Global mRNA expression analysis in myosin II deficient strains of Saccharomyces cerevisiae reveals an impairment of cell integrity functions

<p>Abstract</p> <p>Background</p> <p>The <it>Saccharomyces cerevisiae MYO1 </it>gene encodes the myosin II heavy chain (Myo1p), a protein required for normal cytokinesis in budding yeast. Myo1p deficiency in yeast (<it>myo1Δ</it>) causes a cell separation defect characterized by the formation of attached cells, yet it also causes abnormal budding patterns, formation of enlarged and elongated cells, increased osmotic sensitivity, delocalized chitin deposition, increased chitin synthesis, and hypersensitivity to the chitin synthase III inhibitor Nikkomycin Z. To determine how differential expression of genes is related to these diverse cell wall phenotypes, we analyzed the global mRNA expression profile of <it>myo1Δ </it>strains.</p> <p>Results</p> <p>Global mRNA expression profiles of <it>myo1Δ </it>strains and their corresponding wild type controls were obtained by hybridization to yeast oligonucleotide microarrays. Results for selected genes were confirmed by real time RT-PCR. A total of 547 differentially expressed genes (p ≤ 0.01) were identified with 263 up regulated and 284 down regulated genes in the <it>myo1Δ </it>strains. Gene set enrichment analysis revealed the significant over-representation of genes in the protein biosynthesis and stress response categories. The <it>SLT2/MPK1 </it>gene was up regulated in the microarray, and a <it>myo1Δslt2Δ </it>double mutant was non-viable. Overexpression of ribosomal protein genes <it>RPL30 </it>and <it>RPS31 </it>suppressed the hypersensitivity to Nikkomycin Z and increased the levels of phosphorylated Slt2p in <it>myo1Δ </it>strains. Increased levels of phosphorylated Slt2p were also observed in wild type strains under these conditions.</p> <p>Conclusion</p> <p>Following this analysis of global mRNA expression in yeast <it>myo1Δ </it>strains, we conclude that 547 genes were differentially regulated in <it>myo1Δ </it>strains and that the stress response and protein biosynthesis gene categories were coordinately regulated in this mutant. The <it>SLT2/MPK1 </it>gene was confirmed to be essential for <it>myo1Δ </it>strain viability, supporting that the up regulated stress response genes are regulated by the <it>PKC1 </it>cell integrity pathway. Suppression of Nikkomycin Z hypersensitivity together with Slt2p phosphorylation was caused by the overexpression of ribosomal protein genes <it>RPL30 </it>and <it>RPS31</it>. These ribosomal protein mRNAs were down regulated in the <it>myo1Δ </it>arrays, suggesting that down regulation of ribosomal biogenesis may affect cell integrity in <it>myo1Δ </it>strains.</p

Magnetism of small V clusters embedded in a Cu fcc matrix: an ab initio study

We present extensive first principles density functional theory (DFT) calculations dedicated to analyze the magnetic and electronic properties of small V$_{n}$ clusters (n=1,2,3,4,5,6) embedded in a Cu fcc matrix. We consider different cluster structures such as: i) a single V impurity, ii) several V$_{2}$ dimers having different interatomic distance and varying local atomic environment, iii) V$_{3}$ and iv) V$_{4}$ clusters for which we assume compact as well as 2- and 1-dimensional atomic configurations and finally, in the case of the v) V$_{5}$ and vi) V$_{6}$ structures we consider a square pyramid and a square bipyramid together with linear arrays, respectively. In all cases, the V atoms are embedded as substitutional impurities in the Cu network. In general, and as in the free standing case, we have found that the V clusters tend to form compact atomic arrays within the cooper matrix. Our calculated non spin-polarized density of states at the V sites shows a complex peaked structure around the Fermi level that strongly changes as a function of both the interatomic distance and local atomic environment, a result that anticipates a non trivial magnetic behavior. In fact, our DFT calculations reveal, in each one of our clusters systems, the existence of different magnetic solutions (ferromagnetic, ferrimagnetic, and antiferromagnetic) with very small energy differences among them, a result that could lead to the existence of complex finite-temperature magnetic properties. Finally, we compare our results with recent experimental measurements.Comment: 7 pages and 4 figure

