Identification of nucleotide patterns enriched in secreted RNAs as putative cis-acting elements targeting them to exosome nano-vesicles

<p>Abstract</p> <p>Background</p> <p>Exosomes are nanoscale membrane vesicles released by most cells. They are postulated to be involved in cell–cell communication and genetic reprogramming of their target cells. In addition to proteins and lipids, they release RNA molecules many of which are not present in the donor cells implying a highly selective mode of their packaging into these vesicles. Sequence motifs targeting RNA to the vesicles are currently unknown.</p> <p>Results</p> <p><it>Ab initio</it> approach was applied for computational identification of potential RNA secretory motifs in the primary sequences of exosome-enriched RNAs (eRNAs). Exhaustive motif analysis for the first time revealed unique sequence features of eRNAs. We discovered multiple linear motifs specifically enriched in secreted RNAs. Their potential function as <it>cis</it>-acting elements targeting RNAs to exosomes is proposed. The motifs co-localized in the same transcripts suggesting combinatorial organization of these secretory signals. We investigated associations of the discovered motifs with other RNA parameters. Secreted RNAs were found to have almost twice shorter half-life times on average, in comparison with cytoplasmic RNAs, and the occurrence of some eRNA-specific motifs significantly correlated with this eRNA feature. Also, we found that eRNAs are highly enriched in long noncoding RNAs.</p> <p>Conclusions</p> <p>Secreted RNAs share specific sequence motifs that may potentially function as <it>cis</it>-acting elements targeting RNAs to exosomes. Discovery of these motifs will be useful for our understanding the roles of eRNAs in cell-cell communication and genetic reprogramming of the target cells. It will also facilitate nano-scale vesicle engineering and selective targeting of RNAs of interest to these vesicles for gene therapy purposes.</p

Sex estimation based on the anthropometric measurements of thyroid cartilage using discriminant analysis

Abstract Background The morphometric analysis of the individual bones of the human skeleton can be used to estimate the sex of unidentified corpses. Our aims were as follows: to test whether thyroid cartilage can be used for forensic purposes as a predictor of biological sex; to establish the level of sexual dimorphism of the thyroid cartilage in a sample of adult subjects from a population of European Russia; and to test the accuracy of the morphometric parameters obtained from the thyroid cartilage. Results The thyroid cartilage from 100 adults of known age (50 males and 50 females) was obtained during forensic examination; morphometric tests were conducted using Vernier Digital ROKTOOLS ABS DIN 862 0-200/6 inch with measurement accuracy ± 0.01 mm. The measured parameters were N = 31 for each subject. Intra- and inter-observer reproducibility was tested. Multivariate statistical analysis was applied to the measurements. To check the data set for normal distribution, the Kolmogorov-Smirnov test was used. Finally, to estimate the sex of the observed individuals, a stepwise discriminant analysis was conducted, using the Wilks' lambda selection method. The most significant parameters were the outer distance between bases of inferior horn; the inner distance between distal ends of inferior horns; distance between distal ends of left superior and inferior horns; left superior horn length (distance between left superior horn distal end and base); distance between superior and inferior notches; thyroid angle; left lamina height (vertical line along left lamina middle); horizontal distance between anterior intermedium line and the right lamina posterior edge; distance between inferior thyroid notch and line connecting left and right thyroid laminae; and left superior horn thickness at mid-line. The stepwise discriminant analysis resulted in an equation with ten parameters. Conclusions The results of the current study indicated that in the European Russian population, the equation obtained in the stepwise discriminant analysis makes it possible to predict sex with a probability of 100% on the validation set. On the test set, the resultant accuracy was 100% for females and 100% for males. Our findings confirm the scientific evidence that the thyroid cartilage has a pronounced sexual dimorphism

Improvement of methods for estimation of catchability for trawl survey systems with use of hydroacoustic means (on example of walleye pollock in the Okhotsk Sea)

