Intramolecular integration within Moloney murine leukemia virus DNA

By screening a library of unintegrated, circular Moloney murine leukemia virus (M-MuLV) DNA cloned in lambda phage, we found that approximately 20% of the M-MuLV DNA inserts contained internal sequence deletions or inversions. Restriction enzyme mapping demonstrated tht the deleted segments frequently abutted a long terminal repeat (LTR) sequence, whereas the inverted segments were usually flanked by LTR sequences, suggesting that many of the variants arose as a consequence of M-MuLV DNA molecules integrating within their own DNA. Nucleotide sequencing also suggested that most of the variant inserts were generated by autointegration. One of the recombinant M-MuLV DNA inserts contained a large inverted repeat of a unique M-MuLV sequence abutting an LTR. This molecule was shown by nucleotide sequencing to have arisen by an M-MuLV DNA Molecule integrating within a second M-MuLV DNA molecule before cloning. The autointegrated M-MuLV DNA had generally lost two base pairs from the LTR sequence at each junction with target site DNA, whereas a four-base-pair direct repeat of target site DNA flanked the integrated viral DNA. Nucleotide sequencing of preintegration target site DNA showed that this four-base-pair direct repeat was present only once before integration and was thus reiterated by the integration event. The results obtained from the autointegrated clones were supported by nucleotide sequencing of the host-virus junction of two cloned M-MuLV integrated proviruses obtained from infected rat cells. Detailed analysis of the different unique target site sequences revealed no obvious common features

Viscous cavities

International audienceWe study experimentally the impact of solid spheres in a viscous liquid at moderate Reynolds numbers (Re similar to 5-100). We first determine the drag force by following the slowdown dynamics of projectiles. We then focus on the shape of the free surface: such impacts generate cavities, whose original shape is described and modeled. (C) 2013 American Institute of Physics

Hopping Time Scales and the Phonon-Liquid Electron-Crystal Picture in Thermoelectric Copper Selenide

The suppression of transverse phonons by liquidlike diffusion in superionic conductors has been proposed as a means to dramatically reduce thermal conductivity in thermoelectric materials [H. Lui et al. Nat. Mater. 11, 422 (2012)]. We have measured the ion transport and lattice dynamics in the original phonon-liquid electron-crystal Cu2Se using neutron spectroscopy. We show that hopping time scales are too slow to significantly affect lattice vibrations and that the transverse phonons persist at all temperatures. Substantial changes to the phonon spectrum occur well below the transition to the superionic phase, and the ultralow thermal conductivity is instead attributed to anharmonicity

Cross-Modal Health State Estimation

Individuals create and consume more diverse data about themselves today than any time in history. Sources of this data include wearable devices, images, social media, geospatial information and more. A tremendous opportunity rests within cross-modal data analysis that leverages existing domain knowledge methods to understand and guide human health. Especially in chronic diseases, current medical practice uses a combination of sparse hospital based biological metrics (blood tests, expensive imaging, etc.) to understand the evolving health status of an individual. Future health systems must integrate data created at the individual level to better understand health status perpetually, especially in a cybernetic framework. In this work we fuse multiple user created and open source data streams along with established biomedical domain knowledge to give two types of quantitative state estimates of cardiovascular health. First, we use wearable devices to calculate cardiorespiratory fitness (CRF), a known quantitative leading predictor of heart disease which is not routinely collected in clinical settings. Second, we estimate inherent genetic traits, living environmental risks, circadian rhythm, and biological metrics from a diverse dataset. Our experimental results on 24 subjects demonstrate how multi-modal data can provide personalized health insight. Understanding the dynamic nature of health status will pave the way for better health based recommendation engines, better clinical decision making and positive lifestyle changes.Comment: Accepted to ACM Multimedia 2018 Conference - Brave New Ideas, Seoul, Korea, ACM ISBN 978-1-4503-5665-7/18/1

The spinning ball spiral

International audienceWe discuss the trajectory of a fast revolving solid ball moving in a fluid of comparable density. As the ball slows down owing to drag, its trajectory follows an exponential spiral as long as the rotation speed remains constant: at the characteristic distance L where the ball speed is significantly affected by the drag, the bending of the trajectory increases, surprisingly. Later, the rotation speed decreases, which makes the ball follow a second kind of spiral, also described in the paper. Finally, the use of these highly curved trajectories is shown to be relevant to sports. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft

Most of the response elicited against Wolbachia surface protein in filarial nematode infection is due to the infective larval stage

Immune responses to the intracellular Wolbachia bacteria of filarial nematodes are thought to contribute to the pathologic process of filarial infection. Here, we compare antibody responses of subjects living in an area where lymphatic filariasis is endemic with antibody responses elicited in a murine model of filarial infection, to provide evidence that the infective larval stage (L3), not adult nematodes, are the primary inducer of responses against Wolbachia. In human subjects, antibody responses to Brugia malayi Wolbachia surface protein (WSP) are most often correlated with antibody responses to the L3 stage of B. malayi. Analysis of anti-WSP responses induced in mice by different stages of the rodent filariae Litomosoides sigmodontis shows that the strongest anti-WSP response is elicited by the L3 stage. Although adult filarial nematode death may play a role in the generation of an anti-WSP response, it is the L3 stage that is the major source of immunogenic material, and incoming L3 provide a continual boosting of the anti-WSP response. Significant exposure to the endosymbiotic bacteria may occur earlier in nematode infection than previously thought, and the level of exposure to infective insect bites may be a key determinant of disease progression

Detection of microRNAs in color space

MotivationDeep sequencing provides inexpensive opportunities to characterize the transcriptional diversity of known genomes. The AB SOLiD technology generates millions of short sequencing reads in color-space; that is, the raw data is a sequence of colors, where each color represents 2 nt and each nucleotide is represented by two consecutive colors. This strategy is purported to have several advantages, including increased ability to distinguish sequencing errors from polymorphisms. Several programs have been developed to map short reads to genomes in color space. However, a number of previously unexplored technical issues arise when using SOLiD technology to characterize microRNAs.ResultsHere we explore these technical difficulties. First, since the sequenced reads are longer than the biological sequences, every read is expected to contain linker fragments. The color-calling error rate increases toward the 3(') end of the read such that recognizing the linker sequence for removal becomes problematic. Second, mapping in color space may lead to the loss of the first nucleotide of each read. We propose a sequential trimming and mapping approach to map small RNAs. Using our strategy, we reanalyze three published insect small RNA deep sequencing datasets and characterize 22 new microRNAs.Availability and implementationA bash shell script to perform the sequential trimming and mapping procedure, called SeqTrimMap, is available at: http://www.mirbase.org/tools/seqtrimmap/[email protected] informationSupplementary data are available at Bioinformatics online