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Sample records for autochthonous eukaryotic diversity

  1. Eukaryotic diversity at pH extremes.

    Science.gov (United States)

    Amaral-Zettler, Linda A

    2012-01-01

    Extremely acidic (pH 9) environments support a diversity of single-cell and to a lesser extent, multicellular eukaryotic life. This study compared alpha and beta diversity in eukaryotic communities from seven diverse aquatic environments with pH values ranging from 2 to 11 using massively-parallel pyrotag sequencing targeting the V9 hypervariable region of the 18S ribosomal RNA (rRNA) gene. A total of 946 operational taxonomic units (OTUs) were recovered at a 6% cut-off level (94% similarity) across the sampled environments. Hierarchical clustering of the samples segregated the communities into acidic and alkaline groups. Similarity percentage (SIMPER) analysis followed by indicator OTU analysis (IOA) and non-metric multidimensional scaling (NMDS) were used to determine which characteristic groups of eukaryotic taxa typify acidic or alkaline extremes and the extent to which pH explains eukaryotic community structure in these environments. Spain's Rio Tinto yielded the fewest observed OTUs while Nebraska Sandhills alkaline lakes yielded the most. Distinct OTUs, including metazoan OTUs, numerically dominated pH extreme sites. Indicator OTUs included the diatom Pinnularia and unidentified opisthokonts (Fungi and Filasterea) in the extremely acidic environments, and the ciliate Frontonia across the extremely alkaline sites. Inferred from NMDS, pH explained only a modest fraction of the variation across the datasets, indicating that other factors influence the underlying community structure in these environments. The findings from this study suggest that the ability for eukaryotes to adapt to pH extremes over a broad range of values may be rare, but further study of taxa that can broadly adapt across diverse acidic and alkaline environments, respectively present good models for understanding adaptation and should be targeted for future investigations.

  2. Eukaryotic diversity at pH extremes

    Directory of Open Access Journals (Sweden)

    Linda A. Amaral-Zettler

    2013-01-01

    Full Text Available Extremely acidic (pH<3 and extremely alkaline (pH>9 environments support a diversity of single-cell and to a lesser extent, multicellular eukaryotic life. This study compared alpha and beta diversity in eukaryotic communities from 7 diverse aquatic environments with pH values ranging from 2 to 11 using massively-parallel pyrotag sequencing targeting the V9 hypervariable region of the 18S ribosomal RNA (rRNA gene. A total of 946 Operational Taxonomic Units (OTUs were recovered at a 6% cut-off level (94% similarity across the sampled environments. Hierarchical clustering of the samples segregated the communities into acidic and alkaline groups. Similarity Percentage Analysis (SIMPER followed by Indicator OTU Analysis (IOA and Non-metric Multidimensional Scaling (NMDS were used to determine which characteristic groups of eukaryotic taxa typify acidic or alkaline extremes and the extent to which pH explains eukaryotic community structure in these environments. Spain’s Rio Tinto yielded the fewest observed OTUs while Nebraska Sandhills alkaline lakes yielded the most. Distinct OTUs, including metazoan OTUs, numerically dominated pH extreme sites. Indicator OTUs included the diatom Pinnularia and unidentified opisthokonts (Fungi and Filasterea in the extremely acidic environments, and the ciliate Frontonia across the extremely alkaline sites. Inferred from NMDS, pH explained only a modest fraction of the variation across the datasets, indicating that other factors influence the underlying community structure in these environments. The findings from this study suggest that the ability for eukaryotes to adapt to pH extremes over a broad range of values may be rare, but further study of taxa that can broadly adapt across diverse acidic and alkaline environments respectively present good models for understanding adaptation and should be targeted for future investigations.

  3. Soil eukaryotic functional diversity, a metatranscriptomic approach.

    Science.gov (United States)

    Bailly, Julie; Fraissinet-Tachet, Laurence; Verner, Marie-Christine; Debaud, Jean-Claude; Lemaire, Marc; Wésolowski-Louvel, Micheline; Marmeisse, Roland

    2007-11-01

    To appreciate the functional diversity of communities of soil eukaryotic micro-organisms we evaluated an experimental approach based on the construction and screening of a cDNA library using polyadenylated mRNA extracted from a forest soil. Such a library contains genes that are expressed by each of the different organisms forming the community and represents its metatranscriptome. The diversity of the organisms that contributed to this library was evaluated by sequencing a portion of the 18S rDNA gene amplified from either soil DNA or reverse-transcribed RNA. More than 70% of the sequences were from fungi and unicellular eukaryotes (protists) while the other most represented group was the metazoa. Calculation of richness estimators suggested that more than 180 species could be present in the soil samples studied. Sequencing of 119 cDNA identified genes with no homologues in databases (32%) and genes coding proteins involved in different biochemical and cellular processes. Surprisingly, the taxonomic distribution of the cDNA and of the 18S rDNA genes did not coincide, with a marked under-representation of the protists among the cDNA. Specific genes from such an environmental cDNA library could be isolated by expression in a heterologous microbial host, Saccharomyces cerevisiae. This is illustrated by the functional complementation of a histidine auxotrophic yeast mutant by two cDNA originating possibly from an ascomycete and a basidiomycete fungal species. Study of the metatranscriptome has the potential to uncover adaptations of whole microbial communities to local environmental conditions. It also gives access to an abundant source of genes of biotechnological interest.

  4. An epigenetic toolkit allows for diverse genome architectures in eukaryotes.

    Science.gov (United States)

    Maurer-Alcalá, Xyrus X; Katz, Laura A

    2015-12-01

    Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic tree of life. Here we highlight how the changes in genome architecture in diverse eukaryotes are regulated by epigenetic processes, such as DNA elimination, genome rearrangements, and adaptive changes to genome architecture. The ability to epigenetically modify and regulate genomes has contributed greatly to the diversity of eukaryotes observed today.

  5. Eukaryotic diversity in historical soil samples

    NARCIS (Netherlands)

    Moon-van der Staay, S.Y.; Tzeneva, V.A.; Staay, van der G.W.M.; Vos, de W.M.; Smidt, H.; Hackstein, J.H.P.

    2006-01-01

    The eukaryotic biodiversity in historical air-dried samples of Dutch agricultural soil has been assessed by random sequencing of an 18S rRNA gene library and by denaturing gradient gel electrophoresis. Representatives of nearly all taxa of eukaryotic soil microbes could be identified, demonstrating

  6. Eukaryotic diversity in historical soil samples.

    Science.gov (United States)

    Moon-van der Staay, Seung Yeo; Tzeneva, Vesela A; van der Staay, Georg W M; de Vos, Willem M; Smidt, Hauke; Hackstein, Johannes H P

    2006-09-01

    The eukaryotic biodiversity in historical air-dried samples of Dutch agricultural soil has been assessed by random sequencing of an 18S rRNA gene library and by denaturing gradient gel electrophoresis. Representatives of nearly all taxa of eukaryotic soil microbes could be identified, demonstrating that it is possible to study eukaryotic microbiota in samples from soil archives that have been stored for more than 30 years at room temperature. In a pilot study, 41 sequences were retrieved that could be assigned to fungi and a variety of aerobic and anaerobic protists such as cercozoans, ciliates, xanthophytes (stramenopiles), heteroloboseans, and amoebozoans. A PCR-denaturing gradient gel electrophoresis analysis of samples collected between 1950 and 1975 revealed significant changes in the composition of the eukaryotic microbiota.

  7. Genetic diversity and variability in two Italian autochthonous donkey genetic types assessed by microsatellite markers

    Directory of Open Access Journals (Sweden)

    Donato Matassino

    2014-01-01

    Full Text Available Since 13rd century, Italian domestic autochthonous donkey population has been characterised by Mediterranean grey mousy cruciate ancestral phenotype, currently typical of Amiata donkey (AD genetic type. This phenotype persisted up to the 16th century when a marked introduction of Hispanic and French big sized and dark bay or darkish coloured sires occurred. In the context of a safeguard programme of Latial Equide resources, the aim of this research was to evaluate the genetic diversity and similarity between the AD breed and an autochthonous donkey population native from Lazio, the Viterbese donkey (VD, using molecular markers. A total of 135 animals (50 AD and 85 VD were genetically characterised by using 16 short tandem repeat markers. A high genetic differentiation between populations (FST=0.158; P<0.01 and a low betweenbreeds genetic similarity (0.233±0.085 were observed. Correspondence analysis, the result of STRUCTURE software analysis and analysis of molecular variance would seem to indicate genetically different entities as well. It would be desirable to increase the number of comparison with other breeds to better understand the origin of VD. Moreover, results obtained in this study suggest that the loss of genetic variation observed in VD could mainly derive from unnoticed sub-population structuring (Wahlund effect, rather than to other factors such as inbreeding, null alleles or selection influence.

  8. Censusing marine eukaryotic diversity in the twenty-first century.

    Science.gov (United States)

    Leray, Matthieu; Knowlton, Nancy

    2016-09-01

    The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems.This article is part of the themed issue 'From DNA barcodes to biomes'.

  9. Censusing marine eukaryotic diversity in the twenty-first century

    Science.gov (United States)

    Knowlton, Nancy

    2016-01-01

    The ocean constitutes one of the vastest and richest biomes on our planet. Most recent estimations, all based on indirect approaches, suggest that there are millions of marine eukaryotic species. Moreover, a large majority of these are small (less than 1 mm), cryptic and still unknown to science. However, this knowledge gap, caused by the lack of diagnostic morphological features in small organisms and the limited sampling of the global ocean, is currently being filled, thanks to new DNA-based approaches. The molecular technique of PCR amplification of homologous gene regions combined with high-throughput sequencing, routinely used to census unculturable prokaryotes, is now also being used to characterize whole communities of marine eukaryotes. Here, we review how this methodological advancement has helped to better quantify the magnitude and patterns of marine eukaryotic diversity, with an emphasis on taxonomic groups previously largely overlooked. We then discuss obstacles remaining to achieve a global understanding of marine eukaryotic diversity. In particular, we argue that 18S variable regions do not provide sufficient taxonomic resolution to census marine life, and suggest combining broad eukaryotic surveys targeting the 18S rRNA region with more taxon-focused analyses of hypervariable regions to improve our understanding of the diversity of species, the functional units of marine ecosystems. This article is part of the themed issue ‘From DNA barcodes to biomes’. PMID:27481783

  10. Next-Generation Sequencing Assessment of Eukaryotic Diversity in Oil Sands Tailings Ponds Sediments and Surface Water.

    Science.gov (United States)

    Aguilar, Maria; Richardson, Elisabeth; Tan, BoonFei; Walker, Giselle; Dunfield, Peter F; Bass, David; Nesbø, Camilla; Foght, Julia; Dacks, Joel B

    2016-11-01

    Tailings ponds in the Athabasca oil sands (Canada) contain fluid wastes, generated by the extraction of bitumen from oil sands ores. Although the autochthonous prokaryotic communities have been relatively well characterized, almost nothing is known about microbial eukaryotes living in the anoxic soft sediments of tailings ponds or in the thin oxic layer of water that covers them. We carried out the first next-generation sequencing study of microbial eukaryotic diversity in oil sands tailings ponds. In metagenomes prepared from tailings sediment and surface water, we detected very low numbers of sequences encoding eukaryotic small subunit ribosomal RNA representing seven major taxonomic groups of protists. We also produced and analysed three amplicon-based 18S rRNA libraries prepared from sediment samples. These revealed a more diverse set of taxa, 169 different OTUs encompassing up to eleven higher order groups of eukaryotes, according to detailed classification using homology searching and phylogenetic methods. The 10 most abundant OTUs accounted for > 90% of the total of reads, vs. large numbers of rare OTUs (< 1% abundance). Despite the anoxic and hydrocarbon-enriched nature of the environment, the tailings ponds harbour complex communities of microbial eukaryotes indicating that these organisms should be taken into account when studying the microbiology of the oil sands.

  11. Diversity and antibiotic susceptibility of autochthonous dairy enterococci isolates: Are they safe candidates for autochthonous starter cultures?

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    Amarela eTerzić-Vidojević

    2015-09-01

    Full Text Available Enterococci represent the most controversial group of dairy bacteria. They are found to be the main constituent of many traditional Mediterranean dairy products and contribute to their characteristic taste and flavor. On the other hand, during the last 50 years antibiotic-resistant enterococci have emerged as leading causes of nosocomial infections worldwide. The aim of this study was to determine the diversity, technological properties, antibiotic susceptibility and virulence traits of 636 enterococci previously isolated from 55 artisan dairy products from 12 locations in the Western Balkan countries of Serbia, Croatia and Bosnia and Herzegovina. All strains were identified both by microbiological and molecular methods. The predominant species was Enterococcus durans, followed by E. faecalis and E. faecium. Over 44% of the isolates were resistant to ciprofloxacin and erythromycin, while 26.2% of the isolates were multi-resistant to three or more antibiotics belonging to different families. 185 isolates (29.1% were susceptible to all 13 of the antibiotics tested. The antibiotic-susceptible isolates were further tested for possible virulence genes and the production of biogenic amines. Finally, five enterococci isolates were found to be antibiotic susceptible with good technological characteristics and without virulence traits or the ability to produce biogenic amines, making them possible candidates for biotechnological application as starter cultures in the dairy industry.

  12. MtDNA diversity among four Portuguese autochthonous dog breeds: a fine-scale characterisation

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    Santa-Rita Pedro

    2005-06-01

    Full Text Available Abstract Background The picture of dog mtDNA diversity, as obtained from geographically wide samplings but from a small number of individuals per region or breed, has revealed weak geographic correlation and high degree of haplotype sharing between very distant breeds. We aimed at a more detailed picture through extensive sampling (n = 143 of four Portuguese autochthonous breeds – Castro Laboreiro Dog, Serra da Estrela Mountain Dog, Portuguese Sheepdog and Azores Cattle Dog-and comparatively reanalysing published worldwide data. Results Fifteen haplotypes belonging to four major haplogroups were found in these breeds, of which five are newly reported. The Castro Laboreiro Dog presented a 95% frequency of a new A haplotype, while all other breeds contained a diverse pool of existing lineages. The Serra da Estrela Mountain Dog, the most heterogeneous of the four Portuguese breeds, shared haplotypes with the other mainland breeds, while Azores Cattle Dog shared no haplotypes with the other Portuguese breeds. A review of mtDNA haplotypes in dogs across the world revealed that: (a breeds tend to display haplotypes belonging to different haplogroups; (b haplogroup A is present in all breeds, and even uncommon haplogroups are highly dispersed among breeds and continental areas; (c haplotype sharing between breeds of the same region is lower than between breeds of different regions and (d genetic distances between breeds do not correlate with geography. Conclusion MtDNA haplotype sharing occurred between Serra da Estrela Mountain dogs (with putative origin in the centre of Portugal and two breeds in the north and south of the country-with the Castro Laboreiro Dog (which behaves, at the mtDNA level, as a sub-sample of the Serra da Estrela Mountain Dog and the southern Portuguese Sheepdog. In contrast, the Azores Cattle Dog did not share any haplotypes with the other Portuguese breeds, but with dogs sampled in Northern Europe. This suggested that the

  13. French invasive Asian tiger mosquito populations harbor reduced bacterial microbiota and genetic diversity compared to Vietnamese autochthonous relatives

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    Minard, G.; Tran, F. H.; Van, Van Tran; Goubert, C.; Bellet, C.; Lambert, G.; Kim, Khanh Ly Huynh; Thuy, Trang Huynh Thi; Mavingui, P.; Valiente Moro, C.

    2015-01-01

    The Asian tiger mosquito Aedes albopictus is one of the most significant pathogen vectors of the twenty-first century. Originating from Asia, it has invaded a wide range of eco-climatic regions worldwide. The insect-associated microbiota is now recognized to play a significant role in host biology. While genetic diversity bottlenecks are known to result from biological invasions, the resulting shifts in host-associated microbiota diversity has not been thoroughly investigated. To address this subject, we compared four autochthonous Ae. albopictus populations in Vietnam, the native area of Ae. albopictus, and three populations recently introduced to Metropolitan France, with the aim of documenting whether these populations display differences in host genotype and bacterial microbiota. Population-level genetic diversity (microsatellite markers and COI haplotype) and bacterial diversity (16S rDNA metabarcoding) were compared between field-caught mosquitoes. Bacterial microbiota from the whole insect bodies were largely dominated by Wolbachia pipientis. Targeted analysis of the gut microbiota revealed a greater bacterial diversity in which a fraction was common between French and Vietnamese populations. The genus Dysgonomonas was the most prevalent and abundant across all studied populations. Overall genetic diversities of both hosts and bacterial microbiota were significantly reduced in recently established populations of France compared to the autochthonous populations of Vietnam. These results open up many important avenues of investigation in order to link the process of geographical invasion to shifts in commensal and symbiotic microbiome communities, as such shifts may have dramatic impacts on the biology and/or vector competence of invading hematophagous insects. PMID:26441903

  14. TEM evidence for eukaryotic diversity in mid-Proterozoic oceans

    OpenAIRE

    Javaux, E.J; Knoll, A H; Walter, M.R.

    2004-01-01

    Biomarker molecular fossils in 2770 Ma shales suggest that the Eucarya diverged from other principal domains early in Earth history. Nonetheless, at present, the oldest fossils that can be assigned to an extant eukaryotic clade are filamentous red algae preserved in ca. 1200 Ma cherts from Arctic Canada. Between these records lies a rich assortment of potentially protistan microfossils. Combined light microscopy, scanning electron microscopy, and transmission electron microscopy on 1500-1400 ...

  15. Structural Diversity of Eukaryotic Membrane Cytochrome P450s*

    OpenAIRE

    Johnson, Eric F.; Stout, C. David

    2013-01-01

    X-ray crystal structures are available for 29 eukaryotic microsomal, chloroplast, or mitochondrial cytochrome P450s, including two non-monooxygenase P450s. These structures provide a basis for understanding structure-function relations that underlie their distinct catalytic activities. Moreover, structural plasticity has been characterized for individual P450s that aids in understanding substrate binding in P450s that mediate drug clearance.

  16. What Entamoeba histolytica and Giardia lamblia tell us about the evolution of eukaryotic diversity

    Indian Academy of Sciences (India)

    J Samuelson

    2002-11-01

    Entamoeba histolytica and Giardia lamblia are microaerophilic protists, which have long been considered models of ancient pre-mitochondriate eukaryotes. As transitional eukaryotes, amoebae and giardia appeared to lack organelles of higher eukaryotes and to depend upon energy metabolism appropriate for anaerobic conditions, early in the history of the planet. However, our studies have shown that amoebae and giardia contain splicoeosomal introns, ras-family signal-transduction proteins, ATP-binding casettes (ABC)-family drug transporters, Golgi, and a mitochondrion-derived organelle (amoebae only). These results suggest that most of the organelles of higher eukaryotes were present in the common ancestor of all eukaryotes, and so dispute the notion of transitional eukaryotic forms. In addition, phylogenetic studies suggest many of the genes encoding the fermentation enzymes of amoebae and giardia derive from prokaryotes by lateral gene transfer (LGT). While LGT has recently been shown to be an important determinant of prokaryotic evolution, this is the first time that LGT has been shown to be an important determinant of eukaryotic evolution. Further, amoebae contain cyst wall-associated lectins, which resemble, but are distinct from lectins in the walls of insects (convergent evolution). Giardia have a novel microtubule-associated structure which tethers together pairs of nuclei during cell division. It appears then that amoebae and giardia tell us less about the origins of eukaryotes and more about the origins of eukaryotic diversity.

  17. Microbial eukaryotic distributions and diversity patterns in a deep-sea methane seep ecosystem.

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    Pasulka, Alexis L; Levin, Lisa A; Steele, Josh A; Case, David H; Landry, Michael R; Orphan, Victoria J

    2016-09-01

    Although chemosynthetic ecosystems are known to support diverse assemblages of microorganisms, the ecological and environmental factors that structure microbial eukaryotes (heterotrophic protists and fungi) are poorly characterized. In this study, we examined the geographic, geochemical and ecological factors that influence microbial eukaryotic composition and distribution patterns within Hydrate Ridge, a methane seep ecosystem off the coast of Oregon using a combination of high-throughput 18S rRNA tag sequencing, terminal restriction fragment length polymorphism fingerprinting, and cloning and sequencing of full-length 18S rRNA genes. Microbial eukaryotic composition and diversity varied as a function of substrate (carbonate versus sediment), activity (low activity versus active seep sites), sulfide concentration, and region (North versus South Hydrate Ridge). Sulfide concentration was correlated with changes in microbial eukaryotic composition and richness. This work also revealed the influence of oxygen content in the overlying water column and water depth on microbial eukaryotic composition and diversity, and identified distinct patterns from those previously observed for bacteria, archaea and macrofauna in methane seep ecosystems. Characterizing the structure of microbial eukaryotic communities in response to environmental variability is a key step towards understanding if and how microbial eukaryotes influence seep ecosystem structure and function.

  18. Diversity and dynamics of Antarctic marine microbial eukaryotes under manipulated environmental UV radiation

    NARCIS (Netherlands)

    Piquet, Anouk M. -T.; Bolhuis, Henk; Davidson, Andrew T.; Thomson, Paul G.; Buma, Anita G. J.

    2008-01-01

    In the light of the predicted global climate change, it is essential that the status and diversity of polar microbial communities is described and understood. In the present study, molecular tools were used to investigate the marine eukaryotic communities of Prydz Bay, Eastern Antarctica, from Novem

  19. Phylogenetic diversity and in situ detection of eukaryotes in anaerobic sludge digesters

    Science.gov (United States)

    Matsubayashi, Miri; Shimada, Yusuke; Li, Yu-You; Harada, Hideki

    2017-01-01

    Eukaryotic communities in aerobic wastewater treatment processes are well characterized, but little is known about them in anaerobic processes. In this study, abundance, diversity and morphology of eukaryotes in anaerobic sludge digesters were investigated by quantitative real-time PCR (qPCR), 18S rRNA gene clone library construction and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken from four different anaerobic sludge digesters in Japan. Results of qPCR of rRNA genes revealed that Eukarya accounted from 0.1% to 1.4% of the total number of microbial rRNA gene copy numbers. The phylogenetic affiliations of a total of 251 clones were Fungi, Alveolata, Viridiplantae, Amoebozoa, Rhizaria, Stramenopiles and Metazoa. Eighty-five percent of the clones showed less than 97.0% sequence identity to described eukaryotes, indicating most of the eukaryotes in anaerobic sludge digesters are largely unknown. Clones belonging to the uncultured lineage LKM11 in Cryptomycota of Fungi were most abundant in anaerobic sludge, which accounted for 50% of the total clones. The most dominant OTU in each library belonged to either the LKM11 lineage or the uncultured lineage A31 in Alveolata. Principal coordinate analysis indicated that the eukaryotic and prokaryotic community structures were related. The detection of anaerobic eukaryotes, including the members of the LKM11 and A31 lineages in anaerobic sludge digesters, by CARD-FISH revealed their sizes in the range of 2–8 μm. The diverse and uncultured eukaryotes in the LKM11 and the A31 lineages are common and ecologically relevant members in anaerobic sludge digester. PMID:28264042

  20. A Broad Phylogenetic Survey Unveils the Diversity and Evolution of Telomeres in Eukaryotes

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    Fulnečková, Jana; Ševčíková, Tereza; Fajkus, Jiří; Lukešová, Alena; Lukeš, Martin; Vlček, Čestmír; Lang, B. Franz; Kim, Eunsoo; Eliáš, Marek; Sýkorová, Eva

    2013-01-01

    Telomeres, ubiquitous and essential structures of eukaryotic chromosomes, are known to come in a variety of forms, but knowledge about their actual diversity and evolution across the whole phylogenetic breadth of the eukaryotic life remains fragmentary. To fill this gap, we employed a complex experimental approach to probe telomeric minisatellites in various phylogenetically diverse groups of algae. Our most remarkable results include the following findings: 1) algae of the streptophyte class Klebsormidiophyceae possess the Chlamydomonas-type telomeric repeat (TTTTAGGG) or, in at least one species, a novel TTTTAGG repeat, indicating an evolutionary transition from the Arabidopsis-type repeat (TTTAGGG) ancestral for Chloroplastida; 2) the Arabidopsis-type repeat is also present in telomeres of Xanthophyceae, in contrast to the presence of the human-type repeat (TTAGGG) in other ochrophytes studied, and of the photosynthetic alveolate Chromera velia, consistent with its phylogenetic position close to apicomplexans and dinoflagellates; 3) glaucophytes and haptophytes exhibit the human-type repeat in their telomeres; and 4) ulvophytes and rhodophytes have unusual telomere structures recalcitrant to standard analysis. To obtain additional details on the distribution of different telomere types in eukaryotes, we performed in silico analyses of genomic data from major eukaryotic lineages, utilizing also genome assemblies from our on-going genome projects for representatives of three hitherto unsampled lineages (jakobids, malawimonads, and goniomonads). These analyses confirm the human-type repeat as the most common and possibly ancestral in eukaryotes, but alternative motifs replaced it along the phylogeny of diverse eukaryotic lineages, some of them several times independently. PMID:23395982

  1. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

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    Wang, Jiali; Wang, Fang; Chu, Limin; Wang, Hao; Zhong, Zhiping; Liu, Zhipei; Gao, Jianyong; Duan, Hairong

    2014-01-01

    Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene) of the planktonic microbial eukaryotes (nano- and picoeukaryotes) in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%), whereas Stramenopiles (26.65%) and Alveolates (10.84%) are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%), whereas less represented in other hypersaline lakes such as Gahai (0.50%) and Xiaochaidan (1.15%). Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper) saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

  2. Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME.

    Science.gov (United States)

    Leray, Matthieu; Knowlton, Nancy

    2016-01-01

    PCR amplification followed by deep sequencing of homologous gene regions is increasingly used to characterize the diversity and taxonomic composition of marine eukaryotic communities. This approach may generate millions of sequences for hundreds of samples simultaneously. Therefore, tools that researchers can use to visualize complex patterns of diversity for these massive datasets are essential. Efforts by microbiologists to understand the Earth and human microbiomes using high-throughput sequencing of the 16S rRNA gene has led to the development of several user-friendly, open-source software packages that can be similarly used to analyze eukaryotic datasets. Quantitative Insights Into Microbial Ecology (QIIME) offers some of the most helpful data visualization tools. Here, we describe functionalities to import OTU tables generated with any molecular marker (e.g., 18S, COI, ITS) and associated metadata into QIIME. We then present a range of analytical tools implemented within QIIME that can be used to obtain insights about patterns of alpha and beta diversity for marine eukaryotes.

  3. Genetic diversity of eukaryotic plankton assemblages in Eastern Tibetan Lakes differing by their salinity and altitude.

    Science.gov (United States)

    Wu, Qinglong L; Chatzinotas, Antonis; Wang, Jianjun; Boenigk, Jens

    2009-10-01

    Eukaryotic plankton assemblages in 11 high-mountain lakes located at altitudes of 2,817 to 5,134 m and over a total area of ca. one million square kilometers on the Eastern Tibet Plateau, spanning a salinity gradient from 0.2 (freshwater) to 187.1 g l(-1) (hypersaline), were investigated by cultivation independent methods. Two 18S rRNA gene-based fingerprint approaches, i.e., the terminal restriction fragment length polymorphism and denaturing gradient gel electrophoresis (DGGE) with subsequent band sequencing were applied. Samples of the same lake type (e.g., freshwater) generally shared more of the same bands or T-RFs than samples of different types (e.g., freshwater versus saline). However, a certain number of bands or T-RFs among the samples within each lake were distinct, indicating the potential presence of significant genetic diversity within each lake. PCA indicated that the most significant environmental gradient among the investigated lakes was salinity. The observed molecular profiles could be further explained (17-24%) by ion percentage of chloride, carbonate and bicarbonate, and sulfate, which were also covaried with change of altitude and latitude. Sequence analysis of selected major DGGE bands revealed many sequences (largely protist) that are not related to any known cultures but to uncultured eukaryotic picoplankton and unidentified eukaryotes. One fourth of the retrieved sequences showed eukaryotic plankton, which were found worldwide and detected in low land lakes, were also detected in habitats located above 4,400 m, suggesting a cosmopolitan distribution of these phylotypes. Collectively, our study suggests that there was a high beta-diversity of eukaryotic plankton assemblages in the investigated Tibetan lakes shaped by multiple geographic and environmental factors.

  4. Genetic diversity of eukaryotic microorganisms in Lake Taihu, a large shallow subtropical lake in china.

    Science.gov (United States)

    Chen, Meijun; Chen, Feizhou; Yu, Yang; Ji, Jian; Kong, Fanxiang

    2008-10-01

    We investigated the genetic diversity of eukaryotic microorganisms (0.8-20 microm) by sequencing cloned 18S rRNA genes in six genetic libraries constructed from six locations in Lake Taihu, a large shallow subtropical lake in China. Genetic libraries of eukaryotic ribosomal RNA were screened by restriction fragment length polymorphism (RFLP) analysis, and one clone representative of each RFLP pattern was partially sequenced. A total of 528 clones were clustered into 165 RFLP patterns and finally into 131 operational taxonomic unit (OTUs). Phylogenetic analysis revealed that each library included many unique OTUs, as well as members of distantly related phylogenetic groups. A majority of the clones were from alveolates, stramenopiles, cercozoa, cryptophytes, chlorophytes, and fungi, with members of choanoflagellida, euglenida, centroheliozoa, ancyromonadidae, ichthyosporea, and kathablepharid representing a minor fraction of the library. Six OTUs (15 clones) were not related to any known eukaryotic group. Canonical correspondence analysis suggested that the differences in eukaryotic microorganism community composition of in the six regions were partially related to trophic status, sediment resuspension, and top-down regulation by metazooplankton.

  5. Depth shapes α- and β-diversities of microbial eukaryotes in surficial sediments of coastal ecosystems.

    Science.gov (United States)

    Gong, Jun; Shi, Fei; Ma, Bin; Dong, Jun; Pachiadaki, Maria; Zhang, Xiaoli; Edgcomb, Virginia P

    2015-10-01

    Little is known about the relative influence of historic processes and environmental gradients on shaping the diversity of single-celled eukaryotes in marine benthos. By combining pyrosequencing of 18S ribosomal RNA genes with data on multiple environmental factors, we investigated the diversity of microeukaryotes in surficial sediments of three basins of the Yellow Sea Large Marine Ecosystem. A considerable proportion (about 20%) of reads was affiliated with known parasitoid protists. Dinophyta and Ciliophora appeared dominant in terms of relative proportion of reads and operational taxonomic unit (OTU) richness. Overall, OTU richness of benthic microeukaryotes decreased with increasing water depth and decreasing pH. While community composition was significantly different among basins, partial Mantel tests indicated a depth-decay pattern of community similarity, whereby water depth, rather than geographic distance or environment, shaped β-diversity of benthic microeukaryotes (including both the abundant and the rare biosphere) on a regional scale. Similar hydrographic and mineralogical factors contributed to the biogeography of both the abundant and the rare OTUs. The trace metal vanadium had a significant effect on the biogeography of the rare biosphere. Our study sheds new light on the composition, diversity patterns and underlying mechanisms of single-celled eukaryote distribution in surficial sediments of coastal oceans.

  6. High genetic diversity and novelty in eukaryotic plankton assemblages inhabiting saline lakes in the Qaidam basin.

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    Jiali Wang

    Full Text Available Saline lakes are intriguing ecosystems harboring extremely productive microbial communities in spite of their extreme environmental conditions. We performed a comprehensive analysis of the genetic diversity (18S rRNA gene of the planktonic microbial eukaryotes (nano- and picoeukaryotes in six different inland saline lakes located in the Qaidam Basin. The novelty level are high, with about 11.23% of the whole dataset showing <90% identity to any previously reported sequence in GenBank. At least 4 operational taxonomic units (OTUs in mesosaline lakes, while up to eighteen OTUs in hypersaline lakes show very low CCM and CEM scores, indicating that these sequences are highly distantly related to any existing sequence. Most of the 18S rRNA gene sequence reads obtained in investigated mesosaline lakes is closely related to Holozoa group (48.13%, whereas Stramenopiles (26.65% and Alveolates (10.84% are the next most common groups. Hypersaline lakes in the Qaidam Basin are also dominated by Holozoa group, accounting for 26.65% of the total number of sequence reads. Notably, Chlorophyta group are only found in high abundance in Lake Gasikule (28.00%, whereas less represented in other hypersaline lakes such as Gahai (0.50% and Xiaochaidan (1.15%. Further analysis show that the compositions of planktonic eukaryotic assemblages are also most variable between different sampling sites in the same lake. Out of the parameters, four show significant correlation to this CCA: altitude, calcium, sodium and potassium concentrations. Overall, this study shows important gaps in the current knowledge about planktonic microbial eukaryotes inhabiting Qaidam Basin (hyper saline water bodies. The identified diversity and novelty patterns among eukaryotic plankton assemblages in saline lake are of great importance for understanding and interpreting their ecology and evolution.

  7. Molecular diversity of eukaryotes in municipal wastewater treatment processes as revealed by 18S rRNA gene analysis.

    Science.gov (United States)

    Matsunaga, Kengo; Kubota, Kengo; Harada, Hideki

    2014-01-01

    Eukaryotic communities involved in sewage treatment processes have been investigated by morphological identification, but have not yet been well-characterized using molecular approaches. In the present study, eukaryotic communities were characterized by constructing 18S rRNA gene clone libraries. The phylogenetic affiliations of a total of 843 clones were Alveolata, Fungi, Rhizaria, Euglenozoa, Stramenopiles, Amoebozoa, and Viridiplantae as protozoans and Rotifera, Gastrotricha, and Nematoda as metazoans. Sixty percent of the clones had <97% sequence identity to described eukaryotes, indicating the greater diversity of eukaryotes than previously recognized. A core OTU closely related to Epistylis chrysemydis was identified, and several OTUs were shared by 4-8 libraries. Members of the uncultured lineage LKM11 in Cryptomycota were predominant fungi in sewage treatment processes. This comparative study represents an initial step in furthering understanding of the diversity and role of eukaryotes in sewage treatment processes.

  8. Environmental metabarcoding reveals heterogeneous drivers of microbial eukaryote diversity in contrasting estuarine ecosystems.

    Science.gov (United States)

    Lallias, Delphine; Hiddink, Jan G; Fonseca, Vera G; Gaspar, John M; Sung, Way; Neill, Simon P; Barnes, Natalie; Ferrero, Tim; Hall, Neil; Lambshead, P John D; Packer, Margaret; Thomas, W Kelley; Creer, Simon

    2015-05-01

    Assessing how natural environmental drivers affect biodiversity underpins our understanding of the relationships between complex biotic and ecological factors in natural ecosystems. Of all ecosystems, anthropogenically important estuaries represent a 'melting pot' of environmental stressors, typified by extreme salinity variations and associated biological complexity. Although existing models attempt to predict macroorganismal diversity over estuarine salinity gradients, attempts to model microbial biodiversity are limited for eukaryotes. Although diatoms commonly feature as bioindicator species, additional microbial eukaryotes represent a huge resource for assessing ecosystem health. Of these, meiofaunal communities may represent the optimal compromise between functional diversity that can be assessed using morphology and phenotype-environment interactions as compared with smaller life fractions. Here, using 454 Roche sequencing of the 18S nSSU barcode we investigate which of the local natural drivers are most strongly associated with microbial metazoan and sampled protist diversity across the full salinity gradient of the estuarine ecosystem. In order to investigate potential variation at the ecosystem scale, we compare two geographically proximate estuaries (Thames and Mersey, UK) with contrasting histories of anthropogenic stress. The data show that although community turnover is likely to be predictable, taxa are likely to respond to different environmental drivers and, in particular, hydrodynamics, salinity range and granulometry, according to varied life-history characteristics. At the ecosystem level, communities exhibited patterns of estuary-specific similarity within different salinity range habitats, highlighting the environmental sequencing biomonitoring potential of meiofauna, dispersal effects or both.

  9. Oceanic 18S rDNA sequences from picoplankton reveal unsuspected eukaryotic diversity

    Science.gov (United States)

    Moon-van der Staay, Seung Yeo; De WachterRDanielVaulot, RupertDe WachterR.Daniel

    2001-02-01

    Picoplankton-cells with a diameter of less than 3µm-are the dominant contributors to both primary production and biomass in open oceanic regions. However, compared with the prokaryotes, the eukaryotic component of picoplankton is still poorly known. Recent discoveries of new eukaryotic algal taxa based on picoplankton cultures suggest the existence of many undiscovered taxa. Conventional approaches based on phenotypic criteria have limitations in depicting picoplankton composition due to their tiny size and lack of distinctive taxonomic characters. Here we analyse, using an approach that has been very successful for prokaryotes but has so far seldom been applied to eukaryotes, 35 full sequences of the small-subunit (18S) ribosomal RNA gene derived from a picoplanktonic assemblage collected at a depth of 75m in the equatorial Pacific Ocean, and show that there is a high diversity of picoeukaryotes. Most of the sequences were previously unknown but could still be assigned to important marine phyla including prasinophytes, haptophytes, dinoflagellates, stramenopiles, choanoflagellates and acantharians. We also found a novel lineage, closely related to dinoflagellates and not previously described.

  10. How and why DNA barcodes underestimate the diversity of microbial eukaryotes.

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    Gwenael Piganeau

    Full Text Available BACKGROUND: Because many picoplanktonic eukaryotic species cannot currently be maintained in culture, direct sequencing of PCR-amplified 18S ribosomal gene DNA fragments from filtered sea-water has been successfully used to investigate the astounding diversity of these organisms. The recognition of many novel planktonic organisms is thus based solely on their 18S rDNA sequence. However, a species delimited by its 18S rDNA sequence might contain many cryptic species, which are highly differentiated in their protein coding sequences. PRINCIPAL FINDINGS: Here, we investigate the issue of species identification from one gene to the whole genome sequence. Using 52 whole genome DNA sequences, we estimated the global genetic divergence in protein coding genes between organisms from different lineages and compared this to their ribosomal gene sequence divergences. We show that this relationship between proteome divergence and 18S divergence is lineage dependent. Unicellular lineages have especially low 18S divergences relative to their protein sequence divergences, suggesting that 18S ribosomal genes are too conservative to assess planktonic eukaryotic diversity. We provide an explanation for this lineage dependency, which suggests that most species with large effective population sizes will show far less divergence in 18S than protein coding sequences. CONCLUSIONS: There is therefore a trade-off between using genes that are easy to amplify in all species, but which by their nature are highly conserved and underestimate the true number of species, and using genes that give a better description of the number of species, but which are more difficult to amplify. We have shown that this trade-off differs between unicellular and multicellular organisms as a likely consequence of differences in effective population sizes. We anticipate that biodiversity of microbial eukaryotic species is underestimated and that numerous "cryptic species" will become

  11. Uncultivated microbial eukaryotic diversity: a method to link ssu rRNA gene sequences with morphology.

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    Marissa B Hirst

    Full Text Available Protists have traditionally been identified by cultivation and classified taxonomically based on their cellular morphologies and behavior. In the past decade, however, many novel protist taxa have been identified using cultivation independent ssu rRNA sequence surveys. New rRNA "phylotypes" from uncultivated eukaryotes have no connection to the wealth of prior morphological descriptions of protists. To link phylogenetically informative sequences with taxonomically informative morphological descriptions, we demonstrate several methods for combining whole cell rRNA-targeted fluorescent in situ hybridization (FISH with cytoskeletal or organellar immunostaining. Either eukaryote or ciliate-specific ssu rRNA probes were combined with an anti-α-tubulin antibody or phalloidin, a common actin stain, to define cytoskeletal features of uncultivated protists in several environmental samples. The eukaryote ssu rRNA probe was also combined with Mitotracker® or a hydrogenosomal-specific anti-Hsp70 antibody to localize mitochondria and hydrogenosomes, respectively, in uncultivated protists from different environments. Using rRNA probes in combination with immunostaining, we linked ssu rRNA phylotypes with microtubule structure to describe flagellate and ciliate morphology in three diverse environments, and linked Naegleria spp. to their amoeboid morphology using actin staining in hay infusion samples. We also linked uncultivated ciliates to morphologically similar Colpoda-like ciliates using tubulin immunostaining with a ciliate-specific rRNA probe. Combining rRNA-targeted FISH with cytoskeletal immunostaining or stains targeting specific organelles provides a fast, efficient, high throughput method for linking genetic sequences with morphological features in uncultivated protists. When linked to phylotype, morphological descriptions of protists can both complement and vet the increasing number of sequences from uncultivated protists, including those of

  12. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea

    KAUST Repository

    Pearman, John K.

    2015-11-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore–offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

  13. Extracellular DNA amplicon sequencing reveals high levels of benthic eukaryotic diversity in the central Red Sea.

    Science.gov (United States)

    Pearman, John K; Irigoien, Xabier; Carvalho, Susana

    2016-04-01

    The present study aims to characterize the benthic eukaryotic biodiversity patterns at a coarse taxonomic level in three areas of the central Red Sea (a lagoon, an offshore area in Thuwal and a shallow coastal area near Jeddah) based on extracellular DNA. High-throughput amplicon sequencing targeting the V9 region of the 18S rRNA gene was undertaken for 32 sediment samples. High levels of alpha-diversity were detected with 16,089 operational taxonomic units (OTUs) being identified. The majority of the OTUs were assigned to Metazoa (29.2%), Alveolata (22.4%) and Stramenopiles (17.8%). Stramenopiles (Diatomea) and Alveolata (Ciliophora) were frequent in a lagoon and in shallower coastal stations, whereas metazoans (Arthropoda: Maxillopoda) were dominant in deeper offshore stations. Only 24.6% of total OTUs were shared among all areas. Beta-diversity was generally lower between the lagoon and Jeddah (nearshore) than between either of those and the offshore area, suggesting a nearshore-offshore biodiversity gradient. The current approach allowed for a broad-range of benthic eukaryotic biodiversity to be analysed with significantly less labour than would be required by other traditional taxonomic approaches. Our findings suggest that next generation sequencing techniques have the potential to provide a fast and standardised screening of benthic biodiversity at large spatial and temporal scales.

  14. Eukaryotic microbial diversity of phototrophic microbial mats in two Icelandic geothermalhot springs.

    Science.gov (United States)

    Aguilera, Angeles; Souza-Egipsy, Virginia; González-Toril, Elena; Rendueles, Olaya; Amils, Ricardo

    2010-03-01

    The composition of the eukaryotic community and the three-dimensional structure of diverse phototrophic microbial mats from two hot springs in Iceland (Seltun and Hveradalir geothermal areas) were explored by comparing eukaryotic assemblages from microbial mats. Samples were collected in July 2007 from 15 sampling stations along thermal and pH gradients following both hot springs. Physicochemical data revealed high variability in terms of pH (ranging from 2.8 to 7), with high concentrations of heavy metals, including up to 20 g Fe/l, 80 mg Zn/l, 117 mg Cu/l, and 39 mg Ni/l at the most acidic sampling points. Phylogenetic analysis of 18S rDNA genes revealed a diversity of sequences related to several taxa, including members of the Bacillariophyta, Chlorophyta, Rhodophyta, and Euglenophyta phyla as well as ciliates, amoebae, and stramenopiles. The closest relatives to some of the sequences detected came from acidophilic organisms, even when the samples were collected at circumneutral water locations. Electron microscopy showed that most of the microecosystems analyzed were organized as phototrophic microbial mats in which filamentous cyanobacteria usually appeared as a major component. Deposits of amorphous minerals rich in silica, iron, and aluminium around the filaments were frequently detected.

  15. Lateral transfer of tetrahymanol-synthesizing genes has allowed multiple diverse eukaryote lineages to independently adapt to environments without oxygen

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    Takishita Kiyotaka

    2012-02-01

    Full Text Available Abstract Sterols are key components of eukaryotic cellular membranes that are synthesized by multi-enzyme pathways that require molecular oxygen. Because prokaryotes fundamentally lack sterols, it is unclear how the vast diversity of bacterivorous eukaryotes that inhabit hypoxic environments obtain, or synthesize, sterols. Here we show that tetrahymanol, a triterpenoid that does not require molecular oxygen for its biosynthesis, likely functions as a surrogate of sterol in eukaryotes inhabiting oxygen-poor environments. Genes encoding the tetrahymanol synthesizing enzyme squalene-tetrahymanol cyclase were found from several phylogenetically diverged eukaryotes that live in oxygen-poor environments and appear to have been laterally transferred among such eukaryotes. Reviewers This article was reviewed by Eric Bapteste and Eugene Koonin.

  16. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile

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    D. Joshua eParris

    2014-10-01

    Full Text Available Molecular surveys are revealing diverse eukaryotic assemblages in oxygen-limited ocean waters. These communities may play pivotal ecological roles through autotrophy, feeding, and a wide range of symbiotic associations with prokaryotes. We used 18S rRNA gene sequencing to provide the first snapshot of pelagic microeukaryotic community structure in two cellular size fractions (0.2-1.6 µm, >1.6 µm from seven depths through the anoxic oxygen minimum zone (OMZ off northern Chile. Sequencing of >154,000 amplicons revealed contrasting patterns of phylogenetic diversity across size fractions and depths. Protist and total eukaryote diversity in the >1.6 µm fraction peaked at the chlorophyll maximum in the upper photic zone before declining by ~50% in the OMZ. In contrast, diversity in the 0.2-1.6 µm fraction, though also elevated in the upper photic zone, increased four-fold from the lower oxycline to a maximum at the anoxic OMZ core. Dinoflagellates of the Dinophyceae and endosymbiotic Syndiniales clades dominated the protist assemblage at all depths (~40-70% of sequences. Other protist groups varied with depth, with the anoxic zone community of the larger size fraction enriched in euglenozoan flagellates and acantharean radiolarians (up to 18% and 40% of all sequences, respectively. The OMZ 0.2-1.6 µm fraction was dominated (11-99% by Syndiniales, which exhibited depth-specific variation in composition and total richness despite uniform oxygen conditions. Metazoan sequences, though confined primarily to the 1.6 µm fraction above the OMZ, were also detected within the anoxic zone where groups such as copepods increased in abundance relative to the oxycline and upper OMZ. These data, compared to those from other low-oxygen sites, reveals variation in OMZ microeukaryote composition, helping to identify clades with potential adaptations to oxygen-depletion.

  17. A late origin of the extant eukaryotic diversity: divergence time estimates using rare genomic changes

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    Koonin Eugene V

    2011-05-01

    eukaryotes that is open to comparative-genomic study probably was preceded by hundreds of millions years of evolution that might have included extinct diversity inaccessible to comparative approaches. Reviewers This article was reviewed by William Martin, Herve Philippe (nominated by I. King Jordan, and Romain Derelle.

  18. Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river.

    Science.gov (United States)

    Bricheux, Geneviève; Morin, Loïc; Le Moal, Gwenaël; Coffe, Gérard; Balestrino, Damien; Charbonnel, Nicolas; Bohatier, Jacques; Forestier, Christiane

    2013-06-01

    Despite the recent and significant increase in the study of aquatic microbial communities, little is known about the microbial diversity of complex ecosystems such as running waters. This study investigated the biodiversity of biofilm communities formed in a river with 454 Sequencing™. This river has the particularity of integrating both organic and microbiological pollution, as receiver of agricultural pollution in its upstream catchment area and urban pollution through discharges of the wastewater treatment plant of the town of Billom. Different regions of the small subunit (SSU) ribosomal RNA gene were targeted using nine pairs of primers, either universal or specific for bacteria, eukarya, or archaea. Our aim was to characterize the widest range of rDNA sequences using different sets of polymerase chain reaction (PCR) primers. A first look at reads abundance revealed that a large majority (47-48%) were rare sequences (<5 copies). Prokaryotic phyla represented the species richness, and eukaryotic phyla accounted for a small part. Among the prokaryotic phyla, Proteobacteria (beta and alpha) predominated, followed by Bacteroidetes together with a large number of nonaffiliated bacterial sequences. Bacillariophyta plastids were abundant. The remaining bacterial phyla, Verrucomicrobia and Cyanobacteria, made up the rest of the bulk biodiversity. The most abundant eukaryotic phyla were annelid worms, followed by Diatoms, and Chlorophytes. These latter phyla attest to the abundance of plastids and the importance of photosynthetic activity for the biofilm. These findings highlight the existence and plasticity of multiple trophic levels within these complex biological systems.

  19. Neutral Theory Predicts the Relative Abundance and Diversity of Genetic Elements in a Broad Array of Eukaryotic Genomes

    Science.gov (United States)

    Serra, François; Becher, Verónica; Dopazo, Hernán

    2013-01-01

    It is universally true in ecological communities, terrestrial or aquatic, temperate or tropical, that some species are very abundant, others are moderately common, and the majority are rare. Likewise, eukaryotic genomes also contain classes or “species” of genetic elements that vary greatly in abundance: DNA transposons, retrotransposons, satellite sequences, simple repeats and their less abundant functional sequences such as RNA or genes. Are the patterns of relative species abundance and diversity similar among ecological communities and genomes? Previous dynamical models of genomic diversity have focused on the selective forces shaping the abundance and diversity of transposable elements (TEs). However, ideally, models of genome dynamics should consider not only TEs, but also the diversity of all genetic classes or “species” populating eukaryotic genomes. Here, in an analysis of the diversity and abundance of genetic elements in >500 eukaryotic chromosomes, we show that the patterns are consistent with a neutral hypothesis of genome assembly in virtually all chromosomes tested. The distributions of relative abundance of genetic elements are quite precisely predicted by the dynamics of an ecological model for which the principle of functional equivalence is the main assumption. We hypothesize that at large temporal scales an overarching neutral or nearly neutral process governs the evolution of abundance and diversity of genetic elements in eukaryotic genomes. PMID:23798991

  20. Dynamic genetic features of eukaryotic plankton diversity in the Nakdong River estuary of Korea

    Science.gov (United States)

    Lee, Jee Eun; Chung, Ik Kyo; Lee, Sang-Rae

    2016-08-01

    Estuaries are environments where freshwater and seawater mix and they display various salinity profiles. The construction of river barrages and dams has rapidly changed these environments and has had a wide range of impacts on plankton communities. To understand the dynamics of such communities, researchers need accurate and rapid techniques for detecting plankton species. We evaluated the diversity of eukaryotic plankton over a salinity gradient by applying a metagenomics tool at the Nakdong River estuary in Korea. Environmental samples were collected on three dates during summer and autumn of 2011 at the Eulsukdo Bridge at the mouth of that river. Amplifying the 18S rDNA allowed us to analyze 456 clones and 122 phylotypes. Metagenomic sequences revealed various taxonomic groups and cryptic genetic variations at the intra- and inter-specific levels. By analyzing the same station at each sampling date, we observed that the phylotypes presented a salinity-related pattern of diversity in assemblages. The variety of species within freshwater samples reflected the rapid environmental changes caused by freshwater inputs. Dinophyceae phylotypes accounted for the highest proportion of overall diversity in the seawater samples. Euryhaline diatoms and dinoflagellates were observed in the freshwater, brackish and seawater samples. The biological data for species composition demonstrate the transitional state between freshwater and seawater. Therefore, this metagenomics information can serve as a biological indicator for tracking changes in aquatic environments.

  1. Diversity and dynamics of active microbial eukaryotes in the anoxic zone of a freshwater meromictic lake (Pavin, France

    Directory of Open Access Journals (Sweden)

    CECILE eLEPERE

    2016-02-01

    Full Text Available Microbial eukaryotes play a crucial role in ecosystem functioning and oxygen is considered to be one of the strongest barriers against their local dispersal. However, diversity of microbial eukaryotes in freshwater habitats with oxygen gradients has previously received very little attention. We applied high-throughput sequencing (V4 region of the 18S rRNA gene in conjunction with quantitative PCR (DNA and RNA and fluorescent in situ hybridization analyses, to provide an unique spatio-temporal analysis of microbial eukaryotes diversity and potential activity in a meromictic freshwater lake (lake Pavin. This study revealed a high genetic diversity of unicellular eukaryotes in the permanent anoxic zone of lake Pavin and allowed the discrimination of active vs. inactive components. 42 % of the OTUs (Operational taxonomic Units are exclusively present in the monimolimnion, where Alveolata (Ciliophora and Dinophyceae and Fungi (Dikarya and Chytrids are the most active phyla and are probably represented by species capable of anaerobic metabolism. Pigmented eukaryotes (Haptophyceae and Chlorophyceae are also present and active in this zone, which opens up questions regarding their metabolism.

  2. Diversity of eukaryotic DNA replication origins revealed by genome-wide analysis of chromatin structure.

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    Nicolas M Berbenetz

    2010-09-01

    Full Text Available Eukaryotic DNA replication origins differ both in their efficiency and in the characteristic time during S phase when they become active. The biological basis for these differences remains unknown, but they could be a consequence of chromatin structure. The availability of genome-wide maps of nucleosome positions has led to an explosion of information about how nucleosomes are assembled at transcription start sites, but no similar maps exist for DNA replication origins. Here we combine high-resolution genome-wide nucleosome maps with comprehensive annotations of DNA replication origins to identify patterns of nucleosome occupancy at eukaryotic replication origins. On average, replication origins contain a nucleosome depleted region centered next to the ACS element, flanked on both sides by arrays of well-positioned nucleosomes. Our analysis identified DNA sequence properties that correlate with nucleosome occupancy at replication origins genome-wide and that are correlated with the nucleosome-depleted region. Clustering analysis of all annotated replication origins revealed a surprising diversity of nucleosome occupancy patterns. We provide evidence that the origin recognition complex, which binds to the origin, acts as a barrier element to position and phase nucleosomes on both sides of the origin. Finally, analysis of chromatin reconstituted in vitro reveals that origins are inherently nucleosome depleted. Together our data provide a comprehensive, genome-wide view of chromatin structure at replication origins and suggest a model of nucleosome positioning at replication origins in which the underlying sequence occludes nucleosomes to permit binding of the origin recognition complex, which then (likely in concert with nucleosome modifiers and remodelers positions nucleosomes adjacent to the origin to promote replication origin function.

  3. Antibody to a conserved antigenic target is protective against diverse prokaryotic and eukaryotic pathogens.

    Science.gov (United States)

    Cywes-Bentley, Colette; Skurnik, David; Zaidi, Tanweer; Roux, Damien; Deoliveira, Rosane B; Garrett, Wendy S; Lu, Xi; O'Malley, Jennifer; Kinzel, Kathryn; Zaidi, Tauqeer; Rey, Astrid; Perrin, Christophe; Fichorova, Raina N; Kayatani, Alexander K K; Maira-Litràn, Tomas; Gening, Marina L; Tsvetkov, Yury E; Nifantiev, Nikolay E; Bakaletz, Lauren O; Pelton, Stephen I; Golenbock, Douglas T; Pier, Gerald B

    2013-06-11

    Microbial capsular antigens are effective vaccines but are chemically and immunologically diverse, resulting in a major barrier to their use against multiple pathogens. A β-(1→6)-linked poly-N-acetyl-d-glucosamine (PNAG) surface capsule is synthesized by four proteins encoded in genetic loci designated intercellular adhesion in Staphylococcus aureus or polyglucosamine in selected Gram-negative bacterial pathogens. We report that many microbial pathogens lacking an identifiable intercellular adhesion or polyglucosamine locus produce PNAG, including Gram-positive, Gram-negative, and fungal pathogens, as well as protozoa, e.g., Trichomonas vaginalis, Plasmodium berghei, and sporozoites and blood-stage forms of Plasmodium falciparum. Natural antibody to PNAG is common in humans and animals and binds primarily to the highly acetylated glycoform of PNAG but is not protective against infection due to lack of deposition of complement opsonins. Polyclonal animal antibody raised to deacetylated glycoforms of PNAG and a fully human IgG1 monoclonal antibody that both bind to native and deacetylated glycoforms of PNAG mediated complement-dependent opsonic or bactericidal killing and protected mice against local and/or systemic infections by Streptococcus pyogenes, Streptococcus pneumoniae, Listeria monocytogenes, Neisseria meningitidis serogroup B, Candida albicans, and P. berghei ANKA, and against colonic pathology in a model of infectious colitis. PNAG is also a capsular polysaccharide for Neisseria gonorrhoeae and nontypable Hemophilus influenzae, and protects cells from environmental stress. Vaccination targeting PNAG could contribute to immunity against serious and diverse prokaryotic and eukaryotic pathogens, and the conserved production of PNAG suggests that it is a critical factor in microbial biology.

  4. A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling.

    Science.gov (United States)

    Graham, Linda E; Knack, Jennifer J; Graham, Melissa E; Graham, James M; Zulkifly, Shahrizim

    2015-06-01

    Periphyton dominated by the cellulose-rich filamentous green alga Cladophora forms conspicuous growths along rocky marine and freshwater shorelines worldwide, providing habitat for diverse epibionts. Bacterial epibionts have been inferred to display diverse functions of biogeochemical significance: N-fixation and other redox reactions, phosphorus accumulation, and organic degradation. Here, we report taxonomic diversity of eukaryotic and prokaryotic epibionts and diversity of genes associated with materials cycling in a Cladophora metagenome sampled from Lake Mendota, Dane Co., WI, USA, during the growing season of 2012. A total of 1,060 distinct 16S, 173 18S, and 351 28S rRNA operational taxonomic units, from which >220 genera or species of bacteria (~60), protists (~80), fungi (6), and microscopic metazoa (~80), were distinguished with the use of reference databases. We inferred the presence of several algal taxa generally associated with marine systems and detected Jaoa, a freshwater periphytic ulvophyte previously thought endemic to China. We identified six distinct nifH gene sequences marking nitrogen fixation, >25 bacterial and eukaryotic cellulases relevant to sedimentary C-cycling and technological applications, and genes encoding enzymes in aerobic and anaerobic pathways for vitamin B12 biosynthesis. These results emphasize the importance of Cladophora in providing habitat for microscopic metazoa, fungi, protists, and bacteria that are often inconspicuous, yet play important roles in ecosystem biogeochemistry.

  5. An overview of the phylogeny and diversity of eukaryotes%真核生物系统发育和多样性概观

    Institute of Scientific and Technical Information of China (English)

    Sandra L. BALDAUF

    2008-01-01

    Our understanding of eukaryote biology is dominated by the study of land plants, animals and fungi. However, these are only three isolated fragments of the full diversity of extant eukaryotes. The majority of eukaryotes, in terms of major taxa and probably also sheer numbers of cells, consists of exclusively or predominantly unicellular lineages. A surprising number of these lineages are poorly characterized. Nonetheless, they are fundamental to our understanding of eukaryote biology and the underlying forces that shaped it. This article consists of an overview of the current state of our understanding of the eukaryote tree. This includes the identity of the major groups of eukaryotes, some of their important, defining or simply interesting features and the proposed relationships of these groups to each other.

  6. Diversity and distribution of microbial eukaryotes in the deep tropical and subtropical North Atlantic Ocean

    Science.gov (United States)

    Morgan-Smith, Danielle; Clouse, Melissa A.; Herndl, Gerhard J.; Bochdansky, Alexander B.

    2013-08-01

    Employing a combination of 4',6-diamidino-2-phenylindole and fluorescein isothiocyanate (DAPI-FITC) staining and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH), we distinguished a variety of taxonomic and morphological types of eukaryotic microbes in the central and deep water masses of the tropical and subtropical North Atlantic Ocean. Samples were taken along a transect across the tropical Atlantic, along the equatorial upwelling and into the West-African upwelling region. Samples were collected as deep as 7000 m in the Romanche Fracture Zone within the Mid-Atlantic Ridge. Approximately 50-70% of FISH-identified eukaryotes in deep water masses belong to one of seven groups: kinetoplastids, labyrinthulomycetes, fungi, diplonemids, group II alveolates, MAST 4 (stramenopiles), and an unidentified organism with a peculiar nuclear morphology. A smaller percentage of total eukaryotes was identified in the Central Water, especially in the oxygen minimum zone, than in deep water masses. CARD-FISH probes designed to identify broad taxonomic groups revealed kinetoplastids and fungi were more abundant than noted in previous studies employing 18S rRNA gene clone libraries. Group II alveolates, in contrast, were much less prevalent than previously reported. On a second survey, eukaryotic microbes were enumerated in the deep-sea basins below the North Atlantic subtropical gyre including the Vema Fracture Zone, which is another prominent trench in the Mid-Atlantic Ridge. The abundance of eukaryotes and chlorophyll concentrations were significantly different between the two cruises, which covered very different hydrographic regimes with associated high and low levels of primary production, respectively.

  7. Structural diversity of eukaryotic 18S rRNA and its impact on alignment and phylogenetic reconstruction.

    Science.gov (United States)

    Xie, Qiang; Lin, Jinzhong; Qin, Yan; Zhou, Jianfu; Bu, Wenjun

    2011-02-01

    Ribosomal RNAs are important because they catalyze the synthesis of peptides and proteins. Comparative studies of the secondary structure of 18S rRNA have revealed the basic locations of its many length-conserved and length-variable regions. In recent years, many more sequences of 18S rDNA with unusual lengths have been documented in GenBank. These data make it possible to recognize the diversity of the secondary and tertiary structures of 18S rRNAs and to identify the length-conserved parts of 18S rDNAs. The longest 18S rDNA sequences of almost every known eukaryotic phylum were included in this study. We illustrated the bioinformatics-based structure to show that, the regions that are more length-variable, regions that are less length-variable, the splicing sites for introns, and the sites of A-minor interactions are mostly distributed in different parts of the 18S rRNA. Additionally, this study revealed that some length-variable regions or insertion positions could be quite close to the functional part of the 18S rRNA of Foraminifera organisms. The tertiary structure as well as the secondary structure of 18S rRNA can be more diverse than what was previously supposed. Besides revealing how this interesting gene evolves, it can help to remove ambiguity from the alignment of eukaryotic 18S rDNAs and to improve the performance of 18S rDNA in phylogenetic reconstruction. Six nucleotides shared by Archaea and Eukaryota but rarely by Bacteria are also reported here for the first time, which might further support the supposed origin of eukaryote from archaeans.

  8. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

    Science.gov (United States)

    Hugerth, Luisa W; Muller, Emilie E L; Hu, Yue O O; Lebrun, Laura A M; Roume, Hugo; Lundin, Daniel; Wilmes, Paul; Andersson, Anders F

    2014-01-01

    High-throughput sequencing of ribosomal RNA gene (rDNA) amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level). The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems.

  9. Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

    Directory of Open Access Journals (Sweden)

    Luisa W Hugerth

    Full Text Available High-throughput sequencing of ribosomal RNA gene (rDNA amplicons has opened up the door to large-scale comparative studies of microbial community structures. The short reads currently produced by massively parallel sequencing technologies make the choice of sequencing region crucial for accurate phylogenetic assignments. While for 16S rDNA, relevant regions have been well described, no truly systematic design of 18S rDNA primers aimed at resolving eukaryotic diversity has yet been reported. Here we used 31,862 18S rDNA sequences to design a set of broad-taxonomic range degenerate PCR primers. We simulated the phylogenetic information that each candidate primer pair would retrieve using paired- or single-end reads of various lengths, representing different sequencing technologies. Primer pairs targeting the V4 region performed best, allowing discrimination with paired-end reads as short as 150 bp (with 75% accuracy at genus level. The conditions for PCR amplification were optimised for one of these primer pairs and this was used to amplify 18S rDNA sequences from isolates as well as from a range of environmental samples which were then Illumina sequenced and analysed, revealing good concordance between expected and observed results. In summary, the reported primer sets will allow minimally biased assessment of eukaryotic diversity in different microbial ecosystems.

  10. Metatranscriptomics reveals the diversity of genes expressed by eukaryotes in forest soils.

    Directory of Open Access Journals (Sweden)

    Coralie Damon

    Full Text Available Eukaryotic organisms play essential roles in the biology and fertility of soils. For example the micro and mesofauna contribute to the fragmentation and homogenization of plant organic matter, while its hydrolysis is primarily performed by the fungi. To get a global picture of the activities carried out by soil eukaryotes we sequenced 2×10,000 cDNAs synthesized from polyadenylated mRNA directly extracted from soils sampled in beech (Fagus sylvatica and spruce (Picea abies forests. Taxonomic affiliation of both cDNAs and 18S rRNA sequences showed a dominance of sequences from fungi (up to 60% and metazoans while protists represented less than 12% of the 18S rRNA sequences. Sixty percent of cDNA sequences from beech forest soil and 52% from spruce forest soil had no homologs in the GenBank/EMBL/DDJB protein database. A Gene Ontology term was attributed to 39% and 31.5% of the spruce and beech soil sequences respectively. Altogether 2076 sequences were putative homologs to different enzyme classes participating to 129 KEGG pathways among which several were implicated in the utilisation of soil nutrients such as nitrogen (ammonium, amino acids, oligopeptides, sugars, phosphates and sulfate. Specific annotation of plant cell wall degrading enzymes identified enzymes active on major polymers (cellulose, hemicelluloses, pectin, lignin and glycoside hydrolases represented 0.5% (beech soil-0.8% (spruce soil of the cDNAs. Other sequences coding enzymes active on organic matter (extracellular proteases, lipases, a phytase, P450 monooxygenases were identified, thus underlining the biotechnological potential of eukaryotic metatranscriptomes. The phylogenetic affiliation of 12 full-length carbohydrate active enzymes showed that most of them were distantly related to sequences from known fungi. For example, a putative GH45 endocellulase was closely associated to molluscan sequences, while a GH7 cellobiohydrolase was closest to crustacean sequences, thus

  11. Autochthonous "Bjelovars dried cheese"

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    Slavko Kirin

    2006-12-01

    Full Text Available «Dried cheese» is in autochthonous group of Bjelovar region cheeses which is still produced in rural domestic scale. The name of cheese originates from production procedure - drying for longer or shorter period in airy place after which the cheese is smoked, or is smoked only without drying. This type of cheese is produced in whole central region of Croatia which includes Međimurje, Podravina, Bilogora; Moslavina, Posavina and region around the capital. The aim of this paper is to describe and determine sensory, chemical and microbiological composition to determine its characteristics and production standards. As standards for sensory properties following characteristics can be used: a Outer shape: dimensions: diameter: 140-145 mm, height: 58-61 mm, mass: 700-750 g, equal, rounded shape, smooth skin, equal colour; b Consistency: easily cut, elastic, soft; c Cut: nicely combined white body, few improper holes of equal size; d Odour: pleasant milky acid odour, fairly smoky; e Taste: Fairly milky acidic taste, medium salty, fairly smoky taste. Depending on fat in dry matter content and water content in non fat dry matter, analyzed samples can be characterized as quarter fat, soft and semidry cheese. Higher acidity and saltiness was determined in some samples, microbiological analyses has shown that the most common contaminants are yeasts and moulds.

  12. Early evolution of eukaryote feeding modes, cell structural diversity, and classification of the protozoan phyla Loukozoa, Sulcozoa, and Choanozoa.

    Science.gov (United States)

    Cavalier-Smith, Thomas

    2013-05-01

    I discuss how different feeding modes and related cellular structures map onto the eukaryote evolutionary tree. Centrally important for understanding eukaryotic cell diversity are Loukozoa: ancestrally biciliate phagotrophic protozoa possessing a posterior cilium and ventral feeding groove into which ciliary currents direct prey. I revise their classification by including all anaerobic Metamonada as a subphylum and adding Tsukubamonas. Loukozoa, often with ciliary vanes, are probably ancestral to all protozoan phyla except Euglenozoa and Percolozoa and indirectly to kingdoms Animalia, Fungi, Plantae, and Chromista. I make a new protozoan phylum Sulcozoa comprising subphyla Apusozoa (Apusomonadida, Breviatea) and Varisulca (Diphyllatea; Planomonadida, Discocelida, Mantamonadida; Rigifilida). Understanding sulcozoan evolution clarifies the origins from them of opisthokonts (animals, fungi, Choanozoa) and Amoebozoa, and their evolutionary novelties; Sulcozoa and their descendants (collectively called podiates) arguably arose from Loukozoa by evolving posterior ciliary gliding and pseudopodia in their ventral groove. I explain subsequent independent cytoskeletal modifications, accompanying further shifts in feeding mode, that generated Amoebozoa, Choanozoa, and fungi. I revise classifications of Choanozoa, Conosa (Amoebozoa), and basal fungal phylum Archemycota. I use Choanozoa, Sulcozoa, Loukozoa, and Archemycota to emphasize the need for simply classifying ancestral (paraphyletic) groups and illustrate advantages of this for understanding step-wise phylogenetic advances.

  13. Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

    Science.gov (United States)

    Cooper, Edwin L.; Overstreet, Nicola

    2014-03-01

    Recent evidence supports that prokaryotes exhibit adaptive immunity in the form of CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) and Cas (CRISPR associated proteins). The CRISPR-Cas system confers resistance to exogenous genetic elements such as phages and plasmids by allowing for the recognition and silencing of these genetic elements. Moreover, CRISPR-Cas serves as a memory of past exposures. This suggests that the evolution of the immune system has counterparts among the prokaryotes, not exclusively among eukaryotes. Mathematical models have been proposed which simulate the evolutionary patterns of CRISPR, however large gaps in our understanding of CRISPR-Cas function and evolution still exist. The CRISPR-Cas system is analogous to small RNAs involved in resistance mechanisms throughout the tree of life, and a deeper understanding of the evolution of small RNA pathways is necessary before the relationship between these convergent systems is to be determined. Presented in this review are novel RNAi therapies based on CRISPR-Cas analogs and the potential for future therapies based on CRISPR-Cas system components.

  14. High-throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil-drilling activities.

    Science.gov (United States)

    Lanzén, Anders; Lekang, Katrine; Jonassen, Inge; Thompson, Eric M; Troedsson, Christofer

    2016-09-01

    As global exploitation of available resources increases, operations extend towards sensitive and previously protected ecosystems. It is important to monitor such areas in order to detect, understand and remediate environmental responses to stressors. The natural heterogeneity and complexity of communities means that accurate monitoring requires high resolution, both temporally and spatially, as well as more complete assessments of taxa. Increased resolution and taxonomic coverage is economically challenging using current microscopy-based monitoring practices. Alternatively, DNA sequencing-based methods have been suggested for cost-efficient monitoring, offering additional insights into ecosystem function and disturbance. Here, we applied DNA metabarcoding of eukaryotic communities in marine sediments, in areas of offshore drilling on the Norwegian continental shelf. Forty-five samples, collected from seven drilling sites in the Troll/Oseberg region, were assessed, using the small subunit ribosomal RNA gene as a taxonomic marker. In agreement with results based on classical morphology-based monitoring, we were able to identify changes in sediment communities surrounding oil platforms. In addition to overall changes in community structure, we identified several potential indicator taxa, responding to pollutants associated with drilling fluids. These included the metazoan orders Macrodasyida, Macrostomida and Ceriantharia, as well as several ciliates and other protist taxa, typically not targeted by environmental monitoring programmes. Analysis of a co-occurrence network to study the distribution of taxa across samples provided a framework for better understanding the impact of anthropogenic activities on the benthic food web, generating novel, testable hypotheses of trophic interactions structuring benthic communities.

  15. Size-fractionated diversity of eukaryotic microbial communities in the Eastern Tropical North Pacific oxygen minimum zone.

    Science.gov (United States)

    Duret, Manon T; Pachiadaki, Maria G; Stewart, Frank J; Sarode, Neha; Christaki, Urania; Monchy, Sébastien; Srivastava, Ankita; Edgcomb, Virginia P

    2015-05-01

    Oxygen minimum zones (OMZs) caused by water column stratification appear to expand in parts of the world's ocean, with consequences for marine biogeochemical cycles. OMZ formation is often fueled by high surface primary production, and sinking organic particles can be hotspots of interactions and activity within microbial communities. This study investigated the diversity of OMZ protist communities in two biomass size fractions (>30 and 30-1.6 μm filters) from the world's largest permanent OMZ in the Eastern Tropical North Pacific. Diversity was quantified via Illumina MiSeq sequencing of V4 region of 18S SSU rRNA genes in samples spanning oxygen gradients at two stations. Alveolata and Rhizaria dominated the two size fractions at both sites along the oxygen gradient. Community composition at finer taxonomic levels was partially shaped by oxygen concentration, as communities associated with versus anoxic waters shared only ∼32% of operational taxonomic unit (OTU) (97% sequence identity) composition. Overall, only 9.7% of total OTUs were recovered at both stations and under all oxygen conditions sampled, implying structuring of the eukaryotic community in this area. Size-fractionated communities exhibited different taxonomical features (e.g. Syndiniales Group I in the 1.6-30 μm fraction) that could be explained by the microniches created on the surface-originated sinking particles.

  16. Study of genetic diversity of eukaryotic picoplankton in different oceanic regions by small-subunit rRNA gene cloning and sequencing.

