scholarly journals Optimizing extraction and targeted capture of ancient environmental DNA for reconstructing past environments using the PalaeoChip Arctic-1.0 bait-set

2020 ◽  
pp. 1-24 ◽  
Author(s):  
Tyler J. Murchie ◽  
Melanie Kuch ◽  
Ana T. Duggan ◽  
Marissa L. Ledger ◽  
Kévin Roche ◽  
...  
Keyword(s):  
Extraction Procedure ◽  
Environmental Dna ◽  
Local Environment ◽  
Enzymatic Reactions ◽  
Soil Extraction ◽  
Dna Recovery ◽  
Target Sequencing ◽  
Other Substances ◽  
Targeted Capture

Abstract Sedimentary ancient DNA (sedaDNA) has been established as a viable biomolecular proxy for tracking taxon presence through time in a local environment, even in the total absence of surviving tissues. SedaDNA is thought to survive through mineral binding, facilitating long-term biomolecular preservation, but also challenging DNA isolation. Two common limitations in sedaDNA extraction are the carryover of other substances that inhibit enzymatic reactions, and the loss of authentic sedaDNA when attempting to reduce inhibitor co-elution. Here, we present a sedaDNA extraction procedure paired with targeted enrichment intended to maximize DNA recovery. Our procedure exhibits a 7.7–19.3x increase in on-target plant and animal sedaDNA compared to a commercial soil extraction kit, and a 1.2–59.9x increase compared to a metabarcoding approach. To illustrate the effectiveness of our cold spin extraction and PalaeoChip capture enrichment approach, we present results for the diachronic presence of plants and animals from Yukon permafrost samples dating to the Pleistocene-Holocene transition, and discuss new potential evidence for the late survival (~9700 years ago) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike region of Yukon, Canada. This enrichment approach translates to a more taxonomically diverse dataset and improved on-target sequencing.

scholarly journals PalaeoChip Arctic1.0: An optimised eDNA targeted enrichment approach to reconstructing past environments

2019 ◽  
Author(s):  
Tyler J. Murchie ◽  
Melanie Kuch ◽  
Ana Duggan ◽  
Marissa L. Ledger ◽  
Kévin Roche ◽  
...  
Keyword(s):  
Environmental Dna ◽  
Local Environment ◽  
Fold Increase ◽  
Soil Extraction ◽  
Target Molecules ◽  
Mineral Binding ◽  
Animal Presence ◽  
Long Term Preservation ◽  
Targeted Enrichment

SummaryAncient environmental DNA has been established as a viable biomolecular proxy for tracking taxonomic presence through time in a local environment, even in the total absence of primary tissues. It is thought that sedimentary ancient DNA (sedaDNA) survives through mineral binding. And while these organo-mineral complexes likely facilitate long-term preservation, they also challenge our ability to release and isolate target molecules. Two limitations in sedaDNA extraction impede many palaeoenvironmental reconstructions: the post-extraction carryover of enzymatic inhibitors, and sedaDNA loss when attempting to reduce inhibitor co-elution. Here, we present an optimised eDNA targeted enrichment approach for reconstructing past environments. Our new extraction protocol with targeted enrichment averages a 14.6-fold increase in on-target plant and animal DNA compared to a commercial soil extraction kit, and a 22.6-fold increase compared to a PCR metabarcoding approach. To illustrate the effectiveness of the PalaeoChip Arctic1.0 protocol, we present results of plant and animal presence from permafrost samples and discuss new potential evidence for the late survival (ca. 9685 BP) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike Region of Yukon, Canada. This approach translates to a more diverse and sensitive dataset with increased sequencing efficiency of ecologically informative sedaDNA.

