scholarly journals Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10947
Author(s):  
James A. Fellows Yates ◽  
Thiseas C. Lamnidis ◽  
Maxime Borry ◽  
Aida Andrades Valtueña ◽  
Zandra Fagernäs ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Genomic Data ◽  
Extended Version ◽  
Research Groups ◽  
High Quality ◽  
Diverse Range ◽  
Dna Analyses ◽  
Heterogeneous Landscape ◽  
Analytical Standards

The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.

scholarly journals Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager

2020 ◽  
Author(s):  
James A. Fellows Yates ◽  
Thiseas C. Lamnidis ◽  
Maxime Borry ◽  
Aida Andrades Valtueña ◽  
Zandra Fagernäs ◽  
...  
Keyword(s):  
Ancient Dna ◽  
Genomic Data ◽  
Extended Version ◽  
Research Groups ◽  
Sequencing Data ◽  
High Quality ◽  
Diverse Range ◽  
Heterogeneous Landscape ◽  
Analytical Standards

AbstractThe broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present nf-core/eager, an advanced and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practises. This new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term lifecycle for the pipeline. nf-core/eager will assist in ensuring that ancient DNA sequencing data can be used by a diverse range of research groups and fields.

scholarly journals The First Seal Hunter Families on Gotland - On the Mesolithic Occupation in the Stora Förvar Cave

2021 ◽  
Vol 7 (1) ◽  
pp. 65-87
Author(s):  
Christian Lindqvist ◽  
Göran Possnert
Keyword(s):  
Carbon Isotope ◽  
Ancient Dna ◽  
Subsistence Economy ◽  
Dna Analyses ◽  
Base Camp ◽  
Burial Customs ◽  
Initial Settlement ◽  
Burial Cave

The article presents some results of a joint interdisciplinary researchproject, The Stora Förvar Cave and Gotlands peopling, faunal history and subsistence economy/diet development from the Boreal to the Subatlantic, initiated by Christian Lindqvist in 1991. Its objectives include investigations of a number of crucial issues in a long-term perspective, such as the initial settlement, the early faunal history, the early subsistence economy and diet, but also the character of the Mesolithic-Neolithic shift on Gotland, by means of human and zooosteological, carbon isotope and ancient DNA analyses. The article presents and discusses artefact, osteological, and 13C and 14C data and interpretations concerning the duration and character of the Mesolithic occupation —temporary kill/butchering site, seasonal hunting station, semi-sedentary base camp or burial cave —as well as osteobiographical data on the identified human individuals and their burial customs.

scholarly journals The influence of sample quantity and lysis parameters on the success of ancient DNA extraction from skeletal remains

BioTechniques ◽  
2021 ◽  
Author(s):  
Alina Euskirchen ◽  
Larissa Hartmann ◽  
Janine Mazanec ◽  
Patrick Wittmeier ◽  
Susanne Hummel
Keyword(s):  
Mitochondrial Dna ◽  
Sample Preparation ◽  
Dna Extraction ◽  
Ancient Dna ◽  
Skeletal Remains ◽  
Sample Material ◽  
Chromosomal Dna ◽  
High Quality ◽  
Dna Analyses ◽  
Lysis Time

DNA extraction is of utmost importance in archaeobiology, as it determines the success of further DNA analyses. This study concentrates on the success of ancient DNA extraction using silica spin columns and PCR-based analysis from archaeological skeletal material and investigates the influence of sample quantity, lysis time and lysis temperature during sample preparation. The results show that lysis times ranging from 2 to 48 h are suitable, and that lysis should be carried out at a constant temperature of 56°C. Concerning sample quantity, 10 mg for mitochondrial DNA and 50 mg for chromosomal DNA are sufficient for high quality analyses. Thus invaluable sample material can be saved, and time of sample preparation can be reduced considerably.

scholarly journals Ancient genomes redate the extinction of Sussemionus, a subgenus of Equus, to late Holocene

