scholarly journals In-Depth Analysis Reveals Production of Circular RNAs from Non-Coding Sequences

Cells ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 1806 ◽  
Author(s):  
Annie Robic ◽  
Julie Demars ◽  
Christa Kühn
Keyword(s):  
The Other ◽  
Circular Rnas ◽  
Small Contribution ◽  
Porcine Genome ◽  
Coding Sequences ◽  
Intronic Sequence ◽  
Total Rna ◽  
Depth Analysis ◽  
New Type ◽  
Porcine Testis

The sequencing of total RNA depleted for ribosomal sequences remains the method of choice for the study of circRNAs. Our objective was to characterize non-canonical circRNAs, namely not originating from back splicing and circRNA produced by non-coding genes. To this end, we analyzed a dataset from porcine testis known to contain about 100 intron-derived circRNAs. Labelling reads containing a circular junction and originating from back splicing provided information on the very small contribution of long non-coding genes to the production of canonical circRNAs. Analyses of the other reads revealed two origins for non-canonical circRNAs: (1) Intronic sequences for lariat-derived intronic circRNAs and intron circles, (2) Mono-exonic genes (mostly non-coding) for either a new type of circRNA (including only part of the exon: sub-exonic circRNAs) or, even more rarely, mono-exonic canonical circRNAs. The most complex set of sub-exonic circRNAs was produced by RNase_MRP (ribozyme RNA). We specifically investigated the intronic circRNA of ATXN2L, which is probably an independently transcribed sisRNA (stable intronic sequence RNA). We may be witnessing the emergence of a new non-coding gene in the porcine genome. Our results are evidence that most non-canonical circRNAs originate from non-coding sequences.

An Introduction to Roman Retailing

2018 ◽  
Author(s):  
Steven J. R. Ellis
Keyword(s):  
The Other ◽  
Methodological Framework ◽  
Roman World ◽  
Depth Analysis ◽  
Food And Drink ◽  
The One ◽  
Value Of It

This chapter introduces the topic of retailing in the Roman world and outlines some of the important developments in its study. It establishes why the focus of the book zooms in from retailing in general to the retailing of food and drink in particular; thus from shops to bars. Another aim is to demonstrate the scope of the study, which is an in-depth analysis of specific shops and bars at Pompeii on the one hand, and on the other a broader survey of the retail landscapes of cities throughout the Roman world. Essentially this chapter provides the theoretical and methodological framework for the book, while also arguing for the value of it in the first place.

Hydroxyl-containing bis(sulfonates). Reaction of 1,4-dibromo-2,3-butanedione with water, methanol and sodium sulfite

2021 ◽  
pp. 1-12
Author(s):  
Gerasimos M. Tsivgoulis ◽  
Dimitris G. Vachliotis ◽  
Golfo G. Kordopati ◽  
Panayiotis V. Ioannou
Keyword(s):  
13C Nmr ◽  
Sodium Sulfite ◽  
The Other ◽  
Carbonyl Carbon ◽  
1H And 13C Nmr ◽  
Sodium Sulfonate ◽  
Pure Product ◽  
Methylene Groups ◽  
New Type ◽  
High Yields

Sulfonates are well-known substances with a variety of applications, e.g. as surfactants. On the other hand, bis(sulfonates) bearing hydroxyl or keto group(s) in between the sulfonate groups can be used with or without further modification as starting materials for the preparation of new type of molecules capable to form either complexes or in general supramolecular structures. The synthesis of three hydroxyl-bearing bis(sulfonates), 2-hydroxypropane-1,3-bis(sodium sulfonate) 4, DL-2,3-dihydroxybutane-1,4-bis(sodium sulfonate) 8, and sodium 2,3,4-trihydroxy-1-sulfonate 7 (as by-product) via the Strecker sulfonation are described. Interestingly, under similar conditions, sulfonation of 1,4-dibromo-2,3-butanedione 9 was found to be very complicated and no pure product could be isolated, despite previously reported results on sulfonation of α-halogenated ketones in high yields. There are indications that SO3 2 -  attacks at the carbonyl carbon of 9 followed by rearrangement and expulsion of SO4 2 - . 1,4-dibromo-2,3-butanedione 9, bearing two keto groups next to methylene groups, can potentially exist as enols or in the case of its solution in hydroxylic solvents in the form of hemiketals or geminal diols. This behavior of 9 when is dissolved in CDCl3, CD3OD and D2O was studied by means of UV-Vis, 1H and 13C NMR and the nature of the adducts formed was elucidated.

