 180 [105; 225] days in Group 1, from 266 [200; 367] to 120 [62; 215] days in Group 2. Conclusions: Transarterial chemoembolization with drug-eluting microspheres is an effective treatment for primary and metastatic liver tumors. It should be considered as a palliative therapy, which allows achieving a good antitumor response at different stages of cancer

Reduced purine biosynthesis in humans after their divergence from Neandertals

We analyze the metabolomes of humans, chimpanzees, and macaques in muscle, kidney and three different regions of the brain. Although several compounds in amino acid metabolism occur at either higher or lower concentrations in humans than in the other primates, metabolites downstream of adenylosuccinate lyase, which catalyzes two reactions in purine synthesis, occur at lower concentrations in humans. This enzyme carries an amino acid substitution that is present in all humans today but absent in Neandertals. By introducing the modern human substitution into the genomes of mice, as well as the ancestral, Neandertal-like substitution into the genomes of human cells, we show that this amino acid substitution contributes to much or all of the reduction of de novo synthesis of purines in humans

Efficiency in a forced contribution threshold public good game

We contrast and compare three ways of predicting efficiency in a forced contribution threshold public good game. The three alternatives are based on ordinal potential, quantal response and impulse balance theory. We report an experiment designed to test the respective predictions and find that impulse balance gives the best predictions. A simple expression detailing when enforced contributions result in high or low efficiency is provided