2021 ◽  
Author(s):  
Dawei Cai ◽  
Siqi Zhu ◽  
Mian Gong ◽  
Naifan Zhang ◽  
Jia Wen ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
North America ◽  
Ancient Dna ◽  
Fossil Record ◽  
Late Holocene ◽  
Northern China ◽  
High Quality ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The exceptionally-rich fossil record available for the equid family has provided textbook examples of macroevolutionary changes. Horses, asses and zebras represent three extant subgenus of Equus lineage, while the Sussemionus subgenus is another remarkable Equus lineage ranging from North America to Ethiopia in Pleistocene. We sequenced 26 archaeological specimens from northern China in Holocene showing morphological features reminiscent of Equus ovodovi, a species representative of Sussemionus, and further confirmed them as this species by genetic analyses. Thus, we present the first high-quality complete genome of the Sussemionus that we sequenced to 12.0× depth-of-coverage and demonstrate that it survived until ~3,500 years ago, despite the continued demographic collapse during the Last Glacial Maximum and the great human expansion in East Asia. We also confirmed the Equus tree, and found Sussemionus diverged from the ancestor of non-caballine equids ~2.3-2.7 Million years ago and admixture events could have taken place between them. Our works suggest the small genetic diversity but not the enhanced inbreeding mainly limited the chances of survival of the species, and illustrates how ancient DNA can inform on extinction dynamics and the long-term resilience of species surviving in cryptic population pockets.

ANALYSIS OF ABDOMINAL TYPHOID INCIDENCE IN THE SOUTH REGION OF THE KYRGYZ REPUBLIC

2020 ◽  
pp. 43-48
Author(s):  
Zakirova J.S. ◽  
Nadirbekova R.A. ◽  
Zholdoshev S.T.
Keyword(s):  
Drinking Water ◽  
Typhoid Fever ◽  
Risk Groups ◽  
The Body ◽  
Kyrgyz Republic ◽  
Radiation Factor ◽  
High Quality ◽  
Two Generations ◽  
Immunological Deficiency

The article analyze the long-term morbidity, spread of typhoid fever in the southern regions of the Kyrgyz republic, and remains a permanent epidemic focus in the Jalal-Abad region, where against the low availability of the population to high-quality drinking water, an additional factor on the body for more than two generations and radiation factor, which we confirmed by the spread among the inhabitants of Mailuu-Suu of nosological forms of the syndrome of immunological deficiency, as a predictor of risk groups for infectious diseases, including typhoid fever.

One-step synthesis of high-quality vanadium disulfide quantum dots for long-term lysosome-targetable imaging

2021 ◽  
pp. 130544
Author(s):  
Dan Yang ◽  
Liwen Chen ◽  
Le Wang ◽  
Zhongjie Cui ◽  
Zhuoqi Wen ◽  
...  
Keyword(s):  
Quantum Dots ◽  
High Quality ◽  
One Step

scholarly journals Lyell, the Geikies and Croll's observations on terrestrial glacial sediments and landforms

2021 ◽  
pp. 1-14
Author(s):  
James ROSE
Keyword(s):  
Climate Change ◽  
High Quality ◽  
Glacial Sediments ◽  
Direct Observations ◽  
The Social ◽  
The Status ◽  
Social And Physical Environment ◽  
Glacial Landforms

ABSTRACT Within the context of the work and achievements of James Croll, this paper reviews the records of direct observations of glacial landforms and sediments made by Charles Lyell, Archibald and James Geikie and James Croll himself, in order to evaluate their contributions to the sciences of glacial geology and Quaternary environmental change. The paper outlines the social and physical environment of Croll's youth and contrasts this with the status and experiences of Lyell and the Geikies. It also outlines the character and role of the ‘Glasgow School’ of geologists, who stimulated Croll's interest into the causes of climate change and directed his focus to the glacial and ‘interglacial’ deposits of central Scotland. Contributions are outlined in chronological order, drawing attention to: (i) Lyell's high-quality observations and interpretations of glacial features in Glen Clova and Strathmore and his subsequent rejection of the glacial theory in favour of processes attributed to floating icebergs; (ii) the significant impact of Archibald Geikie's 1863 paper on the ‘glacial drift of Scotland’, which firmly established the land-ice theory; (iii) the fact that, despite James Croll's inherent dislike of geology and fieldwork, he provided high-quality descriptions and interpretations of the landforms and sediments of central Scotland in order to test his theory of climate change; and (iv) the great communication skills of James Geikie, enhanced by contacts and evidence from around the world. It is concluded that whilst direct observations of glacial landforms and sediments were critical to the long-term development of the study of glaciation, the acceptance of this theory was dependent also upon the skills, personality and status of the Geikies and Croll, who developed and promoted the concepts. Sadly, the subsequent rejection of the land-ice concept by Lyell resulted in the same factors challenging the acceptance of the glacial theory.

scholarly journals Unconventional effects of long-term storage of microwave-modified chicken egg white lysozyme preparations

