True Latency Research Articles

The true latency of biomedical research papers

The true latency of biomedical research papers

Bringing Balance: Immune Interactions Regulating Murine Gammaherpesvirus 68 Latency

Abstract Purpose of Review Gammaherpesviruses constitute the chief virus family that is capable of exhibiting true latency. Latency allows the viral genome to override host immune responses and persist despite unfavorable conditions. Due to the species specificity of gammaherpesviruses, murine gammaherpesvirus 68 (MHV68), presents by far the most advanced system for analyzing latency and the impact of the immune response to viral latency in an intact host. Recent Findings Recent publications show that MHV68 utilizes components of the host immune response to promote the establishment of latency. Further, other immune factors, which are classically antiviral, were found to differentially function to promote or restrict MHV68 latency depending on anatomical location or in cell-intrinsic manner. These observations highlight the involvement of varied underlying mechanistic pathways through which host immune factors may interact with MHV68 to regulate latency. Summary Throughout this review, we highlight different ways through which the host immune response both promotes and restricts MHV68 latency.

504. Latent HHV7 Infection Attenuates Beneficial Host-Microbe Interactions in the Human Gut

Abstract Background Human Herpes Virus 7 (HHV7) infection results in a lifelong latent infection with over 95% of adults seropositive for HHV7. Lymphocytes are the best understood host cell type for latent HHV7, with the gastric mucosa another site of latent infection. Herpesviridae latency affects host processes like interferon signaling, antigen presentation, and proliferation—the same host pathways are implicated in the beneficial responses to commensal microbes. Methods Adult human colonic organoids with or without latent HHV7 infection were co-cultured with B. longum in asymmetric oxygen conditions that allow for live interaction (F1). The transcriptional state after 24h of interactions was determined with RNA-sequencing. The transcriptional state was compared between axenic (no microbes) or after co-culture and with or without latent HHV7. F1: Establishing oxygen gradients across epithelial monolayers (A) Schematic of oxygen gradient apparatus (B) Closeup view of individual well (C) Growth of the anaerobe B. longum was identical in the apparatus with hypoxic epithelial compared to full anaerobic growth (D) Butyrate administration protects the epithelium from inflammatory effects of deoxycholate. Results Screening human intestinal organoids (that lack lymphocytes and are strictly of the endodermal lineage) we have generated evidence that intestinal stem cells (ISC) and IEC can be a host cell for latent HHV7 infection in some but not all people (T1). RNA-sequencing reveals that this is true latency, with ISC and IEC containing HHV7 without transcripts from any of the protein-coding genes in the HHV7 genome. Further we have observed that latent HHV7 is mosaic in the gut, not affecting all of the ISC in an individual (T1). In organoid-derived human IEC we have noted co-culture with the commensal bacteria B. longum suppresses key executors of apoptosis and pyroptosis (F2). These same effects are no longer observed with the B. longum is interacting with IEC latently infected with HHV7. A similar pattern was observed with NFkB regulators (F3). T1: Latent HHV7 is found in some intestinal organoids derived from healthy adults From the University of Michigan Translational Tissue Modeling Laboratory (TTML) organoid registry. Each donor is assigned a unique numerical ID. Viral panel is from a commercial multiplex PCR screen. Notably, donor 87 has colonic organoids with and without latent HHV7. F2: Co-culture with the commensal microbe B. longum suppresses most apoptosis and pyroptosis executors only in an organoid without latent HHV7 infection. Fragments per kilobase per millions of reads (FPKM) from RNA-sequencing of fully-differentiated organoid-derived human intestinal epithelium after 24 hours of co-culture with B.longum (Orange) or remaining axenic (without microbes; Blue). Results from cell without (left) or with (right) latent HHV7. F3: Stimulation of the NFkB inhibitor NFKBIA by co-culture with the commensal microbe B. longum is absent in organoids with latent HHV7 infection. Fragments per kilobase per millions of reads (FPKM) from RNA-sequencing of fully-differentiated organoid-derived human intestinal epithelium after 24 hours of co-culture with B.longum (Orange) or remaining axenic (without microbes; Blue). Results from cell without (left) or with (right) latent HHV7. Conclusion Latent HHV7 in the human gut epithelium may attenuate the effect of beneficial microbes like B. longum (F4). The evidence for mosaicism of latent HHV7 in the human gut adds a spatial aspect to these attenuating effects that could be relevant for specific disease processes (e.g. skip lesions in Crohn’s disease). Confirmation of these findings, estimating the true prevalence of latent HHV7 in the gut, and identification of the HHV7 latency mechanism will be required to understand the full implications of these findings. F4: A Model of Latent HHV7 Infection Attenuating Responses to Commensal Microbes. Based on our findings, latent HHV7 infection in the intestinal epithelium may leave the gut mucosa at increased risk for injury by impairing the beneficial response to commensal microbes in a spatially complex manner due to the apparent mosaic nature of latent HHV7 infection in the gut. Disclosures Jonathan L. Golob, MD/PhD, Loxo Oncology: Employment of Spouse.

