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.

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.

Problems of treatment of primary openangle glaucoma in combination with thrombosis of the central retinal vein

GlaucomaNews ◽  
2020 ◽  
pp. 65-69
Author(s):  
T.E. Lipatkina ◽  
◽  
Е.V. Karlova ◽  
A.V. Zolotarev ◽  
◽  
...  
Keyword(s):  
Macular Edema ◽  
Primary Open Angle Glaucoma ◽  
Antihypertensive Drugs ◽  
Open Angle Glaucoma ◽  
Vascular Wall ◽  
Open Angle ◽  
Retinal Edema ◽  
Long Term Preservation ◽  
Central Retinal Vein

Patients with primary open-angle glaucoma (POAG) and ophthalmic hypertension have an increased likelihood of developing occlusions (thrombosis) of the central retinal vein. Different groups of antihypertensive drugs differ in their mechanism of action and may affect concomitant ocular pathology, in particular, retinal edema, which occurs, for example, in occlusion of the central retinal vein. Used in most patients with glaucoma, prostaglandin analogs can contribute to the long-term preservation of macular edema due to the effect on the permeability of the vascular wall. Preparations of other pharmacological groups, reducing the production of aqueous humor, on the contrary, may contribute to its regression. Therefore, the question of choosing a drug for antihypertensive therapy in patients with primary open-angle glaucoma and concomitant macular edema is relevant and is for further study.

Comparison of Polarized and Depolarized Arrest in the Isolated Rat Heart for Long-term Preservation

Circulation ◽  
1997 ◽  
Vol 96 (9) ◽  
pp. 3148-3156 ◽  
Author(s):  
A. K. Snabaitis ◽  
M. J. Shattock ◽  
D. J. Chambers
Keyword(s):  
Rat Heart ◽  
Isolated Rat Heart ◽  
Long Term Preservation ◽  
Isolated Rat

Online Publication of Monuments

2020 ◽  
pp. 355-369
Author(s):  
Willeke Wendrich
Keyword(s):  
Peer Review ◽  
3D Modeling ◽  
Online Publication ◽  
New Technologies ◽  
3D Scanning ◽  
Architectural Drawings ◽  
3D Gis ◽  
Unity 3D ◽  
Long Term Preservation

This chapter outlines the advantages of digital epigraphy in the context of the original monuments. It analyzes the perception of epigraphic publication of monuments, taking into account new technologies. 3DVR models can be created using architectural drawings and measurements (CAD and 3D modeling), 3D scanning, and Structure for Motion (SfM). These systems present different advantages and challenges, which are discussed. Current options for publication include VSim, 3D GIS, and Unity 3D platforms. The issues of peer review of publications and long-term preservation of data are addressed. The chapter concludes with a consideration of the issue of potentially misleading impressions given by 3DVR representations.

scholarly journals Efficient Protocol for Improving the Development of Cryopreserved Embryonic Axes of Chestnut (Castanea sativa Mill.) by Encapsulation–Vitrification

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 231
Author(s):  
Mariam Gaidamashvili ◽  
Eka Khurtsidze ◽  
Tamari Kutchava ◽  
Maurizio Lambardi ◽  
Carla Benelli
Keyword(s):  
Activated Charcoal ◽  
Castanea Sativa ◽  
Alginate Beads ◽  
Embryonic Axes ◽  
Root Regrowth ◽  
Castanea Sativa Mill ◽  
Whole Plants ◽  
Long Term Preservation ◽  
Direct Immersion

An optimized cryopreservation protocol for embryonic axes (EAs) of chestnut (Castanea sativa Mill.) has been developed based on the encapsulation–vitrification procedure. EAs of mature seeds were aseptically dissected and encapsulated in alginate beads with or without 0.3% (w/v) activated charcoal (AC). Embedded EAs were dehydrated with Plant Vitrification Solution 2 for different treatment times up to 120 min, followed by direct immersion in liquid nitrogen. Cryopreserved embryonic axes encapsulated with AC showed higher survival (70%) compared to those encapsulated without AC (50%). Sixty-four percent of embryonic axes, from synthetic seeds with AC, subsequently developed as whole plants. Plantlet regrowth was faster in AC-encapsulated EAs and showed enhanced postcryopreservation shoot and root regrowth over 2 cm after five weeks from rewarming. Results indicate that encapsulation–vitrification with activated charcoal added to the beads is an effective method for the long-term preservation of Castaneasativa embryonic axes.

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