Here, the complete chloroplast genome of Keteleeria fortunei, a vulnerable species in China, was sequenced by next-generation sequencing platform. Its circular genome was 117,183 bp in length and the ...GC content was 38.5%. A total of 101 genes were annotated, including 4 rRNA genes, 20 tRNA genes, and 71 protein coding genes. This study would further our understanding of the genomics and the conservation and utilization of K. fortunei.
Background
With the advent of next-generation sequencing techniques, culture-independent metagenome approaches have now made it possible to predict possible presence of genes in the environmental ...bacteria most of which may be non-cultivable. Short reads obtained from the deep sequencing can be assembled into long contigs some of which include plasmids. Plasmids are the circular double stranded DNA in bacteria and known as one of the major carriers of antibiotic resistance genes.
Objective
Metagenomic analyses, especially focused on plasmids, could help us predict dissemination mechanisms of antibiotic resistance genes in the environment. However, with the availability of a myriad of metagenomic assemblers, the selection of the most appropriate metagenome assembler for the plasmid metagenome study might be challenging. Therefore, in this study, we compared five open source assemblers to suggest most effective way of plasmid metagenome analysis.
Methods
IDBA-UD, MEGAHIT, SPAdes, SOAPdenovo2, and Velvet are compared for conducting plasmid metagenome analyses using two water samples.
Results
Our results clearly showed that abundance and types of antibiotic resistance genes on plasmids varied depending on the selection of assembly tools. IDBA-UD and MEGAHIT demonstrated the overall best assembly statistics with high N50 values with higher portion of longer contigs.
Conclusion
These two assemblers also detected more diverse plasmids. Among the two, MEGAHIT showed more memory efficient assembly, therefore we suggest that the use of MEGAHIT for plasmid metagenome analysis may offer more diverse plasmids with less computer resource required. Here, we also summarized a fundamental plasmid metagenome work flow, especially for antibiotic resistance gene investigation.
De novo genome assembly can be challenging due to inherent properties of the reads, even when using current state-of-the-art assembly tools based on de Bruijn graphs. Often users are not ...bio-informaticians and, in a black box approach, utilise assembly parameters such as contig length and N50 to generate whole genome sequences, potentially resulting in mis-assemblies.
Utilising several assembly tools based on de Bruijn graphs like Velvet, SPAdes and IDBA, we demonstrate that at the optimal N50, mis-assemblies do occur, even when using the multi-k-mer approaches of SPAdes and IDBA. We demonstrate that whole genome mapping can be used to identify these mis-assemblies and can guide the selection of the best k-mer size which yields the highest N50 without mis-assemblies.
We demonstrate the utility of whole genome mapping (WGM) as a tool to identify mis-assemblies and to guide k-mer selection and higher quality de novo genome assembly of bacterial genomes.
New sequencing technologies have opened the way to the discovery and the characterization of pathogenic viruses in clinical samples. However, the use of these new methods can require an amplification ...of viral RNA prior to the sequencing. Among all the available methods, the procedure based on the use of Phi29 polymerase produces a huge amount of amplified DNA. However, its major disadvantage is to generate a large number of chimeric sequences which can affect the assembly step. The pre-process method proposed in this study strongly limits the negative impact of chimeric reads in order to obtain the full-length of viral genomes.
Three different assembly softwares (ABySS, Ray and SPAdes) were tested for their ability to correctly assemble the full-length of viral genomes. Although in all cases, our pre-processed method improved genome assembly, only its combination with the use of SPAdes allowed us to obtain the full-length of the viral genomes tested in one contig.
The proposed pipeline is able to overcome drawbacks due to the generation of chimeric reads during the amplification of viral RNA which considerably improves the assembling of full-length viral genomes.