Stress Incontinence Surgery Does Not Cause Pelvic Malignancy: A Population-Based Cohort Study

We sought to determine if stress urinary incontinence surgery (mesh or nonmesh) is associated with the development of pelvic malignancies later in life. We performed a retrospective cohort study between January 1, 2002 and October 31, 2015 of all women in Ontario, Canada without a history of pelvic malignancy who underwent an index stress incontinence surgery. The primary outcome was a composite of any pelvic malignancy (including urological and gynecological cancers) following stress incontinence surgery. Secondarily, we considered each cancer individually. A survival analysis using a Cox proportional-hazards model with a 3-level categorical exposure (mesh surgery, nonmesh surgery, and control) was performed. Patients were followed until death, emigration or the study end (October 31, 2017). Of the women 74,968 underwent stress urinary incontinence surgery during the study period. There were 5,505,576 women in the control group. Over a median followup of 8.5 years (IQR, 5.5-11.9), 587 pelvic malignancies occurred in the surgery group. Women who underwent stress incontinence surgery had a reduced risk of pelvic malignancy independent of surgery type, compared to controls (Wald type 3 p <0.001; mesh HR, 0.68 [95% CI, 0.62-0.76]; p <0.0001; nonmesh HR, 0.37 [95% CI, 0.29-0.46]; p <0.0001). The individual pelvic cancers similarly demonstrated a reduced risk of malignancy following stress incontinence surgery. At a median followup of 8.5 years, women had no increased risk of pelvic malignancy following either mesh or nonmesh stress urinary incontinence surgery in a large population-based cohort.

Low Latency, Online Processing of the High-Bandwidth Bunch-By-Bunch Observation Data From the Transverse Feedback System in the LHC

During long shutdown 2 (2019-2020) the transverse observation system (ADTObsBox) in the LHC will undergo a substantial upgrade. The purpose of this upgrade is to allow for true low latency, online processing of the 16 data-streams of transverse bunch-by-bunch, turn-by-turn positional data provided by the transverse feedback system in the LHC (ADT). This system makes both offline and online analysis of the data possible, where the emphasis will lie on online analysis, something that the older generation was not designed to provide. The result of the analysis is made available for accelerator physicists, machine operators, and engineers working with LHC. The new system allows users to capture buffers of various lengths for later analysis just like the older generation and it provides a platform for real-time analysis applications to directly capture the data with minimal latency while also providing a heterogeneous computing platform where the applications can utilize CPUs, GPUs and dedicated FPGAs. The analysis applications include bunch-by-bunch instability analysis and passive bunch-by-bunch tune extraction to name a few. The ADTObsBox system uses commodity server technology in combination with FPGA-based PCIe I/O cards. This paper will cover the design and status of the I/O cards, server, firmware, driver, analysis applications and results of early performance testing.

Repeated spontaneous clearance of hepatitis C virus infection in the setting of long-term non-progression of HIV infection.

Hepatitis C Virus (HCV) and human immunodeficiency virus (HIV) are global pandemics that affect 170 million and 35 million individuals, respectively. Up to 45% of individuals infected with HCV clear their infections spontaneously – correlating to factors like aboriginal descent and some host specific immune factors. HIV, however, establishes true latency in infected cells and cannot be cured. In the setting of longterm non-progressors (LTNPs) of HIV, a state of immune preservation and low circulating viral load is established. Regarding HIV/HCV co-infection, little is known about the relationship between spontaneous clearance of HCV infection and long-term control of HIV infection without medical intervention. We describe a case of a HIV-infected female defined as a LTNP in whom spontaneous clearance of HCV was documented on multiple occasions. Similar cases should be documented and identified in an effort to develop novel hypotheses about the natural control of these infections and inform research on immune-based interventions to control them.

