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  • 1
    Series available for loan
    Series available for loan
    Orléans : BRGM
    Associated volumes
    Call number: SR 90.0911(4)
    In: Manuels et methodes
    Type of Medium: Series available for loan
    Pages: 183 S.
    ISBN: 2715900139
    Series Statement: Manuels et méthodes 4
    Language: French
    Location: Lower compact magazine
    Branch Library: GFZ Library
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  • 2
    Monograph available for loan
    Monograph available for loan
    Oxford : North Oxford Acad. Press
    Call number: G 8836
    Type of Medium: Monograph available for loan
    Pages: XI, 190 S. : graph. Darst.
    ISBN: 0946536503
    Series Statement: Studies in geology
    Uniform Title: Les Granites des complexes annulaires
    Language: English
    Location: Upper compact magazine
    Branch Library: GFZ Library
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  • 3
    Monograph available for loan
    Monograph available for loan
    Berlin [u.a.] : Springer
    Call number: PIK B 160-02-0013
    Type of Medium: Monograph available for loan
    Pages: 268 p.
    ISBN: 3540422668
    Series Statement: Population Economics ;
    Branch Library: PIK Library
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  • 4
    Call number: 9780191079993 (e-book)
    Type of Medium: 12
    Pages: 1 online resource (254 pages)
    Edition: First edition
    ISBN: 9780191079993 (e-book)
    Language: English
    Note: Contents Acknowledgments 1 Introduction to environmental DNA (eDNA) 1.1 Definitions 1.2 A brief history of eDNA analysis 1.3 Constraints when working with eDNA 1.4 Workflow in eDNA studies and main methods used 1.5 Environmental DNA as a monitoring tool 2 DNA metabarcode choice and design 2.1 Which DNA metabarcode? 2.2 Properties of the ideal DNA metabarcode 2.3 In silica primer design and testing 2.3.1 Prerequisites 2.3.2 Reference sequences: description, filtering, and formatting for ecoPrimers 2.3.3 In silica primer design with ecoPrimers 2.3.3.1 'Ihe ecoPrimers output 2.3.4 In silica primer testing with ecoPCR 2.3.4.1 The ecoPCR output 2.3.4.2 Filtering of the ecoPCR output 2.3.4.3 Evaluation of primer conservation 2.3.4.4 Taxonomic resolution and Bs index 2.4 Examples of primer pairs available for DNA metabarcoding 3 Reference databases 3.1 Extracting reference databases from EMBL/GenBank/DDBJ 3.1.1 Downloading a local copy of EMBL 3.1.2 Identifying sequences corresponding to the relevant metabarcode 3.2 Marker-specific reference databases 3.2.1 Nuclear rRNA gene reference databases 3.2.2 Eukaryote-specific databases 3.3 Building a local reference database 3.3.1 PCR-based local reference database 3.3.2 Shotgun-based local reference database 3.4 Current challenges and future directions 4 Sampling 4.1 The cycle of eDNA in the environment 4.1.1 State and origin 4.1.2 Fate 4.1.3 Transport 4.2 Sampling design 4.2.1 Focusing on the appropriate DNA population 4.2.2 Defining the sampling strategy 4.3 Sample preservation 5 DNA extraction 5.1 From soil samples 5.2 From sediment 5.3 From litter 5.4 From fecal samples 5.5 From water samples 6 DNA amplification and multiplexing 6.1 Principle of the PCR 6.2 Which polymerase to choose? 6.3 The standard PCR reaction 6.4 The importance of including appropriate controls 6.4.1 Extraction negative controls 6.4.2 PCR negative controls 6.4.3 PCR positive controls 6.4.4 Tagging system controls 6.4.5 Internal controls 6.5 PCR optimization 6.6 How to limit the risk of contamination? 6.7 Blocking oligonucleotides for reducing the amplification of undesirable sequences 6.8 How many PCR replicates? 