Abstract This article summarizes an attempt at reconstructing and using T-shaped wooden spades as well as reflecting on the connection between structures and resource use around Knudmosen near ...Herning. However, an important limitation on this process is that very few spades are dated. The conclusion is that the spades are relatively easy to produce and well suited to digging peat.
Metagenomics is a segment of conventional microbial genomics dedicated to the sequencing and analysis of combined genomic DNA of entire environmental samples. The most critical step of the ...metagenomic data analysis is the reconstruction of individual genes and genomes of the microorganisms in the communities using metagenomic assemblers - computational programs that put together small fragments of sequenced DNA generated by sequencing instruments. Here, we describe the challenges of metagenomic assembly, a wide spectrum of applications in which metagenomic assemblies were used to better understand the ecology and evolution of microbial ecosystems, and present one of the most efficient microbial assemblers, SPAdes that was upgraded to become applicable for metagenomics.
•Boreal birds will experience northward shifts as temperatures become warmer.•As new analytical methods and forecasting tools arise, decision-makers are better equipped to predict the impacts of ...climate change on biodiversity and develop more resilient management strategies through data-informed decision-making.•Our work represents a comprehensive analysis of projected dynamic disturbance-mediated changes combined with boreal bird density models at the ecozone scale and provides realistic short- and long-term projections with important implications for northern biodiversity conservation and management.•Future climate-mitigated distribution shifts and population declines of boreal landbirds will require targeted conservation actions. Our results highlight the importance of the NT as a potential refugium for many boreal-breeding landbird species in Canada.
Climate change presents a major threat to biodiversity globally. Northern ecosystems, such as Canada's boreal forest, are predicted to experience particularly severe climate-induced changes. These changes may reduce the carrying capacity and habitat suitability of the boreal forest for many wildlife species. Boreal birds are susceptible to both direct and indirect effects of climate change, and several studies have predicted northward shifts in species distributions as temperatures become warmer. We forecasted spatially-explicit changes in the densities of 72 boreal landbird species using integrated climate change projections and a forest dynamics model in the Taiga Plains ecozone of the Northwest Territories (NT), Canada, over the 2011–2091 horizon. We 1) identified "winner," "loser," and "bellringer" species over short (2031) and long-term (2091) forecasts, 2) mapped landbird range and density changes under three contrasting Global Circulation Models (GCMs), and 3) quantify differences in landbird density predictions across a latitudinal gradient. Species that showed a moderate increase or decrease in their predicted abundance were considered "winners" and "losers," respectively. Species that showed a marked increase or decrease – a doubling or halving – of their predicted abundance in all three GCMs, were termed "bellringers". From 2011–2031, only 2/72 (2.8%) were considered winners, and 3/72 (4.2%) were losers. From 2011–2091, the abundance of more species was predicted to change: 26/72 (36.1%) were winners, and 10/72 species (13.9%) were losers. Four species were considered bellringers: Gray-cheeked Thrush, White-crowned Sparrow, Fox Sparrow, and American Tree Sparrow. Overall, projected range shifts were strongly oriented along a southeast-to-northwest axis. Shifts to the north and south were evenly distributed among all three GCMs. Our results suggest that future climate-mitigated distribution shifts and population declines of boreal landbirds will require targeted conservation actions. They also highlight the importance of the NT as a potential refugium for many boreal-breeding landbird species in Canada.
Sequence data assembly is a foundational step in high‐throughput sequencing, with untold consequences for downstream analyses. Despite this, few studies have interrogated the many methods for ...assembling phylogenomic UCE data for their comparative efficacy, or for how outputs may be impacted. We study this by comparing the most commonly used assembly methods for UCEs in the under‐studied bee lineage Nomiinae and a representative sampling of relatives. Data for 63 UCE‐only and 75 mixed taxa were assembled with five methods, including ABySS, HybPiper, SPAdes, Trinity and Velvet, and then benchmarked for their relative performance in terms of locus capture parameters and phylogenetic reconstruction. Unexpectedly, Trinity and Velvet trailed the other methods in terms of locus capture and DNA matrix density, whereas SPAdes performed favourably in most assessed metrics. In comparison with SPAdes, the guided‐assembly approach HybPiper generally recovered the highest quality loci but in lower numbers. Based on our results, we formally move Clavinomia to Dieunomiini and render Epinomia once more a subgenus of Dieunomia. We strongly advise that future studies more closely examine the influence of assembly approach on their results, or, minimally, use better‐performing assembly methods such as SPAdes or HybPiper. In this way, we can move forward with phylogenomic studies in a more standardized, comparable manner.
