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RanDeL-Seq: a High-Throughput Method to Map Viral cis- andtrans-Acting Elements
No full textIt has long been known that noncoding genomic regions can be obligate
cis elements acted upon in trans by gene products. In viruses, cis
elements regulate gene expression, encapsidation, and other maturation
processes, but mapping these elements relies on targeted iterative
deletion or laborious prospecting for rare spontaneously occurring
mutants. Here, we introduce a method to comprehensively map viral cis
and trans elements at single-nucleotide resolution by high-throughput
random deletion. Variable-size deletions are randomly generated by
transposon integration, excision, and exonuclease chewback and then
barcoded for tracking via sequencing (i.e., random deletion library
sequencing [RanDeL-seq]). Using RanDeL-seq, we generated and screened
>23,000 HIV-1 variants to generate a single-base resolution map of
HIV-1’s cis and trans elements. The resulting landscape recapitulated
HIV-1’s known cis-acting elements (i.e., long terminal repeat [LTR],
W, and Rev response element [RRE]) and, surprisingly, indicated that
HIV-1’s central DNA flap (i.e., central polypurine tract [cPPT] to
central termination sequence [CTS]) is as critical as the LTR, W, and
RRE for long-term passage. Strikingly, RanDeL-seq identified a
previously unreported similar to 300-bp region downstream of RRE
extending to splice acceptor 7 that is equally critical for sustained
viral passage. RanDeL-seq was also used to construct and screen a
library of >90,000 variants of Zika virus (ZIKV). Unexpectedly,
RanDeL-seq indicated that ZIKV’s cis-acting regions are larger than the
untranscribed (UTR) termini, encompassing a large fraction of the
nonstructural genes. Collectively, RanDeL-seq provides a versatile
framework for generating viral deletion mutants, enabling discovery of
replication mechanisms and development of novel antiviral therapeutics,
particularly for emerging viral infections.
IMPORTANCE Recent studies have renewed interest in developing novel
antiviral therapeutics and vaccines based on defective interfering
particles (DIPs)-a subset of viral deletion mutants that conditionally
replicate. Identifying and engineering DIPs require that viral cis- and
trans-acting elements be accurately mapped. Here, we introduce a
high-throughput method (random deletion library sequencing
[RanDeL-seq]) to comprehensively map cis- and trans-acting elements
within a viral genome. RanDeL-seq identified essential cis elements in
HIV, including the obligate nature of the once-controversial viral
central polypurine tract (cPPT), and identified a new cis region
proximal to the Rev responsive element (RRE). RanDeL-seq also identified
regions of Zika virus required for replication and packaging. RanDeL-seq
is a versatile and comprehensive technique to rapidly map cis and trans
regions of a genome
Author response
No full textDevelopmental programs have the fidelity to form neural circuits with the same structure and function among individuals of the same species. It is less well understood, however, to what extent entire neural circuits of different individuals are similar. Previously, we reported the neuronal connectome of the visual eye circuit from the head of a Platynereis dumerilii larva (Randel et al., 2014). We now report a full-body serial section transmission electron microscopy (ssTEM) dataset of another larva of the same age, for which we describe the connectome of the visual eyes and the larval eyespots. Anatomical comparisons and quantitative analyses of the two circuits reveal a high inter-individual stereotypy of the cell complement, neuronal projections, and synaptic connectivity, including the left-right asymmetry in the connectivity of some neurons. Our work shows the extent to which the eye circuitry in Platynereis larvae is hard-wired
Dynamic variability of the Asian monsoon anticyclone observed in potential vorticity and correlations with tracer distributions
No full text480km transmission of MDM 576-Gb/s 8QAM using a few-mode re-circulating loop
No full textWe demonstrate successful 3-mode-division-multiplexed × 192-Gb/s dual-polarization 8QAM (total 576 Gb/s) transmission over 480 km of few-mode fiber (FMF). This distance was obtained using an all few-mode re-circulating loop containing a 60 km FMF span
A Multi-Language Comparison of Influences on Author Verification using Character N-Grams
No full textWe create a new multi-language corpus for author verification based on Wikipedia talkpages, and evaluate the influence that differences in topic and time have on character n-gram author profiles. Topic alignment between two texts is found to increase author verification precision, and an authors writing style is found to change over time, but not more significantly after 3 years than after 1 year.Information ArchitectureWISElectrical Engineering, Mathematics and Computer Scienc
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe 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
The vanishing author in computer-generated works: a critical analysis of recent Australian case law