    Science.gov (United States)

    Díez, B; Pedrós-Alió, C; Massana, R

    2001-07-01

    Very small eukaryotic organisms (picoeukaryotes) are fundamental components of marine planktonic systems, often accounting for a significant fraction of the biomass and activity in a system. Their identity, however, has remained elusive, since the small cells lack morphological features for identification. We determined the diversity of marine picoeukaryotes by sequencing cloned 18S rRNA genes in five genetic libraries from North Atlantic, Southern Ocean, and Mediterranean Sea surface waters. Picoplankton were obtained by filter size fractionation, a step that excluded most large eukaryotes and recovered most picoeukaryotes. Genetic libraries of eukaryotic ribosomal DNA were screened by restriction fragment length polymorphism analysis, and at least one clone of each operational taxonomic unit (OTU) was partially sequenced. In general, the phylogenetic diversity in each library was rather great, and each library included many different OTUs and members of very distantly related phylogenetic groups. Of 225 eukaryotic clones, 126 were affiliated with algal classes, especially the Prasinophyceae, the Prymnesiophyceae, the Bacillariophyceae, and the Dinophyceae. A minor fraction (27 clones) was affiliated with clearly heterotrophic organisms, such as ciliates, the chrysomonad Paraphysomonas, cercomonads, and fungi. There were two relatively abundant novel lineages, novel stramenopiles (53 clones) and novel alveolates (19 clones). These lineages are very different from any organism that has been isolated, suggesting that there are previously unknown picoeukaryotes. Prasinophytes and novel stramenopile clones were very abundant in all of the libraries analyzed. These findings underscore the importance of attempts to grow the small eukaryotic plankton in pure culture.

  17. MOLECULAR IDENTIFICATION AND GENOTYPING OF CIAUSCOLO AUTOCHTHONOUS MICROFLORA: PRELIMINARY STUDY

    Directory of Open Access Journals (Sweden)

    A. Petruzzelli

    2011-01-01

    Full Text Available The present study reports the results of a preliminary characterization of the bacterial population of Ciauscolo, a typical Italian fermented sausage, traditionally manufactured in Marche region. The bacterial community involved in Ciauscolo fermentation was investigated using both molecular and culturebased methods. The estimation of genotypic intra-species variation of the autochthonous bacteria isolated was also evaluated by using randomly amplified polymorphic DNA (RAPD analysis and unweighted pairgroup method with arithmetic averages (UPGMA cluster analysis. Our findings revealed an high diversity of the autochthonous bacterial population investigated, both at species and strain level.

  18. Metabolic Engineering of Eukaryotic Microalgae: Potential and Challenges come with great diversity

    Directory of Open Access Journals (Sweden)

    Javier A Gimpel

    2015-12-01

    Full Text Available The great phylogenetic diversity of microalgae is corresponded by a wide arrange of interesting and useful metabolites. Nonetheless metabolic engineering in microalgae has been limited, since specific transformation tools must be developed for each species for either the nuclear or chloroplast genomes. Microalgae as production platforms for metabolites offer several advantages over plants and other microorganisms, like the ability of GMO containment and reduced costs in culture media, respectively. Currently, microalgae have proved particularly well suited for the commercial production of omega-3 fatty acids and carotenoids. Therefore most metabolic engineering strategies have been developed for these metabolites. Microalgal biofuels have also drawn great attention recently, resulting in efforts for improving the production of hydrogen and photosynthates, particularly triacylglycerides. Metabolic pathways of microalgae have also been manipulated in order to improve photosynthetic growth under specific conditions and for achieving trophic conversion. Although these pathways are not strictly related to secondary metabolites, the synthetic biology approaches could potentially be translated to this field and will also be discussed.

  19. In Metabolic Engineering of Eukaryotic Microalgae: Potential and Challenges Come with Great Diversity

    Science.gov (United States)

    Gimpel, Javier A.; Henríquez, Vitalia; Mayfield, Stephen P.

    2015-01-01

    The great phylogenetic diversity of microalgae is corresponded by a wide arrange of interesting and useful metabolites. Nonetheless metabolic engineering in microalgae has been limited, since specific transformation tools must be developed for each species for either the nuclear or chloroplast genomes. Microalgae as production platforms for metabolites offer several advantages over plants and other microorganisms, like the ability of GMO containment and reduced costs in culture media, respectively. Currently, microalgae have proved particularly well suited for the commercial production of omega-3 fatty acids and carotenoids. Therefore most metabolic engineering strategies have been developed for these metabolites. Microalgal biofuels have also drawn great attention recently, resulting in efforts for improving the production of hydrogen and photosynthates, particularly triacylglycerides. Metabolic pathways of microalgae have also been manipulated in order to improve photosynthetic growth under specific conditions and for achieving trophic conversion. Although these pathways are not strictly related to secondary metabolites, the synthetic biology approaches could potentially be translated to this field and will also be discussed. PMID:26696985

  20. Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins.

    Science.gov (United States)

    Ruvinsky, Anatoly M; Vakser, Ilya A; Rivera, Mario

    2014-03-21

    diversity in mechanisms of iron traffic suggested by experimental approaches.

  1. Local packing modulates diversity of iron pathways and cooperative behavior in eukaryotic and prokaryotic ferritins

    Energy Technology Data Exchange (ETDEWEB)

    Ruvinsky, Anatoly M., E-mail: anatoly.ruvinsky@astrazeneca.com [Infection Innovative Medicine, AstraZeneca R and D Boston, 35 Gatehouse Drive, Waltham, Massachusetts 02451 (United States); Center for Bioinformatics, The University of Kansas, Lawrence, Kansas 66047 (United States); Vakser, Ilya A. [Center for Bioinformatics, The University of Kansas, Lawrence, Kansas 66047 (United States); Department of Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66047 (United States); Rivera, Mario [Department of Chemistry, The University of Kansas, Lawrence, Kansas 66047 (United States)

    2014-03-21

    diversity in mechanisms of iron traffic suggested by experimental approaches.

  2. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.

    Science.gov (United States)

    Shi, Xiao Li; Lepère, Cécile; Scanlan, David J; Vaulot, Daniel

    2011-04-28

    The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX), which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

  3. Plastid 16S rRNA gene diversity among eukaryotic picophytoplankton sorted by flow cytometry from the South Pacific Ocean.

    Directory of Open Access Journals (Sweden)

    Xiao Li Shi

    Full Text Available The genetic diversity of photosynthetic picoeukaryotes was investigated in the South East Pacific Ocean. Genetic libraries of the plastid 16S rRNA gene were constructed on picoeukaryote populations sorted by flow cytometry, using two different primer sets, OXY107F/OXY1313R commonly used to amplify oxygenic organisms, and PLA491F/OXY1313R, biased towards plastids of marine algae. Surprisingly, the two sets revealed quite different photosynthetic picoeukaryote diversity patterns, which were moreover different from what we previously reported using the 18S rRNA nuclear gene as a marker. The first 16S primer set revealed many sequences related to Pelagophyceae and Dictyochophyceae, the second 16S primer set was heavily biased toward Prymnesiophyceae, while 18S sequences were dominated by Prasinophyceae, Chrysophyceae and Haptophyta. Primer mismatches with major algal lineages is probably one reason behind this discrepancy. However, other reasons, such as DNA accessibility or gene copy numbers, may be also critical. Based on plastid 16S rRNA gene sequences, the structure of photosynthetic picoeukaryotes varied along the BIOSOPE transect vertically and horizontally. In oligotrophic regions, Pelagophyceae, Chrysophyceae, and Prymnesiophyceae dominated. Pelagophyceae were prevalent at the DCM depth and Chrysophyceae at the surface. In mesotrophic regions Pelagophyceae were still important but Chlorophyta contribution increased. Phylogenetic analysis revealed a new clade of Prasinophyceae (clade 16S-IX, which seems to be restricted to hyper-oligotrophic stations. Our data suggest that a single gene marker, even as widely used as 18S rRNA, provides a biased view of eukaryotic communities and that the use of several markers is necessary to obtain a complete image.

  4. Comparative genomic analysis reveals a diverse repertoire of genes involved in prokaryote-eukaryote interactions within the Pseudovibrio genus.

    Directory of Open Access Journals (Sweden)

    Stefano eRomano

    2016-03-01

    Full Text Available Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage.Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus.Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche

  5. Diversity and vertical distribution of microbial eukaryotes in the snow, sea ice and seawater near the North Pole at the end of the polar night

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    Charles eBachy

    2011-05-01

    Full Text Available Our knowledge about the microorganisms living in the high Arctic Ocean is still rudimentary compared to other oceans mostly because of logistical challenges imposed by its inhospitable climate and the presence of a multi-year ice cap. We have used 18S rRNA gene libraries to study the diversity of microbial eukaryotes in the upper part of the water column (0-170 m depth, the sea ice (0-1.5 m depth and the overlying snow from samples collected in the vicinity of the North Pole (N88°35', E015°59 at the very end of the long polar night. We detected very diverse eukaryotes belonging to Alveolata, Fungi, Amoebozoa, Viridiplantae, Metazoa, Rhizaria, Heterokonta and Telonemia. Different alveolates (dinoflagellates and Marine Alveolate Groups I and II species were the most abundant and diverse in gene libraries from water and sea ice, representing 80% of the total number of clones and Operational Taxonomic Units (OTUs. Only contaminants and/or species from continental ecosystems were detected in snow, suggesting wind- and animal- or human-mediated cosmopolitan dispersal of some taxa. By contrast, sea ice and seawater samples harbored a larger and more similar inter-sample protist diversity as compared with snow. The North Pole was found to harbor distinctive eukaryotic communities along the vertical gradient with an unparalleled diversity of core dinoflagellates, largely dominant in libraries from the water column, as compared to other oceanic locations. In contrast, phototrophic organisms typical of Arctic sea ice and plankton, such as diatoms and prasinophytes, were very rare in our samples. This was most likely due to a decrease of their populations after several months of polar night darkness and to the presence of rich populations of diverse grazers. Whereas strict phototrophs were scarce, we identified a variety of likely mixotrophic taxa, which supports the idea that mixotrophy may be important for the survival of diverse protists through the

  6. A survey of PPR proteins identifies DYW domains like those of land plant RNA editing factors in diverse eukaryotes.

    Science.gov (United States)

    Schallenberg-Rüdinger, Mareike; Lenz, Henning; Polsakiewicz, Monika; Gott, Jonatha M; Knoop, Volker

    2013-01-01

    The pentatricopeptide repeat modules of PPR proteins are key to their sequence-specific binding to RNAs. Gene families encoding PPR proteins are greatly expanded in land plants where hundreds of them participate in RNA maturation, mainly in mitochondria and chloroplasts. Many plant PPR proteins contain additional carboxyterminal domains and have been identified as essential factors for specific events of C-to-U RNA editing, which is abundant in the two endosymbiotic plant organelles. Among those carboxyterminal domain additions to plant PPR proteins, the so-called DYW domain is particularly interesting given its similarity to cytidine deaminases. The frequency of organelle C-to-U RNA editing and the diversity of DYW-type PPR proteins correlate well in plants and both were recently identified outside of land plants, in the protist Naegleria gruberi. Here we present a systematic survey of PPR protein genes and report on the identification of additional DYW-type PPR proteins in the protists Acanthamoeba castellanii, Malawimonas jakobiformis, and Physarum polycephalum. Moreover, DYW domains were also found in basal branches of multi-cellular lineages outside of land plants, including the alga Nitella flexilis and the rotifers Adineta ricciae and Philodina roseola. Intriguingly, the well-characterized and curious patterns of mitochondrial RNA editing in the slime mold Physarum also include examples of C-to-U changes. Finally, we identify candidate sites for mitochondrial RNA editing in Malawimonas, further supporting a link between DYW-type PPR proteins and C-to-U editing, which may have remained hitherto unnoticed in additional eukaryote lineages.

  7. Characterization of Bacterial, Archaeal and Eukaryote Symbionts from Antarctic Sponges Reveals a High Diversity at a Three-Domain Level and a Particular Signature for This Ecosystem

    Science.gov (United States)

    Rodríguez-Marconi, Susana; De la Iglesia, Rodrigo; Díez, Beatriz; Fonseca, Cássio A.; Hajdu, Eduardo; Trefault, Nicole

    2015-01-01

    Sponge-associated microbial communities include members from the three domains of life. In the case of bacteria, they are diverse, host specific and different from the surrounding seawater. However, little is known about the diversity and specificity of Eukarya and Archaea living in association with marine sponges. This knowledge gap is even greater regarding sponges from regions other than temperate and tropical environments. In Antarctica, marine sponges are abundant and important members of the benthos, structuring the Antarctic marine ecosystem. In this study, we used high throughput ribosomal gene sequencing to investigate the three-domain diversity and community composition from eight different Antarctic sponges. Taxonomic identification reveals that they belong to families Acarnidae, Chalinidae, Hymedesmiidae, Hymeniacidonidae, Leucettidae, Microcionidae, and Myxillidae. Our study indicates that there are different diversity and similarity patterns between bacterial/archaeal and eukaryote microbial symbionts from these Antarctic marine sponges, indicating inherent differences in how organisms from different domains establish symbiotic relationships. In general, when considering diversity indices and number of phyla detected, sponge-associated communities are more diverse than the planktonic communities. We conclude that three-domain microbial communities from Antarctic sponges are different from surrounding planktonic communities, expanding previous observations for Bacteria and including the Antarctic environment. Furthermore, we reveal differences in the composition of the sponge associated bacterial assemblages between Antarctic and tropical-temperate environments and the presence of a highly complex microbial eukaryote community, suggesting a particular signature for Antarctic sponges, different to that reported from other ecosystems. PMID:26421612

  8. Autochthonous Hepatitis E Virus Infection in Europe: A Matter of Concern for Public Health?

    OpenAIRE

    Echevarría, José-Manuel

    2014-01-01

    Human hepatitis E virus (HHEV) is the proposed name for a diverse group of RNA viruses from the family Hepeviridae that cause acute hepatitis among humans. Waterborne strains are regularly imported into Europe by international travelers, and virus transmission of zoonotic strains via contaminated aliments is involved in autochthonous cases. Therefore, in Europe, hepatitis E displays a unique dual character, having features of both imported and autochthonous infections. Environmental involveme...

  9. Eukaryotic community diversity and spatial variation during drinking water production (by seawater desalination) and distribution in a full-scale network

    KAUST Repository

    Belila, Abdelaziz

    2016-12-01

    Eukaryotic microorganisms are naturally present in many water resources and can enter, grow and colonize water treatment and transport systems, including reservoirs, pipes and premise plumbing. In this study, we explored the eukaryotic microbial community structure in water during the (i) production of drinking water in a seawater desalination plant and (ii) transport of the drinking water in the distribution network. The desalination plant treatment involved pre-treatment (e.g. spruce filters), reverse osmosis (RO) membrane filtration and post-treatment steps (e.g. remineralization). 454 pyrosequencing analysis of the 18S rRNA gene revealed a highly diverse (35 phyla) and spatially variable eukaryotic community during water treatment and distribution. The desalination plant feed water contained a typical marine picoeukaryotic community dominated by Stramenopiles, Alveolates and Porifera. In the desalination plant Ascomycota was the most dominant phylum (15.5% relative abundance), followed by Alveolata (11.9%), unclassified fungi clade (10.9%) and Porifera (10.7%). In the drinking water distribution network, an uncultured fungi phylum was the major group (44.0%), followed by Chordata (17.0%), Ascomycota (11.0%) and Arthropoda (8.0%). Fungi constituted 40% of the total eukaryotic community in the treatment plant and the distribution network and their taxonomic composition was dominated by an uncultured fungi clade (55%). Comparing the plant effluent to the network samples, 84 OTUs (2.1%) formed the core eukaryotic community while 35 (8.4%) and 299 (71.5%) constituted unique OTUs in the produced water at the plant and combined tap water samples from the network, respectively. RO membrane filtration treatment significantly changed the water eukaryotic community composition and structure, highlighting the fact that (i) RO produced water is not sterile and (ii) the microbial community in the final tap water is influenced by the downstream distribution system. The study

  10. [Autochthonous microbiota, probiotics and prebiotics].

    Science.gov (United States)

    Suárez, Juan Evaristo

    2015-02-07

    The autochthonous microbiota is the community of microorganisms that colonizes the skin and mucosal surfaces. The symbiosis is, generally, mutualistic but it can become parasitic due to immune response alterations. The skin microbiota includes bacteria (95%), lipophilic fungi and mites. In the digestive apparatus, each cavity presents its own microbiota, which reaches its target organ during the perinatal period, originating complex and stable communities (homeostasis). The vaginal microbiota varies with the endocrine activity, significantly increasing during the fertile and pregnancy periods, when lactobacilli are the most abundant organisms. Four are the main benefits of the autochthonous microbiota: i) delivery of essential nutrients, such as vitamins and some amino acids; ii) utilization of undigestible diet components, the colonic microbiota degrades complex glycans and fulfils almost 20% of the calories present in a normal diet; iii) development of the immune system: the continuous contact with the immune system maintains it alert and in good shape to repel pathogens efficaciously and iv) microbial antagonism, hinders colonization of our mucosal surfaces by alochthonous, potentially pathogenic, organisms. This works through three mechanisms: colonization interference, production of antimicrobials and co-aggregation with the potential pathogens. The microbiota can, sporadically, produce damages: opportunistic endogenous infections and generation of carcinogenic compounds. Probiotics are "live microorganisms that when administered in adequate amounts, confer a health benefit to the consumer". Prebiotics are undigestible glycans that enhance the growth or activity of the intestinal microbiota, thus generating a health benefit. Synbiotics are mixes of probiotics and prebiotics that exert a synergistic health effect.

  11. Eukaryotic diversity in premise drinking water using 18S rDNA sequencing: implications for health risks

    Science.gov (United States)

    The goal of this study was to characterize microbial eukaryotes over a 12 month period, so as to provide insight into the occurrence of potentially important predators and bacterial hosts in hot and cold premise plumbing. Nearly 6,300 partial (600 bp) 18S rRNA gene sequences from...

  12. Diversity and distribution of eukaryotic microbes in and around a brine pool adjacent to the Thuwal cold seeps in the Red Sea

    KAUST Repository

    Wang, Yong

    2014-02-04

    A hypoxic/suboxic brine pool at a depth of about 850 m was discovered near the Thuwal cold seeps in the Red Sea. Filled with high concentrations of hydrogen sulfide and ammonia, such a brine pool might limit the spread of eukaryotic organisms. Here, we compared the communities of the eukaryotic microbes in a microbial mat, sediments and water samples distributed in 7 sites within and adjacent to the brine pool. Taxonomic classification of the pyrosequenced 18S rRNA amplicon reads showed that fungi highly similar to the species identified along the Arabic coast were almost ubiquitous in the water and sediment samples, supporting their wide distribution in various environments. The microbial mat displayed the highest species diversity and contained grazers and a considerable percentage of unclassified species. Phylogeny-based methods revealed novel lineages representing a majority of the reads from the interface between the sea water and brine pool. Phylogenetic relationships with more reference sequences suggest that the lineages were affiliated with novel Alveolata and Euglenozoa inhabiting the interface where chemosynthetic prokaryotes are highly proliferative due to the strong chemocline and halocline. The brine sediments harbored abundant species highly similar to invertebrate gregarine parasites identified in different oxygen-depleted sediments. Therefore, the present findings support the uniqueness of some microbial eukaryotic groups in this cold seep brine system. 2014 Wang, Zhang, Cao, Shek, Tian, Wong, Batang, Al-suwailem and Qian.

  13. Autochthonous cheeses of Bosnia and Herzegovina

    OpenAIRE

    Zlatan Sarić; Sonja Bijeljac

    2003-01-01

    Despite the migration of people towards cities, autochthonous cheeses in Bosnia and Herzegovina survived. Technologies of these cheeses are simple and adapted to humble mountain limitations. Geographical occasions and rich mountain pastures created a certain participation of ewe's milk cheeses. Communicative isolation of hilly-mountain regions resulted in "closed" cheese production in small households. Autochthonous cheeses in Bosnia and Herzegovina have various origins. Different cheeses are...

  14. Depth matters: Microbial eukaryote diversity and community structure in the eastern North Pacific revealed through environmental gene libraries

    Science.gov (United States)

    Schnetzer, Astrid; Moorthi, Stefanie D.; Countway, Peter D.; Gast, Rebecca J.; Gilg, Ilana C.; Caron, David A.

    2011-01-01

    Protistan community structure was examined from 6 depths (1.5, 20, 42, 150, 500, 880 m) at a coastal ocean site in the San Pedro Channel, California. A total of 856 partial length 18S rDNA protistan sequences from the six clone libraries were analyzed to characterize diversity present at each depth. The sequences were grouped into a total of 259 Operational Taxonomic Units (OTUs) that were inferred using an automated OTU calling program that formed OTUs with approximately species-level distinction (95% sequence similarity). Most OTUs (194 out of 259) were observed at only one specific depth, and only two were present in clone libraries from all depths. OTUs were obtained from 21 major protistan taxonomic groups determined by their closest BLAST matches to identified protists in the NCBI database. Approximately 74% of the detected OTUs belonged to the Chromalveolates, with Group II alveolates making up the largest single group. Protistan assemblages at euphotic depths (1.5, 20 and 42 m) were characterized by the presence of clades that contained phototrophic species (stramenopiles, chlorophytes and haptophytes) as well as consumers (especially ciliates). Assemblages in the lower water column (150, 500 and 800 m) were distinct from communities at shallow depths because of strong contributions from taxa belonging to euglenozoans, acantharians, polycystines and Taxopodida ( Sticholonche spp. and close relatives). Species richness (Chao I estimate) and diversity (Shannon index) were highest within the euphotic zone and at 150 m, and lowest for protistan assemblages located in the oxygen minimum zone (500 and 880 m). Multivariate analyses (Bray-Curtis coefficient) confirmed that protistan assemblage composition differed significantly when samples were grouped into shallow (≤150 m) and deep water assemblages (≥150 m).

  15. Investigating microbial eukaryotic diversity from a global census: insights from a comparison of pyrotag and full-length sequences of 18S rRNA genes.

    Science.gov (United States)

    Lie, Alle A Y; Liu, Zhenfeng; Hu, Sarah K; Jones, Adriane C; Kim, Diane Y; Countway, Peter D; Amaral-Zettler, Linda A; Cary, S Craig; Sherr, Evelyn B; Sherr, Barry F; Gast, Rebecca J; Caron, David A

    2014-07-01

    Next-generation DNA sequencing (NGS) approaches are rapidly surpassing Sanger sequencing for characterizing the diversity of natural microbial communities. Despite this rapid transition, few comparisons exist between Sanger sequences and the generally much shorter reads of NGS. Operational taxonomic units (OTUs) derived from full-length (Sanger sequencing) and pyrotag (454 sequencing of the V9 hypervariable region) sequences of 18S rRNA genes from 10 global samples were analyzed in order to compare the resulting protistan community structures and species richness. Pyrotag OTUs called at 98% sequence similarity yielded numbers of OTUs that were similar overall to those for full-length sequences when the latter were called at 97% similarity. Singleton OTUs strongly influenced estimates of species richness but not the higher-level taxonomic composition of the community. The pyrotag and full-length sequence data sets had slightly different taxonomic compositions of rhizarians, stramenopiles, cryptophytes, and haptophytes, but the two data sets had similarly high compositions of alveolates. Pyrotag-based OTUs were often derived from sequences that mapped to multiple full-length OTUs at 100% similarity. Thus, pyrotags sequenced from a single hypervariable region might not be appropriate for establishing protistan species-level OTUs. However, nonmetric multidimensional scaling plots constructed with the two data sets yielded similar clusters, indicating that beta diversity analysis results were similar for the Sanger and NGS sequences. Short pyrotag sequences can provide holistic assessments of protistan communities, although care must be taken in interpreting the results. The longer reads (>500 bp) that are now becoming available through NGS should provide powerful tools for assessing the diversity of microbial eukaryotic assemblages.

  16. Assessment of fungal diversity in deep-sea sediments by multiple primer approach

    Digital Repository Service at National Institute of Oceanography (India)

    Singh, P; Raghukumar, C.; Verma, P; Shouche, Y.

    -II): sequences and tools for high-throughput rRNA analysis. Nucleic Acids Res 33: D294–D296 11 Connell L, Barrett A, Templeton A, Staudigel H (2009) Fungal diversity associated with an active deep- sea volcano: Vailulu’u Seamount, Samoa. Geomicrobiology J 26..., Philippe H, Gail F, Moreira D (2003) Autochthonous eukaryotic diversity in hydrothermal sediment and experimental microcolonizers at the mid-Atlantic Ridge. Proc Natl Acad Sci USA 2:697-702 López-García P, Rodriguez-Valera F, Pedros-Alio C, Moreira D...

  17. Autochthonous cheeses of Bosnia and Herzegovina

    Directory of Open Access Journals (Sweden)

    Zlatan Sarić

    2003-04-01

    Full Text Available Despite the migration of people towards cities, autochthonous cheeses in Bosnia and Herzegovina survived. Technologies of these cheeses are simple and adapted to humble mountain limitations. Geographical occasions and rich mountain pastures created a certain participation of ewe's milk cheeses. Communicative isolation of hilly-mountain regions resulted in "closed" cheese production in small households. Autochthonous cheeses in Bosnia and Herzegovina have various origins. Different cheeses are produced in different parts of Bosnia and Herzegovina. There are : Travnički cheese, Masni (fat cheese, Presukača, Sirac, Livanjski cheese, Posni (lean cheese, "Suvi" (dry cheese or "Mješinski" full fat cheese matured in sheepskin bag, fresh sour milk cheese "Kiseli" and dried sour milk cheese "Kiseli", Zajednica, Basa, Kalenderovački cheese and goat's milk cheeses (Hard and White soft goat's milk cheese, "Zarica" and Urda. Besides above-mentioned types of cheese in Bosnia and Herzegovina some other autochthonous dairy products are produced: Kajmak (Cream, Maslo (Rendered butter and Zimsko kiselo mlijeko (Winter sour milk. The specificity in Bosnia and Herzegovina is that autochthonous dairy products are still mainly both produced and consumed in small rural households. Exceptions are Travnički cheese and Kajmak that are significantly sold at market. Only Livanjski cheese is manufactured as industry dairy product.

  18. Autochthonous Linguistic Minorities in the Italian Alps:

    Directory of Open Access Journals (Sweden)

    Ernst Steinicke

    2011-08-01

    Full Text Available More than any other area in Western Europe, the Alps, especially the Italian Alps, are home to great ethno-cultural diversity: there, no less than seven autochthonous linguistic minorities coexist side by side with the respective official majority. Now being considered an important cultural heritage by the state as well as by the regions, new legislation offers protection to all ‘linguistic-historic minorities’ in Italy. Our study shows, however, that it is quite difficult to maintain such groups, since it is largely unknown where exactly the minority areas are situated. Based on that, local actor groups in various communities take advantage of this lack of knowledge and declare themselves minority territories although they show no linguistic varieties. An important objective of this project is therefore to present a cartographic representation of this linguistic diversity. Subsequently, the contribution discusses case studies of distinct ethno-linguistic self-awareness. Even though with Law No. 482 a first important step was taken to preserve the linguistic minorities, their progressive decline by territorial and numerical criteria cannot be denied. Today, besides unfavorable bio-demographic factors and “diffuse ethnicity,” other causes are current demographic processes. In this framework the amenity migrants, those new immigrants who have discovered the mountains as a new, desirable settlement space, play a decisive role by reinforcing the assimilation process.Les Alpes, plus précisément les Alpes italiennes, plus que toute autre région d'Europe Occidentale, sont un lieu de grande diversité ethnoculturelle : pas moins de sept minorités linguistiques autochtones y coexistent, côte à côte avec la majorité officielle correspondante. Maintenant considérées comme un héritage culturel important par les états ainsi que par les régions, une nouvelle législation offre une protection à toutes les « minorités linguistiques

  19. Genetic characterization of autochthonous grapevine cultivars from Eastern Turkey by simple sequence repeats (SSRs

    Directory of Open Access Journals (Sweden)

    Sadiye Peral Eyduran

    2016-01-01

    Full Text Available In this research, two well-recognized standard grape cultivars, Cabernet Sauvignon and Merlot, together with eight historical autochthonous grapevine cultivars from Eastern Anatolia in Turkey, were genetically characterized by using 12 pairs of simple sequence repeat (SSR primers in order to evaluate their genetic diversity and relatedness. All of the used SSR primers produced successful amplifications and revealed DNA polymorphisms, which were subsequently utilized to evaluate the genetic relatedness of the grapevine cultivars. Allele richness was implied by the identification of 69 alleles in 8 autochthonous cultivars with a mean value of 5.75 alleles per locus. The average expected heterozygosity and observed heterozygosity were found to be 0.749 and 0.739, respectively. Taking into account the generated alleles, the highest number was recorded in VVC2C3 and VVS2 loci (nine and eight alleles per locus, respectively, whereas the lowest number was recorded in VrZAG83 (three alleles per locus. Two main clusters were produced by using the unweighted pair-group method with arithmetic mean dendrogram constructed on the basis of the SSR data. Only Cabernet Sauvignon and Merlot cultivars were included in the first cluster. The second cluster involved the rest of the autochthonous cultivars. The results obtained during the study illustrated clearly that SSR markers have verified to be an effective tool for fingerprinting grapevine cultivars and carrying out grapevine biodiversity studies. The obtained data are also meaningful references for grapevine domestication.

  20. Autochthonous clams monitoring of Ganzirri Lake (Sicily).

    Science.gov (United States)

    Di Bella, Giuseppa; Cavallaro, Novella; Lo Turco, Vincenzo; Furci, Patrizia; Rando, Rossana; La Pera, Lara; Dugo, Giacomo

    2010-12-01

    Two autochthonous clams, Venerupis aurea laeta and Cerastoderma edule/glaucum, collected for a period of 1 year, from May 2007 to January 2008, were studied in the Cape Peloro lagoon. On the samples, it was evaluated the presence of pathogenic microorganisms and proteins, lipids and yield edible part were determined. It was evaluated the concentration of mineral elements (Cd, Cu, Mn, Se, Pb, Zn) and organic contaminants (∑DDT and PCBs). Salmonella is never present in any sample. Total and faecal coliform values have always been under law limits for alive bivalves mussels production and sale. Zn, Cu, Cd and Pb levels were found in clams where they are slightly lower too. Both species do not show significant changes for Mn and Se. DDT and PCBs traces were discovered in Ganzirri Lake' samples, but in all observed cases, they were below law limits. As a result of all these observations, it is clear that, in recent years, the bivalve's use of Ganzirri Lake does not denote toxicological risk to human health.

  1. Eukaryotic DNA Replicases

    KAUST Repository

    Zaher, Manal S.

    2014-11-21

    The current model of the eukaryotic DNA replication fork includes three replicative DNA polymerases, polymerase α/primase complex (Pol α), polymerase δ (Pol δ), and polymerase ε (Pol ε). The primase synthesizes 8–12 nucleotide RNA primers that are extended by the DNA polymerization activity of Pol α into 30–35 nucleotide RNA-DNA primers. Replication factor C (RFC) opens the polymerase clamp-like processivity factor, proliferating cell nuclear antigen (PCNA), and loads it onto the primer-template. Pol δ utilizes PCNA to mediate highly processive DNA synthesis, while Pol ε has intrinsic high processivity that is modestly stimulated by PCNA. Pol ε replicates the leading strand and Pol δ replicates the lagging strand in a division of labor that is not strict. The three polymerases are comprised of multiple subunits and share unifying features in their large catalytic and B subunits. The remaining subunits are evolutionarily not related and perform diverse functions. The catalytic subunits are members of family B, which are distinguished by their larger sizes due to inserts in their N- and C-terminal regions. The sizes of these inserts vary among the three polymerases, and their functions remain largely unknown. Strikingly, the quaternary structures of Pol α, Pol δ, and Pol ε are arranged similarly. The catalytic subunits adopt a globular structure that is linked via its conserved C-terminal region to the B subunit. The remaining subunits are linked to the catalytic and B subunits in a highly flexible manner.

  2. Determination and inference of eukaryotic transcription factor sequence specificity.

    Science.gov (United States)

    Weirauch, Matthew T; Yang, Ally; Albu, Mihai; Cote, Atina G; Montenegro-Montero, Alejandro; Drewe, Philipp; Najafabadi, Hamed S; Lambert, Samuel A; Mann, Ishminder; Cook, Kate; Zheng, Hong; Goity, Alejandra; van Bakel, Harm; Lozano, Jean-Claude; Galli, Mary; Lewsey, Mathew G; Huang, Eryong; Mukherjee, Tuhin; Chen, Xiaoting; Reece-Hoyes, John S; Govindarajan, Sridhar; Shaulsky, Gad; Walhout, Albertha J M; Bouget, François-Yves; Ratsch, Gunnar; Larrondo, Luis F; Ecker, Joseph R; Hughes, Timothy R

    2014-09-11

    Transcription factor (TF) DNA sequence preferences direct their regulatory activity, but are currently known for only ∼1% of eukaryotic TFs. Broadly sampling DNA-binding domain (DBD) types from multiple eukaryotic clades, we determined DNA sequence preferences for >1,000 TFs encompassing 54 different DBD classes from 131 diverse eukaryotes. We find that closely related DBDs almost always have very similar DNA sequence preferences, enabling inference of motifs for ∼34% of the ∼170,000 known or predicted eukaryotic TFs. Sequences matching both measured and inferred motifs are enriched in chromatin immunoprecipitation sequencing (ChIP-seq) peaks and upstream of transcription start sites in diverse eukaryotic lineages. SNPs defining expression quantitative trait loci in Arabidopsis promoters are also enriched for predicted TF binding sites. Importantly, our motif "library" can be used to identify specific TFs whose binding may be altered by human disease risk alleles. These data present a powerful resource for mapping transcriptional networks across eukaryotes.

  3. The eukaryotic fossil record in deep time

    Science.gov (United States)

    Butterfield, N.

    2011-12-01

    Eukaryotic organisms are defining constituents of the Phanerozoic biosphere, but they also extend well back into the Proterozoic record, primarily in the form of microscopic body fossils. Criteria for identifying pre-Ediacaran eukaryotes include large cell size, morphologically complex cell walls and/or the recognition of diagnostically eukaryotic cell division patterns. The oldest unambiguous eukaryote currently on record is an acanthomorphic acritarch (Tappania) from the Palaeoproterozoic Semri Group of central India. Older candidate eukaryotes are difficult to distinguish from giant bacteria, prokaryotic colonies or diagenetic artefacts. In younger Meso- and Neoproterozoic strata, the challenge is to recognize particular grades and clades of eukaryotes, and to document their macro-evolutionary expression. Distinctive unicellular forms include mid-Neoproterozoic testate amoebae and phosphate biomineralizing 'scale-microfossils' comparable to an extant green alga. There is also a significant record of seaweeds, possible fungi and problematica from this interval, documenting multiple independent experiments in eukaryotic multicellularity. Taxonomically resolved forms include a bangiacean red alga and probable vaucheriacean chromalveolate algae from the late Mesoproterozoic, and populations of hydrodictyacean and siphonocladalean green algae of mid Neoproterozoic age. Despite this phylogenetic breadth, however, or arguments from molecular clocks, there is no convincing evidence for pre-Ediacaran metazoans or metaphytes. The conspicuously incomplete nature of the Proterozoic record makes it difficult to resolve larger-scale ecological and evolutionary patterns. Even so, both body fossils and biomarker data point to a pre-Ediacaran biosphere dominated overwhelming by prokaryotes. Contemporaneous eukaryotes appear to be limited to conspicuously shallow water environments, and exhibit fundamentally lower levels of morphological diversity and evolutionary turnover than

  4. Microbial diversity and metabolic networks in acid mine drainage habitats

    Directory of Open Access Journals (Sweden)

    Celia eMendez-Garcia

    2015-05-01

    Full Text Available Acid mine drainage (AMD emplacements are low-complexity natural systems. Low-pH conditions appear to be the main factor underlying the limited diversity of the microbial populations thriving in these environments, although temperature, ionic composition, total organic carbon and dissolved oxygen are also considered to significantly influence their microbial life. This natural reduction in diversity driven by extreme conditions was reflected in several studies on the microbial populations inhabiting the various micro-environments present in such ecosystems. Early studies based on the physiology of the autochthonous microbiota and the growing success of omics technologies have enabled a better understanding of microbial ecology and function in low-pH mine outflows; however, complementary omics-derived data should be included to completely describe their microbial ecology. Furthermore, recent updates on the distribution of eukaryotes and ultra-micro-archaea demand their inclusion in the microbial characterisation of AMD systems. In this review, we present a complete overview of the bacterial, archaeal (including ultra-micro-archaeal and eukaryotic diversity in these ecosystems and include a thorough depiction of the metabolism and element cycling in AMD habitats. We also review different metabolic network structures at the organismal level, which is necessary to disentangle the role of each member of the AMD communities described thus far.

  5. Development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium

    Energy Technology Data Exchange (ETDEWEB)

    Teixeira, Catarina [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Almeida, C. Marisa R.; Nunes da Silva, Marta [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Bordalo, Adriano A. [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal); Laboratório de Hidrobiologia e Ecologia, Instituto de Ciências Biomédicas Abel Salazar (ICBAS), Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto (Portugal); Mucha, Ana P., E-mail: amucha@ciimar.up.pt [Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas, 289, 4050-123 Porto (Portugal)

    2014-09-15

    Microbial assisted phytoremediation is a promising, though yet poorly explored, new remediation technique. The aim of this study was to develop autochthonous microbial consortia resistant to cadmium that could enhance phytoremediation of salt-marsh sediments contaminated with this metal. The microbial consortia were selectively enriched from rhizosediments colonized by Juncus maritimus and Phragmites australis. The obtained consortia presented similar microbial abundance but a fairly different community structure, showing that the microbial community was a function of the sediment from which the consortia were enriched. The effect of the bioaugmentation with the developed consortia on cadmium uptake, and the microbial community structure associated to the different sediments were assessed using a microcosm experiment. Our results showed that the addition of the cadmium resistant microbial consortia increased J. maritimus metal phytostabilization capacity. On the other hand, in P. australis, microbial consortia amendment promoted metal phytoextraction. The addition of the consortia did not alter the bacterial structure present in the sediments at the end of the experiments. This study provides new evidences that the development of autochthonous microbial consortia for enhanced phytoremediation of salt-marsh sediments contaminated with cadmium might be a simple, efficient, and environmental friendly remediation procedure. Capsule abstract: Development of autochthonous microbial consortia resistant to cadmium that enhanced phytoremediation by salt-marsh plants, without a long term effect on sediment bacterial diversity. - Highlights: • Cd resistant microbial consortia were developed and applied to salt-marsh sediments. • In Phragmites australis the consortia amendment promoted metal phytoextraction. • The consortia addition increased Juncus maritimus phytostabilization capacity. • No long term changes on the rhizosediment bacterial structure were observed.

  6. Autophagy in unicellular eukaryotes

    NARCIS (Netherlands)

    Kiel, J.A.K.W.

    2010-01-01

    Cells need a constant supply of precursors to enable the production of macromolecules to sustain growth and survival. Unlike metazoans, unicellular eukaryotes depend exclusively on the extracellular medium for this supply. When environmental nutrients become depleted, existing cytoplasmic components

  7. Autochthonous and allochthonous contributions of organic carbon to microbial food webs in Svalbard fjords

    KAUST Repository

    Holding, Johnna M.

    2017-03-27

    Rising temperatures in the Arctic Ocean are causing sea ice and glaciers to melt at record breaking rates, which has consequences for carbon cycling in the Arctic Ocean that are yet to be fully understood. Microbial carbon cycling is driven by internal processing of in situ produced organic carbon (OC), however recent research suggests that melt water from sea ice and glaciers could introduce an allochthonous source of OC to the microbial food web with ramifications for the metabolic balance of plankton communities. In this study, we characterized autochthonous and allochthonous sources of OC to the Western Svalbard fjord system using stable isotopes of carbon. We quantified δ13C of eukaryotic and prokaryotic planktonic groups using polar lipid-derived fatty acids as biomarkers in addition to measuring δ13C of marine particulate OC and dissolved OC from glacial runoff. δ13C of bacteria (−22.5‰) was higher than that of glacial runoff OC (−28.5‰) and other phytoplankton groups (−24.7 to −29.1‰), which suggests that marine bacteria preferentially use a third source of OC. We present a Bayesian three-source δ13C mixing model whereby ∼ 60% of bacteria carbon is derived from OC in sea ice, and the remaining carbon is derived from autochthonous production and glacial-derived OC. These results suggest that subsidies of OC from melting glaciers will not likely influence microbial carbon cycling in Svalbard fjords in the future and that further research is needed to determine the effects of melting sea ice on microbial carbon cycling in fjord systems and elsewhere in the Arctic Ocean.

  8. Autochthonous Transmission of Trypanosoma Cruzi in Southern California

    Science.gov (United States)

    Hernandez, Salvador; Flores, Carmen A.; Viana, Gracia M.; Sanchez, Daniel R.; Traina, Mahmoud I.

    2016-01-01

    Trypanosoma cruzi usually infects humans via triatomine insects in Latin America. Vector-borne transmission in the United States is exceedingly rare. We describe (1) the first case of probable autochthonous transmission reported in California in more than 30 years and (2) the first ever reported case in the greater Los Angeles area. PMID:28018928

  9. Authenticity and autochthonous traditions in archaic and Hellenistic poetry

    NARCIS (Netherlands)

    Klooster, Julia

    2016-01-01

    J.J.H. Klooster, ‘Authenticity and autochthonous traditions in archaic and Hellenistic poetry’. In E. Bakker (ed): Authorship, Authority and Authenticity in Archaic and Classical Greek Song. Proceedings of the Network for the Study of Archaic and Classical Greek Song, Vol. 2, Leiden: Brill

  10. Reemergence and Autochthonous Transmission of Dengue Virus, Eastern China, 2014.

    Science.gov (United States)

    Wang, Wen; Yu, Bin; Lin, Xian-Dan; Kong, De-Guang; Wang, Jian; Tian, Jun-Hua; Li, Ming-Hui; Holmes, Edward C; Zhang, Yong-Zhen

    2015-09-01

    In 2014, 20 dengue cases were reported in the cities of Wenzhou (5 cases) and Wuhan (15 cases), China, where dengue has rarely been reported. Dengue virus 1 was detected in 4 patients. Although most of these cases were likely imported, epidemiologic analysis provided evidence for autochthonous transmission.

  11. High level expression of the capsid protein of hepatitis E virus in diverse eukaryotic cells using the Semliki Forest virus replicon.

    Science.gov (United States)

    Torresi, J; Meanger, J; Lambert, P; Li, F; Locarnini, S A; Anderson, D A

    1997-12-01

    The capsid protein of hepatitis E virus (HEV) is encoded by open reading frame 2 (ORF 2) and exhibits variable processing when expressed in insect and COS cells, but nothing is known of its processing in cells relevant to its replication. The full-length ORF 2 protein was expressed at high levels in mammalian cells by insertion of ORF 2 in the Semliki Forest virus (SFV) replicon to generate rSFV/HEV ORF 2K. Expression of the capsid protein was detected readily by metabolic labelling and indirect immunofluorescence in BHK-21 cells transfected with RNA transcripts derived from rSFV/HEV ORF 2K. ORF 2 protein was also expressed at high levels in cells of diverse origin, including liver-derived cell lines Huh7 and HepG2, following infection with recombinant virus derived from cotransfection of BHK-21 cells with the rSFV/HEV ORF 2K and helper SFV replicon RNAs. The addition of hypertonic KCl during metabolic labelling reduced the level of host cell protein synthesis and enhanced the detection of intermediates in ORF 2 protein processing. The wide host range and high level expression directed by SFV replicon particles has particular utility in the analysis of cell-specific factors in the protein processing and assembly of non-cultivable viruses such as HEV.

  12. Atypical mitochondrial inheritance patterns in eukaryotes.

    Science.gov (United States)

    Breton, Sophie; Stewart, Donald T

    2015-10-01

    Mitochondrial DNA (mtDNA) is predominantly maternally inherited in eukaryotes. Diverse molecular mechanisms underlying the phenomenon of strict maternal inheritance (SMI) of mtDNA have been described, but the evolutionary forces responsible for its predominance in eukaryotes remain to be elucidated. Exceptions to SMI have been reported in diverse eukaryotic taxa, leading to the prediction that several distinct molecular mechanisms controlling mtDNA transmission are present among the eukaryotes. We propose that these mechanisms will be better understood by studying the deviations from the predominating pattern of SMI. This minireview summarizes studies on eukaryote species with unusual or rare mitochondrial inheritance patterns, i.e., other than the predominant SMI pattern, such as maternal inheritance of stable heteroplasmy, paternal leakage of mtDNA, biparental and strictly paternal inheritance, and doubly uniparental inheritance of mtDNA. The potential genes and mechanisms involved in controlling mitochondrial inheritance in these organisms are discussed. The linkage between mitochondrial inheritance and sex determination is also discussed, given that the atypical systems of mtDNA inheritance examined in this minireview are frequently found in organisms with uncommon sexual systems such as gynodioecy, monoecy, or andromonoecy. The potential of deviations from SMI for facilitating a better understanding of a number of fundamental questions in biology, such as the evolution of mtDNA inheritance, the coevolution of nuclear and mitochondrial genomes, and, perhaps, the role of mitochondria in sex determination, is considerable.

  13. Autochthonous Hepatitis E Virus Infection in Europe: A Matter of Concern for Public Health?

    Science.gov (United States)

    Echevarría, José-Manuel

    2014-03-01

    Human hepatitis E virus (HHEV) is the proposed name for a diverse group of RNA viruses from the family Hepeviridae that cause acute hepatitis among humans. Waterborne strains are regularly imported into Europe by international travelers, and virus transmission of zoonotic strains via contaminated aliments is involved in autochthonous cases. Therefore, in Europe, hepatitis E displays a unique dual character, having features of both imported and autochthonous infections. Environmental involvement of waterborne and zoonotic diseases puts alimentary safety at risk. In addition, it may lead to serious health problems derived from persistent infection among patients with immune impairment due to organ transplant, cancer, or human immunodeficiency virus infection. Although the European health authorities know at present that HHEV represents a problem worthy of consideration, the actual incidence of the disease in Europe is unknown, and attempts to ascertain the prevalence of the infection is hampered by unresolved technical issues. In order to determine the burden of hepatitis E in Europe, the World Health Organization Regional Office and the European Centre for Disease Prevention and Control should pay specific attention to hepatitis E, and research efforts in the continent should be transnational and collaborative. Development of a specific European network for hepatitis E would help to achieve these goals.

  14. The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

    Energy Technology Data Exchange (ETDEWEB)

    Fritz-Laylin, Lillian K.; Prochnik, Simon E.; Ginger, Michael L.; Dacks, Joel; Carpenter, Meredith L.; Field, Mark C.; Kuo, Alan; Paredez, Alex; Chapman, Jarrod; Pham, Jonathan; Shu, Shengqiang; Neupane, Rochak; Cipriano, Michael; Mancuso, Joel; Tu, Hank; Salamov, Asaf; Lindquist, Erika; Shapiro, Harris; Lucas, Susan; Grigoriev, Igor V.; Cande, W. Zacheus; Fulton, Chandler; Rokhsar, Daniel S.; Dawson, Scott C.

    2010-03-01

    Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likely present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.

  15. Characterization and Technological Features of Autochthonous Coagulase-Negative Staphylococci as Potential Starters for Portuguese Dry Fermented Sausages.

    Science.gov (United States)

    Semedo-Lemsaddek, Teresa; Carvalho, Laura; Tempera, Carolina; Fernandes, Maria H; Fernandes, Maria J; Elias, Miguel; Barreto, António S; Fraqueza, Maria J

    2016-05-01

    The manufacture of dry fermented sausages is an important part of the meat industry in Southern European countries. These products are usually produced in small shops from a mixture of pork, fat, salt, and condiments and are stuffed into natural casings. Meat sausages are slowly cured through spontaneous fermentation by autochthonous microbiota present in the raw materials or introduced during manufacturing. The aim of this work was to evaluate the technological and safety features of coagulase-negative staphylococci (CNS) isolated from Portuguese dry fermented meat sausages in order to select autochthonous starters. Isolates (n = 104) obtained from 2 small manufacturers were identified as Staphylococcus xylosus, Staphylococcus equorum, Staphylococcus saprophyticus, and Staphylococcus carnosus. Genomically diverse isolates (n = 82) were selected for further analysis to determine the ability to produce enzymes (for example, nitrate-reductases, proteases, lipases) and antibiotic susceptibility. Autochthonous CNS producing a wide range of enzymes and showing low antibioresistance were selected as potential starters for future use in the production of dry fermented meat sausages.

  16. Tracking the autochthonous carbon transfer in stream biofilm food webs.

    Science.gov (United States)

    Risse-Buhl, Ute; Trefzger, Nicolai; Seifert, Anne-Gret; Schönborn, Wilfried; Gleixner, Gerd; Küsel, Kirsten

    2012-01-01

    Food webs in the rhithral zone rely mainly on allochthonous carbon from the riparian vegetation. However, autochthonous carbon might be more important in open canopy streams. In streams, most of the microbial activity occurs in biofilms, associated with the streambed. We followed the autochthonous carbon transfer toward bacteria and grazing protozoa within a stream biofilm food web. Biofilms that developed in a second-order stream (Thuringia, Germany) were incubated in flow channels under climate-controlled conditions. Six-week-old biofilms received either ¹³C- or ¹²C-labeled CO₂, and uptake into phospholipid fatty acids was followed. The dissolved inorganic carbon of the flow channel water became immediately labeled. In biofilms grown under 8-h light/16-h dark conditions, more than 50% of the labeled carbon was incorporated in biofilm algae, mainly filamentous cyanobacteria, pennate diatoms, and nonfilamentous green algae. A mean of 29% of the labeled carbon reached protozoan grazer. The testate amoeba Pseudodifflugia horrida was highly abundant in biofilms and seemed to be the most important grazer on biofilm bacteria and algae. Hence, stream biofilms dominated by cyanobacteria and algae seem to play an important role in the uptake of CO₂ and transfer of autochthonous carbon through the microbial food web.

  17. Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

    Energy Technology Data Exchange (ETDEWEB)

    Lykidis, Athanasios

    2006-12-01

    Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymes and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.

  18. On the Diversification of the Translation Apparatus across Eukaryotes

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    Greco Hernández

    2012-01-01

    Full Text Available Diversity is one of the most remarkable features of living organisms. Current assessments of eukaryote biodiversity reaches 1.5 million species, but the true figure could be several times that number. Diversity is ingrained in all stages and echelons of life, namely, the occupancy of ecological niches, behavioral patterns, body plans and organismal complexity, as well as metabolic needs and genetics. In this review, we will discuss that diversity also exists in a key biochemical process, translation, across eukaryotes. Translation is a fundamental process for all forms of life, and the basic components and mechanisms of translation in eukaryotes have been largely established upon the study of traditional, so-called model organisms. By using modern genome-wide, high-throughput technologies, recent studies of many nonmodel eukaryotes have unveiled a surprising diversity in the configuration of the translation apparatus across eukaryotes, showing that this apparatus is far from being evolutionarily static. For some of the components of this machinery, functional differences between different species have also been found. The recent research reviewed in this article highlights the molecular and functional diversification the translational machinery has undergone during eukaryotic evolution. A better understanding of all aspects of organismal diversity is key to a more profound knowledge of life.

  19. Origins and evolution of viruses of eukaryotes: The ultimate modularity

    Energy Technology Data Exchange (ETDEWEB)

    Koonin, Eugene V., E-mail: koonin@ncbi.nlm.nih.gov [National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894 (United States); Dolja, Valerian V., E-mail: doljav@science.oregonstate.edu [Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 (United States); Krupovic, Mart, E-mail: krupovic@pasteur.fr [Institut Pasteur, Unité Biologie Moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Paris 75015 (France)

    2015-05-15

    Viruses and other selfish genetic elements are dominant entities in the biosphere, with respect to both physical abundance and genetic diversity. Various selfish elements parasitize on all cellular life forms. The relative abundances of different classes of viruses are dramatically different between prokaryotes and eukaryotes. In prokaryotes, the great majority of viruses possess double-stranded (ds) DNA genomes, with a substantial minority of single-stranded (ss) DNA viruses and only limited presence of RNA viruses. In contrast, in eukaryotes, RNA viruses account for the majority of the virome diversity although ssDNA and dsDNA viruses are common as well. Phylogenomic analysis yields tangible clues for the origins of major classes of eukaryotic viruses and in particular their likely roots in prokaryotes. Specifically, the ancestral genome of positive-strand RNA viruses of eukaryotes might have been assembled de novo from genes derived from prokaryotic retroelements and bacteria although a primordial origin of this class of viruses cannot be ruled out. Different groups of double-stranded RNA viruses derive either from dsRNA bacteriophages or from positive-strand RNA viruses. The eukaryotic ssDNA viruses apparently evolved via a fusion of genes from prokaryotic rolling circle-replicating plasmids and positive-strand RNA viruses. Different families of eukaryotic dsDNA viruses appear to have originated from specific groups of bacteriophages on at least two independent occasions. Polintons, the largest known eukaryotic transposons, predicted to also form virus particles, most likely, were the evolutionary intermediates between bacterial tectiviruses and several groups of eukaryotic dsDNA viruses including the proposed order “Megavirales” that unites diverse families of large and giant viruses. Strikingly, evolution of all classes of eukaryotic viruses appears to have involved fusion between structural and replicative gene modules derived from different sources

  20. GENEALOGICAL DECOMPOSITION OF THE EFFECTIVE POPULATION SIZE: A CASE STUDY ON CROATIAN AUTOCHTHONOUS CATTLE BREEDS

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    Martin Reljanović

    2015-09-01

    Full Text Available Effective population size (Ne is one of the most important tools used to assess genetic diversity for conservation purposes. Using pedigree data of three Croatian autochthonous cattle breeds (Buša, Istrian and Slavonian Syrmian Podolian the effective maternal (NeF, paternal (NeM and combined maternal-paternal (NeFM population size was estimated. Additionally, we estimated the effective population size based on the census population sex ratio (Nes, the effective population size from the individual increase in inbreeding (NeFi and the effective population size from individual increase in coancestry (NeCi. We compared these sizes with the values obtained for 20 additional cattle populations, as well as with the newly calculated NeFM. The effective population sizes calculated for three autochthonous breeds were consistently the lowest in amongst all the considered cattle breeds. Utilisation of extremely small numbers of breeding males is the main reason for the observed reduction in the effective population size. The decomposition of effective population size into maternal and paternal components is shown to be an informative parameter in detecting the reduction of the effective population size as a consequence of unequal sex contribution. Still, the impact of the pedigree depth and completeness on the NeF, NeM and NeFM estimation remain to be analysed. A large deviation between Nes and all other methods of Ne estimation was observed and it is our recommendation that breeders and stakeholders should consider using alternative methods of Ne estimation when planning breeding programmes as well as in the determination of the endangered status of animal populations.

  1. Eukaryotic association module in phage WO genomes from Wolbachia

    Science.gov (United States)

    Bordenstein, Sarah R.; Bordenstein, Seth R.

    2016-01-01

    Viruses are trifurcated into eukaryotic, archaeal and bacterial categories. This domain-specific ecology underscores why eukaryotic viruses typically co-opt eukaryotic genes and bacteriophages commonly harbour bacterial genes. However, the presence of bacteriophages in obligate intracellular bacteria of eukaryotes may promote DNA transfers between eukaryotes and bacteriophages. Here we report a metagenomic analysis of purified bacteriophage WO particles of Wolbachia and uncover a eukaryotic association module in the complete WO genome. It harbours predicted domains, such as the black widow latrotoxin C-terminal domain, that are uninterrupted in bacteriophage genomes, enriched with eukaryotic protease cleavage sites and combined with additional domains to forge one of the largest bacteriophage genes to date (14,256 bp). To the best of our knowledge, these eukaryotic-like domains have never before been reported in packaged bacteriophages and their phylogeny, distribution and sequence diversity imply lateral transfers between bacteriophage/prophage and animal genomes. Finally, the WO genome sequences and identification of attachment sites will potentially advance genetic manipulation of Wolbachia. PMID:27727237

  2. Intercultural Profiles and Adaptation Among Immigrant and Autochthonous Adolescents.

    Science.gov (United States)

    Inguglia, Cristiano; Musso, Pasquale

    2015-02-01

    Few studies examine relationships between intercultural strategies and adaptation among adolescents using a person-oriented approach. Framed from an intercultural psychology perspective, this study used such an approach in order to examine the influence of intercultural profiles, patterns of relationships among variables related to intercultural strategies, on the adaptation of adolescents of both non-dominant and dominant groups. Two hundred and fifty-six adolescents living in Italy and aged from 14 to 18 participated to the study: 127 immigrants from Tunisia (males = 49.61%) and 129 autochthonous (males = 44.19%). Data were collected through self-report questionnaires. Using cluster analytic methods to identify profiles, the results showed that immigrant adolescents were divided in two acculturation profiles, ethnic and integrated-national, with adolescents belonging to the latter showing higher self-esteem, life satisfaction and sociocultural competence than the former. Also among autochthonous adolescents two acculturation expectation profiles were identified, not-multicultural and multicultural, with adolescents belonging to the latter showing higher self-esteem and life satisfaction than the former. Findings highlight the importance of using multiple indicators in order to gain a more comprehensive understanding of the acculturation process as well as suggesting implications for the social policies in this field.

  3. From grape berries to wine: population dynamics of cultivable yeasts associated to "Nero di Troia" autochthonous grape cultivar.

    Science.gov (United States)

    Garofalo, Carmela; Tristezza, Mariana; Grieco, Francesco; Spano, Giuseppe; Capozzi, Vittorio

    2016-04-01

    The aim of this work was to study the biodiversity of yeasts isolated from the autochthonous grape variety called "Uva di Troia", monitoring the natural diversity from the grape berries to wine during a vintage. Grapes were collected in vineyards from two different geographical areas and spontaneous alcoholic fermentations (AFs) were performed. Different restriction profiles of ITS-5.8S rDNA region, corresponding to Saccharomyces cerevisiae, Issatchenkia orientalis, Metschnikowia pulcherrima, Hanseniaspora uvarum, Candida zemplinina, Issatchenkia terricola, Kluyveromyces thermotolerans, Torulaspora delbrueckii, Metschnikowia chrysoperlae, Pichia fermentans, Hanseniaspora opuntiae and Hanseniaspora guilliermondii, were observed. The yeast occurrences varied significantly from both grape berries and grape juices, depending on the sampling location. Furthermore, samples collected at the end of AF revealed the great predominance of Saccharomyces cerevisiae, with a high intraspecific biodiversity. This is the first report on the population dynamics of 'cultivable' microbiota diversity of "Uva di Troia" cultivar from the grape to the corresponding wine ("Nero di Troia"), and more general for Southern Italian oenological productions, allowing us to provide the basis for an improved management of wine yeasts (with both non-Saccharomyces and Saccharomyces) for the production of typical wines with desired unique traits. A certain geographical-dependent variability has been reported, suggesting the need of local based formulation for autochthonous starter cultures, especially in the proportion of the different species/strains in the design of mixed microbial preparations.

  4. Characterization of autochthonous Lactobacillus paracasei strains on potential probiotic ability

    Directory of Open Access Journals (Sweden)

    Zorica Radulović

    2010-06-01

    Full Text Available Lactic acid bacteria strains isolated from traditional made cheeses constitute a reservoir of unexplored potential in biotechnology. In this study four autochthonous lactobacilli strains, isolated from traditional white brined cheeses and identified as Lactobacillus paracasei (08, 564, 05 and 02, were investigated on potential probiotic ability. The investigation comprised sensitivity to simulated gastrointestinal tract conditions, antimicrobial activity against wide range of pathogens, antibiotic resistance as well as autoaggregation ability. Lactobacillus rhamnosus GG was used as referent strain. Three tested strains grew well in simulated gastrointestinal conditions, but their sensitivity was greater on bile acids and pancreatin compared with pepsin low pH 2.5. The examined strains had different sensitivity to antibiotics, but three strains showed very good antimicrobial activity to pathogens. All strains demonstrated very good autoaggregation ability. For three of four examined strains of Lb. paracasei probiotic potential was similar with referent strain Lb. rhamnosus GG, determined in vitro

  5. Development of an autochthonous starter culture for spreadable goat cheese

    Directory of Open Access Journals (Sweden)

    Florencia FRAU

    Full Text Available Abstract The aim of this work was to select strains of LAB autochthonous from Santiago del Estero to formulate a starter culture for making spreadable goat cheese. Four strains were selected: CRL1799 (Lactobacillus fermentum with high acidifying activity, CRL1803 (Lactobacillus fermentum with high proteolytic activity, CRL1808 (Lactobacillus rhamnosus with production of exopolysaccharide and CRL1785 (Enterococcus faecium with diacetyl-acetoin production. The selected strains showed qualities that make them useful as starter culture in the elaboration of spreadable cheese. This starter culture is an alternative that allows obtaining differentiated products. The inclusion of CRL1808 strains seems to improve the rheology and texture, excluding the use of additives.

  6. AUTOCHTHONOUS APPROACHING IN THE MANAGEMENT OF THE SECURITY RISK

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    Burtescu Emil

    2008-05-01

    Full Text Available An optimal management for a corporation, no matter what size the corporation is, it must contain the management of the security risk. On the importance that is given to the risk management can depend the well functioning of the corporation. An important role in this process has the owner of the business and the way that this one understands the risk. A good understanding of the risk by the owner will have as effect the allocation of sufficient funds to implement controls meant to bring the risk level in order to be an acceptable one. The autochthonous corporations, in a great part even because of the inexistence of reglementations in this domain, have an empiric approach of the phenomena.

  7. Distribuição da diversidade isoenzimática e morfológica da mandioca na agricultura autóctone de Ubatuba Distribution of the isozyme and morphological diversity of cassava in the autochthonous agriculture of Ubatuba

    Directory of Open Access Journals (Sweden)

    Julianno Bergoch Monteiro Sambatti

    2000-03-01

    Full Text Available A diversidade fenotípica de quatro sistemas isoenzimáticos e doze caracteres morfológicos em mandioca (Manihot esculenta Crantz foi quantificada através do índice de Shannon-Weaver para quatro roças de mandioca pertencentes a dois agricultores autóctones no município de Ubatuba-SP. A diversidade total foi repartida entre diversidade dentro de roças e diversidade entre roças, mostrando que a maior parte da diversidade se concentra dentro de roças para a maioria dos caracteres. Entrevistas foram realizadas para verificar se os agricultores reconhecem a existência de plantas de mandioca originadas por semente e a existência de bancos de semente.Phenotypic diversity of four isozymes systems and twelve morphological traits of cassava (Manihot esculenta Crantz were quantified using the Shannon-Weaver diversity index for four cassava gardens of two traditional farmers of Ubatuba,SP, Brazil. The total diversity was partitioned within and among gardens, showing that most of the diversity is concentrated within gardens. Interviews were carried out in order to verify if farmers recognize the existance of cassava plants originated from seeds and seed banks with the surveyed farmers in order to identify, in the present case, mechanisms of genetic diversity amplification.

  8. Expanding the eukaryotic genetic code

    Science.gov (United States)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2013-01-22

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  9. Expanding the eukaryotic genetic code

    Energy Technology Data Exchange (ETDEWEB)

    Chin, Jason W.; Cropp, T. Ashton; Anderson, J. Christopher; Schultz, Peter G.

    2017-02-28

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  10. Endosymbiosis and Eukaryotic Cell Evolution.

    Science.gov (United States)

    Archibald, John M

    2015-10-05

    Understanding the evolution of eukaryotic cellular complexity is one of the grand challenges of modern biology. It has now been firmly established that mitochondria and plastids, the classical membrane-bound organelles of eukaryotic cells, evolved from bacteria by endosymbiosis. In the case of mitochondria, evidence points very clearly to an endosymbiont of α-proteobacterial ancestry. The precise nature of the host cell that partnered with this endosymbiont is, however, very much an open question. And while the host for the cyanobacterial progenitor of the plastid was undoubtedly a fully-fledged eukaryote, how - and how often - plastids moved from one eukaryote to another during algal diversification is vigorously debated. In this article I frame modern views on endosymbiotic theory in a historical context, highlighting the transformative role DNA sequencing played in solving early problems in eukaryotic cell evolution, and posing key unanswered questions emerging from the age of comparative genomics.

  11. Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers.

    Science.gov (United States)

    Pandey, Prashant K; Siddharth, Jay; Verma, Pankaj; Bavdekar, Ashish; Patole, Milind S; Shouche, Yogesh S

    2012-06-01

    The micro-eukaryotic diversity from the human gut was investigated using universal primers directed towards 18S rRNA gene, fecal samples being the source of DNA. The subjects in this study included two breast-fed and two formula-milk-fed infants and their mothers. The study revealed that the infants did not seem to harbour any microeukaryotes in their gut. In contrast, there were distinct eukaryotic microbiota present in the mothers. The investigation is the first of its kind in the comparative study of the human feces to reveal the presence of micro-eukaryotic diversity variance in infants and adults from the Indian subcontinent. The micro-eukaryotes encountered during the investigation include known gut colonizers like Blastocystis and some fungi species. Some of these micro-eukaryotes have been speculated to be involved in clinical manifestations of various diseases. The study is an attempt to highlight the importance of micro-eukaryotes in the human gut.

  12. Autochthonous and Allochthonous Carbon Cycling in a Eutrophic Flow-Through Wetland

    Science.gov (United States)

    Wetland environments are important sites for the cycling and retention of terrestrially derived organic matter and nutrients, the influx of which subsidizes wetland C sequestration, as well as fueling autochthonous C productivity. Wetland treatment of agricultural runoff has been...

  13. Evolutionary origin of eukaryotic cells.

    Science.gov (United States)

    Kostianovsky, M

    2000-01-01

    This article reviews literature on the transition from rudimentary prokaryotic life to eukaryotes. An overview of the differences between these organisms and theories of eukaryogenesis are reviewed. Various methods of investigating the transformation from prokaryotes to eukaryotes are elaborated, including the fossil, the molecular and living records, and examples are given. Lastly, the recent molecular studies and the impact on phylogenetic classification for the tree of life, based on molecular evolution, are discussed.

  14. Italian autochthonous pigs: progress report and research perspectives

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    O. Franci

    2010-04-01

    Full Text Available Characteristics and research perspectives of autochthonous Italian pig are summarised and discussed. Nowadays only six breeds are still farmed (Mora Romagnola, Cinta Senese, Casertana, Calabrese, Nero Siciliano and Sarda, on twenty-one local pig genotypes existing in Italy at beginning of the last century. Recently all the breeds are recorded on the National Pedigree Register. For the genetic conservation of these populations, an adequate management of mating appears fundamental to limit the inbreeding and to increase the genetic variability, as nowadays it is carried out in Cinta Senese that offers the deepest pedigree. For Nero Siciliano and Sarda, individuation of morphological standard and recovery of appropriate genotypes appear also urgent. From the recent literature it is evident that the local breeds are worse than the improved ones in reproductive performance and productive traits as growth rate, feed conversion and carcass composition but they show interesting quality of meat and fat. Among the six breeds Cinta Senese, Mora Romagnola and Casertana seem to show higher body size and faster growth rate. The link with free-range rearing increases the commercial value of products of local pigs, because of both effective characterization and consumer suggestion, but research is helpful to increase the knowledge of their rearing system. The more interesting fields of research seem the following: genetic traceability; feeding traceability; evolution of body composition; sustainable exploitation of natural resources.

  15. Metabolic and biological profile of autochthonous Vitis vinifera L. ecotypes.

    Science.gov (United States)

    Impei, Stefania; Gismondi, Angelo; Canuti, Lorena; Canini, Antonella

    2015-05-01

    Vitis vinifera L. is a plant species rich in phenolic compounds that are usually associated with the health benefits of wine and grape consumption in the diet. Anthocyanins, catechins, flavonol, phenolic acids and stilbenes are key molecular constituents of the Vitis berries, affecting the quality of grape products. The purpose of this work was to identify the metabolic profiles of 37 genetically certified V. vinifera Latial accessions. In particular, qualitative and quantitative analyses of specific secondary metabolites and total phenolic and tannin contents were performed by LC-MS and spectrophotometric analysis. In addition, since plant molecules are well-known for their free radical scavenging properties, the antioxidant effects of the sample extracts were evaluated through two different antiradical assays: DPPH and FRAP tests. Finally, a preliminary screening of the antiproliferative activity of each specimen on HCT-116 human colorectal cancer cells was conducted. All the results showed a great variety and amount of phenolic compounds in all accessions; moreover, we observed a significant correlation in the extracts between the metabolite concentration and bioactivity. Besides, some samples presented extraordinary biological effects, such as reduction of tumor cell growth not associated with cytotoxicity, supporting their use as possible future adjuvants for cancer therapy. In conclusion, the present research increased the scientific knowledge about Italian autochthonous vine ecotypes in order to valorize them and support their reintroduction in the local economic system.

  16. Application of autochthonous mixed starter for controlled Kedong sufu fermentation in pilot plant tests.

    Science.gov (United States)

    Feng, Zhen; Xu, Miao; Zhai, Shuang; Chen, Hong; Li, Ai-li; Lv, Xin-tong; Deng, Hong-ling

    2015-01-01

    Traditional sufu is fermented by back-slopping and back-slopping has many defects. The objective of this study was to apply autochthonous mixed starter to control Kedong sufu fermentation. Sufu was manufactured using back-slopping (batch A) and autochthonous mixed starter (batch B) with Kocuria kristinae F7, Micrococcus luteus KDF1, and Staphylococcus carnosus KDFR1676. Considering physicochemical properties of sufu, 150-day sufu samples from batch A and 90-day sufu samples from batch B met the standard requirements, respectively. Considering sensory characteristics of sufu, 150-day sufu samples from batch A and 90-day sufu samples from batch B showed no significant differences (P > 0.05). The maturation period of sufu was shortened by 60 d. Profiles of free amino acids and peptides partly revealed the mechanism of typical sensory quality and shorter ripening time of sufu manufactured by autochthonous mixed starter. In final products, content of total biogenic amines was reduced by 48%. Autochthonous mixed starter performed better than back-slopping. Fermentation had a positive influence on the quality, safety, and sensory properties of sufu. The application of autochthonous mixed starter does not change the sensory characteristics of traditional fermented sufu. In addition, it reduces maturation period and improves their homogeneity and safety. It is possible to substitute autochthonous mixed starter for back-slopping in the manufacture of sufu.

  17. Characterization of virgin olive oils produced with autochthonous Galician varieties.

    Science.gov (United States)

    Reboredo-Rodríguez, Patricia; González-Barreiro, Carmen; Cancho-Grande, Beatriz; Valli, Enrico; Bendini, Alessandra; Gallina Toschi, Tullia; Simal-Gandara, Jesus

    2016-12-01

    The interest of Galician oil producers (NW Spain) in recovering the ancient autochthonous olive varieties Brava and Mansa has increased substantially in recent years. Virgin olive oils produced by co-crushing both varieties in two different proportions, reflecting the usual and most common practice adopted in this region, have gradually emerged for the production of virgin olive oils. Herein, the sensory and chemical characteristics of such oils were characterized by quality and genuineness-related parameters. The results of chemical analysis are discussed in terms of their effective contribution to the sensory profile, which suggests useful recommendations for olive oil producers to improve the quality of oils. Antioxidant compounds, together with aromas and coloured pigments were determined, and their contribution in determining the functional value and the sensory properties of oils was investigated. In general, given the high levels of phenolic compounds (ranging between 254 and 375mg/kg oil), tocopherols (about 165mg/kg oil) and carotenoids (10-12mg/kg oil); these are oils with long stability, especially under dark storage conditions, because stability is reinforced with the contribution of chlorophylls (15-22mg/kg oil). A major content of phenolic compounds, as well as a predominance of trans-2-hexen-1-al within odor-active compounds (from 897 to 1645μg/kg oil), responsible for bitter sensory notes. This characterization allows to developing new antioxidant-rich and flavour-rich VOOs, when co-crushing with a higher proportion of Brava olives, satisfying the consumers' demand in having access to more healthy dishes and peculiar sensory attributes.

  18. Antimicrobial Susceptibility of Autochthonous Aquatic Vibrio cholerae in Haiti

    Science.gov (United States)

    Baron, Sandrine; Lesne, Jean; Jouy, Eric; Larvor, Emeline; Kempf, Isabelle; Boncy, Jacques; Rebaudet, Stanilas; Piarroux, Renaud

    2016-01-01

    We investigated the antimicrobial susceptibility of 50 environmental isolates of Vibrio cholerae non-O1/non-O139 collected in surface waters in Haiti in July 2012, during an active cholera outbreak. A panel of 16 antibiotics was tested on the isolates using the disk diffusion method and PCR detection of seven resistance-associated genes (strA/B, sul1/2, ermA/B, and mefA). All isolates were susceptible to amoxicillin-clavulanic acid, cefotaxime, imipenem, ciprofloxacin, norfloxacin, amikacin, and gentamicin. Nearly a quarter (22.0%) of the isolates were susceptible to all 16 antimicrobials tested and only 8.0% of the isolates (n = 4) were multidrug-resistant. The highest proportions of resistant isolates were observed for sulfonamide (70.0%), amoxicillin (12.0%), and trimethoprim-sulfamethoxazole (10.0%). One strain was resistant to erythromycin and one to doxycycline, two antibiotics used to treat cholera in Haiti. Among the 50 isolates, 78% possessed at least two resistance-associated genes, and the genes sul1, ermA, and strB were detected in all four multidrug-resistant isolates. Our results clearly indicate that the autochthonous population of V. cholerae non-O1/non-O139 found in surface waters in Haiti shows antimicrobial patterns different from that of the outbreak strain. The presence in the Haitian aquatic environment of V. cholerae non-O1/non-O139 with reduced susceptibility or resistance to antibiotics used in human medicine may constitute a mild public health threat. PMID:27818656

  19. Arabidopsis transcription factors: genome-wide comparative analysis among eukaryotes.

    Science.gov (United States)

    Riechmann, J L; Heard, J; Martin, G; Reuber, L; Jiang, C; Keddie, J; Adam, L; Pineda, O; Ratcliffe, O J; Samaha, R R; Creelman, R; Pilgrim, M; Broun, P; Zhang, J Z; Ghandehari, D; Sherman, B K; Yu, G

    2000-12-15

    The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.