6.9 Multiplexing several metabarcodes within the same PCR 6.10 Multiplexing many samples on the same sequencing lane 6.10.1 Overview of the problem 6.10.2 Strategy 1: single-step PCR with Illumina adapters 6.10.3 Strategy 2: two-step PCR with Illumina adapters 6.10.4 Strategy 3: single-step PCR with tagged primers 7 DNA sequencing 7.1 Overview of the first, second, and third generations of sequencing technologies 7.2 The Illumina technology 7.2.1 Library preparation 7.2.2 Flow cell, bridge PCR, and clusters 7.2.3 Sequencing by synthesis 7.2.4 Quality scores of the sequence reads 8 DNA metabarcoding data analysis 8.1 Basic sequence handling and curation 8.1.1 Sequencing quality 8.1.1.1 The pros and cons of read quality-based filtering 8.1.1.2 Quality trimming software 8.1.2 Paired-end read pairing 8.1.3 Sequence demultiplexing 8.1.4 Sequence dereplication 8.1.5 Rough sequence curation 8.2 Sequence classification 8.2.1 Taxonomic classification 8.2.2 Unsupervised classification 8.2.3 Chimera identification 8.3 Taking advantages of experimental controls 8.3.1 Filtering out potential contaminants 8.3.2 Removing dysfunctional PCRs 8.4 General considerations on ecological analyses 8.4.1 Sampling effort and representativeness 8.4.1.1 Evaluating representativeness of the sequencing per PCR 8.4.1.2 Evaluating representativeness at the sampling unit or site level 8.4.2 Handling samples with varying sequencing depth 8.4.3 Going further and adapting the ecological models to metabarcoding 9 Single-species detection 9.1 Principle of the quantitative PCR (qPCR) 9.1.1 Recording amplicon accumulation in real time via fluorescence measurement 9.1.2 The typical amplification curve 9.1.3 Quantification of target sequences with the Ct method 9.2 Design and testing of qPCR barcodes targeting a single species 9.2.1 1he problem of specificity 9.2.2 qPCR primers and probe 9.2.3 Candidate qPCR barcodes 9.3 Additional experimental considerations 9.3.1 General issues associated with sampling, extraction, and PCR amplification 9.3.2 The particular concerns of contamination and inhibition 10 Environmental DNA for functional diversity 10.1 Functional diversity from DNA metabarcoding 10.1.1 Functional inferences 10.1.2 Targeting active populations 10.2 Metagenomics and metatranscriptomics: sequencing more than a barcode 10.2.1 General sampling constraints 10.2.1.1 Optimization of the number of samples 10.2.1.2 Enrichment in target organisms 10.2.1.3 Enrichment in functional information 10.2.2 General molecular constraints 10.2.3 From sequences to functions 10.2.3.1 Assembling (or not) a metagenome 10.2.3.2 Sorting contigs or reads in broad categories 10.2.3.3 Extracting functional information via taxonomic inferences 10.2.3.4 Functional annotation of metagenomes 11 Some early landmark studies 11.1 Emergence of the concept of eDNA and first results on microorganisms 11.2 Examining metagenomes to explore the functional information carried by eDNA 11.3 Extension to macroorganisms 12 Freshwater ecosystems 12.1 Production, persistence, transport, and delectability of eDNA in freshwater ecosystems 12.1.1 Production 12.1.2 Persistence 12.1.3 Transport/ diffusion distance 12.1.4 Detectability 12.2 Macroinvertebrates 12.3 Diatoms and microeukaryotes 12.4 Aquatic plants 12.5 Fish, amphibians, and other vertebrates 12.5.1 Species detection 12.5.2 Biomass estimates 12.6 Are rivers conveyer belts of biodiversity information? 