Regeneration from duplicating fragments of the Drosophila wing disc

Development ◽  
1981 ◽  
Vol 66 (1) ◽  
pp. 117-126
Author(s):  
Jane Karlsson ◽  
R. J. Smith
Keyword(s):  
Imaginal Disc ◽  
General Rule ◽  
Wing Disc ◽  
The Other ◽  
Posterior Compartment ◽  
Drosophila Wing ◽  
Polar Coordinate ◽  
New Type ◽  
Coordinate Model

It is a general rule that of two complementary Drosophila imaginal disc fragments, one regenerates and the other duplicates. This paper reports an investigation of an exception to this rule. Duplicating fragments from the periphery of the wing disc which lacked presumptive notum were found to regenerate notum structures during and after duplication. The propensity for this was greatest in fragments lying close to the presumptive notum, with the exception of a fragment confined to the posterior compartment, which did not regenerate notum. Structures were added sequentially, and regeneration stopped once most of the notum was present. These results are not easily explained by the polar coordinate model, which states that regeneration cannot occur from duplicating fragments. Since compartments appear to be involved in this type of regeneration as in others, it is suggested that a new type of model is required, one which permits simultaneous regeneration and duplication, and assigns a major role to compartments.

scholarly journals Proteogenomic Analysis of Burkholderia Species Strains 25 and 46 Isolated from Uraniferous Soils Reveals Multiple Mechanisms to Cope with Uranium Stress

Cells ◽  
2018 ◽  
Vol 7 (12) ◽  
pp. 269 ◽  
Author(s):  
Meenakshi Agarwal ◽  
Ashish Pathak ◽  
Rajesh Rathore ◽  
Om Prakash ◽  
Rakesh Singh ◽  
...  
Keyword(s):  
Heavy Metals ◽  
Stress Response ◽  
Proteomic Analysis ◽  
Protein Biosynthesis ◽  
Draft Genome ◽  
Department Of Energy ◽  
Coding Sequences ◽  
Total Rna ◽  
A Genome ◽  
Rna Genes

Two Burkholderia spp. (strains SRS-25 and SRS-46) were isolated from high concentrations of uranium (U) from the U.S. Department of Energy (DOE)-managed Savannah River Site (SRS). SRS contains soil gradients that remain co-contaminated by heavy metals from previous nuclear weapons production activities. Uranium (U) is one of the dominant contaminants within the SRS impacted soils, which can be microbially transformed into less toxic forms. We established microcosms containing strains SRS-25 and SRS-46 spiked with U and evaluated the microbially-mediated depletion with concomitant genomic and proteomic analysis. Both strains showed a rapid depletion of U; draft genome sequences revealed SRS-25 genome to be of approximately 8,152,324 bp, a G + C content of 66.5, containing a total 7604 coding sequences with 77 total RNA genes. Similarly, strain SRS-46 contained a genome size of 8,587,429 bp with a G + C content of 67.1, 7895 coding sequences, with 73 total RNA genes, respectively. An in-depth, genome-wide comparisons between strains 25, 46 and a previously isolated strain from our research (Burkholderia sp. strain SRS-W-2-2016), revealed a common pool of 3128 genes; many were found to be homologues to previously characterized metal resistance genes (e.g., for cadmium, cobalt, and zinc), as well as for transporter, stress/detoxification, cytochromes, and drug resistance functions. Furthermore, proteomic analysis of strains with or without U stress, revealed the increased expression of 34 proteins from strain SRS-25 and 52 proteins from strain SRS-46; similar to the genomic analyses, many of these proteins have previously been shown to function in stress response, DNA repair, protein biosynthesis and metabolism. Overall, this comparative proteogenomics study confirms the repertoire of metabolic and stress response functions likely rendering the ecological competitiveness to the isolated strains for colonization and survival in the heavy metals contaminated SRS soil habitat.

scholarly journals A Hooked-Collar for Bridge Piers Protection: Flow Fields and Scour

Water ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 1251 ◽  
Author(s):  
Su-Chin Chen ◽  
Samkele Tfwala ◽  
Tsung-Yuan Wu ◽  
Hsun-Chuan Chan ◽  
Hsien-Ter Chou
Keyword(s):  
Laboratory Experiments ◽  
Horseshoe Vortex ◽  
Flow Fields ◽  
Bridge Pier ◽  
The Other ◽  
Bridge Piers ◽  
Vortex Strength ◽  
Numerical Tests ◽  
Scour Hole ◽  
New Type