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Grzegorz Leśnierowski ◽  
Tianyu Yang ◽  
Renata Cegielska-Radziejewska
Keyword(s):  
Microwave Radiation ◽  
Egg White ◽  
Process Time ◽  
High Quality ◽  
Chicken Egg ◽  
Egg White Lysozyme ◽  
Physicochemical Changes ◽  
Long Term Storage ◽  
Term Storage

AbstractThermal modification is an effective method that induces significant expansion of the antimicrobial properties and other valuable properties of chicken egg white lysozyme. In our latest research, a new innovative method of enzyme modification was developed, in which microwave radiation was used as an energy source to process liquid lysozyme concentrate (LLC). After modification, high-quality preparations were obtained. However, long-term storage in a concentrated form initiated various processes that caused darkening over time and could also lead to other significant changes to their structure and, consequently, to their functional properties. This necessitated multidirectional research to explain this phenomenon. This paper presents the results of research aimed at assessing the physicochemical changes in the properties of microwave-modified lysozyme in the form of a liquid concentrate after long-term storage under refrigeration conditions. The assessment also considered the conditions under the acidity of the modifying medium and the duration of the microwave modification. The analysis showed that the values of the basic parameters determining the quality and usefulness of the modified enzyme significantly improved during long-term storage of the preparations. The greatest changes were observed in the preparations modified for the longest time and in the most acidic environment (process time 260 s, pH 2.0), the number of oligomers under these conditions increased by 18% after 12 months of holding, and the surface hydrophobicity increased by as much as 31%. In addition, microbiological tests showed that the preparations of microwave-modified lysozyme had an effect on gram-positive bacteria as well as on gram-negative, and this effect was significantly enhanced after 12 months. The results confirm that LLC modification with microwave radiation is a highly efficient method to prepare high-quality and high utility potential lysozyme. Notably, an interesting and important phenomenon was the observation of the unconventional behaviour of the preparations during their long-term storage, which increased their utility potential significantly.

scholarly journals The Passive Microwave Neural Network Precipitation Retrieval Algorithm for Climate Applications (PNPR-CLIM): Design and Verification

2021 ◽  
Vol 13 (9) ◽  
pp. 1701
Author(s):  
Leonardo Bagaglini ◽  
Paolo Sanò ◽  
Daniele Casella ◽  
Elsa Cattani ◽  
Giulia Panegrossi
Keyword(s):  
Neural Network ◽  
Passive Microwave ◽  
Retrieval Algorithm ◽  
Climate Data ◽  
High Quality ◽  
Data Record ◽  
Global Precipitation ◽  
Climate Data Record

This paper describes the Passive microwave Neural network Precipitation Retrieval algorithm for climate applications (PNPR-CLIM), developed with funding from the Copernicus Climate Change Service (C3S), implemented by ECMWF on behalf of the European Union. The algorithm has been designed and developed to exploit the two cross-track scanning microwave radiometers, AMSU-B and MHS, towards the creation of a long-term (2000–2017) global precipitation climate data record (CDR) for the ECMWF Climate Data Store (CDS). The algorithm has been trained on an observational dataset built from one year of MHS and GPM-CO Dual-frequency Precipitation Radar (DPR) coincident observations. The dataset includes the Fundamental Climate Data Record (FCDR) of AMSU-B and MHS brightness temperatures, provided by the Fidelity and Uncertainty in Climate data records from Earth Observation (FIDUCEO) project, and the DPR-based surface precipitation rate estimates used as reference. The combined use of high quality, calibrated and harmonized long-term input data (provided by the FIDUCEO microwave brightness temperature Fundamental Climate Data Record) with the exploitation of the potential of neural networks (ability to learn and generalize) has made it possible to limit the use of ancillary model-derived environmental variables, thus reducing the model uncertainties’ influence on the PNPR-CLIM, which could compromise the accuracy of the estimates. The PNPR-CLIM estimated precipitation distribution is in good agreement with independent DPR-based estimates. A multiscale assessment of the algorithm’s performance is presented against high quality regional ground-based radar products and global precipitation datasets. The regional and global three-year (2015–2017) verification analysis shows that, despite the simplicity of the algorithm in terms of input variables and processing performance, the quality of PNPR-CLIM outperforms NASA GPROF in terms of rainfall detection, while in terms of rainfall quantification they are comparable. The global analysis evidences weaknesses at higher latitudes and in the winter at mid latitudes, mainly linked to the poorer quality of the precipitation retrieval in cold/dry conditions.

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