Biomedical Materials to Repair Retinal Detachments

1985 ◽  
Vol 55 ◽  
Author(s):  
Miguel F. Refojo
Keyword(s):  
Retinal Detachment ◽  
Silicone Rubber ◽  
Methyl Acrylate ◽  
Silicone Oil ◽  
Vitreous Body ◽  
Light Sensitivity ◽  
Scleral Buckling ◽  
Intraocular Injection ◽  
Other Substances

ABSTRACTImplants are essential for the repair of retinal detachments. The implant buckles the wall of the eye and apposes the detached retina with the choroid, thus restoring light sensitivity to the retina. The scleral buckling also relieves traction on the retina from a shrinking vitreous body. The implant materials most commonly used are solid silicone rubber and silicone sponges, but both types have some disadvantages. A poly(hydroxyethyl acrylate-co-methyl acrylate) hydrogel implant with improved properties of softness and antibiotic absorption is also available for retinal detachment surgery. Proliferative vitreoretinopathy involves various conditions of retinal detachment complicated by vitreous fibrosis, which, after vitrectomy, may be treated with intraocular injection of fluids that support the retina against the choroid. For conditions requiring a long-term implant, silicone oil although controversial is the material of choice. Many other substances have been investigated but none better has yet been found.

The value of environmental DNA biobanking for long-term biomonitoring

2018 ◽  
Vol 2 (8) ◽  
pp. 1192-1193 ◽  
Author(s):  
Simon N. Jarman ◽  
Oliver Berry ◽  
Michael Bunce
Keyword(s):  
Environmental Dna

The Resource Development of Yulin Energy and Heavy Chemical Industry Base and Re-Thinking Sustainable City Development

2012 ◽  
Vol 524-527 ◽  
pp. 3264-3268 ◽  
Author(s):  
Zhao Feng Lei ◽  
Bang Yan Li ◽  
Xu Li Lei ◽  
Lun He
Keyword(s):  
Sustainable Development ◽  
Local Environment ◽  
Living Environment ◽  
Energy Resources ◽  
City Development ◽  
Development Mode ◽  
Sustainable City ◽  
The Sustainable Development ◽  
Yulin City

Yulin City, which is rich in energy, is one of the national energy and chemical bases. But with the process of exploitation of resources, it causes serious ecological damage and has grim living environment situation in the local environment. It is in long-term about the sustainable development of city very urgent. This paper analyzes the reputation, ruin and its treatment of the development of energy resources in Yulin City, trying to explore the sustainable development mode which is suit in resource-dependent of area.

scholarly journals Fresh contact: Youth, migration, and atmospheres in India

2018 ◽  
Vol 37 (2) ◽  
pp. 313-330 ◽  
Author(s):  
Jane Dyson
Keyword(s):  
Young People ◽  
Word Meaning ◽  
Local Environment ◽  
Social Nature ◽  
Environmental Setting ◽  
The Social ◽  
Youth Agency ◽  
Indian Village ◽  
High Degree

This paper uses long-term research in an Indian village to develop Karl Mannheim’s notion of each generation’s ‘fresh contact’ with their inherited social and environmental setting. I examine how a generation of young people re-apprehend their local environment following a period of migration. I argue that young people aged between 25 and 34 who have lived outside their locality re-appraise their village economically and spiritually when they return home. I point to the social nature of this ‘fresh contact’, its spatial character, and the high degree of reflexivity that young men display in discussing their own agency as a generation – a point that emerged especially clearly in their discussion of the term ‘ mahaul,’ a Hindi word meaning ‘atmosphere’. The paper contributes to geographical and anthropological work on youth agency by highlighting the utility of notions of fresh contact in specific social conjunctures, such as the migration of a particular cohort. At the same time, it suggests the importance of placing alongside Mannheim’s work an explicit focus on the spatial nature of fresh contact, the sociality that constitutes cohorts as generations, and young people’s reflexive capacity to theorise their generational agency.

scholarly journals Overcoming limitations to environmental DNA studies: A coastal temperate reference sequence database for multiple chloroplast gene regions generated in a single assay.