Fully relativistic calculation of magnetic properties of Fe, Co and Ni adclusters on Ag(100)

We present first principles calculations of the magnetic moments and magnetic anisotropy energies of small Fe, Co and Ni clusters on top of a Ag(100) surface as well as the exchange-coupling energy between two single adatoms of Fe or Co on Ag(100). The calculations are performed fully relativistically using the embedding technique within the Korringa-Kohn-Rostoker method. The magnetic anisotropy and the exchange-coupling energies are calculated by means of the force theorem. In the case of adatoms and dimers of iron and cobalt we obtain enhanced spin moments and, especially, unusually large orbital moments, while for nickel our calculations predict a complete absence of magnetism. For larger clusters, the magnitudes of the local moments of the atoms in the center of the cluster are very close to those calculated for the corresponding monolayers. Similar to the orbital moments, the contributions of the individual atoms to the magnetic anisotropy energy strongly depend on the position, hence, on the local environment of a particular atom within a given cluster. We find strong ferromagnetic coupling between two neighboring Fe or Co atoms and a rapid, oscillatory decay of the exchange-coupling energy with increasing distance between these two adatoms.Comment: 8 pages, ReVTeX + 4 figures (Encapsulated Postscript), submitted to PR

FaMYB123 interacts with FabHLH3 to regulate the late steps of anthocyanin and flavonol biosynthesis during ripening.

In this work, we identified and functionally characterized the strawberry (Fragaria × ananassa) R2R3 MYB transcription factor FaMYB123. As in most genes associated with organoleptic properties of ripe fruit, FaMYB123 expression is ripening-related, receptacle-specific, and antagonistically regulated by ABA and auxin. Knockdown of FaMYB123 expression by RNAi in ripe strawberry fruit receptacles downregulated the expression of enzymes involved in the late steps of anthocyanin/flavonoid biosynthesis. Transgenic fruits showed a parallel decrease in the contents of total anthocyanin and flavonoid, especially malonyl derivatives of pelargonidin and cyanidins. The decrease was concomitant with accumulation of proanthocyanin, propelargonidins, and other condensed tannins associated mainly with green receptacles. Potential coregulation between FaMYB123 and FaMYB10, which may act on different sets of genes for the enzymes involved in anthocyanin production, was explored. FaMYB123 and FabHLH3 were found to interact and to be involved in the transcriptional activation of FaMT1, a gene responsible for the malonylation of anthocyanin components during ripening. Taken together, these results demonstrate that FaMYB123 regulates the late steps of the flavonoid pathway in a specific manner. In this study, a new function for an R2R3 MYB transcription factor, regulating the expression of a gene that encodes a malonyltransferase, has been elucidated.This work was funded by the Spanish Ministerio de Ciencia e Innovacion (AGL2014-55784-C2-2-R and AGL2017-86531-C2-2-R). FJMR is supported by a ‘Margarita Salas’ post-doctoral fellowship (UCOR02MS) from the University of Cordoba (Requalification of the Spanish university system) from the Ministry of Universities financed by the European Union (NexGenerationEU). FJMH is supported by a ‘Juan de la Cierva-Incorporacion’ fellowship (IJC2020- 045526-I), funded by MCIN/AEI/10.13039/501100011033 and the European Union ‘NextGenerationEU’/PRTR. AR-F and SA are on the European Union’s Horizon 2020 Research and Innovation Program, Project PlantaSYST (SGA-CSA No. 739582 under FPA No. 664620). The authors thank Dr. Gema Garc ıa from the Microscopy Unit of UCAIB-IMIBIC for technical help with the microscope. Funding for open access charge: University of Cordoba/CBUA.S

