scholarly journals Genomics in the ecological arena

2010 ◽  
Vol 7 (1) ◽  
pp. 2-3 ◽  
Author(s):  
Luisa Orsini ◽  
Ellen Decaestecker ◽  
Luc De Meester ◽  
Michael E. Pfrender ◽  
John K. Colbourne
Keyword(s):  
Model System ◽  
Model Organisms ◽  
Meeting Report ◽  
Model Species ◽  
Environmental Genomics ◽  
Large Community ◽  
Genomic Tools ◽  
The Times ◽  
First Time ◽  
European University

This meeting report presents the cutting-edge research that is developing around the waterflea Daphnia , an emerging model system in environmental genomics. Daphnia has been a model species in ecology, toxicology and evolution for many years and is supported by a large community of ecologists, evolutionary biologists and ecotoxicologists. Thanks to new advances in genomics and transciptomics and to the sustained efforts of the Daphnia Genomics Consortium (DGC), Daphnia is also rapidly developing as a model system in environmental genomics. Advances in this emerging field were presented at the DGC 2010, held for the first time in a European University. During the meeting, a plethora of elegant studies were presented on the mechanisms of responses to environmental challenges using recently developed genomic tools. The DGC 2010 is a concrete example of the new trends in ecology and evolution. The times are mature for the application of innovative genomic and transcriptomic tools for studies of environmental genomics in non-model organisms.

scholarly journals Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
Luisa Orsini ◽  
Donald Gilbert ◽  
Ram Podicheti ◽  
Mieke Jansen ◽  
James B. Brown ◽  
...  
Keyword(s):  
Daphnia Magna ◽  
Draft Genome ◽  
Model Organisms ◽  
Transcriptome Data ◽  
Rna Seq ◽  
Data Set ◽  
Environmental Genomics ◽  
Environmental Perturbations ◽  
Gene Environment ◽  
Genomic Tools

Abstract The full exploration of gene-environment interactions requires model organisms with well-characterized ecological interactions in their natural environment, manipulability in the laboratory and genomic tools. The waterflea Daphnia magna is an established ecological and toxicological model species, central to the food webs of freshwater lentic habitats and sentinel for water quality. Its tractability and cyclic parthenogenetic life-cycle are ideal to investigate links between genes and the environment. Capitalizing on this unique model system, the STRESSFLEA consortium generated a comprehensive RNA-Seq data set by exposing two inbred genotypes of D. magna and a recombinant cross of these genotypes to a range of environmental perturbations. Gene models were constructed from the transcriptome data and mapped onto the draft genome of D. magna using EvidentialGene. The transcriptome data generated here, together with the available draft genome sequence of D. magna and a high-density genetic map will be a key asset for future investigations in environmental genomics.

scholarly journals Brown Algal Model Organisms

2020 ◽  
Vol 54 (1) ◽  
pp. 71-92
Author(s):  
Susana M. Coelho ◽  
J. Mark Cock
Keyword(s):  
Novel Species ◽  
Classical Model ◽  
Saccharina Japonica ◽  
Model System ◽  
Model Organisms ◽  
Phylogenetic Groups ◽  
The Past ◽  
Genomic Tools ◽  
Modern Genomic ◽  
Multicellular Organisms

Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga Ectocarpus has led to it emerging as a general model system for this group, but additional models, such as Fucus or Dictyota dichotoma, remain of interest for specific biological questions. In addition, Saccharina japonica has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.

scholarly journals Linking genes to communities and ecosystems: Daphnia as an ecogenomic model

2012 ◽  
Vol 279 (1735) ◽  
pp. 1873-1882 ◽  
Author(s):  
Brooks E. Miner ◽  
Luc De Meester ◽  
Michael E. Pfrender ◽  
Winfried Lampert ◽  
Nelson G. Hairston
Keyword(s):  
Evolutionary Dynamics ◽  
Model System ◽  
Causal Chain ◽  
Ecosystem Dynamics ◽  
Model Organisms ◽  
Ecological Interactions ◽  
Evolutionary Changes ◽  
Genomic Tools ◽  
Biological Hierarchy ◽  
Modern Genomic

How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances.