No full textAbstract
The use of software is ubiquitous in the creation of many copyright works, yet the requirement in copyright law that every work have a human author who engages in independent intellectual effort means that its use may prevent copyright subsistence. Several recent Australian cases have refocused attention on authorship as an essential criterion of copyright subsistence, and these cases suggest that much computer-produced output may be authorless and thus lack copyright protection. This article, the first in a two-part series, analyses how each case deals with the question of authorship of computer-produced works and why the use of software diminishes copyright protection for a significant number of computer-generated works. The article critiques the application of conventional notions of human authorship developed in the pre-computer age to modern productions and suggests alternative approaches to authorship that satisfy both the major objectives of copyright policy and the need to adapt to the computer age. The article argues that, without a broader judicial approach to authorship of computer-generated works, Parliament must remedy the lacuna in protection for these ‘authorless’ works. Possible solutions for reform are suggested. In a forthcoming article, the author comprehensively examines those reform proposals
Effect of voluntary exercise on number and volume of cardiomyocytes and their mitochondria in the mouse left ventricle
No full textVoluntary exercise (VE) has a beneficial influence on the heart and mean lifespan. The present study evaluates structural adaptations of cardiomyocytes and their mitochondria due to VE by new, unbiased stereological methods. Female, 7-9-week-old mice were randomly assigned to a control (CG, n = 7) or VE group (EG, n = 7). EG animals were housed in cages with free access to a running wheel and had a mean running distance of 6.7 (1.8) km per day. After 4 weeks, the hearts of all mice were processed for light and electron microscopy. We estimated the number and volume of cardiomyocytes by the disector method and the number and volume of mitochondria by estimation of the Euler number. In comparison to CG, VE did not have an effect on the myocardial volume of the left ventricle (CG: 93 (10), EG: 103 (17) (mm(3))), the number of cardiomyocytes (CG: 2.81 (0.27), EG: 2.82 (0.43) (x10(6))) and their number-weighted mean volume. However, the composition of the cardiomyocytes changed due to VE. The total volume of mitochondria (CG: 21.8 (4.9), EG: 32.2 (4.3) (mm(3)), P < 0.01) and the total number (CG: 3.76 (0.44), EG: 7.02 (1.13) (x10(10)), P < 0.001) were significantly higher in EG than in CG. The mean number-weighted mitochondrial volume was smaller in EG than in CG (P < 0.05). In summary, VE does not alter ventricular volume nor cardiomyocyte volume or number but the oxidative capacity of cardiomyocytes by an increased mitochondrial number and total volume in the left ventricle. These structural changes may participate in the beneficial effects of VE
Diffusive author(s), cohesive author: Analysis of S/N (1994)
No full textThis study indicates the ways in which various aspects of the author(s) are brought forth in Dumb type’s performance art, the S/N production. Previous research has suggested a non-hierarchical organization of Dumb type and the absence of a “privileged author” in Dumb type’s collaborative work, S/N. However, the results that I have investigated from member’s interviews on the creative process of S/N along with my analysis of the recorded images of S/N, indicate a different aspect of the author(s). First, S/N was created through, so to speak, the collective ideas of the members of Dumb type. Further, S/N has at least nine quotations from previous performances, installations, and printed writings, besides the work-in-progress technique. Explicating one of the “author functions” as given by Michel Foucault, each text has plural subjects of the author. However, it has been revealed from members’ interviews that Teiji Furuhashi had a decision-making role in selecting the members’ ideas within the performance. Since then, S/N has had plural subjects of creation; however, Furuhashi is one of the subjects of creation along with the “privileged author.” S/N has plural authors (diffusive authors) yet at the same time, it has a “privileged author,” Teiji Furuhashi (cohesive author)
William Peirce Randel, Le Ku-Klux-Klan, traduit de l'américain par Marie Tadié, Paris, éditions Albin-Michel, 1966. Godfrey Hodgson, « Carpetbaggers » et Ku-Klux-Klan, Les Etats-Unis après la guerre de Sécession, collection « Archives », Paris, René Julliard, 1966
No full textDardel Éric. William Peirce Randel, Le Ku-Klux-Klan, traduit de l'américain par Marie Tadié, Paris, éditions Albin-Michel, 1966. Godfrey Hodgson, « Carpetbaggers » et Ku-Klux-Klan, Les Etats-Unis après la guerre de Sécession, collection « Archives », Paris, René Julliard, 1966. In: Revue d'histoire et de philosophie religieuses, 47e année n°3,1967. pp. 292-293
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