2021 ◽  
Author(s):  
Nicole Foster ◽  
Kor-jent Dijk ◽  
Ed Biffin ◽  
Jennifer Young ◽  
Vicki Thomson ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Dna Barcode ◽  
Environmental Dna ◽  
Reference Sequence ◽  
Reference Database ◽  
Chloroplast Gene ◽  
Coastal Plants ◽  
Reference Databases ◽  
Targeted Capture ◽  
Comprehensive Reference

A proliferation in environmental DNA (eDNA) research has increased the reliance on reference sequence databases to assign unknown DNA sequences to known taxa. Without comprehensive reference databases, DNA extracted from environmental samples cannot be correctly assigned to taxa, limiting the use of this genetic information to identify organisms in unknown sample mixtures. For animals, standard metabarcoding practices involve amplification of the mitochondrial Cytochrome-c oxidase subunit 1 (CO1) region, which is a universally amplifyable region across majority of animal taxa. This region, however, does not work well as a DNA barcode for plants and fungi, and there is no similar universal single barcode locus that has the same species resolution. Therefore, generating reference sequences has been more difficult and several loci have been suggested to be used in parallel to get to species identification. For this reason, we developed a multi-gene targeted capture approach to generate reference DNA sequences for plant taxa across 20 target chloroplast gene regions in a single assay. We successfully compiled a reference database for 93 temperate coastal plants including seagrasses, mangroves, and saltmarshes/samphire’s. We demonstrate the importance of a comprehensive reference database to prevent species going undetected in eDNA studies. We also investigate how using multiple chloroplast gene regions impacts the ability to discriminate between taxa.

scholarly journals Parental effects and the evolution of phenotypic memory

2015 ◽  
Author(s):  
Bram Kuijper ◽  
Rufus A Johnstone
Keyword(s):  
Local Environment ◽  
Parental Effects ◽  
Bet Hedging ◽  
Changing Environments ◽  
Structured Population ◽  
Different Types ◽  
Parental Phenotype ◽  
Selection For ◽  
Nongenetic Inheritance

Abstract Despite growing evidence for nongenetic inheritance, the ecological conditions that favor the evolution of heritable parental or grandparental effects remain poorly understood. Here, we systematically explore the evolution of parental effects in a patch-structured population with locally changing environments. When selection favors the production of a mix of offspring types, this mix differs according to the parental phenotype, implying that parental effects are favored over selection for bet-hedging in which the mixture of offspring phenotypes produced does not depend on the parental phenotype. Positive parental effects (generating a positive correlation between parental and offspring phenotype) are favored in relatively stable habitats and when different types of local environment are roughly equally abundant, and can give rise to long-term parental inheritance of phenotypes. By contrast, unstable habitats can favor negative parental effects (generating a negative correlation between parental and offspring phenotype), and under these circumstances even slight asymmetries in the abundance of local environmental states select for marked asymmetries in transmission fidelity.

scholarly journals Human Body Burden of Heavy Metals and Health Consequences of Pb Exposure in Guiyu, an E-Waste Recycling Town in China

2021 ◽  
Vol 18 (23) ◽  
pp. 12428
Author(s):  
Wenlong Huang ◽  
Xiaoling Shi ◽  
Kusheng Wu
Keyword(s):  
Heavy Metals ◽  
Body Burden ◽  
Local Environment ◽  
Waste Recycling ◽  
The Body ◽  
Health Consequences ◽  
Long Term Effects ◽  
Adaptive Immune ◽  
Pb Exposure

Guiyu accommodates millions of tons of e-waste from overseas and domestic sources each year and is notorious for its e-waste dismantling industry. As a consequence, Guiyu has been described as “the world’s most toxic place” and “junk town”. Informal e-waste recycling activities have caused severe pollution to the local environment and are associated with extensive health problems to the residents. This review provides updated insights on the body burden of heavy metals derived from e-waste and health outcomes resulted from lead (Pb) exposure. The review identified that Guiyu has been highly contaminated by heavy metals, especially Pb. Excessive exposure to Pb has been associated with multi-system and long-term effects in neonates and children, covering nervous, cardiovascular, adaptive immune, and hematologic systems as well as chromosome and DNA damage. Our review indicates strong associations that emphasize the need to develop strong regulations for prevention of exposure and health consequences in Guiyu and similar sites around the world.

scholarly journals A pilot for implementing environmental DNA (eDNA) based methods into environmental and biomonitoring

