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Jaeckisch N.,Alfred Wegener Institute for Polar and Marine Research | Yang I.,Institute For Medizinische Mikrobiologie Und Krankenhaushygiene | Wohlrab S.,Alfred Wegener Institute for Polar and Marine Research | Glockner G.,Berlin Center for Genomics in Biodiversity Research | And 5 more authors.
PLoS ONE | Year: 2011

Many dinoflagellate species are notorious for the toxins they produce and ecological and human health consequences associated with harmful algal blooms (HABs). Dinoflagellates are particularly refractory to genomic analysis due to the enormous genome size, lack of knowledge about their DNA composition and structure, and peculiarities of gene regulation, such as spliced leader (SL) trans-splicing and mRNA transposition mechanisms. Alexandrium ostenfeldii is known to produce macrocyclic imine toxins, described as spirolides. We characterized the genome of A. ostenfeldii using a combination of transcriptomic data and random genomic clones for comparison with other dinoflagellates, particularly Alexandrium species. Examination of SL sequences revealed similar features as in other dinoflagellates, including Alexandrium species. SL sequences in decay indicate frequent retro-transposition of mRNA species. This probably contributes to overall genome complexity by generating additional gene copies. Sequencing of several thousand fosmid and bacterial artificial chromosome (BAC) ends yielded a wealth of simple repeats and tandemly repeated longer sequence stretches which we estimated to comprise more than half of the whole genome. Surprisingly, the repeats comprise a very limited set of 79-97 bp sequences; in part the genome is thus a relatively uniform sequence space interrupted by coding sequences. Our genomic sequence survey (GSS) represents the largest genomic data set of a dinoflagellate to date. Alexandrium ostenfeldii is a typical dinoflagellate with respect to its transcriptome and mRNA transposition but demonstrates Alexandrium-like stop codon usage. The large portion of repetitive sequences and the organization within the genome is in agreement with several other studies on dinoflagellates using different approaches. It remains to be determined whether this unusual composition is directly correlated to the exceptionally genome organization of dinoflagellates with a low amount of histones and histone-like proteins. © 2011 Jaeckisch et al.


Morelli G.,Max Planck Institute For Infektionsbiologie | Morelli G.,Max Planck Institute For Molekulare Genetik | Song Y.,Beijing Institute of Microbiology and Epidemiology | Song Y.,University College Cork | And 28 more authors.
Nature Genetics | Year: 2010

Plague is a pandemic human invasive disease caused by the bacterial agent Yersinia pestis. We here report a comparison of 17 whole genomes of Y. pestis isolates from global sources. We also screened a global collection of 286 Y. pestis isolates for 933 SNPs using Sequenom MassArray SNP typing. We conducted phylogenetic analyses on this sequence variation dataset, assigned isolates to populations based on maximum parsimony and, from these results, made inferences regarding historical transmission routes. Our phylogenetic analysis suggests that Y. pestis evolved in or near China and spread through multiple radiations to Europe, South America, Africa and Southeast Asia, leading to country-specific lineages that can be traced by lineage-specific SNPs. All 626 current isolates from the United States reflect one radiation, and 82 isolates from Madagascar represent a second radiation. Subsequent local microevolution of Y. pestis is marked by sequential, geographically specific SNPs. © 2010 Nature America, Inc. All rights reserved.


Makarova O.,Free University of Berlin | Rodriguez-Rojas A.,Free University of Berlin | Eravci M.,Free University of Berlin | Weise C.,Free University of Berlin | And 5 more authors.
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

Insects show long-lasting antimicrobial immune responses that follow the initial fast-acting cellular processes. These immune responses are discussed to provide a form of phrophylaxis and/or to serve as a safety measure against persisting infections. The duration and components of such longlasting responses have rarely been studied in detail, a necessary prerequisite to understand their adaptive value. Here, we present a 21 day proteomic time course of the mealworm beetle Tenebrio molitor immune-challenged with heat-killed Staphylococcus aureus. The most upregulated peptides are antimicrobial peptides (AMPs), many of which are still highly abundant 21 days after infection. The identified AMPs included toll and imd-mediated AMPs, a significant number of which have no known function against S. aureus or other Gram-positive bacteria. The proteome reflects the selective arena for bacterial infections. The results also corroborate the notion of synergistic interactions in vivo that are difficult to model in vitro. This article is part of the themed issue ‘Evolutionary ecology of arthropod antimicrobial peptides’. © 2016 The Author(s) Published by the Royal Society. All rights reserved.