HIV Infection in the Native and Allograft Kidney: Implications for Management, Diagnosis, and Transplantation.

The native kidney is a reservoir for human immunodeficiency virus (HIV)-1 and a site of viral replication, similar to lymphoid tissue, gut-associated lymphoid tissue or semen. The ability of the virus to persist may result from either a true latency or sequestration in an anatomic site that is not effectively exposed to antiretroviral therapy. The presence of HIV in kidney epithelial cells will lead progressively to end-stage renal disease. For decades, HIV-infected patients were excluded from consideration for kidney transplantation. Hemodialysis and peritoneal dialysis were the only forms of treatment available to these patients. The introduction of combined antiretroviral therapy has changed the overall prognosis of these patients and allowed them to benefit from kidney transplantation without an increased risk of opportunistic infections or cancer. However, we recently established that HIV-1 can infect kidney transplant epithelial cells in the absence of detectable viremia. The presence of HIV in kidney cells can manifest itself in multiple ways, ranging from indolent nephropathy and inflammation to proteinuria with glomerular abnormalities. Because the tools that are available to diagnose the presence of HIV in kidney cells are complex, the rate of infection is certainly underestimated. This finding will certainly have implications in the management of patients, particularly for HIV-positive donors. The purpose of this review is to highlight recent evidence that the allograft kidney can be infected by the virus after transplantation as well as the associated consequences.

Exosomes from uninfected cells activate transcription of latent HIV-1.

HIV-1 infection causes AIDS, infecting millions worldwide. The virus can persist in a state of chronic infection due to its ability to become latent. We have previously shown a link between HIV-1 infection and exosome production. Specifically, we have reported that exosomes transport viral proteins and RNA from infected cells to neighboring uninfected cells. These viral products could then elicit an innate immune response, leading to activation of the Toll-like receptor and NF-κB pathways. In this study, we asked whether exosomes from uninfected cells could activate latent HIV-1 in infected cells. We observed that irrespective of combination antiretroviral therapy, both short- and long-length viral transcripts were increased in wild-type HIV-1–infected cells exposed to purified exosomes from uninfected cells. A search for a possible mechanism for this finding revealed that the exosomes increase RNA polymerase II loading onto the HIV-1 promoter in the infected cells. These viral transcripts, which include trans-activation response (TAR) RNA and a novel RNA that we termed TAR-gag, can then be packaged into exosomes and potentially be exported to neighboring uninfected cells, leading to increased cellular activation. To better decipher the exosome release pathways involved, we used siRNA to suppress expression of ESCRT (endosomal sorting complex required for transport) proteins and found that ESCRT II and IV significantly control exosome release. Collectively, these results imply that exosomes from uninfected cells activate latent HIV-1 in infected cells and that true transcriptional latency may not be possible in vivo, especially in the presence of combination antiretroviral therapy.

At what latency does the phase of brain oscillations influence perception?

Recent evidence has shown a rhythmic modulation of perception: prestimulus ongoing electroencephalography (EEG) phase in the θ (4-8 Hz) and α (8-13 Hz) bands has been directly linked with fluctuations in target detection. In fact, the ongoing EEG phase directly reflects cortical excitability: it acts as a gating mechanism for information flow at the neuronal level. Consequently, the key phase modulating perception should be the one present in the brain when the stimulus is actually being processed. Most previous studies, however, reported phase modulation peaking 100 ms or more before target onset. To explain this discrepancy, we first use simulations showing that contamination of spontaneous oscillatory signals by target-evoked ERP and signal filtering (e.g., wavelet) can result in an apparent shift of the peak phase modulation towards earlier latencies, potentially reaching the prestimulus period. We then present a paradigm based on linear systems analysis which can uncover the true latency at which ongoing EEG phase influences perception. After measuring the impulse response function, we use it to reconstruct (rather than record) the brain activity of human observers during white noise sequences. We can then present targets in those sequences, and reliably estimate EEG phase around these targets without any influence of the target-evoked response. We find that in these reconstructed signals, the important phase for perception is that of fronto-occipital ∼6 Hz background oscillations at about 75 ms after target onset. These results confirm the causal influence of phase on perception at the time the stimulus is effectively processed in the brain.

