HIV-1 gene expression: lessons from provirus and non-integrated DNA

Replication of HIV-1 involves a series of obligatory steps such as reverse transcription of the viral RNA genome into double-stranded DNA, and subsequent integration of the DNA into the human chromatin. Integration is an essential step for HIV-1 replication; yet the natural process of HIV-1 infection generates both integrated and high levels of non-integrated DNA. Although proviral DNA is the template for productive viral replication, the non-integrated DNA has been suggested to be active for limited viral gene synthesis. In this review, the regulation of viral gene expression from proviral DNA will be summarized and issues relating to non-integrated DNA as a template for transcription will be discussed, as will the possible function of pre-integration transcription in HIV-1 replication cycle

The second chance story of HIV-1 DNA: Unintegrated? Not a problem!

Accumulation of high levels of unintegrated viral DNA is a common feature of retroviral infection. It was recently discovered that coinfection of cells with integrated and unintegrated HIV-1 can result in complementation, allowing viral replication in the absence of integration. This new mode of HIV-1 replication has numerous implications for the function of unintegrated viral DNA and its application as a therapeutic vector

The trinity of the cortical actin in the initiation of HIV-1 infection

For an infecting viral pathogen, the actin cortex inside the host cell is the first line of intracellular components that it encounters. Viruses devise various strategies to actively engage or circumvent the actin structure. In this regard, the human immunodeficiency virus-1 (HIV-1) exemplifies command of cellular processes to take control of actin dynamics for the initiation of infection. It has becomes increasingly evident that cortical actin presents itself both as a barrier to viral intracellular migration and as a necessary cofactor that the virus must actively engage, particularly, in the infection of resting CD4 blood T cells, the primary targets of HIV-1. The coercion of this most fundamental cellular component permits infection by facilitating entry, reverse transcription, and nuclear migration, three essential processes for the establishment of viral infection and latency in blood T cells. It is the purpose of this review to examine, in detail, the manifestation of viral dependence on the actin cytoskeleton, and present a model of how HIV utilizes actin dynamics to initiate infection

Specific Marking of HIV-1 Positive Cells using a Rev-dependent Lentiviral Vector Expressing the Green Fluorescent Protein

Most of HIV-responsive expression vectors are based on the HIV promoter, the long terminal repeat (LTR). While responsive to an early HIV protein, Tat, the LTR is also responsive to cellular activation states and to the local chromatin activity where the integration has occurred. This can result in high HIV-independent activity, and has restricted the usefulness of LTR-based reporter to mark HIV positive cells 1,2,3. Here, we constructed an expression lentiviral vector that possesses, in addition to the Tat-responsive LTR, numerous HIV DNA sequences that include the Rev-response element and HIV splicing sites 4,5,6. The vector was incorporated into a lentiviral reporter virus, permitting highly specific detection of replicating HIV in living cell populations. The activity of the vector was measured by expression of the green fluorescence protein (GFP). The application of this vector as reported here offers a novel alternative approach to existing methods, such as in situ PCR or HIV antigen staining, to identify HIV-positive cells. The vector can also express therapeutic genes for basic or clinical experimentation to target HIV-positive cells

Cofilin Activation in Peripheral CD4 T Cells of HIV-1 Infected Patients: A Pilot Study

Cofilin is an actin-depolymerizing factor that regulates actin dynamics critical for T cell migration and T cell activation. In unstimulated resting CD4 T cells, cofilin exists largely as a phosphorylated inactive form. Previously, we demonstrated that during HIV-1 infection of resting CD4 T cells, the viral envelope-CXCR4 signaling activates cofilin to overcome the static cortical actin restriction. In this pilot study, we have extended this in vitro observation and examined cofilin phosphorylation in resting CD4 T cells purified from the peripheral blood of HIV-1-infected patients. Here, we report that the resting T cells from infected patients carry significantly higher levels of active cofilin, suggesting that these resting cells have been primed in vivo in cofilin activity to facilitate HIV-1 infection. HIV-1-mediated aberrant activation of cofilin may also lead to abnormalities in T cell migration and activation that could contribute to viral pathogenesis.Department of Defense (National Defense Science and Engineering Fellowship); National Institute of Allergy and Infectious Diseases (AI069981

Sequence Level Semantics Aggregation for Video Object Detection

Video objection detection (VID) has been a rising research direction in recent years. A central issue of VID is the appearance degradation of video frames caused by fast motion. This problem is essentially ill-posed for a single frame. Therefore, aggregating features from other frames becomes a natural choice. Existing methods rely heavily on optical flow or recurrent neural networks for feature aggregation. However, these methods emphasize more on the temporally nearby frames. In this work, we argue that aggregating features in the full-sequence level will lead to more discriminative and robust features for video object detection. To achieve this goal, we devise a novel Sequence Level Semantics Aggregation (SELSA) module. We further demonstrate the close relationship between the proposed method and the classic spectral clustering method, providing a novel view for understanding the VID problem. We test the proposed method on the ImageNet VID and the EPIC KITCHENS dataset and achieve new state-of-the-art results. Our method does not need complicated postprocessing methods such as Seq-NMS or Tubelet rescoring, which keeps the pipeline simple and clean.Comment: ICCV 2019 camera read