Delhi in Transition, 1821 and Beyond

2018 ◽  
Keyword(s):  
Nineteenth Century ◽  
Lived Experience ◽  
English Translation ◽  
East India Company ◽  
Multiple Sources ◽  
Original Manuscript ◽  
English East India Company ◽  
The Times ◽  
First Time ◽  
The City

Commissioned by the English East India Company to write about contemporary nineteenth-century Delhi, Mirza Sangin Beg walked around the city to capture its highly fascinating urban and suburban extravaganza. Laced with epigraphy and fascinating anecdotes, the city as ‘lived experience’ has an overwhelming presence in his work, Sair-ul Manazil. Sair-ul Manazil dominates the historiography of eighteenth- and nineteenth-century compositions on Delhi in Persian and Urdu, and remains unparalleled in its architecture and detailed content. It deals with the habitations of people, bazars, professions and professionals, places of worship and revelry, and issues of contestation. Over fifty typologies of structures and several institutions that find resonance in the Persian and Ottoman Empires can also be gleaned from Sair-ul Manazil. Interestingly, Beg made no attempt to ‘monumentalize’ buildings; instead, he explored them as spaces reflective of the sociocultural milieu of the times. Delhi in Transition is the first comprehensive English translation of Beg’s work, which was originally published in Persian. It is the only translation to compare the four known versions of Sair-ul Manazil, including the original manuscript located in Berlin, which is being consulted for the first time. It has an exhaustive introduction and extensive notes, along with the use of varied styles in the book to indicate the multiple sources of the text, contextualize Beg’s work for the reader and engage him with the debate concerning the different variants of this unique and eclectic work.

scholarly journals Research on Plants for the Understanding of Diseases of Nuclear and Mitochondrial Origin

2012 ◽  
Vol 2012 ◽  
pp. 1-12 ◽  
Author(s):  
Claudia P. Spampinato ◽  
Diego F. Gomez-Casati
Keyword(s):  
Current Knowledge ◽  
Model System ◽  
Human Diseases ◽  
Model Organisms ◽  
Human Cell Lines ◽  
Molecular Defects ◽  
Human Genes ◽  
Clinical Disorders ◽  
Mitochondrial Origin ◽  
Experimental Findings

Different model organisms, such asEscherichia coli,Saccharomyces cerevisiae,Caenorhabditis elegans,Drosophila melanogaster, mouse, cultured human cell lines, among others, were used to study the mechanisms of several human diseases. Since human genes and proteins have been structurally and functionally conserved in plant organisms, the use of plants, especiallyArabidopsis thaliana, as a model system to relate molecular defects to clinical disorders has recently increased. Here, we briefly review our current knowledge of human diseases of nuclear and mitochondrial origin and summarize the experimental findings of plant homologs implicated in each process.

Effect of Oxidized Myofibrils Protein Subjected to Mutiple Freeze-Thaw Cycles on N-Nitrosamine Formation in In Vitro Model System

2012 ◽  
Vol 550-553 ◽  
pp. 1590-1594 ◽  
Author(s):  
Hua Yang ◽  
Pei Pei Meng ◽  
Rui Wang ◽  
Pei Ran Li ◽  
Peng Li ◽  
...  
Keyword(s):  
Sodium Nitrite ◽  
Protein Carbonyl ◽  
Model System ◽  
Model Systems ◽  
Secondary Amines ◽  
Freeze Thaw ◽  
Heavy Chains ◽  
Carcinogenic Substance ◽  
The Times

N-nitrosamine is a kind of carcinogenic substance, which is possibly formed in the reaction of nitrites with amino acids or secondary amines. Two in vitro model systems were designed to evaluate the influence of oxidized myofibrils protein subjected to repeated freeze-thaw cycles (0, 1, 2, 3, 4, 7, 10 times) on N-nitrosamine formation. Model system I contains diethylamine and sodium nitrite, while model system II contains only sodium nitrite as reaction solution. Oxidized myofibrils protein were added to both systems. The results revealed that as the number of freeze-thaw cycles increased, cross-linking of myosin heavy chains and the content of protein carbonyl increased, but the content of protein sulfydryl decreased, which indicates oxidization of protein occurred. The concentration of N-nitrosodiethylamine increased as the number of freeze-thaw cycles increased, especially after four cycles. Oxidized myofibrils protein promoted the formation of N-nitrosodiethylamine. The more the times of freeze-thaw cycles were subjected, the more oxidization of myofibrils protein occurred and the higher yield of the N-nitrosodiethylamine.

Profaning the Sacred: The Unorthodox Financial Activities of Catholic Clerics During the Napoleonic Period, 1796–1814

2021 ◽  
Vol 51 (4) ◽  
pp. 523-542
Author(s):  
Christopher Korten
Keyword(s):  
Precious Metals ◽  
Religious Communities ◽  
Critical Periods ◽  
For Profit ◽  
Sacred And Profane ◽  
The Rich ◽  
The Times ◽  
First Time ◽  
Insight Into