13 Marine environments 13.1 Environmental DNA cycle and transport in marine ecosystems 13.2 Marine microbial diversity 13.3 Environmental DNA for marine macroorganisms 14 Terrestrial ecosystems 14.1 Delectability, persistence, and mobility of eDNA in soil 14.2 Plant community characterization 14.3 Earthworm community characterization 14.4 Bacterial community or metagenome characterization 14.5 Multitaxa diversity surveys 1 5 Paleoenvironments 15.1 Lake sediments 15.1.1 Pollen, macrofossils, and DNA metabarcoding 15.1.2 Plants and mammals from Lake Anteme 15.1.3 Viability in the ice-free corridor in North America 15.2 Permafrost 15.2.1 Overview of the emergence of permafrost as a source of eDNA 15.2.2 Large-scale analysis of permafrost samples for reconstructing past plant communities 15.3 Archaeological midden material 15.3.1 Bulk archaeological fish bones from Madagascar 15.3.2 Midden from Greenland to assess past human diet 16 Host-associated microbiota 16.1 DNA dynamics 16.2 Early molecular-based works 16.3 Post-holobiont works 17 Diet analysis 17.1 Some seminal diet studies 17.1.1 Proof of concept-analyzing herbivore diet using next-generation sequencing 17.1.2 Assessing the efficiency of conservation actions in Bialowieza forest 17.1.3 Characterizing carnivore diet, or how to disentangle predator and prey eDNA 17.1.4 Analyzing an omnivorous diet, or integrating several diets in a single one 17.2 Methodological and experimental specificities of eDNA diet analyses 17.2.1 eDNAsources 17.2.1.1 Feces 17.2.1.2 Gut content 17.2.1.3 Whole body 17.2.2 Quantitative aspects 17.2.2.1 Relationship between the amount of ingested food and DNA quantity in the sample 17.2.2.2 Quantifying DNA with PCR and next-generation sequencing 17.2.2.3 Empirical correction of abundances 17.2.3 Diet as a sample of the existing biodiversity 17.2.4 Problematic diets 18 Analysis of bulk samples 18.1 What is a bulk sample? 18.2 Case studies 18.2.1 Bulk insect samples for biodiversity monitoring 18.2.2 Nematode diversity in tropical rainforest 18.2.3 Marine metawan diversity in benthic ecosystems 18.3 Metabarcoding markers for bulk samples 18.4 Alternative strategies 19 The future of eDNA metabarcoding 19.1 PCR-based approaches 19.1.1 Singl
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  • 5
    Keywords: rocks ; granitoids ; petrogenesis ; granite petrogenesis
    Description / Table of Contents: 6 February 2019 --- Performing process-oriented investigations involving mass transfer using Rcrust: a new phase equilibrium modelling tool / Matthew Mayne, Gary Stevens, Jean-François Moyen and Tim Johnson / Geological Society, London, Special Publications, 491, https://doi.org/10.1144/SP491-2018-85 --- Water-assisted production of late-orogenic trondhjemites at magmatic and subsolidus conditions / Patrizia Fiannacca, Miguel Angelo Stipp Basei, Rosolino Cirrincione, Antonino Pezzino and Damiano Russo / Geological Society, London, Special Publications, 491, https://doi.org/10.1144/SP491-2018-113 --- The dual origin of I-type granites: The contribution from laboratory experiments / Antonio Castro / Geological Society, London, Special Publications, 491, https://doi.org/10.1144/SP491-2018-110 --- Whole-rock geochemical modelling of granite genesis – the current state of play / Vojtech Janousek and Jean-François Moyen / Geological Society, London, Special Publications, 491, https://doi.org/10.1144/SP491-2018-160 --- Granites and crustal heat budget / Jean-Francois Moyen / Geological Society, London, Special Publications, 491, https://doi.org/10.1144/SP491-2018-148
    Edition: online first
    Language: English
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  • 6
    ISSN: 1420-9055
    Keywords: Nutrient limitation ; primary production ; ocean, mediterranean ; micronanoplankton ; ultraplankton
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract Enrichment experiments were carried out on seawater samples from the Israeli coast to characterise the nature of nutrient limitation. Phytoplankton chlorophyll, ATP, PC, PN, PP and bicarbonate and orthophosphate uptake rates indicate that phosphorus limitation is more extreme than that of nitrogen. A large increase in total nitrogen observed with P enrichment suggests that a substantial nitrogen fixation is mediated by picocyanobacteria in this kind of oligotrophic mediterranean waters.