Exosomes from uninfected cells activate transcription of latent HIV-1

HIV-1 infection causes AIDS, infecting millions worldwide. The virus can persist in a state of chronic infection due to its ability to become latent. We have previously shown a link between HIV-1 infection and exosome production. Specifically, we have reported that exosomes transport viral proteins and RNA from infected cells to neighboring uninfected cells. These viral products could then elicit an innate immune response, leading to activation of the Toll-like receptor and NF-κB pathways. In this study, we asked whether exosomes from uninfected cells could activate latent HIV-1 in infected cells. We observed that irrespective of combination antiretroviral therapy, both short- and long-length viral transcripts were increased in wild-type HIV-1-infected cells exposed to purified exosomes from uninfected cells. A search for a possible mechanism for this finding revealed that the exosomes increase RNA polymerase II loading onto the HIV-1 promoter in the infected cells. These viral transcripts, which include trans-activation response (TAR) RNA and a novel RNA that we termed TAR-gag, can then be packaged into exosomes and potentially be exported to neighboring uninfected cells, leading to increased cellular activation. To better decipher the exosome release pathways involved, we used siRNA to suppress expression of ESCRT (endosomal sorting complex required for transport) proteins and found that ESCRT II and IV significantly control exosome release. Collectively, these results imply that exosomes from uninfected cells activate latent HIV-1 in infected cells and that true transcriptional latency may not be possible in vivo, especially in the presence of combination antiretroviral therapy.

At What Latency Does the Phase of Brain Oscillations Influence Perception?

Recent evidence has shown a rhythmic modulation of perception: prestimulus ongoing electroencephalography (EEG) phase in the θ (4–8 Hz) and α (8–13 Hz) bands has been directly linked with fluctuations in target detection. In fact, the ongoing EEG phase directly reflects cortical excitability: it acts as a gating mechanism for information flow at the neuronal level. Consequently, the key phase modulating perception should be the one present in the brain when the stimulus is actually being processed. Most previous studies, however, reported phase modulation peaking 100 ms or more before target onset. To explain this discrepancy, we first use simulations showing that contamination of spontaneous oscillatory signals by target-evoked ERP and signal filtering (e.g., wavelet) can result in an apparent shift of the peak phase modulation towards earlier latencies, potentially reaching the prestimulus period. We then present a paradigm based on linear systems analysis which can uncover the true latency at which ongoing EEG phase influences perception. After measuring the impulse response function, we use it to reconstruct (rather than record) the brain activity of human observers during white noise sequences. We can then present targets in those sequences, and reliably estimate EEG phase around these targets without any influence of the target-evoked response. We find that in these reconstructed signals, the important phase for perception is that of fronto-occipital ∼6 Hz background oscillations at about 75 ms after target onset. These results confirm the causal influence of phase on perception at the time the stimulus is effectively processed in the brain.

Repeated Spontaneous Clearance of Hepatitis C Virus (HCV) Infection in the Setting of Long-Term Non-Progression of Human Immunodeficiency Virus (HIV) Infection

1.1.Introduction: HCV and HIV are global pandemics that affect 170 million and 35 million individuals, respectively. Up to 45% of individuals infected with HCV clear their infections spontaneously – correlating to factors like female sex, aboriginal descent, symptomatic acute hepatitis and some host specific immune factors. HIV, however, establishes true latency in infected cells, and therefore cannot be cured. In the setting of long-term non-progressors (LTNPs) of HIV, a state of immune preservation and low circulating viral load is established. Regarding HIV/HCV co- infection, little is known about the relationship between spontaneous clearance of HCV infection and long-term control of HIV infection without the benefit of antiretroviral therapy. 1.2.Case Presentation: We describe a case of a HIV-infected female who was an established LTNP in whom spontaneous clearance of HCV was documented on multiple occasions. 1.3.Conclusion: Similar cases of HIV LTNPs who may be exposed repeatedly to HCV and fail to establish productive infections should be documented and identified in an effort to develop novel hypotheses about natural control of both HIV and HCV. In the future, this could inform research on immune-based interventions to control these infections.