This article reveals for the first time how Catholic clerics survived financially during the Napoleonic period in Italy (1796–1814). Despite the very rich, 200-year historiography on one of the Church's most critical periods, there is almost nothing on how religious clerics coped at this time. Their institutions had been despoiled by the French, often in collaboration with locals, negating traditional forms of clerical income, such as alms or rental income from non-ecclesiastical properties. This caused clerics to search out unorthodox – at times, non-canonical – ways of eking out a living, either for themselves, their religious communities or both, as such distinctions were often blurred. Masses were monetized and traded; ecclesiastical paraphernalia composed of precious metals were smelted and commodified, and relics were sold for profit. The uncovering of these controversial acts by men who in normal times were upstanding reveals the desperation of the times and provides insight into the rich discussion on determining the degrees of separation (and overlap) between the sacred and profane.

scholarly journals ISMB 2003 Bio-ontologies SIG and Sixth Annual Bio-ontologies Meeting Report

2003 ◽  
Vol 4 (6) ◽  
pp. 663-666 ◽  
Author(s):  
Phillip Lord ◽  
Robert Stevens
Keyword(s):  
North America ◽  
Peer Review ◽  
Interest Group ◽  
Text Analysis ◽  
Special Interest ◽  
Text Processing ◽  
Global Politics ◽  
Meeting Report ◽  
The Many ◽  
First Time

The Annual Bio-Ontologies meeting (http://www.cs.man.ac.uk/˜stevens/meeting03/) has now been running for 6 consecutive years, as a special interest group (SIG) of the much larger ISMB conference. It met in Brisbane, Australia, this summer, the first time it was held outside North America or Europe. The bio-ontologies meeting is 1 day long and normally has around 100 attendees. This year there were many fewer, no doubt a result of the distance, global politics and SARS. The meeting consisted of a series of 30 min talks with no formal peer review or publication. Talks ranged in style from fairly formal and complete pieces of work, through works in progress, to the very informal and discursive. Each year's meeting has a theme and this year it was ‘ontologies, and text processing’. There is a tendency for those submitting talks to ignore the theme completely, but this year's theme obviously struck a chord, as half the programme was about ontologies and text analysis (http://www.cs.man.ac.uk/˜stevensr/meeting03/programme.html). Despite the smaller size of the meeting, the programme was particularly strong this year, meaning that the tension between allowing time for the many excellent talks, discussion and questions from the floor was particular keenly felt. A happy problem to have!

Orishatukeh Faduma and the New Theology

1994 ◽  
Vol 63 (1) ◽  
pp. 60-80 ◽  
Author(s):  
Moses Nathaniel Moore
Keyword(s):  
Nineteenth Century ◽  
Historical Development ◽  
Christian Ethics ◽  
Comparative Religion ◽  
Religion And Science ◽  
Historical Significance ◽  
Dark Continent ◽  
Theological Orientation ◽  
The Times ◽  
First Time

In 1890 theBoston Heraldcarried the following review of an article entitled “Thoughts for the Times or The New Theology”: “A curiosity is a paper by a native African, Orishatukeh Faduma, on ‘Thoughts for the Times,’ by which he means the new theology. This is the first time that a criticof the new theology has turned up from the dark continent, and is a curious and significant paper. When a native can write like this on subjects in which he has been obliged to educate himself, it means that we are to say nothing more against the intelligence of the African race.” While correct in noting the historical significance of Faduma's efforts, the reviewer's condescension disclosed his failure to appreciate and understand the sophistication and depth of Faduma' theological analysis and agenda. Faduma's critique of elements of the New Theology did not entail his rejection of this controversial theological synthesis which emerged during the last quarter of the nineteenth century. Rather, his comments on religion and science, the historicalcritical method, comparative religion, missiology, the historical development of Christianity, and Christian ethics reveal that he essentially shared the theological orientation of its formulators.

scholarly journals A Nanoscale Model System for the Human Myelin Sheath

2021 ◽  
Author(s):  
Matthias Hoffmann ◽  
David Haselberger ◽  
Tommy Hofmann ◽  
Lisa Müller ◽  
Kevin Janson ◽  
...  
Keyword(s):  
Basic Protein ◽  
Model System ◽  
Myelin Proteins ◽  
Membrane Systems ◽  
Lipid Interactions ◽  
Functional Studies ◽  
Complex Lipid ◽  
Central Nervous Systems ◽  
Lipid Environment ◽  
First Time

Here, we for the first time establish nanodiscs with the challenging lipid composition of myelin of the peripheral or central nervous systems, respectively (PNS and CNS, both containing >40% cholesterol, which so far has been thought to be detrimental for nanodisc formation).Thus, we prove that more complex lipid model membrane systems are in general accessible through nanodiscs and can study protein-lipid interactions in myelin and factors driving myelin formation or degradation using combinations of myelin proteins in a highly controlled lipid environment resembling myelin’s cytoplasmic leaflet. For the functional studies, initial proof-of-principle experiments using myelin basic protein have been performed. <br>

Sign in / Sign up

Export Citation Format

Share Document