We benchmarked the hybrid assembly approaches of MaSuRCA, SPAdes, and Unicycler for bacterial pathogens using Illumina and Oxford Nanopore sequencing by determining genome completeness and accuracy, ...antimicrobial resistance (AMR), virulence potential, multilocus sequence typing (MLST), phylogeny, and pan genome. Ten bacterial species (10 strains) were tested for simulated reads of both mediocre- and low-quality, whereas 11 bacterial species (12 strains) were tested for real reads.
Unicycler performed the best for achieving contiguous genomes, closely followed by MaSuRCA, while all SPAdes assemblies were incomplete. MaSuRCA was less tolerant of low-quality long reads than SPAdes and Unicycler. The hybrid assemblies of five antimicrobial-resistant strains with simulated reads provided consistent AMR genotypes with the reference genomes. The MaSuRCA assembly of Staphylococcus aureus with real reads contained msr(A) and tet(K), while the reference genome and SPAdes and Unicycler assemblies harbored blaZ. The AMR genotypes of the reference genomes and hybrid assemblies were consistent for the other five antimicrobial-resistant strains with real reads. The numbers of virulence genes in all hybrid assemblies were similar to those of the reference genomes, irrespective of simulated or real reads. Only one exception existed that the reference genome and hybrid assemblies of Pseudomonas aeruginosa with mediocre-quality long reads carried 241 virulence genes, whereas 184 virulence genes were identified in the hybrid assemblies of low-quality long reads. The MaSuRCA assemblies of Escherichia coli O157:H7 and Salmonella Typhimurium with mediocre-quality long reads contained 126 and 118 virulence genes, respectively, while 110 and 107 virulence genes were detected in their MaSuRCA assemblies of low-quality long reads, respectively. All approaches performed well in our MLST and phylogenetic analyses. The pan genomes of the hybrid assemblies of S. Typhimurium with mediocre-quality long reads were similar to that of the reference genome, while SPAdes and Unicycler were more tolerant of low-quality long reads than MaSuRCA for the pan-genome analysis. All approaches functioned well in the pan-genome analysis of Campylobacter jejuni with real reads.
Our research demonstrates the hybrid assembly pipeline of Unicycler as a superior approach for genomic analyses of bacterial pathogens using Illumina and Oxford Nanopore sequencing.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Most research on boreal populations of woodland caribou (Rangifer tarandus caribou) has been conducted in areas of high anthropogenic disturbance. However, a large portion of the species' range ...overlaps relatively pristine areas primarily affected by natural disturbances, such as wildfire. Climate‐driven habitat change is a key concern for the conservation of boreal‐dependent species, where management decisions have yet to consider knowledge from multiple ecological domains integrated into a cohesive and spatially explicit forecast of species‐specific habitat and demography. We used a novel ecological forecasting framework to provide climate‐sensitive projections of habitat and demography for five boreal caribou monitoring areas within the Northwest Territories (NWT), Canada, over 90 years. Importantly, we quantify uncertainty around forecasted mean values. Our results suggest habitat suitability may increase in central and southwest regions of the NWT's Taiga Plains ecozone but decrease in southern and northwestern regions driven by conversion of coniferous to deciduous forests. We do not project that boreal caribou population growth rates will change despite forecasted changes to habitat suitability. Our results emphasize the importance of efforts to protect and restore northern boreal caribou habitat despite climate uncertainty while highlighting expected spatial variations that are important considerations for local people who rely on them. An ability to reproduce previous work, and critical thought when incorporating sources of uncertainty, will be important to refine forecasts, derive management decisions, and improve conservation efficacy for northern species at risk.