  20. Eukaryotic vs. prokaryotic chemosensory systems.

    Science.gov (United States)

    Sbarbati, Andrea; Merigo, Flavia; Osculati, Francesco

    2010-04-01

    In the last decades, microbiologists demonstrated that microorganisms possess chemosensory capabilities and communicate with each other via chemical signals. In parallel, it was demonstrated that solitary eukaryotic chemosensory cells are diffusely located on the mucosae of digestive and respiratory apparatuses. It is now evident that on the mucosal surfaces of vertebrates, two chemoreceptorial systems (i.e. eukaryotic and prokaryotic) coexist in a common microenvironment. To date, it is not known if the two chemosensory systems reciprocally interact and compete for detection of chemical cues. This appears to be a fruitful field of study and future researches must consider that the mucosal epithelia possess more chemosensory capabilities than previously supposed.

  1. Lateral transfer of eukaryotic ribosomal RNA genes: an emerging concern for molecular ecology of microbial eukaryotes.

    Science.gov (United States)

    Yabuki, Akinori; Toyofuku, Takashi; Takishita, Kiyotaka

    2014-07-01

    Ribosomal RNA (rRNA) genes are widely utilized in depicting organismal diversity and distribution in a wide range of environments. Although a few cases of lateral transfer of rRNA genes between closely related prokaryotes have been reported, it remains to be reported from eukaryotes. Here, we report the first case of lateral transfer of eukaryotic rRNA genes. Two distinct sequences of the 18S rRNA gene were detected from a clonal culture of the stramenopile, Ciliophrys infusionum. One was clearly derived from Ciliophrys, but the other gene originated from a perkinsid alveolate. Genome-walking analyses revealed that this alveolate-type rRNA gene is immediately adjacent to two protein-coding genes (ubc12 and usp39), and the origin of both genes was shown to be a stramenopile (that is, Ciliophrys) in our phylogenetic analyses. These findings indicate that the alveolate-type rRNA gene is encoded on the Ciliophrys genome and that eukaryotic rRNA genes can be transferred laterally.

  2. Nitrate storage and dissimilatory nitrate reduction by eukaryotic microbes

    DEFF Research Database (Denmark)

    Kamp, Anja; Høgslund, Signe; Risgaard-Petersen, Nils;

    2015-01-01

    The microbial nitrogen cycle is one of the most complex and environmentally important element cycles on Earth and has long been thought to be mediated exclusively by prokaryotic microbes. Rather recently, it was discovered that certain eukaryotic microbes are able to store nitrate intracellularly...... and use it for dissimilatory nitrate reduction in the absence of oxygen. The paradigm shift that this entailed is ecologically significant because the eukaryotes in question comprise global players like diatoms, foraminifers, and fungi. This review article provides an unprecedented overview of nitrate...... storage and dissimilatory nitrate reduction by diverse marine eukaryotes placed into an eco-physiological context. The advantage of intracellular nitrate storage for anaerobic energy conservation in oxygen-depleted habitats is explained and the life style enabled by this metabolic trait is described...

  3. Active eukaryotes in microbialites from Highborne Cay, Bahamas, and Hamelin Pool (Shark Bay), Australia.

    Science.gov (United States)

    Edgcomb, Virginia P; Bernhard, Joan M; Summons, Roger E; Orsi, William; Beaudoin, David; Visscher, Pieter T

    2014-02-01

    Microbialites are organosedimentary structures that are formed through the interaction of benthic microbial communities and sediments and include mineral precipitation. These lithifying microbial mat structures include stromatolites and thrombolites. Exuma Sound in the Bahamas, and Hamelin Pool in Shark Bay, Western Australia, are two locations where significant stands of modern microbialites exist. Although prokaryotic diversity in these structures is reasonably well documented, little is known about the eukaryotic component of these communities and their potential to influence sedimentary fabrics through grazing, binding and burrowing activities. Accordingly, comparisons of eukaryotic communities in modern stromatolitic and thrombolitic mats can potentially provide insight into the coexistence of both laminated and clotted mat structures in close proximity to one another. Here we examine this possibility by comparing eukaryotic diversity based on Sanger and high-throughput pyrosequencing of small subunit ribosomal RNA (18S rRNA) genes. Analyses were based on total RNA extracts as template to minimize input from inactive or deceased organisms. Results identified diverse eukaryotic communities particularly stramenopiles, Alveolata, Metazoa, Amoebozoa and Rhizaria within different mat types at both locations, as well as abundant and diverse signatures of eukaryotes with eukaryotic diversity, particularly in hypersaline Hamelin Pool. There was evidence of vertical structuring of protist populations and foraminiferal diversity was highest in bioturbated/clotted thrombolite mats of Highborne Cay.

  4. Dyneins across eukaryotes: a comparative genomic analysis.

    Science.gov (United States)

    Wickstead, Bill; Gull, Keith

    2007-12-01

    Dyneins are large minus-end-directed microtubule motors. Each dynein contains at least one dynein heavy chain (DHC) and a variable number of intermediate chains (IC), light intermediate chains (LIC) and light chains (LC). Here, we used genome sequence data from 24 diverse eukaryotes to assess the distribution of DHCs, ICs, LICs and LCs across Eukaryota. Phylogenetic inference identified nine DHC families (two cytoplasmic and seven axonemal) and six IC families (one cytoplasmic). We confirm that dyneins have been lost from higher plants and show that this is most likely because of a single loss of cytoplasmic dynein 1 from the ancestor of Rhodophyta and Viridiplantae, followed by lineage-specific losses of other families. Independent losses in Entamoeba mean that at least three extant eukaryotic lineages are entirely devoid of dyneins. Cytoplasmic dynein 2 is associated with intraflagellar transport (IFT), but in two chromalveolate organisms, we find an IFT footprint without the retrograde motor. The distribution of one family of outer-arm dyneins accounts for 2-headed or 3-headed outer-arm ultrastructures observed in different organisms. One diatom species builds motile axonemes without any inner-arm dyneins (IAD), and the unexpected conservation of IAD I1 in non-flagellate algae and LC8 (DYNLL1/2) in all lineages reveals a surprising fluidity to dynein function.

  5. Distinct gene number-genome size relationships for eukaryotes and non-eukaryotes: gene content estimation for dinoflagellate genomes.

    Directory of Open Access Journals (Sweden)

    Yubo Hou

    Full Text Available The ability to predict gene content is highly desirable for characterization of not-yet sequenced genomes like those of dinoflagellates. Using data from completely sequenced and annotated genomes from phylogenetically diverse lineages, we investigated the relationship between gene content and genome size using regression analyses. Distinct relationships between log(10-transformed protein-coding gene number (Y' versus log(10-transformed genome size (X', genome size in kbp were found for eukaryotes and non-eukaryotes. Eukaryotes best fit a logarithmic model, Y' = ln(-46.200+22.678X', whereas non-eukaryotes a linear model, Y' = 0.045+0.977X', both with high significance (p0.91. Total gene number shows similar trends in both groups to their respective protein coding regressions. The distinct correlations reflect lower and decreasing gene-coding percentages as genome size increases in eukaryotes (82%-1% compared to higher and relatively stable percentages in prokaryotes and viruses (97%-47%. The eukaryotic regression models project that the smallest dinoflagellate genome (3x10(6 kbp contains 38,188 protein-coding (40,086 total genes and the largest (245x10(6 kbp 87,688 protein-coding (92,013 total genes, corresponding to 1.8% and 0.05% gene-coding percentages. These estimates do not likely represent extraordinarily high functional diversity of the encoded proteome but rather highly redundant genomes as evidenced by high gene copy numbers documented for various dinoflagellate species.

  6. Eukaryotic microorganisms in cold environments. Examples from Pyrenean glaciers

    Directory of Open Access Journals (Sweden)

    Laura eGarcia-Descalzo

    2013-03-01

    Full Text Available Little is known about the viability of eukaryotic microorganisms preserved in icy regions. Here we report on the diversity of microbial eukaryotes in ice samples derived from four Pyrenean glaciers. The species composition of eukaryotic communities in these glaciers is unknown mostly because of the presence of a multi-year ice cap, and it is not clear whether they harbor the same populations. The recent deglaciation of these areas is allowing an easy access to glacial layers that correspond to the Little Ice Age although some isolated deposits are attributed to previous glacial cycles. In this study, we use molecular 18S rRNA-based approaches to characterize some of the microbial eukaryotic populations associated with Pyrenean glaciers. Firstly, we performed a chemical and microscopical characterization of ice samples. Secondly, molecular analyses revealed interesting protist genetic diversity in glaciers. In order to understand the microbial composition of the ice samples the eukaryotic communities resident in the glacial samples were examined by amplifying community DNA and constructing clone libraries with 18S rRNA primers. After removal of potential chimeric sequences and derreplication of identical sequences, phylogenetic analysis demonstrated that several different protists could be identified. Protist diversity was more phylum rich in Aneto and Monte Perdido glaciers. The dominant taxonomic groups across all samples (> 1 % of all sequences were Viridiplantae and Rhizaria. Significant variations in relative abundances of protist phyla between higher and lower glaciers were observed. At the genus level, significant differences were also recorded for the dominant genera Chloromonas, Raphidonema , Heteromita , Koliella and Bodomorpha. In addition, protist community structure showed significant differences between glaciers. The relative abundances of protist groups at different taxonomic levels correlated with the altitude and area of glaciers

  7. Microbiological changes and diversity in autochthonous non-toxigenic Corynebacterium diphtheriae isolated in France.

    Science.gov (United States)

    Farfour, E; Badell, E; Dinu, S; Guillot, S; Guiso, N

    2013-10-01

    Autochtonous toxigenic Corynebacterium diphtheriae have disappeared in mainland France, but non-toxigenic C. diphtheriae are still circulating. Using phenotypic and molecular tools, we retrospectively characterized 103 non-toxigenic C. diphtheriae collected in mainland France and highlight several changes. The proportion of C. diphtheriae belfanti increased between 1977 and 2011 and it is the most frequent biotype recovered in recent years. Resistance to ciprofloxacin has increased and most isolates with decreased sensitivity belong to the belfanti biotype. Using multilocus sequence typing, we demonstrate that French isolates are distributed in a large number of sequence types and identify three distinct lineages. C. diphtheriae mitis and gravis form lineage I while C. diphtheriae belfanti forms lineages II and III. Almost all isolates of lineage II are part of a unique clonal complex or are very close to it. Most French isolates have a dtxR sequence homologous to that of toxigenic isolates, suggesting that if lyzogenised by a corynephage, they can express diphtheria toxin.

  8. Defensins: antifungal lessons from eukaryotes

    Directory of Open Access Journals (Sweden)

    Patrícia M. Silva

    2014-03-01

    Full Text Available Over the last years, antimicrobial peptides (AMPs have been the focus of intense research towards the finding of a viable alternative to current antifungal drugs. Defensins are one of the major families of AMPs and the most represented among all eukaryotic groups, providing an important first line of host defense against pathogenic microorganisms. Several of these cysteine-stabilized peptides present a relevant effect against fungi. Defensins are the AMPs with the broader distribution across all eukaryotic kingdoms, namely, Fungi, Plantæ and Animalia, and were recently shown to have an ancestor in a bacterial organism. As a part of the host defense, defensins act as an important vehicle of information between innate and adaptive immune system and have a role in immunomodulation. This multidimensionality represents a powerful host shield, hard for microorganisms to overcome using single approach resistance strategies. Pathogenic fungi resistance to conventional antimycotic drugs is becoming a major problem. Defensins, as other AMPs, have shown to be an effective alternative to the current antimycotic therapies, demonstrating potential as novel therapeutic agents or drug leads. In this review, we summarize the current knowledge on some eukaryotic defensins with antifungal action. An overview of the main targets in the fungal cell and the mechanism of action of these AMPs (namely, the selectivity for some fungal membrane components are presented. Additionally, recent works on antifungal defensins structure, activity and citotoxicity are also reviewed.

  9. Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

    Directory of Open Access Journals (Sweden)

    Turk Vito

    2009-11-01

    Full Text Available Abstract Background The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea. Results We have identified in silico the full complement of the cystatin superfamily in more than 2100 prokaryotic and eukaryotic genomes. The analysis of numerous eukaryotic genomes has provided strong evidence for the emergence of this superfamily in the ancestor of eukaryotes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. While stefins remain encoded by a single or a small number of genes throughout the eukaryotes, the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications. In the cystatin superfamily we discovered twenty vertebrate-specific and three angiosperm-specific orthologous families, indicating that functional diversification has occurred only in multicellular eukaryotes. In vertebrate orthologous families, the prevailing trends were loss of the ancestral inhibitory activity and acquisition of novel functions in innate immunity. Bacterial cystatins and stefins may be emergency inhibitors that enable survival of bacteria in the host, defending them from the host's proteolytic activity. Conclusion This study challenges the current view on the classification, origin and evolution of the cystatin superfamily and provides valuable insights into their functional diversification. The findings of this comprehensive study provide guides for future

  10. Eukaryotic versus prokaryotic marine picoplankton ecology.

    Science.gov (United States)

    Massana, Ramon; Logares, Ramiro

    2013-05-01

    Marine microorganisms contribute markedly to global biomass and ecosystem function. They include a diverse collection of organisms differing in cell size and in evolutionary history. In particular, microbes within the picoplankton are similar in size but belong to two drastically different cellular plans, the prokaryotes and the eukaryotes. Compared with larger organisms, prokaryotes and picoeukaryotes share ecological features, such as high specific activity, large and constant abundances, and high dispersal potential. Still, there are some aspects where their different cell organization influences their ecological performance. First, prokaryotes have a huge metabolic versatility and are involved in all biogeochemical cycles, whereas picoeukaryotes are metabolically less flexible but can exploit diverse predatory life strategies due to their phagocytic capacity. Second, sexual reproduction is absent in prokaryotes but may be present in picoeukaryotes, thus determining different evolutionary diversification dynamics and making species limits clearer in picoeukaryotes. Finally, it is plausible that picoeukaryotes are less flexible to enter a reversible state of low metabolic activity, thus picoeukaryote assemblages may have fewer rare species and may be less resilient to environmental change. In summary, lumping together pico-sized microbes may be convenient for some ecological studies, but it is also important to keep in mind their differences.

  11. Characterization of Fiore Sardo cheese manufactured with the addition of autochthonous cultures.

    Science.gov (United States)

    Pisano, M Barbara; Elisabetta Fadda, M; Deplano, Maura; Corda, Arianna; Casula, Maddalena; Cosentino, Sofia

    2007-08-01

    This work evaluated the effect of adjunct autochthonous cultures on the chemical, microbiological and sensory characteristics of Fiore Sardo cheese during ripening. A total of twelve batches of cheeses were manufactured according to the technical Disciplinary of Fiore Sardo cheese, with and without different combinations of autochthonous strains isolated from the native microflora of artisanal Fiore Sardo. There were no significant differences in the cheese compositional parameters between experimental and control cheeses, but the addition of cultures led to a statistically significant decrease in pH values in experimental cheeses. The evolution of total mesophilic bacteria, total coliforms and lactic acid bacteria were significantly influenced by the addition of autochthonous cultures in most of the experimental cheeses. As for sensory characteristics, all the experimental cheeses reported significantly higher scores especially for shape, texture, interior openings, taste and aftertaste. This study demonstrated the beneficial effect of the addition of selected autochthonous cultures in accelerating the disappearance of undesirable flora and improving the typical sensory characteristics of the cheese, and confirmed the importance of ewes' milk as a source of technologically interesting strains that could be used to ensure a higher quality of artisanal cheese productions.

  12. CRYOPRESERVATION OF RAM SPERM FROM AUTOCHTHONOUS BREEDS DURING A NON-MATING SEASON

    Directory of Open Access Journals (Sweden)

    Milko SABEV

    2007-07-01

    Full Text Available It is possible to collect and successfully cryopreserve ejaculates in a non-mating season from rams of the autochthonous breeds Karakachan, Cooper-red Shumen and Karnobat-local, raised in Bulgaria. Studies are in progress aiming the elaboration of optimal cryoprotective extenders and freezing technology.

  13. A strategy to potentiate Cd phytoremediation by saltmarsh plants - autochthonous bioaugmentation.

    Science.gov (United States)

    Nunes da Silva, Marta; Mucha, Ana P; Rocha, A Cristina; Teixeira, Catarina; Gomes, Carlos R; Almeida, C Marisa R

    2014-02-15

    The recovery of estuarine environments is in need. Phytoremediation could be a valid option to reduce pollution while preserving natural biodiversity. In this work, estuarine sediments colonized by Juncus maritimus or Phragmites australis were spiked with cadmium in the absence and in the presence of an autochthonous microbial consortium resistant to the metal. The aim of this study was to increase the potential for cadmium phytoremediation that these two halophyte plants have shown. Experiments were carried out in greenhouses with an automatic irrigation system that simulated estuarine tidal cycles. After 2 months, Cd concentration in P. australis stems increased up to 7 times when the rhizosphere was inoculated with the microbial consortium. So, P. australis phytoextraction potential was increased through autochthonous bioaugmentation. As for J. maritimus, up to 48% more Cd (total amount) was observed in its belowground tissues after being subjected to autochthonous bioaugmentation. Therefore, the phytostabilization potential of this plant was promoted. For both plants this increase in cadmium uptake did not cause significant signs of toxicity. Therefore, the addition of autochthonous microorganisms resistant to cadmium seems to be a valuable strategy to potentiate phytoremediation of this metal in saltmarshes, being useful for the recovery of moderately impacted estuaries. This will contribute for an effective management of these areas. Research on this topic regarding estuarine ecosystems, especially saltmarshes, is, to our knowledge, inexistent.

  14. Towards a palaeoecological model of the Mesoproterozoic Taoudeni Basin, Mauritania, Northwestern Africa: implications for early eukaryote evolution

    Science.gov (United States)

    Beghin, Jérémie; Guilbaud, Romain; Poulton, Simon W.; Gueneli, Nur; Brocks, Jochen J.; Storme, Jean-Yves; Blanpied, Christian; Javaux, Emmanuelle J.

    2016-04-01

    The mid-Proterozoic rock record preserves a relatively moderate diversity of early eukaryotes, despite the early evolution of fundamental features of the eukaryotic cell. Common hypotheses involve the redox state of stratified oceans with oxic shallow waters, euxinic mid-depth waters, and anoxic and ferruginous deep waters during this time period. Mid-Proterozoic eukaryotes would have found suitable ecological niches in estuarine, fluvio-deltaic and coastal shallow marine environments near nutrient sources, while N2-fixing photoautotrophs bacteria would have been better competitors than eukaryotic algae in nutrient-poor niches. Here, we present the first palaeoecological model of the late Mesoproterozoic Taoudeni Basin, Mauritania, Northwestern Africa. Previous palaeontological studies in the basin reported stromatolites, a low diversity of microfossils - including one species of presumed eukaryotes: verrucae-bearing acritarch - and biomarkers of anoxygenic phototrophic purple and green sulfur bacteria, cyanobacteria and microaerophilic methanotrophs. However, no biomarkers diagnostic for crown group eukaryotes were reported so far. In addition to exceptionally well preserved microbial mats showing chain-like aggregates of pyrite grains, we observed a total of sixty-two morphotaxa including nine presumed prokaryotes, thirty-five possible prokaryotes or eukaryotes, fifteen unambiguous species of eukaryotes - ornamented and process-bearing acritarchs, multicellular morphotaxon, putative VSMs, large budding vesicles, and vesicles with a sophisticated excystment structure: the pylome - and three remains of structured kerogen. Here, we combined the geological context (sedimentological features and lithofacies), iron speciation (n = 156) - with the aim of reconstructing palaeoredox environmental conditions -, and microfossils quantitative analysis (n = 61). Sediments were deposited under shallow waters in pericratonic (western basin) and epicratonic (eastern basin

  15. Will enhanced turbulence in inland waters result in elevated production of autochthonous dissolved organic matter?

    Science.gov (United States)

    Zhou, Yongqiang; Zhou, Jian; Jeppesen, Erik; Zhang, Yunlin; Qin, Boqiang; Shi, Kun; Tang, Xiangming; Han, Xiaoxia

    2016-02-01

    Biological activity in lakes is strongly influenced by hydrodynamic conditions, not least turbulence intensity; which increases the encounter rate between plankter and nutrient patches. To investigate whether enhanced turbulence in shallow and eutrophic lakes may result in elevated biological production of autochthonous chromophoric dissolved organic matter (CDOM), a combination of field campaigns and mesocosm experiments was used. Parallel factor analysis identified seven components: four protein-like, one microbial humic-like and two terrestrial humic-like components. During our field campaigns, elevated production of autochthonous CDOM was recorded in open water with higher wind speed and wave height than in inner bays, implying that elevated turbulence resulted in increased production of autochthonous CDOM. Confirming the field campaign results, in the mesocosm experiment enhanced turbulence resulted in a remarkably higher microbial humic-like C1 and tryptophan-like C3 (pproduction of autochthonous CDOM. This is consistent with the significantly higher mean concentrations of chlorophyll-a (Chl-a) and dissolved organic carbon (DOC) and the enhanced phytoplanktonic alkaline phosphatase activity (PAPA) recorded in the experimental turbulence groups than in the control group (p<0.05). The C:N ratio (from 3.34 to 25.72 with a mean of 13.13±4.08) for the mesocosm CDOM samples further suggested their probable autochthonous origin. Our results have implications for the understanding of CDOM cycling in shallow aquatic ecosystems influenced by wind-induced waves, in which the enhanced turbulence associated with extreme weather conditions may be further stimulated by the predicted global climate change.

  16. Temporal dynamics and decay of putatively allochthonous and autochthonous viral genotypes in contrasting freshwater lakes.

    Science.gov (United States)

    Hewson, Ian; Barbosa, Jorge G; Brown, Julia M; Donelan, Ryan P; Eaglesham, James B; Eggleston, Erin M; LaBarre, Brenna A

    2012-09-01

    Aquatic viruses play important roles in the biogeochemistry and ecology of lacustrine ecosystems; however, their composition, dynamics, and interactions with viruses of terrestrial origin are less extensively studied. We used a viral shotgun metagenomic approach to elucidate candidate autochthonous (i.e., produced within the lake) and allochthonous (i.e., washed in from other habitats) viral genotypes for a comparative study of their dynamics in lake waters. Based on shotgun metagenomes prepared from catchment soil and freshwater samples from two contrasting lakes (Cayuga Lake and Fayetteville Green Lake), we selected two putatively autochthonous viral genotypes (phycodnaviruses likely infecting algae and cyanomyoviruses likely infecting picocyanobacteria) and two putatively allochthonous viral genotypes (geminiviruses likely infecting terrestrial plants and circoviruses infecting unknown hosts but common in soil libraries) for analysis by genotype-specific quantitative PCR (TaqMan) applied to DNAs from viruses in the viral size fraction of lake plankton, i.e., 0.2 μm > virus > 0.02 μm. The abundance of autochthonous genotypes largely reflected expected host abundance, while the abundance of allochthonous genotypes corresponded with rainfall and storm events in the respective catchments, suggesting that viruses with these genotypes may have been transported to the lake in runoff. The decay rates of allochthonous and autochthonous genotypes, assessed in incubations where all potential hosts were killed, were generally lower (0.13 to 1.50% h(-1)) than those reported for marine virioplankton but similar to those for freshwater virioplankton. Both allochthonous and autochthonous viral genotypes were detected at higher concentrations in subsurface sediments than at the water-sediment interface. Our data indicate that putatively allochthonous viruses are present in lake plankton and sediments, where their temporal dynamics reflect active transport to the lake during

  17. Evolutionary position of breviate amoebae and the primary eukaryote divergence.

    Science.gov (United States)

    Minge, Marianne A; Silberman, Jeffrey D; Orr, Russell J S; Cavalier-Smith, Thomas; Shalchian-Tabrizi, Kamran; Burki, Fabien; Skjaeveland, Asmund; Jakobsen, Kjetill S

    2009-02-22

    Integration of ultrastructural and molecular sequence data has revealed six supergroups of eukaryote organisms (excavates, Rhizaria, chromalveolates, Plantae, Amoebozoa and opisthokonts), and the root of the eukaryote evolutionary tree is suggested to lie between unikonts (Amoebozoa, opisthokonts) and bikonts (the other supergroups). However, some smaller lineages remain of uncertain affinity. One of these unassigned taxa is the anaerobic, free-living, amoeboid flagellate Breviata anathema, which is of key significance as it is unclear whether it is a unikont (i.e. possibly the deepest branching amoebozoan) or a bikont. To establish its evolutionary position, we sequenced thousands of Breviata genes and calculated trees using 78 protein sequences. Our trees and specific substitutions in the 18S RNA sequence indicate that Breviata is related to other Amoebozoa, thereby significantly increasing the cellular diversity of this phylum and establishing Breviata as a deep-branching unikont. We discuss the implications of these results for the ancestral state of Amoebozoa and eukaryotes generally, demonstrating that phylogenomics of phylogenetically 'nomadic' species can elucidate key questions in eukaryote evolution. Furthermore, mitochondrial genes among the Breviata ESTs demonstrate that Breviata probably contains a modified anaerobic mitochondrion. With these findings, remnants of mitochondria have been detected in all putatively deep-branching amitochondriate organisms.

  18. Molecular typing of fecal eukaryotic microbiota of human infants and their respective mothers

    Indian Academy of Sciences (India)

    Prashant K Pandey; Jay Siddharth; Pankaj Verma; Ashish Bavdekar; Milind S Patole; Yogesh S Shouche

    2012-06-01

    The micro-eukaryotic diversity from the human gut was investigated using universal primers directed towards 18S rRNA gene, fecal samples being the source of DNA. The subjects in this study included two breast-fed and two formula-milk-fed infants and their mothers. The study revealed that the infants did not seem to harbour any micro-eukaryotes in their gut. In contrast, there were distinct eukaryotic microbiota present in the mothers. The investigation is the first of its kind in the comparative study of the human feces to reveal the presence of micro-eukaryotic diversity variance in infants and adults from the Indian subcontinent. The micro-eukaryotes encountered during the investigation include known gut colonizers like Blastocystis and some fungi species. Some of these micro-eukaryotes have been speculated to be involved in clinical manifestations of various diseases. The study is an attempt to highlight the importance of micro-eukaryotes in the human gut.

  19. Autochthonous microbe-assisted phytoremediation of brown coal mine overburden soil

    Science.gov (United States)

    Hamidović, Saud; Teodorović, Smilja; Lalević, Blažo; Karličić, Vera; Jovanović, Ljubinko; Kiković, Dragan; Raičević, Vera

    2015-04-01

    One of the largest brown coal mines in Bosnia and Herzegovina (BiH), Kakanj, has been exploited for over a hundred years. As a consequence of decades of exploitation, severe biocenosis disturbance and degradation of the entire ecosystem have occurred, resulting in overburden soil formation. A significant challenge in remediation of degraded mining areas is difficulty in creating conditions favorable for vegetation growth. Thus, numerous remediation technologies have focused on increasing soil nutrient composition, as well as the number and activity of plant growth-promoting bacteria (PGPB), given that they stimulate host plant growth by increasing the availability of essential nutrients (phosphorus, nitrogen, manganese, iron), producing phytohormones, and providing protection from pathogens. The main objective of this research was to characterize autochthonous plant and microbial overburden communities and access their ability to restore these contaminated soils. Phytocenological analysis of vegetation and plant species was performed according to Flora Europaea (2001), from 2011 - 2013. Our results show that plant species were not detected at mine overburden soil in 2011. However, we detected presence of a single plant species, Amaranthus albus L., in 2012. Further, we recorded the presence of five families (Amaranthaceae, Chenopodiaceae, Convolvulaceae, Poaceae and Polygonaceae) in 2013. Microbial abundance and enzymatic activity were also examined during the same period. The diversity of microbial populations in the first year was rather small. Two Bacillus spp., B. simplex and a B. cereus group member, indigenous to mine overburden were isolated and identified using standard macroscopic and microscopic, as well as molecular techniques (Hamidovic et al., submitted). Phosphate solubilizing activity of bacteria was tested on National Botanical Research Institute's phosphate growth medium (1999). Production of ammonia was determined in peptone water with Nessler

  20. Open Questions on the Origin of Eukaryotes.

    Science.gov (United States)

    López-García, Purificación; Moreira, David

    2015-11-01

    Despite recent progress, the origin of the eukaryotic cell remains enigmatic. It is now known that the last eukaryotic common ancestor was complex and that endosymbiosis played a crucial role in eukaryogenesis at least via the acquisition of the alphaproteobacterial ancestor of mitochondria. However, the nature of the mitochondrial host is controversial, although the recent discovery of an archaeal lineage phylogenetically close to eukaryotes reinforces models proposing archaea-derived hosts. We argue that, in addition to improved phylogenomic analyses with more comprehensive taxon sampling to pinpoint the closest prokaryotic relatives of eukaryotes, determining plausible mechanisms and selective forces at the origin of key eukaryotic features, such as the nucleus or the bacterial-like eukaryotic membrane system, is essential to constrain existing models.

  1. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

    Science.gov (United States)

    Gnad, Florian; Forner, Francesca; Zielinska, Dorota F; Birney, Ewan; Gunawardena, Jeremy; Mann, Matthias

    2010-12-01

    High accuracy mass spectrometry has proven to be a powerful technology for the large scale identification of serine/threonine/tyrosine phosphorylation in the living cell. However, despite many described phosphoproteomes, there has been no comparative study of the extent of phosphorylation and its evolutionary conservation in all domains of life. Here we analyze the results of phosphoproteomics studies performed with the same technology in a diverse set of organisms. For the most ancient organisms, the prokaryotes, only a few hundred proteins have been found to be phosphorylated. Applying the same technology to eukaryotic species resulted in the detection of thousands of phosphorylation events. Evolutionary analysis shows that prokaryotic phosphoproteins are preferentially conserved in all living organisms, whereas-site specific phosphorylation is not. Eukaryotic phosphosites are generally more conserved than their non-phosphorylated counterparts (with similar structural constraints) throughout the eukaryotic domain. Yeast and Caenorhabditis elegans are two exceptions, indicating that the majority of phosphorylation events evolved after the divergence of higher eukaryotes from yeast and reflecting the unusually large number of nematode-specific kinases. Mitochondria present an interesting intermediate link between the prokaryotic and eukaryotic domains. Applying the same technology to this organelle yielded 174 phosphorylation sites mapped to 74 proteins. Thus, the mitochondrial phosphoproteome is similarly sparse as the prokaryotic phosphoproteomes. As expected from the endosymbiotic theory, phosphorylated as well as non-phosphorylated mitochondrial proteins are significantly conserved in prokaryotes. However, mitochondrial phosphorylation sites are not conserved throughout prokaryotes, consistent with the notion that serine/threonine phosphorylation in prokaryotes occurred relatively recently in evolution. Thus, the phosphoproteome reflects major events in the

  2. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers.

    Science.gov (United States)

    Hadziavdic, Kenan; Lekang, Katrine; Lanzen, Anders; Jonassen, Inge; Thompson, Eric M; Troedsson, Christofer

    2014-01-01

    High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. Full primer universality is difficult or impossible to achieve and studies using different primer sets make biodiversity comparisons problematic. The aim of this study was to design and optimize universal eukaryotic primers that could be used as a standard in future biodiversity studies. Using the alignment of all eukaryotic sequences from the publicly available SILVA database, we generated a full characterization of variable versus conserved regions in the 18S rRNA gene. All variable regions within this gene were analyzed and our results suggested that the V2, V4 and V9 regions were best suited for biodiversity assessments. Previously published universal eukaryotic primers as well as a number of self-designed primers were mapped to the alignment. Primer selection will depend on sequencing technology used, and this study focused on the 454 pyrosequencing GS FLX Titanium platform. The results generated a primer pair yielding theoretical matches to 80% of the eukaryotic and 0% of the prokaryotic sequences in the SILVA database. An empirical test of marine sediments using the AmpliconNoise pipeline for analysis of the high throughput sequencing data yielded amplification of sequences for 71% of all eukaryotic phyla with no isolation of prokaryotic sequences. To our knowledge this is the first characterization of the complete 18S rRNA gene using all eukaryotes present in the SILVA database, providing a robust test for universal eukaryotic primers. Since both in silico and empirical tests using high throughput sequencing retained high inclusion of eukaryotic phyla and exclusion of prokaryotes, we conclude that these primers are well suited for assessing eukaryote diversity, and can be used as a standard in biodiversity studies.

  3. Characterization of the 18S rRNA gene for designing universal eukaryote specific primers.

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    Kenan Hadziavdic

    Full Text Available High throughput sequencing technology has great promise for biodiversity studies. However, an underlying assumption is that the primers used in these studies are universal for the prokaryotic or eukaryotic groups of interest. Full primer universality is difficult or impossible to achieve and studies using different primer sets make biodiversity comparisons problematic. The aim of this study was to design and optimize universal eukaryotic primers that could be used as a standard in future biodiversity studies. Using the alignment of all eukaryotic sequences from the publicly available SILVA database, we generated a full characterization of variable versus conserved regions in the 18S rRNA gene. All variable regions within this gene were analyzed and our results suggested that the V2, V4 and V9 regions were best suited for biodiversity assessments. Previously published universal eukaryotic primers as well as a number of self-designed primers were mapped to the alignment. Primer selection will depend on sequencing technology used, and this study focused on the 454 pyrosequencing GS FLX Titanium platform. The results generated a primer pair yielding theoretical matches to 80% of the eukaryotic and 0% of the prokaryotic sequences in the SILVA database. An empirical test of marine sediments using the AmpliconNoise pipeline for analysis of the high throughput sequencing data yielded amplification of sequences for 71% of all eukaryotic phyla with no isolation of prokaryotic sequences. To our knowledge this is the first characterization of the complete 18S rRNA gene using all eukaryotes present in the SILVA database, providing a robust test for universal eukaryotic primers. Since both in silico and empirical tests using high throughput sequencing retained high inclusion of eukaryotic phyla and exclusion of prokaryotes, we conclude that these primers are well suited for assessing eukaryote diversity, and can be used as a standard in biodiversity studies.

  4. Selection of an autochthonous Saccharomyces strain starter for alcoholic fermentation of Sherry base wines.

    Science.gov (United States)

    Rodríguez-Palero, María Jesús; Fierro-Risco, Jesús; Codón, Antonio C; Benítez, Tahía; Valcárcel, Manuel J

    2013-06-01

    Several indigenous Saccharomyces strains from musts were isolated in the Jerez de la Frontera region, at the end of spontaneous fermentation, in order to select the most suitable autochthonous yeast starter, during the 2007 vintage. Five strains were chosen for their oenological abilities and fermentative kinetics to elaborate a Sherry base wine. The selected autochthonous strains were characterized by molecular methods: electrophoretic karyotype and random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) and by physiological parameters: fermentative power, ethanol production, sugar consumption, acidity and volatile compound production, sensory quality, killer phenotype, desiccation, and sulphur dioxide tolerance. Laboratory- and pilot-scale fermentations were conducted with those autochthonous strains. One of them, named J4, was finally selected over all others for industrial fermentations. The J4 strain, which possesses exceptional fermentative properties and oenological qualities, prevails in industrial fermentations, and becomes the principal biological agent responsible for winemaking. Sherry base wine, industrially manufactured by means of the J4 strain, was analyzed, yielding, together with its sensory qualities, final average values of 0.9 g/l sugar content, 13.4 % (v/v) ethanol content and 0.26 g/l volatile acidity content; apart from a high acetaldehyde production, responsible for the distinctive aroma of "Fino". This base wine was selected for "Fino" Sherry elaboration and so it was fortified; it is at present being subjected to biological aging by the so-called "flor" yeasts. The "flor" velum formed so far is very high quality. To the best of our knowledge, this is the first study covering from laboratory to industrial scale of characterization and selection of autochthonous starter intended for alcoholic fermentation in Sherry base wines. Since the 2010 vintage, the indigenous J4 strain is employed to industrially manufacture a

  5. Caciotta della Garfagnana cheese: selection and evaluation of autochthonous mesophilic lactic acid bacteria as starter cultures

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    Domenico Cerri

    2011-04-01

    Full Text Available The aim of this study was to isolate, identify and select, with respect to acidification and proteolytic activities, the autochthonous mesophilic lactic acid bacteria (LAB present in milk and Caciotta della Garfagnana, a cheese produced either with raw or thermised cow’s milk in small dairies and family plants of Garfagnana (Tuscany, to obtain LAB strains with attributes suitable to be employed as starter cultures in this type of cheese, particularly when thermised milk is used to control spoilage microflora. Samples of raw milk, curd and cheese were collected from three representative farmers of the production area and used to isolate autochthonous LAB. Phenotypic and genotypic (species-specific PCR assay identification of isolated LAB was done. Twenty-eight strains of LAB isolated from milk, curd and cheese were screened for acidifying and proteolytic activities. LAB strains with the better attributes were used as mesophilic starter cultures in technological trials: experimental cheeses manufactured with the addition of autochthonous LAB and control cheeses were compared for LAB and pH evolution. Experimental cheeses presented a significant increase in the mesophilic lactic acid microflora up to 14 days of ripening and significantly lower pH values up to seven days of ripening. The use of wild selected mesophilic lactic acid bacteria, together with thermisation of milk, for the Caciotta della Garfagnana looks very promising and could help to both standardise the production and improve quality and traditional characteristics of this type of cheese.

  6. Caciotta della Garfagnana cheese: selection and evaluation of autochthonous mesophilic lactic acid bacteria as starter cultures

    Directory of Open Access Journals (Sweden)

    Barbara Turchi

    2011-05-01

    Full Text Available he aim of this study was to isolate, identify and select, with respect to acidification and proteolytic activities, the autochthonous mesophilic lactic acid bacteria (LAB present in milk and Caciotta della Garfagnana, a cheese produced either with raw or thermised cow’s milk in small dairies and family plants of Garfagnana (Tuscany, to obtain LAB strains with attributes suitable to be employed as starter cultures in this type of cheese, particularly when thermised milk is used to control spoilage microflora. Samples of raw milk, curd and cheese were collected from three representative farmers of the production area and used to isolate autochthonous LAB. Phenotypic and genotypic (species-specific PCR assay identification of isolated LAB was done. Twenty-eight strains of LAB isolated from milk, curd and cheese were screened for acidifying and proteolytic activities. LAB strains with the better attributes were used as mesophilic starter cultures in technological trials: experimental cheeses manufactured with the addition of autochthonous LAB and control cheeses were compared for LAB and pH evolution. Experimental cheeses presented a significant increase in the mesophilic lactic acid microflora up to 14 days of ripening and significantly lower pH values up to seven days of ripening. The use of wild selected mesophilic lactic acid bacteria, together with thermisation of milk, for the Caciotta della Garfagnana looks very promising and could help to both standardise the production and improve quality and traditional characteristics of this type of cheese.

  7. Selection of autochthonous sour cherry (Prunus cerasus L. genotypes in Feketić region

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    Radičević Sanja

    2012-01-01

    Full Text Available Autochthonous genotypes of fruit species are very important source of genetic variability and valuable material for breeding work. Fruit Research Institute-Čačak has a long tradition of studying autochthonous genotypes of temperate fruits sporadically spread and preserved in some localities in Serbia. Over 2005-2006, the following properties of nine autochthonous sour cherry genotypes grown in Feketic region were investigated: flowering and ripening time, pomological properties, biochemical composition of fruits and field resistance to causal agents of cherry diseases - cherry leaf spot (Blumeriella jaapii (Rehm. v. Arx., shot-hole (Clasterosporium carpophilum (Lév. Aderh. and brown rot (Monilinia laxa /Ader et Ruhl./ Honey ex Whetz.. The genotypes were tested for the presence of Prune dwarf virus and Prunus necrotic ring spot virus. In majority of genotypes fruits were large, with exceptional organoleptical properties, whereas ripening time was in the first ten or twenty days of June. The highest fruit weight was observed in F-1 genotype (8.1 g. The highest soluble solids and total sugars content were found in F- 4 genotype (17.60% and 14.25%, respectively. As for field resistance to causal agents of diseases and good pomo-technological properties, F-1, F-2, F-3, F-7 and F-8 genotypes were singled out. [Projekat Ministarstva nauke Republike Srbije, br. TR31064

  8. Low molecular weight peptides derived from sarcoplasmic proteins produced by an autochthonous starter culture in a beaker sausage model

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    Constanza M. López

    2015-06-01

    Significance: The selection of a specific autochthonous starter culture guarantees the hygiene and typicity of fermented sausages. The identification of new peptides as well as new target proteins by means of peptidomics represents a significant step toward the elucidation of the role of microorganisms in meat proteolysis. Moreover, these peptides may be further used as biomarkers capable to certify the use of the applied autochthonous starter culture described here.

  9. Eu-Detect: An algorithm for detecting eukaryotic sequences in metagenomic data sets

    Indian Academy of Sciences (India)

    Monzoorul Haque Mohammed; Sudha Chadaram Dinakar; Dinakar Komanduri; Tarini Shankar Ghosh; Sharmila S Mande

    2011-09-01

    Physical partitioning techniques are routinely employed (during sample preparation stage) for segregating the prokaryotic and eukaryotic fractions of metagenomic samples. In spite of these efforts, several metagenomic studies focusing on bacterial and archaeal populations have reported the presence of contaminating eukaryotic sequences inmetagenomic data sets. Contaminating sequences originate not only from genomes of micro-eukaryotic species but also from genomes of (higher) eukaryotic host cells. The latter scenario usually occurs in the case of host-associatedmetagenomes. Identification and removal of contaminating sequences is important, since these sequences not only impact estimates of microbial diversity but also affect the accuracy of several downstream analyses. Currently, the computational techniques used for identifying contaminating eukaryotic sequences, being alignment based, are slow, inefficient, and require huge computing resources. In this article, we present Eu-Detect, an alignment-free algorithm that can rapidly identify eukaryotic sequences contaminating metagenomic data sets. Validation results indicate that on a desktop with modest hardware specifications, the Eu-Detect algorithm is able to rapidly segregate DNA sequence fragments of prokaryotic and eukaryotic origin, with high sensitivity. A Web server for the Eu-Detect algorithm is available at http://metagenomics.atc.tcs.com/Eu-Detect/.

  10. Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica Mine, Mexico.

    Science.gov (United States)

    Ragon, Marie; Van Driessche, Alexander E S; García-Ruíz, Juan M; Moreira, David; López-García, Purificación

    2013-01-01

    The Naica Mine in northern Mexico is famous for its giant gypsum crystals, which may reach up to 11 m long and contain fluid inclusions that might have captured microorganisms during their formation. These crystals formed under particularly stable geochemical conditions in cavities filled by low salinity hydrothermal water at 54-58°C. We have explored the microbial diversity associated to these deep, saline hydrothermal waters collected in the deepest (ca. 700-760 m) mineshafts by amplifying, cloning and sequencing small-subunit ribosomal RNA genes using primers specific for archaea, bacteria, and eukaryotes. Eukaryotes were not detectable in the samples and the prokaryotic diversity identified was very low. Two archaeal operational taxonomic units (OTUs) were detected in one sample. They clustered with, respectively, basal Thaumarchaeota lineages and with a large clade of environmental sequences branching at the base of the Thermoplasmatales within the Euryarchaeota. Bacterial sequences belonged to the Candidate Division OP3, Firmicutes and the Alpha- and Beta-proteobacteria. Most of the lineages detected appear autochthonous to the Naica system, since they had as closest representatives environmental sequences retrieved from deep sediments or the deep subsurface. In addition, the high GC content of 16S rRNA gene sequences belonging to the archaea and to some OP3 OTUs suggests that at least these lineages are thermophilic. Attempts to amplify diagnostic functional genes for methanogenesis (mcrA) and sulfate reduction (dsrAB) were unsuccessful, suggesting that those activities, if present, are not important in the aquifer. By contrast, genes encoding archaeal ammonium monooxygenase (AamoA) were amplified, suggesting that Naica Thaumarchaeota are involved in nitrification. These organisms are likely thermophilic chemolithoautotrophs adapted to thrive in an extremely energy-limited environment.

  11. Microbial diversity in the deep-subsurface hydrothermal aquifer feeding the giant gypsum crystal-bearing Naica mine, Mexico

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    Marie eRagon

    2013-03-01

    Full Text Available The Naica mine in Northern Mexico is famous for its giant gypsum crystals, which may reach up to 11 m long and contain fluid inclusions that might have captured microorganisms during their formation. These crystals formed under particularly stable geochemical conditions in cavities filled by low salinity hydrothermal water at 54-58°C. We have explored the microbial diversity associated to these deep, saline hydrothermal waters collected in the deepest (ca. 700-760 m mineshafts by amplifying, cloning and sequencing small-subunit ribosomal RNA genes using primers specific for archaea, bacteria and eukaryotes. Eukaryotes were not detectable in the samples and the prokaryotic diversity identified was very low. Two archaeal operational taxonomic units (OTUs were detected in one sample. They clustered with, respectively, basal Thaumarchaeota lineages and with a large clade of environmental sequences branching at the base of the Thermoplasmatales within the Euryarchaeota. Bacterial sequences belonged to the Candidate Division OP3, Firmicutes and the Alpha- and Beta-Proteobacteria. Most of the lineages detected appear autochthonous to the Naica system, since they had as closest representatives environmental sequences retrieved from deep sediments or the deep subsurface. In addition, the high GC content of 16S rRNA gene sequences belonging to the archaea and to some OP3 OTUs suggests that at least these lineages are thermophilic. Attempts to amplify diagnostic functional genes for methanogenesis (mcrA and sulfate reduction (dsrAB were unsuccessful, suggesting that those activities, if present, are not important in the aquifer. By contrast, genes encoding archaeal ammonium monooxygenase (AamoA were amplified, suggesting that Naica Thaumarchaeota are involved in nitrification. These organisms are likely thermophilic chemolithoautotrophs adapted to thrive in an extremely energy-limited environment.

  12. Nucleoporin Nup98: a gatekeeper in the eukaryotic kingdoms.

    Science.gov (United States)

    Iwamoto, Masaaki; Asakawa, Haruhiko; Hiraoka, Yasushi; Haraguchi, Tokuko

    2010-06-01

    The nucleoporin Nup98 is an essential component of the nuclear pore complex. This peripheral nucleoporin with its Gly-Leu-Phe-Gly (GLFG) repeat domain contributes to nuclear-cytoplasmic trafficking, including mRNA export. In addition, accumulating studies indicate that Nup98 plays roles in several important biological events such as gene expression, mitotic checkpoint, and pathogenesis. Nup98 is well conserved among organisms belonging to the fungi and animal kingdoms. These kingdoms belong to the eukaryotic supergroup Opisthokonta. However, there is considerable diversity in the Nup98 orthologs expressed in organisms belonging to other eukaryotic supergroups. Intriguingly, in ciliates, a unicellular organism having two functionally distinct nuclei, GLFG-Nup98 is present in one of the nuclei and a distinct Nup98 ortholog is present in the other nucleus, and these different Nup98s participate in a nucleus-selective transport mechanism. In this review, we focus on Nup98 function and discuss how this nucleoporin has evolved in eukaryotic kingdoms.

  13. The twilight of Heliozoa and rise of Rhizaria, an emerging supergroup of amoeboid eukaryotes

    Science.gov (United States)

    Nikolaev, Sergey I.; Berney, Cédric; Fahrni, José F.; Bolivar, Ignacio; Polet, Stephane; Mylnikov, Alexander P.; Aleshin, Vladimir V.; Petrov, Nikolai B.; Pawlowski, Jan

    2004-01-01

    Recent molecular phylogenetic studies revealed the extraordinary diversity of single-celled eukaryotes. However, the proper assessment of this diversity and accurate reconstruction of the eukaryote phylogeny are still impeded by the lack of molecular data for some major groups of easily identifiable and cultivable protists. Among them, amoeboid eukaryotes have been notably absent from molecular phylogenies, despite their diversity, complexity, and abundance. To partly fill this phylogenetic gap, we present here combined small-subunit ribosomal RNA and actin sequence data for the three main groups of “Heliozoa” (Actinophryida, Centrohelida, and Desmothoracida), the heliozoan-like Sticholonche, and the radiolarian group Polycystinea. Phylogenetic analyses of our sequences demonstrate the polyphyly of heliozoans, which branch either as an independent eukaryotic lineage (Centrohelida), within stramenopiles (Actinophryida), or among cercozoans (Desmothoracida), in broad agreement with previous ultrastructure-based studies. Our data also provide solid evidence for the existence of the Rhizaria, an emerging supergroup of mainly amoeboid eukaryotes that includes desmothoracid heliozoans, all radiolarians, Sticholonche, and foraminiferans, as well as various filose and reticulose amoebae and some flagellates. PMID:15148395

  14. How many novel eukaryotic 'kingdoms'? Pitfalls and limitations of environmental DNA surveys

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    Pawlowski Jan

    2004-06-01

    Full Text Available Abstract Background Over the past few years, the use of molecular techniques to detect cultivation-independent, eukaryotic diversity has proven to be a powerful approach. Based on small-subunit ribosomal RNA (SSU rRNA gene analyses, these studies have revealed the existence of an unexpected variety of new phylotypes. Some of them represent novel diversity in known eukaryotic groups, mainly stramenopiles and alveolates. Others do not seem to be related to any molecularly described lineage, and have been proposed to represent novel eukaryotic kingdoms. In order to review the evolutionary importance of this novel high-level eukaryotic diversity critically, and to test the potential technical and analytical pitfalls and limitations of eukaryotic environmental DNA surveys (EES, we analysed 484 environmental SSU rRNA gene sequences, including 81 new sequences from sediments of the small river, the Seymaz (Geneva, Switzerland. Results Based on a detailed screening of an exhaustive alignment of eukaryotic SSU rRNA gene sequences and the phylogenetic re-analysis of previously published environmental sequences using Bayesian methods, our results suggest that the number of novel higher-level taxa revealed by previously published EES was overestimated. Three main sources of errors are responsible for this situation: (1 the presence of undetected chimeric sequences; (2 the misplacement of several fast-evolving sequences; and (3 the incomplete sampling of described, but yet unsequenced eukaryotes. Additionally, EES give a biased view of the diversity present in a given biotope because of the difficult amplification of SSU rRNA genes in some taxonomic groups. Conclusions Environmental DNA surveys undoubtedly contribute to reveal many novel eukaryotic lineages, but there is no clear evidence for a spectacular increase of the diversity at the kingdom level. After re-analysis of previously published data, we found only five candidate lineages of possible novel

  15. Bacterial proteins pinpoint a single eukaryotic root.

    Science.gov (United States)

    Derelle, Romain; Torruella, Guifré; Klimeš, Vladimír; Brinkmann, Henner; Kim, Eunsoo; Vlček, Čestmír; Lang, B Franz; Eliáš, Marek

    2015-02-17

    The large phylogenetic distance separating eukaryotic genes and their archaeal orthologs has prevented identification of the position of the eukaryotic root in phylogenomic studies. Recently, an innovative approach has been proposed to circumvent this issue: the use as phylogenetic markers of proteins that have been transferred from bacterial donor sources to eukaryotes, after their emergence from Archaea. Using this approach, two recent independent studies have built phylogenomic datasets based on bacterial sequences, leading to different predictions of the eukaryotic root. Taking advantage of additional genome sequences from the jakobid Andalucia godoyi and the two known malawimonad species (Malawimonas jakobiformis and Malawimonas californiana), we reanalyzed these two phylogenomic datasets. We show that both datasets pinpoint the same phylogenetic position of the eukaryotic root that is between "Unikonta" and "Bikonta," with malawimonad and collodictyonid lineages on the Unikonta side of the root. Our results firmly indicate that (i) the supergroup Excavata is not monophyletic and (ii) the last common ancestor of eukaryotes was a biflagellate organism. Based on our results, we propose to rename the two major eukaryotic groups Unikonta and Bikonta as Opimoda and Diphoda, respectively.

  16. Safety improvement and preservation of typical sensory qualities of traditional dry fermented sausages using autochthonous starter cultures.

    Science.gov (United States)

    Talon, Régine; Leroy, Sabine; Lebert, Isabelle; Giammarinaro, Philippe; Chacornac, Jean-Paul; Latorre-Moratalla, Mariluz; Vidal-Carou, Carmen; Zanardi, Emanuela; Conter, Mauro; Lebecque, Annick

    2008-08-15

    Traditional dry fermented sausages are manufactured without addition of starter cultures in small-scale processing units, their fermentation relying on indigenous microflora. Characterisation and control of these specific bacteria are essential for the sensory quality and the safety of the sausages. The aim of this study was to develop an autochthonous starter culture that improves safety while preserving the typical sensory characteristics of traditional sausages. An autochthonous starter composed of Lactobacillus sakei, Staphylococcus equorum and Staphylococcus succinus isolated from a traditional fermented sausage was developed. These strains were tested for their susceptibility to antibiotics and their production of biogenic amines. This starter was evaluated in situ at the French traditional processing unit where the strains had been isolated. Effects of the autochthonous starter were assessed by analysing the microbial, physico-chemical, biochemical and sensory characteristics of the sausages. Inoculation with the chosen species was confirmed using known species-specific PCR assays for L. sakei and S. equorum and a species-specific PCR assay developed in this study for S. succinus. Strains were monitored by pulse-field gel electrophoresis typing. Addition of autochthonous microbial starter cultures improved safety compared with the traditional natural fermentation of sausages, by inhibiting the pathogen Listeria monocytogenes, decreasing the level of biogenic amines and by limiting fatty acid and cholesterol oxidation. Moreover, autochthonous starter did not affect the typical sensory quality of the traditional sausages. This is the first time to our knowledge that selection, development and validation in situ of autochthonous starter cultures have been carried out, and also the first time that S. equorum together with S. succinus have been used as starter cultures for meat fermentation. Use of autochthonous starter cultures is an effective tool for limiting

  17. Complementing the Eukaryotic Protein Interactome.

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    Robert Pesch

    Full Text Available Protein interaction networks are important for the understanding of regulatory mechanisms, for the explanation of experimental data and for the prediction of protein functions. Unfortunately, most interaction data is available only for model organisms. As a possible remedy, the transfer of interactions to organisms of interest is common practice, but it is not clear when interactions can be transferred from one organism to another and, thus, the confidence in the derived interactions is low. Here, we propose to use a rich set of features to train Random Forests in order to score transferred interactions. We evaluated the transfer from a range of eukaryotic organisms to S. cerevisiae using orthologs. Directly transferred interactions to S. cerevisiae are on average only 24% consistent with the current S. cerevisiae interaction network. By using commonly applied filter approaches the transfer precision can be improved, but at the cost of a large decrease in the number of transferred interactions. Our Random Forest approach uses various features derived from both the target and the source network as well as the ortholog annotations to assign confidence values to transferred interactions. Thereby, we could increase the average transfer consistency to 85%, while still transferring almost 70% of all correctly transferable interactions. We tested our approach for the transfer of interactions to other species and showed that our approach outperforms competing methods for the transfer of interactions to species where no experimental knowledge is available. Finally, we applied our predictor to score transferred interactions to 83 targets species and we were able to extend the available interactome of B. taurus, M. musculus and G. gallus with over 40,000 interactions each. Our transferred interaction networks are publicly available via our web interface, which allows to inspect and download transferred interaction sets of different sizes, for various

  18. Study of features of the biochemical composition of red vine leaves of autochthonous varieties in Russia

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    Oganesyants Lev

    2015-01-01

    Full Text Available One of the fields of processing industries’ activities is the use of secondary resources. The use the vegetative parts of grape plants may become an important component in solving this task. Such vegetative parts, first of all, include red grape leaves, which provide a large reserve of antioxidants and other biologically useful substances. The Russian Research Institute of Brewing and Wine Industry has carried out the detailed study of the features of the biochemical composition of red vine leaves of autochthonous varieties cultivated in the Rostov region of Russia. Cold winters are considered to be the major stress for the grape plants. Under these conditions, leaves accumulate large amount of biologically active substances, including trans-resveratrol, which provide significant advantage compared with the harvest from grapes cultivated in areas where the plants are not protected during winter. Comparative studies on the biochemical composition of red vine leaves of autochthonous and European varieties were conducted, including on the use of bioassay systems in vitro. It was found that extracts of red vine leaves of autochthonous varieties have a marked effect on the rate of glutathione reductase and pyruvate kinase reactions that are demonstrating their angioprotective and energizing properties. The increase in the rate of the catalase reaction indicates the manifestation of antioxidant properties. The technology of CO2 – and highly concentrated hydrophilic extracts production from red vine leaves that preserves biologically active compounds to the maximum extent possible. The extracts are used for the manufacture of soft drinks that have the venomotor action and may be applied in the process of the manufacture of fat products with extended shelf life, as well as the main raw material for the preparations with the pronounced angioprotective effect.

  19. Crystal structure of the eukaryotic ribosome.

    Science.gov (United States)

    Ben-Shem, Adam; Jenner, Lasse; Yusupova, Gulnara; Yusupov, Marat

    2010-11-26

    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.

  20. Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics.

    Science.gov (United States)

    Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

    2014-01-27

    The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi [corrected] . at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi [corrected]. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi [corrected].

  1. Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Lamellomorpha sp. indicated by metagenomics

    Science.gov (United States)

    Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

    2014-01-01

    The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Lamellomorpha sp. at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Lamellomorpha sp.. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Lamellomorpha sp..

  2. [Clinical study of prejudicing autochthonous speech act (thought)--acceleration of the activity in the remission process of schizophrenia].

    Science.gov (United States)

    Kato, S

    1997-01-01

    Schizophrenics occasionally experience guilty feeling at having insulted someone such as having said "You fool" or "Die" to a new acquaintance. They also experience guilty feeling from autochthonous thought, a feeling of having prejudiced his neighbour. This latter autochthonous thought is considered to be closely related with the former prejudicing speech act. The author would provisionally call these phenomenons of prejudice, prejudicing autochthonous speech act (or prejudicing autochthonous thought), particularly in the case in which the object of prejudice is an intimate real other, or a co-presenting other. Based on his own nine cases, the author has first described the clinical characteristics of this symptom, and then developed psychopathological considerations to draw a attention to the therapeutic importance of this symptom. On the symptomatological ground, the prejudicing autochthonous speech act (thought) belongs to psychomotor verbal hallucinations (J. Séglas), more precisely to the soliloquy type of this hallucination. On the clinical ground, this symptom is likely to follow auditory hallucination caused by an acute state or that of recovery period from this state. Furthermore, it is not infrequent that general improvement as well as remission follow the appearance of this symptom. This symptomatological change of the center of gravity, that is, the gradual transition from auditory hallucination to prejudicing autochthonous speech act (thought) is considered to correspond to a change of the patient's position in relation to others. This position, once experienced passively, is now experienced actively. In other words, the patient, coming out of an acute psychotic state and opening to an intersubjective world, is confronted with a high tension relationship with others. The prejudicing autochthonous speech act (thought) appears in this situation, to restore the patient's own subjectivity in coping with the pressure of real others. In this case, this

  3. Impact of autochthonous music on the creation of tourist destination image

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    Željko Blagus

    2010-06-01

    Full Text Available This paper tries to determine to what extent autochthonous music may contribute to the creation of the image of a tourist destination. In other words, it aims at demostrating how the Croatian Međimurje County may become recognizable as a tourist destination on the basis of its ethnographic heritage, which exists even today in different ways. The first part of the paper deals with the role of image in the choice of destination and defines the term “destination image”. A particular emphasis is placed on the analysis of the impact of autochthonous music on the image of the Međimurje County. It proves the thesis that autochthonous music plays an important role in the presentation and dissemination of the recognizable image of Međimurje. As shown in this paper, the music of Međimurje is a resource characterized by dynamism, change and adaptability. It is also a source of inspiration of numerous musicians and, thanks to its uniqueness in terms of authenticity, representativeness or rarity, it becomes a quality symbol of the environment in which it came to be. In this sense, the paper offers an insight into the way in which the music of Međimurje might be used to improve the understanding and acceptance of certain communication content by making the message clearer and easier to understand. It is evident that the market evaluated the autochthonous music of Međimurje in the past and will continue to evaluate it to an increasing extent in the future, so claims about its incompatibility with commercialism and utilitarianism may only be accepted conditionally. The second part of the paper includes a description of the methodological frame of the field research that has been conducted as well as a report on its results. In this way, the analysis of the role which the music of Međimurje plays in the creation of image acquires its concrete meaning, since the results of the research can be interpreted with regard to their assumptions and their

  4. Sex and the eukaryotic cell cycle is consistent with a viral ancestry for the eukaryotic nucleus.

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    Bell, Philip John Livingstone

    2006-11-07

    The origin of the eukaryotic cell cycle, including mitosis, meiosis, and sex are as yet unresolved aspects of the evolution of the eukaryotes. The wide phylogenetic distribution of both mitosis and meiosis suggest that these processes are integrally related to the origin of the earliest eukaryotic cells. According to the viral eukaryogenesis (VE) hypothesis, the eukaryotes are a composite of three phylogenetically unrelated organisms: a viral lysogen that evolved into the nucleus, an archaeal cell that evolved into the eukaryotic cytoplasm, and an alpha-proteobacterium that evolved into the mitochondria. In the extended VE hypothesis presented here, the eukaryotic cell cycle arises as a consequence of the derivation of the nucleus from a lysogenic DNA virus.

  5. Transfer of DNA from Bacteria to Eukaryotes

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    Benoît Lacroix

    2016-07-01

    Full Text Available Historically, the members of the Agrobacterium genus have been considered the only bacterial species naturally able to transfer and integrate DNA into the genomes of their eukaryotic hosts. Yet, increasing evidence suggests that this ability to genetically transform eukaryotic host cells might be more widespread in the bacterial world. Indeed, analyses of accumulating genomic data reveal cases of horizontal gene transfer from bacteria to eukaryotes and suggest that it represents a significant force in adaptive evolution of eukaryotic species. Specifically, recent reports indicate that bacteria other than Agrobacterium, such as Bartonella henselae (a zoonotic pathogen, Rhizobium etli (a plant-symbiotic bacterium related to Agrobacterium, or even Escherichia coli, have the ability to genetically transform their host cells under laboratory conditions. This DNA transfer relies on type IV secretion systems (T4SSs, the molecular machines that transport macromolecules during conjugative plasmid transfer and also during transport of proteins and/or DNA to the eukaryotic recipient cells. In this review article, we explore the extent of possible transfer of genetic information from bacteria to eukaryotic cells as well as the evolutionary implications and potential applications of this transfer.

  6. Efficient method to optimize antibodies using avian leukosis virus display and eukaryotic cells.

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    Yu, Changming; Pike, Gennett M; Rinkoski, Tommy A; Correia, Cristina; Kaufmann, Scott H; Federspiel, Mark J

    2015-08-11

    Antibody-based therapeutics have now had success in the clinic. The affinity and specificity of the antibody for the target ligand determines the specificity of therapeutic delivery and off-target side effects. The discovery and optimization of high-affinity antibodies to important therapeutic targets could be significantly improved by the availability of a robust, eukaryotic display technology comparable to phage display that would overcome the protein translation limitations of microorganisms. The use of eukaryotic cells would improve the diversity of the displayed antibodies that can be screened and optimized as well as more seamlessly transition into a large-scale mammalian expression system for clinical production. In this study, we demonstrate that the replication and polypeptide display characteristics of a eukaryotic retrovirus, avian leukosis virus (ALV), offers a robust, eukaryotic version of bacteriophage display. The binding affinity of a model single-chain Fv antibody was optimized by using ALV display, improving affinity >2,000-fold, from micromolar to picomolar levels. We believe ALV display provides an extension to antibody display on microorganisms and offers virus and cell display platforms in a eukaryotic expression system. ALV display should enable an improvement in the diversity of properly processed and functional antibody variants that can be screened and affinity-optimized to improve promising antibody candidates.

  7. Antibiotic susceptibility and antimicrobial activity of autochthonous starter cultures as safety parameters for fresh cheese production

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    Dora Bučan

    2013-11-01

    Full Text Available The antibiotic susceptibility and antimicrobial activity, as food safety parameters important for application of autochthonous lactic acid bacteria (LAB, that previously satisfied technological criteria for functional starter cultures in fresh cheese production were examined. Soluble whole cell protein patterns of autochthonous LAB strains from fresh cheese, obtained by SDS-PAGE, revealed the presence of two predominant strains, which were identified as Lactobacillus fermentum A8 and Enterococcus faecium A7. These strains were not resistant and shown susceptibility to antibiotics: ampicillin, bacitracin, penicillin G, azithromycin, chloramphenicol, clarithromycin, clindamycin, spiramycin, tetracycline, streptomycin, neomycin, gentamicin, erythromycin, rifampicin and novobiocin. Lb. fermentum A8 strain displayed phenotypic resistance to vancomycin, but this resistance is intrinsic, not transferable and it is acceptable from the safety aspect. The capacity of Lb. fermentum A8 and Ec. faecium A7 to inhibit growth of test-microorganisms Listeria monocytogenes ATCC 11911, Escherichia coli 3014, Salmonella enterica serovar Typhimurium FP1 and Staphylococcus aureus 3048, was also analysed. According to obtained results, Lb. fermentum A8 and Ec. faecium A7 are safe from the aspect of spreading antibiotic resistance and could be useful as bioprotective cultures that inhibit common bacterial food contaminants, including L. monocytogenes.

  8. Combined Treatment Effects of Radiation and Immunotherapy: Studies in an Autochthonous Prostate Cancer Model

    Energy Technology Data Exchange (ETDEWEB)

    Wada, Satoshi [Department of Oncology, James Buchanan Brady Urological Institute, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland (United States); Harris, Timothy J.; Tryggestad, Erik [Department of Radiation Oncology and Molecular Radiation Sciences, James Buchanan Brady Urological Institute, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland (United States); Yoshimura, Kiyoshi [Department of Oncology, James Buchanan Brady Urological Institute, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland (United States); Zeng, Jing [Department of Radiation Oncology and Molecular Radiation Sciences, James Buchanan Brady Urological Institute, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland (United States); Yen, Hung-Rong; Getnet, Derese; Grosso, Joseph F.; Bruno, Tullia C. [Department of Oncology, James Buchanan Brady Urological Institute, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland (United States); De Marzo, Angelo M. [Department of Pathology, James Buchanan Brady Urological Institute, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland (United States); Department of Urology, James Buchanan Brady Urological Institute, Johns Hopkins Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland (United States); and others

    2013-11-15

    Purpose: To optimize the combination of ionizing radiation and cellular immunotherapy using a preclinical autochthonous model of prostate cancer. Methods and Materials: Transgenic mice expressing a model antigen under a prostate-specific promoter were treated using a platform that integrates cone-beam CT imaging with 3-dimensional conformal therapy. Using this technology we investigated the immunologic and therapeutic effects of combining ionizing radiation with granulocyte/macrophage colony-stimulating factor-secreting cellular immunotherapy for prostate cancer in mice bearing autochthonous prostate tumors. Results: The combination of ionizing radiation and immunotherapy resulted in a significant decrease in pathologic tumor grade and gross tumor bulk that was not evident with either single-modality therapy. Furthermore, combinatorial therapy resulted in improved overall survival in a preventive metastasis model and in the setting of established micrometastases. Mechanistically, combined therapy resulted in an increase of the ratio of effector-to-regulatory T cells for both CD4 and CD8 tumor-infiltrating lymphocytes. Conclusions: Our preclinical model establishes a potential role for the use of combined radiation-immunotherapy in locally advanced prostate cancer, which warrants further exploration in a clinical setting.

  9. The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation.

    Science.gov (United States)

    Roger, Andrew J; Hug, Laura A

    2006-06-29

    Determining the relationships among and divergence times for the major eukaryotic lineages remains one of the most important and controversial outstanding problems in evolutionary biology. The sequencing and phylogenetic analyses of ribosomal RNA (rRNA) genes led to the first nearly comprehensive phylogenies of eukaryotes in the late 1980s, and supported a view where cellular complexity was acquired during the divergence of extant unicellular eukaryote lineages. More recently, however, refinements in analytical methods coupled with the availability of many additional genes for phylogenetic analysis showed that much of the deep structure of early rRNA trees was artefactual. Recent phylogenetic analyses of a multiple genes and the discovery of important molecular and ultrastructural phylogenetic characters have resolved eukaryotic diversity into six major hypothetical groups. Yet relationships among these groups remain poorly understood because of saturation of sequence changes on the billion-year time-scale, possible rapid radiations of major lineages, phylogenetic artefacts and endosymbiotic or lateral gene transfer among eukaryotes. Estimating the divergence dates between the major eukaryote lineages using molecular analyses is even more difficult than phylogenetic estimation. Error in such analyses comes from a myriad of sources including: (i) calibration fossil dates, (ii) the assumed phylogenetic tree, (iii) the nucleotide or amino acid substitution model, (iv) substitution number (branch length) estimates, (v) the model of how rates of evolution change over the tree, (vi) error inherent in the time estimates for a given model and (vii) how multiple gene data are treated. By reanalysing datasets from recently published molecular clock studies, we show that when errors from these various sources are properly accounted for, the confidence intervals on inferred dates can be very large. Furthermore, estimated dates of divergence vary hugely depending on the methods

  10. Effect of autochthonous lactic acid bacteria starters on health-promoting and sensory properties of tomato juices.

    Science.gov (United States)

    Di Cagno, Raffaella; Surico, Rosalinda F; Paradiso, Annalisa; De Angelis, Maria; Salmon, Jean-Christophe; Buchin, Solange; De Gara, Laura; Gobbetti, Marco

    2009-01-15

    Strains of Lactobacillus plantarum, Weissella cibaria/confusa, Lactobacillus brevis, Pediococcus pentosaceous, Lactobacillus sp. and Enterococcus faecium/faecalis were identified from raw tomatoes by Biolog System, partial 16S rRNA gene sequence and subjected to typing by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) analysis. Ten autochthonous strains were singly used to ferment tomato juice (TJ) via a protocol which included fermentation at 25 degrees C for 17 h and further storage at 4 degrees C for 40 days. Unstarted TJ and TJ fermented with an allochthonous strain of L. plantarum were used as the controls. All autochthonous strains grew well in TJ reaching cell densities ca. 10,000 and 10 times higher than unstarted TJ and TJ fermented with the allochthonous strain. Viscosity of TJs fermented with autochthonous strains was generally the highest, especially when started with W. cibaria/confusa which synthesized exo-polysaccharides. Overall, unstarted TJ and TJ fermented with the allochthonous strain showed marked decreases of ascorbic acid (ASC), glutathione (GSH) and total antioxidant activity (TTA) during storage. On the contrary, several TJs fermented with autochthonous strains, especially with L. plantarum POM1 and POM 35, maintained elevated values of ASC, GSH and TAA. The variation of color indexes mirrored the above behavior. TJs fermented with the above two autochthonous strains were compared to controls based on volatile components through Purge and Trap or Solid Phase Microextraction Gas Chromatography-Mass Spectrometry (PT or SPME-GC/MS) analysis. As shown by Principal Component Analysis a large number of volatiles belonging to various chemical classes markedly differentiated TJs fermented with autochthonous strains with respect to controls.

  11. The independent prokaryotic origins of eukaryotic fructose-1, 6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle

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    Jiang Yong-Hai

    2012-10-01

    Full Text Available Abstract Background In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP and sedoheptulose-1, 7-bisphosphate (SBP are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (F/SBPase, while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (FBPase and sedoheptulose-1, 7-bisphosphatase (SBPase, respectively. It was proposed that these two eukaryotic enzymes arose from the divergence of a common ancestral eubacterial bifunctional F/SBPase of mitochondrial origin. However, no specific affinity between SBPase and eubacterial FBPase or F/SBPase can be observed in the previous phylogenetic analyses, and it is hard to explain why SBPase and/or F/SBPase are/is absent from most extant nonphotosynthetic eukaryotes according to this scenario. Results Domain analysis indicated that eubacterial F/SBPase of two different resources contain distinct domains: proteobacterial F/SBPases contain typical FBPase domain, while cyanobacterial F/SBPases possess FBPase_glpX domain. Therefore, like prokaryotic FBPase, eubacterial F/SBPase can also be divided into two evolutionarily distant classes (Class I and II. Phylogenetic analysis based on a much larger taxonomic sampling than previous work revealed that all eukaryotic SBPase cluster together and form a close sister group to the clade of epsilon-proteobacterial Class I FBPase which are gluconeogenesis-specific enzymes, while all eukaryotic chloroplast FBPase group together with eukaryotic cytosolic FBPase and form another distinct clade which then groups with the Class I FBPase of diverse eubacteria. Motif analysis of these enzymes also supports these phylogenetic correlations. Conclusions There are two evolutionarily distant classes of eubacterial bifunctional F/SBPase. Eukaryotic FBPase and SBPase do not diverge from either of them but have two independent origins

  12. Microbial eukaryote plankton communities of high-mountain lakes from three continents exhibit strong biogeographic patterns.