A new type of collar, the hooked-collar, was studied through experiments and numerical methods. Tests were conducted using a hooked collar of a width of 1.25b and a height of 0.25b, where b is the bridge-pier width. The hooked-collar efficiency was evaluated by testing different hooked-collar placements within the bridge-pier, which were compared to the bridge-pier without any collar. A double hooked-collar configuration, one placed at the bed level and the other buried 0.25b, was the most efficient at reducing the scour hole. In other cases, a hooked-collar positioned 0.25b above the bed slightly reduced the scour hole and had similar scour patterns when compared to the pier without the hooked-collar. The flow fields along the vertical symmetrical plane in the experiments are also presented. Laboratory experiments and numerical tests show that maximal downflow is highly reduced along with a corresponding decrease in horseshoe vortex strength for the experiments with the hooked-collar, compared to cases without the hooked-collar. The flow fields reveal that the maximum turbulent kinetic energy decreases with the installation of the hooked-collar.

scholarly journals KARAKTERISTIK ORGANIOLEPTIK OTAK-OTAK IKAN YANG DIBERI EDIBLE COATING KARAGINAN DENGAN PENAMBAHAN ASAP CAIR

2015 ◽  
Vol 4 (2) ◽  
Author(s):  
Eka Irma Q Bariah ◽  
Siegfried Berhimpon ◽  
Eunike Louisje Mongi
Keyword(s):  
Environmentally Friendly ◽  
Food Product ◽  
Edible Coating ◽  
The Other ◽  
Liquid Smoke ◽  
Organoleptic Characteristics ◽  
Randomized Design ◽  
New Type ◽  
Completely Randomized Design

Edible coating is a new type of packaging made of biopolymer. The advantages of edible coating is enable to protect the food product, the original appearance of the product can be maintained and the product can be eaten as well as environmentally friendly. The study aim was to look at the organoleptic characteristics of fish cake coated with edible coating of carrageenan were given a liquid smoke. The treatments  given were variation of carrageenan concentration i,e. 0%, 1%, 1,5%, 2%, 2,5%, 3%. The experiment was designed using a Completely Randomized Design (CRD). To determine the effect of treatments, the data were tested using organoleptical tests consists of hedonic and texture.The results shown that hedonic test of the appearance and color of the raw sample have significant effect (p>0,05), while the other test showed no significant effect (p>0,05). However, the organoleptical score for taste, smell and texture shown a tendency that the fish cake coated, have  higher score than without coated. Keywords: Edible coating, Carrageenan, Fish cake, Liquid smoke.

scholarly journals Unequal signal and coding joint formation in human V(D)J recombination.

1993 ◽  
Vol 13 (7) ◽  
pp. 3900-3906 ◽  
Author(s):  
G H Gauss ◽  
M R Lieber
Keyword(s):  
Cell Lines ◽  
Relative Efficiency ◽  
Chromosomal Rearrangements ◽  
The Other ◽  
Combined Effects ◽  
Recombination Activity ◽  
Coding Sequences ◽  
Joint Formation ◽  
Differential Reaction ◽  
Endogenous Loci

Substrates for studying V(D)J recombination in human cells and two human pre-B-cell lines that have active V(D)J recombination activity are described. Using these substrates, we have been able to analyze the relative efficiency of signal joint and coding joint formation. Coding joint formation was five- to sixfold less efficient than signal joint formation in both cell lines. This imbalance between the two halves of the reaction was demonstrated on deletional substrates, where each joint is assayed individually. In both cell lines, the inversional reaction (which requires formation of both a signal and a coding joint) was more than 20-fold less efficient than signal joint formation alone. The signal and coding sequences are identical in all of these substrates. Hence, the basis for these differential reaction ratios appears to be that coding joint and signal joint formation are both inefficient and their combined effects are such that inversions (two-joint reactions) reflect the product of these inefficiencies. Physiologically, these results have two implications. First, they show how signal and coding joint formation efficiencies can affect the ratio of deletional to inversional products at endogenous loci. Second, the fact that not all signal and coding joints go to completion implies that the recombinase is generating numerous broken ends. Such unresolved ends may participate in pathologic chromosomal rearrangements even when the other half of the same reaction may have proceeded to resolution.

Orthonormal basis of wavelets with customizable frequency bands

2016 ◽  
Vol 14 (06) ◽  
pp. 1650050 ◽  
Author(s):  
Hiroshi Toda ◽  
Zhong Zhang
Keyword(s):  
Frequency Domain ◽  
Infinite Number ◽  
Orthonormal Basis ◽  
The Other ◽  
Just Intonation ◽  
Frequency Bands ◽  
Orthonormal Bases ◽  
Major Scale ◽  
Dilation Factor ◽  
New Type

We already proved the existence of an orthonormal basis of wavelets having an irrational dilation factor with an infinite number of wavelet shapes, and based on its theory, we proposed an orthonormal basis of wavelets with an arbitrary real dilation factor. In this paper, with the development of these fundamentals, we propose a new type of orthonormal basis of wavelets with customizable frequency bands. Its frequency bands can be freely designed with arbitrary bounds in the frequency domain. For example, we show two types of orthonormal bases of wavelets. One of them has an irrational dilation factor, and the other is designed based on the major scale in just intonation.