Dziallas C.,Copenhagen University | Allgaier M.,Leibniz Institute of Freshwater Ecology and Inland Fisheries | Allgaier M.,Berlin Center for Genomics in Biodiversity Research | Monaghan M.T.,Leibniz Institute of Freshwater Ecology and Inland Fisheries | And 3 more authors.
Frontiers in Microbiology | Year: 2012

Mutual interactions in the form of symbioses can increase the fitness of organisms and provide them with the capacity to occupy new ecological niches. The formation of obligate symbioses allows for rapid evolution of new life forms including multitrophic consortia. Microbes are important components of many known endosymbioses and their short generation times and strong potential for genetic exchange may be important drivers of speciation. Hosts provide endo-and ectosymbionts with stable, nutrient-rich environments, and protection from grazers. This is of particular importance in aquatic ecosystems, which are often highly variable, harsh, and nutrient-deficient habitats. It is therefore not surprising that symbioses are widespread in both marine and freshwater environments. Symbioses in aquatic ciliates are good model systems for exploring symbiont-host interactions. Many ciliate species are globally distributed and have been intensively studied in the context of plastid evolution. Their relatively large cell size offers an ideal habitat for numerous microorganisms with different functional traits including commensalism and parasitism. Phagocytosis facilitates the formation of symbiotic relationships, particularly since some ingested microorganisms can escape the digestion. For example, photoautotrophic algae and methanogens represent endosymbionts that greatly extend the biogeochemical functions of their hosts. Consequently, symbiotic relationships between protists and prokaryotes are widespread and often result in new ecological functions of the symbiotic communities. This enables ciliates to thrive under a wide range of environmental conditions including ultraoligotrophic or anoxic habitats. We summarize the current understanding of this exciting research topic to identify the many areas in which knowledge is lacking and to stimulate future research by providing an overview on new methodologies and by formulating a number of emerging questions in this field. © 2012 Dziallas, Allgaier, Monaghan and Grossart.


News Article | October 31, 2016
Site: www.eurekalert.org

While fungi are well known for being essential in cycling carbon and nutrients, there are only about 100,000 described species in contrast to the 1.5 to 3 millions, assumed to exist on Earth. Of these, barely 3000 fungi belong to aquatic habitats. In fact, freshwater fungi have been researched so little, it is only now that an international research team provide the first lake-wide fungal diversity estimate in the open access journal MycoKeys. Over the spring and the early summer of 2010, a large team of scientists, led by Dr Christian Wurzbacher and Dr Norman Warthmann, affiliated with the Leibniz-Institute of Freshwater Ecology and Inland Fisheries and the Berlin Center for Genomics in Biodiversity Research, Germany (currently at University of Gothenburg, Sweden, and the Australian National University, Australia, respectively), collected a total of 216 samples from 54 locations, encompassing eight different habitats within Lake Stechlin in North-East Germany. Having recovered samples on three occasions over the course of the study, their aim was to test how habitat specificity affects the fungal community and whether fungal groups would reflect the availability of particulate organic matter as substrate. Unlike previous studies of aquatic fungi that compared water samples among different lakes or seasons, theirs would compare the diversity among habitats within a single lake. This included the study of fungi living in the water and the sediments, as well as fungi living on the surfaces of plants and other animals. As a result, the scientists concluded that every type of habitat, i.e. sediments, biofilms, and submerged macrophytes (large aquatic plants), has a specific fungal community that varies more than initially expected. Of these, lake biofilms, representing a group of microorganisms, whose cells stick to each other, and cling together to a surface, turned out to be the hotspots for aquatic fungi. "Our study provides the first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition," the scientists summarise. "Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body." Wurzbacher C, Warthmann N, Bourne EC, Attermeyer K, Allgaier M, Powell JR, Detering H, Mbedi S, Grossart H-P, Monaghan MT (2016) High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany). MycoKeys 16: 17-44. https:/


Escalera-Zamudio M.,Leibniz Institute for Zoo and Wildlife Research | Lisandra Zepeda Mendoza M.,Copenhagen University | Heeger F.,Berlin Center for Genomics in Biodiversity Research | Loza-Rubio E.,National Research Center Disciplinaria en Microbiologia Animal | And 7 more authors.
Journal of Virology | Year: 2015

The Desmodus rotundus endogenous betaretrovirus (DrERV) is fixed in the vampire bat D. rotundus population and in other phyllostomid bats but is not present in all species from this family. DrERV is not phylogenetically related to Old World bat betaretroviruses but to betaretroviruses from rodents and New World primates, suggesting recent cross-species transmission. A recent integration age estimation of the provirus in some taxa indicates that an exogenous counterpart might have been in recent circulation. © 2015, American Society for Microbiology.