    Science.gov (United States)

    Filker, Sabine; Sommaruga, Ruben; Vila, Irma; Stoeck, Thorsten

    2016-05-01

    Microbial eukaryotes hold a key role in aquatic ecosystem functioning. Yet, their diversity in freshwater lakes, particularly in high-mountain lakes, is relatively unknown compared with the marine environment. Low nutrient availability, low water temperature and high ultraviolet radiation make most high-mountain lakes extremely challenging habitats for life and require specific molecular and physiological adaptations. We therefore expected that these ecosystems support a plankton diversity that differs notably from other freshwater lakes. In addition, we hypothesized that the communities under study exhibit geographic structuring. Our rationale was that geographic dispersal of small-sized eukaryotes in high-mountain lakes over continental distances seems difficult. We analysed hypervariable V4 fragments of the SSU rRNA gene to compare the genetic microbial eukaryote diversity in high-mountain lakes located in the European Alps, the Chilean Altiplano and the Ethiopian Bale Mountains. Microbial eukaryotes were not globally distributed corroborating patterns found for bacteria, multicellular animals and plants. Instead, the plankton community composition emerged as a highly specific fingerprint of a geographic region even on higher taxonomic levels. The intraregional heterogeneity of the investigated lakes was mirrored in shifts in microbial eukaryote community structure, which, however, was much less pronounced compared with interregional beta-diversity. Statistical analyses revealed that on a regional scale, environmental factors are strong predictors for plankton community structures in high-mountain lakes. While on long-distance scales (>10 000 km), isolation by distance is the most plausible scenario, on intermediate scales (up to 6000 km), both contemporary environmental factors and historical contingencies interact to shift plankton community structures.

  13. Gene Discovery for Synthetic Biology: Exploring the Novel Natural Product Biosynthetic Capacity of Eukaryotic Microalgae.

    Science.gov (United States)

    O'Neill, E C; Saalbach, G; Field, R A

    2016-01-01

    Eukaryotic microalgae are an incredibly diverse group of organisms whose sole unifying feature is their ability to photosynthesize. They are known for producing a range of potent toxins, which can build up during harmful algal blooms causing damage to ecosystems and fisheries. Genome sequencing is lagging behind in these organisms because of their genetic complexity, but transcriptome sequencing is beginning to make up for this deficit. As more sequence data becomes available, it is apparent that eukaryotic microalgae possess a range of complex natural product biosynthesis capabilities. Some of the genes concerned are responsible for the biosynthesis of known toxins, but there are many more for which we do not know the products. Bioinformatic and analytical techniques have been developed for natural product discovery in bacteria and these approaches can be used to extract information about the products synthesized by algae. Recent analyses suggest that eukaryotic microalgae produce many complex natural products that remain to be discovered.

  14. Marine biofilm bacteria evade eukaryotic predation by targeted chemical defense.

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    Carsten Matz

    Full Text Available Many plants and animals are defended from predation or herbivory by inhibitory secondary metabolites, which in the marine environment are very common among sessile organisms. Among bacteria, where there is the greatest metabolic potential, little is known about chemical defenses against bacterivorous consumers. An emerging hypothesis is that sessile bacterial communities organized as biofilms serve as bacterial refuge from predation. By testing growth and survival of two common bacterivorous nanoflagellates, we find evidence that chemically mediated resistance against protozoan predators is common among biofilm populations in a diverse set of marine bacteria. Using bioassay-guided chemical and genetic analysis, we identified one of the most effective antiprotozoal compounds as violacein, an alkaloid that we demonstrate is produced predominately within biofilm cells. Nanomolar concentrations of violacein inhibit protozoan feeding by inducing a conserved eukaryotic cell death program. Such biofilm-specific chemical defenses could contribute to the successful persistence of biofilm bacteria in various environments and provide the ecological and evolutionary context for a number of eukaryote-targeting bacterial metabolites.

  15. Mercury dilution by autochthonous organic matter in a fertilized mangrove wetland.

    Science.gov (United States)

    Machado, Wilson; Sanders, Christian J; Santos, Isaac R; Sanders, Luciana M; Silva-Filho, Emmanoel V; Luiz-Silva, Wanilson

    2016-06-01

    A dated sediment core from a highly-fertilized mangrove wetland located in Cubatão (SE Brazil) presented a negative correlation between mercury (Hg) and organic carbon contents. This is an unusual result for a metal with well-known affinity to organic matter. A dilution of Hg concentrations by autochthonous organic matter explained this observation, as revealed by carbon stable isotopes signatures (δ(13)C). Mercury dilution by the predominant mangrove-derived organic matter counterbalanced the positive influences of algal-derived organic matter and clay contents on Hg levels, suggesting that deleterious effects of Hg may be attenuated. Considering the current paradigm on the positive effect of organic matter on Hg concentrations in coastal sediments and the expected increase in mangrove organic matter burial due to natural and anthropogenic stimulations of primary production, predictions on the influences of organic matter on Hg accumulation in mangrove wetlands deserve caution.

  16. INFLUENCE OF AUTOCHTHONOUS SACCHAROMYCES SPP. STRAINS ON THE SULFUR DIOXIDE CONCENTRATION IN WINE

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    Josip BELJAK

    2008-11-01

    Full Text Available The aim of this work was to study the infl uence of 8 autochthonous yeasts strains on the sulfur dioxide formation. For this purpose grape must from the Traminer, Muller Turgau and Chardonnay grapes was used. Yeast strains used were cultivated at the Department for Microbiology, Faculty of Agriculture, University of Zagreb. Five of them were H2S negative and three H2S positive. Tested yeast strains produced from 19 up to 45 mg/l of sulfur dioxide. The highest sulfur dioxide producer was one of the H2S positive yeast strains. The results indicated the initial sugar concentration to be very important for the ratio of sulfur dioxide production. Yeasts were more effi cient at higher sugar levels.

  17. Strongyloidiasis in a young French woman raises concern about possible ongoing autochthonous transmission in Spain

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    Alexandre Duvignaud

    2016-01-01

    Full Text Available Strongyloidiasis is one of the most common geohelminth infections in tropical and subtropical areas. Accurate diagnosis remains challenging, leading to an overall underestimation of strongyloidiasis prevalence. The possibility of ongoing autochthonous transmission in some temperate areas and especially in southern Europe is still debated, and data supporting this hypothesis are scarce. The case of a young French woman, who had travelled frequently to Spain and had acquired Strongyloides stercoralis infection as revealed by gastrointestinal symptoms and hypereosinophilia, is reported here. Physicians should keep in mind the risk of being infected in some areas of southern Europe, even if low, in order to avoid the life-threatening manifestations of strongyloidiasis favoured by pathological or therapeutic immunosuppression.

  18. Screening for ligninolytic enzymes from autochthonous fungi and applications for decolorization of Remazole Marine Blue

    Science.gov (United States)

    Erden, Emre; Ucar, M. Cigdem; Gezer, Tekin; Pazarlioglu, Nurdan Kasikara

    2009-01-01

    This study presents new and alternative fungal strains for the production of ligninolytic enzymes which have great potential to use in industrial and biotechnological processes. Thirty autochthonous fungal strains were harvested from Bornova-Izmir in Turkiye. In the fresh fruitbody extracts laccase, manganese peroxidase and lignin peroxidase activities, which are the principal enzymes responsible for ligninocellulose degradation by Basidiomycetes, were screened. Spores of some of the basidiomycetes species such as Cortinarius sp., Trametes versicolor, Pleurotus ostreatus, Abortiporus biennis, Lyophyllum subglobisporium, Ramaria stricta, Ganoderma carnosum, Lactarius delicious ve Lepista nuda were isolated and investigated optimum cultivation conditions in submerged fermentation for high yields of ligninolytic enzyme production. In addition, isolated fungal strains were monitored on agar plates whether having the capability of decolorization of a textile dye Remazol Marine Blue. PMID:24031371

  19. Do consumers from Međimurje region recognize their autochthonous Turoš cheese?

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    Kristijan Valkaj

    2013-11-01

    Full Text Available The aim of this study was to determine whether consumers from the Međimurje region recognise and distinguish the autochthonous cheese called Turoš from similar cheeses like Prgica and Kvargl originating from regions neighbouring to Međimurje. Chemical, textural and microbiological properties of all three cheeses were given. Preference tests with 200 consumers using a face-to-face survey and a two-step procedure were performed. The blind taste test showed that 97 % of the respondents recognised differences between the tasted samples, and almost half of them preferred the Turoš cheese. Similarly, the informed test showed that a significantly higher number of the respondents preferred the Turoš cheese in comparison to Kvargl and Prgica. Statistical analyses showed no significant differences between respondents’ preferences in the blind and the informed tests.

  20. Effect of autochthonous starter cultures on the biogenic amine content of ewe's milk cheese throughout ripening.

    Science.gov (United States)

    Renes, E; Diezhandino, I; Fernández, D; Ferrazza, R E; Tornadijo, M E; Fresno, J M

    2014-12-01

    Cheese is among the most commonly implicated foods associated with biogenic amines poisoning. The aim of this study was to evaluate the effects of the type of autochthonous starter culture and ripening time on the concentration of biogenic amines (histamine, tyramine, putrescine, cadaverine, tryptamine, β-phenylethylamine, spermine and spermidine) in cheeses made from pasteurized ewe's milk. 4 cheese batches were made, in duplicate, and ripened for 7 months. The biogenic amines of 40 cheeses were analysed by high performance liquid chromatography. The predominant biogenic amines determined at the end of the ripening time were phenylethylamine, spermine and tryptamine. Together, these accounted for 81% of the total of biogenic amines studied. The type of starter culture used to make the ewe's cheese had a significant effect (p culture made up entirely of Lactococcus lactis subsp. lactis and L. lactis subsp. cremoris or of the same in combination with Lactobacillus plantarum.

  1. [Autochthonous acute viral and bacterial infections of the central nervous system (meningitis and encephalitis)].

    Science.gov (United States)

    Pérez-Ruiz, Mercedes; Vicente, Diego; Navarro-Marí, José María

    2008-07-01

    Rapid diagnosis of acute viral and bacterial infections of the central nervous system (meningitis and encephalitis) is highly important for the clinical management of the patient and helps to establish early therapy that may solve life-threatening situations, to avoid unnecessary empirical treatments, to reduce hospital stay, and to facilitate appropriate interventions in the context of public health. Molecular techniques, especially real-time polymerase chain reaction, have become the fastest and most sensitive diagnostic procedures for autochthonous viral meningitis and encephalitis, and their role is becoming increasingly important for the diagnosis and control of most frequent acute bacterial meningitides. Automatic and closed systems may encourage the widespread and systematic use of molecular techniques for the diagnosis of these neurological syndromes in most laboratories.

  2. Seasonal variation of allochthonous and autochthonous energy inputs in an alpine stream

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    Stefano Fenoglio

    2014-10-01

    Full Text Available Despite the enormous importance of alpine streams, information about many aspects of their ecology is still insufficient. Alpine lotic systems differ in many environmental characteristics from those lower down, for example because above tree line streams drain catchments where terrestrial vegetation is scarce and allochthonous organic input is expected to be small. The main objectives of this study were to examine seasonal variation of autochthonous and allochthonous energetic inputs and their relationship with macroinvertebrate communities in the Po river, an alpine non-glacial stream (NW Italy. For one year, samplings were monthly performed in a homogeneous 100 m stream reach for discharge, autochthonous energy input (benthic chlorophyll a, allochthonous energy input (coarse particulate organic matter, abundance and structure of benthic macroinvertebrate community. Chlorophyll a concentrations were in the range of what reported for other alpine streams, but presented a time-lag with respect to what has been reported for glacial-fed mountain rivers. CPOM amounts were lower than those in lowland, forested streams of the same area but exhibited an intriguing, different seasonal variability, probably reported for the first time, with a maximum in spring and a minimum in winter. We collected 29,950 macroinvertebrates belonging to 13 families and 10 orders. Benthic communities were essentially dominated by Ephemeroptera, Plecoptera and Diptera. Scrapers was the most important FFG, but also Shredders were well represented. Relationships between chlorophyll a concentrations, CPOM availability and macroinvertebrate community characteristics were analysed and discussed considering the existence of different top-down or bottom-up regulation mechanisms. This study confirms that benthic algae constitute an essential resource for macroinvertebrates in alpine streams above the tree line but also underlines the importance of terrestrial organic input, a

  3. Dietary preferences of two seagrass inhabiting gastropods: Allochthonous vs autochthonous resources

    Science.gov (United States)

    Doropoulos, C.; Hyndes, G. A.; Lavery, P. S.; Tuya, F.

    2009-06-01

    The movement of allochthonous resources between habitats can provide important trophic linkages in marine landscapes. In coastal south-western Australia, the kelp Ecklonia radiata is removed from reefs and accumulates in large quantities in neighbouring seagrass meadows. This study investigated the feeding preferences and grazing rates of two locally abundant gastropods, Pyrene bidentata and Cantharidus lepidus, which exhibit inverse distribution patterns with proximity to reefs in seagrass meadows, to determine whether allochthonous kelp has the potential to contribute to the seagrass food web. Using laboratory choice and no-choice feeding experiments, we tested whether detached kelp is consumed preferentially, and at greater rates, by these two species than autochthonous resources (i.e. seagrass, epiphytic red macroalgae and seagrass periphyton). Both species displayed a preference for macroalgae and seagrass periphyton over seagrass leaves. In choice experiments, neither species displayed any clear preference between kelp (fresh or aged), red macroalgae or periphyton (consumption rates ranged between 0.39 and 3.64 mg ind -1 day -1), but consumption rates were always higher relative to seagrass. In no-choice experiments, P. bidentata displayed minimal consumption of seagrass, but consumed fresh and aged kelp, red macroalgae and seagrass periphyton at similar rates (2.00-7.22 mg ind -1 day -1). In comparison, C. lepidus consumed periphyton at far greater rates than any other food source (3.61 vs 0.33-1.10 mg ind -1 day -1). The results indicate that both P. bidentata and C. lepidus showed a clear preference for macroalgae and periphyton over seagrass, but no consistent preference towards any autochthonous or allochthonous algal resource. Reef-derived kelp therefore has the potential to contribute to the food web of seagrass meadows, and subsidise secondary production.

  4. Positive effects of bacterial diversity on ecosystem functioning driven by complementarity effects in a bioremediation context.

    Directory of Open Access Journals (Sweden)

    Patrick A Venail

    Full Text Available Despite their importance as ecosystem drivers, our understanding of the influence of bacterial diversity on ecosystem functioning is limited. After identifying twelve bacterial strains from two petroleum-contaminated sites, we experimentally explored the impact of biodiversity on total density by manipulating the number of strains in culture. Irrespective of the origin of the bacteria relative to the contaminant, biodiversity positively influenced total density. However, bacteria cultured in the crude oil of their origin (autochthonous reached higher densities than bacteria from another origin (allochthonous and the relationship between diversity and density was stronger for autochthonous bacteria. By measuring the relative contribution of each strain to total density we showed that the observed positive effect of increasing diversity on total density was mainly due to positive interactions among species and not the presence of a particular species. Our findings can be explained by the complex chemical composition of crude oil and the necessity of a diverse array of organisms with complementary enzymatic capacities to achieve its degradation. The long term exposure to a contaminant may have allowed different bacteria to become adapted to the use of different fractions of the crude, resulting in higher complementarity in resource use in autochthonous bacteria compared to allochthonous ones. Our results could help improve the success of bioaugmentation as a bioremediation technique by suggesting the use of a diversified set of autochthonous organisms.

  5. Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes

    Directory of Open Access Journals (Sweden)

    Reddy Anireddy SN

    2006-01-01

    Full Text Available Abstract Background Kinesins, a superfamily of molecular motors, use microtubules as tracks and transport diverse cellular cargoes. All kinesins contain a highly conserved ~350 amino acid motor domain. Previous analysis of the completed genome sequence of one flowering plant (Arabidopsis has resulted in identification of 61 kinesins. The recent completion of genome sequencing of several photosynthetic and non-photosynthetic eukaryotes that belong to divergent lineages offers a unique opportunity to conduct a comprehensive comparative analysis of kinesins in plant and non-plant systems and infer their evolutionary relationships. Results We used the kinesin motor domain to identify kinesins in the completed genome sequences of 19 species, including 13 newly sequenced genomes. Among the newly analyzed genomes, six represent photosynthetic eukaryotes. A total of 529 kinesins was used to perform comprehensive analysis of kinesins and to construct gene trees using the Bayesian and parsimony approaches. The previously recognized 14 families of kinesins are resolved as distinct lineages in our inferred gene tree. At least three of the 14 kinesin families are not represented in flowering plants. Chlamydomonas, a green alga that is part of the lineage that includes land plants, has at least nine of the 14 known kinesin families. Seven of ten families present in flowering plants are represented in Chlamydomonas, indicating that these families were retained in both the flowering-plant and green algae lineages. Conclusion The increase in the number of kinesins in flowering plants is due to vast expansion of the Kinesin-14 and Kinesin-7 families. The Kinesin-14 family, which typically contains a C-terminal motor, has many plant kinesins that have the motor domain at the N terminus, in the middle, or the C terminus. Several domains in kinesins are present exclusively either in plant or animal lineages. Addition of novel domains to kinesins in lineage

  6. Eukaryotic membrane protein overproduction in Lactococcus lactis

    NARCIS (Netherlands)

    Kunji, Edmund R.S.; Chan, Ka Wai; Slotboom, Dirk Jan; Floyd, Suzanne; O’Connor, Rosemary; Monné, Magnus

    2005-01-01

    Eukaryotic membrane proteins play many vital roles in the cell and are important drug targets. Approximately 25% of all genes identified in the genome are known to encode membrane proteins, but the vast majority have no assigned function. Although the generation of structures of soluble proteins has

  7. Evidence for a Minimal Eukaryotic Phosphoproteome?

    NARCIS (Netherlands)

    Diks, Sander H.; Parikh, Kaushal; van der Sijde, Marijke; Joore, Jos; Ritsema, Tita; Peppelenbosch, Maikel P.

    2007-01-01

    Background. Reversible phosphorylation catalysed by kinases is probably the most important regulatory mechanism in eukaryotes. Methodology/Principal Findings. We studied the in vitro phosphorylation of peptide arrays exhibiting the majority of PhosphoBase-deposited protein sequences, by factors in c

  8. Eukaryotic and prokaryotic microbial communities during microalgal biomass production.

    Science.gov (United States)

    Lakaniemi, Aino-Maija; Hulatt, Chris J; Wakeman, Kathryn D; Thomas, David N; Puhakka, Jaakko A

    2012-11-01

    Eukaryotic and bacterial communities were characterized and quantified in microalgal photobioreactor cultures of freshwater Chlorella vulgaris and marine Dunaliella tertiolecta. The microalgae exhibited good growth, whilst both cultures contained diverse bacterial communities. Both cultures included Proteobacteria and Bacteroidetes, while C. vulgaris cultures also contained Actinobacteria. The bacterial genera present in the cultures were different due to different growth medium salinities and possibly different extracellular products. Bacterial community profiles were relatively stable in D. tertiolecta cultures but not in C. vulgaris cultures likely due to presence of ciliates (Colpoda sp.) in the latter. The presence of ciliates did not, however, cause decrease in total number of C. vulgaris or bacteria during 14 days of cultivation. Quantitative PCR (qPCR) reliably showed relative microalgal and bacterial cell numbers in the batch cultures with stable microbial communities, but was not effective when bacterial communities varied. Raw culture samples were successfully used as qPCR templates.

  9. Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill.

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    Holly M Bik

    Full Text Available Benthic habitats harbour a significant (yet unexplored diversity of microscopic eukaryote taxa, including metazoan phyla, protists, algae and fungi. These groups are thought to underpin ecosystem functioning across diverse marine environments. Coastal marine habitats in the Gulf of Mexico experienced visible, heavy impacts following the Deepwater Horizon oil spill in 2010, yet our scant knowledge of prior eukaryotic biodiversity has precluded a thorough assessment of this disturbance. Using a marker gene and morphological approach, we present an intensive evaluation of microbial eukaryote communities prior to and following oiling around heavily impacted shorelines. Our results show significant changes in community structure, with pre-spill assemblages of diverse Metazoa giving way to dominant fungal communities in post-spill sediments. Post-spill fungal taxa exhibit low richness and are characterized by an abundance of known hydrocarbon-degrading genera, compared to prior communities that contained smaller and more diverse fungal assemblages. Comparative taxonomic data from nematodes further suggests drastic impacts; while pre-spill samples exhibit high richness and evenness of genera, post-spill communities contain mainly predatory and scavenger taxa alongside an abundance of juveniles. Based on this community analysis, our data suggest considerable (hidden initial impacts across Gulf beaches may be ongoing, despite the disappearance of visible surface oil in the region.

  10. Large variability of bathypelagic microbial eukaryotic communities across the world’s oceans

    KAUST Repository

    Pernice, Massimo C.

    2015-10-09

    In this work, we study the diversity of bathypelagic microbial eukaryotes (0.8–20 μm) in the global ocean. Seawater samples from 3000 to 4000 m depth from 27 stations in the Atlantic, Pacific and Indian Oceans were analyzed by pyrosequencing the V4 region of the 18S ribosomal DNA. The relative abundance of the most abundant operational taxonomic units agreed with the results of a parallel metagenomic analysis, suggesting limited PCR biases in the tag approach. Although rarefaction curves for single stations were seldom saturated, the global analysis of all sequences together suggested an adequate recovery of bathypelagic diversity. Community composition presented a large variability among samples, which was poorly explained by linear geographic distance. In fact, the similarity between communities was better explained by water mass composition (26% of the variability) and the ratio in cell abundance between prokaryotes and microbial eukaryotes (21%). Deep diversity appeared dominated by four taxonomic groups (Collodaria, Chrysophytes, Basidiomycota and MALV-II) appearing in different proportions in each sample. Novel diversity amounted to 1% of the pyrotags and was lower than expected. Our study represents an essential step in the investigation of bathypelagic microbial eukaryotes, indicating dominating taxonomic groups and suggesting idiosyncratic assemblages in distinct oceanic regions.

    The ISME Journal advance online publication, 9 October 2015; doi:10.1038/ismej.2015.170

  11. Large-scale patterns in biodiversity of microbial eukaryotes from the abyssal sea floor.

    Science.gov (United States)

    Scheckenbach, Frank; Hausmann, Klaus; Wylezich, Claudia; Weitere, Markus; Arndt, Hartmut

    2010-01-05

    Eukaryotic microbial life at abyssal depths remains "uncharted territory" in eukaryotic microbiology. No phylogenetic surveys have focused on the largest benthic environment on this planet, the abyssal plains. Moreover, knowledge of the spatial patterns of deep-sea community structure is scanty, and what little is known originates primarily from morphology-based studies of foraminiferans. Here we report on the great phylogenetic diversity of microbial eukaryotic communities of all 3 abyssal plains of the southeastern Atlantic Ocean--the Angola, Cape, and Guinea Abyssal Plains--from depths of 5,000 m. A high percentage of retrieved clones had no close representatives in genetic databases. Many clones were affiliated with parasitic species. Furthermore, differences between the communities of the Cape Abyssal Plain and the other 2 abyssal plains point to environmental gradients apparently shaping community structure at the landscape level. On a regional scale, local species diversity showed much less variation. Our study provides insight into the community composition of microbial eukaryotes on larger scales from the wide abyssal sea floor realm and marks a direction for more detailed future studies aimed at improving our understanding of deep-sea microbes at the community and ecosystem levels, as well as the ecological principles at play.

  12. Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees

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    Bernad Lucia

    2009-11-01

    Full Text Available Abstract Background Sequencing projects have allowed diverse retroviruses and LTR retrotransposons from different eukaryotic organisms to be characterized. It is known that retroviruses and other retro-transcribing viruses evolve from LTR retrotransposons and that this whole system clusters into five families: Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao and Caulimoviridae. Phylogenetic analyses usually show that these split into multiple distinct lineages but what is yet to be understood is how deep evolution occurred in this system. Results We combined phylogenetic and graph analyses to investigate the history of LTR retroelements both as a tree and as a network. We used 268 non-redundant LTR retroelements, many of them introduced for the first time in this work, to elucidate all possible LTR retroelement phylogenetic patterns. These were superimposed over the tree of eukaryotes to investigate the dynamics of the system, at distinct evolutionary times. Next, we investigated phenotypic features such as duplication and variability of amino acid motifs, and several differences in genomic ORF organization. Using this information we characterized eight reticulate evolution markers to construct phenotypic network models. Conclusion The evolutionary history of LTR retroelements can be traced as a time-evolving network that depends on phylogenetic patterns, epigenetic host-factors and phenotypic plasticity. The Ty1/Copia and the Ty3/Gypsy families represent the oldest patterns in this network that we found mimics eukaryotic macroevolution. The emergence of the Bel/Pao, Retroviridae and Caulimoviridae families in this network can be related with distinct inflations of the Ty3/Gypsy family, at distinct evolutionary times. This suggests that Ty3/Gypsy ancestors diversified much more than their Ty1/Copia counterparts, at distinct geological eras. Consistent with the principle of preferential attachment, the connectivities among phenotypic markers, taken as

  13. Towards New Antifolates Targeting Eukaryotic Opportunistic Infections

    Energy Technology Data Exchange (ETDEWEB)

    Liu, J.; Bolstad, D; Bolstad, E; Wright, D; Anderson, A

    2009-01-01

    Trimethoprim, an antifolate commonly prescribed in combination with sulfamethoxazole, potently inhibits several prokaryotic species of dihydrofolate reductase (DHFR). However, several eukaryotic pathogenic organisms are resistant to trimethoprim, preventing its effective use as a therapeutic for those infections. We have been building a program to reengineer trimethoprim to more potently and selectively inhibit eukaryotic species of DHFR as a viable strategy for new drug discovery targeting several opportunistic pathogens. We have developed a series of compounds that exhibit potent and selective inhibition of DHFR from the parasitic protozoa Cryptosporidium and Toxoplasma as well as the fungus Candida glabrata. A comparison of the structures of DHFR from the fungal species Candida glabrata and Pneumocystis suggests that the compounds may also potently inhibit Pneumocystis DHFR.

  14. Statistical characteristics of eukaryotic intron database

    Institute of Scientific and Technical Information of China (English)

    HE Miao; LI Jidong; ZHANG Shanghong

    2006-01-01

    A database called eukaryotic intron database (EID) was developed based on the data from GenBank.Studies on the statistical characteristics of EID show that there were 103,848 genes,478,484 introns,and 582,332 exons,with an average of 4.61 introns and 5.61 exons per gene.Introns of 40-120 nt in length were abundant in the database.Results of the statistical analysis on the data from nine model species showed that in eukaryotes,higher species do not necessarily have more introns or exons in a gene than lower species.Furthermore,characteristics of EID,such as intron phase,distribution of different splice sites,and the relationship between genome size and intron proportion or intron density,have been studied.

  15. Immunodetection of Murine Lymphotoxins in Eukaryotic Cells.

    Science.gov (United States)

    Boitchenko, Veronika E.; Korobko, Vyacheslav G.; Prassolov, Vladimir S.; Kravchenko, Vladimir V.; Kuimov, Alexander N.; Turetskaya, Regina L.; Kuprash, Dmitry V.; Nedospasov, Sergei A.

    2000-10-01

    Lymphotoxins alpha and beta (LTalpha and LTbeta) are members of tumor necrosis factor superfamily. LT heterotrimers exist on the surface of lymphocytes and signal through LTbeta receptor while soluble LTalpha homotrimer can signal through TNF receptors p55 and p75. LT-, as well as TNF-mediated signaling are important for the organogenesis and maintenance of microarchitecture of secondary lymphoid organs in mice and has been implicated in the mechanism of certain inflammatory syndromes in humans. In this study we describe the generation of eukaryotic expression plasmids encoding murine LTalpha and LTbeta genes and a prokaryotic expression construct for murine LTalpha. Using recombinant proteins expressed by these vectors as tools for antisera selection, we produced and characterized several polyclonal antibodies capable of detecting LT proteins in eukaryotic cells.

  16. Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome

    OpenAIRE

    Lu Chen; Tovar-Corona, Jaime M.; Urrutia, Araxi O.

    2012-01-01

    Alternative splicing (AS) is a common posttranscriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. The release of the human genome draft revealed a much smaller number of genes than anticipated. Because of its potential role in expanding protein diversity, interest in alternative splicing has been increasing over the last decade. Although recent studies have shown that 94% human multiexon genes undergo AS, evolution of...

  17. Evaluation of autochthonous bioaugmentation and biostimulation during microcosm-simulated oil spills.

    Science.gov (United States)

    Nikolopoulou, M; Pasadakis, N; Kalogerakis, N

    2013-07-15

    Oil spills are treated as a widespread problem that poses a great threat to any ecosystem. Following first response actions, bioremediation has emerged as the best strategy for combating oil spills and can be enhanced by the following two complementary approaches: bioaugmentation and biostimulation. Bioaugmentation is one of the most controversial issues of bioremediation. Studies that compare the relative performance of bioaugmentation and biostimulation suggest that nutrient addition alone has a greater effect on oil biodegradation than the addition of microbial products because the survival and degradation ability of microbes introduced to a contaminated site are highly dependent on environmental conditions. Microbial populations grown in rich media under laboratory conditions become stressed when exposed to field conditions in which nutrient concentrations are substantially lower. There is increasing evidence that the best approach to overcoming these barriers is the use of microorganisms from the polluted area, an approach proposed as autochthonous bioaugmentation (ABA) and defined as a bioaugmentation technology that exclusively uses microorganisms indigenous to the sites (soil, sand, and water) slated for decontamination. In this work, we examined the effectiveness of strategies combining autochthonous bioaugmentation with biostimulation for successful remediation of polluted marine environments. Seawater was collected from a pristine area (Agios Onoufrios Beach, Chania) and was placed in a bioreactor with 1% v/v crude oil to facilitate the adaptation of the indigenous microorganism population. The pre-adapted consortium and the indigenous population were tested in combination with inorganic or lipophilic nutrients in the presence (or absence) of biosurfactants (rhamnolipids) during 90-day long experiments. Chemical analysis (gas chromatography-mass spectrometry) of petroleum hydrocarbons confirmed the results of previous work demonstrating that the

  18. Arsenic and antimony transporters in eukaryotes.

    Science.gov (United States)

    Maciaszczyk-Dziubinska, Ewa; Wawrzycka, Donata; Wysocki, Robert

    2012-01-01

    Arsenic and antimony are toxic metalloids, naturally present in the environment and all organisms have developed pathways for their detoxification. The most effective metalloid tolerance systems in eukaryotes include downregulation of metalloid uptake, efflux out of the cell, and complexation with phytochelatin or glutathione followed by sequestration into the vacuole. Understanding of arsenic and antimony transport system is of high importance due to the increasing usage of arsenic-based drugs in the treatment of certain types of cancer and diseases caused by protozoan parasites as well as for the development of bio- and phytoremediation strategies for metalloid polluted areas. However, in contrast to prokaryotes, the knowledge about specific transporters of arsenic and antimony and the mechanisms of metalloid transport in eukaryotes has been very limited for a long time. Here, we review the recent advances in understanding of arsenic and antimony transport pathways in eukaryotes, including a dual role of aquaglyceroporins in uptake and efflux of metalloids, elucidation of arsenic transport mechanism by the yeast Acr3 transporter and its role in arsenic hyperaccumulation in ferns, identification of vacuolar transporters of arsenic-phytochelatin complexes in plants and forms of arsenic substrates recognized by mammalian ABC transporters.

  19. In situ expression of eukaryotic ice-binding proteins in microbial communities of Arctic and Antarctic sea ice

    Science.gov (United States)

    Uhlig, Christiane; Kilpert, Fabian; Frickenhaus, Stephan; Kegel, Jessica U; Krell, Andreas; Mock, Thomas; Valentin, Klaus; Beszteri, Bánk

    2015-01-01

    Ice-binding proteins (IBPs) have been isolated from various sea-ice organisms. Their characterisation points to a crucial role in protecting the organisms in sub-zero environments. However, their in situ abundance and diversity in natural sea-ice microbial communities is largely unknown. In this study, we analysed the expression and phylogenetic diversity of eukaryotic IBP transcripts from microbial communities of Arctic and Antarctic sea ice. IBP transcripts were found in abundances similar to those of proteins involved in core cellular processes such as photosynthesis. Eighty-nine percent of the IBP transcripts grouped with known IBP sequences from diatoms, haptophytes and crustaceans, but the majority represented novel sequences not previously characterized in cultured organisms. The observed high eukaryotic IBP expression in natural eukaryotic sea ice communities underlines the essential role of IBPs for survival of many microorganisms in communities living under the extreme conditions of polar sea ice. PMID:25885562

  20. An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin

    OpenAIRE

    Thiergart, T.; Landan, G; Schenk, M.; Dagan, T.; Martin, W F

    2012-01-01

    To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the a...

  1. Widespread vertical transmission and associated host sex-ratio distortion within the eukaryotic phylum Microspora.

    Science.gov (United States)

    Terry, Rebecca S; Smith, Judith E; Sharpe, Rosie G; Rigaud, Thierry; Littlewood, D Timothy J; Ironside, Joseph E; Rollinson, David; Bouchon, Didier; MacNeil, Calum; Dick, Jaimie T A; Dunn, Alison M

    2004-09-01

    Vertical transmission (VT) and associated manipulation of host reproduction are widely reported among prokaryotic endosymbionts. Here, we present evidence for widespread use of VT and associated sex-ratio distortion in a eukaryotic phylum. The Microspora are an unusual and diverse group of eukaryotic parasites that infect all animal phyla. Following our initial description of a microsporidian that feminizes its crustacean host, we survey the diversity and distribution of VT within the Microspora. We find that vertically transmitted microsporidia are ubiquitous in the amphipod hosts sampled and that they are also diverse, with 11 species of microsporidia detected within 16 host species. We found that infections were more common in females than males, suggesting that host sex-ratio distortion occurs in five out of eight parasite species tested. Phylogenetic reconstruction demonstrates that VT occurs in all major lineages of the phylum Microspora and that sex-ratio distorters are found on multiple branches of the phylogenetic tree. We propose that VT is either an ancestral trait or evolves with peculiar frequency in this phylum. If the association observed here between VT and host sex-ratio distortion holds true across other host taxa, these eukaryotic parasites may join the bacterial endosymbionts in their importance as sex-ratio distorters.

  2. Nitrogen fixation in eukaryotes – New models for symbiosis

    Directory of Open Access Journals (Sweden)

    Lockhart Peter

    2007-04-01

    Full Text Available Abstract Background Nitrogen, a component of many bio-molecules, is essential for growth and development of all organisms. Most nitrogen exists in the atmosphere, and utilisation of this source is important as a means of avoiding nitrogen starvation. However, the ability to fix atmospheric nitrogen via the nitrogenase enzyme complex is restricted to some bacteria. Eukaryotic organisms are only able to obtain fixed nitrogen through their symbiotic interactions with nitrogen-fixing prokaryotes. These symbioses involve a variety of host organisms, including animals, plants, fungi and protists. Results We have compared the morphological, physiological and molecular characteristics of nitrogen fixing symbiotic associations of bacteria and their diverse hosts. Special features of the interaction, e.g. vertical transmission of symbionts, grade of dependency of partners and physiological modifications have been considered in terms of extent of co-evolution and adaptation. Our findings are that, despite many adaptations enabling a beneficial partnership, most symbioses for molecular nitrogen fixation involve facultative interactions. However, some interactions, among them endosymbioses between cyanobacteria and diatoms, show characteristics that reveal a more obligate status of co-evolution. Conclusion Our review emphasises that molecular nitrogen fixation, a driving force for interactions and co-evolution of different species, is a widespread phenomenon involving many different organisms and ecosystems. The diverse grades of symbioses, ranging from loose associations to highly specific intracellular interactions, might themselves reflect the range of potential evolutionary fates for symbiotic partnerships. These include the extreme evolutionary modifications and adaptations that have accompanied the formation of organelles in eukaryotic cells: plastids and mitochondria. However, age and extensive adaptation of plastids and mitochondria complicate the

  3. First record of autochthonous canine ehrlichiosis caused by Ehrlichia canis in Romania.

    Science.gov (United States)

    Morar, Doru; Dărăbuş, Gheorghe; Imre, Mirela; Ilie, Marius Stelian; Imre, Kálmán

    2015-06-01

    This case study describes the first genetically confirmed and clinically manifested autochthonous Ehrlichia canis infection in a 9-year-old female mixed-breed dog from Romania. Health screening of the dog included clinical examination, evaluation of stained peripheral blood smear and hematologic variables, as well as serologic testing and molecular analysis. Clinical signs included fever, apathy, dehydration, pale mucous membranes, and weakness. The microscopic examination of the blood smear and immunologic assays for Borrelia burgdorferi, Anaplasma phagocytophilum, and E canis antibodies, and for Dirofilaria immitis antigen yielded negative results. Hematologic abnormalities included moderate nonregenerative anemia, leucopenia with neutropenia, and moderate thrombocytopenia. The biochemical abnormalities identified were hypoalbuminemia, and mildly increased serum enzyme activities of AST and ALT. In addition, increased urea and creatinine levels associated with low urine specific gravity and proteinuria were also present. Nested PCR amplification of the partial E canis 16S rRNA gene demonstrated the presence of this rickettsial pathogen in the dog's blood, which subsequently was confirmed through sequencing based on the 100% homology with GenBank deposited E canis isolates. After specific treatment with doxycycline (10 mg/kg, orally, SID) for one month, the proteinuria, and hematologic and serum biochemical abnormalities with the exception of mild azotemia resolved. This report supports the geographical expansion of canine ehrlichiosis caused by E canis in nonendemic regions of Europe.

  4. Study on the reproductive capacity of bulls of the autochthonous Rhodope Shorthorn cattle breed

    Directory of Open Access Journals (Sweden)

    Radka Malinova

    2015-06-01

    Full Text Available The sperm production of bulls from the autochthonous Rhodope Shorthorn cattle breed was studied. The breed is among the smallest in Europe, the average weight of the cows ranging from 200 to 250 kg, and of the bulls from 330 to 370 kg. It was found that during the first 6 months from the start of exploitation, at the age of the bulls from 18 to 24 months, AI bulls had high reproductive capacity. The ejaculate volume was 1,74±0,09 ml in average (LS, the percentage of motile spermatozoa was 74,3±3,48% and the concentration 1268±13,1 x 106/ml. It was established that the bull had a significant impact on the reproductive performance, but the individual differences in the main characteristics were not high – motility 71,8-77,0%, concentration – 1222-1324 х 106/ml. The season also had a significant effect on the percentage of motile spermatozoa. Within the period from January to June, the highest reproductive capacity of the bulls was observed from February to May and the lowest in June.

  5. Determinants of the intention to purchase an autochthonous local lamb breed: Spanish case study.

    Science.gov (United States)

    Gracia, Azucena; Maza, María Teresa

    2015-12-01

    The aim of the paper is to study consumers' acceptability for a lamb meat from a local autochthonous breed. An intention to purchase model was developed based on the Theory of Planned Behavior (TPB) and estimated using data from a survey conducted in Spain. Results indicated that consumers were willing to buy this lamb meat because 86% of respondents said that they probably/definitely would buy it, although only 23% would if the meat is not available in their usual meat store. Then, the lack of availability in the market is an aspect limiting its consumption. The most important factors explaining the intention to purchase for consumers who would purchase this meat if it were not available in their usual store are the importance attached to the animal breed and their social embeddedness with the local area. An appropriate food policy would be to inform consumers about the importance of the animal breed in the quality of the meat and the local origin.

  6. Improving the antioxidant properties of quinoa flour through fermentation with selected autochthonous lactic acid bacteria.

    Science.gov (United States)

    Rizzello, Carlo Giuseppe; Lorusso, Anna; Russo, Vito; Pinto, Daniela; Marzani, Barbara; Gobbetti, Marco

    2017-01-16

    Lactic acid bacteria strains, previously isolated from the same matrix, were used to ferment quinoa flour aiming at exploiting the antioxidant potential. As in vitro determined on DPPH and ABTS radicals, the scavenging activity of water/salt-soluble extracts (WSE) from fermented doughs was significantly (Pquinoa dough fermented with Lactobacillus plantarum T0A10. The corresponding WSE was subjected to Reverse Phase Fast Protein Liquid Chromatography, and 32 fractions were collected and subjected to in vitro assays. The most active fraction was resistant to further hydrolysis by digestive enzymes. Five peptides, having sizes from 5 to 9 amino acid residues, were identified by nano-Liquid Chromatography-Electrospray Ionisation-Mass Spectra/Mass Spectra. The sequences shared compositional features which are typical of antioxidant peptides. As shown by determining cell viability and radical scavenging activity (MTT and DCFH-DA assays, respectively), the purified fraction showed antioxidant activity on human keratinocytes NCTC 2544 artificially subjected to oxidative stress. This study demonstrated the capacity of autochthonous lactic acid bacteria to release peptides with antioxidant activity through proteolysis of native quinoa proteins. Fermentation of the quinoa flour with a selected starter might be considered suitable for novel applications as functional food ingredient, dietary supplement or pharmaceutical preparations.

  7. Alkaline bioleaching of municipal solid waste incineration fly ash by autochthonous extremophiles.

    Science.gov (United States)

    Ramanathan, Thulasya; Ting, Yen-Peng

    2016-10-01

    The increasing demand for energy and the generation of solid waste have caused an alarming rise in fly ash production globally. Since heavy metals continue to be in demand for the production of materials, resource recovery from the recycling of these wastes has the potential to delay the depletion of natural ores. The use of microorganisms for the leaching of metals, in a process called bioleaching, is an eco-friendly and economical way to treat the metal-laden wastes. Bioleaching of fly ash is challenging due largely to the alkaline nature and toxic levels of heavy metals which are detrimental to microbial growth and bioleaching activity. The present work reports the isolation of indigenous bacteria from a local fly ash landfill site and their bioleaching performance. 38 autochthonous strains of bacteria were isolated from eight samples collected and plated on five different media. 18 of the isolates showed bioleaching potential, with significant alkaline pH or fly ash tolerance. Genetic characterization of the strains revealed a dominance of Firmicutes, with Alkalibacterium sp. TRTYP6 showing highest fly ash tolerance of up to 20% w/v fly ash, and growth over a pH range 8-12.5. The organism selectively recovered about 52% Cu from the waste. To the best of our knowledge, this is the first time a study on bioleaching with extreme alkaliphiles is reported.

  8. Use of autochthonous lactic acid bacteria starters to ferment mango juice for promoting its probiotic roles.

    Science.gov (United States)

    Liao, Xue-Yi; Guo, Li-Qiong; Ye, Zhi-Wei; Qiu, Ling-Yan; Gu, Feng-Wei; Lin, Jun-Fang

    2016-05-18

    Strains of Leuconostoc mesenteroides, Pediococcus pentosaceus, and Lactobacillus brevis were identified from mango fruits by partial 16S rDNA gene sequence. Based on the ability of producing mannitol and diacetyl, Leuconostoc mesenteroides MPL18 and MPL39 were selected within the lactic acid bacteria isolates, and used as mixed starters to ferment mango juice (MJ). Both the autochthonous strains grew well in fermented mango juice (FMJ) and remained viable at 9.81 log cfu mL(-1) during 30 days of storage at 4°C. The content of total sugar of FMJ was lower than that of MJ, while the concentration of mannitol was higher than that of MJ, and the concentration of diacetyl was 3.29 ± 0.12 mg L(-1). Among detected organic acids including citric acid, gallic acid, lactic acid, and acetic acid, only citric acid and gallic acid were found in MJ, while all detected organic acids were found in FMJ. The concentration of lactic acid of FMJ was the highest (78.62 ± 13.66 mM) among all detected organic acids. The DPPH radical scavenging capacity of FMJ was higher than that of MJ. Total phenolic compounds were better preserved in FMJ. The acidity and sweetness had a noticeable impact on the overall acceptance of the treated sample.

  9. The potential of autochthonous microbial culture encapsulation in a confined environment for phenol biodegradation.

    Science.gov (United States)

    Azaizeh, Hassan; Kurzbaum, Eyal; Said, Ons; Jaradat, Husain; Menashe, Ofir

    2015-10-01

    Olive mill wastewater (OMWW) is claimed to be one of the most polluting effluents produced by agro-food industries, providing high contaminants load that encase cytotoxic agents such as phenolic and polyphenolic compounds. Therefore, a significant and continuous stress episode is induced once the mixed liquor of the wastewater treatment plants (WWTP's) is being exposed to OMWW. The use of bio-augmentation treatment procedures can be useful to eliminate or reduce such stress episodes. In this study, we have estimated the use of autochthonous biomass implementation within small bioreactor platform (SBP) particles as a bio-augmentation method to challenge against WWTPs stress episodes. Our results showed that SBP particles significantly reduced the presence of various phenolics: tannic, gallic and caffeic acid in a synthetic medium and in crude OMWW matrix. Moreover, the SBP particles succeeded to biodegrade a very high concentration of phenol blend (3000 mg L(-1)). Our findings indicated that the presence of the SBP microfiltration membrane has reduced the phenol biodegradation rate by 50 % compared to the same suspended culture. Despite the observed reduction in biodegradation rate, encapsulation in a confined environment can offer significant values such as overcoming the grazing forcers and dilution, thus achieving a long-term sufficient biomass. The potential for reducing stress episodes caused by cytotoxic agents through bio-augmentation treatment procedure using the SBP technology is discussed.

  10. Complex archaea that bridge the gap between prokaryotes and eukaryotes.

    Science.gov (United States)

    Spang, Anja; Saw, Jimmy H; Jørgensen, Steffen L; Zaremba-Niedzwiedzka, Katarzyna; Martijn, Joran; Lind, Anders E; van Eijk, Roel; Schleper, Christa; Guy, Lionel; Ettema, Thijs J G

    2015-05-14

    The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.

  11. Prokaryotic and eukaryotic community structure in field and cultured microbialites from the alkaline Lake Alchichica (Mexico.

    Directory of Open Access Journals (Sweden)

    Estelle Couradeau

    Full Text Available The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both field samples collected along a depth gradient (0-14 m depth and long-term-maintained laboratory aquaria. Using small subunit (SSU rRNA gene libraries and fingerprinting methods, we detected a wide diversity of bacteria and protists contrasting with a minor fraction of archaea. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms. Cyanobacterial diversity varied with depth, Oscillatoriales dominating shallow and intermediate microbialites and Pleurocapsales the deepest samples. The early-branching Gloeobacterales represented significant proportions in aquaria microbialites. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated in biomass, heterotrophic lineages were more diverse. We detected members of up to 21 bacterial phyla or candidate divisions, including lineages possibly involved in microbialite formation, such as sulfate-reducing Deltaproteobacteria but also Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia. Heterotrophic eukaryotes were dominated by Fungi (including members of the basal Rozellida or Cryptomycota, Choanoflagellida, Nucleariida, Amoebozoa, Alveolata and Stramenopiles. The diversity and relative abundance of many eukaryotic lineages suggest an unforeseen role for protists in microbialite ecology. Many lineages from lake microbialites were successfully maintained in aquaria. Interestingly, the diversity detected in aquarium microbialites was higher than

  12. Phylogeny of choanozoa, apusozoa, and other protozoa and early eukaryote megaevolution.

    Science.gov (United States)

    Cavalier-Smith, Thomas; Chao, Ema E-Y

    2003-05-01

    The primary diversification of eukaryotes involved protozoa, especially zooflagellates-flagellate protozoa without plastids. Understanding the origins of the higher eukaryotic kingdoms (two purely heterotrophic, Animalia and Fungi, and two primarily photosynthetic, Plantae and Chromista) depends on clarifying evolutionary relationships among the phyla of the ancestral kingdom Protozoa. We therefore sequenced 18S rRNA genes from 10 strains from the protozoan phyla Choanozoa and Apusozoa. Eukaryote diversity is encompassed by three early-radiating, arguably monophyletic groups: Amoebozoa, opisthokonts, and bikonts. Our taxon-rich rRNA phylogeny for eukaryotes allowing for intersite rate variation strongly supports the opisthokont clade (animals, Choanozoa, Fungi). It agrees with the view that Choanozoa are sisters of or ancestral to animals and reveals a novel nonflagellate choanozoan lineage, Ministeriida, sister either to choanoflagellates, traditionally considered animal ancestors, or to animals. Maximum likelihood trees suggest that within animals Placozoa are derived from medusozoan Cnidaria (we therefore place Placozoa as a class within subphylum Medusozoa of the Cnidaria) and hexactinellid sponges evolved from demosponges. The bikont and amoebozoan radiations are both very ill resolved. Bikonts comprise the kingdoms Plantae and Chromista and three major protozoan groups: alveolates, excavates, and Rhizaria. Our analysis weakly suggests that Apusozoa, represented by Ancyromonas and the apusomonads ( Apusomonas and the highly diverse and much more ancient genus Amastigomonas, from which it evolved), are not closely related to other Rhizaria and may be the most divergent bikont lineages. Although Ancyromonas and apusomonads appear deeply divergent in 18S rRNA trees, the trees neither refute nor support the monophyly of Apusozoa. The bikont phylum Cercozoa weakly but consistently appears as sister to Retaria (Foraminifera; Radiolaria), together forming a hitherto

  13. [Highest level of division in the organism classification. 1. Prokaryotes and eukaryotes].

    Science.gov (United States)

    Shatalkin, A I

    2004-01-01

    The works on the general classification of all organisms are considered as a convenient opportunity to sum up numerous data obtained in organic world studying. The present stage is characterized by rapid development of the molecular reconstructions that have already caused considerable changes in our classification practice. These changes look especially impressive at studying the organism cellular structure. The great massive of new data allow us to compare Prokaryotes and Eukaryotes on the nucleic acids and especially proteins whose number in Eukaryote cell approaches to several thousands. Basing on the structure of macromolecules one can hypothesize with great certainty about Prokaryote or Eukaryotes origin. The article presents the detailed characteristic of Prokaryotes or Eukaryotes with the emphasis placed on the comparative analysis of biological macromolecules. Among specially considered cellular structures and processes are cell wall, intracellular components, cellular cycle, nucleus, DNA compactness, replication, genome organization, transcription, posttranscriptional modifications, introns, ribosomes and translation, cytoskeleton, mitosis, cytokinesis, cellular organelles, intracellular membranes systems, modes of nutrition, sexual condition. The macromolecular analysis let to carry out the homology of structures and to find out some new connections. It was shown that typology considered as a search for morphological patterns within the biodiversity structure has almost exhausted the subject. It was directed mostly to distinguishing "main" group in contrast with intermediate and aberrant ones, which were considered as minor phenomenon. At present due to macromolecules systematics it is able to estimate the whole diversity of forms including typologically transitive.

  14. Prokaryotes Versus Eukaryotes: Who is Hosting Whom?

    Science.gov (United States)

    Tellez, Guillermo

    2014-01-01

    Microorganisms represent the largest component of biodiversity in our world. For millions of years, prokaryotic microorganisms have functioned as a major selective force shaping eukaryotic evolution. Microbes that live inside and on animals outnumber the animals' actual somatic and germ cells by an estimated 10-fold. Collectively, the intestinal microbiome represents a "forgotten organ," functioning as an organ inside another that can execute many physiological responsibilities. The nature of primitive eukaryotes was drastically changed due to the association with symbiotic prokaryotes facilitating mutual coevolution of host and microbe. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. From termites and honey bees to ruminants and mammals, depending on novel biochemistries provided by the prokaryotic microbiome, the association helps to metabolize several nutrients that the host cannot digest and converting these into useful end products (such as short-chain fatty acids), a process, which has huge impact on the biology and homeostasis of metazoans. More importantly, in a direct and/or indirect way, the intestinal microbiota influences the assembly of gut-associated lymphoid tissue, helps to educate immune system, affects the integrity of the intestinal mucosal barrier, modulates proliferation and differentiation of its epithelial lineages, regulates angiogenesis, and modifies the activity of enteric as well as the central nervous system. Despite these important effects, the mechanisms by which the gut microbial community influences the host's biology remain almost entirely unknown. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes, which encourage us to postulate: who is hosting whom?

  15. Prokaryotes versus Eukaryotes: Who is hosting whom?

    Directory of Open Access Journals (Sweden)

    Guillermo eTellez

    2014-10-01

    Full Text Available Microorganisms represent the largest component of biodiversity in our world. For millions of years, prokaryotic microorganisms have functioned as a major selective force shaping eukaryotic evolution. Microbes that live inside and on animals outnumber the animals’ actual somatic and germ cells by an estimated 10-fold. Collectively, the intestinal microbiome represents a ‘forgotten organ’, functioning as an organ inside another that can execute many physiological responsibilities. The nature of primitive eukaryotes was drastically changed due to the association with symbiotic prokaryotes facilitating mutual coevolution of host and microbe. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. From termites and honey bees to ruminants and mammals, depending on novel biochemistries provided by the prokaryotic microbiome, the association helps to metabolize several nutrients that the host cannot digest and converting these into useful end products (such as short chain fatty acids, a process which has huge impact on the biology and homeostasis of metazoans. More importantly, in a direct and/or indirect way, the intestinal microbiota influences the assembly of gut-associated lymphoid tissue, helps to educate immune system, affects the integrity of the intestinal mucosal barrier, modulates proliferation and differentiation of its epithelial lineages, regulates angiogenesis, and modifies the activity of enteric as well as the central nervous system,. Despite these important effects, the mechanisms by which the gut microbial community influences the host’s biology remains almost entirely unknown. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes which encourage us to postulate: Who is

  16. Expression of eukaryotic polypeptides in chloroplasts

    Energy Technology Data Exchange (ETDEWEB)

    Mayfield, Stephen P

    2013-06-04

    The present invention relates to a gene expression system in eukaryotic and prokaryotic cells, preferably plant cells and intact plants. In particular, the invention relates to an expression system having a RB47 binding site upstream of a translation initiation site for regulation of translation mediated by binding of RB47 protein, a member of the poly(A) binding protein family. Regulation is further effected by RB60, a protein disulfide isomerase. The expression system is capable of functioning in the nuclear/cytoplasm of cells and in the chloroplast of plants. Translation regulation of a desired molecule is enhanced approximately 100 fold over that obtained without RB47 binding site activation.

  17. Amplification and characterization of eukaryotic structural genes.

    Science.gov (United States)

    Maniatis, T; Efstratiadis, A; Sim, G K; Kafatos, F

    1978-05-01

    An approach to the study of eukaryotic structural genes which are differentially expressed during development is described. This approach involves the isolation and amplification of mRNA sequences by in vitro conversion of mRNA to double-stranded cDNA followed by molecular cloning in bacterial plasmids. This procedure provides highly specific hybridization probes that can be used to identify genes and their contiguous DNA sequences in genomic DNA, and to detect specific RNA transcripts during development. The nature of the method allows the isolation of individual mRNA sequences from a complex population of molecules at different stages of development.

  18. The ecology of viruses that infect eukaryotic algae.

    Science.gov (United States)

    Short, Steven M

    2012-09-01

    Because viruses of eukaryotic algae are incredibly diverse, sweeping generalizations about their ecology are rare. These obligate parasites infect a range of algae and their diversity can be illustrated by considering that isolates range from small particles with ssRNA genomes to much larger particles with 560 kb dsDNA genomes. Molecular research has also provided clues about the extent of their diversity especially considering that genetic signatures of algal viruses in the environment rarely match cultivated viruses. One general concept in algal virus ecology that has emerged is that algal viruses are very host specific and most infect only certain strains of their hosts; with the exception of viruses of brown algae, evidence for interspecies infectivity is lacking. Although some host-virus systems behave with boom-bust oscillations, complex patterns of intraspecies infectivity can lead to host-virus coexistence obfuscating the role of viruses in host population dynamics. Within the framework of population dynamics, host density dependence is an important phenomenon that influences virus abundances in nature. Variable burst sizes of different viruses also influence their abundances and permit speculations about different life strategies, but as exceptions are common in algal virus ecology, life strategy generalizations may not be broadly applicable. Gaps in knowledge of virus seasonality and persistence are beginning to close and investigations of environmental reservoirs and virus resilience may answer questions about virus inter-annual recurrences. Studies of algal mortality have shown that viruses are often important agents of mortality reinforcing notions about their ecological relevance, while observations of the surprising ways viruses interact with their hosts highlight the immaturity of our understanding. Considering that just two decades ago algal viruses were hardly acknowledged, recent progress affords the optimistic perspective that future studies

  19. Asgard archaea illuminate the origin of eukaryotic cellular complexity.

    Science.gov (United States)

    Zaremba-Niedzwiedzka, Katarzyna; Caceres, Eva F; Saw, Jimmy H; Bäckström, Disa; Juzokaite, Lina; Vancaester, Emmelien; Seitz, Kiley W; Anantharaman, Karthik; Starnawski, Piotr; Kjeldsen, Kasper U; Stott, Matthew B; Nunoura, Takuro; Banfield, Jillian F; Schramm, Andreas; Baker, Brett J; Spang, Anja; Ettema, Thijs J G

    2017-01-19

    The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota. Asgard archaea affiliate with eukaryotes in phylogenomic analyses, and their genomes are enriched for proteins formerly considered specific to eukaryotes. Notably, thorarchaeal genomes encode several homologues of eukaryotic membrane-trafficking machinery components, including Sec23/24 and TRAPP domains. Furthermore, we identify thorarchaeal proteins with similar features to eukaryotic coat proteins involved in vesicle biogenesis. Our results expand the known repertoire of 'eukaryote-specific' proteins in Archaea, indicating that the archaeal host cell already contained many key components that govern eukaryotic cellular complexity.

  20. Fruit Morphological Changes during Pit Hardening in Autochthonous Istrian Olive (Olea europaea L. Cultivars

    Directory of Open Access Journals (Sweden)

    Marin Krapac

    2014-02-01

    Full Text Available Endocarp lignification is important fruit growth phenophase since after its completion fruit starts with oil accumulation. The information about duration of endocarp lignification is important for timing of management practices, irrigation and pest control in oil cultivars, and fruit thinning in table cultivars to obtain uniform fruit weight and size. In this study, fruit length, width and weight of four Istrian autochthonous olive cultivars (‘Buža’, ‘Puntoža’, ‘Rošinjola’ and ‘Istarska bjelica’ were measured. Samples were taken from olive collection orchard of the Institute of Agriculture and Tourism in Poreč in equal growing conditions. The aim of the research was to define an olive fruit growth dynamics during pit hardening. Fruit weight in all cultivars was increasing during endocarp lignification (from 7th to 28th July. The highest percentage in the weight growth in the first week had cultivars ‘Buža’ (48.5% and ‘Rošinjola’ (44.6% while in the second week maximum was reached by cultivars ‘Puntoža’ (44.2% and ‘Istarska bjelica’ (42%. The highest increase in total fruit mass was detected in ‘Puntoža’ (1.30 g and the least at ‘Rošinjola’ (0.56 g. Maximum increase in length (L and width (W had ‘Puntoža’ (L: 7.13 mm; W: 4.23 mm and the least ‘Istarska bjelica’ (L: 2.48 mm; W: 2.70 mm.

  1. Polychlorinated biphenyl (PCB) anaerobic degradation in marine sediments: microcosm study and role of autochthonous microbial communities.

    Science.gov (United States)

    Matturro, Bruna; Ubaldi, Carla; Grenni, Paola; Caracciolo, Anna Barra; Rossetti, Simona

    2016-07-01

    Polychlorobiphenyl (PCB) biodegradation was followed for 1 year in microcosms containing marine sediments collected from Mar Piccolo (Taranto, Italy) chronically contaminated by this class of hazardous compounds. The microcosms were performed under strictly anaerobic conditions with or without the addition of Dehalococcoides mccartyi, the main microorganism known to degrade PCBs through the anaerobic reductive dechlorination process. Thirty PCB congeners were monitored during the experiments revealing that the biodegradation occurred in all microcosms with a decrease in hepta-, hexa-, and penta-chlorobiphenyls (CBs) and a parallel increase in low chlorinated PCBs (tri-CBs and tetra-CBs). The concentrations of the most representative congeners detected in the original sediment, such as 245-245-CB and 2345-245-CB, and of the mixture 2356-34-CB+234-245-CB, decreased by 32.5, 23.8, and 46.7 %, respectively, after only 70 days of anaerobic incubation without any bioaugmentation treatment. Additionally, the structure and population dynamics of the microbial key players involved in the biodegradative process and of the entire mixed microbial community were accurately defined by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH) in both the original sediment and during the operation of the microcosm. The reductive dehalogenase genes of D. mccartyi, specifically involved in PCB dechlorination, were also quantified using real-time PCR (qPCR). Our results demonstrated that the autochthonous microbial community living in the marine sediment, including D. mccartyi (6.32E+06 16S rRNA gene copy numbers g(-1) sediment), was able to efficiently sustain the biodegradation of PCBs when controlled anaerobic conditions were imposed.

  2. RNA Export through the NPC in Eukaryotes.

    Science.gov (United States)

    Okamura, Masumi; Inose, Haruko; Masuda, Seiji

    2015-03-20

    In eukaryotic cells, RNAs are transcribed in the nucleus and exported to the cytoplasm through the nuclear pore complex. The RNA molecules that are exported from the nucleus into the cytoplasm include messenger RNAs (mRNAs), ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), small nuclear RNAs (snRNAs), micro RNAs (miRNAs), and viral mRNAs. Each RNA is transported by a specific nuclear export receptor. It is believed that most of the mRNAs are exported by Nxf1 (Mex67 in yeast), whereas rRNAs, snRNAs, and a certain subset of mRNAs are exported in a Crm1/Xpo1-dependent manner. tRNAs and miRNAs are exported by Xpot and Xpo5. However, multiple export receptors are involved in the export of some RNAs, such as 60S ribosomal subunit. In addition to these export receptors, some adapter proteins are required to export RNAs. The RNA export system of eukaryotic cells is also used by several types of RNA virus that depend on the machineries of the host cell in the nucleus for replication of their genome, therefore this review describes the RNA export system of two representative viruses. We also discuss the NPC anchoring-dependent mRNA export factors that directly recruit specific genes to the NPC.

  3. Consistent mutational paths predict eukaryotic thermostability

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    van Noort Vera

    2013-01-01

    Full Text Available Abstract Background Proteomes of thermophilic prokaryotes have been instrumental in structural biology and successfully exploited in biotechnology, however many proteins required for eukaryotic cell function are absent from bacteria or archaea. With Chaetomium thermophilum, Thielavia terrestris and Thielavia heterothallica three genome sequences of thermophilic eukaryotes have been published. Results Studying the genomes and proteomes of these thermophilic fungi, we found common strategies of thermal adaptation across the different kingdoms of Life, including amino acid biases and a reduced genome size. A phylogenetics-guided comparison of thermophilic proteomes with those of other, mesophilic Sordariomycetes revealed consistent amino acid substitutions associated to thermophily that were also present in an independent lineage of thermophilic fungi. The most consistent pattern is the substitution of lysine by arginine, which we could find in almost all lineages but has not been extensively used in protein stability engineering. By exploiting mutational paths towards the thermophiles, we could predict particular amino acid residues in individual proteins that contribute to thermostability and validated some of them experimentally. By determining the three-dimensional structure of an exemplar protein from C. thermophilum (Arx1, we could also characterise the molecular consequences of some of these mutations. Conclusions The comparative analysis of these three genomes not only enhances our understanding of the evolution of thermophily, but also provides new ways to engineer protein stability.

  4. Eukaryotic and Prokaryotic Cytoskeletons: Structure and Mechanics

    Science.gov (United States)

    Gopinathan, Ajay

    2013-03-01

    The eukaryotic cytoskeleton is an assembly of filamentous proteins and a host of associated proteins that collectively serve functional needs ranging from spatial organization and transport to the production and transmission of forces. These systems can exhibit a wide variety of non-equilibrium, self-assembled phases depending on context and function. While much recent progress has been made in understanding the self-organization, rheology and nonlinear mechanical properties of such active systems, in this talk, we will concentrate on some emerging aspects of cytoskeletal physics that are promising. One such aspect is the influence of cytoskeletal network topology and its dynamics on both active and passive intracellular transport. Another aspect we will highlight is the interplay between chirality of filaments, their elasticity and their interactions with the membrane that can lead to novel conformational states with functional implications. Finally we will consider homologs of cytoskeletal proteins in bacteria, which are involved in templating cell growth, segregating genetic material and force production, which we will discuss with particular reference to contractile forces during cell division. These prokaryotic structures function in remarkably similar yet fascinatingly different ways from their eukaryotic counterparts and can enrich our understanding of cytoskeletal functioning as a whole.

  5. Strong eukaryotic IRESs have weak secondary structure.

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    Xuhua Xia

    Full Text Available BACKGROUND: The objective of this work was to investigate the hypothesis that eukaryotic Internal Ribosome Entry Sites (IRES lack secondary structure and to examine the generality of the hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: IRESs of the yeast and the fruit fly are located in the 5'UTR immediately upstream of the initiation codon. The minimum folding energy (MFE of 60 nt RNA segments immediately upstream of the initiation codons was calculated as a proxy of secondary structure stability. MFE of the reverse complements of these 60 nt segments was also calculated. The relationship between MFE and empirically determined IRES activity was investigated to test the hypothesis that strong IRES activity is associated with weak secondary structure. We show that IRES activity in the yeast and the fruit fly correlates strongly with the structural stability, with highest IRES activity found in RNA segments that exhibit the weakest secondary structure. CONCLUSIONS: We found that a subset of eukaryotic IRESs exhibits very low secondary structure in the 5'-UTR sequences immediately upstream of the initiation codon. The consistency in results between the yeast and the fruit fly suggests a possible shared mechanism of cap-independent translation initiation that relies on an unstructured RNA segment.

  6. Spy: a new group of eukaryotic DNA transposons without target site duplications.

    Science.gov (United States)

    Han, Min-Jin; Xu, Hong-En; Zhang, Hua-Hao; Feschotte, Cédric; Zhang, Ze

    2014-06-24

    Class 2 or DNA transposons populate the genomes of most eukaryotes and like other mobile genetic elements have a profound impact on genome evolution. Most DNA transposons belong to the cut-and-paste types, which are relatively simple elements characterized by terminal-inverted repeats (TIRs) flanking a single gene encoding a transposase. All eukaryotic cut-and-paste transposons so far described are also characterized by target site duplications (TSDs) of host DNA generated upon chromosomal insertion. Here, we report a new group of evolutionarily related DNA transposons called Spy, which also include TIRs and DDE motif-containing transposase but surprisingly do not create TSDs upon insertion. Instead, Spy transposons appear to transpose precisely between 5'-AAA and TTT-3' host nucleotides, without duplication or modification of the AAATTT target sites. Spy transposons were identified in the genomes of diverse invertebrate species based on transposase homology searches and structure-based approaches. Phylogenetic analyses indicate that Spy transposases are distantly related to IS5, ISL2EU, and PIF/Harbinger transposases. However, Spy transposons are distinct from these and other DNA transposon superfamilies by their lack of TSD and their target site preference. Our findings expand the known diversity of DNA transposons and reveal a new group of eukaryotic DDE transposases with unusual catalytic properties.

  7. Differential utilization of allochthonous and autochthonous carbon by aquatic insects of two shrub-steppe desert spring-streams: A stable carbon isotope analysis and critique of the method

    Energy Technology Data Exchange (ETDEWEB)

    Mize, A.L. [Old Dominion Univ., Norfolk, VA (United States)

    1993-06-01

    The purpose of this study is to assess whether the carbon supporting stream food webs comes principally from terrestrial sources or is produced within the stream. Lacking data to resolve the allochthonous/autochthonous issue with any finality, stream ecologists have alternately postulated that stream carbon was principally autochthonous or principally allochthonous. Others argued that autochthonous and allochthonous carbon resources cannot be separated and that the allochthonous/autochthonous dependence issue is unresolvable. Many investigators have seized upon stable carbon isotopes technology as the tool to resolve the controversy. Unfortunately most investigators have conceded that the results are rarely quantitative and that the qualitative relationships are ambiguous. This study points out the fallacies of trying to conjure single isotopic values for either allochthonous or autochthonous carbon. It suggests that stable carbon isotope technology is not reliable in establishing specific consumer/food source relations and that it is not suitable for assessing allochthonous/autochthonous carbon dependence in freshwater streams.

  8. Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes

    OpenAIRE

    2008-01-01

    Abstract Background Chlamydiae are obligate intracellular bacteria of protists, invertebrates and vertebrates, but have not been found to date in photosynthetic eukaryotes (algae and embryophytes). Genes of putative chlamydial origin, however, are present in significant numbers in sequenced genomes of photosynthetic eukaryotes. It has been suggested that such genes were acquired by an ancient horizontal gene transfer from Chlamydiae to the ancestor of photosynthetic eukaryotes. To further tes...

  9. Alternative Splicing: A Potential Source of Functional Innovation in the Eukaryotic Genome

    Directory of Open Access Journals (Sweden)

    Lu Chen

    2012-01-01

    Full Text Available Alternative splicing (AS is a common posttranscriptional process in eukaryotic organisms, by which multiple distinct functional transcripts are produced from a single gene. The release of the human genome draft revealed a much smaller number of genes than anticipated. Because of its potential role in expanding protein diversity, interest in alternative splicing has been increasing over the last decade. Although recent studies have shown that 94% human multiexon genes undergo AS, evolution of AS and thus its potential role in functional innovation in eukaryotic genomes remain largely unexplored. Here we review available evidence regarding the evolution of AS prevalence and functional role. In addition we stress the need to correct for the strong effect of transcript coverage in AS detection and set out a strategy to ultimately elucidate the extent of the role of AS in functional innovation on a genomic scale.

  10. The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups.

    Science.gov (United States)

    Koonin, Eugene V; Wolf, Yuri I; Nagasaki, Keizo; Dolja, Valerian V

    2008-12-01

    The recent discovery of RNA viruses in diverse unicellular eukaryotes and developments in evolutionary genomics have provided the means for addressing the origin of eukaryotic RNA viruses. The phylogenetic analyses of RNA polymerases and helicases presented in this Analysis article reveal close evolutionary relationships between RNA viruses infecting hosts from the Chromalveolate and Excavate supergroups and distinct families of picorna-like viruses of plants and animals. Thus, diversification of picorna-like viruses probably occurred in a 'Big Bang' concomitant with key events of eukaryogenesis. The origins of the conserved genes of picorna-like viruses are traced to likely ancestors including bacterial group II retroelements, the family of HtrA proteases and DNA bacteriophages.

  11. Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes

    Directory of Open Access Journals (Sweden)

    Butler Margaret I

    2006-10-01

    Full Text Available Abstract Background Inteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi. Results We identified seven intein coding sequences within nuclear genes coding for the second largest subunits of RNA polymerase. These sequences were found in diverse eukaryotes: one is in the second largest subunit of RNA polymerase I (RPA2 from the ascomycete fungus Phaeosphaeria nodorum, one is in the RNA polymerase III (RPC2 of the slime mould Dictyostelium discoideum and four intein coding sequences are in RNA polymerase II genes (RPB2, one each from the green alga Chlamydomonas reinhardtii, the zygomycete fungus Spiromyces aspiralis and the chytrid fungi Batrachochytrium dendrobatidis and Coelomomyces stegomyiae. The remaining intein coding sequence is in a viral relic embedded within the genome of the oomycete Phytophthora ramorum. The Chlamydomonas and Dictyostelium inteins are the first nuclear-encoded inteins found outside of the fungi. These new inteins represent a unique dataset: they are found in homologous proteins that form a paralogous group. Although these paralogues diverged early in eukaryotic evolution, their sequences can be aligned over most of their length. The inteins are inserted at multiple distinct sites, each of which corresponds to a highly conserved region of RNA polymerase. This dataset supports earlier work suggesting that inteins preferentially occur in highly conserved regions of their host proteins. Conclusion The identification of these new inteins

  12. Arsenic transport in prokaryotes and eukaryotic microbes.

    Science.gov (United States)

    Rosen, Barry P; Tamás, Markus J

    2010-01-01

    Aquaporins (AQPs) and aquaglyceroporins facilitate transport of a broad spectrum of substrates such as water, glycerol and other small uncharged solutes. More recently, AQPs ave also been shown to facilitate diffusion of metalloids such as arsenic (As) and antimony (Sb). At neutral pH, the trivalent forms of these metalloids are structurally similar to glycerol and hence they can enter cells through AQPs. As- and Sb-containing compounds are toxic to cells, yet both metalloids are used as chemotherapeutic agents for treating acute promyelocytic leukemia and diseases caused by protozoan parasites. In this chapter, we will review the role of AQPs and other proteins in metalloid transport in prokaryotes and eukaryotic microbes.

  13. Protein splicing and its evolution in eukaryotes

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    Starokadomskyy P. L.

    2010-02-01

    Full Text Available Inteins, or protein introns, are parts of protein sequences that are post-translationally excised, their flanking regions (exteins being spliced together. This process was called protein splicing. Originally inteins were found in prokaryotic or unicellular eukaryotic organisms. But the general principles of post-translation protein rearrangement are evolving yielding different post-translation modification of proteins in multicellular organisms. For clarity, these non-intein mediated events call either protein rearrangements or protein editing. The most intriguing example of protein editing is proteasome-mediated splicing of antigens in vertebrates that may play important role in antigen presentation. Other examples of protein rearrangements are maturation of Hg-proteins (critical receptors in embryogenesis as well as maturation of several metabolic enzymes. Despite a lack of experimental data we try to analyze some intriguing examples of protein splicing evolution.