    Type of Medium: Electronic Resource
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  • 7
    Publication Date: 2007-10-08
    Description: The Kerguelen Archipelago is made up of a stack of thick piles of Tertiary flood basalts intruded by transitional to alkaline igneous centres at various times since 30 Ma ago. In the SW, the Rallier-du-Baty Peninsula is mostly occupied by two silicic ring complexes, each with an average diameter of 15 km, comprising dissected calderas cross-cut by subvolcanic cupolas. Previous radiometric determinations yield ages ranging from 15.4 to 7.4 Ma in the southern centre, and 6.2 to 4.9 Ma in the northern one. The felsic ring dykes were injected by coeval mafic magmas, forming, successively, swarms of early mafic enclaves, disrupted synplutonic cone sheets, and late cone-sheets. After the emplacement and subsequent unroofing of the plutonic ring complexes, abundant and thick trachytic pyroclastic flows and falls were emitted from the younger caldera volcanoes, while hawaiite and mugearite lava flows were erupted from marginal maars and cones. Huge trachyte ignimbritic flows filled the glacial valleys in the central Peninsula, and capped lacustrine deposits and older lava flows, while related pumice falls are widespread throughout the archipelago. This powerful plinian eruption took place after the network of glacial valleys was established, but before the Little Ice Age that occurred during the last centuries. In the south of the peninsula, even younger trachytic formations are exposed, and fumarolic vents are still active. The growth mechanisms of a caldera-related ring complex can be explained as a repetitive sequence of two eruptive episodes. The first episode of hydrofracturing, induced by volatile exsolution within the evolving magma chamber, creates a vertical circular fracture zone, along which highly vesiculated magmas are emitted during explosive eruptive events occurring at the surface in a caldera volcano. It is followed by a second episode of cauldron-subsidence of a crustal block down to the degassed magma chamber, induced by pressure release. Downward movement of the crustal block favours the emplacement at shallow depths within the older caldera-filling formations, of discrete magmatic sheets characterized by a 16-km mean diameter and a 1-km mean thickness, corresponding to an average unit volume of 200 km3. Actually, the estimated volumes of the different igneous episodes within the Rallier-du-Baty nested ring complex vary from 60 to 900 km3, and correspond to the production during 15 Ma of about 2800 {+/-} 850 km3 of new materials and a net crustal growth of about 100 {+/-} 30 x 103 m3 per year.
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  • 8
    ISSN: 1573-5052
    Keywords: Mediterranean forests ; Changes ; Disturbances ; Human activities ; Dynamic models
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract The development of socio-economic activity over the past ten years in the Mediterranean region has induced severe changes in the main natural forest ecosystems. In the northern Mediterranean, rural depopulation has accelerated since the end of the second World War, particularly since the establishment of Common Market agricultural policies, and led to an under-utilization of species causing a strong biological resurgence of the forest, even at high altitudes. This means that, at the present time, the extension of expansion model coniferous forests is favored by their capacities for spatial, biological and ecological selection. Along with this, the under-utilization of sclerophyllous (resistance model) and deciduous (stabilization model) oak coppices has led to the establishment of new forest structures and architectures which are notably different from the main climatic groups defined up to now by phytosociological and synchronic methods. Two new forms of disturbances have appeared: increasingly important wild fires have replaced disturbances caused by burn beating and are at the origin of the very strong spatial and temporal heterogeneity of current forest species. In addition, the geographical continuity of the main groups of same-aged sclerophyllous and deciduous species, due to their non-use over the past ten years, has accelerated a phytosanitary imbalance by an increase in the action of pests. In the southern Mediterranean, particularly in North Africa, demographic pressure and grazing have widely disturbed the main forest ecosystems which show a continual regression of their surface. Many forest tree species with a low spatial and biological selection, such as Mediterranean firs and black pines (Pinus nigra subsp. mauritanica), are threatened with extinction, as are the deciduous oak forests which, considering the climatic stress and edaphic constraints, are permanently in a state of imbalance. Human disturbances induce a complete modification of structures and architectures tending towards the installation of simplified forest models (trees-grasses) where tree regeneration is nearly impossible. The sclerophyllous coppices well-adapted to stress are also threatened by shorter and shorter cutting cycles and by the high usage of tree canopies for grazing. The forest understory structures have witnessed a decrease in their characteristic sylvatic species and the matorralization of most of the forests can be seen by the replacement of typical forest groups by preforest groups (Tetraclinis forests, Aleppo pine forests). New geopedological constraints linked to the removal of the surface soil layer combined with regular climatic stress (duration of drought periods) strongly decrease the resilience of these ecosystems which are under continual pressure (unbalanced models). In diverse regions, particulary in semi-arid bioclimates, hyperdegradation affects the shrub cover which disappears for a time in favor of perennial grasses (forest steppization): Andropogon div. sp., Ampelodesmos, Stipa div. sp. In all bioclimatic groups, the increase in grazing pressure throughout the southern Mediterranean ecosystems can even lead to the total disappearance of perennial species from the ecosystem with the exception of the dominant tree. Regardless of the altitude or ecosystem, invasive therophytes are then the only plants to occupy the understory and indicate hyperdegradation (forest therophytization).
    Type of Medium: Electronic Resource
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    European journal of forest research 51 (1929), S. 509-521 
    ISSN: 1612-4677
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 0030-493X
    Keywords: Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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