1,721,088 research outputs found
RNA-Seq sample dataset for studying gene circuit host interaction
No full textRNA-Seq sample preparation and sequencing
E. coli NCM3722 cultures were grown and growth stopped 4 hrs post day dilution by adding 1/10 volume of 5% phenol 95% ethanol (v/v). Cells were harvested by centrifugation (4500 x g for 30 min). Supernatants were discarded and pellets drained by gravity flow for 5 min. Pellets wet weights were measured by subtracting the weights of cognate empty tubes. There are 7 samples in total containing 6 different plasmid constructs in the E. coli host. Samples 1 and 2 are biological replicates of the same construct (AND gate in pSB3K3), Sample 3 (Inputs-gfp in pSB3K3), Sample 4 (empty pSB3K3), Sample 5 (AND gate in pSB4K5), Sample 6 (Inputs-gfp in pSB4K5), Sample 7 (empty pSB4K5). The pellet cell samples were frozen at -80 °C before sent out on dry ice to vertis Biotechnologie AG for RNA-Seq. In brief, the cell pellets were incubated with lysozyme for 15 min at room temperature. The total RNA was then isolated using the mirVana RNA isolation kit (Invitrogen) including DNase treatment. Primary transcript enrichment was achieved by rRNA depletion and treatment with Terminator exonuclease (Epicentre) to remove other processed RNAs. RNA was fragmented using RNaseIII and cDNA libraries were built including PCR amplification with barcoded sequencing adaptors. Samples were pooled in approximately equimolar amounts to form one cDNA pool. The cDNA pool was sequenced on an Illumina HiSeq 2000 machine. The short sequence alignment software "Bowtie" (19) was used to map RNA-Seq reads (about 20 million each sample) on the E. coli MG1655 annotated genome (NCBI accession number NC_000913) and the cognate plasmid circuit sequences of each sample. The number of mapped reads for each gene was determined according to their annotated location features (NCBI gff format). The expression levels of genes were subsequently determined using the normalized measure of RPKM (Reads Per Kilobase of transcript per Million mapped reads). Read mapping were visualized using the Integrative Genomics Viewer tool (IGV).RNA-Seq dataset for 7 cell samples, sequenced on Illumina 2500 platform
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Source data and scripts for "A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction"
No full textSplit inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augment a mini-Mu transposon-based screening approach and devise the intein-assisted bisection mapping (IBM) method. IBM robustly reveals clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further show that the use of inteins expands functional sequence space for splitting a protein. We also demonstrate the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins, and that basal activities of highly active proteins can be mitigated by splitting them. Our work offers a generalizable and systematic route towards creating split protein-intein fusions for synthetic biology.Ho, Trevor Y. H.; Wang, Baojun. (2021). Source data and scripts for "A systematic approach to inserting split inteins for Boolean logic gate engineering and basal activity reduction", [dataset]. University of Edinburgh. School of Biological Sciences. Centre for Synthetic and Systems Biology. https://doi.org/10.7488/ds/3001
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Full text linkWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
P1 phagemid-based delivery of Cas9 antimicrobial into Shigella flexneri
Full text linkA bacteriophage P1 phagemid system allowed efficient packaging of a DNA-sequence
specific, Cas9 antimicrobial into transducing particles, which could be used to infect and kill
pathogenic bacteria, such as Shigella flexneri. Although the transduction of a cas9 phagemid
yielded significant antimicrobial effect on S. flexneri, the phagemid lysates produced a
significant non-Cas9-mediated cytotoxic effect, which might be attributed to the presence of
wildtype P1 phage and/or other cytotoxic factors in phagemid lysates. Treatment of
phagemid lysates with a low concentration of polythene glycol (PEG) reduced the titre of
wildtype P1 phage and led to a lower cytotoxicity of phagemid lysates on S. flexneri cells.
Mutations introduced into the P1 lytic origin of replication (oriL) inhibited its lytic stage DNA
replication, yet the mutant was incapable of producing phagemid transducing particles.
Deletion of the DNA packaging site, pac, from the P1 genome significantly reduced the titre
of wildtype P1 phage. A Δpac mutation, however, did not reduce the cytotoxicity of phagemid
lysates significantly, when used for treatment of S. flexneri in vitro and in a zebrafish larvae
infection model. An alternative P4 cosmid system allowed efficient packaging of cas9
construct into transducing units without the contamination of host and/or phage DNA.
Contrastingly, treatment of S. flexneri with P4 cosmid lysates gave negligible cytotoxic killing
of the bacterial cells, suggesting that the non-Cas9-mediated killing effect might be attributed
to impurities associated with the P1 phagemid transducing units and/or due to inherent
properties of P1 transduction. Nevertheless, the versatility of the P1 phagemid system
allowed an inducible Cpf1-mediated, vector curing function to be incorporated into the
phagemid while retaining its Cas9-mediated antimicrobial effect on S. flexneri cells.
Furthermore, the P1 cas9 phagemid was compatible with the ΔnadC autotrophy
complementation system, providing antibiotic-free maintenance and selection of the modified
vector in ΔnadC E. coli. Taken together, the phagemid and/or cosmid system that produces
pure transducing particles might be the key to achieving a high Cas9 antimicrobial effect on
S. flexneri cells with negligible lysate cytotoxicity
- …