The intracellular domain of β-dystroglycan mediates the nucleolar stress response by suppressing UBF transcriptional activity

β-dystroglycan (β-DG) is a key component of multiprotein complexes in the plasma membrane and nuclear envelope. In addition, β-DG undergoes two successive proteolytic cleavages that result in the liberation of its intracellular domain (ICD) into the cytosol and nucleus. However, stimuli-inducing ICD cleavage and the physiological relevance of this proteolytic fragment are largely unknown. In this study we show for the first time that β-DG ICD is targeted to the nucleolus where it interacts with the nuclear proteins B23 and UBF (central factor of Pol I-mediated rRNA gene transcription) and binds to rDNA promoter regions. Interestingly DG silencing results in reduced B23 and UBF levels and aberrant nucleolar morphology. Furthermore, β-DG ICD cleavage is induced by different nucleolar stressors, including oxidative stress, acidosis, and UV irradiation, which implies its participation in the response to nucleolar stress. Consistent with this idea, overexpression of β-DG elicited mislocalization and decreased levels of UBF and suppression of rRNA expression, which in turn provoked altered ribosome profiling and decreased cell growth. Collectively our data reveal that β-DG ICD acts as negative regulator of rDNA transcription by impeding the transcriptional activity of UBF, as a part of the protective mechanism activated in response to nucleolar stress

Benchmarking scientific performance by decomposing leadership of Cuban and Latin American institutions in Public Health

This is a post-peer-review, pre-copyedit version of an article published in Scientometrics. The final authenticated version is available online at: http://dx.doi.org/10.1007/s11192-015-1831-z”.Comparative benchmarking with bibliometric indicators can be an aid in decision-making with regard to research management. This study aims to characterize scientific performance in a domain (Public Health) by the institutions of a country (Cuba), taking as reference world output and regional output (other Latin American centers) during the period 2003–2012. A new approach is used here to assess to what extent the leadership of a specific institution can change its citation impact. Cuba was found to have a high level of specialization and scientific leadership that does not match the low international visibility of Cuban institutions. This leading output appears mainly in non-collaborative papers, in national journals; publication in English is very scarce and the rate of international collaboration is very low. The Instituto de Medicina Tropical Pedro Kouri stands out, alone, as a national reference. Meanwhile, at the regional level, Latin American institutions deserving mention for their high autonomy in normalized citation would include Universidad de Buenos Aires (ARG), Universidade Federal de Pelotas (BRA), Consejo Nacional de Investigaciones Cientı´ficas y Te´cnicas (ARG), Instituto Oswaldo Cruz (BRA) and the Centro de Pesquisas Rene Rachou (BRA). We identify a crucial aspect that can give rise to misinterpretations of data: a high share of leadership cannot be considered positive for institutions when it is mainly associated with a high proportion of non-collaborative papers and a very low level of performance. Because leadership might be questionable in some cases, we propose future studies to ensure a better interpretation of findings.This work was made possible through financing by the scholarship funds for international mobility between Andalusian and IberoAmerican Universities and the SCImago GroupPeer reviewe

Interactive Effect of UVR and Phosphorus on the Coastal Phytoplankton Community of the Western Mediterranean Sea: Unravelling Eco- Physiological Mechanisms

Versión del editor4,411

BIOFRAG: A new database for analysing BIOdiversity responses to forest FRAGmentation