News Article | December 23, 2015
Site: phys.org

Fathers are able to adjust to increasing temperatures within their own lifetime and do transmit this information to their offspring. This has now been shown for the first time in a wild animal. The findings were the result of a project within the Joint Initiative for Research and Innovation and have been published in the scientific journal Molecular Ecology. Male wild guinea pigs respond to increasing temperatures with biochemical modifications attached to their genome and pass this "epigenetic" information to the next generation, and most likely even the following one. In order to study their response to changing environmental conditions, male wild guinea pigs were kept for two months at an ambient temperature raised by ten degrees. It was subsequently examined whether any biochemical changes had occurred in the genome (DNA) of their liver in result of that heat treatment sons sired by the males before and after the rise in temperature were also examined for such possible biochemical changes of the genome of their liver and also in the genomes of their testicles. The joint scientists team from the Leibniz Institute for Zoo and Wildlife Research (IZW), the Berlin Center for Genomics in Biodiversity Research (BeGenDiv) and the Californian company Zymo Research detected significant differences in the methylation of the DNA (a biochemical modification of the genome) of the wild guinea pigs when comparing the genomes prior to and after exposure to increased temperatures. These differences were especially found in genes encoding proteins responsible for protection against heat damage. The magic word which describes this process is "epigenetics" (Greek: epi = upon, over, above; genetics = study of heredity) – a molecular mechanism which regulates the switching-on of genes in response to environmental changes without changing the sequence of the DNA's building blocks. "We believe that the transfer of epigenetic information from father to sons prepares the latter for changes in environmental conditions such as a rise in temperature. This is particularly important with regards to a possible adaptive response to climate change. Epigenetic mechanisms could therefore be crucial for the fitness and survival of the offspring," says Alexandra Weyrich, researcher at the IZW. As the mother-child relationship in mammals during and after pregnancy is particularly intense, previous research focused mainly on the transfer of maternal epigenetic information. "However, in most wild mammal species, including wild guinea pigs, it is the males who leave their ancestral habitats and quickly adjust to varying environmental conditions such as temperatures during the search for females and new territories," explains Weyrich. The rapid adjustment to environmental changes is, among other things, possible through epigenetic modifications such as the methylation or demethylation of the DNA. Unlike the "genetic code" (the sequence of the DNA's building blocks), epigenetic modifications are flexible and can therefore be used as a "switch" in response to environmental changes. The new findings show that some of these acquired epigenetic modifications can be robust enough to be passed onto offspring. The current study shows that fathers pass on epigenetic changes in their DNA to their sons. Explore further: Environmental change leaves its footprint in the epigenome More information: Alexandra Weyrich et al. Paternal intergenerational epigenetic response to heat exposure in male Wild guinea pigs, Molecular Ecology (2015). DOI: 10.1111/mec.13494


News Article | October 31, 2016
Site: phys.org

What is in the water? Not only Theodor Fontane had once been fascinated by this sight, when he wrote about his famous lake monster. Sharing his inspiration, scientists wanted to know what fungi can thrive underwater and where exactly. Credit: Christian Wurzbacher While fungi are well known for being essential in cycling carbon and nutrients, there are only about 100,000 described species in contrast to the 1.5 to 3 millions, assumed to exist on Earth. Of these, barely 3000 fungi belong to aquatic habitats. In fact, freshwater fungi have been researched so little, it is only now that an international research team provide the first lake-wide fungal diversity estimate in the open access journal MycoKeys. Over the spring and the early summer of 2010, a large team of scientists, led by Dr Christian Wurzbacher and Dr Norman Warthmann, affiliated with the Leibniz-Institute of Freshwater Ecology and Inland Fisheries and the Berlin Center for Genomics in Biodiversity Research, Germany (currently at University of Gothenburg, Sweden, and the Australian National University, Australia, respectively), collected a total of 216 samples from 54 locations, encompassing eight different habitats within Lake Stechlin in North-East Germany. Having recovered samples on three occasions over the course of the study, their aim was to test how habitat specificity affects the fungal community and whether fungal groups would reflect the availability of particulate organic matter as substrate. Unlike previous studies of aquatic fungi that compared water samples among different lakes or seasons, theirs would compare the diversity among habitats within a single lake. This included the study of fungi living in the water and the sediments, as well as fungi living on the surfaces of plants and other animals. As a result, the scientists concluded that every type of habitat, i.e. sediments, biofilms, and submerged macrophytes (large aquatic plants), has a specific fungal community that varies more than initially expected. Of these, lake biofilms, representing a group of microorganisms, whose cells stick to each other, and cling together to a surface, turned out to be the hotspots for aquatic fungi. "Our study provides the first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition," the scientists summarise. "Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body." Explore further: Top 50 most wanted fungi: New search function zooms in on the dark fungal diversity More information: Christian Wurzbacher et al, High habitat-specificity in fungal communities in oligo-mesotrophic, temperate Lake Stechlin (North-East Germany), MycoKeys (2016). DOI: 10.3897/mycokeys.16.9646