Rev-dependent lentiviral expression vector

BACKGROUND: HIV-responsive expression vectors are all based on the HIV promoter, the long terminal repeat (LTR). While responsive to an early HIV protein, Tat, the LTR is also responsive to cellular activation states and to the local chromatin activity where the integration has occurred. This can result in high HIV-independent activity, and has restricted the use of LTR-based reporter vectors to cloned cells, where aberrantly high expressing (HIV-negative) cells can be eliminated. Enhancements in specificity would increase opportunities for expression vector use in detection of HIV as well as in experimental gene expression in HIV-infected cells. RESULTS: We have constructed an expression vector that possesses, in addition to the Tat-responsive LTR, numerous HIV DNA sequences that include the Rev-response element and HIV splicing sites that are efficiently used in human cells. It also contains a reading frame that is removed by cellular splicing activity in the absence of HIV Rev. The vector was incorporated into a lentiviral reporter virus, permitting detection of replicating HIV in living cell populations. The activity of the vector was measured by expression of green fluorescence protein (GFP) reporter and by PCR of reporter transcript following HIV infection. The vector displayed full HIV dependency. CONCLUSION: As with the earlier developed Tat-dependent expression vectors, the Rev system described here is an exploitation of an evolved HIV process. The inclusion of Rev-dependency renders the LTR-based expression vector highly dependent on the presence of replicating HIV. The application of this vector as reported here, an HIV-dependent reporter virus, offers a novel alternative approach to existing methods, in situ PCR or HIV antigen staining, to identify HIV-positive cells. The vector permits examination of living cells, can express any gene for basic or clinical experimentation, and as a pseudo-typed lentivirus has access to most cell types and tissues

Mining and Predicting Smart Device User Behavior

Three types of user behavior are mined in this paper: application usage, smart device usage and periodicity of user behavior. When mining application usage, the application installation, most frequently used applications and application correlation are analyzed. The application usage is long-tailed. When mining the device usage, the mean, variance and autocorrelation are calculated both for duration and interval. Both the duration and interval are long-tailed but only duration satisfies power-law distribution. Meanwhile, the autocorrelation of both duration and interval is weak, which makes predicting user behavior based on adjacent behavior not so reasonable in related works. Then DFT (Discrete Fourier Transform) is utilized to analyze the periodicity of user behavior and results show that the most obvious periodicity is 24 hours, which is in agreement with related works. Based on the results above, an improved user behavior predicting model is proposed based on Chebyshev inequality. Experiment results show that the performance is good in accurate rate and recall rate

Selective killing of HIV-1-positive macrophages and T cells by the Rev-dependent lentivirus carrying anthrolysin O from Bacillus anthracis

<p>Abstract</p> <p>Background</p> <p>The ability of Human Immunodeficiency Virus (HIV) to persist in the body has proven to be a long-standing challenge to virus eradication. Current antiretroviral therapy cannot selectively destroy infected cells; it only halts active viral replication. With therapeutic cessation or interruption, viral rebound occurs, and invariably, viral loads return to pre-treatment levels. The natural reservoirs harboring replication-competent HIV-1 include CD4 T cells and macrophages. In particular, cells from the macrophage lineage resist HIV-1-mediated killing and support sustained viral production. To develop a complementary strategy to target persistently infected cells, this proof-of-concept study explores an HIV-1 Rev-dependent lentiviral vector carrying a bacterial hemolysin, <it>anthrolysin O </it>(<it>anlO</it>) from <it>Bacillus anthracis</it>, to achieve selective killing of HIV-1- infected cells.</p> <p>Results</p> <p>We demonstrate that in the Rev-dependent lentiviral vector, <it>anlO </it>expression is exclusively dependent on Rev, a unique HIV-1 protein present only in infected cells. Intracellular expression and oligomerization of AnlO result in membrane pore formation and cytolysis. We have further overcome a technical hurdle in producing a Revdependent AnlO lentivirus, through the use of β-cyclodextrin derivatives to inhibit direct killing of producer cells by AnlO. Using HIV-1-infected macrophages and T cells as a model, we demonstrate that this Rev-dependent AnlO lentivirus diminishes HIV-1- positive cells.</p> <p>Conclusion</p> <p>The Rev-dependent lentiviral vector has demonstrated its specificity in targeting persistently infected cells. The choice of <it>anlO </it>as the first suicidal gene tested in this vector is based on its cytolytic activity in macrophages and T cells. We conclude that Rev-regulated expression of suicidal genes in HIV-1-positive cells is possible, although future <it>in vivo </it>delivery of this system needs to address numerous safety issues.</p