The junctional complex in the intestine of Sagitta setosa (Chaetognatha): the paired septate junction

1980 ◽  
Vol 42 (1) ◽  
pp. 227-246
Author(s):  
M. Duvert ◽  
D. Gros ◽  
C. Salat
Keyword(s):  
Uranyl Acetate ◽  
The Other ◽  
Septate Junction ◽  
Junctional Complex ◽  
Outer Diameter ◽  
Central Ring ◽  
Straight Path ◽  
New Type ◽  
Pleated Sheet ◽  
Tight Formation

The junctional complex of the intestine of Sagitta setosa has been studied in tissues stained with uranyl acetate or after lanthanum impregnation, and by freeze-cleavage. All types of junctions have been characterized in both perpendicular and tangential planes. From the apex to the base of the cell the following junctions occur in this order: a zonula adhaerens; a septate junction where the septa occur in pairs; a pleated sheet septate junction; and numerous gap junctions of the A-type. From the upper part of the cells inwards to the septate junction, the membranes follow a relatively straight path. In the lower part of the cells the membranes are deeply interdigitating. At the intersection between 3 cells a very different junction is to be observed where small units, periodically disposed, bind the membranes of the 3 adjoining cells. Each unit is composed of 3 short segments which bind the cell membranes to a central ring 16.6 +/− 2.3 nm in outer diameter. The paired septate junction constitutes a new type. Its main features are that the septa are paired and occur in 2 formations, one the ‘loose formation’, with elements between the septa of each pair, and the other, a ‘tight formation’. After lanthanum impregnation, the thickness of each septum is seen to be about 3 nm and the undulation period 12.6 +/− 1.6 nm. On freeze-fractures 10-nm particles are found on crests on the PF face and in furrows on the EF face. The possible significance of this type of junction is discussed. The junctional complex described is analogous to those found in various invertebrate epithelia.

An Encounter with the Other: A Thematic Analysis of Accounts of DMT Experiences from a Naturalistic Field Study

2021 ◽  
Author(s):  
Pascal Michael ◽  
David Luke ◽  
Oliver Robinson
Keyword(s):  
Field Study ◽  
Thematic Analysis ◽  
Conscious Experience ◽  
The Other ◽  
Structured Interviews ◽  
Depth Analysis ◽  
Death Experience ◽  
Extraordinary Experiences ◽  
Alien Abduction ◽  
Increasing Trends

Introduction: N, N-Dimethyltryptamine (DMT) is an endogenous serotonergic psychedelic capable of producing radical shifts in conscious experience. Increasing trends in its use, as well as new trials administering DMT to patients, indicate the growing importance of a thorough elucidation of the phenomenology the drug may occasion. This is particularly in light of the hyper-real, otherworldly, and often ontologically challenging yet potentially transformative, nature of the experience, not least encounters with apparently non-self social agents. Laboratory studies have been limited by clinical setting and lacking qualitative analyses, while online surveys’ limitations lie in retrospective design, recreational use, and both of which not guaranteeing ‘breakthrough’ experiences. Methods: We report on the first naturalistic field study of DMT use including its qualitative analysis. Screened, healthy, anonymised and experienced DMT users (40-75mg inhaled) were observed during their non-clinical use of the drug at home. Semi-structured interviews using the micro-phenomenological technique were employed immediately after their experience. This paper reports on the thematic analysis of one major domain of the breakthrough experiences elicited; the ‘other’. Thirty-six post-DMT experience interviews with mostly Caucasian (83%) males (8 female) of average 37 years were predominantly inductively coded. Results: Invariably, profound and highly intense experiences occurred. The main overarching category comprised the encounter with other ‘beings’ (94% of reports), with further subordinate themes including the entities’ role, appearance, demeanour, communication and interaction; while the other over-arching category comprised experiences of emerging into other ‘worlds’ (100% of reports), in turn consisting of the scene, the content and quality of the immersive spaces. Discussion: The present study provides a systematic and in-depth analysis of the features of the otherworldly encounter within the breakthrough DMT experience, as well as elaborating on the resonances with both previous DMT studies and other types of extraordinary experiences which also entail entity encounters. These include the alien abduction, folkloric, shamanic and near-death experience. Putative neural mechanisms of these features of the DMT experience and its promise as a psychotherapeutic agent are discussed in light of such findings.

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