Successful extraction of insect DNA from recent copal inclusions: limits and perspectives.
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ABSTRACT:
SUBMITTER: Modi A
PROVIDER: S-EPMC7994385 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Insects preserved in copal, the sub-fossilized resin precursor of amber, have potential value in molecular ecological studies of recently-extinct species and of extant species that have never been collected as living specimens. The objective of the work reported in this paper was therefore to determine if ancient DNA is present in insects preserved in copal. We prepared DNA libraries from two stingless bees (Apidae: Meliponini: Trigonisca ameliae) preserved in 'Anthropocene' Colombian copal, dated to 'post-Bomb' and 10,612±62 cal yr BP, respectively, and obtained sequence reads using the GS Junior 454 System. Read numbers were low, but were significantly higher for DNA extracts prepared from crushed insects compared with extracts obtained by a non-destructive method. The younger specimen yielded sequence reads up to 535 nucleotides in length, but searches of these sequences against the nucleotide database revealed very few significant matches. None of these hits was to stingless bees though one read of 97 nucleotides aligned with two non-contiguous segments of the mitochondrial cytochrome oxidase subunit I gene of the East Asia bumblebee Bombus hypocrita. The most significant hit was for 452 nucleotides of a 470-nucleotide read that aligned with part of the genome of the root-nodulating bacterium Bradyrhizobium japonicum. The other significant hits were to proteobacteria and an actinomycete. Searches directed specifically at Apidae nucleotide sequences only gave short and insignificant alignments. All of the reads from the older specimen appeared to be artefacts. We were therefore unable to obtain any convincing evidence for the preservation of ancient DNA in either of the two copal inclusions that we studied, and conclude that DNA is not preserved in this type of material. Our results raise further doubts about claims of DNA extraction from fossil insects in amber, many millions of years older than copal.
| S-EPMC3770633 | biostudies-literature
Project description:Fluid inclusions in evaporite minerals (halite, gypsum, etc.) potentially preserve genetic records of microbial diversity and changing environmental conditions of Earth's hydrosphere for nearly one billion years. Here we describe a robust protocol for surface sterilization and retrieval of DNA from fluid inclusions in halite that, unlike previously published methods, guarantees removal of potentially contaminating surface-bound DNA. The protocol involves microscopic visualization of cell structures, deliberate surface contamination followed by surface sterilization with acid and bleach washes, and DNA extraction using Amicon centrifugal filters. Methods were verified on halite crystals of four different ages from Saline Valley, California (modern, 36 ka, 64 ka, and 150 ka), with retrieval of algal and archaeal DNA, and characterization of the algal community using ITS1 sequences. The protocol we developed opens up new avenues for study of ancient microbial ecosystems in fluid inclusions, understanding microbial evolution across geological time, and investigating the antiquity of life on earth and other parts of the solar system.
| S-EPMC3111412 | biostudies-literature
Project description:The loss of biodiversity during the Anthropocene is a constant topic of discussion, especially in the top biodiversity hotspots, such as Madagascar. In this regard, the study of preserved organisms through time, like those included in "Madagascar copal", is of relevance. "Madagascar copal" originated from the leguminous tree Hymenaea verrucosa, which produced and produces resin abundantly. In the last 20 years, interest has focused on the scientific study of its biological inclusions, mainly arthropods, described in dozens of publications. The age and origin of the deposits of "Madagascar copal" have not yet been resolved. Our objectives are to determine its age and geographical origin, and thus increase its scientific value as a source of biological/palaeobiological information. Although Hymenaea was established in Madagascar during the Miocene, we did not find geological deposits of copal or amber in the island. It is plausible that the evolution of those deposits was negatively conditioned by the type of soil, by the climate, and by the development of soil/litter microorganisms, which inhibit preservation of the resin pieces in the litter and subsoil over 300 years. Our results indicate that "Madagascar copal" is a Recent resin, up to a few hundred years old, that originated from Hymenaea trees growing in the lowland coastal forests, one of the most endangered ecosystems in the world. The included and preserved biota is representative of that ecosystem today and during historical times. Inclusions in this Recent resin do not have the palaeontological significance that has been mistakenly attributed to them, but they do have relevant implications for studies regarding Anthropocene biodiversity loss in this hottest hotspot.
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Project description:DNA extraction method targeted loci environmental
| PRJNA315949 | ENA
Project description:Purpose of reviewEnvironmental pollutants are threat to human beings. Pollutants can lead to human health and environment hazards. The purpose of this review is to summarize the work done on detection of environmental pollutants using DNA nanosensors and challenges in the areas that can be focused for safe environment.Recent findingsMost of the DNA-based nanosensors designed so far use DNA as recognition element. ssDNA, dsDNA, complementary mismatched DNA, aptamers, and G-quadruplex DNA are commonly used as probes in nanosensors. More and more DNA sequences are being designed that can specifically detect various pollutants even simultaneously in complex milk, wastewater, soil, blood, tap water, river, and pond water samples. The feasibility of direct detection, ease of designing, and analysis makes DNA nanosensors fit for future point-of-care applications.SummaryDNA nanosensors are easy to design and have good sensitivity. DNA component and nanomaterials can be designed in a controlled manner to detect various environmental pollutants. This review identifies the recent advances in DNA nanosensor designing and opportunities available to design nanosensors for unexplored pathogens, antibiotics, pesticides, GMO, heavy metals, and other toxic pollutant.