  14. Eukaryotic protein production in designed storage organelles

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    Saloheimo Markku

    2009-01-01

    Full Text Available Abstract Background Protein bodies (PBs are natural endoplasmic reticulum (ER or vacuole plant-derived organelles that stably accumulate large amounts of storage proteins in seeds. The proline-rich N-terminal domain derived from the maize storage protein γ zein (Zera is sufficient to induce PBs in non-seed tissues of Arabidopsis and tobacco. This Zera property opens up new routes for high-level accumulation of recombinant proteins by fusion of Zera with proteins of interest. In this work we extend the advantageous properties of plant seed PBs to recombinant protein production in useful non-plant eukaryotic hosts including cultured fungal, mammalian and insect cells. Results Various Zera fusions with fluorescent and therapeutic proteins accumulate in induced PB-like organelles in all eukaryotic systems tested: tobacco leaves, Trichoderma reesei, several mammalian cultured cells and Sf9 insect cells. This accumulation in membranous organelles insulates both recombinant protein and host from undesirable activities of either. Recombinant protein encapsulation in these PBs facilitates stable accumulation of proteins in a protected sub-cellular compartment which results in an enhancement of protein production without affecting the viability and development of stably transformed hosts. The induced PBs also retain the high-density properties of native seed PBs which facilitate the recovery and purification of the recombinant proteins they contain. Conclusion The Zera sequence provides an efficient and universal means to produce recombinant proteins by accumulation in ER-derived organelles. The remarkable cross-kingdom conservation of PB formation and their biophysical properties should have broad application in the manufacture of non-secreted recombinant proteins and suggests the existence of universal ER pathways for protein insulation.

  15. Autochthonous bioaugmentation with environmental samples rich in hydrocarbonoclastic bacteria for bench-scale bioremediation of oily seawater and desert soil.

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    Ali, Nedaa; Dashti, Narjes; Salamah, Samar; Al-Awadhi, Husain; Sorkhoh, Naser; Radwan, Samir

    2016-05-01

    Oil-contaminated seawater and desert soil batches were bioaugmented with suspensions of pea (Pisum sativum) rhizosphere and soil with long history of oil pollution. Oil consumption was measured by gas-liquid chromatography. Hydrocarbonoclastic bacteria in the bioremediation batches were counted using a mineral medium with oil vapor as a sole carbon source and characterized by their 16S ribosomal RNA (rRNA)-gene sequences. Most of the oil was consumed during the first 2-4 months, and the oil-removal rate decreased or ceased thereafter due to nutrient and oxygen depletion. Supplying the batches with NaNO3 (nitrogen fertilization) at a late phase of bioremediation resulted in reenhanced oil consumption and bacterial growth. In the seawater batches bioaugmented with rhizospheric suspension, the autochthonous rhizospheric bacterial species Microbacterium oxidans and Rhodococcus spp. were established and contributed to oil-removal. The rhizosphere-bioaugmented soil batches selectively favored Arthrobacter nitroguajacolicus, Caulobacter segnis, and Ensifer adherens. In seawater batches bioaugmented with long-contaminated soil, the predominant oil-removing bacterium was the marine species Marinobacter hydrocarbonoclasticus. In soil batches on the other hand, the autochthonous inhabitants of the long-contaminated soil, Pseudomonas and Massilia species were established and contributed to oil removal. It was concluded that the use of rhizospheric bacteria for inoculating seawater and desert soil and of bacteria in long-contaminated soil for inoculating desert soil follows the concept of "autochthonous bioaugmentation." Inoculating seawater with bacteria in long-contaminated soil, on the other hand, merits the designation "allochthonous bioaugmentation."

  16. An evolutionary network of genes present in the eukaryote common ancestor polls genomes on eukaryotic and mitochondrial origin.

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    Thiergart, Thorsten; Landan, Giddy; Schenk, Marc; Dagan, Tal; Martin, William F

    2012-01-01

    To test the predictions of competing and mutually exclusive hypotheses for the origin of eukaryotes, we identified from a sample of 27 sequenced eukaryotic and 994 sequenced prokaryotic genomes 571 genes that were present in the eukaryote common ancestor and that have homologues among eubacterial and archaebacterial genomes. Maximum-likelihood trees identified the prokaryotic genomes that most frequently contained genes branching as the sister to the eukaryotic nuclear homologues. Among the archaebacteria, euryarchaeote genomes most frequently harbored the sister to the eukaryotic nuclear gene, whereas among eubacteria, the α-proteobacteria were most frequently represented within the sister group. Only 3 genes out of 571 gave a 3-domain tree. Homologues from α-proteobacterial genomes that branched as the sister to nuclear genes were found more frequently in genomes of facultatively anaerobic members of the rhiozobiales and rhodospirilliales than in obligate intracellular ricketttsial parasites. Following α-proteobacteria, the most frequent eubacterial sister lineages were γ-proteobacteria, δ-proteobacteria, and firmicutes, which were also the prokaryote genomes least frequently found as monophyletic groups in our trees. Although all 22 higher prokaryotic taxa sampled (crenarchaeotes, γ-proteobacteria, spirochaetes, chlamydias, etc.) harbor genes that branch as the sister to homologues present in the eukaryotic common ancestor, that is not evidence of 22 different prokaryotic cells participating at eukaryote origins because prokaryotic "lineages" have laterally acquired genes for more than 1.5 billion years since eukaryote origins. The data underscore the archaebacterial (host) nature of the eukaryotic informational genes and the eubacterial (mitochondrial) nature of eukaryotic energy metabolism. The network linking genes of the eukaryote ancestor to contemporary homologues distributed across prokaryotic genomes elucidates eukaryote gene origins in a dialect

  17. Blocking Modification of Eukaryotic Initiation 5A2 Antagonizes Cervical Carcinoma via Inhibition of RhoA/ROCK Signal Transduction Pathway.

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    Liu, Xiaojun; Chen, Dong; Liu, Jiamei; Chu, Zhangtao; Liu, Dongli

    2016-09-07

    Cervical carcinoma is one of the leading causes of cancer-related death for female worldwide. Eukaryotic initiation factor 5A2 belongs to the eukaryotic initiation factor 5A family and is proposed to be a key factor involved in the development of diverse cancers. In the current study, a series of in vivo and in vitro investigations were performed to characterize the role of eukaryotic initiation factor 5A2 in oncogenesis and metastasis of cervical carcinoma. The expression status of eukaryotic initiation factor 5A2 in 15 cervical carcinoma patients was quantified. Then, the effect of eukaryotic initiation factor 5A2 knockdown on in vivo tumorigenicity ability, cell proliferation, cell cycle distribution, and cell mobility of HeLa cells was measured. To uncover the mechanism driving the function of eukaryotic initiation factor 5A2 in cervical carcinoma, expression of members within RhoA/ROCK pathway was detected, and the results were further verified with an RhoA overexpression modification. The level of eukaryotic initiation factor 5A2 in cervical carcinoma samples was significantly higher than that in paired paratumor tissues (P ROCK I, and ROCK II were downregulated. The above-mentioned changes in eukaryotic initiation factor 5A2 knockdown cells were alleviated by the overexpression of RhoA. The major findings outlined in the current study confirmed the potential of eukaryotic initiation factor 5A2 as a promising prognosis predictor and therapeutic target for cervical carcinoma treatment. Also, our data inferred that eukaryotic initiation factor 5A2 might function in carcinogenesis of cervical carcinoma through an RhoA/ROCK-dependent manner.

  18. Characterization of Carbapenem-Resistant Enterobacteriaceae with High Rate of Autochthonous Transmission in the Arabian Peninsula.

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    Ágnes Sonnevend

    Full Text Available To establish the role of local transmission versus possible pathogen import due to previous foreign exposure in infections caused by carbapenem non-susceptible Enterobacteriaceae in the Arabian Peninsula, 200 independent isolates collected in 16 hospitals of Saudi Arabia, Kuwait, Oman and the United Arab Emirates were studied. All strains were multidrug resistant; 42.5% of them also qualified as extremely drug resistant. The frequency of various carbapenemases varied according to the participating countries, but in the collection, as a whole, blaNDM-1 was the most frequently encountered carbapenemase gene (46.5% followed by blaOXA-48-like gene (32.5%. A comparatively high rate (8.9% of multi-clonal strains carrying both blaNDM and blaOXA-48-like genes in the United Arab Emirates, representing the most resistant subgroup, was encountered. No KPC-expressing isolates were detected. Three major clones of blaNDM-1 carrying Klebsiella pneumoniae of ST152 (n = 22, Saudi Arabia, ST14 (n = 7, United Arab Emirates and ST147 types (n = 9, Oman were identified, the latter two clones carrying similar, but not identical HI1b incompatibility type plasmids of >170 kb. While from 78.6% of the cases with documented foreign hospitalization blaNDM positive strains were isolated, these strains formed only 25.6% of all the isolates expressing this enzyme. In fact, 56.8% of the NDM, 75.7% of OXA-48-like and 90.9% of VIM positive strains were recovered from patients without documented foreign exposure, neither in the form of travel or prior hospitalization abroad, suggesting a high rate of autochthonous infections. This, considering the extensive links of these countries to the rest of the world, predicts that trends in the local epidemiology of carbapenem resistant strains may increasingly affect the spread of these pathogens on the global scale. These results call for improved surveillance of carbapenem resistant Enterobacteriaceae in the countries of the Arabian

  19. [Epidemic of autochthonous hepatic and intestinal amebiasis in a place near Grenoble].

    Science.gov (United States)

    Ambroise-Thomas, P; Goullier, A; Grillot, R; Lascaud, D; Rivoire, L; Perrin, Y

    1975-01-01

    We had the opportunity of studying an epidemic of autochthonous amoebiasis occurring in the autumn of 1974 in a small town of 4000 inhabitants 30 km from Grenoble. Attention was originally attracted by the occurrence in this town of two cases of hepatic amoebiasis and one of intestinal amoebiasis identified by rectoscopy. Systematic investigations (coproctic examinations and serological tests for amoebiasis by indirect antibody fluorescence) were then carried out on everyone in the locality with digestive disorders which were possibly referable to amoebiasis, and on the other members of their families. A total number of 148 coproctic examinations were made and in two cases revealed the presence of vegetative forms of Entamoeba histolytica. In both cases the infestation provoked few symptoms (asthenia, vague abdominal discomfort, intermittent and apparently banal diarrhoea). On the other hand 20 out of 94 serological tests revealed positive results, 14 of which were equal to or greater than a titre of 1/100, a level at which all risks of non-specificity are virtually ruled out under our experimental conditions. Material reasons made it impossible to subject these cases to repeated faecal checks, but in two of them at least the rectoscopic appearances were very suggestive of subacute intestinal amoebiasis. Moreover, amoebic disease appears to be well confirmed by the results obtained among the patients as a whole by treatment with Metroinidazole. A variety of hypotheses on the origin of this epidemic have been put forward and then abandoned (market garden produce, receipt by certain families of exotic frut from overseas). In actual fact water seems to be the point of departure, for, although specimens of water taken at 7 different levels in the water supply system failed to reveal the presence of a single amoeba, bacteriological analyses during autumn 1974 showed signs of faecal contamination. The locality, which is situated at the foot of the Chartreuse massif

  20. Role of self-sufficiency, productivity and diversification on the economic sustainability of farming systems with autochthonous sheep breeds in less favoured areas in Southern Europe.

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    Ripoll-Bosch, R; Joy, M; Bernués, A

    2014-08-01

    Traditional mixed livestock cereal- and pasture-based sheep farming systems in Europe are threatened by intensification and specialisation processes. However, the intensification process does not always yield improved economic results or efficiency. This study involved a group of farmers that raised an autochthonous sheep breed (Ojinegra de Teruel) in an unfavourable area of North-East Spain. This study aimed to typify the farms and elucidate the existing links between economic performance and certain sustainability indicators (i.e. productivity, self-sufficiency and diversification). Information was obtained through direct interviews with 30 farms (73% of the farmers belonging to the breeders association). Interviews were conducted in 2009 and involved 32 indicators regarding farm structure, management and economic performance. With a principal component analysis, three factors were obtained explaining 77.9% of the original variance. This factors were named as inputs/self-sufficiency, which included the use of on-farm feeds, the amount of variable costs per ewe and economic performance; productivity, which included lamb productivity and economic autonomy; and productive orientation, which included the degree of specialisation in production. A cluster analysis identified the following four groups of farms: high-input intensive system; low-input self-sufficient system; specialised livestock system; and diversified crops-livestock system. In conclusion, despite the large variability between and within groups, the following factors that explain the economic profitability of farms were identified: (i) high feed self-sufficiency and low variable costs enhance the economic performance (per labour unit) of the farms; (ii) animal productivity reduces subsidy dependence, but does not necessarily imply better economic performance; and (iii) diversity of production enhances farm flexibility, but is not related to economic performance.

  1. The COG database: an updated version includes eukaryotes

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    Sverdlov Alexander V

    2003-09-01

    Full Text Available Abstract Background The availability of multiple, essentially complete genome sequences of prokaryotes and eukaryotes spurred both the demand and the opportunity for the construction of an evolutionary classification of genes from these genomes. Such a classification system based on orthologous relationships between genes appears to be a natural framework for comparative genomics and should facilitate both functional annotation of genomes and large-scale evolutionary studies. Results We describe here a major update of the previously developed system for delineation of Clusters of Orthologous Groups of proteins (COGs from the sequenced genomes of prokaryotes and unicellular eukaryotes and the construction of clusters of predicted orthologs for 7 eukaryotic genomes, which we named KOGs after eukaryotic orthologous groups. The COG collection currently consists of 138,458 proteins, which form 4873 COGs and comprise 75% of the 185,505 (predicted proteins encoded in 66 genomes of unicellular organisms. The eukaryotic orthologous groups (KOGs include proteins from 7 eukaryotic genomes: three animals (the nematode Caenorhabditis elegans, the fruit fly Drosophila melanogaster and Homo sapiens, one plant, Arabidopsis thaliana, two fungi (Saccharomyces cerevisiae and Schizosaccharomyces pombe, and the intracellular microsporidian parasite Encephalitozoon cuniculi. The current KOG set consists of 4852 clusters of orthologs, which include 59,838 proteins, or ~54% of the analyzed eukaryotic 110,655 gene products. Compared to the coverage of the prokaryotic genomes with COGs, a considerably smaller fraction of eukaryotic genes could be included into the KOGs; addition of new eukaryotic genomes is expected to result in substantial increase in the coverage of eukaryotic genomes with KOGs. Examination of the phyletic patterns of KOGs reveals a conserved core represented in all analyzed species and consisting of ~20% of the KOG set. This conserved portion of the

  2. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence.

    Science.gov (United States)

    Koonin, Eugene V

    2017-02-10

    Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation. The nucleic acid-guided defense systems include prokaryotic Argonaute (pAgo)-centered innate immunity and CRISPR-Cas adaptive immunity as well as diverse branches of RNA interference (RNAi) in eukaryotes. The archaeal pAgo machinery is the direct ancestor of eukaryotic RNAi that, however, acquired additional components, such as Dicer, and enormously diversified through multiple duplications. In contrast, eukaryotes lack any heritage of the CRISPR-Cas systems, conceivably, due to the cellular toxicity of some Cas proteins that would get activated as a result of operon disruption in eukaryotes. The adaptive immunity function in eukaryotes is taken over partly by the PIWI RNA branch of RNAi and partly by protein-based immunity. In this review, I briefly discuss the interplay between homology and analogy in the evolution of RNA- and DNA-guided immunity, and attempt to formulate some general evolutionary principles for this ancient class of defense systems.

  3. Causes and consequences of eukaryotization through mutualistic endosymbiosis and compartmentalization

    NARCIS (Netherlands)

    Hengeveld, R.; Fedonkin, M.A.

    2004-01-01

    This paper reviews and extends ideas of eukaryotization by endosymbiosis. These ideas are put within an historical context of processes that may have led up to eukaryotization and those that seem to have resulted from this process. Our starting point for considering the emergence and development of

  4. Molecular paleontology and complexity in the last eukaryotic common ancestor.

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    Koumandou, V Lila; Wickstead, Bill; Ginger, Michael L; van der Giezen, Mark; Dacks, Joel B; Field, Mark C

    2013-01-01

    Eukaryogenesis, the origin of the eukaryotic cell, represents one of the fundamental evolutionary transitions in the history of life on earth. This event, which is estimated to have occurred over one billion years ago, remains rather poorly understood. While some well-validated examples of fossil microbial eukaryotes for this time frame have been described, these can provide only basic morphology and the molecular machinery present in these organisms has remained unknown. Complete and partial genomic information has begun to fill this gap, and is being used to trace proteins and cellular traits to their roots and to provide unprecedented levels of resolution of structures, metabolic pathways and capabilities of organisms at these earliest points within the eukaryotic lineage. This is essentially allowing a molecular paleontology. What has emerged from these studies is spectacular cellular complexity prior to expansion of the eukaryotic lineages. Multiple reconstructed cellular systems indicate a very sophisticated biology, which by implication arose following the initial eukaryogenesis event but prior to eukaryotic radiation and provides a challenge in terms of explaining how these early eukaryotes arose and in understanding how they lived. Here, we provide brief overviews of several cellular systems and the major emerging conclusions, together with predictions for subsequent directions in evolution leading to extant taxa. We also consider what these reconstructions suggest about the life styles and capabilities of these earliest eukaryotes and the period of evolution between the radiation of eukaryotes and the eukaryogenesis event itself.

  5. Inhibition of Listeria monocytogenes and Escherichia coli O157:H7 in liquid broth medium and during processing of fermented sausage using autochthonous starter cultures.

    Science.gov (United States)

    Pragalaki, T; Bloukas, J G; Kotzekidou, P

    2013-11-01

    The antimicrobial effect of two autochthonous starter cultures of Lactobacillus sakei was evaluated in vitro (in liquid broth medium) and in situ assays. The inactivation of foodborne pathogens Listeria monocytogenes (serotype 4ab No 10) and Escherichia coli O157:H7 ATCC 43888 was investigated during the production of fermented sausage according to a typical Greek recipe using L. sakei strains as starter cultures. The inactivation kinetics were modeled using GInaFiT, a freeware tool to assess microbial survival curves. By the end of the ripening period, the inhibition of L. monocytogenes was significant in treatments with L. sakei 8416 and L. sakei 4413 compared to the control treatment. A 2.2-log reduction of the population of E. coli O157:H7 resulted from the autochthonous starter culture L. sakei 4413 during sausage processing. The use of the autochthonous starter cultures constitutes an additional improvement to the microbial safety by reducing foodborne pathogens.

  6. A new definition of health? An open letter of autochthonous peoples and medical anthropologists to the WHO.

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    Charlier, P; Coppens, Y; Malaurie, J; Brun, L; Kepanga, M; Hoang-Opermann, V; Correa Calfin, J A; Nuku, G; Ushiga, M; Schor, X E; Deo, S; Hassin, J; Hervé, C

    2017-01-01

    Currently, for many practitioners (hospital and liberals) and researchers (including public health), the WHO definition of health is outdated: first it seems more utopian than pragmatic; then, it proves unsuitable for a large part of the world population. There is clearly a need to refine this definition or propose additional criteria to be more relevant or discriminating. In this perspective, what can indigenous people offer in the elaboration of a new definition of health? In this article, leaders or representatives of autochthonous peoples, anthropologists and physicians from many cultural origins (Amazonia, Patagonia, Papua New-Guinea, Inuit, North-American Indian, sub-Saharan Africa, India, China, Melanesia and Polynesia) have tried to identify and explain several key concepts that WHO should reintegrate into its new definition of health: human equilibrium in nature, accepted spirituality and adaptation. On the sidelines of the application of COP21 decisions that should give back to man his place into the environment, autochthonous people leaders, anthropologists and MDs explain why these three concepts are fundamental and universal health determinants, and need to be included in a new WHO definition of health.

  7. Behavior of Staphylococcus aureus and autochthone microbiota in fresh sausages added of sodium nitrite and stored under refrigeration

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    Lucyanne Maria Moraes Correia

    2014-10-01

    Full Text Available Fresh sausages are cured meat products that may be contaminated with Staphylococcus aureus during the manufacturing procedure, which is frequently related with inadequate handling practices. The use of nitrite in meat products has proven efficacy against Clostridium botulinum, and studies indicate that bactericidal action against S. aureus depends on factors that are intrinsic and extrinsic to the product. The objective of the present study was to evaluate the effect of nitrite concentration, and pH on S. aureus and psychrotrophic autochthone microbiota in fresh sausages stored at different times and temperatures. Fresh sausage were produced at nitrite concentrations 50, 150 and 200ppm and contaminated with S. aureus. The sausages were storage at refrigeration (7 and 12°C and the quantification of S. aureus and psychrotrophic microorganisms was carried out on days 0, 2, 4, 7, and 10. Results showed that nitrite concentrations and the temperatures used had minimal effect on the multiplication of S. aureus and psychrotrophic autochthone microbiota. Final counts depended only on the length of storage: at the end of 10 days, counts were statistically similar in the different groups, showing that temperature and nitrite concentrations used did not control microbial growth effectively. It is suggested that the product should be stored below 7°C or at freezing temperatures for greater microbiological stability

  8. Energetics and genetics across the prokaryote-eukaryote divide

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    Lane Nick

    2011-06-01

    Full Text Available Abstract Background All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont. Results The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote. Conclusions The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes. Reviewers This article was reviewed by

  9. An investigation into eukaryotic pseudouridine synthases.

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    King, Ross D; Lu, Chuan

    2014-08-01

    A common post-transcriptional modification of RNA is the conversion of uridine to its isomer pseudouridine. We investigated the biological significance of eukaryotic pseudouridine synthases using the yeast Saccharomyces cerevisiae. We conducted a comprehensive statistical analysis on growth data from automated perturbation (gene deletion) experiments, and used bi-logistic curve analysis to characterise the yeast phenotypes. The deletant strains displayed different alteration in growth properties, including in some cases enhanced growth and/or biphasic growth curves not seen in wild-type strains under matched conditions. These results demonstrate that disrupting pseudouridine synthases can have a significant qualitative effect on growth. We further investigated the significance of post-transcriptional pseudouridine modification through investigation of the scientific literature. We found that (1) In Toxoplasma gondii, a pseudouridine synthase gene is critical in cellular differentiation between the two asexual forms: Tachyzoites and bradyzoites; (2) Mutation of pseudouridine synthase genes has also been implicated in human diseases (mitochondrial myopathy and sideroblastic anemia (MLASA); dyskeratosis congenita). Taken together, these results are consistent with pseudouridine synthases having a Gene Ontology function of "biological regulation".

  10. Genetic and pathological characteristics of Cryptococcus gattii and Cryptococcus neoformans var. neoformans from meningoencephalitis in autochthonous goats and mouflons, Sardinia, Italy.

    Science.gov (United States)

    Maestrale, Caterina; Masia, Mariangela; Pintus, Davide; Lollai, Stefano; Kozel, Thomas R; Gates-Hollingsworth, Marcellene A; Cancedda, Maria Giovanna; Cabras, Pierangela; Pirino, Salvatore; D'Ascenzo, Vittoria; Ligios, Ciriaco

    2015-06-12

    In this study, we examined in Sardinia the brain of 555 autochthonous sheep, 50 goats, and 4 mouflons which were found affected by neurological signs. We found 6 goats and one mouflon with meningoencephalitis caused by Cryptococcus sp. There was no evidence of cryptococcal infections in any of the examined sheep. MLST genotyping on Cryptococcus sp. isolates identified Cryptococcus gatti genotype AFLP4/VGI and Cryptococcus neoformans var. neoformans genotype AFLP2/VNIV. Phylogenetically, all Cryptococcus gattii isolates fell within the autochthonous animal, human and environmental Mediterranean isolate cluster, forming a distinct branch along with environmental strains from Alicante, in the southern Mediterranean coast of Spain.

  11. LeuT: a prokaryotic stepping stone on the way to a eukaryotic neurotransmitter transporter structure.

    Science.gov (United States)

    Singh, Satinder K

    2008-01-01

    Ion-coupled secondary transport is utilized by a broad range of integral membrane proteins to catalyze the energetically unfavorable movement of solute molecules across a lipid bilayer. Members of the solute carrier 6 (SLC6) family, present in both prokaryotes and eukaryotes, are sodium-coupled symporters that play crucial roles in processes as diverse as nutrient uptake and neurotransmitter clearance. The crystal structure of LeuT, a bacterial member of this family, provided the first atomic-level glimpse into overall architecture, pinpointed the substrate and sodium binding sites and implicated candidate helices and residues in the "gating" conformational changes that accompany ion binding and release. The structure is consistent with a wealth of elegant biochemical data on the eukaryotic counterparts and has for the first time permitted the construction of accurate homology models that can be directly tested experimentally. Sequence identity is especially high near the substrate and sodium binding sites and, thus, molecular insights within these regions have been substantial. However, there are several topics relevant to transport mechanism, inhibition and regulation that structure/function studies of LeuT cannot adequately address, suggesting the need for a eukaryotic transporter crystal structure.

  12. Snapshot of the eukaryotic gene expression in muskoxen rumen--a metatranscriptomic approach.

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    Meng Qi

    Full Text Available BACKGROUND: Herbivores rely on digestive tract lignocellulolytic microorganisms, including bacteria, fungi and protozoa, to derive energy and carbon from plant cell wall polysaccharides. Culture independent metagenomic studies have been used to reveal the genetic content of the bacterial species within gut microbiomes. However, the nature of the genes encoded by eukaryotic protozoa and fungi within these environments has not been explored using metagenomic or metatranscriptomic approaches. METHODOLOGY/PRINCIPAL FINDINGS: In this study, a metatranscriptomic approach was used to investigate the functional diversity of the eukaryotic microorganisms within the rumen of muskoxen (Ovibos moschatus, with a focus on plant cell wall degrading enzymes. Polyadenylated RNA (mRNA was sequenced on the Illumina Genome Analyzer II system and 2.8 gigabases of sequences were obtained and 59129 contigs assembled. Plant cell wall degrading enzyme modules including glycoside hydrolases, carbohydrate esterases and polysaccharide lyases were identified from over 2500 contigs. These included a number of glycoside hydrolase family 6 (GH6, GH48 and swollenin modules, which have rarely been described in previous gut metagenomic studies. CONCLUSIONS/SIGNIFICANCE: The muskoxen rumen metatranscriptome demonstrates a much higher percentage of cellulase enzyme discovery and an 8.7x higher rate of total carbohydrate active enzyme discovery per gigabase of sequence than previous rumen metagenomes. This study provides a snapshot of eukaryotic gene expression in the muskoxen rumen, and identifies a number of candidate genes coding for potentially valuable lignocellulolytic enzymes.

  13. New organelles by gene duplication in a biophysical model of eukaryote endomembrane evolution.

    Science.gov (United States)

    Ramadas, Rohini; Thattai, Mukund

    2013-06-04

    Extant eukaryotic cells have a dynamic traffic network that consists of diverse membrane-bound organelles exchanging matter via vesicles. This endomembrane system arose and diversified during a period characterized by massive expansions of gene families involved in trafficking after the acquisition of a mitochondrial endosymbiont by a prokaryotic host cell >1.8 billion years ago. Here we investigate the mechanistic link between gene duplication and the emergence of new nonendosymbiotic organelles, using a minimal biophysical model of traffic. Our model incorporates membrane-bound compartments, coat proteins and adaptors that drive vesicles to bud and segregate cargo from source compartments, and SNARE proteins and associated factors that cause vesicles to fuse into specific destination compartments. In simulations, arbitrary numbers of compartments with heterogeneous initial compositions segregate into a few compositionally distinct subsets that we term organelles. The global structure of the traffic system (i.e., the number, composition, and connectivity of organelles) is determined completely by local molecular interactions. On evolutionary timescales, duplication of the budding and fusion machinery followed by loss of cross-interactions leads to the emergence of new organelles, with increased molecular specificity being necessary to maintain larger organellar repertoires. These results clarify potential modes of early eukaryotic evolution as well as more recent eukaryotic diversification.

  14. A Pseudomonas aeruginosa type VI secretion phospholipase D effector targets both prokaryotic and eukaryotic cells.

    Science.gov (United States)

    Jiang, Feng; Waterfield, Nicholas R; Yang, Jian; Yang, Guowei; Jin, Qi

    2014-05-14

    Widely found in animal and plant-associated proteobacteria, type VI secretion systems (T6SSs) are potentially capable of facilitating diverse interactions with eukaryotes and/or other bacteria. Pseudomonas aeruginosa encodes three distinct T6SS haemolysin coregulated protein (Hcp) secretion islands (H1, H2, and H3-T6SS), each involved in different aspects of the bacterium's interaction with other organisms. Here we describe the characterization of a P. aeruginosa H3-T6SS-dependent phospholipase D effector, PldB, and its three tightly linked cognate immunity proteins. PldB targets the periplasm of prokaryotic cells and exerts an antibacterial activity. Surprisingly, PldB also facilitates intracellular invasion of host eukaryotic cells by activation of the PI3K/Akt pathway, revealing it to be a trans-kingdom effector. Our findings imply a potentially widespread T6SS-mediated mechanism, which deploys a single phospholipase effector to influence both prokaryotic cells and eukaryotic hosts.

  15. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.

    Directory of Open Access Journals (Sweden)

    Florence Guillière

    Full Text Available While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.

  16. IRES-mediated translation of membrane proteins and glycoproteins in eukaryotic cell-free systems.

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    Andreas K Brödel

    Full Text Available Internal ribosome entry site (IRES elements found in the 5' untranslated region of mRNAs enable translation initiation in a cap-independent manner, thereby representing an alternative to cap-dependent translation in cell-free protein expression systems. However, IRES function is largely species-dependent so their utility in cell-free systems from different species is rather limited. A promising approach to overcome these limitations would be the use of IRESs that are able to recruit components of the translation initiation apparatus from diverse origins. Here, we present a solution to this technical problem and describe the ability of a number of viral IRESs to direct efficient protein expression in different eukaryotic cell-free expression systems. The IRES from the intergenic region (IGR of the Cricket paralysis virus (CrPV genome was shown to function efficiently in four different cell-free systems based on lysates derived from cultured Sf21, CHO and K562 cells as well as wheat germ. Our results suggest that the CrPV IGR IRES-based expression vector is universally applicable for a broad range of eukaryotic cell lysates. Sf21, CHO and K562 cell-free expression systems are particularly promising platforms for the production of glycoproteins and membrane proteins since they contain endogenous microsomes that facilitate the incorporation of membrane-spanning proteins and the formation of post-translational modifications. We demonstrate the use of the CrPV IGR IRES-based expression vector for the enhanced synthesis of various target proteins including the glycoprotein erythropoietin and the membrane proteins heparin-binding EGF-like growth factor receptor as well as epidermal growth factor receptor in the above mentioned eukaryotic cell-free systems. CrPV IGR IRES-mediated translation will facilitate the development of novel eukaryotic cell-free expression platforms as well as the high-yield synthesis of desired proteins in already established

  17. HIV-1 Replication and the Cellular Eukaryotic Translation Apparatus

    Directory of Open Access Journals (Sweden)

    Santiago Guerrero

    2015-01-01

    Full Text Available Eukaryotic translation is a complex process composed of three main steps: initiation, elongation, and termination. During infections by RNA- and DNA-viruses, the eukaryotic translation machinery is used to assure optimal viral protein synthesis. Human immunodeficiency virus type I (HIV-1 uses several non-canonical pathways to translate its own proteins, such as leaky scanning, frameshifting, shunt, and cap-independent mechanisms. Moreover, HIV-1 modulates the host translation machinery by targeting key translation factors and overcomes different cellular obstacles that affect protein translation. In this review, we describe how HIV-1 proteins target several components of the eukaryotic translation machinery, which consequently improves viral translation and replication.

  18. Rooting the eukaryote tree by using a derived gene fusion.

    Science.gov (United States)

    Stechmann, Alexandra; Cavalier-Smith, Thomas

    2002-07-05

    Single-gene trees have failed to locate the root of the eukaryote tree because of systematic biases in sequence evolution. Structural genetic data should yield more reliable insights into deep phylogenetic relationships. We searched major protist groups for the presence or absence of a gene fusion in order to locate the root of the eukaryote tree. In striking contrast to previous molecular studies, we show that all eukaryote groups ancestrally with two cilia (bikonts) are evolutionarily derived. The root lies between bikonts and opisthokonts (animals, Fungi, Choanozoa). Amoebozoa either diverged even earlier or are sister of bikonts or (less likely) opisthokonts.

  19. Post-Triassic para-autochthoneity of the Yukon-Tanana Terrane: paleomagnetism of the Early Cretaceous Quiet Lake batholith

    Science.gov (United States)

    Symons, D. T. A.; McCausland, P. J. A.; Kawasaki, K.; Hart, C. J. R.

    2015-10-01

    Was the Yukon-Tanana Terrane (YTT), a California-sized part of south-central Yukon, an autochthonous or para-autochthonous part of northern British Columbia in the Early Cretaceous or was it part of a proposed allochthonous `Baja B.C.' continent offshore of southern California? To answer this fundamental question, a paleomagnetic study has been completed on 347 specimens from 24 sites in the 114.7 ± 1.1 Ma Quiet Lake batholith. This 1300 km2 pluton is composed mostly of massive medium-to-coarse grained biotite quartz monzonite that exhibits no evidence of either deformation or metamorphism, and that intrudes metamorphosed pre-Cretaceous basement rocks of the YTT in southern Yukon. The paleomagnetic analysis utilized thermal and alternating field step demagnetization, and saturation isothermal remanence methods. A well-defined characteristic remanent magnetization (ChRM) direction was isolated throughout the 500-585 °C temperature range at Decl. = 340.6°, Incl. = 77.4° (N = 14 sites, k = 51.2, A95 = 5.6°). The ChRM resides in magnetite with a low titanium content and is interpreted to be a primary thermoremanent magnetization. After correction for 490 km of geologically demonstrable dextral displacement on the inboard Tintina fault zone, the Quiet Lake batholith's paleopole is not significantly different at 95 per cent confidence from the co-eval 115 Ma reference paleopole for North America, giving non-significant translation and rotation estimates of 1.4° ± 5.1° (1σ) northwestwards and 10° ± 13° (1σ) clockwise, respectively. Thus, this is the first Early Cretaceous paleopole to show clearly that the YTT in Yukon is a para-autochthon that was part of North America's continental margin at that time. Further, after correction for Tintina fault displacement, the eight available Mesozoic YTT paleopoles agree closely with the North American apparent polar wander path (APWP). In contrast, the 22 paleopoles from the Intermontane Belt show the expected

  20. Membranes, energetics, and evolution across the prokaryote-eukaryote divide

    Science.gov (United States)

    Lynch, Michael; Marinov, Georgi K

    2017-01-01

    The evolution of the eukaryotic cell marked a profound moment in Earth’s history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes. Thus, although the origin of the mitochondrion was a key event in evolutionary history, there is no reason to think membrane bioenergetics played a direct, causal role in the transition from prokaryotes to eukaryotes and the subsequent explosive diversification of cellular and organismal complexity. DOI: http://dx.doi.org/10.7554/eLife.20437.001 PMID:28300533

  1. The structure and function of the eukaryotic ribosome.

    Science.gov (United States)

    Wilson, Daniel N; Doudna Cate, Jamie H

    2012-05-01

    Structures of the bacterial ribosome have provided a framework for understanding universal mechanisms of protein synthesis. However, the eukaryotic ribosome is much larger than it is in bacteria, and its activity is fundamentally different in many key ways. Recent cryo-electron microscopy reconstructions and X-ray crystal structures of eukaryotic ribosomes and ribosomal subunits now provide an unprecedented opportunity to explore mechanisms of eukaryotic translation and its regulation in atomic detail. This review describes the X-ray crystal structures of the Tetrahymena thermophila 40S and 60S subunits and the Saccharomyces cerevisiae 80S ribosome, as well as cryo-electron microscopy reconstructions of translating yeast and plant 80S ribosomes. Mechanistic questions about translation in eukaryotes that will require additional structural insights to be resolved are also presented.

  2. Giant viruses and the origin of modern eukaryotes.

    Science.gov (United States)

    Forterre, Patrick; Gaïa, Morgan

    2016-06-01

    Several authors have suggested that viruses from the NucleoCytoplasmic Large DNA Viruses group (NCLDV) have played an important role in the origin of modern eukaryotes. Notably, the viral eukaryogenesis theory posits that the nucleus originated from an ancient NCLDV-related virus. Focusing on the viral factory instead of the virion adds credit to this hypothesis, but also suggests alternative scenarios. Beside a role in the emergence of the nucleus, ancient NCLDV may have provided new genes and/or chromosomes to the proto-eukaryotic lineage. Phylogenetic analyses suggest that NCLDV informational proteins, related to those of Archaea and Eukarya, were either recruited by ancient NCLDV from proto-eukaryotes and/or transferred to proto-eukaryotes, in agreement with the antiquity of NCLDV and their possible role in eukaryogenesis.

  3. Construction and expression of recombined human AFP eukaryotic expression vector

    Institute of Scientific and Technical Information of China (English)

    Li-Wang Zhang; Yang-Lin Pan; Stephen M Festein; Jun Ren; Liang Zhang; Hong-Mei Zhang; Bin Jin; Bo-Rong Pan; Xiao-Ming Si; Yan-Jun Zhang; Zhong-Hua Wang

    2003-01-01

    AIM: To construct a recombined human AFP eukaryotic expression vector for the purpose of gene therapy and target therapy of hepatocellular carcinoma (HCC).METHODS: The full length AFP-cDNA of prokaryotic vector was digested, and subcloned to the multi-clony sites of the eukaryotic vector. The constructed vector was confirmed by enzymes digestion and electrophoresis, and the product expressed was detected by electrochemiluminescence and immunofluorescence methods.RESULTS: The full length AFP-cDNA successfully cloned to the eukaryotic vector through electrophoresis, 0.9723 IU/ml AFP antigen was detected in the supernatant of AFPCHO by electrochemiluminescence method. Compared with the control groups, the differences were significant (P<0.05).AFP antigen molecule was observed in the plasma of AFPCHO by immunofluorescence staining.CONCLUSION: The recombined human AFP eukaryotic expression vector can express in CHO cell line. It provides experimental data for gene therapy and target therapy of hepatocellular carcinoma.

  4. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae.

    NARCIS (Netherlands)

    Wijffels, R.H.; Kruse, O.; Hellingwerf, K.J.

    2013-01-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments. Cyanobacteria are promising host organisms fo

  5. Language Contact and Language Conflict in Autochthonous Language Minority Settings in the EU: A Preliminary Round-Up of Guiding Principles and Research Desiderata

    Science.gov (United States)

    Darquennes, Jeroen

    2010-01-01

    This contribution deals with language contact and language conflict in autochthonous language minority settings in the European Union. It rounds up a number of concepts that guide macro-socio-linguistic and macrocontact-linguistic research on language minorities. The description of these concepts results in a list of research desiderata.

  6. Autochthonous cultivars of Emilia Romagna region and their clones: Comparison of the chemical and sensory properties of olive oils.

    Science.gov (United States)

    Rotondi, Annalisa; Lapucci, Chiara; Morrone, Lucia; Neri, Luisa

    2017-06-01

    The olive species (Olea europaea L.) is characterized by significant phenotypic and genetic variability the genetic matrix has a strong influence on several important extra virgin olive oil (EVOO) chemical components. Four clones from cultivars autochthonous of the Emilia Romagna region were selected for their notable performance in terms of agronomical characteristics, and the quality of the olive oil produced was studied in detail. In particular, we analyzed the fatty acid composition, the phenolic profile and the sensory analysis of the oils from these clones and compared them with the oils from the respective cultivars. Most of the new clones, all already provided with a genetic and sanitary certification, exhibited overall higher qualitative standards than the cultivars, producing monovarietal oils interesting both nutritionally and from a sensory point of view, and furthermore with a beneficial effect on health.

  7. Massive expansion of the calpain gene family in unicellular eukaryotes

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    Zhao Sen

    2012-09-01

    Full Text Available Abstract Background Calpains are Ca2+-dependent cysteine proteases that participate in a range of crucial cellular processes. Dysfunction of these enzymes may cause, for instance, life-threatening diseases in humans, the loss of sex determination in nematodes and embryo lethality in plants. Although the calpain family is well characterized in animal and plant model organisms, there is a great lack of knowledge about these genes in unicellular eukaryote species (i.e. protists. Here, we study the distribution and evolution of calpain genes in a wide range of eukaryote genomes from major branches in the tree of life. Results Our investigations reveal 24 types of protein domains that are combined with the calpain-specific catalytic domain CysPc. In total we identify 41 different calpain domain architectures, 28 of these domain combinations have not been previously described. Based on our phylogenetic inferences, we propose that at least four calpain variants were established in the early evolution of eukaryotes, most likely before the radiation of all the major supergroups of eukaryotes. Many domains associated with eukaryotic calpain genes can be found among eubacteria or archaebacteria but never in combination with the CysPc domain. Conclusions The analyses presented here show that ancient modules present in prokaryotes, and a few de novo eukaryote domains, have been assembled into many novel domain combinations along the evolutionary history of eukaryotes. Some of the new calpain genes show a narrow distribution in a few branches in the tree of life, likely representing lineage-specific innovations. Hence, the functionally important classical calpain genes found among humans and vertebrates make up only a tiny fraction of the calpain family. In fact, a massive expansion of the calpain family occurred by domain shuffling among unicellular eukaryotes and contributed to a wealth of functionally different genes.

  8. Chlamydial genes shed light on the evolution of photoautotrophic eukaryotes

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    Melkonian Michael

    2008-07-01

    Full Text Available Abstract Background Chlamydiae are obligate intracellular bacteria of protists, invertebrates and vertebrates, but have not been found to date in photosynthetic eukaryotes (algae and embryophytes. Genes of putative chlamydial origin, however, are present in significant numbers in sequenced genomes of photosynthetic eukaryotes. It has been suggested that such genes were acquired by an ancient horizontal gene transfer from Chlamydiae to the ancestor of photosynthetic eukaryotes. To further test this hypothesis, an extensive search for proteins of chlamydial origin was performed using several recently sequenced algal genomes and EST databases, and the proteins subjected to phylogenetic analyses. Results A total of 39 proteins of chlamydial origin were retrieved from the photosynthetic eukaryotes analyzed and their identity verified through phylogenetic analyses. The distribution of the chlamydial proteins among four groups of photosynthetic eukaryotes (Viridiplantae, Rhodoplantae, Glaucoplantae, Bacillariophyta was complex suggesting multiple acquisitions and losses. Evidence is presented that all except one of the chlamydial genes originated from an ancient endosymbiosis of a chlamydial bacterium into the ancestor of the Plantae before their divergence into Viridiplantae, Rhodoplantae and Glaucoplantae, i.e. more than 1.1 BYA. The chlamydial proteins subsequently spread through secondary plastid endosymbioses to other eukaryotes. Of 20 chlamydial proteins recovered from the genomes of two Bacillariophyta, 10 were of rhodoplant, and 10 of viridiplant origin suggesting that they were acquired by two different secondary endosymbioses. Phylogenetic analyses of concatenated sequences demonstrated that the viridiplant secondary endosymbiosis likely occurred before the divergence of Chlorophyta and Streptophyta. Conclusion We identified 39 proteins of chlamydial origin in photosynthetic eukaryotes signaling an ancient invasion of the ancestor of the

  9. Exploitation of sweet cherry (Prunus avium L.) puree added of stem infusion through fermentation by selected autochthonous lactic acid bacteria.

    Science.gov (United States)

    Di Cagno, Raffaella; Surico, Rosalinda Fortunata; Minervini, Giovanna; Rizzello, Carlo Giuseppe; Lovino, Raffaella; Servili, Maurizio; Taticchi, Agnese; Urbani, Sefania; Gobbetti, Marco

    2011-08-01

    Strains of Lactobacillus plantarum, Pediococcus acidilactici, Pediococcus pentosaceus and Leuconostoc mesenteroides subsp. mesenteroides were identified from 8 cultivars of sweet cherry by partial 16S rRNA gene sequence and subjected to typing by Random Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) analysis. Representative isolates from each species and each cultivar were screened based on the kinetics of growth on cherry puree added of (10%, v/v) stem infusion (CP-SI). A protocol for processing and storage of CP-SI, which included fermentation by selected autochthonous P. pentosaceus SWE5 and L. plantarum FP3 (started CP-SI) or spontaneous fermentation (unstarted CP-SI), was set up. Starters grew and remained viable at elevated cell numbers (ca. 9.0 log cfu g(-1)) during 60 days of storage at 4 °C. The number of presumptive lactic acid bacteria of the unstarted CP-SI did not exceed the value of ca. 3.0 log cfu g(-1). Consumption of carbohydrates (e.g., glucose and fructose) by starter lactic acid bacteria was limited as well as it was the lactic acid fermentation. Consumption of organic acids (e.g., malic acid) and free amino acids was evident, especially, throughout storage. Compared to CP-SI before processing, the concentrations of total phenolic compounds and anthocyanins did not vary in the started CP-SI. The concentration of anthocyanins slightly decreased in the unstarted CP-SI. The antioxidant activity, expressed as the scavenging activity toward DPPH radical, was found at highest level in the started CP-SI which approached that found in CP-SI before processing. During storage, viscosity and, especially, color indexes of started CP-SI were higher than those found in the unstarted CP-SI. Fermentation by autochthonous lactic acid bacteria seemed to also positively interfere with the sensory attributes of CP-SI.

  10. Similarities and Differences in the Glycosylation Mechanisms in Prokaryotes and Eukaryotes

    Directory of Open Access Journals (Sweden)

    Anne Dell

    2010-01-01

    Full Text Available Recent years have witnessed a rapid growth in the number and diversity of prokaryotic proteins shown to carry N- and/or O-glycans, with protein glycosylation now considered as fundamental to the biology of these organisms as it is in eukaryotic systems. This article overviews the major glycosylation pathways that are known to exist in eukarya, bacteria and archaea. These are (i oligosaccharyltransferase (OST-mediated N-glycosylation which is abundant in eukarya and archaea, but is restricted to a limited range of bacteria; (ii stepwise cytoplasmic N-glycosylation that has so far only been confirmed in the bacterial domain; (iii OST-mediated O-glycosylation which appears to be characteristic of bacteria; and (iv stepwise O-glycosylation which is common in eukarya and bacteria. A key aim of the review is to integrate information from the three domains of life in order to highlight commonalities in glycosylation processes. We show how the OST-mediated N- and O-glycosylation pathways share cytoplasmic assembly of lipid-linked oligosaccharides, flipping across the ER/periplasmic/cytoplasmic membranes, and transferring “en bloc” to the protein acceptor. Moreover these hallmarks are mirrored in lipopolysaccharide biosynthesis. Like in eukaryotes, stepwise O-glycosylation occurs on diverse bacterial proteins including flagellins, adhesins, autotransporters and lipoproteins, with O-glycosylation chain extension often coupled with secretory mechanisms.

  11. Similarities and differences in the glycosylation mechanisms in prokaryotes and eukaryotes.

    Science.gov (United States)

    Dell, Anne; Galadari, Alaa; Sastre, Federico; Hitchen, Paul

    2010-01-01

    Recent years have witnessed a rapid growth in the number and diversity of prokaryotic proteins shown to carry N- and/or O-glycans, with protein glycosylation now considered as fundamental to the biology of these organisms as it is in eukaryotic systems. This article overviews the major glycosylation pathways that are known to exist in eukarya, bacteria and archaea. These are (i) oligosaccharyltransferase (OST)-mediated N-glycosylation which is abundant in eukarya and archaea, but is restricted to a limited range of bacteria; (ii) stepwise cytoplasmic N-glycosylation that has so far only been confirmed in the bacterial domain; (iii) OST-mediated O-glycosylation which appears to be characteristic of bacteria; and (iv) stepwise O-glycosylation which is common in eukarya and bacteria. A key aim of the review is to integrate information from the three domains of life in order to highlight commonalities in glycosylation processes. We show how the OST-mediated N- and O-glycosylation pathways share cytoplasmic assembly of lipid-linked oligosaccharides, flipping across the ER/periplasmic/cytoplasmic membranes, and transferring "en bloc" to the protein acceptor. Moreover these hallmarks are mirrored in lipopolysaccharide biosynthesis. Like in eukaryotes, stepwise O-glycosylation occurs on diverse bacterial proteins including flagellins, adhesins, autotransporters and lipoproteins, with O-glycosylation chain extension often coupled with secretory mechanisms.

  12. Mussel biofiltration effects on attached bacteria and unicellular eukaryotes in fish-rearing seawater

    Science.gov (United States)

    Voudanta, Eleni; Monchy, Sebastién; Delegrange, Alice; Vincent, Dorothée; Genitsaris, Savvas; Christaki, Urania

    2016-01-01

    Mussel biofiltration is a widely used approach for the mitigation of aquaculture water. In this study, we investigated the effect of mussel biofiltration on the communities of particle-associated bacteria and unicellular eukaryotes in a sea bass aquaculture in southern North Sea. We assessed the planktonic community changes before and after biofiltration based on the diversity of the 16S and 18S rRNA genes by using next generation sequencing technologies. Although there was no overall reduction in the operational taxonomic units (OTU) numbers between the control (no mussels) and the test (with mussels) tanks, a clear reduction in the relative abundance of the top three most dominant OTUs in every sampling time was observed, ranging between 2–28% and 16–82% for Bacteria and Eukarya, respectively. The bacterial community was dominated by OTUs related to phytoplankton blooms and/or high concentrations of detritus. Among the eukaryotes, several fungal and parasitic groups were found. Their relative abundance in most cases was also reduced from the control to the test tanks; a similar decreasing pattern was also observed for both major higher taxa and functional (trophic) groups. Overall, this study showed the effectiveness of mussel biofiltration on the decrease of microbiota abundance and diversity in seawater fueling fish farms. PMID:27069786

  13. Living at the Limits: Evidence for Microbial Eukaryotes Thriving under Pressure in Deep Anoxic, Hypersaline Habitats

    Directory of Open Access Journals (Sweden)

    Thorsten Stoeck

    2014-01-01

    Full Text Available The advent of molecular tools in microbial ecology paved the way to exploit the diversity of microbes in extreme environments. Here, we review these tools as applied in one of the most polyextreme habitats known on our planet, namely, deep hypersaline anoxic basins (DHABs, located at ca. 3000–3500 m depth in the Eastern Mediterranean Sea. Molecular gene signatures amplified from environmental DHAB samples identified a high degree of genetic novelty, as well as distinct communities in the DHABs. Canonical correspondence analyses provided strong evidence that salinity, ion composition, and anoxia were the strongest selection factors shaping protistan community structures, largely preventing cross-colonization among the individual basins. Thus, each investigated basin represents a unique habitat (“isolated islands of evolution”, making DHABs ideal model sites to test evolutionary hypotheses. Fluorescence in situ hybridization assays using specifically designed probes revealed that the obtained genetic signatures indeed originated from indigenous polyextremophiles. Electron microscopy imaging revealed unknown ciliates densely covered with prokaryote ectosymbionts, which may enable adaptations of eukaryotes to DHAB conditions. The research reviewed here significantly advanced our knowledge on polyextremophile eukaryotes, which are excellent models for a number of biological research areas, including ecology, diversity, biotechnology, evolutionary research, physiology, and astrobiology.

  14. A statistical anomaly indicates symbiotic origins of eukaryotic membranes.

    Science.gov (United States)

    Bansal, Suneyna; Mittal, Aditya

    2015-04-01

    Compositional analyses of nucleic acids and proteins have shed light on possible origins of living cells. In this work, rigorous compositional analyses of ∼5000 plasma membrane lipid constituents of 273 species in the three life domains (archaea, eubacteria, and eukaryotes) revealed a remarkable statistical paradox, indicating symbiotic origins of eukaryotic cells involving eubacteria. For lipids common to plasma membranes of the three domains, the number of carbon atoms in eubacteria was found to be similar to that in eukaryotes. However, mutually exclusive subsets of same data show exactly the opposite-the number of carbon atoms in lipids of eukaryotes was higher than in eubacteria. This statistical paradox, called Simpson's paradox, was absent for lipids in archaea and for lipids not common to plasma membranes of the three domains. This indicates the presence of interaction(s) and/or association(s) in lipids forming plasma membranes of eubacteria and eukaryotes but not for those in archaea. Further inspection of membrane lipid structures affecting physicochemical properties of plasma membranes provides the first evidence (to our knowledge) on the symbiotic origins of eukaryotic cells based on the "third front" (i.e., lipids) in addition to the growing compositional data from nucleic acids and proteins.

  15. An Evolutionary Framework for Understanding the Origin of Eukaryotes.

    Science.gov (United States)

    Blackstone, Neil W

    2016-04-27

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real-the endosymbiosis that led to the mitochondrion is often described as "non-Darwinian" because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious-all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  16. Single Cell Genomics and Transcriptomics for Unicellular Eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Ciobanu, Doina; Clum, Alicia; Singh, Vasanth; Salamov, Asaf; Han, James; Copeland, Alex; Grigoriev, Igor; James, Timothy; Singer, Steven; Woyke, Tanja; Malmstrom, Rex; Cheng, Jan-Fang

    2014-03-14

    Despite their small size, unicellular eukaryotes have complex genomes with a high degree of plasticity that allow them to adapt quickly to environmental changes. Unicellular eukaryotes live with prokaryotes and higher eukaryotes, frequently in symbiotic or parasitic niches. To this day their contribution to the dynamics of the environmental communities remains to be understood. Unfortunately, the vast majority of eukaryotic microorganisms are either uncultured or unculturable, making genome sequencing impossible using traditional approaches. We have developed an approach to isolate unicellular eukaryotes of interest from environmental samples, and to sequence and analyze their genomes and transcriptomes. We have tested our methods with six species: an uncharacterized protist from cellulose-enriched compost identified as Platyophrya, a close relative of P. vorax; the fungus Metschnikowia bicuspidate, a parasite of water flea Daphnia; the mycoparasitic fungi Piptocephalis cylindrospora, a parasite of Cokeromyces and Mucor; Caulochytrium protosteloides, a parasite of Sordaria; Rozella allomycis, a parasite of the water mold Allomyces; and the microalgae Chlamydomonas reinhardtii. Here, we present the four components of our approach: pre-sequencing methods, sequence analysis for single cell genome assembly, sequence analysis of single cell transcriptomes, and genome annotation. This technology has the potential to uncover the complexity of single cell eukaryotes and their role in the environmental samples.

  17. An Evolutionary Framework for Understanding the Origin of Eukaryotes

    Science.gov (United States)

    Blackstone, Neil W.

    2016-01-01

    Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes. PMID:27128953

  18. Crystal structure of eukaryotic ribosome and its complexes with inhibitors.

    Science.gov (United States)

    Yusupova, Gulnara; Yusupov, Marat

    2017-03-19

    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.

  19. An Evolutionary Framework for Understanding the Origin of Eukaryotes

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    Neil W. Blackstone

    2016-04-01

    Full Text Available Two major obstacles hinder the application of evolutionary theory to the origin of eukaryotes. The first is more apparent than real—the endosymbiosis that led to the mitochondrion is often described as “non-Darwinian” because it deviates from the incremental evolution championed by the modern synthesis. Nevertheless, endosymbiosis can be accommodated by a multi-level generalization of evolutionary theory, which Darwin himself pioneered. The second obstacle is more serious—all of the major features of eukaryotes were likely present in the last eukaryotic common ancestor thus rendering comparative methods ineffective. In addition to a multi-level theory, the development of rigorous, sequence-based phylogenetic and comparative methods represents the greatest achievement of modern evolutionary theory. Nevertheless, the rapid evolution of major features in the eukaryotic stem group requires the consideration of an alternative framework. Such a framework, based on the contingent nature of these evolutionary events, is developed and illustrated with three examples: the putative intron proliferation leading to the nucleus and the cell cycle; conflict and cooperation in the origin of eukaryotic bioenergetics; and the inter-relationship between aerobic metabolism, sterol synthesis, membranes, and sex. The modern synthesis thus provides sufficient scope to develop an evolutionary framework to understand the origin of eukaryotes.

  20. Sterol Synthesis in Diverse Bacteria.

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    Wei, Jeremy H; Yin, Xinchi; Welander, Paula V

    2016-01-01

    Sterols are essential components of eukaryotic cells whose biosynthesis and function has been studied extensively. Sterols are also recognized as the diagenetic precursors of steranes preserved in sedimentary rocks where they can function as geological proxies for eukaryotic organisms and/or aerobic metabolisms and environments. However, production of these lipids is not restricted to the eukaryotic domain as a few bacterial species also synthesize sterols. Phylogenomic studies have identified genes encoding homologs of sterol biosynthesis proteins in the genomes of several additional species, indicating that sterol production may be more widespread in the bacterial domain than previously thought. Although the occurrence of sterol synthesis genes in a genome indicates the potential for sterol production, it provides neither conclusive evidence of sterol synthesis nor information about the composition and abundance of basic and modified sterols that are actually being produced. Here, we coupled bioinformatics with lipid analyses to investigate the scope of bacterial sterol production. We identified oxidosqualene cyclase (Osc), which catalyzes the initial cyclization of oxidosqualene to the basic sterol structure, in 34 bacterial genomes from five phyla (Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia) and in 176 metagenomes. Our data indicate that bacterial sterol synthesis likely occurs in diverse organisms and environments and also provides evidence that there are as yet uncultured groups of bacterial sterol producers. Phylogenetic analysis of bacterial and eukaryotic Osc sequences confirmed a complex evolutionary history of sterol synthesis in this domain. Finally, we characterized the lipids produced by Osc-containing bacteria and found that we could generally predict the ability to synthesize sterols. However, predicting the final modified sterol based on our current knowledge of sterol synthesis was difficult. Some bacteria

  1. The inadequacy of morphology for species and genus delineation in microbial eukaryotes: an example from the parabasalian termite symbiont coronympha.

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    James T Harper

    Full Text Available BACKGROUND: For the majority of microbial eukaryotes (protists, algae, there is no clearly superior species concept that is consistently applied. In the absence of a practical biological species concept, most species and genus level delineations have historically been based on morphology, which may lead to an underestimate of the diversity of microbial eukaryotes. Indeed, a growing body of molecular evidence, such as barcoding surveys, is beginning to support the conclusion that significant cryptic species diversity exists. This underestimate of diversity appears to be due to a combination of using morphology as the sole basis for assessing diversity and our inability to culture the vast majority of microbial life. Here we have used molecular markers to assess the species delineations in two related but morphologically distinct genera of uncultivated symbionts found in the hindgut of termites. METHODOLOGY/PRINCIPAL FINDINGS: Using single-cell isolation and environmental PCR, we have used a barcoding approach to characterize the diversity of Coronympha and Metacoronympha symbionts in four species of Incisitermes termites, which were also examined using scanning electron microscopy and light microcopy. Despite the fact that these genera are significantly different in morphological complexity and structural organisation, we find they are two life history stages of the same species. At the same time, we show that the symbionts from different termite hosts show an equal or greater level of sequence diversity than do the hosts, despite the fact that the symbionts are all classified as one species. CONCLUSIONS/SIGNIFICANCE: The morphological information used to describe the diversity of these microbial symbionts is misleading at both the genus and species levels, and led to an underestimate of species level diversity as well as an overestimate of genus level diversity. The genus 'Metacoronympha' is invalid and appears to be a life history stage of

  2. Fungal diversity from various marine habitats deduced through culture-independent studies

    Digital Repository Service at National Institute of Oceanography (India)

    Manohar, C.S.; Raghukumar, C.

    Studies on the molecular diversity of the micro-eukaryotic community have shown that fungi occupy a central position in a large number of marine habitats. Environmental surveys using molecular tools have shown the presence of fungi from a large...

  3. cAMP and cGMP signaling: sensory systems with prokaryotic roots adopted by eukaryotic cilia.

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    Johnson, Jacque-Lynne F; Leroux, Michel R

    2010-08-01

    An exciting discovery of the new millennium is that primary cilia, organelles found on most eukaryotic cells, play crucial roles in vertebrate development by modulating Hedgehog, Wnt and PDGF signaling. Analysis of the literature and sequence databases reveals that the ancient signal transduction pathway, which uses cGMP in eukaryotes or related cyclic di-GMP in bacteria, exists in virtually all eukaryotes. However, many eukaryotes that secondarily lost cilia during evolution, including flowering plants, slime molds and most fungi, lack otherwise evolutionarily conserved cGMP signaling components. Based on this intriguing phylogenetic distribution, the presence of cGMP signaling proteins within cilia, and the indispensable roles that cGMP plays in transducing environmental signals in divergent ciliated cells (e.g. vertebrate photoreceptors and Caenorhabditis elegans sensory neurons), we propose that cGMP signaling has a strong ciliary basis. cAMP signaling, also inherent to bacteria and crucial for cilium-dependent olfaction, similarly appears to have widespread usage in diverse cilia. Thus, we argue here that both cyclic nucleotides play essential and potentially ubiquitous roles in modulating ciliary functions.

  4. Eukaryote-to-eukaryote gene transfer gives rise to genome mosaicism in euglenids

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    Weber Andreas PM

    2011-04-01

    Full Text Available Abstract Background Euglenophytes are a group of photosynthetic flagellates possessing a plastid derived from a green algal endosymbiont, which was incorporated into an ancestral host cell via secondary endosymbiosis. However, the impact of endosymbiosis on the euglenophyte nuclear genome is not fully understood due to its complex nature as a 'hybrid' of a non-photosynthetic host cell and a secondary endosymbiont. Results We analyzed an EST dataset of the model euglenophyte Euglena gracilis using a gene mining program designed to detect laterally transferred genes. We found E. gracilis genes showing affinity not only with green algae, from which the secondary plastid in euglenophytes evolved, but also red algae and/or secondary algae containing red algal-derived plastids. Phylogenetic analyses of these 'red lineage' genes suggest that E. gracilis acquired at least 14 genes via eukaryote-to-eukaryote lateral gene transfer from algal sources other than the green algal endosymbiont that gave rise to its current plastid. We constructed an EST library of the aplastidic euglenid Peranema trichophorum, which is a eukaryovorous relative of euglenophytes, and also identified 'red lineage' genes in its genome. Conclusions Our data show genome mosaicism in E. gracilis and P. trichophorum. One possible explanation for the presence of these genes in these organisms is that some or all of them were independently acquired by lateral gene transfer and contributed to the successful integration and functioning of the green algal endosymbiont as a secondary plastid. Alternative hypotheses include the presence of a phagocytosed alga as the single source of those genes, or a cryptic tertiary endosymbiont harboring secondary plastid of red algal origin, which the eukaryovorous ancestor of euglenophytes had acquired prior to the secondary endosymbiosis of a green alga.

  5. Molecular phylogeny of centrohelid heliozoa, a novel lineage of bikont eukaryotes that arose by ciliary loss.

    Science.gov (United States)

    Cavalier-Smith, Thomas; Chao, Ema E-Y

    2003-04-01

    Recent molecular and cellular evidence indicates that eukaryotes comprise three major lineages: the probably ancestrally uniciliate protozoan phylum Amoebozoa; the ancestrally posteriorly uniciliate opisthokont clade (animals, Choanozoa, and fungi); and a very diverse ancestrally biciliate clade, the bikonts-plants, chromalveolates, and excavate and rhizarian Protozoa. As Heliozoa are the only eukaryote phylum not yet placed on molecular sequence trees, we have sequenced the 18S rRNA genes of three centrohelid heliozoa, Raphidiophrys ambigua, Heterophrys marina, and Chlamydaster sterni, to investigate their phylogenetic position. Phylogenetic analysis by distance and maximum likelihood methods allowing for intersite rate variation and invariable sites confirms that centrohelid heliozoa are a robust clade that does not fall within any other phyla. In particular, they are decisively very distant from the heterokont pedinellid chromists, at one time thought to be related to heliozoa, and lack the unique heterokont signature sequence. They also appear not to be specifically related to either Amoebozoa or Radiolaria, with which they have sometimes been classified, so it is desirable to retain Heliozoa as a separate protozoan phylum. Even though centrohelids have no cilia or centrioles, the centrohelid clade branches among the bikont eukaryotes, but there is no strong bootstrap support for any particular position. Distance trees usually place centrohelids as sisters to haptophytes, whereas parsimony puts them as sisters to red algae, but there is no reason to think that either position is correct; both have very low bootstrap support. Quartet puzzling places them with fairly low support as sisters to the apusozoan zooflagellate Ancyromonas. As Ancyromonas is the only other eukaryote that shares the character combination of flat plate-like mitochondrial cristae and kinetocyst-type extrusomes with centrohelids, this position is biologically plausible, but because of weak

  6. Predation and eukaryote cell origins: a coevolutionary perspective.

    Science.gov (United States)

    Cavalier-Smith, T

    2009-02-01

    Cells are of only two kinds: bacteria, with DNA segregated by surface membrane motors, dating back approximately 3.5Gy; and eukaryotes, which evolved from bacteria, possibly as recently as 800-850My ago. The last common ancestor of eukaryotes was a sexual phagotrophic protozoan with mitochondria, one or two centrioles and cilia. Conversion of bacteria (=prokaryotes) into a eukaryote involved approximately 60 major innovations. Numerous contradictory ideas about eukaryogenesis fail to explain fundamental features of eukaryotic cell biology or conflict with phylogeny. Data are best explained by the intracellular coevolutionary theory, with three basic tenets: (1) the eukaryotic cytoskeleton and endomembrane system originated through cooperatively enabling the evolution of phagotrophy; (2) phagocytosis internalised DNA-membrane attachments, unavoidably disrupting bacterial division; recovery entailed the evolution of the nucleus and mitotic cycle; (3) the symbiogenetic origin of mitochondria immediately followed the perfection of phagotrophy and intracellular digestion, contributing greater energy efficiency and group II introns as precursors of spliceosomal introns. Eukaryotes plus their archaebacterial sisters form the clade neomura, which evolved from a radically modified derivative of an actinobacterial posibacterium that had replaced the ancestral eubacterial murein peptidoglycan by N-linked glycoproteins, radically modified its DNA-handling enzymes, and evolved cotranslational protein secretion, but not the isoprenoid-ether lipids of archaebacteria. I focus on this phylogenetic background and on explaining how in response to novel phagotrophic selective pressures and ensuing genome internalisation this prekaryote evolved efficient digestion of prey proteins by retrotranslocation and 26S proteasomes, then internal digestion by phagocytosis, lysosomes, and peroxisomes, and eukaryotic vesicle trafficking and intracellular compartmentation.

  7. Genome-wide analysis of eukaryote thaumatin-like proteins (TLPs with an emphasis on poplar

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    Duplessis Sébastien

    2011-02-01

    Full Text Available Abstract Background Plant inducible immunity includes the accumulation of a set of defense proteins during infection called pathogenesis-related (PR proteins, which are grouped into families termed PR-1 to PR-17. The PR-5 family is composed of thaumatin-like proteins (TLPs, which are responsive to biotic and abiotic stress and are widely studied in plants. TLPs were also recently discovered in fungi and animals. In the poplar genome, TLPs are over-represented compared with annual species and their transcripts strongly accumulate during stress conditions. Results Our analysis of the poplar TLP family suggests that the expansion of this gene family was followed by diversification, as differences in expression patterns and predicted properties correlate with phylogeny. In particular, we identified a clade of poplar TLPs that cluster to a single 350 kb locus of chromosome I and that are up-regulated by poplar leaf rust infection. A wider phylogenetic analysis of eukaryote TLPs - including plant, animal and fungi sequences - shows that TLP gene content and diversity increased markedly during land plant evolution. Mapping the reported functions of characterized TLPs to the eukaryote phylogenetic tree showed that antifungal or glycan-lytic properties are widespread across eukaryote phylogeny, suggesting that these properties are shared by most TLPs and are likely associated with the presence of a conserved acidic cleft in their 3D structure. Also, we established an exhaustive catalog of TLPs with atypical architectures such as small-TLPs, TLP-kinases and small-TLP-kinases, which have potentially developed alternative functions (such as putative receptor kinases for pathogen sensing and signaling. Conclusion Our study, based on the most recent plant genome sequences, provides evidence for TLP gene family diversification during land plant evolution. We have shown that the diverse functions described for TLPs are not restricted to specific clades but seem

  8. Genetic diversity of bacteria associated with the hindgut of the terrestrial crustacean Porcellio scaber (Crustacea: Isopoda).

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    Kostanjsek, Rok; Strus, Jasna; Avgustin, Gorazd

    2002-06-01

    Molecular approaches were used to examine the genetic diversity of bacteria associated with the gut wall of the terrestrial isopod Porcellio scaber and to determine whether an autochthonous microflora exists in the P. scaber hindgut. 16S ribosomal genes were amplified from the total DNA isolated from thoroughly washed papillate regions of the hindgut, where the highest concentrations of bacteria are commonly found. The amplified genes were cloned, sequenced and phylogenetically analysed. The results implied an unexpectedly large diversity of microflora associated with the cuticle of the hindgut. Almost half of the retrieved sequences were found to be less than 80% homologous with any of the known sequences available at DNA data banks. Most of these sequences were clustered in one of three groups, and were clearly distant from the sequences of other bacterial taxa, indicating that they could represent novel bacterial species or even genera. More than two thirds of the sequences were found to be phylogenetically related to sequences from bacteria typically isolated from human and animal intestines, e.g. streptococci, enterococci, and members of the genus Bacteroides. The majority of the remaining sequences were most closely related to typical soil bacteria, e.g. bacilli and pseudomonads. The facts that a large proportion of the retrieved sequences was related to the sequences of bacteria, which are autochthonous to intestinal ecosystems, and that bacteria, specifically attached to the cuticular spines, were observed, indicate that truly autochthonous bacteria may well be present in the hindgut of P. scaber.

  9. Eukaryotic Community Distribution and Its Relationship to Water Physicochemical Parameters in an Extreme Acidic Environment, Río Tinto (Southwestern Spain)†

    Science.gov (United States)

    Aguilera, Angeles; Manrubia, Susanna C.; Gómez, Felipe; Rodríguez, Nuria; Amils, Ricardo

    2006-01-01

    The correlation between water physicochemical parameters and eukaryotic benthic composition was examined in Río Tinto. Principal component analysis showed a high inverse relationship between pH and most of the heavy metals analyzed as well as Dunaliella sp., while Chlamydomonas sp. abundance was positively related. Zn, Cu, and Ni clustered together and showed a strong inverse correlation with the diversity coefficient and most of the species analyzed. These eukaryotic communities seem to be more influenced by the presence of heavy metals than by the pH. PMID:16885283

  10. The Sec translocon mediated protein transport in prokaryotes and eukaryotes.

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    Denks, Kärt; Vogt, Andreas; Sachelaru, Ilie; Petriman, Narcis-Adrian; Kudva, Renuka; Koch, Hans-Georg

    2014-01-01

    Protein transport via the Sec translocon represents an evolutionary conserved mechanism for delivering cytosolically-synthesized proteins to extra-cytosolic compartments. The Sec translocon has a three-subunit core, termed Sec61 in Eukaryotes and SecYEG in Bacteria. It is located in the endoplasmic reticulum of Eukaryotes and in the cytoplasmic membrane of Bacteria where it constitutes a channel that can be activated by multiple partner proteins. These partner proteins determine the mechanism of polypeptide movement across the channel. During SRP-dependent co-translational targeting, the ribosome threads the nascent protein directly into the Sec channel. This pathway is in Bacteria mainly dedicated for membrane proteins but in Eukaryotes also employed by secretory proteins. The alternative pathway, leading to post-translational translocation across the Sec translocon engages an ATP-dependent pushing mechanism by the motor protein SecA in Bacteria and a ratcheting mechanism by the lumenal chaperone BiP in Eukaryotes. Protein transport and biogenesis is also assisted by additional proteins at the lateral gate of SecY/Sec61α and in the lumen of the endoplasmic reticulum or in the periplasm of bacterial cells. The modular assembly enables the Sec complex to transport a vast array of substrates. In this review we summarize recent biochemical and structural information on the prokaryotic and eukaryotic Sec translocons and we describe the remarkably complex interaction network of the Sec complexes.

  11. Evolution of DNA replication protein complexes in eukaryotes and Archaea.

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    Nicholas Chia

    Full Text Available BACKGROUND: The replication of DNA in Archaea and eukaryotes requires several ancillary complexes, including proliferating cell nuclear antigen (PCNA, replication factor C (RFC, and the minichromosome maintenance (MCM complex. Bacterial DNA replication utilizes comparable proteins, but these are distantly related phylogenetically to their archaeal and eukaryotic counterparts at best. METHODOLOGY/PRINCIPAL FINDINGS: While the structures of each of the complexes do not differ significantly between the archaeal and eukaryotic versions thereof, the evolutionary dynamic in the two cases does. The number of subunits in each complex is constant across all taxa. However, they vary subtly with regard to composition. In some taxa the subunits are all identical in sequence, while in others some are homologous rather than identical. In the case of eukaryotes, there is no phylogenetic variation in the makeup of each complex-all appear to derive from a common eukaryotic ancestor. This is not the case in Archaea, where the relationship between the subunits within each complex varies taxon-to-taxon. We have performed a detailed phylogenetic analysis of these relationships in order to better understand the gene duplications and divergences that gave rise to the homologous subunits in Archaea. CONCLUSION/SIGNIFICANCE: This domain level difference in evolution suggests that different forces have driven the evolution of DNA replication proteins in each of these two domains. In addition, the phylogenies of all three gene families support the distinctiveness of the proposed archaeal phylum Thaumarchaeota.