Habitat fragmentation studies are producing inconsistent and complex results across which it is nearly impossible to synthesise. Consistent analytical techniques can be applied to primary datasets, if stored in a flexible database that allows simple data retrieval for subsequent analyses. Method: We developed a relational database linking data collected in the field to taxonomic nomenclature, spatial and temporal plot attributes and further environmental variables (e.g. information on biogeographic region. Typical field assessments include measures of biological variables (e.g. presence, abundance, ground cover) of one species or a set of species linked to a set of plots in fragments of a forested landscape. Conclusion: The database currently holds records of 5792 unique species sampled in 52 landscapes in six of eight biogeographic regions: mammals 173, birds 1101, herpetofauna 284, insects 2317, other arthropods: 48, plants 1804, snails 65. Most species are found in one or two landscapes, but some are found in four. Using the huge amount of primary data on biodiversity response to fragmentation becomes increasingly important as anthropogenic pressures from high population growth and land demands are increasing. This database can be queried to extract data for subsequent analyses of the biological response to forest fragmentation with new metrics that can integrate across the components of fragmented landscapes. Meta-analyses of findings based on consistent methods and metrics will be able to generalise over studies allowing inter-comparisons for unified answers. The database can thus help researchers in providing findings for analyses of trade-offs between land use benefits and impacts on biodiversity and to track performance of management for biodiversity conservation in human-modified landscapes.Fil: Pfeifer, Marion. Imperial College London; Reino UnidoFil: Lefebvre, Veronique. Imperial College London; Reino UnidoFil: Gardner, Toby A.. Stockholm Environment Institute; SueciaFil: Arroyo Rodríguez, Víctor. Universidad Nacional Autónoma de México; MéxicoFil: Baeten, Lander. University of Ghent; BélgicaFil: Banks Leite, Cristina. Imperial College London; Reino UnidoFil: Barlow, Jos. Lancaster University; Reino UnidoFil: Betts, Matthew G.. State University of Oregon; Estados UnidosFil: Brunet, Joerg. Swedish University of Agricultural Sciences; SueciaFil: Cerezo Blandón, Alexis Mauricio. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Métodos Cuantitativos y Sistemas de Información; ArgentinaFil: Cisneros, Laura M.. University of Connecticut; Estados UnidosFil: Collard, Stuart. Nature Conservation Society of South Australia; AustraliaFil: D´Cruze, Neil. The World Society for the Protection of Animals; Reino UnidoFil: Da Silva Motta, Catarina. Ministério da Ciência, Tecnologia, Inovações. Instituto Nacional de Pesquisas da Amazônia; BrasilFil: Duguay, Stephanie. Carleton University; CanadáFil: Eggermont, Hilde. University of Ghent; BélgicaFil: Eigenbrod, Félix. University of Southampton; Reino UnidoFil: Hadley, Adam S.. State University of Oregon; Estados UnidosFil: Hanson, Thor R.. No especifíca;Fil: Hawes, Joseph E.. University of East Anglia; Reino UnidoFil: Heartsill Scalley, Tamara. United State Department of Agriculture. Forestry Service; Puerto RicoFil: Klingbeil, Brian T.. University of Connecticut; Estados UnidosFil: Kolb, Annette. Universitat Bremen; AlemaniaFil: Kormann, Urs. Universität Göttingen; AlemaniaFil: Kumar, Sunil. State University of Colorado - Fort Collins; Estados UnidosFil: Lachat, Thibault. Swiss Federal Institute for Forest; SuizaFil: Lakeman Fraser, Poppy. Imperial College London; Reino UnidoFil: Lantschner, María Victoria. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Bahía Blanca; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Patagonia Norte. Estación Experimental Agropecuaria San Carlos de Bariloche; ArgentinaFil: Laurance, William F.. James Cook University; AustraliaFil: Leal, Inara R.. Universidade Federal de Pernambuco; BrasilFil: Lens, Luc. University of Ghent; BélgicaFil: Marsh, Charles J.. University of Leeds; Reino UnidoFil: Medina Rangel, Guido F.. Universidad Nacional de Colombia; ColombiaFil: Melles, Stephanie. University of Toronto; CanadáFil: Mezger, Dirk. Field Museum of Natural History; Estados UnidosFil: Oldekop, Johan A.. University of Sheffield; Reino UnidoFil: Overal , Williams L.. Museu Paraense Emílio Goeldi. Departamento de Entomologia; BrasilFil: Owen, Charlotte. Imperial College London; Reino UnidoFil: Peres, Carlos A.. University of East Anglia; Reino UnidoFil: Phalan, Ben. University of Southampton; Reino UnidoFil: Pidgeon, Anna Michle. University of Wisconsin; Estados UnidosFil: Pilia, Oriana. Imperial College London; Reino UnidoFil: Possingham, Hugh P.. Imperial College London; Reino Unido. The University Of Queensland; AustraliaFil: Possingham, Max L.. No especifíca;Fil: Raheem, Dinarzarde C.. Royal Belgian Institute of Natural Sciences; Bélgica. Natural History Museum; Reino UnidoFil: Ribeiro, Danilo B.. Universidade Federal do Mato Grosso do Sul; BrasilFil: Ribeiro Neto, Jose D.. Universidade Federal de Pernambuco; BrasilFil: Robinson, Douglas W.. State University of Oregon; Estados UnidosFil: Robinson, Richard. Manjimup Research Centre; AustraliaFil: Rytwinski, Trina. Carleton University; CanadáFil: Scherber, Christoph. Universität Göttingen; AlemaniaFil: Slade, Eleanor M.. University of Oxford; Reino UnidoFil: Somarriba, Eduardo. Centro Agronómico Tropical de Investigación y Enseñanza; Costa RicaFil: Stouffer, Philip C.. State University of Louisiana; Estados UnidosFil: Struebig, Matthew J.. University of Kent; Reino UnidoFil: Tylianakis, Jason M.. University College London; Estados Unidos. Imperial College London; Reino UnidoFil: Teja, Tscharntke. Universität Göttingen; AlemaniaFil: Tyre, Andrew J.. Universidad de Nebraska - Lincoln; Estados UnidosFil: Urbina Cardona, Jose N.. Pontificia Universidad Javeriana; ColombiaFil: Vasconcelos, Heraldo L.. Universidade Federal de Uberlandia; BrasilFil: Wearn, Oliver. Imperial College London; Reino Unido. The Zoological Society of London; Reino UnidoFil: Wells, Konstans. University of Adelaide; AustraliaFil: Willig, Michael R.. University of Connecticut; Estados UnidosFil: Wood, Eric. University of Wisconsin; Estados UnidosFil: Young, Richard P.. Durrell Wildlife Conservation Trust; Reino UnidoFil: Bradley, Andrew V.. Imperial College London; Reino UnidoFil: Ewers, Robert M.. Imperial College London; Reino Unid