Iron Age pit zone alignments are a relatively newly recognized type of system and research has focused primarily on why the pits were dug. There are numerous proposals, although the general ...perception of them as a kind of defence system hasnot changed since it was put forward by Eriksen and Rindel in 2001. But an experimental archaeological approach is, as of yet, untested, and by asking the ‘how’ before the ‘why’ the enigmatic tracts of thousands of pit-holes can be analysed froma new angle. Thus, in this article, the focus moves from the collective pit zone alignments to each individual pit-hole and the process involved in digging same. Systematic studies of spades, attempts to reconstruct double-spades, experimentsdigging pit-holes and the construction and use of parts of pit zone alignments helps make it probable that the inhabitants of a village from the pre-Roman Iron Age would have been able to dig a stretch of 100 metres by 4 metres of a pit zonealignment, broadly equivalent to seven holes, in 1 day. The experiments also made it clear that the pit zone alignment did not constitute an obstacle to sheep or cattle, and that they only, under exceptional circumstances, were an obstacle to people. But most significant was the insight gained into the process of digging the holes in terms of the organization of work, which undoubtedly lay behind the excavation work.
Iron Age pit zone alignments are a relatively newly recognized type of system and research has focused primarily on why the pits were dug. There are numerous proposals, although the general ...perception of them as a kind of defence system has not changed since it was put forward by Eriksen and Rindel in 2001. But an experimental archaeological approach is, as of yet, untested, and by asking the 'how' before the 'why' the enigmatic tracts of thousands of pit-holes can be analysed from a new angle. Thus, in this article, the focus moves from the collective pit zone alignments to each individual pit-hole and the process involved in digging same. Systematic studies of spades, attempts to reconstruct double-spades, experiments digging pit-holes and the construction and use of parts of pit zone alignments helps make it probable that the inhabitants of a village from the pre-Roman Iron Age would have been able to dig a stretch of 100 metres by 4 metres of a pit zone alignment, broadly equivalent to seven holes, in 1 day. The experiments also made it clear that the pit zone alignment did not constitute an obstacle to sheep or cattle, and that they only, under exceptional circumstances, were an obstacle to people. But most significant was the insight gained into the process of digging the holes in terms of the organization of work, which undoubtedly lay behind the excavation work
The purpose of this study is to examine the kinds of reasoning that African American young men learn and develop when playing Spades, a common cultural practice in African American communities. The ...qualitative study found that the Spades players routinely consider multiple variables and their mathematical relationships when making decisions. The variables considered by the players when bidding include card strength, the number of cards held in any particular suit, player bidding tendencies, player levels of expertise, the current score of the game, and the level of confidence in one’s partner. The paper claims that the forms of reasoning explored in this study connect well to those of scientists who engage in modeling: a central practice in science. A major implication is that model-based instruction in science classrooms is akin to cultural modeling (Lee in
American Educational Research Journal
, 38(1), 97–141,
2001
), as the pedagogy leverages the assets and resources of African American young men learned through cultural practice. Such pedagogies could therefore have a positive effect upon engagement and achievement of African American young men in science.
В статье представлен искусствоведческий анализ ряда работ отечественных режиссеров, в фокусе творческого интереса которых находится «Пиковая дама» Пушкина-Чайковского. Опираясь на методы ...интерпретации и реинтерпретации, автор останавливается на таких художественных образцах, как фильм-балет «Три карты», созданный по мотивам повести А.С. Пушкина «Пиковая дама» на музыку К. Молчанова (1983), опера «Пиковая дама» в постановке Ш. Херхайма и М. Янсонса (Амстердам, 2016) и Х. Нойен-фельса и М. Янсонса (Зальцбург, 2018), а также игровое кино С. Подгаевского («Пиковая дама. Черный обряд»), П. Лунгина («Дама пик»), А. Домогарова-младшего («Пиковая дама. Зазеркалье»), выпущенное в прокат в период с 2015 по 2018 гг. Выявляя в каждом из указанных произведений наличие таких визуальных символов, как вода и зеркало, автор ставит перед собой задачу разобраться в том, насколько их очевидное присутствие в обозначенных художественных образцах дает возможность квалифицировать их либо с позиции интерпретации, либо - реинтерпретации первоисточника.
The study examines the resources related to science that African American young men learn and develop by playing a card game called Spades, a common cultural practice in African American communities ...that dates back to the Civil War Era. The qualitative study examines what the Spades players at a local high school consider when making decisions about what cards to play. A significant finding is that the players use, learn and develop resources such as the ability to make observations, draw inferences, and use empirical data to inform future actions and decisions. Such reasoning bears a resemblance to central practices of science and challenges long held deficit views of African American young men. Implications of the research findings are discussed.
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