  12. Flagellar motility in eukaryotic human parasites.

    Science.gov (United States)

    Krüger, Timothy; Engstler, Markus

    2015-10-01

    A huge variety of protists rely on one or more motile flagella to either move themselves or move fluids and substances around them. Many of these flagellates have evolved a symbiotic or parasitic lifestyle. Several of the parasites have adapted to human hosts, and include agents of prevalent and serious diseases. These unicellular parasites have become specialised in colonising a wide range of biological niches within humans. They usually have diverse transmission cycles, and frequently manifest a variety of distinct morphological stages. The motility of the single or multiple flagella plays important but understudied roles in parasite transmission, host invasion, dispersal, survival, proliferation and pathology. In this review we provide an overview of the important human pathogens that possess a motile flagellum for at least part of their life cycle. We highlight recently published studies that aim to elucidate motility mechanisms, and their relevance for human disease. We then bring the physics of swimming at the microscale into context, emphasising the importance of interdisciplinary approaches for a full understanding of flagellate motility - especially in light of the parasites' microenvironments and population dynamics. Finally, we summarise some important technological aspects, describing challenges for the field and possibilities for motility analyses in the future.

  13. The rise and fall of the autochthonous self: from Italian Renaissance art and Shakespeare to Heidegger, Lacan, and intersubjectivism.

    Science.gov (United States)

    Chessick, Richard D

    2010-01-01

    This article addresses the unresolved question of the existence of a private core autochthonous self, as it has been described by Winnicott, Modell, and others. The postmodern version of the self has eliminated this concept entirely, relegating the self to a changing and unstable display, or regarding it as totally chaotic, or even an illusion. The question is raised whether by returning to the origins of this notion of a private self and then tracing its apparent dissolution it might be possible to discover some evidence that it still exists. The methodology used is that of obtaining knowledge directly through the arts and the claim is made that because empirical science has clamored to be the only source of knowledge, we have lost what could be obtained by direct intuitive seeing and experiencing the works of creative geniuses. To explore the rise of the autochthonous self this article provides an examination of the shift from Gothic art to Italian Renaissance art, a time which engendered the origin of "man" with his or her elusive private individual self that then became expressed in changing works of art. As this spread north, Shakespeare appeared and similarly invented and illustrated in his characters the private individual self, a concept not appreciated or recognized before the renaissance. But as science arose and Western civilization began to decline, a corresponding disillusionment with "man" took place. The self began to be viewed as solely a social construction with no core except perhaps a genetic endowment. This was accompanied by a reduction in the concept of the human as a valuable and precious living being and was replaced by regarding the human as an object of control and exploitation. After the Second World War a movement in contemporary United States psychoanalysis gradually replaced the ideas of Freud and his emphasis on the "I" in the psychoanalytic process, with forms of relational therapy, assuming that the self was ab initio

  14. Comparative analysis of eukaryotic marine microbial assemblages from 18S rRNA gene and gene transcript clone libraries by using different methods of extraction.

    Science.gov (United States)

    Koid, Amy; Nelson, William C; Mraz, Amy; Heidelberg, Karla B

    2012-06-01

    Eukaryotic marine microbes play pivotal roles in biogeochemical nutrient cycling and ecosystem function, but studies that focus on the protistan biogeography and genetic diversity lag-behind studies of other microbes. 18S rRNA PCR amplification and clone library sequencing are commonly used to assess diversity that is culture independent. However, molecular methods are not without potential biases and artifacts. In this study, we compare the community composition of clone libraries generated from the same water sample collected at the San Pedro Ocean Time Series (SPOTs) station in the northwest Pacific Ocean. Community composition was assessed using different cell lysis methods (chemical and mechanical) and the extraction of different nucleic acids (DNA and RNA reverse transcribed to cDNA) to build Sanger ABI clone libraries. We describe specific biases for ecologically important phylogenetic groups resulting from differences in nucleic acid extraction methods that will inform future designs of eukaryotic diversity studies, regardless of the target sequencing platform planned.

  15. Horizontal gene transfer in the evolution of photosynthetic eukaryotes

    Institute of Scientific and Technical Information of China (English)

    Jinling HUANG; Jipei YUE

    2013-01-01

    Horizontal gene transfer (HGT) may not only create genome mosaicism,but also introduce evolutionary novelties to recipient organisms.HGT in plastid genomes,though relatively rare,still exists.HGT-derived genes are particularly common in unicellular photosynthetic eukaryotes and they also occur in multicellular plants.In particular,ancient HGT events occurring during the early evolution of primary photosynthetic eukaryotes were probably frequent.There is clear evidence that anciently acquired genes played an important role in the establishment of primary plastids and in the transition of plants from aquatic to terrestrial environments.Although algal genes have often been used to infer historical plastids in plastid-lacking eukaryotes,reliable approaches are needed to distinguish endosymbionts-derived genes from those independently acquired from preferential feeding or other activities.

  16. Interaction of tRNA with Eukaryotic Ribosome

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    Dmitri Graifer

    2015-03-01

    Full Text Available This paper is a review of currently available data concerning interactions of tRNAs with the eukaryotic ribosome at various stages of translation. These data include the results obtained by means of cryo-electron microscopy and X-ray crystallography applied to various model ribosomal complexes, site-directed cross-linking with the use of tRNA derivatives bearing chemically or photochemically reactive groups in the CCA-terminal fragment and chemical probing of 28S rRNA in the region of the peptidyl transferase center. Similarities and differences in the interactions of tRNAs with prokaryotic and eukaryotic ribosomes are discussed with concomitant consideration of the extent of resemblance between molecular mechanisms of translation in eukaryotes and bacteria.

  17. Alternative splicing: a pivotal step between eukaryotic transcription and translation.

    Science.gov (United States)

    Kornblihtt, Alberto R; Schor, Ignacio E; Alló, Mariano; Dujardin, Gwendal; Petrillo, Ezequiel; Muñoz, Manuel J

    2013-03-01

    Alternative splicing was discovered simultaneously with splicing over three decades ago. Since then, an enormous body of evidence has demonstrated the prevalence of alternative splicing in multicellular eukaryotes, its key roles in determining tissue- and species-specific differentiation patterns, the multiple post- and co-transcriptional regulatory mechanisms that control it, and its causal role in hereditary disease and cancer. The emerging evidence places alternative splicing in a central position in the flow of eukaryotic genetic information, between transcription and translation, in that it can respond not only to various signalling pathways that target the splicing machinery but also to transcription factors and chromatin structure.

  18. Regulation of eukaryotic DNA replication and nuclear structure

    Institute of Scientific and Technical Information of China (English)

    WUJIARUI

    1999-01-01

    In eukaryote,nuclear structure is a key component for the functions of eukaryotic cells.More and more evidences show that the nuclear structure plays important role in regulating DNA replication.The nuclear structure provides a physical barrier for the replication licensing,participates in the decision where DNA replication initiates,and organizes replication proteins as replication factory for DNA replication.Through these works,new concepts on the regulation of DNA replication have emerged,which will be discussed in this minireview.

  19. AUTOCHTHONOUS BIOFACIES IN THE PLIOCENE LORETO BASIN, BAJA CALIFORNIA SUR, MEXICO

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    MICHELE PIAZZA

    1998-07-01

    Full Text Available The present paper examines the molluscan and/or echinoid assemblages recovered from two lithostratigraphic units (Piedras Rodadas Sandstone and Arroyo de Arce Norte Sandstone outcropping in the Pliocene Loreto Basin, Baja California Sur, Mexico. Ten biofacies have been identified, i.e. Trachycardium procerum-Trachycardium senticosum Biofacies, Chione compta-Transennella modesta Biofacies, Laevicardium elenense-Chione kelletii Biofacies, Xenophora sp. 1-Strombus subgracilior Biofacies, Crassostrea californica osunai Biofacies, Myrakeena angelica Biofacies, Vermetid-Nodipecten Biofacies, Argopecten abietis abietis Biofacies, Aequipecten dallasi Biofacies and Encope Biofacies. The first four biofacies have been defined on the basis of statistical analyses (cluster analysis, MDS. The other six, which are monospecific or definitely low-diversity, were already identified during field work. The deduced paleoecological bearing of biofacies, largely relying upon the comparison to their closest modern counterparts, provides the basis for the paleoenvironmental reconstruction. The latter also considers sedimentological evidence and is framed within the tectonic and sedimentary context recently proposed by American workers. Biofacies point toward environments differing in terms of substrate texture, presence/absence of vegetal cover, energy level, variously distributed within the low tide mark-40 m bathymetric range. 

  20. First description of autochthonous canine visceral leishmaniasis in the metropolitan region of Vitória, State of Espírito Santo, Brazil

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    Marco André Loureiro Tonini

    2012-12-01

    Full Text Available INTRODUCTION: We investigated autochthonous canine visceral leishmaniasis (CVL in the metropolitan region of Vitória (MRV, an area in which a human case was previously reported. METHODS: Serological, parasitological, and molecular tests were performed in 201 dogs. RESULTS: Twenty-six (13% and 12 (6% dogs were identified as positive using in-house enzyme-linked immunosorbent assay (ELISA and rK39 tests, respectively. Two dogs had a positive culture for Leishmania chagasi, and 4 were polymerase chain reaction (PCR-positive for Leishmania spp. One positive dog belonged to the aforementioned patient. CONCLUSIONS: Although the responsible vector was not found, our results provide evidence of autochthonous CVL in the MRV, a non-endemic area for VL.

  1. Characterisation of extra virgin olive oils from Galician autochthonous varieties and their co-crushings with Arbequina and Picual cv.

    Science.gov (United States)

    Reboredo-Rodríguez, P; González-Barreiro, C; Cancho-Grande, B; Fregapane, G; Salvador, M D; Simal-Gándara, J

    2015-06-01

    The current trend of the olive oil market is the production of high quality extra from traditional minor olive varieties with peculiar and differentiated characteristics (especially with respect to the aromatic and phenolic composition). In this way, the interest of Galician oil producers (NW Spain) in recovering old autochthonous Local olive fruits has increased substantially in recent years. In order to investigate the potential of the Local olives by either producing high quality monovarietal oils or mixing with the most widespread olives in Galicia (Arbequina and Picual cv.), quality indices, and fatty acid composition as well as volatile and phenolic profiles were determined and compared. All EVOOs studied in this work can be considered as "extra virgin olive oil" due to quality indices fell within the ranges established in legislation. Picual and Local olive oils as well as those resulting from their co-crushing reach values which are required by EU legislation to add the specific health claim on the oil label. Co-crushing Picual:Local (80:20) provided a significant enhancement of grass and apple nuances and a decrease of banana notes with respect to Picual oils. The co-crushing process improved sensory and health properties of Picual extra virgin olive oils. The effect of co-crushing on phenolics, ester volatiles and banana nuances cannot be easily modulated, contrary to quality indices and fatty acid composition, both changing linearly in strict correlation with the fruit mass ratio.

  2. Schistosomal myeloradiculopathy in a low-prevalence area: 27 cases (14 autochthonous in Campinas, São Paulo, Brazil

    Directory of Open Access Journals (Sweden)

    André Ricardo Ribas Freitas

    2010-07-01

    Full Text Available Schistosomal myeloradiculopathy (SMR is a form of schistosomiasis that is not linked with a high worm burden but rather is found in patients who have been sporadically exposed to Schistosoma mansoni. This paper aims to determine the occurrence of SMR in a low-endemic area with urban transmission in Campinas, São Paulo, Brazil. A retrospective study was performed, identifying confirmed cases in the two largest public hospitals on the region. Patients were diagnosed with SMR using standardised criteria, common clinical parameters, evidence of schistosomal infection and exclusion of other causes of myelopathy. A total of 27 patients were identified; 19 (85.2% were men and four (14.8% were women, ranging from 13-57 years of age (mean = 31.2; standard deviation = 12.8. Patients were classified as autochthonous (n = 14; 51.9% or allochthonous (n = 11; 40.7% and epidemiological data could not be obtained for two patients (7.4%. The clinical parameters of these patients were not different from previous studies. The sensitivity of serum immune reactions, cerebrospinal fluid immune reactions and parasitological stool examinations in identifying infected individuals was 87.5%, 93.8% and 40%, respectively. The epidemiological importance of these findings and their relationship with the control policies of schistosomiasis are discussed.

  3. Schistosomal myeloradiculopathy in a low-prevalence area: 27 cases (14 autochthonous) in Campinas, São Paulo, Brazil.

    Science.gov (United States)

    Freitas, André Ricardo Ribas; Oliveira, Augusto César Penalva; Silva, Luiz Jacintho

    2010-07-01

    Schistosomal myeloradiculopathy (SMR) is a form of schistosomiasis that is not linked with a high worm burden but rather is found in patients who have been sporadically exposed to Schistosoma mansoni. This paper aims to determine the occurrence of SMR in a low-endemic area with urban transmission in Campinas, São Paulo, Brazil. A retrospective study was performed, identifying confirmed cases in the two largest public hospitals on the region. Patients were diagnosed with SMR using standardised criteria, common clinical parameters, evidence of schistosomal infection and exclusion of other causes of myelopathy. A total of 27 patients were identified; 19 (85.2%) were men and four (14.8%) were women, ranging from 13-57 years of age (mean = 31.2; standard deviation = 12.8). Patients were classified as autochthonous (n = 14; 51.9%) or allochthonous (n = 11; 40.7%) and epidemiological data could not be obtained for two patients (7.4%). The clinical parameters of these patients were not different from previous studies. The sensitivity of serum immune reactions, cerebrospinal fluid immune reactions and parasitological stool examinations in identifying infected individuals was 87.5%, 93.8% and 40%, respectively. The epidemiological importance of these findings and their relationship with the control policies of schistosomiasis are discussed.

  4. The Genetic History of Peruvian Quechua‐Lamistas and Chankas: Uniparental DNA Patterns among Autochthonous Amazonian and Andean Populations

    Science.gov (United States)

    Sandoval, José R.; Lacerda, Daniela R.; Acosta, Oscar; Jota, Marilza S.; Robles‐Ruiz, Paulo; Salazar‐Granara, Alberto; Vieira, Pedro Paulo R.; Paz‐y‐Miño, César; Fujita, Ricardo

    2016-01-01

    Summary This study focuses on the genetic history of the Quechua‐Lamistas, inhabitants of the Lamas Province in the San Martin Department, Peru, who speak their own distinct variety of the Quechua family of languages. It has been suggested that different pre‐Columbian ethnic groups from the Peruvian Amazonia, like the Motilones or “shaven heads”, assimilated the Quechua language and then formed the current native population of Lamas. However, many Quechua‐Lamistas claim to be direct descendants of the Chankas, a famous pre‐Columbian indigenous group that escaped from Inca rule in the Andes. To investigate the Quechua‐Lamistas and Chankas’ ancestries, we compared uniparental genetic profiles (17 STRs of Q‐M3 Y‐chromosome and mtDNA complete control region haplotypes) among autochthonous Amazonian and Andean populations from Peru, Bolivia and Ecuador. The phylogeographic and population genetic analyses indicate a fairly heterogeneous ancestry for the Quechua‐Lamistas, while they are closely related to their neighbours who speak Amazonian languages, presenting no direct relationships with populations from the region where the ancient Chankas lived. On the other hand, the genetic profiles of self‐identified Chanka descendants living in Andahuaylas (located in the Apurimac Department, Peru, in the Central Andes) were closely related to those living in Huancavelica and the assumed Chanka Confederation area before the Inca expansion. PMID:26879156

  5. Antioxidant Properties and Flavonoid Profile in Leaves of Calabrian Lavandula multifida L., an Autochthon Plant of Mediterranean Southern Regions.

    Science.gov (United States)

    Panuccio, Maria Rosaria; Fazio, Angela; Papalia, Teresa; Barreca, Davide

    2016-04-01

    Lavandula multifida is a rare short-lived plant characteristic of Mediterranean basin able to survive in hot and arid climatic conditions on poorly evolved limestone soils. In this work, we characterize the enzymatic antioxidant system and phenolic composition, as well as the antioxidant properties of L. multifida fresh leaves. Enzymatic patterns show high level of peroxidases, ascorbate peroxidase, and dehydroascorbate reductase activities, when compared with L. angustifolia. The same trend is evident in total carotenoids, ascorbic acid, and reduced glutathione, and in the total antioxidant capacity assay. Moreover, RP-DAD-HPLC analyses of EtOH extract, obtained from fresh leaves, reveal main components, carvacrol, vitexin, and 7- or 8-glucoside derivatives of hypolaetin, scutellarein, luteolin, isoscutellarein, apigenin, and chrysoeriol. The analysis of this autochthon plant depicted a series of strategies adopted by L. multifida to survive in its stressful natural habitat and richness in health-promoting compounds that can be a resource for the preservation of this variety in dangerous of extinction.

  6. Potential antimicrobial and antiproliferative activities of autochthonous starter cultures and protease EPg222 in dry-fermented sausages.

    Science.gov (United States)

    Fernández, Margarita; Ruiz-Moyano, Santiago; Benito, María José; Martín, Alberto; Hernández, Alejandro; Córdoba, María de Guía

    2016-05-18

    This work studied the presence of nitrogen compounds with bioactive properties in Iberian pork sausages that were manufactured using different autochthonous starter cultures (Pediococcus acidilactici MS200 and Staphylococcus vitulus RS34) and protease EPg222. Nitrogen compounds were extracted and evaluated for their antimicrobial effect against spoilage and pathogenic bacteria, such as Bacillus cereus, Escherichia coli, Salmonella choleraesuis, Staphylococcus aureus and Listeria monocytogenes, and antiproliferative activity on the HT-29 colon adenocarcinoma cell line. Dry-fermented sausages elaborated with starter cultures P200S34 and protease EPg222 generate extracts that cause inhibition of the growth of pathogens reaching 25% inhibition of Bacillus cereus, making this a promising tool for biocontrol in the meat industry. On the other hand, the inoculation of well-adapted starter cultures with high proteolytic activity also increased the antiproliferative activity of these extracts, around 45% inhibition at 72 h, mainly due to an increase in free amino acids, such as Lys and Pro, but also small peptides.

  7. Eukaryotic tRNAs fingerprint invertebrates vis-à-vis vertebrates.

    Science.gov (United States)

    Mitra, Sanga; Das, Pijush; Samadder, Arpa; Das, Smarajit; Betai, Rupal; Chakrabarti, Jayprokas

    2015-01-01

    During translation, aminoacyl-tRNA synthetases recognize the identities of the tRNAs to charge them with their respective amino acids. The conserved identities of 58,244 eukaryotic tRNAs of 24 invertebrates and 45 vertebrates in genomic tRNA database were analyzed and their novel features extracted. The internal promoter sequences, namely, A-Box and B-Box, were investigated and evidence gathered that the intervention of optional nucleotides at 17a and 17b correlated with the optimal length of the A-Box. The presence of canonical transcription terminator sequences at the immediate vicinity of tRNA genes was ventured. Even though non-canonical introns had been reported in red alga, green alga, and nucleomorph so far, fairly motivating evidence of their existence emerged in tRNA genes of other eukaryotes. Non-canonical introns were seen to interfere with the internal promoters in two cases, questioning their transcription fidelity. In a first of its kind, phylogenetic constructs based on tRNA molecules delineated and built the trees of the vast and diverse invertebrates and vertebrates. Finally, two tRNA models representing the invertebrates and the vertebrates were drawn, by isolating the dominant consensus in the positional fluctuations of nucleotide compositions.

  8. Functional Subunits of Eukaryotic Chaperonin CCT/TRiC in Protein Folding

    Directory of Open Access Journals (Sweden)

    M. Anaul Kabir

    2011-01-01

    Full Text Available Molecular chaperones are a class of proteins responsible for proper folding of a large number of polypeptides in both prokaryotic and eukaryotic cells. Newly synthesized polypeptides are prone to nonspecific interactions, and many of them make toxic aggregates in absence of chaperones. The eukaryotic chaperonin CCT is a large, multisubunit, cylindrical structure having two identical rings stacked back to back. Each ring is composed of eight different but similar subunits and each subunit has three distinct domains. CCT assists folding of actin, tubulin, and numerous other cellular proteins in an ATP-dependent manner. The catalytic cooperativity of ATP binding/hydrolysis in CCT occurs in a sequential manner different from concerted cooperativity as shown for GroEL. Unlike GroEL, CCT does not have GroES-like cofactor, rather it has a built-in lid structure responsible for closing the central cavity. The CCT complex recognizes its substrates through diverse mechanisms involving hydrophobic or electrostatic interactions. Upstream factors like Hsp70 and Hsp90 also work in a concerted manner to transfer the substrate to CCT. Moreover, prefoldin, phosducin-like proteins, and Bag3 protein interact with CCT and modulate its function for the fine-tuning of protein folding process. Any misregulation of protein folding process leads to the formation of misfolded proteins or toxic aggregates which are linked to multiple pathological disorders.

  9. MutL homologs in restriction-modification systems and the origin of eukaryotic MORC ATPases

    Directory of Open Access Journals (Sweden)

    Aravind L

    2008-03-01

    Full Text Available Abstract The provenance and biochemical roles of eukaryotic MORC proteins have remained poorly understood since the discovery of their prototype MORC1, which is required for meiotic nuclear division in animals. The MORC family contains a combination of a gyrase, histidine kinase, and MutL (GHKL and S5 domains that together constitute a catalytically active ATPase module. We identify the prokaryotic MORCs and establish that the MORC family belongs to a larger radiation of several families of GHKL proteins (paraMORCs in prokaryotes. Using contextual information from conserved gene neighborhoods we show that these proteins primarily function in restriction-modification systems, in conjunction with diverse superfamily II DNA helicases and endonucleases. The common ancestor of these GHKL proteins, MutL and topoisomerase ATPase modules appears to have catalyzed structural reorganization of protein complexes and concomitant DNA-superstructure manipulations along with fused or standalone nuclease domains. Furthermore, contextual associations of the prokaryotic MORCs and their relatives suggest that their eukaryotic counterparts are likely to carry out chromatin remodeling by DNA superstructure manipulation in response to epigenetic signals such as histone and DNA methylation. Reviewers This article was reviewed by Arcady Mushegian and Gaspar Jekely.

  10. Eukaryotic Organisms in Extreme Acidic Environments, the Río Tinto Case

    Science.gov (United States)

    Angeles Aguilera, Angeles

    2013-07-01

    A major issue in microbial ecology is to identify the limits of life for growth and survival, and to understand the molecular mechanisms that define these limits. Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons. Some are basic and revolve around the idea that extreme environments are believed to reflect early Earth conditions. Others are related to the biotechnological potential of extremophiles. In this regard, the study of extremely acidic environments has become increasingly important since environmental acidity is often caused by microbial activity. Highly acidic environments are relatively scarce worldwide and are generally associated with volcanic activity or mining operations. For most acidic environments, low pH facilitates metal solubility, and therefore acidic waters tend to have high concentrations of heavy metals. However, highly acidic environments are usually inhabited by acidophilic and acidotolerant eukaryotic microorganisms such as algae, amoebas, ciliates, heliozoan and rotifers, not to mention filamentous fungi and yeasts. Here, we review the general trends concerning the diversity and ecophysiology of eukaryotic acidophilic microorganims, as well as summarize our latest results on this topic in one of the largest extreme acidic rivers, Río Tinto (SW, Spain).

  11. Eukaryotic Organisms in Extreme Acidic Environments, the Río Tinto Case

    Directory of Open Access Journals (Sweden)

    Angeles Aguilera

    2013-07-01

    Full Text Available A major issue in microbial ecology is to identify the limits of life for growth and survival, and to understand the molecular mechanisms that define these limits. Thus, interest in the biodiversity and ecology of extreme environments has grown in recent years for several reasons. Some are basic and revolve around the idea that extreme environments are believed to reflect early Earth conditions. Others are related to the biotechnological potential of extremophiles. In this regard, the study of extremely acidic environments has become increasingly important since environmental acidity is often caused by microbial activity. Highly acidic environments are relatively scarce worldwide and are generally associated with volcanic activity or mining operations. For most acidic environments, low pH facilitates metal solubility, and therefore acidic waters tend to have high concentrations of heavy metals. However, highly acidic environments are usually inhabited by acidophilic and acidotolerant eukaryotic microorganisms such as algae, amoebas, ciliates, heliozoan and rotifers, not to mention filamentous fungi and yeasts. Here, we review the general trends concerning the diversity and ecophysiology of eukaryotic acidophilic microorganims, as well as summarize our latest results on this topic in one of the largest extreme acidic rivers, Río Tinto (SW, Spain.

  12. Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements).

    Science.gov (United States)

    Giresi, Paul G; Lieb, Jason D

    2009-07-01

    The binding of sequence-specific regulatory factors and the recruitment of chromatin remodeling activities cause nucleosomes to be evicted from chromatin in eukaryotic cells. Traditionally, these active sites have been identified experimentally through their sensitivity to nucleases. Here we describe the details of a simple procedure for the genome-wide isolation of nucleosome-depleted DNA from human chromatin, termed FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements). We also provide protocols for different methods of detecting FAIRE-enriched DNA, including use of PCR, DNA microarrays, and next-generation sequencing. FAIRE works on all eukaryotic chromatin tested to date. To perform FAIRE, chromatin is crosslinked with formaldehyde, sheared by sonication, and phenol-chloroform extracted. Most genomic DNA is crosslinked to nucleosomes and is sequestered to the interphase, whereas DNA recovered in the aqueous phase corresponds to nucleosome-depleted regions of the genome. The isolated regions are largely coincident with the location of DNaseI hypersensitive sites, transcriptional start sites, enhancers, insulators, and active promoters. Given its speed and simplicity, FAIRE has utility in establishing chromatin profiles of diverse cell types in health and disease, isolating DNA regulatory elements en masse for further characterization, and as a screening assay for the effects of small molecules on chromatin organization.

  13. Autochthonous sporadic acute hepatitis E caused by two distinct subgenotype 3b hepatitis E virus strains with only 90% nucleotide identity.

    Science.gov (United States)

    Yamaguchi, Yasuko; Takagi, Hitoshi; Suzuki, Yuhei; Maruhashi, Kyoko; Kosone, Takashi; Kakizaki, Satoru; Sato, Ken; Yamada, Masanobu; Nagashima, Shigeo; Takahashi, Masaharu; Okamoto, Hiroaki

    2017-04-01

    Hepatitis E, which is caused by hepatitis E virus (HEV), is a public health concern in Japan, where the zoonotic food-borne transmission of HEV from domestic pigs and wild boars plays an important role. A 44-year-old Japanese man with autochthonous sporadic acute hepatitis E was admitted with general fatigue and moderate liver dysfunction. In the present study, two distinct HEV strains were recovered from the patient, who had consumed the raw or undercooked pig liver and intestine two or three times per week for 3 months before the disease onset. The recovered HEV strains were segregated into two clusters within subgenotype 3b, the open reading frame (ORF)1 and ORF2 sequences of which each showed ~10% difference, indicating HEV mixed infection. Because most notified patients with clinical HEV infection in Japan are diagnosed based on the detection of IgA-class HEV antibodies and because serum samples from only a limited number of HEV-infected patients are subjected to HEV RNA detection and nucleotide sequencing, it is very likely that patients with HEV mixed infection remain largely overlooked. The identification of sources of autochthonous HEV infection remains an important goal. Continued efforts to trace the sources of acute or chronic autochthonous HEV infection are warranted.

  14. Burkholderia type VI secretion systems have distinct roles in eukaryotic and bacterial cell interactions.

    Directory of Open Access Journals (Sweden)

    Sandra Schwarz

    Full Text Available Bacteria that live in the environment have evolved pathways specialized to defend against eukaryotic organisms or other bacteria. In this manuscript, we systematically examined the role of the five type VI secretion systems (T6SSs of Burkholderia thailandensis (B. thai in eukaryotic and bacterial cell interactions. Consistent with phylogenetic analyses comparing the distribution of the B. thai T6SSs with well-characterized bacterial and eukaryotic cell-targeting T6SSs, we found that T6SS-5 plays a critical role in the virulence of the organism in a murine melioidosis model, while a strain lacking the other four T6SSs remained as virulent as the wild-type. The function of T6SS-5 appeared to be specialized to the host and not related to an in vivo growth defect, as ΔT6SS-5 was fully virulent in mice lacking MyD88. Next we probed the role of the five systems in interbacterial interactions. From a group of 31 diverse bacteria, we identified several organisms that competed less effectively against wild-type B. thai than a strain lacking T6SS-1 function. Inactivation of T6SS-1 renders B. thai greatly more susceptible to cell contact-induced stasis by Pseudomonas putida, Pseudomonas fluorescens and Serratia proteamaculans-leaving it 100- to 1000-fold less fit than the wild-type in competition experiments with these organisms. Flow cell biofilm assays showed that T6S-dependent interbacterial interactions are likely relevant in the environment. B. thai cells lacking T6SS-1 were rapidly displaced in mixed biofilms with P. putida, whereas wild-type cells persisted and overran the competitor. Our data show that T6SSs within a single organism can have distinct functions in eukaryotic versus bacterial cell interactions. These systems are likely to be a decisive factor in the survival of bacterial cells of one species in intimate association with those of another, such as in polymicrobial communities present both in the environment and in many infections.

  15. Localization of checkpoint and repair proteins in eukaryotes

    DEFF Research Database (Denmark)

    Lisby, Michael; Rothstein, Rodney

    2005-01-01

    In eukaryotes, the cellular response to DNA damage depends on the type of DNA structure being recognized by the checkpoint and repair machinery. DNA ends and single-stranded DNA are hallmarks of double-strand breaks and replication stress. These two structures are recognized by distinct sets of p...

  16. Tracking Eukaryotic Production and Burial Through Time with Zinc Isotopes

    Science.gov (United States)

    Tang, T. Y. S.; Planavsky, N.; Owens, J. D.; Love, G. D.; Lyons, T.; Peterson, L. C.; Knoll, A. H.; Dupont, C. L.; Reinhard, C.; Zumberge, A.

    2015-12-01

    Zinc is an important, often co-limiting nutrient for eukaryotes in the oceans today. Given the importance of Zn in the modern oceans, we developed a Zn isotope approach to track the extent of Zn limitation and eukaryotic production through Earth's history. Specifically, we use the isotopic systematics of the pyrite (δ66Znpyr), rock extracts (bitumen) and kerogen pyrolysate (δ66Znorg) within euxinic black shales. We show that δ66Znpyr of euxinic core-top muds from the Cariaco basin capture the global deep seawater signature, validating its use as a seawater proxy. Additionally, we propose that Δ66Znpyr-org can be used to track surface water zinc bioavailability. Detailed studies of short-lived oceanic anoxic events such as Cretaceous OAE2, which punctuate an otherwise dominantly oxic Phanerozoic world, exhibit dramatic shifts in seawater δ66Zn and organic bound zinc. Such perturbations are consistent with the demise of eukaryotes under a nitrogen stressed regime, in which cyanobacteria carry the competitive advantage. Contradictory to previous models, however, our data suggest that zinc remained largely bioavailable throughout these anoxic intervals despite significant drawdown of the global reservoir. The framework developed from studies of the modern, Cenozoic, and Mesozoic can be used to track the Precambrian evolution of the marine Zn cycle and the rise of eukaryotic algae to ecological dominance.

  17. Potential of industrial biotechnology with cyanobacteria and eukaryotic microalgae

    NARCIS (Netherlands)

    Wijffels, R.H.; Kruse, O.; Hellingwerf, K.J.

    2013-01-01

    Both cyanobacteria and eukaryotic microalgae are promising organisms for sustainable production of bulk products such as food, feed, materials, chemicals and fuels. In this review we will summarize the potential and current biotechnological developments.Cyanobacteria are promising host organisms for

  18. Monitoring disulfide bond formation in the eukaryotic cytosol

    DEFF Research Database (Denmark)

    Østergaard, Henrik; Tachibana, Christine; Winther, Jakob R.

    2004-01-01

    Glutathione is the most abundant low molecular weight thiol in the eukaryotic cytosol. The compartment-specific ratio and absolute concentrations of reduced and oxidized glutathione (GSH and GSSG, respectively) are, however, not easily determined. Here, we present a glutathione-specific green flu...

  19. Abundance of eukaryotic microbes in the deep subtropical North Atlantic

    NARCIS (Netherlands)

    Morgan-Smith, D.; Herndl, G.J.; van Aken, H.M.; Bochdansky, A.B.

    2011-01-01

    The meso- and bathypelagic ocean comprises the largest habitat on earth, yet we know very little about the distribution and activity of protists in this environment. These small eukaryotes are responsible for controlling bacterial abundance in the surface ocean and are major players in the material

  20. A new inhibitor of apoptosis from vaccinia virus and eukaryotes.

    NARCIS (Netherlands)

    Gubser, C.; Bergamaschi, D.; Hollinshead, M.; Lu, X.; Kuppeveld, F.J.M. van; Smith, G.L.

    2007-01-01

    A new apoptosis inhibitor is described from vaccinia virus, camelpox virus, and eukaryotic cells. The inhibitor is a hydrophobic, multiple transmembrane protein that is resident in the Golgi and is named GAAP (Golgi anti-apoptotic protein). Stable expression of both viral GAAP (v-GAAP) and human GAA

  1. Automatic generation of gene finders for eukaryotic species

    DEFF Research Database (Denmark)

    Terkelsen, Kasper Munch; Krogh, A.

    2006-01-01

    Background The number of sequenced eukaryotic genomes is rapidly increasing. This means that over time it will be hard to keep supplying customised gene finders for each genome. This calls for procedures to automatically generate species-specific gene finders and to re-train them as the quantity...

  2. Geminin: a major DNA replication safeguard in higher eukaryotes

    DEFF Research Database (Denmark)

    Melixetian, Marina; Helin, Kristian

    2004-01-01

    Eukaryotes have evolved multiple mechanisms to restrict DNA replication to once per cell cycle. These mechanisms prevent relicensing of origins of replication after initiation of DNA replication in S phase until the end of mitosis. Most of our knowledge of mechanisms controlling prereplication...

  3. Tus-Ter as a tool to study site-specific DNA replication perturbation in eukaryotes

    DEFF Research Database (Denmark)

    Larsen, Nicolai B; Hickson, Ian D; Mankouri, Hocine W

    2014-01-01

    The high-affinity binding of the Tus protein to specific 21-bp sequences, called Ter, causes site-specific, and polar, DNA replication fork arrest in E coli. The Tus-Ter complex serves to coordinate DNA replication with chromosome segregation in this organism. A number of recent and ongoing studies...... have demonstrated that Tus-Ter can be used as a heterologous tool to generate site-specific perturbation of DNA replication when reconstituted in eukaryotes. Here, we review these recent findings and explore the molecular mechanism by which Tus-Ter mediates replication fork (RF) arrest in the budding...... yeast, S. cerevisiae. We propose that Tus-Ter is a versatile, genetically tractable, and regulatable RF blocking system that can be utilized for disrupting DNA replication in a diverse range of host cells....

  4. Highly hydrophilic proteins in prokaryotes and eukaryotes are common during conditions of water deficit.

    Science.gov (United States)

    Garay-Arroyo, A; Colmenero-Flores, J M; Garciarrubio, A; Covarrubias, A A

    2000-02-25

    The late embryogenesis abundant (LEA) proteins are plant proteins that are synthesized at the onset of desiccation in maturing seeds and in vegetative organs exposed to water deficit. Here, we show that most LEA proteins are comprised in a more widespread group, which we call "hydrophilins." The defining characteristics of hydrophilins are high glycine content (>6%) and a high hydrophilicity index (>1.0). By data base searching, we show that this criterion selectively differentiates most known LEA proteins as well as additional proteins from different taxons. We found that within the genomes of Escherichia coli and Saccharomyces cerevisiae, only 5 and 12 proteins, respectively, meet our criterion. Despite their deceivingly loose definition, hydrophilins usually represent stress. Evidence for the participation of one of the E. coli hydrophilins in the adaptive response to hyperosmotic conditions is presented. Apparently, hydrophilins represent analogous adaptations to a common problem in such diverse taxons as prokaryotes and eukaryotes.

  5. The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

    Science.gov (United States)

    Dreos, René; Ambrosini, Giovanna; Groux, Romain; Cavin Périer, Rouaïda; Bucher, Philipp

    2017-01-01

    We present an update of the Eukaryotic Promoter Database EPD (http://epd.vital-it.ch), more specifically on the EPDnew division, which contains comprehensive organisms-specific transcription start site (TSS) collections automatically derived from next generation sequencing (NGS) data. Thanks to the abundant release of new high-throughput transcript mapping data (CAGE, TSS-seq, GRO-cap) the database could be extended to plant and fungal species. We further report on the expansion of the mass genome annotation (MGA) repository containing promoter-relevant chromatin profiling data and on improvements for the EPD entry viewers. Finally, we present a new data access tool, ChIP-Extract, which enables computational biologists to extract diverse types of promoter-associated data in numerical table formats that are readily imported into statistical analysis platforms such as R. PMID:27899657

  6. Molecular Data are Transforming Hypotheses on the Origin and Diversification of Eukaryotes.

    Science.gov (United States)

    Tekle, Yonas I; Parfrey, Laura Wegener; Katz, Laura A

    2009-06-01

    The explosion of molecular data has transformed hypotheses on both the origin of eukaryotes and the structure of the eukaryotic tree of life. Early ideas about the evolution of eukaryotes arose through analyses of morphology by light microscopy and later electron microscopy. Though such studies have proven powerful at resolving more recent events, theories on origins and diversification of eukaryotic life have been substantially revised in light of analyses of molecular data including gene and, increasingly, whole genome sequences. By combining these approaches, progress has been made in elucidating both the origin and diversification of eukaryotes. Yet many aspects of the evolution of eukaryotic life remain to be illuminated.

  7. Soil eukaryotic microorganism succession as affected by continuous cropping of peanut--pathogenic and beneficial fungi were selected.

    Directory of Open Access Journals (Sweden)

    Mingna Chen

    Full Text Available Peanut is an important oil crop worldwide and shows considerable adaptability but growth and yield are negatively affected by continuous cropping. Soil micro-organisms are efficient bio-indicators of soil quality and plant health and are critical to the sustainability of soil-based ecosystem function and to successful plant growth. In this study, 18S rRNA gene clone library analyses were employed to study the succession progress of soil eukaryotic micro-organisms under continuous peanut cultivation. Eight libraries were constructed for peanut over three continuous cropping cycles and its representative growth stages. Cluster analyses indicated that soil micro-eukaryotic assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. Six eukaryotic groups were found and fungi predominated in all libraries. The fungal populations showed significant dynamic change and overall diversity increased over time under continuous peanut cropping. The abundance and/or diversity of clones affiliated with Eurotiales, Hypocreales, Glomerales, Orbiliales, Mucorales and Tremellales showed an increasing trend with continuous cropping but clones affiliated with Agaricales, Cantharellales, Pezizales and Pyxidiophorales decreased in abundance and/or diversity over time. The current data, along with data from previous studies, demonstrated that the soil microbial community was affected by continuous cropping, in particular, the pathogenic and beneficial fungi that were positively selected over time, which is commonplace in agro-ecosystems. The trend towards an increase in fungal pathogens and simplification of the beneficial fungal community could be important factors contributing to the decline in peanut growth and yield over many years of continuous cropping.

  8. Soil eukaryotic microorganism succession as affected by continuous cropping of peanut--pathogenic and beneficial fungi were selected.

    Science.gov (United States)

    Chen, Mingna; Li, Xiao; Yang, Qingli; Chi, Xiaoyuan; Pan, Lijuan; Chen, Na; Yang, Zhen; Wang, Tong; Wang, Mian; Yu, Shanlin

    2012-01-01

    Peanut is an important oil crop worldwide and shows considerable adaptability but growth and yield are negatively affected by continuous cropping. Soil micro-organisms are efficient bio-indicators of soil quality and plant health and are critical to the sustainability of soil-based ecosystem function and to successful plant growth. In this study, 18S rRNA gene clone library analyses were employed to study the succession progress of soil eukaryotic micro-organisms under continuous peanut cultivation. Eight libraries were constructed for peanut over three continuous cropping cycles and its representative growth stages. Cluster analyses indicated that soil micro-eukaryotic assemblages obtained from the same peanut cropping cycle were similar, regardless of growth period. Six eukaryotic groups were found and fungi predominated in all libraries. The fungal populations showed significant dynamic change and overall diversity increased over time under continuous peanut cropping. The abundance and/or diversity of clones affiliated with Eurotiales, Hypocreales, Glomerales, Orbiliales, Mucorales and Tremellales showed an increasing trend with continuous cropping but clones affiliated with Agaricales, Cantharellales, Pezizales and Pyxidiophorales decreased in abundance and/or diversity over time. The current data, along with data from previous studies, demonstrated that the soil microbial community was affected by continuous cropping, in particular, the pathogenic and beneficial fungi that were positively selected over time, which is commonplace in agro-ecosystems. The trend towards an increase in fungal pathogens and simplification of the beneficial fungal community could be important factors contributing to the decline in peanut growth and yield over many years of continuous cropping.

  9. Eukaryotes dominate new production in the Sargasso Sea

    Science.gov (United States)

    Fawcett, S. E.; Lomas, M. W.; Ward, B. B.; Casey, J. R.; Sigman, D. M.

    2010-12-01

    The vast subtropical ocean gyres are considered unproductive “deserts” due to the extremely low concentrations of essential nutrients in their sunlit surface waters. Because of intense upper ocean stratification, phytoplankton growth in the subtropical gyres is limited by the slow supply of nitrate from below, and is assumed to be supported predominantly by “regenerated” nitrogen (N): ammonium and other reduced N sources recycled in surface waters. The phytoplankton assemblage of the subtropical Sargasso Sea is dominated by the prokaryotic cyanobacteria, Prochlorococcus and Synechococcus, which occur in very high cell numbers compared to the rarer, and usually larger, eukaryotic algae. Coupling flow cytometry and a new high-sensitivity method for N isotope analysis, we measure the 15N/14N of major phytoplankton taxa and other biologically distinct particle populations collected from the surface waters of the Sargasso Sea during the stratified summer period. We find that the cyanobacteria and eukaryotic phytoplankton show distinct N isotope signatures, indicating that they utilize different sources of N for growth. Prochlorococcus and Synechococcus have a uniformly low 15N/14N, consistent with the expectation that these phytoplankton rely on regenerated N. However, the 15N/14N of eukaryotic phytoplankton is higher and more variable, with a mean 15N/14N comparable to the new nitrate supply from below, indicating that eukaryotes dominate the consumption of this nitrate and rely on it for more than half of their N requirement. Using our measured 15N/14N values for the various sorted autotrophic populations, we calculate eukaryote-specific summer f-ratios of 0.6-0.67 and total community summer f-ratios of 0.15-0.23. These values are higher than those based on comparison of primary production and sediment-trap derived organic carbon (C) export, and agree well with annual f-ratio estimates implied by geochemical tracers. The high 15N/14N of eukaryotic biomass can

  10. The phagotrophic origin of eukaryotes and phylogenetic classification of Protozoa.

    Science.gov (United States)

    Cavalier-Smith, T

    2002-03-01

    Eukaryotes and archaebacteria form the clade neomura and are sisters, as shown decisively by genes fragmented only in archaebacteria and by many sequence trees. This sisterhood refutes all theories that eukaryotes originated by merging an archaebacterium and an alpha-proteobacterium, which also fail to account for numerous features shared specifically by eukaryotes and actinobacteria. I revise the phagotrophy theory of eukaryote origins by arguing that the essentially autogenous origins of most eukaryotic cell properties (phagotrophy, endomembrane system including peroxisomes, cytoskeleton, nucleus, mitosis and sex) partially overlapped and were synergistic with the symbiogenetic origin of mitochondria from an alpha-proteobacterium. These radical innovations occurred in a derivative of the neomuran common ancestor, which itself had evolved immediately prior to the divergence of eukaryotes and archaebacteria by drastic alterations to its eubacterial ancestor, an actinobacterial posibacterium able to make sterols, by replacing murein peptidoglycan by N-linked glycoproteins and a multitude of other shared neomuran novelties. The conversion of the rigid neomuran wall into a flexible surface coat and the associated origin of phagotrophy were instrumental in the evolution of the endomembrane system, cytoskeleton, nuclear organization and division and sexual life-cycles. Cilia evolved not by symbiogenesis but by autogenous specialization of the cytoskeleton. I argue that the ancestral eukaryote was uniciliate with a single centriole (unikont) and a simple centrosomal cone of microtubules, as in the aerobic amoebozoan zooflagellate Phalansterium. I infer the root of the eukaryote tree at the divergence between opisthokonts (animals, Choanozoa, fungi) with a single posterior cilium and all other eukaryotes, designated 'anterokonts' because of the ancestral presence of an anterior cilium. Anterokonts comprise the Amoebozoa, which may be ancestrally unikont, and a vast

  11. Auxin transport inhibitors impair vesicle motility and actin cytoskeleton dynamics in diverse eukaryotes

    NARCIS (Netherlands)

    P. Dhonukshe (Pankaj); I. Grigoriev (Ilya); R. Fischer (Rainer); M. Tominaga (Motoki); D.G. Robinson (David); J. Hašek (Jiří); T. Paciorek (Tomasz); J. Petrášek (Jan); D. Seifertová (Daniela); R. Tejos (Ricardo); L.A. Meisel (Lee); E. Zažímalová (Eva); T.W.J. Gadella (Theodorus); Y.D. Stierhof; T. Ueda (Takashi); K. Oiwa (Kazuhiro); A.S. Akhmanova (Anna); R. Brock (Roland); A. Spang (Anne); J. Friml (Jiří)

    2008-01-01

    textabstractMany aspects of plant development, including patterning and tropisms, are largely dependent on the asymmetric distribution of the plant signaling molecule auxin. Auxin transport inhibitors (ATIs), which interfere with directional auxin transport, have been essential tools in formulating

  12. FIST: a sensory domain for diverse signal transduction pathways in prokaryotes and ubiquitin signaling in eukaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Borziak, Kirill [ORNL; Jouline, Igor B [ORNL

    2007-01-01

    Motivation: Sensory domains that are conserved among Bacteria, Archaea and Eucarya are important detectors of common signals detected by living cells. Due to their high sequence divergence, sensory domains are difficult to identify. We systematically look for novel sensory domains using sensitive profile-based searches initi-ated with regions of signal transduction proteins where no known domains can be identified by current domain models. Results: Using profile searches followed by multiple sequence alignment, structure prediction, and domain architecture analysis, we have identified a novel sensory domain termed FIST, which is present in signal transduction proteins from Bacteria, Archaea and Eucarya. Remote similarity to a known ligand-binding fold and chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids.

  13. Eukaryotic beta-alanine synthases are functionally related but have a high degree of structural diversity

    DEFF Research Database (Denmark)

    Gojkovic, Zoran; Sandrini, Michael; Piskur, Jure

    2001-01-01

    beta -Alanine synthase (EC 3.5.1.6), which catalyzes the final step of pyrimidine catabolism, has only been characterized in mammals. A Saccharomyces kluyveri pyd3 mutant that is unable to grow on N-carbamy-beta -alanine as the sole nitrogen source and exhibits diminished beta -alanine synthase...... no pyrimidine catabolic pathway, it enabled growth on N-carbamyl- beta -alanine as the sole nitrogen source. The D. discoideum and D. melanogaster PYD3 gene products are similar to mammalian beta -alanine synthases. In contrast, the S. kluyveri protein is quite different from these and more similar to bacterial...... N- carbamyl amidohydrolases. All three beta -alanine synthases are to some degree related to various aspartate transcarbamylases, which catalyze the second step of the de novo pyrimidine biosynthetic pathway. PYD3 expression in yeast seems to be inducible by dihydrouracil and N-carbamyl-beta...

  14. Micro-Eukaryote Diversity in Freshwater Ponds That Harbor the Amphibian Pathogen "Batrachochytrium Dendrobatidis" ("Bd")

    Science.gov (United States)

    Lauer, Antje; McConnel, Lonnie; Singh, Navdeep

    2012-01-01

    We designed a microbiology project that fully engaged undergraduate biology students, high school students, and their teachers in a summer research program as part of the Research Education Vitalizing Science University Program conducted at California State University Bakersfield. Modern molecular biological methods and microscopy were used to…

  15. MicroRNA-16 suppresses metastasis in an orthotopic, but not autochthonous, mouse model of soft tissue sarcoma

    Directory of Open Access Journals (Sweden)

    Mohit Sachdeva

    2015-08-01

    Full Text Available MicroRNAs (miRNAs can regulate tumor cell invasion and metastasis in a tumor-specific manner. We recently demonstrated that global downregulation of miRNAs after deleting dicer can promote development of distant metastases in a mouse model of primary soft tissue sarcoma (STS. In this study, we identified miRNAs that are differentially downregulated in metastatic STS in both human and mouse, and investigated the role of these miRNAs in metastasis. miRNA- TaqMan PCR arrays showed a global downregulation of miRNAs in metastatic human sarcomas. Similar analysis in mouse metastatic sarcomas revealed overlap for several downregulated miRNAs including miR-16, miR-103, miR-146a, miR-223, miR-342 and miR-511. Restoration of these downregulated miRNAs in mouse primary sarcoma cell lines showed that miR-16, but not other downregulated miRNAs, was able to significantly suppress both migration and invasion in vitro, without altering cell proliferation. In addition, orthotopic transplantation of a sarcoma cell line stably expressing miR-16 into the muscle of immunocompromised mice revealed that restoration of miR-16 can significantly decrease lung metastasis in vivo. However, no change in the rate of lung metastasis was observed when miR-16 was deleted in mouse primary sarcomas at sarcoma initiation. Taken together, these results indicate that miR-16 can have metastasis-suppressing properties both in vitro and in vivo. However, the loss-of-function experiments in autochthonous tumors indicate that loss of miR-16 is not sufficient to promote metastasis in vivo.

  16. The Indian origin of paternal haplogroup R1a1* substantiates the autochthonous origin of Brahmins and the caste system.

    Science.gov (United States)

    Sharma, Swarkar; Rai, Ekta; Sharma, Prithviraj; Jena, Mamata; Singh, Shweta; Darvishi, Katayoon; Bhat, Audesh K; Bhanwer, A J S; Tiwari, Pramod Kumar; Bamezai, Rameshwar N K

    2009-01-01

    Many major rival models of the origin of the Hindu caste system co-exist despite extensive studies, each with associated genetic evidences. One of the major factors that has still kept the origin of the Indian caste system obscure is the unresolved question of the origin of Y-haplogroup R1a1*, at times associated with a male-mediated major genetic influx from Central Asia or Eurasia, which has contributed to the higher castes in India. Y-haplogroup R1a1* has a widespread distribution and high frequency across Eurasia, Central Asia and the Indian subcontinent, with scanty reports of its ancestral (R*, R1* and R1a*) and derived lineages (R1a1a, R1a1b and R1a1c). To resolve these issues, we screened 621 Y-chromosomes (of Brahmins occupying the upper-most caste position and schedule castes/tribals occupying the lower-most positions) with 55 Y-chromosomal binary markers and seven Y-microsatellite markers and compiled an extensive dataset of 2809 Y-chromosomes (681 Brahmins, and 2128 tribals and schedule castes) for conclusions. A peculiar observation of the highest frequency (up to 72.22%) of Y-haplogroup R1a1* in Brahmins hinted at its presence as a founder lineage for this caste group. Further, observation of R1a1* in different tribal population groups, existence of Y-haplogroup R1a* in ancestors and extended phylogenetic analyses of the pooled dataset of 530 Indians, 224 Pakistanis and 276 Central Asians and Eurasians bearing the R1a1* haplogroup supported the autochthonous origin of R1a1 lineage in India and a tribal link to Indian Brahmins. However, it is important to discover novel Y-chromosomal binary marker(s) for a higher resolution of R1a1* and confirm the present conclusions.

  17. First Proliferative Kidney Disease outbreak in Austria, linking to the aetiology of Black Trout Syndrome threatening autochthonous trout populations.

    Science.gov (United States)

    Gorgoglione, Bartolomeo; Kotob, Mohamed H; Unfer, Günter; El-Matbouli, Mansour

    2016-05-01

    Proliferative Kidney Disease (PKD) was diagnosed in juvenile autochthonous brown trout Salmo trutta for the first time in Austria during summer 2014. Cytology showed Tetracapsuloides bryosalmonae sporoblasts, and histology revealed sporogonic (coelozoic) and extrasporogonic (histozoic) stages. Analysis of malacosporean ribosomal small subunit revealed that this strain is closely related to European isolates, although its source is unknown. Infection and high pathogenicity were reproduced upon a pre-restocking test with specific pathogen free (SPF) juvenile trout, resulting in 100% mortality between 28 and 46 d post exposure (dpe), with high ectoparasitosis. Fish showed grade 2 of the Kidney Swelling Index and grade 3 of the PKD histological assessment. T. bryosalmonae enzootic waters were demonstrated in further locations along the River Kamp, with infected bryozoans retrieved up to 6 km upstream of the farm with the PKD outbreak. Fredericella sultana colonies collected from these locations were cultivated in laboratory conditions. Released malacospores successfully induced PKD, and contextually Black Trout Syndrome (BTS), in SPF brown trout. In the absence of co-infections mortality occurred between 59 and 98 dpe, with kidneys enlarged up to 6.74% of total body weight (normal 1.23%). This study confirms the first isolation of a pathogenic myxozoan from an Austrian river tributary of the Danube, where its 2-host life cycle is fully occurring. Its immunosuppressant action could link PKD as a key factor in the multifactorial aetiology of BTS. This T. bryosalmonae isolation provides an impetus to undertake further multi-disciplinary research, aiming to assess the impact of PKD and BTS spreading to central European regions.

  18. AMPELOGRAPHIC CHARACTERIZATION OF THE AUTOCHTHONOUS GRAPE CULTIVAR “KALLMET” IN MAL��SIA E MADHE, ALBANIA

    Directory of Open Access Journals (Sweden)

    Bardhosh Ferraj

    2012-06-01

    Full Text Available “Kallmet” is one of the most sprout autochthonous wine grape cultivar in the North-western and Central part of Albania. Study was conducted in three consecutive years, 2009-2011, in Malësia e Madhe, 250 m above the sea level, in the North-western part of Albania, in a 10 years old vineyard. For evaluation of the main characteristics the IPGRI Descriptors of Grapevine was used. Form of the new shoot tip of “Kallmet” is half-open, with no anthocianic coloration, and densely prostrate hairs. The upper surface colour of new leaf is green with bronze spots. Flower type is functional female, and the first florescence appears at the 4-5th nodes. Mature leaf size is medium, leaf shape is pentangular, shape of the lateral teeth is convex in both sides, shape of the base sinus is half-open, shape of the upper lateral sinus is closed, and the depth of the upper lateral sinus is 63 mm. Bunch weight is small and bunch density is medium. “Kallmet” has medium-sized spherical deep red to violet berry with soft colourless pulp. Berries are not uniform and there occur a high rate of millerandage because of the lack of pollination during flowering time. Grape yield is 155 kv ha-1, grape must content is 67 ml/100 g fresh grape, sugar content is 21%, total acidity 5.7 g/l. The time of bud break is medium, while the number of inflorescences for fruit-bearing offshoot is 1.7. The annual vegetative growth is 180 cm. “Kallmet” leaves are susceptible to Plasmopara viticola, while the berries appear a relatively high resistance to Plasmopara viticola, and high resistance to Uncinula necator and Botrytis cynerea.

  19. Identity, Diversity and Diversity Management

    DEFF Research Database (Denmark)

    Holck, Lotte; Muhr, Sara Louise; Villeseche, Florence

    2016-01-01

    The purpose of this paper is to examine the relationship between the identity and diversity literatures and discuss how a better understanding of the theoretical connections between the two informs both diversity research and diversity management practices. Design/methodology/approach – Literature...... review followed by a discussion of the theoretical and practical consequences of connecting the identity and diversity literatures. Findings – The authors inform future research in three ways. First, by showing how definitions of identity influence diversity theorizing in specific ways. Second......, the authors explore how such definitions entail distinct foci regarding how diversity should be analyzed and interventions actioned. Third, the authors discuss how theoretical coherence between definitions of identity and diversity perspectives – as well as knowledge about a perspective’s advantages...

  20. Microfossils' diversity from the Proterozoic Taoudeni Basin, Mauritania

    Science.gov (United States)

    Beghin, Jérémie; Houzay, Jean-Pierre; Blanpied, Christian; Javaux, Emmanuelle

    2014-05-01

    Prokaryotes and microscopic eukaryotes are known to have appeared well before the Cambrian's adaptative radiation which flourished perceptibly as a generalized macroscopic world. What do we know about the trigger events which stimulated eukaryotic diversification during the Proterozoic? Biological innovations or environmental changes, and indeed probably both (Knoll et al., 2006), played a fundamental role controlling this important step of life's evolution on Earth. Javaux (2011), proposed a diversification pattern of early eukaryotes divided into three steps and focusing on different taxonomic levels, from stem group to within crown group, of the domain Eukarya. Here, we present a new, exquisitely preserved and morphologically diverse assemblage of organic-walled microfossils from the 1.1 Ga El Mreiti Group of the Taoudeni Basin (Mauritania). The assemblage includes beautifully preserved microbial mats comprising pyritized filaments, prokaryotic filamentous sheaths and filaments, microfossils of uncertain biological affinity including smooth isolated and colonial sphaeromorphs (eukaryotes and/or prokaryotes), diverse protists (ornamented and process-bearing acritarchs), as well multicellular microfossils interpreted in the literature as possible xanthophyte algae. Several taxa are reported for the first time in Africa, but are known worldwide. This study improves microfossil diversity previously reported by Amard (1986) and shows purported xanthophyte algae contrary to a previous biomarker study suggesting the absence of eukaryotic algae, other than acritarchs, in the basin (Blumenberg et al., 2012). This new microfossil assemblage and others provide, all together, evidences of early and worldwide diversification of eukaryotes. Thereby, those first qualitative results also provide a basis for further and larger quantitative studies on the Taoudeni Basin. To better understand the palaeobiology (stem or crown group, aerobic or anaerobic metabolism) and

  1. Arthropod Diversity in a Tropical Forest

    DEFF Research Database (Denmark)

    Basset, Yves; Cizek, Lukas; Cuénoud, Philippe;

    2012-01-01

    Most eukaryotic organisms are arthropods. Yet, their diversity in rich terrestrial ecosystems is still unknown. Here we produce tangible estimates of the total species richness of arthropods in a tropical rainforest. Using a comprehensive range of structured protocols, we sampled the phylogenetic......,000 arthropod species. Notably, just 1 hectare of rainforest yields >60% of the arthropod biodiversity held in the wider landscape. Models based on plant diversity fitted the accumulated species richness of both herbivore and nonherbivore taxa exceptionally well. This lends credence to global estimates...

  2. Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry

    OpenAIRE

    2008-01-01

    Recent years have witnessed major upheavals in views about early eukaryotic evolution. One very significant finding was that mitochondria, including hydrogenosomes and the newly discovered mitosomes, are just as ubiquitous and defining among eukaryotes as the nucleus itself. A second important advance concerns the readjustment, still in progress, about phylogenetic relationships among eukaryotic groups and the roughly six new eukaryotic supergroups that are currently at the focus of much atte...

  3. Myosin domain evolution and the primary divergence of eukaryotes.

    Science.gov (United States)

    Richards, Thomas A; Cavalier-Smith, Thomas

    2005-08-25

    Eukaryotic cells have two contrasting cytoskeletal and ciliary organizations. The simplest involves a single cilium-bearing centriole, nucleating a cone of individual microtubules (probably ancestral for unikonts: animals, fungi, Choanozoa and Amoebozoa). In contrast, bikonts (plants, chromists and all other protozoa) were ancestrally biciliate with a younger anterior cilium, converted every cell cycle into a dissimilar posterior cilium and multiple ciliary roots of microtubule bands. Here we show by comparative genomic analysis that this fundamental cellular dichotomy also involves different myosin molecular motors. We found 37 different protein domain combinations, often lineage-specific, and many previously unidentified. The sequence phylogeny and taxonomic distribution of myosin domain combinations identified five innovations that strongly support unikont monophyly and the primary bikont/unikont bifurcation. We conclude that the eukaryotic cenancestor (last common ancestor) had a cilium, mitochondria, pseudopodia, and myosins with three contrasting domain combinations and putative functions.

  4. "Race for the Surface": Eukaryotic Cells Can Win.

    Science.gov (United States)

    Pham, Vy T H; Truong, Vi Khanh; Orlowska, Anna; Ghanaati, Shahram; Barbeck, Mike; Booms, Patrick; Fulcher, Alex J; Bhadra, Chris M; Buividas, Ričardas; Baulin, Vladimir; Kirkpatrick, C James; Doran, Pauline; Mainwaring, David E; Juodkazis, Saulius; Crawford, Russell J; Ivanova, Elena P

    2016-08-31

    With an aging population and the consequent increasing use of medical implants, managing the possible infections arising from implant surgery remains a global challenge. Here, we demonstrate for the first time that a precise nanotopology provides an effective intervention in bacterial cocolonization enabling the proliferation of eukaryotic cells on a substratum surface, preinfected by both live Gram-negative, Pseudomonas aeruginosa, and Gram-positive, Staphylococcus aureus, pathogenic bacteria. The topology of the model black silicon (bSi) substratum not only favors the proliferation of eukaryotic cells but is biocompatible, not triggering an inflammatory response in the host. The attachment behavior and development of filopodia when COS-7 fibroblast cells are placed in contact with the bSi surface are demonstrated in the dynamic study, which is based on the use of real-time sequential confocal imaging. Bactericidal nanotopology may enhance the prospect for further development of inherently responsive antibacterial nanomaterials for bionic applications such as prosthetics and implants.

  5. Characterization of prokaryotic and eukaryotic promoters usinghidden Markov models

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, Pierre; Brunak, Søren

    1996-01-01

    that bind to them. We find that HMMs trained on such subclasses of Escherichia coli promoters (specifically, the so-called sigma-70 and sigma-54 classes) give an excellent classification of unknown promoters with respect to sigma-class. HMMs trained on eukaryotic sequences from human genes also model nicely......In this paper we utilize hidden Markov models (HMMs) and information theory to analyze prokaryotic and eukaryotic promoters. We perform this analysis with special emphasis on the fact that promoters are divided into a number of different classes, depending on which polymerase-associated factors...... have at the same time the ability to find clusters and the ability to model the sequential structure in the input data. This is highly relevant in situations where the variance in the data is high, as is the case for the subclass structure in for example promoter sequences....

  6. Characterization of prokaryotic and eukaryotic promoters using hidden Markov models

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, P.; Chauvin, Y.

    1996-01-01

    that bind to them. We find that HMMs trained on such subclasses of Escherichia coli promoters (specifically, the so-called sigma 70 and sigma 54 classes) give an excellent classification of unknown promoters with respect to sigma-class. HMMs trained on eukaryotic sequences from human genes also model nicely......In this paper we utilize hidden Markov models (HMMs) and information theory to analyze prokaryotic and eukaryotic promoters. We perform this analysis with special emphasis on the fact that promoters are divided into a number of different classes, depending on which polymerase-associated factors...... have at the same time the ability to find clusters and the ability to model the sequential structure in the input data. This is highly relevant in situations where the variance in the data is high, as is the case for the subclass structure in for example promoter sequences....

  7. Analyses of RNA Polymerase II genes from free-living protists: phylogeny, long branch attraction, and the eukaryotic big bang.

    Science.gov (United States)

    Dacks, Joel B; Marinets, Alexandra; Ford Doolittle, W; Cavalier-Smith, Thomas; Logsdon, John M

    2002-06-01

    The phylogenetic relationships among major eukaryotic protist lineages are largely uncertain. Two significant obstacles in reconstructing eukaryotic phylogeny are long-branch attraction (LBA) effects and poor taxon sampling of free-living protists. We have obtained and analyzed gene sequences encoding the largest subunit of RNA Polymerase II (RPB1) from Naegleria gruberi (a heterolobosean), Cercomonas ATCC 50319 (a cercozoan), and Ochromonas danica (a heterokont); we have also analyzed the RPB1 gene from the nucleomorph (nm) genome of Guillardia theta (a cryptomonad). Using a variety of phylogenetic methods our analysis shows that RPB1s from Giardia intestinalis and Trichomonas vaginalis are probably subject to intense LBA effects. Thus, the deep branching of these taxa on RPB1 trees is questionable and should not be interpreted as evidence favoring their early divergence. Similar effects are discernable, to a lesser extent, with the Mastigamoeba invertens RPB1 sequence. Upon removal of the outgroup and these problematic sequences, analyses of the remaining RPB1s indicate some resolution among major eukaryotic groups. The most robustly supported higher-level clades are the opisthokonts (animals plus fungi) and the red algae plus the cryptomonad nm-the latter result gives added support to the red algal origin of cryptomonad chloroplasts. Clades comprising Dictyostelium discoideum plus Acanthamoeba castellanii (Amoebozoa) and Ochromonas plus Plasmodium falciparum (chromalveolates) are consistently observed and moderately supported. The clades supported by our RPB1 analyses are congruent with other data, suggesting that bona fide phylogenetic relationships are being resolved. Thus, the RPB1 gene has apparently retained some phylogenetically meaningful signal, making it worthwhile to obtain sequences from more diverse protist taxa. Additional RPB1 data, especially in combination with other genes, should provide further resolution of branching orders among protist

  8. A high-affinity molybdate transporter in eukaryotes.

    Science.gov (United States)

    Tejada-Jiménez, Manuel; Llamas, Angel; Sanz-Luque, Emanuel; Galván, Aurora; Fernández, Emilio

    2007-12-11

    Molybdenum is an essential element for almost all living beings, which, in the form of a molybdopterin-cofactor, participates in the active site of enzymes involved in key reactions of carbon, nitrogen, and sulfur metabolism. This metal is taken up by cells in form of the oxyanion molybdate. Bacteria acquire molybdate by an ATP-binding-cassette (ABC) transport system in a widely studied process, but how eukaryotic cells take up molybdenum is unknown because molybdate transporters have not been identified so far. Here, we report a eukaryotic high-affinity molybdate transporter, encoded by the green alga Chlamydomonas reinhardtii gene MoT1. An antisense RNA strategy over the MoT1 gene showed that interference of the expression of this gene leads to the inhibition of molybdate transport activity and, in turn, of the Mo-containing enzyme nitrate reductase, indicating a function of MoT1 in molybdate transport. MOT1 functionality was also shown by heterologous expression in Saccharomyces cerevisiae. Molybdate uptake mediated by MOT1 showed a K(m) of approximately 6 nM, which is the range of the lowest K(m) values reported and was activated in the presence of nitrate. Analysis of deduced sequence from the putative protein coded by MoT1 showed motifs specifically conserved in similar proteins present in the databases, and defines a family of membrane proteins in both eukaryotes and prokaryotes probably involved in molybdate transport and distantly related to plant sulfate transporters SULTR. These findings represent an important step in the understanding of molybdate transport, a crucial process in eukaryotic cells.

  9. Eukaryotic protein domains as functional units of cellular evolution

    DEFF Research Database (Denmark)

    Jin, Jing; Xie, Xueying; Chen, Chen;

    2009-01-01

    domain compositions and functional properties, termed "domain clubs," which we use to compare multiple eukaryotic proteomes. This analysis shows that different domain types can take distinct evolutionary trajectories, which correlate with the conservation, gain, expansion, or decay of particular...... of different domain types to assess the molecular compartment occupied by each domain. This reveals that specific subsets of domains demarcate particular cellular processes, such as growth factor signaling, chromatin remodeling, apoptotic and inflammatory responses, or vesicular trafficking. We suggest...

  10. A 3D Hydrodynamic Model for Cytokinesis of Eukaryotic Cells

    Science.gov (United States)

    2014-08-01

    division or binary fission, which is the primary method for reproduction. For eukaryotic cells, it’s called cell mitotic process or mitosis . At the late...of cytokinesis in animal, yeast and plant cells. Experimental observations have provide us with a basic picture of cell mitosis . For eu- karyotic... mitosis and cytokinesis in mammalian cells. 2014 Special Focus on Rho GTPases, page e29770, 2014. [7] Ulrike S. Eggert, Timothy J. Mitchison, and

  11. Sulfate assimilation in eukaryotes: fusions, relocations and lateral transfers

    Directory of Open Access Journals (Sweden)

    Durnford Dion G

    2008-02-01

    Full Text Available Abstract Background The sulfate assimilation pathway is present in photosynthetic organisms, fungi, and many bacteria, providing reduced sulfur for the synthesis of cysteine and methionine and a range of other metabolites. In photosynthetic eukaryotes sulfate is reduced in the plastids whereas in aplastidic eukaryotes the pathway is cytosolic. The only known exception is Euglena gracilis, where the pathway is localized in mitochondria. To obtain an insight into the evolution of the sulfate assimilation pathway in eukaryotes and relationships of the differently compartmentalized isoforms we determined the locations of the pathway in lineages for which this was unknown and performed detailed phylogenetic analyses of three enzymes involved in sulfate reduction: ATP sulfurylase (ATPS, adenosine 5'-phosphosulfate reductase (APR and sulfite reductase (SiR. Results The inheritance of ATPS, APR and the related 3'-phosphoadenosine 5'-phosphosulfate reductase (PAPR are remarkable, with multiple origins in the lineages that comprise the opisthokonts, different isoforms in chlorophytes and streptophytes, gene fusions with other enzymes of the pathway, evidence a eukaryote to prokaryote lateral gene transfer, changes in substrate specificity and two reversals of cellular location of host- and endosymbiont-originating enzymes. We also found that the ATPS and APR active in the mitochondria of Euglena were inherited from its secondary, green algal plastid. Conclusion Our results reveal a complex history for the enzymes of the sulfate assimilation pathway. Whilst they shed light on the origin of some characterised novelties, such as a recently described novel isoform of APR from Bryophytes and the origin of the pathway active in the mitochondria of Euglenids, the many distinct and novel isoforms identified here represent an excellent resource for detailed biochemical studies of the enzyme structure/function relationships.

  12. Non-coding RNAs: the architects of eukaryotic complexity.

    Science.gov (United States)

    Mattick, J S

    2001-11-01

    Around 98% of all transcriptional output in humans is non-coding RNA. RNA-mediated gene regulation is widespread in higher eukaryotes and complex genetic phenomena like RNA interference, co-suppression, transgene silencing, imprinting, methylation, and possibly position-effect variegation and transvection, all involve intersecting pathways based on or connected to RNA signaling. I suggest that the central dogma is incomplete, and that intronic and other non-coding RNAs have evolved to comprise a second tier of gene expression in eukaryotes, which enables the integration and networking of complex suites of gene activity. Although proteins are the fundamental effectors of cellular function, the basis of eukaryotic complexity and phenotypic variation may lie primarily in a control architecture composed of a highly parallel system of trans-acting RNAs that relay state information required for the coordination and modulation of gene expression, via chromatin remodeling, RNA-DNA, RNA-RNA and RNA-protein interactions. This system has interesting and perhaps informative analogies with small world networks and dataflow computing.

  13. Study of intrachromosomal duplications among the eukaryote genomes.

    Science.gov (United States)

    Achaz, G; Netter, P; Coissac, E

    2001-12-01

    Complete eukaryote chromosomes were investigated for intrachromosomal duplications of nucleotide sequences. The analysis was performed by looking for nonexact repeats on two complete genomes, Saccharomyces cerevisiae and Caenorhabditis elegans, and four partial ones, Drosophila melanogaster, Plasmodium falciparum, Arabidopsis thaliana, and Homo sapiens. Through this analysis, we show that all eukaryote chromosomes exhibit similar characteristics for their intrachromosomal repeats, suggesting similar dynamics: many direct repeats have their two copies physically close together, and these close direct repeats are more similar and shorter than the other repeats. On the contrary, there are almost no close inverted repeats. These results support a model for the dynamics of duplication. This model is based on a continuous genesis of tandem repeats and implies that most of the distant and inverted repeats originate from these tandem repeats by further chromosomal rearrangements (insertions, inversions, and deletions). Remnants of these predicted rearrangements have been brought out through fine analysis of the chromosome sequence. Despite these dynamics, shared by all eukaryotes, each genome exhibits its own style of intrachromosomal duplication: the density of repeated elements is similar in all chromosomes issued from the same genome, but is different between species. This density was further related to the relative rates of duplication, deletion, and mutation proper to each species. One should notice that the density of repeats in the X chromosome of C. elegans is much lower than in the autosomes of that organism, suggesting that the exchange between homologous chromosomes is important in the duplication process.

  14. Eukaryotic penelope-like retroelements encode hammerhead ribozyme motifs.

    Science.gov (United States)

    Cervera, Amelia; De la Peña, Marcos

    2014-11-01

    Small self-cleaving RNAs, such as the paradigmatic Hammerhead ribozyme (HHR), have been recently found widespread in DNA genomes across all kingdoms of life. In this work, we found that new HHR variants are preserved in the ancient family of Penelope-like elements (PLEs), a group of eukaryotic retrotransposons regarded as exceptional for encoding telomerase-like retrotranscriptases and spliceosomal introns. Our bioinformatic analysis revealed not only the presence of minimalist HHRs in the two flanking repeats of PLEs but also their massive and widespread occurrence in metazoan genomes. The architecture of these ribozymes indicates that they may work as dimers, although their low self-cleavage activity in vitro suggests the requirement of other factors in vivo. In plants, however, PLEs show canonical HHRs, whereas fungi and protist PLEs encode ribozyme variants with a stable active conformation as monomers. Overall, our data confirm the connection of self-cleaving RNAs with eukaryotic retroelements and unveil these motifs as a significant fraction of the encoded information in eukaryotic genomes.