News Article | November 6, 2016
Site: www.sciencedaily.com

While fungi are well known for being essential in cycling carbon and nutrients, there are only about 100,000 described species in contrast to the 1.5 to 3 millions, assumed to exist on Earth. Of these, barely 3000 fungi belong to aquatic habitats. In fact, freshwater fungi have been researched so little, it is only now that an international research team provide the first lake-wide fungal diversity estimate in the open access journal MycoKeys. Over the spring and the early summer of 2010, a large team of scientists, led by Dr Christian Wurzbacher and Dr Norman Warthmann, affiliated with the Leibniz-Institute of Freshwater Ecology and Inland Fisheries and the Berlin Center for Genomics in Biodiversity Research, Germany (currently at University of Gothenburg, Sweden, and the Australian National University, Australia, respectively), collected a total of 216 samples from 54 locations, encompassing eight different habitats within Lake Stechlin in North-East Germany. Having recovered samples on three occasions over the course of the study, their aim was to test how habitat specificity affects the fungal community and whether fungal groups would reflect the availability of particulate organic matter as substrate. Unlike previous studies of aquatic fungi that compared water samples among different lakes or seasons, theirs would compare the diversity among habitats within a single lake. This included the study of fungi living in the water and the sediments, as well as fungi living on the surfaces of plants and other animals. As a result, the scientists concluded that every type of habitat, i.e. sediments, biofilms, and submerged macrophytes (large aquatic plants), has a specific fungal community that varies more than initially expected. Of these, lake biofilms, representing a group of microorganisms, whose cells stick to each other, and cling together to a surface, turned out to be the hotspots for aquatic fungi. "Our study provides the first estimate of lake-wide fungal diversity and highlights the important contribution of habitat heterogeneity to overall diversity and community composition," the scientists summarise. "Habitat diversity should be considered in any sampling strategy aiming to assess the fungal diversity of a water body."


Sommer S.,Leibniz Institute for Zoo and Wildlife Research | Courtiol A.,Leibniz Institute for Zoo and Wildlife Research | Mazzoni C.J.,Leibniz Institute for Zoo and Wildlife Research | Mazzoni C.J.,Berlin Center for Genomics in Biodiversity Research
BMC Genomics | Year: 2013

Background: The Major Histocompatibility Complex (MHC) is the most important genetic marker to study patterns of adaptive genetic variation determining pathogen resistance and associated life history decisions. It is used in many different research fields ranging from human medical, molecular evolutionary to functional biodiversity studies. Correct assessment of the individual allelic diversity pattern and the underlying structural sequence variation is the basic requirement to address the functional importance of MHC variability. Next-generation sequencing (NGS) technologies are likely to replace traditional genotyping methods to a great extent in the near future but first empirical studies strongly indicate the need for a rigorous quality control pipeline. Strict approaches for data validation and allele calling to distinguish true alleles from artefacts are required.Results: We developed the analytical methodology and validated a data processing procedure which can be applied to any organism. It allows the separation of true alleles from artefacts and the evaluation of genotyping reliability, which in addition to artefacts considers for the first time the possibility of allelic dropout due to unbalanced amplification efficiencies across alleles. Finally, we developed a method to assess the confidence level per genotype a-posteriori, which helps to decide which alleles and individuals should be included in any further downstream analyses. The latter method could also be used for optimizing experiment designs in the future.Conclusions: Combining our workflow with the study of amplification efficiency offers the chance for researchers to evaluate enormous amounts of NGS-generated data in great detail, improving confidence over the downstream analyses and subsequent applications. © 2013 Sommer et al.; licensee BioMed Central Ltd.

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