The essay explores problems of translating Russian classical Literature into English. It happens that even one word is capable of changing if not the plot, then the profound philosophical message of ...a text. The double meaning, direct and indirect, of certain words, and their connections with other parts of the text that remain unnoticed, eventually lead to oversimplifying and narrowing the dimension and scale of the composition as a whole in the perception of readers incapable of comprehending the original. Comparative analyses of only two words in several translations of Dostoevsky’s Crime and Punishment show the complexity and the responsibility of translations, especially the translation of a literary work, where the words rise into “divine height” of their signified and hidden meanings.
"The construction of opera scenarios involves the development of a dramatic and narrative framework upon which an opera is built. These scenarios serve as the foundation for the libretto, music, ...staging, and overall production of the opera. In this introduction, we will explore the principles and procedures that guide the creation of opera scenarios. In summary, constructing an opera scenario is a complex and collaborative process that involves the careful consideration of narrative, character, music, and cultural context. The principles and procedures outlined here provide a foundation for the creation of opera scenarios that can captivate audiences and convey the depth of human emotion through music and drama. Over time, the evolution of the singing voice follows a phenomenon of symbiosis between words and music. The intertwining of the act of speaking with that of singing is constantly found in the concerns of the creators in ancient monody, Greek declamation, Gregorian chant, in the polyphonic style, in the opera performance as well as in all the ramifications of the vocal genre. Keywords: opera scenario construction, musical drama, analysis of the libretto, Eugene Onegin, The Queen of Spades."
The pathless harbourless spade Brodber, Erna May
The Sociological review (Keele),
05/2020, Letnik:
68, Številka:
3
Journal Article
Recenzirano
Migration studies have generally painted the African Jamaican as the group that migrates, this being supposedly a post-emancipation act undertaken to better one’s self economically. This article ...maintains that Jamaicans of all ethnicities and races have been involved in migration: it is a part of the culture and from the earliest post Columbian times. The article posits that the true distinction in migration between races and ethnicities inheres in the geographic end product of migration: others travel to reconnect with ancestral lands but the African Jamaican has no such options as yet and travels to spaces perceived as the ancestral preserves of their former enslavers. In their travels they meet other Africans of the diaspora, like them raised on the margins of the society as has been the nature of enslavement in the New World. The article asks the question: what is the outcome of such meetings carrying as they all do the historical experience of marginality in the societies in which they have been enslaved? The article offers no answer but shares the journey to arriving at one.
Abstract
Lichens are valuable models in symbiosis research and promising sources of biosynthetic genes for biotechnological applications. Most lichenized fungi grow slowly, resist aposymbiotic ...cultivation, and are poor candidates for experimentation. Obtaining contiguous, high-quality genomes for such symbiotic communities is technically challenging. Here, we present the first assembly of a lichen holo-genome from metagenomic whole-genome shotgun data comprising both PacBio long reads and Illumina short reads. The nuclear genomes of the two primary components of the lichen symbiosis—the fungus Umbilicaria pustulata (33 Mb) and the green alga Trebouxia sp. (53 Mb)—were assembled at contiguities comparable to single-species assemblies. The analysis of the read coverage pattern revealed a relative abundance of fungal to algal nuclei of ∼20:1. Gap-free, circular sequences for all organellar genomes were obtained. The bacterial community is dominated by Acidobacteriaceae and encompasses strains closely related to bacteria isolated from other lichens. Gene set analyses showed no evidence of horizontal gene transfer from algae or bacteria into the fungal genome. Our data suggest a lineage-specific loss of a putative gibberellin-20-oxidase in the fungus, a gene fusion in the fungal mitochondrion, and a relocation of an algal chloroplast gene to the algal nucleus. Major technical obstacles during reconstruction of the holo-genome were coverage differences among individual genomes surpassing three orders of magnitude. Moreover, we show that GC-rich inverted repeats paired with nonrandom sequencing error in PacBio data can result in missing gene predictions. This likely poses a general problem for genome assemblies based on long reads.
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