  15. Evolution of filamentous plant pathogens: gene exchange across eukaryotic kingdoms.

    Science.gov (United States)

    Richards, Thomas A; Dacks, Joel B; Jenkinson, Joanna M; Thornton, Christopher R; Talbot, Nicholas J

    2006-09-19

    Filamentous fungi and oomycetes are eukaryotic microorganisms that grow by producing networks of thread-like hyphae, which secrete enzymes to break down complex nutrients, such as wood and plant material, and recover the resulting simple sugars and amino acids by osmotrophy. These organisms are extremely similar in both appearance and lifestyle and include some of the most economically important plant pathogens . However, the morphological similarity of fungi and oomycetes is misleading because they represent some of the most distantly related eukaryote evolutionary groupings, and their shared osmotrophic growth habit is interpreted as being the result of convergent evolution . The fungi branch with the animals, whereas the oomycetes branch with photosynthetic algae as part of the Chromalveolata . In this report, we provide strong phylogenetic evidence that multiple horizontal gene transfers (HGT) have occurred from filamentous ascomycete fungi to the distantly related oomycetes. We also present evidence that a subset of the associated gene families was initially the product of prokaryote-to-fungi HGT. The predicted functions of the gene products associated with fungi-to-oomycete HGT suggest that this process has played a significant role in the evolution of the osmotrophic, filamentous lifestyle on two separate branches of the eukaryote tree.

  16. DNA polymerase zeta (polζ) in higher eukaryotes

    Institute of Scientific and Technical Information of China (English)

    Gregory N Gan; John P Wittschieben; Birgitte φ Wittschieben; Richard D Wood

    2008-01-01

    Most current knowledge about DNA polymerase zeta (pol ζ) comes from studies of the enzyme in the budding yeast Saccharomyces cerevisiae, where polζ consists of a complex of the catalytic subunit Rev3 with Rev7, which associates with Rev1. Most spontaneous and induced mutagenesis in yeast is dependent on these gene products, and yeast pol can mediate translesion DNA synthesis past some adducts in DNA templates. Study of the homologous gene products in higher eukaryotes is in a relatively early stage, but additional functions for the eukaryotic proteins are already appar-ent. Suppression of vertebrate REV3L function not only reduces induced point mutagenesis but also causes larger-scale genuine instability by raising the frequency of spontaneous chromosome translocations. Disruption of Rev3L function is tolerated in Drosophila, Arabidopsis, and in vertebrate cell lines under some conditions, but is incompatible with mouse embryonic development. Functions for REV3L and REV7(MAD2B) in higher eukaryotes have been suggested not only in translesion DNA synthesis but also in some forms of homologous recombination, repair ofinterstrand DNA erosslinks, somatic hypermutation of immunoglobulin genes and cell-cycle control. This review discusses recent devel-opments in these areas.

  17. Oceanographic structure drives the assembly processes of microbial eukaryotic communities.

    Science.gov (United States)

    Monier, Adam; Comte, Jérôme; Babin, Marcel; Forest, Alexandre; Matsuoka, Atsushi; Lovejoy, Connie

    2015-03-17

    Arctic Ocean microbial eukaryote phytoplankton form subsurface chlorophyll maximum (SCM), where much of the annual summer production occurs. This SCM is particularly persistent in the Western Arctic Ocean, which is strongly salinity stratified. The recent loss of multiyear sea ice and increased particulate-rich river discharge in the Arctic Ocean results in a greater volume of fresher water that may displace nutrient-rich saltier waters to deeper depths and decrease light penetration in areas affected by river discharge. Here, we surveyed microbial eukaryotic assemblages in the surface waters, and within and below the SCM. In most samples, we detected the pronounced SCM that usually occurs at the interface of the upper mixed layer and Pacific Summer Water (PSW). Poorly developed SCM was seen under two conditions, one above PSW and associated with a downwelling eddy, and the second in a region influenced by the Mackenzie River plume. Four phylogenetically distinct communities were identified: surface, pronounced SCM, weak SCM and a deeper community just below the SCM. Distance-decay relationships and phylogenetic structure suggested distinct ecological processes operating within these communities. In the pronounced SCM, picophytoplanktons were prevalent and community assembly was attributed to water mass history. In contrast, environmental filtering impacted the composition of the weak SCM communities, where heterotrophic Picozoa were more numerous. These results imply that displacement of Pacific waters to greater depth and increased terrigenous input may act as a control on SCM development and result in lower net summer primary production with a more heterotroph dominated eukaryotic microbial community.

  18. Enzymes involved in organellar DNA replication in photosynthetic eukaryotes

    Directory of Open Access Journals (Sweden)

    Takashi eMoriyama

    2014-09-01

    Full Text Available Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.

  19. Membrane remodeling and organization: Elements common to prokaryotes and eukaryotes.

    Science.gov (United States)

    Vega-Cabrera, Luz A; Pardo-López, Liliana

    2017-02-01

    Membrane remodeling processes in eukaryotes, such as those involved in endocytosis and intracellular trafficking, are mediated by a large number of structural, accessory and regulatory proteins. These processes occur in all cell types, enabling the exchange of signals and/or nutrients with the external medium and with neighboring cells; likewise, they are required for the intracellular trafficking of various cargo molecules between organelles, as well as the recycling of these structures. Recent studies have demonstrated that some elements of the molecular machinery involved in regulating and mediating endocytosis in eukaryotic cells are also present in some bacteria, where they participate in processes such as cell division, sporulation and signal transduction. However, the mechanism whereby this prokaryotic machinery carries out such functions has barely begun to be elucidated. This review summarizes recent information about the cytoskeletal and membrane-organizing proteins for which bacterial homologs have been identified; given their known functions, they may be considered to be part of an ancestral membrane organization system that first emerged in prokaryotes and which further evolved into the more complex regulatory networks operating in eukaryotes. © 2017 IUBMB Life, 69(2):55-62, 2017.

  20. Chromatin—a global buffer for eukaryotic gene control

    Directory of Open Access Journals (Sweden)

    Yuri M. Moshkin

    2015-09-01

    Full Text Available Most of eukaryotic DNA is embedded into nucleosome arrays formed by DNA wrapped around a core histone octamer. Nucleosome is a fundamental repeating unit of chromatin guarding access to the genetic information. Here, I will discuss two facets of nucleosome in eukaryotic gene control. On the one hand, nucleosome acts as a regulatory unit, which controls gene switches through a set of post-translational modifications occurring on histone tails. On the other hand, global configuration of nucleosome arrays with respect to nucleosome positioning, spacing and turnover acts as a tuning parameter for all genomic functions. A “histone code” hypothesis extents the Jacob-Monod model for eukaryotic gene control; however, when considering factors capable of reconfiguring entire nucleosome array, such as ATP-dependent chromatin remodelers, this model becomes limited. Global changes in nucleosome arrays will be sensed by every gene, yet the transcriptional responses might be specific and appear as gene targeted events. What determines such specificity is unclear, but it’s likely to depend on initial gene settings, such as availability of transcription factors, and on configuration of new nucleosome array state.

  1. Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae).

    OpenAIRE

    Cavalier-Smith, T

    2003-01-01

    Chloroplasts originated just once, from cyanobacteria enslaved by a biciliate protozoan to form the plant kingdom (green plants, red and glaucophyte algae), but subsequently, were laterally transferred to other lineages to form eukaryote-eukaryote chimaeras or meta-algae. This process of secondary symbiogenesis (permanent merger of two phylogenetically distinct eukaryote cells) has left remarkable traces of its evolutionary role in the more complex topology of the membranes surrounding all no...

  2. Diversity Management

    DEFF Research Database (Denmark)

    Ravazzani, Silvia

    2016-01-01

    This entry provides an overview of diversity management which, in the context of organizations, consists in the strategic process of harnessing the potential of all employees to create an inclusive environment and, at the same time, contribute to meeting organizational goals. The entry first...... describes the complex construct of diversity that has been variously conceptualized in the literature, embracing multiple social and informational diversity dimensions such as gender, age, culture, values, and workstyle. This is followed by illustration of the historical development of diversity-management...... discourse and practice, and possible overarching approaches guiding organizations. It goes on to elucidate elements linked to the implementation of diversity management: positive and negative outcomes, most spread practices including communication, and contingency factors shaping the understanding...

  3. PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

    Science.gov (United States)

    Decelle, Johan; Romac, Sarah; Stern, Rowena F; Bendif, El Mahdi; Zingone, Adriana; Audic, Stéphane; Guiry, Michael D; Guillou, Laure; Tessier, Désiré; Le Gall, Florence; Gourvil, Priscillia; Dos Santos, Adriana L; Probert, Ian; Vaulot, Daniel; de Vargas, Colomban; Christen, Richard

    2015-11-01

    Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing.

  4. Origin of phagotrophic eukaryotes as social cheaters in microbial biofilms

    Directory of Open Access Journals (Sweden)

    Jékely Gáspár

    2007-01-01

    Full Text Available Abstract Background The origin of eukaryotic cells was one of the most dramatic evolutionary transitions in the history of life. It is generally assumed that eukaryotes evolved later then prokaryotes by the transformation or fusion of prokaryotic lineages. However, as yet there is no consensus regarding the nature of the prokaryotic group(s ancestral to eukaryotes. Regardless of this, a hardly debatable fundamental novel characteristic of the last eukaryotic common ancestor was the ability to exploit prokaryotic biomass by the ingestion of entire cells, i.e. phagocytosis. The recent advances in our understanding of the social life of prokaryotes may help to explain the origin of this form of total exploitation. Presentation of the hypothesis Here I propose that eukaryotic cells originated in a social environment, a differentiated microbial mat or biofilm that was maintained by the cooperative action of its members. Cooperation was costly (e.g. the production of developmental signals or an extracellular matrix but yielded benefits that increased the overall fitness of the social group. I propose that eukaryotes originated as selfish cheaters that enjoyed the benefits of social aggregation but did not contribute to it themselves. The cheaters later evolved into predators that lysed other cells and eventually became professional phagotrophs. During several cycles of social aggregation and dispersal the number of cheaters was contained by a chicken game situation, i.e. reproductive success of cheaters was high when they were in low abundance but was reduced when they were over-represented. Radical changes in cell structure, including the loss of the rigid prokaryotic cell wall and the development of endomembranes, allowed the protoeukaryotes to avoid cheater control and to exploit nutrients more efficiently. Cellular changes were buffered by both the social benefits and the protective physico-chemical milieu of the interior of biofilms. Symbiosis

  5. A large factory-scale application of selected autochthonous lactic acid bacteria for PDO Pecorino Siciliano cheese production.

    Science.gov (United States)

    Guarcello, Rosa; Carpino, Stefania; Gaglio, Raimondo; Pino, Alessandra; Rapisarda, Teresa; Caggia, Cinzia; Marino, Giovanni; Randazzo, Cinzia L; Settanni, Luca; Todaro, Massimo

    2016-10-01

    The main hypothesis of this study was that the autochthonous lactic acid bacteria (LAB) selected for their dairy traits are able to stabilize the production of PDO (Protected Denomination of Origin) Pecorino Siciliano cheese, preserving its typicality. The experimental plan included the application of a multi-strain lactic acid bacteria (LAB) culture, composed of starter (Lactococcus lactis subsp. lactis CAG4 and CAG37) and non starter (Enterococcus faecalis PSL71, Lactococcus garviae PSL67 and Streptococcus macedonicus PSL72) strains, during the traditional production of cheese at large scale level in six factories located in different areas of Sicily. The cheese making processes were followed from milk to ripened cheeses and the effects of the added LAB were evaluated on the microbiological, chemico-physical and sensorial characteristics of the final products. Results highlighted a high variability for all investigated parameters and the dominance of LAB cocci in bulk milk samples. The experimental curds showed a faster pH drop than control curds and the levels of LAB estimated in 5-month ripened experimental cheeses (7.59 and 7.27 Log CFU/g for rods and cocci, respectively) were higher than those of control cheeses (7.02 and 6.61 Log CFU/g for rods and cocci, respectively). The comparison of the bacterial isolates by randomly amplified polymorphic DNA (RAPD)-PCR evidenced the dominance of the added starter lactococci over native milk and vat LAB, while the added non starter LAB were found at almost the same levels of the indigenous strains. The sensory evaluation showed that the mixed LAB culture did not influence the majority of the sensory attributes of the cheeses and that each factory produced cheeses with unique characteristics. Finally, the multivariate statistical analysis based on all parameters evaluated on the ripened cheeses showed the dissimilarities and the relationships among cheeses. Thus, the main hypothesis of the work was accepted since the

  6. Role of eukaryotic-like serine/threonine kinases in bacterial cell division and morphogenesis.

    Science.gov (United States)

    Manuse, Sylvie; Fleurie, Aurore; Zucchini, Laure; Lesterlin, Christian; Grangeasse, Christophe

    2016-01-01

    Bacteria possess a repertoire of versatile protein kinases modulating diverse aspects of their physiology by phosphorylating proteins on various amino acids including histidine, cysteine, aspartic acid, arginine, serine, threonine and tyrosine. One class of membrane serine/threonine protein kinases possesses a catalytic domain sharing a common fold with eukaryotic protein kinases and an extracellular mosaic domain found in bacteria only, named PASTA for 'Penicillin binding proteins And Serine/Threonine kinase Associated'. Over the last decade, evidence has been accumulating that these protein kinases are involved in cell division, morphogenesis and developmental processes in Firmicutes and Actinobacteria. However, observations differ from one species to another suggesting that a general mechanism of activation of their kinase activity is unlikely and that species-specific regulation of cell division is at play. In this review, we survey the latest research on the structural aspects and the cellular functions of bacterial serine/threonine kinases with PASTA motifs to illustrate the diversity of the regulatory mechanisms controlling bacterial cell division and morphogenesis.

  7. Everyday Diversity

    Directory of Open Access Journals (Sweden)

    Christina Ho

    2015-03-01

    Full Text Available The Cosmopolitan Civil Societies Journal has been an important forum for discussing issues around cultural diversity. Articles on cultural diversity have been present in virtually every issue of the journal. These have ranged from conceptual pieces on cosmopolitanism, identity, dialogue, prejudice, pluralism, cultural and social capital and social inclusion, to articles embedded in empirical research on ethnic precincts and segregation in cities, experiences of religious minorities, immigrant entrepreneurs, and more. Over its five year history, the journal has also had themed editions on cultural diversity issues, including one on embracing diversity in sport, and another on the Chinese in Australian politics. The scope of this work has been wide, and authors have brought a range of disciplinary and methodological approaches to the journal.   The purpose of this paper is to draw together some of the work that has been published around cultural diversity, particularly relating to everyday experiences of cosmopolitanism and racism. Focusing on everyday social relations has been an important part of recent scholarship on cultural diversity in Australia (e.g. Wise and Velayutham 2009. In contrast to research framed around multicultural policy or mediated representations of diversity, the scholarship of the ‘everyday’ aims to explore people’s lived experiences and daily interactions with others.

  8. The Evolutionary History of R2R3-MYB Proteins Across 50 Eukaryotes: New Insights Into Subfamily Classification and Expansion.

    Science.gov (United States)

    Du, Hai; Liang, Zhe; Zhao, Sen; Nan, Ming-Ge; Tran, Lam-Son Phan; Lu, Kun; Huang, Yu-Bi; Li, Jia-Na

    2015-06-05

    R2R3-MYB proteins (2R-MYBs) are one of the main transcription factor families in higher plants. Since the evolutionary history of this gene family across the eukaryotic kingdom remains unknown, we performed a comparative analysis of 2R-MYBs from 50 major eukaryotic lineages, with particular emphasis on land plants. A total of 1548 candidates were identified among diverse taxonomic groups, which allowed for an updated classification of 73 highly conserved subfamilies, including many newly identified subfamilies. Our results revealed that the protein architectures, intron patterns, and sequence characteristics were remarkably conserved in each subfamily. At least four subfamilies were derived from early land plants, 10 evolved from spermatophytes, and 19 from angiosperms, demonstrating the diversity and preferential expansion of this gene family in land plants. Moreover, we determined that their remarkable expansion was mainly attributed to whole genome and segmental duplication, where duplicates were preferentially retained within certain subfamilies that shared three homologous intron patterns (a, b, and c) even though up to 12 types of patterns existed. Through our integrated distributions, sequence characteristics, and phylogenetic tree analyses, we confirm that 2R-MYBs are old and postulate that 3R-MYBs may be evolutionarily derived from 2R-MYBs via intragenic domain duplication.

  9. The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes.

    Directory of Open Access Journals (Sweden)

    Estienne C Swart

    Full Text Available The macronuclear genome of the ciliate Oxytricha trifallax displays an extreme and unique eukaryotic genome architecture with extensive genomic variation. During sexual genome development, the expressed, somatic macronuclear genome is whittled down to the genic portion of a small fraction (∼5% of its precursor "silent" germline micronuclear genome by a process of "unscrambling" and fragmentation. The tiny macronuclear "nanochromosomes" typically encode single, protein-coding genes (a small portion, 10%, encode 2-8 genes, have minimal noncoding regions, and are differentially amplified to an average of ∼2,000 copies. We report the high-quality genome assembly of ∼16,000 complete nanochromosomes (∼50 Mb haploid genome size that vary from 469 bp to 66 kb long (mean ∼3.2 kb and encode ∼18,500 genes. Alternative DNA fragmentation processes ∼10% of the nanochromosomes into multiple isoforms that usually encode complete genes. Nucleotide diversity in the macronucleus is very high (SNP heterozygosity is ∼4.0%, suggesting that Oxytricha trifallax may have one of the largest known effective population sizes of eukaryotes. Comparison to other ciliates with nonscrambled genomes and long macronuclear chromosomes (on the order of 100 kb suggests several candidate proteins that could be involved in genome rearrangement, including domesticated MULE and IS1595-like DDE transposases. The assembly of the highly fragmented Oxytricha macronuclear genome is the first completed genome with such an unusual architecture. This genome sequence provides tantalizing glimpses into novel molecular biology and evolution. For example, Oxytricha maintains tens of millions of telomeres per cell and has also evolved an intriguing expansion of telomere end-binding proteins. In conjunction with the micronuclear genome in progress, the O. trifallax macronuclear genome will provide an invaluable resource for investigating programmed genome rearrangements, complementing

  10. Effect of environmental variables on eukaryotic microbial community structure of land-fast Arctic sea ice.

    Science.gov (United States)

    Eddie, Brian; Juhl, Andrew; Krembs, Christopher; Baysinger, Charles; Neuer, Susanne

    2010-03-01

    Sea ice microbial community structure affects carbon and nutrient cycling in polar seas, but its susceptibility to changing environmental conditions is not well understood. We studied the eukaryotic microbial community in sea ice cores recovered near Point Barrow, AK in May 2006 by documenting the composition of the community in relation to vertical depth within the cores, as well as light availability (mainly as variable snow cover) and nutrient concentrations. We applied a combination of epifluorescence microscopy, denaturing gradient gel electrophoresis and clone libraries of a section of the 18S rRNA gene in order to compare the community structure of the major eukaryotic microbial phylotypes in the ice. We find that the community composition of the sea ice is more affected by the depth horizon in the ice than by light availability, although there are significant differences in the abundance of some groups between light regimes. Epifluorescence microscopy shows a shift from predominantly heterotrophic life styles in the upper ice to autotrophy prevailing in the bottom ice. This is supported by the statistical analysis of the similarity between the samples based on the denaturing gradient gel electrophoresis banding patterns, which shows a clear difference between upper and lower ice sections with respect to phylotypes and their proportional abundance. Clone libraries constructed using diatom-specific primers confirm the high diversity of diatoms in the sea ice, and support the microscopic counts. Evidence of protistan grazing upon diatoms was also found in lower sections of the core, with implications for carbon and nutrient recycling in the ice.

  11. Potential and pitfalls of eukaryotic metagenome skimming: a test case for lichens.

    Science.gov (United States)

    Greshake, Bastian; Zehr, Simonida; Dal Grande, Francesco; Meiser, Anjuli; Schmitt, Imke; Ebersberger, Ingo

    2016-03-01

    Whole-genome shotgun sequencing of multispecies communities using only a single library layout is commonly used to assess taxonomic and functional diversity of microbial assemblages. Here, we investigate to what extent such metagenome skimming approaches are applicable for in-depth genomic characterizations of eukaryotic communities, for example lichens. We address how to best assemble a particular eukaryotic metagenome skimming data, what pitfalls can occur, and what genome quality can be expected from these data. To facilitate a project-specific benchmarking, we introduce the concept of twin sets, simulated data resembling the outcome of a particular metagenome sequencing study. We show that the quality of genome reconstructions depends essentially on assembler choice. Individual tools, including the metagenome assemblers Omega and MetaVelvet, are surprisingly sensitive to low and uneven coverages. In combination with the routine of assembly parameter choice to optimize the assembly N50 size, these tools can preclude an entire genome from the assembly. In contrast, MIRA, an all-purpose overlap assembler, and SPAdes, a multisized de Bruijn graph assembler, facilitate a comprehensive view on the individual genomes across a wide range of coverage ratios. Testing assemblers on a real-world metagenome skimming data from the lichen Lasallia pustulata demonstrates the applicability of twin sets for guiding method selection. Furthermore, it reveals that the assembly outcome for the photobiont Trebouxia sp. falls behind the a priori expectation given the simulations. Although the underlying reasons remain still unclear, this highlights that further studies on this organism require special attention during sequence data generation and downstream analysis.

  12. Understanding Diversity

    NARCIS (Netherlands)

    D.L. van Knippenberg (Daan)

    2007-01-01

    textabstractDaan van Knippenberg is Professor of Organizational Behavior at RSM Erasmus University, Erasmus University Rotterdam, The Netherlands. His research interests include work group performance, especially work group diversity and group decision making, leadership, in particular the roles of

  13. Gender Diversities

    DEFF Research Database (Denmark)

    Agustin, Lise Rolandsen; Siim, Birte

    2014-01-01

    The article analyses the European Year for Combating Poverty and Social Exclusion (2010) (EY 2010) with the aim of identifying the nature of gender diversities in EU policies. We argue that the EU handles issues related to gender and diversity in particular ways; this approach is characterized...... by non-citizen/citizen and redistribution/recognition divisions. Employing intersectionality as the methodological approach to gender diversities, the article shows how gender and ethnicity are articulated in the policy-making process which led to the adoption of EY 201, the activities undertaken during...... the EY 2010, and the evaluation of EY 2010. The case study is suitable for developing a dynamic multi-level model for analysing gendered diversities at the transnationmal level: It illustrates how the EU policy frame interacts with particular national contexts in promoting or hundering the advancement...

  14. Targeted metagenomics and ecology of globally important uncultured eukaryotic phytoplankton.

    Science.gov (United States)

    Cuvelier, Marie L; Allen, Andrew E; Monier, Adam; McCrow, John P; Messié, Monique; Tringe, Susannah G; Woyke, Tanja; Welsh, Rory M; Ishoey, Thomas; Lee, Jae-Hyeok; Binder, Brian J; DuPont, Chris L; Latasa, Mikel; Guigand, Cédric; Buck, Kurt R; Hilton, Jason; Thiagarajan, Mathangi; Caler, Elisabet; Read, Betsy; Lasken, Roger S; Chavez, Francisco P; Worden, Alexandra Z

    2010-08-17

    Among eukaryotes, four major phytoplankton lineages are responsible for marine photosynthesis; prymnesiophytes, alveolates, stramenopiles, and prasinophytes. Contributions by individual taxa, however, are not well known, and genomes have been analyzed from only the latter two lineages. Tiny "picoplanktonic" members of the prymnesiophyte lineage have long been inferred to be ecologically important but remain poorly characterized. Here, we examine pico-prymnesiophyte evolutionary history and ecology using cultivation-independent methods. 18S rRNA gene analysis showed pico-prymnesiophytes belonged to broadly distributed uncultivated taxa. Therefore, we used targeted metagenomics to analyze uncultured pico-prymnesiophytes sorted by flow cytometry from subtropical North Atlantic waters. The data reveal a composite nuclear-encoded gene repertoire with strong green-lineage affiliations, which contrasts with the evolutionary history indicated by the plastid genome. Measured pico-prymnesiophyte growth rates were rapid in this region, resulting in primary production contributions similar to the cyanobacterium Prochlorococcus. On average, pico-prymnesiophytes formed 25% of global picophytoplankton biomass, with differing contributions in five biogeographical provinces spanning tropical to subpolar systems. Elements likely contributing to success include high gene density and genes potentially involved in defense and nutrient uptake. Our findings have implications reaching beyond pico-prymnesiophytes, to the prasinophytes and stramenopiles. For example, prevalence of putative Ni-containing superoxide dismutases (SODs), instead of Fe-containing SODs, seems to be a common adaptation among eukaryotic phytoplankton for reducing Fe quotas in low-Fe modern oceans. Moreover, highly mosaic gene repertoires, although compositionally distinct for each major eukaryotic lineage, now seem to be an underlying facet of successful marine phytoplankton.

  15. Insights into the Initiation of Eukaryotic DNA Replication.

    Science.gov (United States)

    Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

    2015-01-01

    The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2-7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2-7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2-7 complex. Sld3 recruits Cdc45 to Mcm2-7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2-7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2-7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted.

  16. Telomeric position effect--a third silencing mechanism in eukaryotes.

    Directory of Open Access Journals (Sweden)

    J Greg Doheny

    Full Text Available Eukaryotic chromosomes terminate in telomeres, complex nucleoprotein structures that are required for chromosome integrity that are implicated in cellular senescence and cancer. The chromatin at the telomere is unique with characteristics of both heterochromatin and euchromatin. The end of the chromosome is capped by a structure that protects the end and is required for maintaining proper chromosome length. Immediately proximal to the cap are the telomere associated satellite-like (TAS sequences. Genes inserted into the TAS sequences are silenced indicating the chromatin environment is incompatible with transcription. This silencing phenomenon is called telomeric position effect (TPE. Two other silencing mechanisms have been identified in eukaryotes, suppressors position effect variegation [Su(vars, greater than 30 members] and Polycomb group proteins (PcG, approximately 15 members. We tested a large number of each group for their ability to suppress TPE [Su(TPE]. Our results showed that only three Su(vars and only one PcG member are involved in TPE, suggesting silencing in the TAS sequences occurs via a novel silencing mechanism. Since, prior to this study, only five genes have been identified that are Su(TPEs, we conducted a candidate screen for Su(TPE in Drosophila by testing point mutations in, and deficiencies for, proteins involved in chromatin metabolism. Screening with point mutations identified seven new Su(TPEs and the deficiencies identified 19 regions of the Drosophila genome that harbor suppressor mutations. Chromatin immunoprecipitation experiments on a subset of the new Su(TPEs confirm they act directly on the gene inserted into the telomere. Since the Su(TPEs do not overlap significantly with either PcGs or Su(vars, and the candidates were selected because they are involved generally in chromatin metabolism and act at a wide variety of sites within the genome, we propose that the Su(TPE represent a third, widely used, silencing

  17. Interaction of Low Temperature Plasmas with Prokaryotic and Eukaryotic Cells

    Science.gov (United States)

    Laroussi, Mounir

    2008-10-01

    Due to promising possibilities for their use in medical applications such as wound healing, surface modification of biocompatible materials, and the sterilization of reusable heat-sensitive medical instruments, low temperature plasmas and plasma jets are making big strides as a technology that can potentially be used in medicine^1-2. At this stage of research, fundamental questions about the effects of plasma on prokaryotic and eukaryotic cells are still not completely answered. An in-depth understanding of the pathway whereby cold plasma interact with biological cells is necessary before real applications can emerge. In this paper, first an overview of non-equilibrium plasma sources (both low and high pressures) will be presented. Secondly, the effects of plasma on bacterial cells will be discussed. Here, the roles of the various plasma agents in the inactivation process will be outlined. In particular, the effects of UV and that of various reactive species (O3, O, OH) are highlighted. Thirdly, preliminary findings on the effects of plasma on few types of eukaryotic cells will be presented. How plasma affects eukaryotic cells, such as mammalian cells, is very important in applications where the viability/preservation of the cells could be an issue (such as in wound treatment). Another interesting aspect is the triggering of apoptosis (programmed cell death). Some investigators have claimed that plasma is able to induce apoptosis in some types of cancer cells. If successfully replicated, this can open up a novel method of cancer treatment. In this talk however, I will briefly focus more on the wound healing potential of cold plasmas. ^1E. A. Blakely, K. A. Bjornstad, J. E. Galvin, O. R. Monteiro, and I. G. Brown, ``Selective Neuron Growth on Ion Implanted and Plasma Deposited Surfaces'', In Proc. IEEE Int. Conf. Plasma Sci., (2002), p. 253. ^2M. Laroussi, ``Non-thermal Decontamination of Biological Media by Atmospheric Pressure Plasmas: Review, Analysis, and

  18. Mosaic origin of the heme biosynthesis pathway in photosynthetic eukaryotes.

    Science.gov (United States)

    Oborník, Miroslav; Green, Beverley R

    2005-12-01

    Heme biosynthesis represents one of the most essential metabolic pathways in living organisms, providing the precursors for cytochrome prosthetic groups, photosynthetic pigments, and vitamin B(12). Using genomic data, we have compared the heme pathway in the diatom Thalassiosira pseudonana and the red alga Cyanidioschyzon merolae to those of green algae and higher plants, as well as to those of heterotrophic eukaryotes (fungi, apicomplexans, and animals). Phylogenetic analyses showed the mosaic character of this pathway in photosynthetic eukaryotes. Although most of the algal and plant enzymes showed the expected plastid (cyanobacterial) origin, at least one of them (porphobilinogen deaminase) appears to have a mitochondrial (alpha-proteobacterial) origin. Another enzyme, glutamyl-tRNA synthase, obviously originated in the eukaryotic nucleus. Because all the plastid-targeted sequences consistently form a well-supported cluster, this suggests that genes were either transferred from the primary endosymbiont (cyanobacteria) to the primary host nucleus shortly after the primary endosymbiotic event or replaced with genes from other sources at an equally early time, i.e., before the formation of three primary plastid lineages. The one striking exception to this pattern is ferrochelatase, the enzyme catalyzing the first committed step to heme and bilin pigments. In this case, two red algal sequences do not cluster either with the other plastid sequences or with cyanobacterial sequences and appear to have a proteobacterial origin like that of the apicomplexan parasites Plasmodium and Toxoplasma. Although the heterokonts also acquired their plastid via secondary endosymbiosis from a red alga, the diatom has a typical plastid-cyanobacterial ferrochelatase. We have not found any remnants of the plastidlike heme pathway in the nonphotosynthetic heterokonts Phytophthora ramorum and Phytophthora sojae.

  19. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  20. Insights into the Initiation of Eukaryotic DNA Replication

    Science.gov (United States)

    Bruck, Irina; Perez-Arnaiz, Patricia; Colbert, Max K; Kaplan, Daniel L

    2015-01-01

    The initiation of DNA replication is a highly regulated event in eukaryotic cells to ensure that the entire genome is copied once and only once during S phase. The primary target of cellular regulation of eukaryotic DNA replication initiation is the assembly and activation of the replication fork helicase, the 11-subunit assembly that unwinds DNA at a replication fork. The replication fork helicase, called CMG for Cdc45-Mcm2–7, and GINS, assembles in S phase from the constituent Cdc45, Mcm2–7, and GINS proteins. The assembly and activation of the CMG replication fork helicase during S phase is governed by 2 S-phase specific kinases, CDK and DDK. CDK stimulates the interaction between Sld2, Sld3, and Dpb11, 3 initiation factors that are each required for the initiation of DNA replication. DDK, on the other hand, phosphorylates the Mcm2, Mcm4, and Mcm6 subunits of the Mcm2–7 complex. Sld3 recruits Cdc45 to Mcm2–7 in a manner that depends on DDK, and recent work suggests that Sld3 binds directly to Mcm2–7 and also to single-stranded DNA. Furthermore, recent work demonstrates that Sld3 and its human homolog Treslin substantially stimulate DDK phosphorylation of Mcm2. These data suggest that the initiation factor Sld3/Treslin coordinates the assembly and activation of the eukaryotic replication fork helicase by recruiting Cdc45 to Mcm2–7, stimulating DDK phosphorylation of Mcm2, and binding directly to single-stranded DNA as the origin is melted. PMID:26710261

  1. The effect of negative autoregulation on eukaryotic gene expression

    Science.gov (United States)

    Nevozhay, Dmitry; Adams, Rhys; Murphy, Kevin; Josic, Kresimir; Balázsi, G. Ábor

    2009-03-01

    Negative autoregulation is a frequent motif in gene regulatory networks, which has been studied extensively in prokaryotes. Nevertheless, some effects of negative feedback on gene expression in eukaryotic transcriptional networks remain unknown. We studied how the strength of negative feedback regulation affects the characteristics of gene expression in yeast cells carrying synthetic transcriptional cascades. We observed a drastic reduction of gene expression noise and a change in the shape of the dose-response curve. We explained these experimentally observed effects by stochastic simulations and a simple set of algebraic equations.

  2. Septins and the lateral compartmentalization of eukaryotic membranes.

    Science.gov (United States)

    Caudron, Fabrice; Barral, Yves

    2009-04-01

    Eukaryotic cells from neurons and epithelial cells to unicellular fungi frequently rely on cellular appendages such as axons, dendritic spines, cilia, and buds for their biology. The emergence and differentiation of these appendages depend on the formation of lateral diffusion barriers at their bases to insulate their membranes from the rest of the cell. Here, we review recent progress regarding the molecular mechanisms and functions of such barriers. This overview underlines the importance and conservation of septin-dependent diffusion barriers, which coordinately compartmentalize both plasmatic and internal membranes. We discuss their role in memory establishment and the control of cellular aging.

  3. Recognition of extremophilic archaeal viruses by eukaryotic cells

    DEFF Research Database (Denmark)

    Uldahl, Kristine Buch; Wu, Linping; Hall, Arnaldur

    2016-01-01

    followed viral uptake, intracellular trafficking and cell viability in human endothelial cells of brain (hCMEC/D3 cells) and umbilical vein (HUVEC) origin. Whereas SMV1 is efficiently internalized into both types of human cells, SSV2 differentiates between HUVECs and hCMEC/D3 cells, thus opening a path......Viruses from the third domain of life, Archaea, exhibit unusual features including extreme stability that allow their survival in harsh environments. In addition, these species have never been reported to integrate into human or any other eukaryotic genomes, and could thus serve for exploration...

  4. Efficacy of Origanum vulgare L. and Rosmarinus officinalis L. essential oils in combination to control postharvest pathogenic Aspergilli and autochthonous mycoflora in Vitis labrusca L. (table grapes).

    Science.gov (United States)

    de Sousa, Larissa Lima; de Andrade, Sonálle Carolina Albuquerque; Athayde, Ana Júlia Alves Aguiar; de Oliveira, Carlos Eduardo Vasconcelos; de Sales, Camila Veríssimo; Madruga, Marta Suely; de Souza, Evandro Leite

    2013-08-01

    This study evaluated the efficacy of the application of the essential oils of Origanum vulgare L. (OVEO) and Rosmarinus officinalis L. (ROEO) alone and in combination to inhibit Aspergillus flavus URM 4540 and Aspergillus niger URM 5842 in fungal growth media and on Vitis labrusca L. (table grapes). The influence on the autochthonous mycoflora and the physical, physicochemical and sensory characteristics of the grapes during storage (25°C, 12days and 12°C, 24days) were also studied. The application of the essential oils in different concentrations (Minimum Inhibitory Concentration - MIC, 1/2 MIC+1/2 MIC and 1/4 MIC+1/4 MIC) inhibited the mycelial growth and spore germination of the test fungi and inhibited the growth of the assayed fungal strains in artificially contaminated grapes and the autochthonous mycoflora of grapes stored at both room and cold temperatures. In general, the application of OVEO and/or ROEO at sub-lethal concentrations preserved the quality of grapes as measured by their physical, physicochemical and sensory attributes throughout the assessed storage time. These results demonstrate the potential of the combination of OVEO and ROEO at sub-lethal concentrations to control postharvest pathogenic fungi in fruits, particularly, A. flavus and A. niger in table grapes.

  5. Taxonomic structure of the yeasts and lactic acid bacteria microbiota of pineapple (Ananas comosus L. Merr.) and use of autochthonous starters for minimally processing.

    Science.gov (United States)

    Di Cagno, Raffaella; Cardinali, Gainluigi; Minervini, Giovanna; Antonielli, Livio; Rizzello, Carlo Giuseppe; Ricciuti, Patrizia; Gobbetti, Marco

    2010-05-01

    Pichia guilliermondii was the only identified yeast in pineapple fruits. Lactobacillus plantarum and Lactobacillus rossiae were the main identified species of lactic acid bacteria. Typing of lactic acid bacteria differentiated isolates depending on the layers. L. plantarum 1OR12 and L. rossiae 2MR10 were selected within the lactic acid bacteria isolates based on the kinetics of growth and acidification. Five technological options, including minimal processing, were considered for pineapple: heating at 72 degrees C for 15 s (HP); spontaneous fermentation without (FP) or followed by heating (FHP), and fermentation by selected autochthonous L. plantarum 1OR12 and L. rossiae 2MR10 without (SP) or preceded by heating (HSP). After 30 days of storage at 4 degrees C, HSP and SP had a number of lactic acid bacteria 1000 to 1,000,000 times higher than the other processed pineapples. The number of yeasts was the lowest in HSP and SP. The Community Level Catabolic Profiles of processed pineapples indirectly confirmed the capacity of autochthonous starters to dominate during fermentation. HSP and SP also showed the highest antioxidant activity and firmness, the better preservation of the natural colours and were preferred for odour and overall acceptability.

  6. Engineering key components in a synthetic eukaryotic signal transduction pathway.

    Science.gov (United States)

    Antunes, Mauricio S; Morey, Kevin J; Tewari-Singh, Neera; Bowen, Tessa A; Smith, J Jeff; Webb, Colleen T; Hellinga, Homme W; Medford, June I

    2009-01-01

    Signal transduction underlies how living organisms detect and respond to stimuli. A goal of synthetic biology is to rewire natural signal transduction systems. Bacteria, yeast, and plants sense environmental aspects through conserved histidine kinase (HK) signal transduction systems. HK protein components are typically comprised of multiple, relatively modular, and conserved domains. Phosphate transfer between these components may exhibit considerable cross talk between the otherwise apparently linear pathways, thereby establishing networks that integrate multiple signals. We show that sequence conservation and cross talk can extend across kingdoms and can be exploited to produce a synthetic plant signal transduction system. In response to HK cross talk, heterologously expressed bacterial response regulators, PhoB and OmpR, translocate to the nucleus on HK activation. Using this discovery, combined with modification of PhoB (PhoB-VP64), we produced a key component of a eukaryotic synthetic signal transduction pathway. In response to exogenous cytokinin, PhoB-VP64 translocates to the nucleus, binds a synthetic PlantPho promoter, and activates gene expression. These results show that conserved-signaling components can be used across kingdoms and adapted to produce synthetic eukaryotic signal transduction pathways.

  7. EuPathDB: the eukaryotic pathogen genomics database resource

    Science.gov (United States)

    Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y.; Brestelli, John; Brunk, Brian P.; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S.; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C.; Lawrence, Cris; Li, Wei; Pinney, Deborah F.; Pulman, Jane A.; Roos, David S.; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J.; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

    2017-01-01

    The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host–pathogen interactions. PMID:27903906

  8. EuPathDB: the eukaryotic pathogen genomics database resource.

    Science.gov (United States)

    Aurrecoechea, Cristina; Barreto, Ana; Basenko, Evelina Y; Brestelli, John; Brunk, Brian P; Cade, Shon; Crouch, Kathryn; Doherty, Ryan; Falke, Dave; Fischer, Steve; Gajria, Bindu; Harb, Omar S; Heiges, Mark; Hertz-Fowler, Christiane; Hu, Sufen; Iodice, John; Kissinger, Jessica C; Lawrence, Cris; Li, Wei; Pinney, Deborah F; Pulman, Jane A; Roos, David S; Shanmugasundram, Achchuthan; Silva-Franco, Fatima; Steinbiss, Sascha; Stoeckert, Christian J; Spruill, Drew; Wang, Haiming; Warrenfeltz, Susanne; Zheng, Jie

    2017-01-04

    The Eukaryotic Pathogen Genomics Database Resource (EuPathDB, http://eupathdb.org) is a collection of databases covering 170+ eukaryotic pathogens (protists & fungi), along with relevant free-living and non-pathogenic species, and select pathogen hosts. To facilitate the discovery of meaningful biological relationships, the databases couple preconfigured searches with visualization and analysis tools for comprehensive data mining via intuitive graphical interfaces and APIs. All data are analyzed with the same workflows, including creation of gene orthology profiles, so data are easily compared across data sets, data types and organisms. EuPathDB is updated with numerous new analysis tools, features, data sets and data types. New tools include GO, metabolic pathway and word enrichment analyses plus an online workspace for analysis of personal, non-public, large-scale data. Expanded data content is mostly genomic and functional genomic data while new data types include protein microarray, metabolic pathways, compounds, quantitative proteomics, copy number variation, and polysomal transcriptomics. New features include consistent categorization of searches, data sets and genome browser tracks; redesigned gene pages; effective integration of alternative transcripts; and a EuPathDB Galaxy instance for private analyses of a user's data. Forthcoming upgrades include user workspaces for private integration of data with existing EuPathDB data and improved integration and presentation of host-pathogen interactions.

  9. Universal Temporal Profile of Replication Origin Activation in Eukaryotes

    Science.gov (United States)

    Goldar, Arach

    2011-03-01

    The complete and faithful transmission of eukaryotic genome to daughter cells involves the timely duplication of mother cell's DNA. DNA replication starts at multiple chromosomal positions called replication origin. From each activated replication origin two replication forks progress in opposite direction and duplicate the mother cell's DNA. While it is widely accepted that in eukaryotic organisms replication origins are activated in a stochastic manner, little is known on the sources of the observed stochasticity. It is often associated to the population variability to enter S phase. We extract from a growing Saccharomyces cerevisiae population the average rate of origin activation in a single cell by combining single molecule measurements and a numerical deconvolution technique. We show that the temporal profile of the rate of origin activation in a single cell is similar to the one extracted from a replicating cell population. Taking into account this observation we exclude the population variability as the origin of observed stochasticity in origin activation. We confirm that the rate of origin activation increases in the early stage of S phase and decreases at the latter stage. The population average activation rate extracted from single molecule analysis is in prefect accordance with the activation rate extracted from published micro-array data, confirming therefore the homogeneity and genome scale invariance of dynamic of replication process. All these observations point toward a possible role of replication fork to control the rate of origin activation.

  10. Eukaryotic snoRNAs: a paradigm for gene expression flexibility.

    Science.gov (United States)

    Dieci, Giorgio; Preti, Milena; Montanini, Barbara

    2009-08-01

    Small nucleolar RNAs (snoRNAs) are one of the most ancient and numerous families of non-protein-coding RNAs (ncRNAs). The main function of snoRNAs - to guide site-specific rRNA modification - is the same in Archaea and all eukaryotic lineages. In contrast, as revealed by recent genomic and RNomic studies, their genomic organization and expression strategies are the most varied. Seemingly snoRNA coding units have adopted, in the course of evolution, all the possible ways of being transcribed, thus providing a unique paradigm of gene expression flexibility. By focusing on representative fungal, plant and animal genomes, we review here all the documented types of snoRNA gene organization and expression, and we provide a comprehensive account of snoRNA expressional freedom by precisely estimating the frequency, in each genome, of each type of genomic organization. We finally discuss the relevance of snoRNA genomic studies for our general understanding of ncRNA family evolution and expression in eukaryotes.

  11. Eukaryotic Replisome Components Cooperate to Process Histones During Chromosome Replication

    Directory of Open Access Journals (Sweden)

    Magdalena Foltman

    2013-03-01

    Full Text Available DNA unwinding at eukaryotic replication forks displaces parental histones, which must be redeposited onto nascent DNA in order to preserve chromatin structure. By screening systematically for replisome components that pick up histones released from chromatin into a yeast cell extract, we found that the Mcm2 helicase subunit binds histones cooperatively with the FACT (facilitiates chromatin transcription complex, which helps to re-establish chromatin during transcription. FACT does not associate with the Mcm2-7 helicase at replication origins during G1 phase but is subsequently incorporated into the replisome progression complex independently of histone binding and uniquely among histone chaperones. The amino terminal tail of Mcm2 binds histones via a conserved motif that is dispensable for DNA synthesis per se but helps preserve subtelomeric chromatin, retain the 2 micron minichromosome, and support growth in the absence of Ctf18-RFC. Our data indicate that the eukaryotic replication and transcription machineries use analogous assemblies of multiple chaperones to preserve chromatin integrity.

  12. Specific features of protein biosynthesis in higher eukaryotes

    Directory of Open Access Journals (Sweden)

    El’skaya A. V.

    2013-05-01

    Full Text Available Over 40 years of studies in the field of higher eukaryotic translation are summarized in the review. Among the pioneer results obtained we should especially accentuate the following: i discovery of the adaptation of tRNAs and aminoacyl-tRNA synthetases (ARSs cellular pools to the synthesis of specific proteins and modulation of the elongation rate by rare isoacceptor tRNAs; ii the chaperone-like properties of the translation components (ribosomes and elongation factor eEF1A; characterization of high molecular weight complexes of ARSs; iii functional compartmentalization, including channeling of tRNA in eukaryotic cells; iv molecular mechanisms of channeling mediated by different non-canonical complexes involving eEF1A, tRNA and aminoacyl-tRNA synthetases; v characterization of the crystal structure of eEF1A2; vi comparison of spatial structure, molecular dynamics, tyrosine phosphorylation and abilities to interact with different protein partners of the eEF1A1 and eEF1A2 isoforms; vii discovery of the microRNA-mediated control of the expression of the proto-oncogenic eEF1A2 isoform in cancer cells; viii examination of the cancer-related changes in translation elongation complex eEF1H and mechanisms of oncogene PTI-1 action; ix discovery of the third tRNA binding site on mammals ribosomes and the allosteric interaction of the 80S ribosomal A and E sites.

  13. Marine fungi: their ecology and molecular diversity.

    Science.gov (United States)

    Richards, Thomas A; Jones, Meredith D M; Leonard, Guy; Bass, David

    2012-01-01

    Fungi appear to be rare in marine environments. There are relatively few marine isolates in culture, and fungal small subunit ribosomal DNA (SSU rDNA) sequences are rarely recovered in marine clone library experiments (i.e., culture-independent sequence surveys of eukaryotic microbial diversity from environmental DNA samples). To explore the diversity of marine fungi, we took a broad selection of SSU rDNA data sets and calculated a summary phylogeny. Bringing these data together identified a diverse collection of marine fungi, including sequences branching close to chytrids (flagellated fungi), filamentous hypha-forming fungi, and multicellular fungi. However, the majority of the sequences branched with ascomycete and basidiomycete yeasts. We discuss evidence for 36 novel marine lineages, the majority and most divergent of which branch with the chytrids. We then investigate what these data mean for the evolutionary history of the Fungi and specifically marine-terrestrial transitions. Finally, we discuss the roles of fungi in marine ecosystems.

  14. Construction and identification of eukaryotic eukaryotic expression plasmid pcdna3.1-bace and its transient expression in cells

    Institute of Scientific and Technical Information of China (English)

    Huilin Gong; Guanjun Zhang; Weijiang Dong

    2006-01-01

    Objective: To generate eukaryotic expression vector of pcDNA3.1-BACE and obtain its transient expression in COS-7 cells and high expression in the neuroblastoma SK-N-SH cells. Methods: A 1503 bp cDNA fragment was amplified from the total RNA of human neuroblastoma by RT-PCR method and cloned into plasmid pcDNA3.1. The vector was identified by digestion with restriction enzymes BamHI and XhoI and sequenced by Sanger-dideoxy-mediated chain termination. The expression of BACE gene was detected by immunocytochemistry method. Results: The results showed that the cDNAfragment included 1503 bp total coding region. The recombinant eukaryotic cell expression vector of pcDNA3.1-BACE was constructed successfully,and the sequence of insert was identical to the published sequence. The COS-7 cells and the neuroblastoma SK-N-SH cells transfected with the pcDNA3.1-BACE plasmid expressed high level of BACE protein in cytoplasm. Conclusion: The recombinant plasmid pcDNA3.1-BACE can provide very useful tool for researching the reason of Alzheimer's disease and lays the important foundation for preventing the AD laterly.

  15. Methods for identifying and mapping recent segmental and gene duplications in eukaryotic genomes.

    Science.gov (United States)

    Khaja, Razi; MacDonald, Jeffrey R; Zhang, Junjun; Scherer, Stephen W

    2006-01-01

    The aim of this chapter is to provide instruction for analyzing and mapping recent segmental and gene duplications in eukaryotic genomes. We describe a bioinformatics-based approach utilizing computational tools to manage eukaryotic genome sequences to characterize and understand the evolutionary fates and trajectories of duplicated genes. An introduction to bioinformatics tools and programs such as BLAST, Perl, BioPerl, and the GFF specification provides the necessary background to complete this analysis for any eukaryotic genome of interest.

  16. Diversity's Calling

    Science.gov (United States)

    Cooper, Kenneth J.

    2011-01-01

    This article discusses how a Harvard-educated scholar of English and poetry, Dr. M. Lee Pelton puts a prominent face on changes that are underway at Boston's Emerson College. Faced with a public controversy over its limited faculty diversity, Emerson College has responded with a spate of hirings and promotions of minorities, capped by the…

  17. Generational diversity.

    Science.gov (United States)

    Kramer, Linda W

    2010-01-01

    Generational diversity has proven challenges for nurse leaders, and generational values may influence ideas about work and career planning. This article discusses generational gaps, influencing factors and support, and the various generational groups present in today's workplace as well as the consequences of need addressing these issues. The article ends with a discussion of possible solutions.

  18. Outbreak of autochthonous canine visceral leishmaniasis in Santa Catarina, Brazil Surto autóctone de leishmaniose visceral canina no Estado de Santa Catarina

    Directory of Open Access Journals (Sweden)

    Mário Steindel

    2013-04-01

    Full Text Available The present study reports the first outbreak of autochthonous canine visceral leishmaniasis in Florianópolis, Santa Catarina, southern Brazil. Following the report of two cases of CVL, the Control Center of Zoonotic Diseases conducted a serological survey by ELISA and IFAT assays in seven districts of the Santa Catarina Island. Eleven seropositive dogs of autochthonous transmission were used in the present study. Infection by Leishmania sp. was confirmed by parasitological examination of bone marrow, liver, spleen and lymph nodes, culture in Schneider's medium and PCR. Leishmania sp. isolates were characterized by PCR-RFLP and hybridization with specific probes, allowing for the identification of Leishmania infantum. Autochthonous transmission of this disease in an area with high tourist traffic presents a major public health concern and signifies the emergence of an important zoonosis in southern Brazil. Therefore, the implementation of surveillance and control measures is imperative to prevent the spread of the disease among the canine population as well as transmission to the human population.O presente estudo relata o primeiro surto autóctone de leishmaniose visceral canina (LCV em Florianópolis, Santa Catarina, Brasil. Durante levantamento soro-epidemiológico realizado pelo Centro de Controle de Doenças Zoonóticas (CCZ envolvendo 2.124 cães, 29 (1,37% foram soropositivos para VL (ELISA + RIFI. Onze cães positivos por transmissão autóctone foram utilizados no presente estudo. A confirmação da infecção por Leishmania sp. foi realizada pelo exame parasitológico da medula óssea, fígado, baço e linfonodos, cultura em meio Schneider e PCR. Os isolados de Leishmania sp. foram caracterizados por PCR-RFLP e hibridação com sondas específicas, permitindo a identificação de Leishmania infantum. A transmissão autóctone da LCV em uma área com grande fluxo turístico como Florianópolis representa um preocupante risco à saúde p

  19. Bacterial scaffolds assemble novel higher-order complexes to reengineer eukaryotic cell processes.

    Science.gov (United States)

    Lesser, Cammie F; Leong, John M

    2011-07-05

    Many microbial pathogens use specialized secretion systems to inject proteins referred to as effectors directly into eukaryotic host cells. These effectors directly target various eukaryotic signaling pathways and cellular processes, often by mimicking the activity of host cell proteins. Effectors of pathogenic Escherichia coli and Salmonella typhimurium can also act as molecular scaffolds that not only recruit but also directly regulate the activity and localization of multiple eukaryotic proteins. By assembling and localizing disparate signaling pathways, the bacteria can reengineer host cell processes to generate novel processes not previously observed in eukaryotic cells.

  20. An Interactive Exercise To Learn Eukaryotic Cell Structure and Organelle Function.

    Science.gov (United States)

    Klionsky, Daniel J.; Tomashek, John J.

    1999-01-01

    Describes a cooperative, interactive problem-solving exercise for studying eukaryotic cell structure and function. Highlights the dynamic aspects of movement through the cell. Contains 15 references. (WRM)

  1. A general strategy to construct small molecule biosensors in eukaryotes.

    Science.gov (United States)

    Feng, Justin; Jester, Benjamin W; Tinberg, Christine E; Mandell, Daniel J; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J; Rios, Xavier; Medford, June I; Church, George M; Fields, Stanley; Baker, David

    2015-12-29

    Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes.

  2. Saccharomyces cerevisiae: a versatile eukaryotic system in virology

    Directory of Open Access Journals (Sweden)

    Breinig Tanja

    2007-10-01

    Full Text Available Abstract The yeast Saccharomyces cerevisiae is a well-established model system for understanding fundamental cellular processes relevant to higher eukaryotic organisms. Less known is its value for virus research, an area in which Saccharomyces cerevisiae has proven to be very fruitful as well. The present review will discuss the main achievements of yeast-based studies in basic and applied virus research. These include the analysis of the function of individual proteins from important pathogenic viruses, the elucidation of key processes in viral replication through the development of systems that allow the replication of higher eukayotic viruses in yeast, and the use of yeast in antiviral drug development and vaccine production.

  3. Prevention of DNA re-replication in eukaryotic cells

    Institute of Scientific and Technical Information of China (English)

    Lan N. Truong; Xiaohua Wu

    2011-01-01

    DNA replication is a highly regulated process involving a number of licensing and replication factors that function in a carefully orchestrated manner to faithfully replicate DNA during every cell cycle. Loss of proper licensing control leads to deregulated DNA replication including DNA re-replication, which can cause genome instability and tumorigenesis. Eukaryotic organisms have established several conserved mechanisms to prevent DNA re-replication and to counteract its potentially harmful effects. These mechanisms include tightly controlled regulation of licensing factors and activation of cell cycle and DNA damage checkpoints.Deregulated licensing control and its associated compromised checkpoints have both been observed in tumor cells, indicating that proper functioning of these pathways is essential for maintaining genome stability. In this review, we discuss the regulatory mechanisms of licensing control, the deleterious consequences when both licensing and checkpoints are compromised, and present possible mechanisms to prevent re-replication in order to maintain genome stability.

  4. Eukaryotic Mismatch Repair in Relation to DNA Replication.

    Science.gov (United States)

    Kunkel, Thomas A; Erie, Dorothy A

    2015-01-01

    Three processes act in series to accurately replicate the eukaryotic nuclear genome. The major replicative DNA polymerases strongly prevent mismatch formation, occasional mismatches that do form are proofread during replication, and rare mismatches that escape proofreading are corrected by mismatch repair (MMR). This review focuses on MMR in light of increasing knowledge about nuclear DNA replication enzymology and the rate and specificity with which mismatches are generated during leading- and lagging-strand replication. We consider differences in MMR efficiency in relation to mismatch recognition, signaling to direct MMR to the nascent strand, mismatch removal, and the timing of MMR. These studies are refining our understanding of relationships between generating and repairing replication errors to achieve accurate replication of both DNA strands of the nuclear genome.

  5. Synthetic biology tools for bioprospecting of natural products in eukaryotes.

    Science.gov (United States)

    Unkles, Shiela E; Valiante, Vito; Mattern, Derek J; Brakhage, Axel A

    2014-04-24

    Filamentous fungi have the capacity to produce a battery of natural products of often unknown function, synthesized by complex metabolic pathways. Unfortunately, most of these pathways appear silent, many in intractable organisms, and their products consequently unidentified. One basic challenge is the difficulty of expressing a biosynthesis pathway for a complex natural product in a heterologous eukaryotic host. Here, we provide a proof-of concept solution to this challenge and describe how the entire penicillin biosynthesis pathway can be expressed in a heterologous host. The method takes advantage of a combination of improved yeast in vivo cloning technology, generation of polycistronic mRNA for the gene cluster under study, and an amenable and easily manipulated fungal host, i.e., Aspergillus nidulans. We achieve expression from a single promoter of the pathway genes to yield a large polycistronic mRNA by using viral 2A peptide sequences to direct successful cotranslational cleavage of pathway enzymes.

  6. Soil fertility controls the size-specific distribution of eukaryotes.

    Science.gov (United States)

    Mulder, Christian

    2010-05-01

    The large range of body-mass values of soil organisms provides a tool to assess the organization of soil ecological communities. Relationships between log-transformed body mass M and log-transformed numerical abundance N of all eukaryotes occurring under organic pastures, mature grasslands, and seminatural heathlands in the Netherlands were investigated. The observed allometry of (M,N) assemblages of below-ground communities strongly reflects the availability of primary macronutrients and essential micronutrients. This log-linear model describes the continuous variation in the allometric slope of animals and fungi along an increasing soil fertility gradient. The aggregate contribution of small invertebrates (M soil explains 72% of these shifts but the nitrogen concentration explains only 36%, with copper and zinc as intermediate predictors (59% and 49%, respectively). Empirical evidence supports common responses of invertebrates to the rates of resource supply and, possibly, to the above-ground primary production of ecosystems.

  7. Kinetic model of DNA replication in eukaryotic organisms

    CERN Document Server

    Herrick, J; Bensimon, A; Herrick, John; Bechhoefer, John; Bensimon, Aaron

    2001-01-01

    We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of different data within a simple theoretical framework. This allows one, for the first time, to determine the parameters governing the DNA replication program in a eukaryote on a genome-wide basis. In particular, we have determined the frequency of origin activation in time and space during the cell cycle. Although we focus on a specific stage of development, this model can easily be adapted to describe replication in many other organisms, including budding yeast.

  8. New thioredoxin targets in the unicellular photosynthetic eukaryote Chlamydomonas reinhardtii

    Science.gov (United States)

    Lemaire, Stéphane D.; Guillon, Blanche; Le Maréchal, Pierre; Keryer, Eliane; Miginiac-Maslow, Myroslawa; Decottignies, Paulette

    2004-01-01

    Proteomics were used to identify the proteins from the eukaryotic unicellular green alga Chlamydomonas reinhardtii that can be reduced by thioredoxin. These proteins were retained specifically on a thioredoxin affinity column made of a monocysteinic thioredoxin mutant able to form mixed disulfides with its targets. Of a total of 55 identified targets, 29 had been found previously in higher plants or Synechocystis, but 26 were new targets. Biochemical tests were performed on three of them, showing a thioredoxin-dependent activation of isocitrate lyase and isopropylmalate dehydrogenase and a thioredoxin-dependent deactivation of catalase that is redox insensitive in Arabidopsis. In addition, we identified a Ran protein, a previously uncharacterized nuclear target in a photosynthetic organism. The metabolic and evolutionary implications of these findings are discussed. PMID:15123830

  9. Pi sensing and signalling: from prokaryotic to eukaryotic cells.

    Science.gov (United States)

    Qi, Wanjun; Baldwin, Stephen A; Muench, Stephen P; Baker, Alison

    2016-06-15

    Phosphorus is one of the most important macronutrients and is indispensable for all organisms as a critical structural component as well as participating in intracellular signalling and energy metabolism. Sensing and signalling of phosphate (Pi) has been extensively studied and is well understood in single-cellular organisms like bacteria (Escherichia coli) and Saccharomyces cerevisiae In comparison, the mechanism of Pi regulation in plants is less well understood despite recent advances in this area. In most soils the available Pi limits crop yield, therefore a clearer understanding of the molecular basis underlying Pi sensing and signalling is of great importance for the development of plants with improved Pi use efficiency. This mini-review compares some of the main Pi regulation pathways in prokaryotic and eukaryotic cells and identifies similarities and differences among different organisms, as well as providing some insight into future research.

  10. Ancient photosynthetic eukaryote biofilms in an Atacama Desert coastal cave

    Science.gov (United States)

    Azua-Bustos, A.; Gonzalez-Silva, C.; Mancilla, R.A.; Salas, L.; Palma, R.E.; Wynne, J.J.; McKay, C.P.; Vicuna, R.

    2009-01-01

    Caves offer a stable and protected environment from harsh and changing outside prevailing conditions. Hence, they represent an interesting habitat for studying life in extreme environments. Here, we report the presence of a member of the ancient eukaryote red algae Cyanidium group in a coastal cave of the hyperarid Atacama Desert. This microorganism was found to form a seemingly monospecific biofilm growing under extremely low photon flux levels. Our work suggests that this species, Cyanidium sp. Atacama, is a new member of a recently proposed novel monophyletic lineage of mesophilic "cave" Cyanidium sp., distinct from the remaining three other lineages which are all thermo-acidophilic. The cave described in this work may represent an evolutionary island for life in the midst of the Atacama Desert. ?? Springer Science + Business Media, LLC 2009.

  11. Enhancer Sharing Promotes Neighborhoods of Transcriptional Regulation Across Eukaryotes

    Science.gov (United States)

    Quintero-Cadena, Porfirio; Sternberg, Paul W.

    2016-01-01

    Enhancers physically interact with transcriptional promoters, looping over distances that can span multiple regulatory elements. Given that enhancer–promoter (EP) interactions generally occur via common protein complexes, it is unclear whether EP pairing is predominantly deterministic or proximity guided. Here, we present cross-organismic evidence suggesting that most EP pairs are compatible, largely determined by physical proximity rather than specific interactions. By reanalyzing transcriptome datasets, we find that the transcription of gene neighbors is correlated over distances that scale with genome size. We experimentally show that nonspecific EP interactions can explain such correlation, and that EP distance acts as a scaling factor for the transcriptional influence of an enhancer. We propose that enhancer sharing is commonplace among eukaryotes, and that EP distance is an important layer of information in gene regulation. PMID:27799341

  12. Biological Influence of Deuterium on Procariotic and Eukaryotic Cells

    Directory of Open Access Journals (Sweden)

    Oleg Mosin

    2014-03-01

    Full Text Available Biologic influence of deuterium (D on cells of various taxonomic groups of prokaryotic and eukaryotic microorganisms realizing methylotrophic, chemoheterotrophic, photo-organotrophic, and photosynthetic ways of assimilation of carbon substrates are investigated at growth on media with heavy water (D2О. The method of step by step adaptation technique of cells to D2О was developed, consisting in plating of cells on 2 % agarose nutrient media containing increasing gradient of concentration of D2О (from 0 up to 98 % D2O and the subsequent selection of stable to D2O cells. In the result of that technique were obtained adapted to maximum concentration of D2O cells, biological material of which instead of hydrogen contained deuterium with levels of enrichment 92–97,5 at.% D.

  13. Features of the biotechnologically relevant polyamide family "cyanophycins" and their biosynthesis in prokaryotes and eukaryotes.

    Science.gov (United States)

    Frommeyer, Maja; Wiefel, Lars; Steinbüchel, Alexander

    2016-01-01

    Cyanophycin, inclusions in cyanobacteria discovered by the Italian scientist Borzi in 1887, were characterized as a polyamide consisting of aspartic acid and arginine. Its synthesis in cyanobacteria was analyzed regarding growth conditions, responsible gene product, requirements, polymer structure and properties. Heterologous expression of diverse cyanophycin synthetases (CphA) in Escherichia coli enabled further enzyme characterization. Cyanophycin is a polyamide with variable composition and physiochemical properties dependent on host and cultivation conditions in contrast to the extracellular polyamides poly-γ-glutamic acid and poly-ε-l-lysine. Furthermore, recombinant prokaryotes and transgenic eukaryotes, including plants expressing different cphA genes, were characterized as suitable for production of insoluble cyanophycin regarding higher yields and modified composition for other requirements and applications. In addition, cyanophycin was characterized as a source for the synthesis of polyaspartic acid or N-containing bulk chemicals and dipeptides upon chemical treatment or degradation by cyanophycinases, respectively. Moreover, water-soluble cyanophycin derivatives with altered amino acid composition were isolated from transgenic plants, yeasts and recombinant bacteria. Thereby, the range of dipeptides could be extended by biological processes and by chemical modification, thus increasing the range of applications for cyanophycin and its dipeptides, including agriculture, food supplementations, medical and cosmetic purposes, synthesis of the polyacrylate substitute poly(aspartic acid) and other applications.

  14. Evolutionary Pattern of N-Glycosylation Sequon Numbers in Eukaryotic ABC Protein Superfamilies

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Buus, Ole Thomsen; Wollenweber, Bernd

    2010-01-01

    Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins and their underly......Many proteins contain a large number of NXS/T sequences (where X is any amino acid except proline) which are the potential sites of asparagine (N) linked glycosylation. However, the patterns of occurrence of these N-glycosylation sequons in related proteins or groups of proteins...... and their underlying causes have largely been unexplored. We computed the actual and probabilistic occurrence of NXS/T sequons in ABC protein superfamilies from eight diverse eukaryotic organisms. The ABC proteins contained significantly higher NXS/T sequon numbers compared to respective genome-wide average......-against the recent findings of only threonine specific Darwinian selection of sequons in proteins. The occurrence of sequons was positively correlated with the frequency of sequon specific amino acids and negatively correlated with proline and the NPS/T sequences. Further, the NPS/T sequences were significantly...

  15. The chaperonin genes of jakobid and jakobid-like flagellates: implications for eukaryotic evolution.

    Science.gov (United States)

    Archibald, John M; O'Kelly, Charles J; Doolittle, W Ford

    2002-04-01

    The jakobids are free-living mitochondriate protists that share ultrastructural features with certain amitochondriate groups and possess the most bacterial-like mitochondrial genomes described thus far. Jakobids belong to a diverse group of mitochondriate and amitochondriate eukaryotes, the excavate taxa. The relationships among the various excavate taxa and their relationships to other putative deep-branching protist groups are largely unknown. With the hope of clarifying these issues, we have isolated the cytosolic chaperonin CCTalpha gene from the jakobid Reclinomonas americana (strains 50394 and 50283), the jakobid-like malawimonad Malawimonas jakobiformis, two heteroloboseans (Acrasis rosea and Naegleria gruberi), a euglenozoan (Trypanosoma brucei), and a parabasalid (Monocercomonas sp.). We also amplified the CCTdelta gene from M. jakobiformis. The Reclinomonas and Malawimonas sequences presented here are among the first nuclear protein-coding genes to be described from these organisms. Unlike other putative early diverging protist lineages, a high density of spliceosomal introns was found in the jakobid and malawimonad CCTs-similar to that observed in vertebrate protein-coding genes. An analysis of intron positions in CCT genes from protists, plants, animals, and fungi suggests that many of the intron-sparse or intron-lacking protist lineages may not be primitively so but have lost spliceosomal introns during their evolutionary history. In phylogenetic trees constructed from CCTalpha protein sequences, R. americana (but not M. jakobiformis) shows a weak but consistent affinity for the Heterolobosea and Euglenozoa.

  16. Structure of a eukaryotic SWEET transporter in a homotrimeric complex.

    Science.gov (United States)

    Tao, Yuyong; Cheung, Lily S; Li, Shuo; Eom, Joon-Seob; Chen, Li-Qing; Xu, Yan; Perry, Kay; Frommer, Wolf B; Feng, Liang

    2015-11-12

    Eukaryotes rely on efficient distribution of energy and carbon skeletons between organs in the form of sugars. Glucose in animals and sucrose in plants serve as the dominant distribution forms. Cellular sugar uptake and release require vesicular and/or plasma membrane transport proteins. Humans and plants use proteins from three superfamilies for sugar translocation: the major facilitator superfamily (MFS), the sodium solute symporter family (SSF; only in the animal kingdom), and SWEETs. SWEETs carry mono- and disaccharides across vacuolar or plasma membranes. Plant SWEETs play key roles in sugar translocation between compartments, cells, and organs, notably in nectar secretion, phloem loading for long distance translocation, pollen nutrition, and seed filling. Plant SWEETs cause pathogen susceptibility possibly by sugar leakage from infected cells. The vacuolar Arabidopsis thaliana AtSWEET2 sequesters sugars in root vacuoles; loss-of-function mutants show increased susceptibility to Pythium infection. Here we show that its orthologue, the vacuolar glucose transporter OsSWEET2b from rice (Oryza sativa), consists of an asymmetrical pair of triple-helix bundles, connected by an inversion linker transmembrane helix (TM4) to create the translocation pathway. Structural and biochemical analyses show OsSWEET2b in an apparent inward (cytosolic) open state forming homomeric trimers. TM4 tightly interacts with the first triple-helix bundle within a protomer and mediates key contacts among protomers. Structure-guided mutagenesis of the close paralogue SWEET1 from Arabidopsis identified key residues in substrate translocation and protomer crosstalk. Insights into the structure-function relationship of SWEETs are valuable for understanding the transport mechanism of eukaryotic SWEETs and may be useful for engineering sugar flux.

  17. New universal rules of eukaryotic translation initiation fidelity.

    Directory of Open Access Journals (Sweden)

    Hadas Zur

    Full Text Available The accepted model of eukaryotic translation initiation begins with the scanning of the transcript by the pre-initiation complex from the 5'end until an ATG codon with a specific nucleotide (nt context surrounding it is recognized (Kozak rule. According to this model, ATG codons upstream to the beginning of the ORF should affect translation. We perform for the first time, a genome-wide statistical analysis, uncovering a new, more comprehensive and quantitative, set of initiation rules for improving the cost of translation and its efficiency. Analyzing dozens of eukaryotic genomes, we find that in all frames there is a universal trend of selection for low numbers of ATG codons; specifically, 16-27 codons upstream, but also 5-11 codons downstream of the START ATG, include less ATG codons than expected. We further suggest that there is selection for anti optimal ATG contexts in the vicinity of the START ATG. Thus, the efficiency and fidelity of translation initiation is encoded in the 5'UTR as required by the scanning model, but also at the beginning of the ORF. The observed nt patterns suggest that in all the analyzed organisms the pre-initiation complex often misses the START ATG of the ORF, and may start translation from an alternative initiation start-site. Thus, to prevent the translation of undesired proteins, there is selection for nucleotide sequences with low affinity to the pre-initiation complex near the beginning of the ORF. With the new suggested rules we were able to obtain a twice higher correlation with ribosomal density and protein levels in comparison to the Kozak rule alone (e.g. for protein levels r=0.7 vs. r=0.31; p<10(-12.

  18. Eukaryotic and prokaryotic contributions to colonic hydrogen sulfide synthesis.

    Science.gov (United States)

    Flannigan, Kyle L; McCoy, Kathy D; Wallace, John L

    2011-07-01

    Hydrogen sulfide (H(2)S) is an important modulator of many aspects of digestive function, both in health and disease. Colonic tissue H(2)S synthesis increases markedly during injury and inflammation and appears to contribute to resolution. Some of the bacteria residing in the colon can also produce H(2)S. The extent to which bacterial H(2)S synthesis contributes to what is measured as colonic H(2)S synthesis is not clear. Using conventional and germ-free mice, we have delineated the eukaryotic vs. prokaryotic contributions to colonic H(2)S synthesis, both in healthy and colitic mice. Colonic tissue H(2)S production is entirely dependent on the presence of the cofactor pyridoxal 5'-phosphate (vitamin B(6)), while bacterial H(2)S synthesis appears to occur independent of this cofactor. As expected, approximately one-half of the H(2)S produced by feces is derived from eukaryotic cells. While colonic H(2)S synthesis is markedly increased when the tissue is inflamed, and, in proportion to the extent of inflammation, fecal H(2)S synthesis does not change and tissue granulocytes do not appear to be the source of the elevated H(2)S production. Rats fed a B vitamin-deficient diet for 6 wk exhibited significantly diminished colonic H(2)S synthesis, but fecal H(2)S synthesis was not different from that of rats on the control diet. Our results demonstrate that H(2)S production by colonic bacteria does not contribute significantly to what is measured as colonic tissue H(2)S production, using the acetate trapping assay system employed in this study.

  19. Autochthonous arbuscular mycorrhizal fungi and Bacillus thuringiensis from a degraded Mediterranean area can be used to improve physiological traits and performance of a plant of agronomic interest under drought conditions.

    Science.gov (United States)

    Armada, Elisabeth; Azcón, Rosario; López-Castillo, Olga M; Calvo-Polanco, Mónica; Ruiz-Lozano, Juan Manuel

    2015-05-01

    Studies have shown that some microorganisms autochthonous from stressful environments are beneficial when used with autochthonous plants, but these microorganisms rarely have been tested with allochthonous plants of agronomic interest. This study investigates the effectiveness of drought-adapted autochthonous microorganisms [Bacillus thuringiensis (Bt) and a consortium of arbuscular mycorrhizal (AM) fungi] from a degraded Mediterranean area to improve plant growth and physiology in Zea mays under drought stress. Maize plants were inoculated or not with B. thuringiensis, a consortium of AM fungi or a combination of both microorganisms. Plants were cultivated under well-watered conditions or subjected to drought stress. Several physiological parameters were measured, including among others, plant growth, photosynthetic efficiency, nutrients content, oxidative damage to lipids, accumulation of proline and antioxidant compounds, root hydraulic conductivity and the expression of plant aquaporin genes. Under drought conditions, the inoculation of Bt increased significantly the accumulation of nutrients. The combined inoculation of both microorganisms decreased the oxidative damage to lipids and accumulation of proline induced by drought. Several maize aquaporins able to transport water, CO2 and other compounds were regulated by the microbial inoculants. The impact of these microorganisms on plant drought tolerance was complementary, since Bt increased mainly plant nutrition and AM fungi were more active improving stress tolerance/homeostatic mechanisms, including regulation of plant aquaporins with several putative physiological functions. Thus, the use of autochthonous beneficial microorganisms from a degraded Mediterranean area is useful to protect not only native plants against drought, but also an agronomically important plant such as maize.