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Project description:The International Council for Harmonisation (ICH) E6(R2) (International Council for Harmonisation (ICH). ICH harmonised guideline: integrated addendum to ICH E6(R1): guideline for good clinical practice E6(R2). 2016. https://database.ich.org/sites/default/files/E6_R2_Addendum.pdf . Accessed 5 Dec 2019) introduced Quality Tolerance Limits (QTLs) to the industry, and in doing so, modernized quality control for clinical trials. QTLs provide measured feedback on clinical trial parameters previously only used by statistical and clinical functions to track trial progress toward endpoints. Elevating these measures as part of the Quality Management System (QMS) provides greater visibility across clinical trial functions and the enterprise as well as to measures that are important indicators of the state of participant protection and reliability of trial results. In support of this new requirement, TransCelerate developed a framework to guide industry sponsors and their agents in implementing QTLs. This QTL Framework is intended to aid industry's ability to improve the quality of clinical research through the implementation of QTLs in a way that helps protect trial participants and reliability of trial results while meeting Health Authority (HA) expectations. The framework is intended to maximize efficiency and minimize confusion in the implementation of QTLs. The framework includes proposed approaches for implementation of QTLs for a clinical trial as defined in Section 5.0.4 and 5.0.7 of ICH E6(R2) (International Council for Harmonisation (ICH). ICH harmonised guideline: integrated addendum to ICH E6(R1): guideline for good clinical practice E6(R2). 2016. https://database.ich.org/sites/default/files/E6_R2_Addendum.pdf . Accessed 5 Dec 2019) and considerations for setting thresholds.
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Project description:Hantaviruses are important zoonotic pathogens of public health importance that are found on all continents except Antarctica and are associated with hemorrhagic fever with renal syndrome (HFRS) in the Old World and hantavirus pulmonary syndrome (HPS) in the New World. Despite the significant disease burden they cause, no FDA-approved specific therapeutics or vaccines exist against these lethal viruses. The lack of available interventions is largely due to an incomplete understanding of hantavirus pathogenesis and molecular mechanisms of virus replication, including cellular entry. Hantavirus Gn/Gc glycoproteins are the only viral proteins exposed on the surface of virions and are necessary and sufficient to orchestrate virus attachment and entry. In vitro studies have implicated integrins (?1-3), DAF/CD55, and gC1qR as candidate receptors that mediate viral attachment for both Old World and New World hantaviruses. Recently, protocadherin-1 (PCDH1) was demonstrated as a requirement for cellular attachment and entry of New World hantaviruses in vitro and lethal HPS in vivo, making it the first clade-specific host factor to be identified. Attachment of hantavirus particles to cellular receptors induces their internalization by clathrin-mediated, dynamin-independent, or macropinocytosis-like mechanisms, followed by particle trafficking to an endosomal compartment where the fusion of viral and endosomal membranes can occur. Following membrane fusion, which requires cholesterol and acid pH, viral nucleocapsids escape into the cytoplasm and launch genome replication. In this review, we discuss the current mechanistic understanding of hantavirus entry, highlight gaps in our existing knowledge, and suggest areas for future inquiry.
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Project description:Medulloblastoma is the most common embryonal tumor of the central nervous system in childhood. Combined multimodality approaches, including surgery, radiation, and chemotherapy, have improved the outcome of medulloblastoma. Advances in genomic research have shown that medulloblastoma is not a biologically or clinically discrete entity. Previously, the risk was divided according to histology, presence of metastasis, degree of resection, and age at diagnosis. Through the development of integrated genomics, new biology-based risk stratification methods have recently been proposed. It is also important to understand the genetic predisposition of patients with medulloblastoma. Therefore, treatment goal aimed to improve the survival rate with minimal additional adverse effects and reduced long-term sequelae. It is necessary to incorporate genetic findings into the standard of care, and clinical trials that reflect this need to be conducted.
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Project description:The 2011 eruption of Nabro volcano, Eritrea, produced one of the largest volcanic sulphur inputs to the atmosphere since the 1991 eruption of Mt. Pinatubo, yet has received comparatively little scientific attention. Nabro forms part of an off-axis alignment, broadly perpendicular to the Afar Rift, and has a history of large-magnitude explosive silicic eruptions, as well as smaller more mafic ones. Here, we present and analyse extensive petrological data obtained from samples of trachybasaltic tephra erupted during the 2011 eruption to assess the pre-eruptive magma storage system and explain the large sulphur emission. We show that the eruption involved two texturally distinct batches of magma, one of which was more primitive and richer in sulphur than the other, which was higher in water (up to 2.5 wt%). Modelling of the degassing and crystallisation histories demonstrates that the more primitive magma rose rapidly from depth and experienced degassing crystallisation, while the other experienced isobaric cooling in the crust at around 5 km depth. Interaction between the two batches occurred shortly before the eruption. The eruption itself was likely triggered by recharge-induced destabilisation of vertically extensive mush zone under the volcano. This could potentially account for the large volume of sulphur released. Some of the melt inclusions are volatile undersaturated, and suggest that the original water content of the magma was around 1.3 wt%, which is relatively high for an intraplate setting, but consistent with seismic studies of the Afar plume. This eruption was smaller than some geological eruptions at Nabro, but provides important insights into the plumbing systems and dynamics of off-axis volcanoes in Afar.
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