In commercial fishery, catching properties of fishing gears are developed mostly for effective catch of fish, rather than for precise measurement of fish distribution density in water, so a problem of catchability exists and this parameter should be determined for each fishing gear. Various methods for estimation of catchability for trawl survey systems are considered. The experimental method of its estimation (comparing of fish density in towed volume determined by other tools with trawl catch) is considered as the most authentic. Scheme and algorithm of the measurements and calculations are described for standard hydroacoustic tools, as scientific echosounder ЕК-60, and software is developed for recalculation of trawl catch to equivalent acoustic units of fish density in the towed volume of water. Results of the catchability estimation for the trawl RT/TM 57/360 used for walleye pollock stock assessment in the Okhotsk Sea are analyzed. Mean value of the catchability coefficient in this case varies from 0.42 to 0.81, generally increasing with depth but decreasing both at the sea surface and on the depth > 200 m. These results correspond well with the model of fish behavior in the noise field of vessel: the low catchability at the sea surface and its increasing with depth could be caused by avoiding reaction of fish to the noise and its moving to deeper layers. Besides, the catchability coefficient for pollock depends on fish size and time of day: it increases with the fish length but decreases for the largest individuals. Influence of the noise field of vessel on selectivity of survey trawls is modeled and there is shown that the depths of the maximum concentration of small-sized and large-sized pollock do not coincide. The developed software and received results are universal means for estimation of the catchability for trawls in all conditions of trawling, they allow to choose optimum mode for survey trawling in dependence on fish species, depth of trawling, and type of vessels and trawl

A "saddle-node" bifurcation scenario for birth or destruction of a Smale-Williams solenoid

Formation or destruction of hyperbolic chaotic attractor under parameter variation is considered with an example represented by Smale--Williams solenoid in stroboscopic Poincar\'{e} map of two alternately excited non-autonomous van der Pol oscillators. The transition occupies a narrow but finite parameter interval and progresses in such way that periodic orbits constituting a "skeleton" of the attractor undergo saddle-node bifurcation events involving partner orbits from the attractor and from a non-attracting invariant set, which forms together with its stable manifold a basin boundary of the attractor.Comment: 7 pages, 7 figures, 1 tabl

Mean field approximation of two coupled populations of excitable units

The analysis on stability and bifurcations in the macroscopic dynamics exhibited by the system of two coupled large populations comprised of $N$ stochastic excitable units each is performed by studying an approximate system, obtained by replacing each population with the corresponding mean-field model. In the exact system, one has the units within an ensemble communicating via the time-delayed linear couplings, whereas the inter-ensemble terms involve the nonlinear time-delayed interaction mediated by the appropriate global variables. The aim is to demonstrate that the bifurcations affecting the stability of the stationary state of the original system, governed by a set of 4N stochastic delay-differential equations for the microscopic dynamics, can accurately be reproduced by a flow containing just four deterministic delay-differential equations which describe the evolution of the mean-field based variables. In particular, the considered issues include determining the parameter domains where the stationary state is stable, the scenarios for the onset and the time-delay induced suppression of the collective mode, as well as the parameter domains admitting bistability between the equilibrium and the oscillatory state. We show how analytically tractable bifurcations occurring in the approximate model can be used to identify the characteristic mechanisms by which the stationary state is destabilized under different system configurations, like those with symmetrical or asymmetrical inter-population couplings.Comment: 5 figure