  20. Evaluation of an autochthonous starter culture on the production of a traditional dry fermented sausage from Chaco (Argentina) at a small-scale facility.

    Science.gov (United States)

    Palavecino Prpich, Noelia Z; Garro, Oscar A; Romero, Mara; Judis, María A; Cayré, María E; Castro, Marcela P

    2016-05-01

    The performance of a mixed starter culture, SAS-1, comprised of the autochthonous strains Lactobacillus sakei ACU-2 and Staphylococcus vitulinus ACU-10, was evaluated into the production process of a traditional dry sausage. Microbiological, physicochemical and sensory analyses were carried out to accomplish this goal. Results showed an improvement in performance through the introduction of SAS-1; adding mixed starter culture rapidly decreased pH, inhibited the growth of contaminant microorganisms and enhanced the beneficial ones, diminished TBARS, and highlighted color and aroma attributes. However, most influential organoleptic descriptors among consumer acceptance were not affected by the addition of the starter. This starter culture would represent a valuable tool to improve the homogeneity of artisanal manufacture of this traditional food.

  1. Confirmation of Sigillaria Brongniart as a coal-forming plant in Cathaysia: occurrence from an Early Permian autochthonous peat-forming flora in Inner Mongolia

    Energy Technology Data Exchange (ETDEWEB)

    Wang, J.; Feng, Z.; Zhang, Y.; Wang, S.J. [Chinese Academy of Sciences, Nanjing (China)

    2009-07-15

    A common lycopsid genus, Sigillaria Brongniart, has been recorded most frequently in peat-forming forests in Europe and North America, but rarely in China. Although Sigillaria, in China, has been found in coal balls and used as evidence that it was a coalforming element, it has never been recorded as compression/impressions in peat-forming settings. Recent investigation of an Early Permian autochthonous peat-forming flora of the Taiyuan Formation near Wuda, Inner Mongolia, has provided evidence that Sigillaria could be a major element of peat-forming vegetation in China. Sigillaria is the only arborescent lycopsid acting as a major contributor to peat/coal formation. The genus Sigillaria is another element that China has in common with the Palaeozoic low-land floras of Europe and North America, enhancing the common floral aspects between the tropical swamp vegetations of the east and west regions of the Palaeotethys Ocean.

  2. Troubling Diversity?

    DEFF Research Database (Denmark)

    Jæger, Kirsten; Jensen, Annie Aarup

    2009-01-01

    Focussing on the cultural encounter between nurses and ethnic minority patients in Danish hospitals, this paper presents the results of a comprehensive analysis of nursing discourses on cultural difference and intercultural contact. Articles from the Danish professional journal ‘The Nurse......', published in the period from 2000 to 2008, pertaining to cultural contact and intercultural understanding have been analyzed in order to uncover nurses' experience of ethnic and cultural diversity and the ways, in which these experiences challenge their cultural and professional expertise. Results...... are related to recent contributions to diversity management theory and intercultural communication theory, calling for a strengthened focus on the historical, political, and social dimensions of intercultural contact. In continuation of these trends, an alternative, theoretical framework...

  3. Influence of oligomeric herbicidal ionic liquids with MCPA and Dicamba anions on the community structure of autochthonic bacteria present in agricultural soil

    Energy Technology Data Exchange (ETDEWEB)

    Ławniczak, Ł., E-mail: lukasz.k.lawniczak@wp.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Syguda, A., E-mail: Anna.Syguda@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Borkowski, A., E-mail: a.borkowski@uw.edu.pl [Faculty of Geology, University of Warsaw, 02-089 Warsaw (Poland); Cyplik, P., E-mail: pcyplik@wp.pl [Department of Biotechnology and Food Microbiology, University of Life Sciences in Poznan, 60-627 Poznan (Poland); Marcinkowska, K., E-mail: k.marcinkowska@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Wolko, Ł., E-mail: wolko@o2.pl [Department of Biochemistry and Biotechnology, Poznań University of Life Sciences in Poznan, 60-632 Poznan (Poland); Praczyk, T., E-mail: t.praczyk@iorpib.poznan.pl [Institute of Plant Protection - National Research Institute, Poznan 60-318 (Poland); Chrzanowski, Ł., E-mail: Lukasz.Chrzanowski@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland); Pernak, J., E-mail: Juliusz.Pernak@put.poznan.pl [Department of Chemical Technology, Poznan University of Technology, 60-965 Poznan (Poland)

    2016-09-01

    The aim of this study was to evaluate the impact of selected herbicidal ionic liquids (HILs), which exhibit high efficacy in terms of weed control and low toxicity, but may be persistent due to limited biodegradability, on the community structure of autochthonic bacteria present in agricultural soil. Four different oligomeric HILs (with two types of cations and different ratio of herbicidal anions) were synthesized and characterized by employing {sup 1}H and {sup 13}C NMR. The results of biodegradation assay indicated that none of the tested HILs could be classified as readily biodegradable (biodegradation rate ranged from 0 to 7%). The conducted field studies confirmed that the herbicidal efficacy of the HILs was higher compared to the reference herbicide mixture by 10 to 30%, depending on the dose and weed species. After termination of field studies, the soil treated with the tested HILs was subjected to next generation sequencing in order to investigate the potential changes in the bacterial community structure. Proteobacteria was the dominant phylum in all studied samples. Treatment with the studied HILs resulted in an increase of Actinobacteria compared to the reference herbicidal mixture. Differenced among the studied HILs were generally associated with a significantly higher abundance of Bacteroidetes in case of 1-HIL-Dicamba 1/3 and Firmicutes in case of 2-HIL-Dicamba 1/3. - Highlights: • Impact of herbicidal ionic liquids on bacterial community structure was studied. • Oligomeric herbicidal ionic liquids were effective but not readily biodegradable. • Next generation sequencing was used to evaluate shifts in bacterial abundance. • Treatment during field trials resulted in changes at class and species level. • Use of herbicidal ionic liquids affects the structure of autochthonic soil bacteria.

  4. Therapeutic efficacy of antigen-specific vaccination and toll-like receptor stimulation against established transplanted and autochthonous melanoma in mice.

    Science.gov (United States)

    Tormo, Damia; Ferrer, Aleix; Bosch, Pilar; Gaffal, Evelyn; Basner-Tschakarjan, Etiena; Wenzel, Jörg; Tüting, Thomas

    2006-05-15

    Malignant melanoma is an attractive model disease for the development of antigen-specific immunotherapy because many antigens recognized by tumor-specific T cells have been identified. In C57BL/6 mice, genetic immunization with recombinant adenovirus encoding xenogeneic human tyrosinase-related protein 2 (Ad-hTRP2) induces protective but not therapeutic cellular immunity against growth of transplanted B16 melanoma cells. Here, we additionally applied CpG DNA and synthetic double-stranded RNA, which activate the innate immune system via Toll-like receptors (TLR). Both adenoviral vaccination and peritumoral injections of TLR ligands were required for rejection of established B16 melanoma in the skin. To more closely mimic the clinical situation in patients with melanoma, we evaluated this combined immunotherapeutic strategy in genetically modified mice, which overexpress hepatocyte growth factor (HGF) and carry an oncogenic mutation in the cyclin-dependent kinase 4 (CDK4)(R24C). HGF x CDK4(R24C) mice rapidly develop multiple invasive melanomas in the skin following neonatal carcinogen treatment, which spontaneously metastasize to lymph nodes and lungs. Vaccination with Ad-hTRP2 followed by injections of TLR ligands resulted in delayed growth of autochthonous primary melanomas in the skin and reduction in the number of spontaneous lung metastases but did not induce tumor regression. Carcinogen-treated HGF x CDK4(R24C) mice bearing multiple autochthonous melanomas did not reject transplanted B16 melanoma despite treatment with Ad-hTRP2 and TLR ligands, suggesting the development of tumor immunotolerance. Further investigations in our novel genetic melanoma model may help to better understand the role of the immune system in the pathogenesis and treatment of this life-threatening disease.

  5. Peroxicretion: a novel secretion pathway in the eukaryotic cell

    NARCIS (Netherlands)

    Sagt, C.M.J.; Ten Haaft, P.J.T; Minneboo, I.M.; Hartog, M.P.; Damveld, R.A.; Van der Laan, J.M.; Akeroyd, M; Wenzel, T.J.; Luesken, F.A.; Veenhuis, M.; Van der Klei, I.; De Winde, J.H.

    2009-01-01

    Background: Enzyme production in microbial cells has been limited to secreted enzymes or intracellular enzymes followed by expensive down stream processing. Extracellular enzymes consists mainly of hydrolases while intracellular enzymes exhibit a much broader diversity. If these intracellular enzyme

  6. Peroxicretion : a novel secretion pathway in the eukaryotic cell

    NARCIS (Netherlands)

    Sagt, Cees M.J.; Haaft, Peter J. ten; Minneboo, Ingeborg M.; Hartog, Miranda P.; Damveld, Robbert A.; Laan, Jan Metske van der; Akeroyd, Michiel; Wenzel, Thibaut J.; Luesken, Francisca A.; Veenhuis, Marten; Klei, Ida van der; Winde, Johannes H. de

    2009-01-01

    Background: Enzyme production in microbial cells has been limited to secreted enzymes or intracellular enzymes followed by expensive down stream processing. Extracellular enzymes consists mainly of hydrolases while intracellular enzymes exhibit a much broader diversity. If these intracellular enzyme

  7. Influence of autochthonous micro-organisms on sorption and remobilization of technetium and selenium. Final report; Einfluss der autochthonen Mikroflora auf die Sorption und Remobilisierung des Technetiums und des Selens. Abschlussbericht

    Energy Technology Data Exchange (ETDEWEB)

    Maue, G.; Stroetmann, I.; Dott, W. [Technische Univ. Berlin (Germany). Fachgebiet Umwelthygiene; Taute, T.; Winkler, A.; Pekdeger, A. [Freie Univ. Berlin (Germany). Fachrichtung Rohstoff- und Umweltgeologie

    1996-10-31

    Within this research project the influence of autochthonous mirco-organisms on immobilization and remobilization of Technetium and Selenium was investigated. Both redoxsensitive radionuclides are part of the waste of nuclear fuel (Tc app. 6%). Former investigations have shown, that immobilization behaviour of both elements could be influenced by micro-organisms. It has not been known, if the autochthonous (or in situ) organisms from greater depth do also have an influence on radionuclide mobility. The autochthonous populations of micro-organisms in deep sediments and their influence on the migration of Tc and Se were investigated in this study. For this reason recirculation column experiments were carried out. Absolutely sterile and anaerobic handling was necessary for the sampling and the further treatment of the sediments and waters used in the experiments. Therefor special methods for sampling, storage and handling had been developed. The results of recirculation column test with autochthonous micro-organisms were compared with sterile parallel tests and were verified with the results of an elaborated version of the hydrogeochemical equilibration code PHREEQE. It was shown that the autochthonous micro-organisms had only very little influence on the migration behaviour. The reason is the very low population (less than 10 E+6 CFU). Nevertheless it has to be taken into consideration, that conventional laboratory experiments for the estimation of the retention capacities of sediments for hazardous waste lead to an overestimation, if the sediments are contaminated with allochthonous micro-organisms (CFU=colony forming units). (orig.) [Deutsch] In dem Forschungsvorhaben wurde der Einfluss der autochthonen Mikroorgansimen auf die Mobilitaet von Technetium und Selen untersucht. Beide redoxsensitiven Radionuklide sind im Abfall von Kernbrennelementen enthalten (Tc ca. 6%). Aus vorangegangenen Forschungsarbeiten ist bekannt, dass die Mobilitaet der beiden Elemente durch

  8. Doing Diversity

    DEFF Research Database (Denmark)

    Just, Sine Nørholm; Christiansen, Tanja Juul

    2012-01-01

    Questions of agency in text–audience relations are less studied than other aspects of rhetorical agency. We suggest conceptualizing and analyzing the relationship between texts and audiences from the perspective of performativity, as it has been developed by Judith Butler. Thus, we argue that tex...... demonstrate the explanatory potential of the performative framework. Subsequently, we discuss how the concept of personae may provide a basis for alternatives to the restrictive positioning that currently dominates diversity management rhetoric....

  9. Teaching Diversity

    OpenAIRE

    Kay Young McChesney

    2015-01-01

    This article is targeted to faculty teaching race and ethnicity, racism, diversity, and multicultural courses. Many students equate race with skin color. The premise of this article is that to teach students about the social construction of race, teachers must first know enough science to teach students that race is not biological. This article examines the biology of race by showing how advances in DNA sequencing led ...

  10. A versatile selection system for folding competent proteins using genetic complementation in a eukaryotic host

    DEFF Research Database (Denmark)

    Lyngsø, C.; Kjaerulff, S.; Muller, S.

    2010-01-01

    Recombinant expression of native or modified eukaryotic proteins is pivotal for structural and functional studies and for industrial and pharmaceutical production of proteins. However, it is often impeded by the lack of proper folding. Here, we present a stringent and broadly applicable eukaryotic...... demonstrated using a complex insertion mutant library of TNF-alpha, from which different folding competent mutant proteins were uncovered....

  11. Large-scale analysis of phosphorylation site occupancy in eukaryotic proteins

    DEFF Research Database (Denmark)

    Rao, R Shyama Prasad; Møller, Ian Max

    2012-01-01

    maximum randomness. An analysis of phosphorylation motifs indicated that just 40 motifs and a much lower number of associated kinases might account for nearly 50% of the known phosphorylations in eukaryotic proteins. Our results provide a broad picture of the phosphorylation sites in eukaryotic proteins....

  12. Ecological Diversity in South American Mammals: Their Geographical Distribution Shows Variable Associations with Phylogenetic Diversity and Does Not Follow the Latitudinal Richness Gradient.

    Directory of Open Access Journals (Sweden)

    Paula Nilda Fergnani

    Full Text Available The extent to which the latitudinal gradient in species richness may be paralleled by a similar gradient of increasing functional or phylogenetic diversity is a matter of controversy. We evaluated whether taxonomic richness (TR is informative in terms of ecological diversity (ED, an approximation to functional diversity and phylogenetic diversity (AvPD using data on 531 mammal species representing South American old autochthonous (marsupials, xenarthrans, mid-Cenozoic immigrants (hystricognaths, primates and newcomers (carnivorans, artiodactyls. If closely related species are ecologically more similar than distantly related species, AvPD will be a strong predictor of ED; however, lower ED than predicted from AvPD may be due to species retaining most of their ancestral characters, suggesting niche conservatism. This pattern could occur in tropical rainforests for taxa of tropical affinity (old autochthonous and mid-Cenozoic immigrants and in open and arid habitats for newcomers. In contrast, higher ED than expected from AvPD could occur, possibly in association with niche evolution, in arid and open habitats for taxa of tropical affinity and in forested habitats for newcomers. We found that TR was a poor predictor of ED and AvPD. After controlling for TR, there was considerable variability in the extent to which AvPD accounted for ED. Taxa of tropical affinity did not support the prediction of ED deficit within tropical rainforests, rather, they showed a mosaic of regions with an excess of ED interspersed with zones of ED deficit within the tropics; newcomers showed ED deficit in arid and open regions. Some taxa of tropical affinity showed excess of ED in tropical desert areas (hystricognaths or temperate semideserts (xenarthrans; newcomers showed excess of ED at cold-temperate latitudes in the Northern Hemisphere. This result suggests that extreme climatic conditions at both temperate and tropical latitudes may have promoted niche evolution in

  13. Ecological Diversity in South American Mammals: Their Geographical Distribution Shows Variable Associations with Phylogenetic Diversity and Does Not Follow the Latitudinal Richness Gradient.

    Science.gov (United States)

    Fergnani, Paula Nilda; Ruggiero, Adriana

    2015-01-01

    The extent to which the latitudinal gradient in species richness may be paralleled by a similar gradient of increasing functional or phylogenetic diversity is a matter of controversy. We evaluated whether taxonomic richness (TR) is informative in terms of ecological diversity (ED, an approximation to functional diversity) and phylogenetic diversity (AvPD) using data on 531 mammal species representing South American old autochthonous (marsupials, xenarthrans), mid-Cenozoic immigrants (hystricognaths, primates) and newcomers (carnivorans, artiodactyls). If closely related species are ecologically more similar than distantly related species, AvPD will be a strong predictor of ED; however, lower ED than predicted from AvPD may be due to species retaining most of their ancestral characters, suggesting niche conservatism. This pattern could occur in tropical rainforests for taxa of tropical affinity (old autochthonous and mid-Cenozoic immigrants) and in open and arid habitats for newcomers. In contrast, higher ED than expected from AvPD could occur, possibly in association with niche evolution, in arid and open habitats for taxa of tropical affinity and in forested habitats for newcomers. We found that TR was a poor predictor of ED and AvPD. After controlling for TR, there was considerable variability in the extent to which AvPD accounted for ED. Taxa of tropical affinity did not support the prediction of ED deficit within tropical rainforests, rather, they showed a mosaic of regions with an excess of ED interspersed with zones of ED deficit within the tropics; newcomers showed ED deficit in arid and open regions. Some taxa of tropical affinity showed excess of ED in tropical desert areas (hystricognaths) or temperate semideserts (xenarthrans); newcomers showed excess of ED at cold-temperate latitudes in the Northern Hemisphere. This result suggests that extreme climatic conditions at both temperate and tropical latitudes may have promoted niche evolution in mammals.

  14. Bacterial Vesicle Secretion and the Evolutionary Origin of the Eukaryotic Endomembrane System.

    Science.gov (United States)

    Gould, Sven B; Garg, Sriram G; Martin, William F

    2016-07-01

    Eukaryotes possess an elaborate endomembrane system with endoplasmic reticulum, nucleus, Golgi, lysosomes, peroxisomes, autophagosomes, and dynamic vesicle traffic. Theories addressing the evolutionary origin of eukaryotic endomembranes have overlooked the outer membrane vesicles (OMVs) that bacteria, archaea, and mitochondria secrete into their surroundings. We propose that the eukaryotic endomembrane system originated from bacterial OMVs released by the mitochondrial ancestor within the cytosol of its archaeal host at eukaryote origin. Confined within the host's cytosol, OMVs accumulated naturally, fusing either with each other or with the host's plasma membrane. This matched the host's archaeal secretory pathway for cotranslational protein insertion with outward bound mitochondrial-derived vesicles consisting of bacterial lipids, forging a primordial, secretory endoplasmic reticulum as the cornerstone of the eukaryotic endomembrane system. VIDEO ABSTRACT.

  15. Diverse Multilateralism

    DEFF Research Database (Denmark)

    Wuthnow, Joel; Li, Xin; Qi, Lingling

    2012-01-01

    This article addresses Chinas multilateral diplomacy by identifying four distinct strategies: watching, engaging, circumventing, and shaping. The typology builds on two literatures: power transition theory, and the more recent “assertiveness” discourse in the West. Drawing from a range of cases...... in both the economic and security domains, the article argues that China’s multilateralism is diverse, and that it cannot be un-problematically characterized as either status-quo or revisionist in nature. However, the general trend appears to be towards engagement, but with an assertive tact as China...

  16. Exposing diversity

    DEFF Research Database (Denmark)

    Nørtoft, Kamilla; Nordentoft, Helle Merete

    . A prominent research theme in health care studies is, therefore, to explicate the gap between theory and practice. The question this paper addresses is how a learning environment can be designed to bridge this theory-practice gap, expose the differences in situated interactions and qualify health...... in the homes of older people and in pedagogical institutions targeting older people. In the paper we look at the potentials and challenges in working with ethnographic video narratives as a pedagogical tool. Our findings indicate that the use of video narratives has the potential to expose the diversity...

  17. Hidden Diversity Revealed : Genomic, Transcriptomic and Functional Studies of Diplomonads

    OpenAIRE

    2012-01-01

    The diplomonads are a diverse group of eukaryotic microbes found in oxygen limited environments such as the intestine of animals were they may cause severe disease. Among them, the prominent human parasite Giardia intestinalis non-invasively colonizes the small intestine of humans and animals where it induces the gastrointestinal disease giardiasis. Two of the eight genetic groups of G. intestinalis, assemblage A and B, are known to infect humans and have zoonotic potential. At the start of p...

  18. The Evolutionary History of MAPL (Mitochondria-Associated Protein Ligase and Other Eukaryotic BAM/GIDE Domain Proteins.

    Directory of Open Access Journals (Sweden)

    Jeremy G Wideman

    Full Text Available MAPL (mitochondria-associated protein ligase, also called MULAN/GIDE/MUL1 is a multifunctional mitochondrial outer membrane protein found in human cells that contains a unique BAM (beside a membrane domain and a C-terminal RING-finger domain. MAPL has been implicated in several processes that occur in animal cells such as NF-kB activation, innate immunity and antiviral signaling, suppression of PINK1/parkin defects, mitophagy in skeletal muscle, and caspase-dependent apoptosis. Previous studies demonstrated that the BAM domain is present in diverse organisms in which most of these processes do not occur, including plants, archaea, and bacteria. Thus the conserved function of MAPL and its BAM domain remains an open question. In order to gain insight into its conserved function, we investigated the evolutionary origins of MAPL by searching for homologues in predicted proteomes of diverse eukaryotes. We show that MAPL proteins with a conserved BAM-RING architecture are present in most animals, protists closely related to animals, a single species of fungus, and several multicellular plants and related green algae. Phylogenetic analysis demonstrated that eukaryotic MAPL proteins originate from a common ancestor and not from independent horizontal gene transfers from bacteria. We also determined that two independent duplications of MAPL occurred, one at the base of multicellular plants and another at the base of vertebrates. Although no other eukaryote genome examined contained a verifiable MAPL orthologue, BAM domain-containing proteins were identified in the protists Bigelowiella natans and Ectocarpus siliculosis. Phylogenetic analyses demonstrated that these proteins are more closely related to prokaryotic BAM proteins and therefore likely arose from independent horizontal gene transfers from bacteria. We conclude that MAPL proteins with BAM-RING architectures have been present in the holozoan and viridiplantae lineages since their very beginnings

  19. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity

    Directory of Open Access Journals (Sweden)

    Mitali Das

    2014-01-01

    Full Text Available As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM 2–7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the “MCM paradox.” Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  20. Structural genomics of eukaryotic targets at a laboratory scale.

    Science.gov (United States)

    Busso, Didier; Poussin-Courmontagne, Pierre; Rosé, David; Ripp, Raymond; Litt, Alain; Thierry, Jean-Claude; Moras, Dino

    2005-01-01

    Structural genomics programs are distributed worldwide and funded by large institutions such as the NIH in United-States, the RIKEN in Japan or the European Commission through the SPINE network in Europe. Such initiatives, essentially managed by large consortia, led to technology and method developments at the different steps required to produce biological samples compatible with structural studies. Besides specific applications, method developments resulted mainly upon miniaturization and parallelization. The challenge that academic laboratories faces to pursue structural genomics programs is to produce, at a higher rate, protein samples. The Structural Biology and Genomics Department (IGBMC - Illkirch - France) is implicated in a structural genomics program of high eukaryotes whose goal is solving crystal structures of proteins and their complexes (including large complexes) related to human health and biotechnology. To achieve such a challenging goal, the Department has established a medium-throughput pipeline for producing protein samples suitable for structural biology studies. Here, we describe the setting up of our initiative from cloning to crystallization and we demonstrate that structural genomics may be manageable by academic laboratories by strategic investments in robotic and by adapting classical bench protocols and new developments, in particular in the field of protein expression, to parallelization.

  1. Rule-based design of synthetic transcription factors in eukaryotes.

    Science.gov (United States)

    Purcell, Oliver; Peccoud, Jean; Lu, Timothy K

    2014-10-17

    To design and build living systems, synthetic biologists have at their disposal an increasingly large library of naturally derived and synthetic parts. These parts must be combined together in particular orders, orientations, and spacings to achieve desired functionalities. These structural constraints can be viewed as grammatical rules describing how to assemble parts together into larger functional units. Here, we develop a grammar for the design of synthetic transcription factors (sTFs) in eukaryotic cells and implement it within GenoCAD, a Computer-Aided Design (CAD) software for synthetic biology. Knowledge derived from experimental evidence was captured in this grammar to guide the user to create designer transcription factors that should operate as intended. The grammar can be easily updated and refined as our experience with using sTFs in different contexts increases. In combination with grammars that define other synthetic systems, we anticipate that this work will enable the more reliable, efficient, and automated design of synthetic cells with rich functionalities.

  2. MCM Paradox: Abundance of Eukaryotic Replicative Helicases and Genomic Integrity.

    Science.gov (United States)

    Das, Mitali; Singh, Sunita; Pradhan, Satyajit; Narayan, Gopeshwar

    2014-01-01

    As a crucial component of DNA replication licensing system, minichromosome maintenance (MCM) 2-7 complex acts as the eukaryotic DNA replicative helicase. The six related MCM proteins form a heterohexamer and bind with ORC, CDC6, and Cdt1 to form the prereplication complex. Although the MCMs are well known as replicative helicases, their overabundance and distribution patterns on chromatin present a paradox called the "MCM paradox." Several approaches had been taken to solve the MCM paradox and describe the purpose of excess MCMs distributed beyond the replication origins. Alternative functions of these MCMs rather than a helicase had also been proposed. This review focuses on several models and concepts generated to solve the MCM paradox coinciding with their helicase function and provides insight into the concept that excess MCMs are meant for licensing dormant origins as a backup during replication stress. Finally, we extend our view towards the effect of alteration of MCM level. Though an excess MCM constituent is needed for normal cells to withstand stress, there must be a delineation of the threshold level in normal and malignant cells. This review also outlooks the future prospects to better understand the MCM biology.

  3. Searching for the role of protein phosphatases in eukaryotic microorganisms

    Directory of Open Access Journals (Sweden)

    da-Silva A.M.

    1999-01-01

    Full Text Available Preference for specific protein substrates together with differential sensitivity to activators and inhibitors has allowed classification of serine/threonine protein phosphatases (PPs into four major types designated types 1, 2A, 2B and 2C (PP1, PP2A, PP2B and PP2C, respectively. Comparison of sequences within their catalytic domains has indicated that PP1, PP2A and PP2B are members of the same gene family named PPP. On the other hand, the type 2C enzyme does not share sequence homology with the PPP members and thus represents another gene family, known as PPM. In this report we briefly summarize some of our studies about the role of serine/threonine phosphatases in growth and differentiation of three different eukaryotic models: Blastocladiella emersonii, Neurospora crassa and Dictyostelium discoideum. Our observations suggest that PP2C is the major phosphatase responsible for dephosphorylation of amidotransferase, an enzyme that controls cell wall synthesis during Blastocladiella emersonii zoospore germination. We also report the existence of a novel acid- and thermo-stable protein purified from Neurospora crassa mycelia, which specifically inhibits the PP1 activity of this fungus and mammals. Finally, we comment on our recent results demonstrating that Dictyostelium discoideum expresses a gene that codes for PP1, although this activity has never been demonstrated biochemically in this organism.

  4. Chloroplast membrane transport: interplay of prokaryotic and eukaryotic traits.

    Science.gov (United States)

    Vothknecht, Ute C; Soll, Jürgen

    2005-07-18

    Chloroplasts are specific plant organelles of prokaryotic origin. They are separated from the surrounding cell by a double membrane, which represents an effective barrier for the transport of metabolites and proteins. Specific transporters in the inner envelope membrane have been described, which facilitate the exchange of metabolites. In contrast, the outer envelope has been viewed for a long time as a molecular sieve that offers a mere size constriction to the passage of molecules. This view has been challenged lately, and a number of specific and regulated pore proteins of the outer envelope (OEPs) have been identified. These pores seem to have originated by adaptation of outer membrane proteins of the cyanobacterial ancestor of the chloroplast. In a similar fashion, the transport of proteins across the two envelope membranes is achieved by two hetero-oligomeric protein complexes called Toc (translocon in the outer envelope of chloroplasts) and Tic (translocon in the inner envelope of chloroplasts). The phylogenetic provenance of the translocon components is less clear, but at least the channel protein of the Toc translocon is of cyanobacterial origin. Characteristic of cyanobacteria and chloroplasts is furthermore a specialized internal membrane system, the thylakoids, on which the components of the photosynthetic machinery are located. Despite the importance of this membrane, very little is known about its phylogenetic origin or the manner of its synthesis. Vipp1 appears to be a ubiquitous component of thylakoid formation, while in chloroplasts of land plants, additionally a vesicle transport system of eukaryotic origin might be involved in this process.

  5. A new inhibitor of apoptosis from vaccinia virus and eukaryotes.

    Directory of Open Access Journals (Sweden)

    Caroline Gubser

    2007-02-01

    Full Text Available A new apoptosis inhibitor is described from vaccinia virus, camelpox virus, and eukaryotic cells. The inhibitor is a hydrophobic, multiple transmembrane protein that is resident in the Golgi and is named GAAP (Golgi anti-apoptotic protein. Stable expression of both viral GAAP (v-GAAP and human GAAP (h-GAAP, which is expressed in all human tissues tested, inhibited apoptosis induced by intrinsic and extrinsic apoptotic stimuli. Conversely, knockout of h-GAAP by siRNA induced cell death by apoptosis. v-GAAP and h-GAAP display overlapping functions as shown by the ability of v-GAAP to complement for the loss of h-GAAP. Lastly, deletion of the v-GAAP gene from vaccinia virus did not affect virus replication in cell culture, but affected virus virulence in a murine infection model. This study identifies a new regulator of cell death that is highly conserved in evolution from plants to insects, amphibians, mammals, and poxviruses.

  6. The emerging roles of inositol pyrophosphates in eukaryotic cell physiology

    Indian Academy of Sciences (India)

    Swarna Gowri Thota; Rashna Bhandari

    2015-09-01

    Inositol pyrophosphates are water soluble derivatives of inositol that contain pyrophosphate or diphosphate moieties in addition to monophosphates. The best characterised inositol pyrophosphates, are IP7 (diphosphoinositol pentakisphosphate or PP-IP5), and IP8 (bisdiphosphoinositol tetrakisphosphate or (PP)2-IP4). These energy-rich small molecules are present in all eukaryotic cells, from yeast to mammals, and are involved in a wide range of cellular functions including apoptosis, vesicle trafficking, DNA repair, osmoregulation, phosphate homeostasis, insulin sensitivity, immune signalling, cell cycle regulation, and ribosome synthesis. Identified more than 20 years ago, there is still only a rudimentary understanding of the mechanisms by which inositol pyrophosphates participate in these myriad pathways governing cell physiology and homeostasis. The unique stereochemical and bioenergetic properties these molecules possess as a consequence of the presence of one or two pyrophosphate moieties in the vicinity of densely packed monophosphates are likely to form the molecular basis for their participation in multiple signalling and metabolic pathways. The aim of this review is to provide first time researchers in this area with an introduction to inositol pyrophosphates and a comprehensive overview on their cellular functions.

  7. Characterization of Binding Sites of Eukaryotic Transcription Factors

    Institute of Scientific and Technical Information of China (English)

    Jiang Qian; Jimmy Lin; Donald J. Zack

    2006-01-01

    To explore the nature of eukaryotic transcription factor (TF) binding sites and determine how they differ from surrounding DNA sequences, we examined four features associated with DNA binding sites: G+C content, pattern complexity,palindromic structure, and Markov sequence ordering. Our analysis of the regulatory motifs obtained from the TRANSFAC database, using yeast intergenic sequences as background, revealed that these four features show variable enrichment in motif sequences. For example, motif sequences were more likely to have palindromic structure than were background sequences. In addition, these features were tightly localized to the regulatory motifs, indicating that they are a property of the motif sequences themselves and are not shared by the general promoter "environment" in which the regulatory motifs reside. By breaking down the motif sequences according to the TF classes to which they bind, more specific associations were identified. Finally, we found that some correlations, such as G+C content enrichment, were species-specific, while others, such as complexity enrichment, were universal across the species examined. The quantitative analysis provided here should increase our understanding of protein-DNA interactions and also help facilitate the discovery of regulatory motifs through bioinformatics.

  8. Circular permutation of a synthetic eukaryotic chromosome with the telomerator

    Science.gov (United States)

    Mitchell, Leslie A.; Boeke, Jef D.

    2014-01-01

    Chromosome engineering is a major focus in the fields of systems biology, genetics, synthetic biology, and the functional analysis of genomes. Here, we describe the “telomerator,” a new synthetic biology device for use in Saccharomyces cerevisiae. The telomerator is designed to inducibly convert circular DNA molecules into mitotically stable, linear chromosomes replete with functional telomeres in vivo. The telomerator cassette encodes convergent yeast telomere seed sequences flanking the I-SceI homing endonuclease recognition site in the center of an intron artificially transplanted into the URA3 selectable/counterselectable auxotrophic marker. We show that inducible expression of the homing endonuclease efficiently generates linear molecules, identified by using a simple plate-based screening method. To showcase its functionality and utility, we use the telomerator to circularly permute a synthetic yeast chromosome originally constructed as a circular molecule, synIXR, to generate 51 linear variants. Many of the derived linear chromosomes confer unexpected phenotypic properties. This finding indicates that the telomerator offers a new way to study the effects of gene placement on chromosomes (i.e., telomere proximity). However, that the majority of synIXR linear derivatives support viability highlights inherent tolerance of S. cerevisiae to changes in gene order and overall chromosome structure. The telomerator serves as an important tool to construct artificial linear chromosomes in yeast; the concept can be extended to other eukaryotes. PMID:25378705

  9. A general strategy to construct small molecule biosensors in eukaryotes

    Science.gov (United States)

    Feng, Justin; Jester, Benjamin W; Tinberg, Christine E; Mandell, Daniel J; Antunes, Mauricio S; Chari, Raj; Morey, Kevin J; Rios, Xavier; Medford, June I; Church, George M; Fields, Stanley; Baker, David

    2015-01-01

    Biosensors for small molecules can be used in applications that range from metabolic engineering to orthogonal control of transcription. Here, we produce biosensors based on a ligand-binding domain (LBD) by using a method that, in principle, can be applied to any target molecule. The LBD is fused to either a fluorescent protein or a transcriptional activator and is destabilized by mutation such that the fusion accumulates only in cells containing the target ligand. We illustrate the power of this method by developing biosensors for digoxin and progesterone. Addition of ligand to yeast, mammalian, or plant cells expressing a biosensor activates transcription with a dynamic range of up to ~100-fold. We use the biosensors to improve the biotransformation of pregnenolone to progesterone in yeast and to regulate CRISPR activity in mammalian cells. This work provides a general methodology to develop biosensors for a broad range of molecules in eukaryotes. DOI: http://dx.doi.org/10.7554/eLife.10606.001 PMID:26714111

  10. Discrepancy variation of dinucleotide microsatellite repeats in eukaryotic genomes.

    Science.gov (United States)

    Gao, Huan; Cai, Shengli; Yan, Binlun; Chen, Baiyao; Yu, Fei

    2009-01-01

    To address whether there are differences of variation among repeat motif types and among taxonomic groups, we present here an analysis of variation and correlation of dinucleotide microsatellite repeats in eukaryotic genomes. Ten taxonomic groups were compared, those being primates, mammalia (excluding primates and rodentia), rodentia, birds, fish, amphibians and reptiles, insects, molluscs, plants and fungi, respectively. The data used in the analysis is from the literature published in the Journal of Molecular Ecology Notes. Analysis of variation reveals that there are no significant differences between AC and AG repeat motif types. Moreover, the number of alleles correlates positively with the copy number in both AG and AC repeats. Similar conclusions can be obtained from each taxonomic group. These results strongly suggest that the increase of SSR variation is almost linear with the increase of the copy number of each repeat motif. As well, the results suggest that the variability of SSR in the genomes of low-ranking species seem to be more than that of high-ranking species, excluding primates and fungi.

  11. Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

    DEFF Research Database (Denmark)

    Irimia, Manuel; Rukov, Jakob Lewin; Penny, David;

    2007-01-01

    Alternative splicing has been reported in various eukaryotic groups including plants, apicomplexans, diatoms, amoebae, animals and fungi. However, whether widespread alternative splicing has evolved independently in the different eukaryotic groups or was inherited from their last common ancestor...

  12. Evaluation of DNA extraction methods for freshwater eukaryotic microalgae.

    Science.gov (United States)

    Eland, Lucy E; Davenport, Russell; Mota, Cesar R

    2012-10-15

    The use of molecular methods to investigate microalgal communities of natural and engineered freshwater resources is in its infancy, with the majority of previous studies carried out by microscopy. Inefficient or differential DNA extraction of microalgal community members can lead to bias in downstream community analysis. Three commercially available DNA extraction kits have been tested on a range of pure culture freshwater algal species with diverse cell walls and mixed algal cultures taken from eutrophic waste stabilization ponds (WSP). DNA yield and quality were evaluated, along with DNA suitability for amplification of 18S rRNA gene fragments by polymerase chain reaction (PCR). QiagenDNeasy(®) Blood and Tissue kit (QBT), was found to give the highest DNA yields and quality. Denaturant Gradient Gel Electrophoresis (DGGE) was used to assess the diversity of communities from which DNA was extracted. No significant differences were found among kits when assessing diversity. QBT is recommended for use with WSP samples, a conclusion confirmed by further testing on communities from two tropical WSP systems. The fixation of microalgal samples with ethanol prior to DNA extraction was found to reduce yields as well as diversity and is not recommended.

  13. Diversity Measures

    Directory of Open Access Journals (Sweden)

    MSc. Mentor Ademaj

    2012-06-01

    Full Text Available Diversity measures are a type of non-criminal measures foreseen in the Chapter IV of the Code of Juvenile Justice, which may be imposed on juvenile perpetrators of criminal acts. These measures can be applied in cases of minor offenses, for which is foreseen the criminal sanction with a fine or imprisonment up to three years or for criminal offenses committed by negligence for which is foreseen the sentence up to five years of imprisonment, except those cases that result in death. With the imposition of these measures is intended to prevent criminal proceedings against juveniles whenever is possible, rehabilitation and reintegration of juvenile in his/her community and the prevention of recidivist behaviour. Competent authority to impose them is the public prosecutor, the juvenile judge and juvenile court. And they are executed by the Kosovo Correctional Service.

  14. Optimizing diversity

    CERN Document Server

    Frein, Yannick; Sebo, Andras

    2007-01-01

    We consider the problem of minimizing the size of a family of sets G such that every subset of 1,...,n can be written as a disjoint union of at most k members of G, where k and n are given numbers. This problem originates in a real-world application aiming at the diversity of industrial production. At the same time, the minimum of G so that every subset of 1,...,n is the union of two sets in G has been asked by Erdos and studied recently by Furedi and Katona without requiring the disjointness of the sets. A simple construction providing a feasible solution is conjectured to be optimal for this problem for all values of n and k and regardless of the disjointness requirement; we prove this conjecture in special cases including all (n,k) for which n <= 3k holds, and some individual values of n and k.

  15. Phenolic characterization and antioxidant capacity of ten autochthonous vines grown in southern Italy / Caratterizzazione fenolica e potere antiossidante di dieci vitigni autoctoni allevati nel Sud Italia

    Directory of Open Access Journals (Sweden)

    Milella Rosa Anna

    2016-01-01

    phenolic profile of ten autochthonous vines grown in two different areas of South Italy. By spectrophotometric analysis it has been possible to analyze quali-quantitive characteristics of such substances, while by ORAC method (Oxygen Radical Absorbance Capacity we have measured, in vitro, the antioxidant action. The oenological potential has been evaluated, in relation to polyphenols content, of ten Vitis Vinifera varieties belonging to autochthonous vines of Basilicata, grown in espalier and tent in two areas: in the vineyard of Val d'Agri (PZ, in Basilicata, and in South-East Bari area, in Rutigliano (Ba, in Puglia. The ten varieties belonging to Southern Italy autochthonous vines include four black grapes and six white grapes. Data obtained on total polyphenols content, view of the considerable variability encountered, allow us to affirm that the polyphenolic ripening of wine grapes, thus the reaching of the maximum level, is very influenced by the “terroir”, defined as the cultivation area or environment, by season trend, by cultivation techniques and by the different vines nutritional conditions. The same holds true for the antioxidant activity of the 10 wine grapes varieties of this study, since it is closely related to the polyphenol

  16. Computational identification of four spliceosomal snRNAs from the deep-branching eukaryote Giardia intestinalis.

    Directory of Open Access Journals (Sweden)

    Xiaowei Sylvia Chen

    Full Text Available RNAs processing other RNAs is very general in eukaryotes, but is not clear to what extent it is ancestral to eukaryotes. Here we focus on pre-mRNA splicing, one of the most important RNA-processing mechanisms in eukaryotes. In most eukaryotes splicing is predominantly catalysed by the major spliceosome complex, which consists of five uridine-rich small nuclear RNAs (U-snRNAs and over 200 proteins in humans. Three major spliceosomal introns have been found experimentally in Giardia; one Giardia U-snRNA (U5 and a number of spliceosomal proteins have also been identified. However, because of the low sequence similarity between the Giardia ncRNAs and those of other eukaryotes, the other U-snRNAs of Giardia had not been found. Using two computational methods, candidates for Giardia U1, U2, U4 and U6 snRNAs were identified in this study and shown by RT-PCR to be expressed. We found that identifying a U2 candidate helped identify U6 and U4 based on interactions between them. Secondary structural modelling of the Giardia U-snRNA candidates revealed typical features of eukaryotic U-snRNAs. We demonstrate a successful approach to combine computational and experimental methods to identify expected ncRNAs in a highly divergent protist genome. Our findings reinforce the conclusion that spliceosomal small-nuclear RNAs existed in the last common ancestor of eukaryotes.

  17. Kingdoms Protozoa and Chromista and the eozoan root of the eukaryotic tree.

    Science.gov (United States)

    Cavalier-Smith, Thomas

    2010-06-23

    I discuss eukaryotic deep phylogeny and reclassify the basal eukaryotic kingdom Protozoa and derived kingdom Chromista in the light of multigene trees. I transfer the formerly protozoan Heliozoa and infrakingdoms Alveolata and Rhizaria into Chromista, which is sister to kingdom Plantae and arguably originated by synergistic double internal enslavement of green algal and red algal cells. I establish new subkingdoms (Harosa; Hacrobia) for the expanded Chromista. The protozoan phylum Euglenozoa differs immensely from other eukaryotes in its nuclear genome organization (trans-spliced multicistronic transcripts), mitochondrial DNA organization, cytochrome c-type biogenesis, cell structure and arguably primitive mitochondrial protein-import and nuclear DNA prereplication machineries. The bacteria-like absence of mitochondrial outer-membrane channel Tom40 and DNA replication origin-recognition complexes from trypanosomatid Euglenozoa roots the eukaryotic tree between Euglenozoa and all other eukaryotes (neokaryotes), or within Euglenozoa. Given their unique properties, I segregate Euglenozoa from infrakingdom Excavata (now comprising only phyla Percolozoa, Loukozoa, Metamonada), grouping infrakingdoms Euglenozoa and Excavata as the ancestral protozoan subkingdom Eozoa. I place phylum Apusozoa within the derived protozoan subkingdom Sarcomastigota. Clarifying early eukaryote evolution requires intensive study of properties distinguishing Euglenozoa from neokaryotes and Eozoa from neozoa (eukaryotes except Eozoa; ancestrally defined by haem lyase).

  18. Horizontal transfer of a eukaryotic plastid-targeted protein gene to cyanobacteria

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    Keeling Patrick J

    2007-06-01

    Full Text Available Abstract Background Horizontal or lateral transfer of genetic material between distantly related prokaryotes has been shown to play a major role in the evolution of bacterial and archaeal genomes, but exchange of genes between prokaryotes and eukaryotes is not as well understood. In particular, gene flow from eukaryotes to prokaryotes is rarely documented with strong support, which is unusual since prokaryotic genomes appear to readily accept foreign genes. Results Here, we show that abundant marine cyanobacteria in the related genera Synechococcus and Prochlorococcus acquired a key Calvin cycle/glycolytic enzyme from a eukaryote. Two non-homologous forms of fructose bisphosphate aldolase (FBA are characteristic of eukaryotes and prokaryotes respectively. However, a eukaryotic gene has been inserted immediately upstream of the ancestral prokaryotic gene in several strains (ecotypes of Synechococcus and Prochlorococcus. In one lineage this new gene has replaced the ancestral gene altogether. The eukaryotic gene is most closely related to the plastid-targeted FBA from red algae. This eukaryotic-type FBA once replaced the plastid/cyanobacterial type in photosynthetic eukaryotes, hinting at a possible functional advantage in Calvin cycle reactions. The strains that now possess this eukaryotic FBA are scattered across the tree of Synechococcus and Prochlorococcus, perhaps because the gene has been transferred multiple times among cyanobacteria, or more likely because it has been selectively retained only in certain lineages. Conclusion A gene for plastid-targeted FBA has been transferred from red algae to cyanobacteria, where it has inserted itself beside its non-homologous, functional analogue. Its current distribution in Prochlorococcus and Synechococcus is punctate, suggesting a complex history since its introduction to this group.

  19. Energy metabolism among eukaryotic anaerobes in light of Proterozoic ocean chemistry.

    Science.gov (United States)

    Mentel, Marek; Martin, William

    2008-08-27

    Recent years have witnessed major upheavals in views about early eukaryotic evolution. One very significant finding was that mitochondria, including hydrogenosomes and the newly discovered mitosomes, are just as ubiquitous and defining among eukaryotes as the nucleus itself. A second important advance concerns the readjustment, still in progress, about phylogenetic relationships among eukaryotic groups and the roughly six new eukaryotic supergroups that are currently at the focus of much attention. From the standpoint of energy metabolism (the biochemical means through which eukaryotes gain their ATP, thereby enabling any and all evolution of other traits), understanding of mitochondria among eukaryotic anaerobes has improved. The mainstream formulations of endosymbiotic theory did not predict the ubiquity of mitochondria among anaerobic eukaryotes, while an alternative hypothesis that specifically addressed the evolutionary origin of energy metabolism among eukaryotic anaerobes did. Those developments in biology have been paralleled by a similar upheaval in the Earth sciences regarding views about the prevalence of oxygen in the oceans during the Proterozoic (the time from ca 2.5 to 0.6 Ga ago). The new model of Proterozoic ocean chemistry indicates that the oceans were anoxic and sulphidic during most of the Proterozoic. Its proponents suggest the underlying geochemical mechanism to entail the weathering of continental sulphides by atmospheric oxygen to sulphate, which was carried into the oceans as sulphate, fueling marine sulphate reducers (anaerobic, hydrogen sulphide-producing prokaryotes) on a global scale. Taken together, these two mutually compatible developments in biology and geology underscore the evolutionary significance of oxygen-independent ATP-generating pathways in mitochondria, including those of various metazoan groups, as a watermark of the environments within which eukaryotes arose and diversified into their major lineages.

  20. Comparative analysis of serine/arginine-rich proteins across 27 eukaryotes: insights into sub-family classification and extent of alternative splicing.

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    Dale N Richardson

    Full Text Available Alternative splicing (AS of pre-mRNA is a fundamental molecular process that generates diversity in the transcriptome and proteome of eukaryotic organisms. SR proteins, a family of splicing regulators with one or two RNA recognition motifs (RRMs at the N-terminus and an arg/ser-rich domain at the C-terminus, function in both constitutive and alternative splicing. We identified SR proteins in 27 eukaryotic species, which include plants, animals, fungi and "basal" eukaryotes that lie outside of these lineages. Using RNA recognition motifs (RRMs as a phylogenetic marker, we classified 272 SR genes into robust sub-families. The SR gene family can be split into five major groupings, which can be further separated into 11 distinct sub-families. Most flowering plants have double or nearly double the number of SR genes found in vertebrates. The majority of plant SR genes are under purifying selection. Moreover, in all paralogous SR genes in Arabidopsis, rice, soybean and maize, one of the two paralogs is preferentially expressed throughout plant development. We also assessed the extent of AS in SR genes based on a splice graph approach (http://combi.cs.colostate.edu/as/gmap_SRgenes. AS of SR genes is a widespread phenomenon throughout multiple lineages, with alternative 3' or 5' splicing events being the most prominent type of event. However, plant-enriched sub-families have 57%-88% of their SR genes experiencing some type of AS compared to the 40%-54% seen in other sub-families. The SR gene family is pervasive throughout multiple eukaryotic lineages, conserved in sequence and domain organization, but differs in gene number across lineages with an abundance of SR genes in flowering plants. The higher number of alternatively spliced SR genes in plants emphasizes the importance of AS in generating splice variants in these organisms.

  1. Phylogenetic analysis of P5 P-type ATPases, a eukaryotic lineage of secretory pathway pumps

    DEFF Research Database (Denmark)

    Møller, Annette; Asp, Torben; Holm, Preben Bach

    2008-01-01

    Eukaryotes encompass a remarkable variety of organisms and unresolved lineages. Different phylogenetic analyses have lead to conflicting conclusions as to the origin and associations between lineages and species. In this work, we investigated evolutionary relationship of a family of cation pumps...... exclusive for the secretory pathway of eukaryotes by combining the identification of lineage-specific genes with phylogenetic evolution of common genes. Sequences of P5 ATPases, which are regarded to be cation pumps in the endoplasmic reticulum (ER), were identified in all eukaryotic lineages but not in any...

  2. Novel eukaryotic enzymes modifying cell-surface biopolymers

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    Aravind L

    2010-01-01

    Full Text Available Abstract Background Eukaryotic extracellular matrices such as proteoglycans, sclerotinized structures, mucus, external tests, capsules, cell walls and waxes contain highly modified proteins, glycans and other composite biopolymers. Using comparative genomics and sequence profile analysis we identify several novel enzymes that could be potentially involved in the modification of cell-surface glycans or glycoproteins. Results Using sequence analysis and conservation we define the acyltransferase domain prototyped by the fungal Cas1p proteins, identify its active site residues and unify them to the superfamily of classical 10TM acyltransferases (e.g. oatA. We also identify a novel family of esterases (prototyped by the previously uncharacterized N-terminal domain of Cas1p that have a similar fold as the SGNH/GDSL esterases but differ from them in their conservation pattern. Conclusions We posit that the combined action of the acyltransferase and esterase domain plays an important role in controlling the acylation levels of glycans and thereby regulates their physico-chemical properties such as hygroscopicity, resistance to enzymatic hydrolysis and physical strength. We present evidence that the action of these novel enzymes on glycans might play an important role in host-pathogen interaction of plants, fungi and metazoans. We present evidence that in plants (e.g. PMR5 and ESK1 the regulation of carbohydrate acylation by these acylesterases might also play an important role in regulation of transpiration and stress resistance. We also identify a subfamily of these esterases in metazoans (e.g. C7orf58, which are fused to an ATP-grasp amino acid ligase domain that is predicted to catalyze, in certain animals, modification of cell surface polymers by amino acid or peptides. Reviewers This article was reviewed by Gaspar Jekely and Frank Eisenhaber

  3. Novel eukaryotic enzymes modifying cell-surface biopolymers

    Science.gov (United States)

    2010-01-01

    Background Eukaryotic extracellular matrices such as proteoglycans, sclerotinized structures, mucus, external tests, capsules, cell walls and waxes contain highly modified proteins, glycans and other composite biopolymers. Using comparative genomics and sequence profile analysis we identify several novel enzymes that could be potentially involved in the modification of cell-surface glycans or glycoproteins. Results Using sequence analysis and conservation we define the acyltransferase domain prototyped by the fungal Cas1p proteins, identify its active site residues and unify them to the superfamily of classical 10TM acyltransferases (e.g. oatA). We also identify a novel family of esterases (prototyped by the previously uncharacterized N-terminal domain of Cas1p) that have a similar fold as the SGNH/GDSL esterases but differ from them in their conservation pattern. Conclusions We posit that the combined action of the acyltransferase and esterase domain plays an important role in controlling the acylation levels of glycans and thereby regulates their physico-chemical properties such as hygroscopicity, resistance to enzymatic hydrolysis and physical strength. We present evidence that the action of these novel enzymes on glycans might play an important role in host-pathogen interaction of plants, fungi and metazoans. We present evidence that in plants (e.g. PMR5 and ESK1) the regulation of carbohydrate acylation by these acylesterases might also play an important role in regulation of transpiration and stress resistance. We also identify a subfamily of these esterases in metazoans (e.g. C7orf58), which are fused to an ATP-grasp amino acid ligase domain that is predicted to catalyze, in certain animals, modification of cell surface polymers by amino acid or peptides. Reviewers This article was reviewed by Gaspar Jekely and Frank Eisenhaber PMID:20056006

  4. Cryptic sex in the smallest eukaryotic marine green alga.

    Science.gov (United States)

    Grimsley, Nigel; Péquin, Bérangère; Bachy, Charles; Moreau, Hervé; Piganeau, Gwenaël

    2010-01-01

    Ostreococcus spp. are common worldwide oceanic picoeukaryotic pelagic algae. The complete genomes of three strains from different ecological niches revealed them to represent biologically distinct species despite their identical cellular morphologies (cryptic species). Their tiny genomes (13 Mb), with approximately 20 chromosomes, are colinear and densely packed with coding sequences, but no sexual life cycle has been described. Seventeen new strains of one of these species, Ostreococcus tauri, were isolated from 98 seawater samplings from the NW Mediterranean by filtering, culturing, cloning, and plating for single colonies and identification by sequencing their ribosomal 18S gene. In order to find the genetic markers for detection of polymorphisms and sexual recombination, we used an in silico approach to screen available genomic data. Intergenic regions of DNA likely to evolve neutrally were analyzed following polymerase chain reaction amplification of sequences using flanking primers from adjacent conserved coding sequences that were present as syntenic pairs in two different species of Ostreococcus. Analyses of such DNA regions from eight marker loci on two chromosomes from each strain revealed that the isolated O. tauri clones were haploid and that the overall level of polymorphism was approximately 0.01. Four different genetic tests for recombination showed that sexual exchanges must be inferred to account for the between-locus and between-chromosome marker combinations observed. However, our data suggest that sexual encounters are infrequent because we estimate the frequency of meioses/mitoses among the sampled strains to be 10(-6). Ostreococcus tauri and related species encode and express core genes for mitosis and meiosis, but their mechanisms of cell division and recombination, nevertheless, remain enigmatic because a classical eukaryotic spindle with 40 canonical microtubules would be much too large for the available approximately 0.9-microm(3) cellular

  5. Phenylalanine hydroxylase (PAH) from the lower eukaryote Leishmania major.

    Science.gov (United States)

    Lye, Lon-Fye; Kang, Song Ok; Nosanchuk, Joshua D; Casadevall, Arturo; Beverley, Stephen M

    2011-01-01

    Aromatic amino acid hydroxylases (AAAH) typically use tetrahydrobiopterin (H(4)B) as the cofactor. The protozoan parasite Leishmania major requires biopterin for growth and expresses strong salvage and regeneration systems to maintain H(4)B levels. Here we explored the consequences of genetic manipulation of the sole L. major phenylalanine hydroxylase (PAH) to explore whether it could account for the Leishmania H(4)B requirement. L. major PAH resembles AAAHs of other organisms, bearing eukaryotic-type domain organization, and conservation of key catalytic residues including those implicated in pteridine binding. A pah(-) null mutant and an episomal complemented overexpressing derivative (pah-/+PAH) were readily obtained, and metabolic labeling studies established that PAH was required to hydroxylate Phe to Tyr. Neither WT nor overexpressing lines were able to hydroxylate radiolabeled tyrosine or tryptophan, nor to synthesize catecholamines. WT but not pah(-) parasites showed reactivity with an antibody to melanin when grown with l-3,4-dihydroxyphenylalanine (L-DOPA), although the reactive product is unlikely to be melanin sensu strictu. WT was auxotrophic for Phe, Trp and Tyr, suggesting that PAH activity was insufficient to meet normal Tyr requirements. However, pah(-) showed an increased sensitivity to Tyr deprivation, while the pah(-)/+PAH overexpressor showed increased survival and could be adapted to grow well without added Tyr. pah(-) showed no alterations in H(4)B-dependent differentiation, as established by in vitro metacyclogenesis, or survival in mouse or macrophage infections. Thus Leishmania PAH may mitigate but not alleviate Tyr auxotrophy, but plays no essential role in the steps of the parasite infectious cycle. These findings suggest PAH is unlikely to explain the Leishmania requirement for biopterin.

  6. The Superoxide Reductase from the Early Diverging Eukaryote Giardia Intestinalis

    Energy Technology Data Exchange (ETDEWEB)

    Cabelli, D.E.; Testa, F.; Mastronicola, D.; Bordi, E.; Pucillo, L.P.; Sarti, P.; Saraiva, L.M.; Giuffre, A.; Teixeira, M.

    2011-10-15

    Unlike superoxide dismutases (SODs), superoxidereductases (SORs) eliminate superoxide anion (O{sub 2}{sup {sm_bullet}-}) not through its dismutation, but via reduction to hydrogen peroxide (H{sub 2}O{sub 2}) in the presence of an electron donor. The microaerobic protist Giardia intestinalis, responsible for a common intestinal disease in humans, though lacking SOD and other canonical reactive oxygen species-detoxifying systems, is among the very few eukaryotes encoding a SOR yet identified. In this study, the recombinant SOR from Giardia (SOR{sub Gi}) was purified and characterized by pulse radiolysis and stopped-flow spectrophotometry. The protein, isolated in the reduced state, after oxidation by superoxide or hexachloroiridate(IV), yields a resting species (T{sub final}) with Fe{sup 3+} ligated to glutamate or hydroxide depending on pH (apparent pK{sub a} = 8.7). Although showing negligible SOD activity, reduced SOR{sub Gi} reacts with O{sub 2}{sup {sm_bullet}-} with a pH-independent second-order rate constant k{sub 1} = 1.0 x 10{sup 9} M{sup -1} s{sup -1} and yields the ferric-(hydro)peroxo intermediate T{sub 1}; this in turn rapidly decays to the T{sub final} state with pH-dependent rates, without populating other detectable intermediates. Immunoblotting assays show that SOR{sub Gi} is expressed in the disease-causing trophozoite of Giardia. We propose that the superoxide-scavenging activity of SOR in Giardia may promote the survival of this air-sensitive parasite in the fairly aerobic proximal human small intestine during infection.

  7. Structural and biomechanical basis of mitochondrial movement in eukaryotic cells

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    Wu M

    2013-10-01

    Full Text Available Min Wu,1 Aruna Kalyanasundaram,2 Jie Zhu1 1Laboratory of Biomechanics and Engineering, Institute of Biophysics, College of Science, Northwest A&F University, Yangling, Shaanxi, People's Republic of China; 2College of Pharmacology, University of Illinois at Chicago, Chicago, IL, USA Abstract: Mitochondria serve as energy-producing organelles in eukaryotic cells. In addition to providing the energy supply for cells, the mitochondria are also involved in other processes, such as proliferation, differentiation, information transfer, and apoptosis, and play an important role in regulation of cell growth and the cell cycle. In order to achieve these functions, the mitochondria need to move to the corresponding location. Therefore, mitochondrial movement has a crucial role in normal physiologic activity, and any mitochondrial movement disorder will cause irreparable damage to the organism. For example, recent studies have shown that abnormal movement of the mitochondria is likely to be the reason for Charcot–Marie–Tooth disease, amyotrophic lateral sclerosis, Alzheimer's disease, Huntington's disease, Parkinson's disease, and schizophrenia. So, in the cell, especially in the particular polarized cell, the appropriate distribution of mitochondria is crucial to the function and survival of the cell. Mitochondrial movement is mainly associated with the cytoskeleton and related proteins. However, those components play different roles according to cell type. In this paper, we summarize the structural basis of mitochondrial movement, including microtubules, actin filaments, motor proteins, and adaptin, and review studies of the biomechanical mechanisms of mitochondrial movement in different types of cells. Keywords: mitochondrial movement, microtubules, actin filaments, motor proteins, adaptin

  8. MetWAMer: eukaryotic translation initiation site prediction

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    Brendel Volker

    2008-09-01

    Full Text Available Abstract Background Translation initiation site (TIS identification is an important aspect of the gene annotation process, requisite for the accurate delineation of protein sequences from transcript data. We have developed the MetWAMer package for TIS prediction in eukaryotic open reading frames of non-viral origin. MetWAMer can be used as a stand-alone, third-party tool for post-processing gene structure annotations generated by external computational programs and/or pipelines, or directly integrated into gene structure prediction software implementations. Results MetWAMer currently implements five distinct methods for TIS prediction, the most accurate of which is a routine that combines weighted, signal-based translation initiation site scores and the contrast in coding potential of sequences flanking TISs using a perceptron. Also, our program implements clustering capabilities through use of the k-medoids algorithm, thereby enabling cluster-specific TIS parameter utilization. In practice, our static weight array matrix-based indexing method for parameter set lookup can be used with good results in data sets exhibiting moderate levels of 5'-complete coverage. Conclusion We demonstrate that improvements in statistically-based models for TIS prediction can be achieved by taking the class of each potential start-methionine into account pending certain testing conditions, and that our perceptron-based model is suitable for the TIS identification task. MetWAMer represents a well-documented, extensible, and freely available software system that can be readily re-trained for differing target applications and/or extended with existing and novel TIS prediction methods, to support further research efforts in this area.

  9. Teaching Diversity

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    Kay Young McChesney

    2015-10-01

    Full Text Available This article is targeted to faculty teaching race and ethnicity, racism, diversity, and multicultural courses. Many students equate race with skin color. The premise of this article is that to teach students about the social construction of race, teachers must first know enough science to teach students that race is not biological. This article examines the biology of race by showing how advances in DNA sequencing led to genetics research that supports arguments that race is not biological. DNA comparisons show that all human populations living today are one species that came from Africa. The article explains the migration of humans out of Africa about 60,000 years ago and how they populated Australia, then Asia, Europe, and the Americas. The article shows how recent research maps the timing of the migration and admixture of specific population groups into Europe and India. The article shows how a mutation in one nucleotide can result in a trait like blue eyes, or Hemoglobin S (which confers resistance to malaria, which can be subject to evolution through natural selection. DNA comparisons show how natural selection shaped the genetics of human skin color to adapt to less UV light in the northern latitudes of Europe and Asia. The article shows that there is no relation between skin color or other “racial” characteristics and complex traits like intelligence. The science in this article will help teachers explain that as race is not biological, race is socially constructed and culturally enacted.

  10. pico-PLAZA, a genome database of microbial photosynthetic eukaryotes.

    Science.gov (United States)

    Vandepoele, Klaas; Van Bel, Michiel; Richard, Guilhem; Van Landeghem, Sofie; Verhelst, Bram; Moreau, Hervé; Van de Peer, Yves; Grimsley, Nigel; Piganeau, Gwenael

    2013-08-01

    With the advent of next generation genome sequencing, the number of sequenced algal genomes and transcriptomes is rapidly growing. Although a few genome portals exist to browse individual genome sequences, exploring complete genome information from multiple species for the analysis of user-defined sequences or gene lists remains a major challenge. pico-PLAZA is a web-based resource (http://bioinformatics.psb.ugent.be/pico-plaza/) for algal genomics that combines different data types with intuitive tools to explore genomic diversity, perform integrative evolutionary sequence analysis and study gene functions. Apart from homologous gene families, multiple sequence alignments, phylogenetic trees, Gene Ontology, InterPro and text-mining functional annotations, different interactive viewers are available to study genome organization using gene collinearity and synteny information. Different search functions, documentation pages, export functions and an extensive glossary are available to guide non-expert scientists. To illustrate the versatility of the platform, different case studies are presented demonstrating how pico-PLAZA can be used to functionally characterize large-scale EST/RNA-Seq data sets and to perform environmental genomics. Functional enrichments analysis of 16 Phaeodactylum tricornutum transcriptome libraries offers a molecular view on diatom adaptation to different environments of ecological relevance. Furthermore, we show how complementary genomic data sources can easily be combined to identify marker genes to study the diversity and distribution of algal species, for example in metagenomes, or to quantify intraspecific diversity from environmental strains.

  11. Antioxidative and antihypertensive activities of pig meat before and after cooking and in vitro gastrointestinal digestion: Comparison between Italian autochthonous pig Suino Nero Lucano and a modern crossbred pig.

    Science.gov (United States)

    Simonetti, Amalia; Gambacorta, Emilio; Perna, Annamaria

    2016-12-01

    The aim of this study was to evaluate and compare antioxidative and antihypertensive activities of Longissimus dorsi muscle from Suino Nero Lucano (SNL) and a modern crossbred (CG) pigs, before and after cooking and in vitro gastrointestinal digestion. Pig meat showed antioxidative and antihypertensive activities, heat treatment decreased the thiols content but at the same time increased angiotensin I-converting enzyme (ACE) inhibitory activity, and in vitro gastrointestinal digestion enhanced the biological activity of meat. Autochthonous SNL meat showed a higher nutraceutical quality compared to CG meat, highlighting a greater potential beneficial physiological effect on human health. The results of this study indicate that the pig meat, in particular autochthonous pig meat, may be considered a functional food since it is a good source of antioxidative and antihypertensive peptides.

  12. Application and validation of autochthonous Lactobacillus plantarum starter cultures for controlled malolactic fermentation and its influence on the aromatic profile of cherry wines.

    Science.gov (United States)

    Sun, Shu Yang; Gong, Han Sheng; Liu, Wen Li; Jin, Cheng Wu

    2016-05-01

    Lactic acid bacteria (LAB) used for malolactic fermentation (MLF) has a great effect on the production and quality of cherry wines. The present study used an autochthonous Lb. plantarum strain of SGJ-24 which was isolated from spontaneous MLF cherry wines and selected by its best MLF performance and tolerance, to investigate its effect on the kinetic of vinification and on chemical and volatile characteristics of Rainer and May Duck cherry wines, in comparison with a commercial Oenococcus oeni strain of 31 MBR. Monitoring of MLF was carried out by measuring cell viability and malic acid metabolism, and results showed that for both cherry varieties, SGJ-24 can significantly minimize MLF duration. After fermentation, wine samples were chemically characterized and analyzed for volatile profiles. Results demonstrated that no negative impact on the analytical parameters has been found, and a general increase of volatile esters and terpenes was observed when SGJ-24 was involved. Sensory analysis revealed that the global aromatic intensity was enhanced by the introduction of SGJ-24. All these data suggested that the application of Lb. plantarum strain of SGJ-24 as a worthwhile alternative LAB species for Rainer and May Duck cherry winemaking.

  13. Iranian wheat flours from rural and industrial mills: Exploitation of the chemical and technology features, and selection of autochthonous sourdough starters for making breads.

    Science.gov (United States)

    Pontonio, Erica; Nionelli, Luana; Curiel, José Antonio; Sadeghi, Alireza; Di Cagno, Raffaella; Gobbetti, Marco; Rizzello, Carlo Giuseppe

    2015-05-01

    This study aimed at describing the main chemical and technology features of eight Iranian wheat flours collected from industrial and artisanal mills. Their suitability for bread making was investigated using autochthonous sourdough starters. Chemical analyses showed high concentration of fibers and ash, and technology aptitude for making breads. As shown through 2-DE analyses, gliadin and glutenin subunits were abundant and varied among the flours. According to the back slopping procedure, type I sourdoughs were prepared from Iranian flours, and lactic acid bacteria were typed and identified. Strains of Pediococcus pentosaceus, Weissella cibaria, Weissella confusa, and Leuconostoc citreum were the most abundant. Based on the kinetics of growth and acidification, quotient of fermentation and concentration of total free amino acids, lactic acid bacteria were selected and used as sourdough mixed starters for bread making. Compared to spontaneous fermentation, sourdoughs fermented with selected and mixed starters favored the increase of the concentrations of organic acids and total free amino acids, the most suitable quotient of fermentation, and the most intense phytase and antioxidant activities. Although the high concentration of fibers, selected and mixed starters improved the textural features of the breads. This study might had contribute to the exploitation of the potential of Iranian wheat flours and to extend the use of sourdough, showing positive technology, nutritional and, probably, economic repercussions.

  14. Microbiological quality and safety of raw milk and soft cheese and detection of autochthonous lactic acid bacteria with antagonistic activity against Listeria monocytogenes, Salmonella Spp., and Staphylococcus aureus.

    Science.gov (United States)

    Ortolani, Maria Beatriz Tassinari; Yamazi, Anderson Keizo; Moraes, Paula Mendonça; Viçosa, Gabriela Nogueira; Nero, Luís Augusto

    2010-02-01

    This study aimed to characterize the microbiological quality and safety of raw milk and soft cheese, verifying possible associations between microbial populations, and the detection of lactic acid bacteria (LAB) with antagonistic activity against foodborne pathogens. Raw milk (n = 36) and soft cheese (n = 18) samples were collected and submitted for the analysis of mesophilic aerobes, total coliforms, Escherichia coli, LAB, coagulase-positive Staphylococcus (CPS), Listeria monocytogenes, and Salmonella spp. In all, 389 LAB isolates were randomly selected and submitted for antagonistic tests against L. monocytogenes, St. aureus, Salmonella Typhimurium, and Lactobacillus sakei. The samples presented high counts of mesophilic aerobes, total coliforms, and LAB, and also high and significant correlation indices between these populations. Low levels of CPS and E. coli were observed, as well as an absence of Salmonella spp. and L. monocytogenes. A substantial portion of the analyzed samples presented LAB cultures with antagonistic activity, but not against Salmonella Typhimurium. The obtained results indicate the antimicrobial potential of the autochthonous microbiota of raw milk and soft cheese. Despite the spoilage potential, the LAB present in the studied food products can be isolated and properly characterized as antagonistic cultures, to be used in bioconservation studies for pathogen control in foods.

  15. Effect of autochthonous starter cultures isolated from Siahmazgi cheese on physicochemical, microbiological and volatile compound profiles and sensorial attributes of sucuk, a Turkish dry-fermented sausage.

    Science.gov (United States)

    Kargozari, Mina; Moini, Sohrab; Akhondzadeh Basti, Afshin; Emam-Djomeh, Zahra; Gandomi, Hassan; Revilla Martin, Isabel; Ghasemlou, Mehran; Carbonell-Barrachina, Angel A

    2014-05-01

    The effect of adding autochthonous starter cultures isolated from Siahmazgi cheese, on the physicochemical parameters and microbial counts of sucuk was investigated during the ripening period. SPME-GC/MS was used in volatile compound analysis and a trained group of panelists carried out sensory analysis of the final product. After preliminary screening, three strains of Lactobacillus plantarum, which possess desirable technological properties, were used to prepare three starter cultures: LBP7, LBP10 and LBP14. The addition of LBP7 and LBP14 starter cultures had a significant effect (Pactivity during the ripening of sausages was not affected by the various starters. The texture profiles of all sausages were similar except for LBP10, which showed lower hardness and gumminess during ripening. Under the conditions of the study, volatile compounds were mainly from spices, and no marked differences were found among inoculated sausages. However, sensory evaluation revealed that most of the sensory attributes were scored higher for inoculated sausages than for the control ones. Therefore, LBP7 and LBP14 could be promising candidates for inclusion as starter cultures for the manufacture of sucuk.

  16. Helminth communities of the autochthonous mustelids Mustela lutreola and M. putorius and the introduced Mustela vison in south-western France.

    Science.gov (United States)

    Torres, J; Miquel, J; Fournier, P; Fournier-Chambrillon, C; Liberge, M; Fons, R; Feliu, C

    2008-12-01

    This study presents the first comprehensive helminthological data on three sympatric riparian mustelids (the European mink Mustela lutreola, the polecat M. putorius and the American mink M. vison) in south-western France. One hundred and twenty-four specimens (45 M. lutreola, 37 M. putorius and 42 M. vison) from eight French departments were analysed. Globally, 15 helminth species were detected: Troglotrema acutum, Pseudamphistomum truncatum, Euryhelmis squamula, Euparyphium melis and Ascocotyle sp. (Trematoda), Taenia tenuicollis (Cestoda), Eucoleus aerophilus, Pearsonema plica, Aonchotheca putorii, Strongyloides mustelorum, Molineus patens, Crenosoma melesi, Filaroides martis and Skrjabingylus nasicola (Nematoda) and larval stages of Centrorhynchus species (Acanthocephala). The autochthonous European mink harboured the highest species richness (13 species) followed by the polecat with 11 species. The introduced American mink presented the most depauperate helminth community (nine species). The prevalence and worm burden of most of the helminths found in M. putorius and M. lutreola were also higher than those of M. vison. Some characteristics of their helminth communities were compared to relatively nearby populations (Spain) and other very distant populations (Belarus). This comparison emphasized M. patens as the most frequent parasite in all of the analysed mustelid populations. It was possible to conclude that the invasive M. vison contributes to the maintenance of the life cycle of the pathogenic T. acutum and S. nasicola helminths, with possible implications for the conservation of the endangered European mink.

  17. Phenolic Compounds, Antioxidant Activity, and Other Characteristics of Extra Virgin Olive Oils from Ital