The use of single-cell RNA-Seq to understand virus-host interactions.

Single-cell analyses allow uncovering cellular heterogeneity, not only per se, but also in response to viral infection. Similarly, single cell transcriptome analyses (scRNA-Seq) can highlight specific signatures, identifying cell subsets with particular phenotypes, which are relevant in the understanding of virus-host interactions

Exploring viral infection using single-cell sequencing.

Single-cell sequencing (SCS) has emerged as a valuable tool to study cellular heterogeneity in diverse fields, including virology. By studying the viral and cellular genome and/or transcriptome, the dynamics of viral infection can be investigated at single cell level. Most studies have explored the impact of cell-to-cell variation on the viral life cycle from the point of view of the virus, by analyzing viral sequences, and from the point of view of the cell, mainly by analyzing the cellular host transcriptome. In this review, we will focus on recent studies that use single-cell sequencing to explore viral diversity and cell variability in response to viral replication

LEDGF/p75 TATA-less promoter is driven by the transcription factor Sp1.

PSIP1 (PC4 and SFRS1 interacting protein 1) encodes two splice variants: lens epithelium-derived growth factor or p75 (LEDGF/p75) and p52. PSIP1 gene products were shown to be involved in transcriptional regulation, affecting a plethora of cellular processes, including cell proliferation, cell survival, and stress response. Furthermore, LEDGF/p75 has implications for various diseases and infections, including autoimmunity, leukemia, embryo development, psoriasis, and human immunodeficiency virus integration. Here, we reported the first characterization of the PSIP1 promoter. Using 5' RNA ligase-mediated rapid amplification of cDNA ends, we identified novel transcription start sites in different cell types. Using a luciferase reporter system, we identified regulatory elements controlling the expression of LEDGF/p75 and p52. These include (i) minimal promoters (-112/+59 and +609/+781) that drive the basal expression of LEDGF/p75 and of the shorter splice variant p52, respectively; (ii) a sequence (+319/+397) that may control the ratio of LEDGF/p75 expression to p52 expression; and (iii) a strong enhancer (-320/-207) implicated in the modulation of LEDGF/p75 transcriptional activity. Computational, biochemical, and genetic approaches enabled us to identify the transcription factor Sp1 as a key modulator of the PSIP1 promoter, controlling LEDGF/p75 transcription through two binding sites at -72/-64 and -46/-36. Overall, our results provide initial data concerning LEDGF/p75 promoter regulation, giving new insights to further understand its biological function and opening the door for new therapeutic strategies in which LEDGF/p75 is involved

Single-Cell RNA-Seq Reveals Transcriptional Heterogeneity in Latent and Reactivated HIV-Infected Cells.

Despite effective treatment, HIV can persist in latent reservoirs, which represent a major obstacle toward HIV eradication. Targeting and reactivating latent cells is challenging due to the heterogeneous nature of HIV-infected cells. Here, we used a primary model of HIV latency and single-cell RNA sequencing to characterize transcriptional heterogeneity during HIV latency and reactivation. Our analysis identified transcriptional programs leading to successful reactivation of HIV expression

Rilocalizzazione di terremoti, modelli 3D di Vp, Vp/Vs e Qp nell’area geotermica di Larderello.

L'area geotermica di Larderello è caratterizzata da un elevato flusso di calore (tra 120 e 1000 mW/m2) e geologicamente caratterizzata da bacini postorogenici riempiti da depositi neogenici, risultato di un diffuso assottigliamento crostale accompagnato da risalite di materiale dal mantello superiore fino a profondità di pochi chilometri

Seismic preprocessing and amplitude cross-calibration for a time-lapse amplitude study on seismic data from the Oseberg reservoir

The cross-calibration of different vintage data is an important prerequisite in attempting to determine the time-lapse seismic effects induced by hydrocarbon production in a reservoir. This paper reports the preprocessing and cross-calibration procedures adopted to modify the data of four seismic vintages (1982, 1989, 1992 and 1999) from the Oseberg field in the North Sea, for optimal conditions for a time-lapse seismic amplitude analysis. The final results, in terms of time-lapse variations, of acoustic impedance and of amplitude-versus-offset, are illustrated for selected data sets. The application of preprocessing to each individual vintage data set reduces the effects of the different acquisition and noise conditions, and leads to consistency in the amplitude response of the four vintages. This consistency facilitates the final amplitude cross-calibration that is carried out using, as reference, the Cretaceous horizon reflections above the Brent reservoir. Such cross-calibration can be considered as vintage-consistent residual amplitude correction. Acoustic impedance sections, intercept and gradie nt amplitude-versus-offset attributes and coherent amplitude-versus-offset estimates are computed on the final cross-calibrated data. The results, shown for three spatially coincident 2D lines selected from the 1982, 1989 and 1999 data sets, clearly indicate gas-cap expansion resulting from oil production. Such expansion is manifested as a decrease in acoustic impedance and a modification of the amplitude-versus-offset trends in the apical part of the reservoir

Three-dimensional tomography and rock properties of the Larderello-Travale

In a geothermal area, a detailed knowledge of the three-dimensional velocity structures aids the managementof the field and the further development of the geothermal source. Here,we present a high-resolution study of the three-dimensional S-wave velocity structures from microearthquake travel times for the Larderello-Travale geothermal field, Italy.We have also deduced the Vp/Vs and Vp ×Vs parameters for this area toemphasize the deep variations in the physical rock properties due to fluid content and porosity. Furthermore, effective porousmedium modelling has been performed for site-relevant lithologies, to improve our interpretation of the results in terms of rock physics signatures. This has allowed us to estimate the variation range of the seismological parameters investigated, as well as their sensitivity for suitable rock under specific physical conditions. LowVp/Vs anomalies, arising froma lower Vp compared to Vs, dominate the geothermal field of Larderello-Travale. These have been interpreted as due to steam-bearing formations. On the contrary, analysis of Vp ×Vs images provides information on the relative changes in rock porosity at depth. Comparison of tomographic section images with previously interpreted seismic lines suggests that the reflective ‘K-horizon’ delineates a transition between zones that have different porosities or crack gatherings. The ‘K-horizon’ also lies on low Vp/Vs anomalies, which suggests a steam saturation zone, despite the reduced porosity at this depth

Analysis of HIV-1 expression level and sense of transcription by high-throughput sequencing of the infected cell.

Next-generation sequencing offers an unprecedented opportunity to jointly analyze cellular and viral transcriptional activity without prerequisite knowledge of the nature of the transcripts. SupT1 cells were infected with a vesicular stomatitis virus G envelope protein (VSV-G)-pseudotyped HIV vector. At 24 h postinfection, both cellular and viral transcriptomes were analyzed by serial analysis of gene expression followed by high-throughput sequencing (SAGE-Seq). Read mapping resulted in 33 to 44 million tags aligning with the human transcriptome and 0.23 to 0.25 million tags aligning with the genome of the HIV-1 vector. Thus, at peak infection, 1 transcript in 143 is of viral origin (0.7%), including a small component of antisense viral transcription. Of the detected cellular transcripts, 826 (2.3%) were differentially expressed between mock- and HIV-infected samples. The approach also assessed whether HIV-1 infection modulates the expression of repetitive elements or endogenous retroviruses. We observed very active transcription of these elements, with 1 transcript in 237 being of such origin, corresponding on average to 123,123 reads in mock-infected samples (0.40%) and 129,149 reads in HIV-1-infected samples (0.45%) mapping to the genomic Repbase repository. This analysis highlights key details in the generation and interpretation of high-throughput data in the setting of HIV-1 cellular infection