2021 ◽  
Vol 4 ◽  
Author(s):  
Tiina Laamanen ◽  
Veera Norros ◽  
Sanna Suikkanen ◽  
Mikko Tolkkinen ◽  
Kristiina Vuorio ◽  
...  
Keyword(s):  
Best Practices ◽  
Information Exchange ◽  
State Of The Art ◽  
Environmental Dna ◽  
Bulk Sample ◽  
The State ◽  
Molecular Techniques ◽  
Future Research ◽  
Dna Metabarcoding

Environmental DNA (eDNA) and other molecular based approaches are revolutionizing the field of biomonitoring. These approaches undergo rapid modifications, and it is crucial to develop the best practices by sharing the newest information and knowledge. In our ongoing project we: assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. assess the state-of-the-art of eDNA methods at Finnish Environment Institute SYKE; identify concrete next steps towards the long-term aim of implementing eDNA methods into environmental and biomonitoring; promote information exchange on eDNA methods and advance future research efforts both within SYKE and with our national and international partners. Scientific background Well-functioning and intact natural ecosystems are essential for human well-being, provide a variety of ecosystem services and contain a high diversity of organisms. However, human activities such as eutrophication, pollution, land-use or invasive species, are threatening the state and functioning of ecosystems from local to global scale (e.g. Benateau et al. 2019; Reid et al. 2018; Vörösmarty et al. 2010). New molecular techniques in the field and in the laboratory have enabled sampling and identification of much of terrestrial, marine and freshwater biodiversity. These include environmental DNA (eDNA, e.g. Valentini et al. 2016) and bulk-sample DNA metabarcoding approaches (e.g. Elbrecht et al. 2017) and targeted RNA-based methods (e.g. Mäki and Tiirola 2018). The eDNA technique uses DNA that is released from organisms into their environment, from which a signal of organisms’ presence in the system can be obtained. For example, in aquatic ecosystems, eDNA is typically extracted from sediment or filtered water samples (e.g. Deiner et al. 2016), and this approach is distinguished from bulk DNA metabarcoding, where organisms are directly identified from e.g. complete biological monitoring samples (e.g. Elbrecht et al. 2017). Despite the demonstrated potential of environmental and bulk-sample DNA metabarcoding approaches in recent years, there are still significant bottlenecks to their routine use that need to be addressed (e.g. Pawlowski et al. 2020). Methods and implementati on The project is divided into three work packages: WP1 Gathering existing knowledge, identifying knowledge gaps and proposing best practices, WP2 Roadmap to implementation and WP3 eDNA monitoring pilot. Please see more details in the Fig. 1

scholarly journals The dimensionality of plant–plant competition

2021 ◽  
Author(s):  
Daniel B Stouffer ◽  
Oscar Godoy ◽  
Giulio Valentino B Dalla Riva ◽  
Margaret Mayfield
Keyword(s):  
A Priori ◽  
Plant Competition ◽  
Experimental Studies ◽  
Local Environment ◽  
Effective Number ◽  
Competing Species ◽  
Term Survival ◽  
Long Run ◽  
High Diversity

To avoid extinction, every species must be able to exploit available resources at least as well as the other species in its community. All else being equal, theory predicts that the more distinct the niches of such co-occurring and competing species, the more species that can persist in the long run. However, both theoretical and experimental studies define a priori the nature and number of resources over which species compete. It therefore remains unclear whether or not species in empirically realistic contexts are actually exploiting all or some of the niches available to them. Here we provide a mathematical solution to this long-standing problem. Specifically, we show how to use the interactions between sets of co-occurring plant species to quantify their implied "niche dimensionality": the effective number of resources over which those species appear to be competing. We then apply this approach to quantify the niche dimensionality of 12 plant assemblages distributed across the globe. Contrary to conventional wisdom, we found that the niche dimensionality in these systems was much lower than the number of competing species. However, two high-resolution experiments also show that changes in the local environment induce a reshuffling of plant's competitive roles and hence act to increase the assemblages' effective niche dimensionality. Our results therefore indicate that homogeneous environments are unlikely to be able to maintain high diversity and also shows how environmental variation impacts species' niches and hence their opportunities for long-term survival.

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