Anti-proliferative effect of Rosmarinus officinalis L. extract on human melanoma A375 cells

Rosemary (Rosmarinus officinalis L.) has been used since ancient times in traditional medicine, while nowadays various rosemary formulations are increasingly exploited by alternative medicine to cure or prevent a wide range of health disorders. Rosemary's bioproperties have prompted scientific investigation, which allowed us to ascertain antioxidant, anti-inflammatory, cytostatic, and cytotoxic activities of crude extracts or of pure components. Although there is a growing body of experimental work, information about rosemary's anticancer properties, such as chemoprotective or anti-proliferative effects on cancer cells, is very poor, especially concerning the mechanism of action. Melanoma is a skin tumor whose diffusion is rapidly increasing in the world and whose malignancy is reinforced by its high resistance to cytotoxic agents; hence the availability of new cytotoxic drugs would be very helpful to improve melanoma prognosis. Here we report on the effect of a rosemary hydroalcoholic extract on the viability of the human melanoma A375 cell line. Main components of rosemary extract were identified by liquid chromatography coupled to tandem mass spectrometry (LC/ESI-MS/MS) and the effect of the crude extract or of pure components on the proliferation of cancer cells was tested by MTT and Trypan blue assays. The effect on cell cycle was investigated by using flow cytometry, and the alteration of the cellular redox state was evaluated by intracellular ROS levels and protein carbonylation analysis. Furthermore, in order to get information about the molecular mechanisms of cytotoxicity, a comparative proteomic investigation was performed