Evaluation of handwriting peculiarities utilizing laser speckle contrast imaging

Functional handwriting is a process involving various complex interactions between physical, cognitive and sensory systems. Since muscular motion is of a peculiar nature for each person, handwriting properties, such as pencil pressure and speed of writing, can be considered as a unique marker of identity. Moreover, impairments of handwriting in many cases are connected to neurodevelopmental disorders such as attention deficit hyperactivity disorder, developmental coordination disorder, autism spectrum disorders, Parkinson's disease, etc. From this point of view, investigations of handwriting kinematics and pressure can be highly important for both forensic science and medicine. Commonly, the kinematic and pressure features of handwriting are evaluated using a graphics tablet with a stylus or electronic pens. The production of such devices is quite expensive. Therefore, the development of new methods for individual handwriting analysis is an important and current goal. Laser speckle contrast imaging (LSCI) is a powerful method, which is sensitive to both motion and pressure. Since the developed technique requires the use of only a simple laser diode and camera for image acquisition, LSCI is a cost-effective and practical tool for handwriting analysis. In the current letter we present a robust LSCI-based method for handwriting pressure and kinematics evaluation. The introduced approach was validated by an Archimedean spiral writing task

Experimental investigation of two-phase gas-liquid flow in microchannel with T-junction

Using high-speed video recording and the method of dual laser scanning the gas-liquid flow was investigated in rectangular microchannels with an aspect ratio of 2.35 and 1.26. Experiments were earned out for the vertical flow of ethanol-nitrogen mixture in a microchannel with a cross section of 553×235 µm and for the horizontal flow of water-nitrogen mixture in a microchannel with a cross section of 315×250 µm. The T-mixer was used at the channel's inlet for gas-liquid flow formation. It was observed that elongated bubble, transition, and annular flows are the main regimes for a microchannel with a hydraulic diameter substantially less than the capillary constant. Using laser scanning, the maps of flow regimes for ethanol-nitrogen and water–nitrogen mixtures were obtained and discussed

Multispectral anti-reflection coatings based on YbF3/ZnS materials on ZnGeP2 substrate by the IBS method for Mid-IR laser applications

A multispectral anti-reflective coating of high radiation strength for laser applications in the IR spectrum for nonlinear ZnGeP2 crystals has been developed for the first time. The coating was constructed using YbF3/ZnS. The developed coating was obtained by a novel approach using ion-beam deposition of these materials on a ZnGeP2 substrate. It has a high LIDT of more than 2 J/cm2. Optimal layer deposition regimes were found for high film density and low absorption, and good adhesion of the coating to the substrate was achieved. At the same time, there was no dissociation of the double compound under high-energy ions

Terahertz signatures of ultrafast Dirac fermion relaxation at the surface of topological insulators

Topologically protected surface states present rich physics and promising spintronic, optoelectronic, and photonic applications that require a proper understanding of their ultrafast carrier dynamics. Here, we investigate these dynamics in topological insulators (TIs) of the bismuth and antimony chalcogenide family, where we isolate the response of Dirac fermions at the surface from the response of bulk carriers by combining photoexcitation with below-bandgap terahertz (THz) photons and TI samples with varying Fermi level, including one sample with the Fermi level located within the bandgap. We identify distinctly faster relaxation of charge carriers in the topologically protected Dirac surface states (few hundred femtoseconds), compared to bulk carriers (few picoseconds). In agreement with such fast cooling dynamics, we observe THz harmonic generation without any saturation effects for increasing incident fields, unlike graphene which exhibits strong saturation. This opens up promising avenues for increased THz nonlinear conversion efficiencies, and high-bandwidth optoelectronic and spintronic information and communication applications.Parts of this research were carried out at ELBE at the Helmholtz-Zentrum Dresden-Rossendorf e.V., a member of the Helmholtz Association. The films are grown in IRE RAS within the framework of the state task. This work was supported by the RFBR grants Nos. 18-29-20101, 19-02-00598. N.A., S.K., and I.I. acknowledge support from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 737038 (TRANSPIRE). T.V.A.G.O. and L.M.E. acknowledge the support by the Würzburg-Dresden Cluster of Excellence on Complexity and Topology in Quantum Matter (ct.qmat). K.-J.T. acknowledges funding from the European Union’s Horizon 2020 research and innovation program under Grant Agreement No. 804349 (ERC StG CUHL) and financial support through the MAINZ Visiting Professorship. ICN2 was supported by the Severo Ochoa program from Spanish MINECO Grant No. SEV-2017-0706