Single-Trial Evoked Potential Estimation Using Iterative Principal Component Analysis

In this paper, we have presented an iterative principal component analysis (PCA) method to obtain single trial evoked potential. The performance of the iterative PCA has been compared with the performance of other iterative component analysis methods, such as independent component analysis, canonical correlation analysis (CCA), and the second-order blind identification, using simulated data at different signal-to-noise ratios as well as actual recordings of visual evoked potentials. In both the simulated and real cases, iterative PCA and CCA perform better than the other methods to estimate the amplitudes. In the estimated trials of the proposed method, the latency of the evoked potentials lies between ±4 ms range of true latency in about 90% of the case; but for other methods, this percentage is around 60%.

Counteracting effects of cellular Notch and Epstein-Barr virus EBNA2: implications for stromal effects on virus-host interactions.

ABSTRACTA number of diverse environmental cues have been linked to B lymphocyte differentiation and activation. One such cue, Notch-2, may be particularly relevant to the biology of infection with Epstein-Barr virus (EBV), which colonizes the B cell compartment. Activated Notch and EBV nuclear antigen 2 (EBNA2) both function as transcriptional activators by virtue of their interactions with the transcription factor RBP-Jκ. Although EBNA2 and activated Notch appear to have partially overlapping functions, we now report that activated Notch counteracts a crucial EBNA2 function both in newly infected primary B cells and in lymphoblastoid cell lines (LCLs). EBNA2 is directly responsible for the initiation of transcription of the majority of EBV proteins associated with type III latency, leading to the outgrowth of LCLs. One of the key proteins driving this outgrowth is latent membrane protein 1 (LMP1), which is regulated by an EBNA2-responsive element within its ED-L1 promoter. Activation of Notch-2 via Delta-like ligand 1 inhibits EBNA2-mediated initiation of LMP1 transcription. Furthermore, ligated Notch-2 also efficiently turns off LMP1 expression from the ED-L1 promoter in LCLs already expressing LMP1. Modulation of EBV gene expression by Notch was not confined to EBNA2-dependent events. Activated Notch-2 also inhibited EBV entry into the lytic cycle in a B cell non-Hodgkin's lymphoma line by upregulating the cellular transcription factor Zeb2, which represses the transcription of BZLF1. These results support the concept that in vivo, cumulative signals from the microenvironment downregulate EBV gene expression in B cells to the latency 0 gene expression profile observed in B cells entering the peripheral blood.IMPORTANCE Experimental infection of resting B cells by Epstein-Barr virus leads to the growth transformation program of virus gene expression and the outgrowth of lymphoblastoid cell lines. Previous studies at the single-cell level revealed complex cellular and viral signaling networks regulating transcription of the viral genome. This study demonstrates that viral gene expression can also be radically altered by molecules expressed on stromal cells in the microenvironment of lymphoid tissue, specifically, Delta-like ligand 1 on stromal cells ligating Notch-2 on infected B cells. Activation of Notch interferes with the transactivation function of EBNA2, downregulates the expression of LMP1 and LMP2a, and inhibits the activation of lytic virus replication in a B cell non-Hodgkin's lymphoma line by preventing expression of BZLF1. The significance of these observations is that they indicate new mechanisms whereby the microenvironment in normal lymphoid tissue may facilitate the repression of viral gene expression, enabling establishment of true latency in memory B cells.

Latent and Delayed Action Polymerization Systems

Various approaches to latent polymerization processes are described. In order to highlight recent advances in this field, the discussion is subdivided into chapters dedicated to diverse classes of polymers, namely polyurethanes, polyamides, polyesters, polyacrylates, epoxy resins, and metathesis-derived polymers. The described latent initiating systems encompass metal-containing as well as purely organic compounds that are activated by external triggers such as light, heat, or mechanical force. Special emphasis is put on the different chemical venues that can be taken to achieve true latency, which include masked N-heterocyclic carbenes, latent metathesis catalysts, and photolatent radical initiators, among others. Scientific challenges and the advantageous application of latent polymerization processes are discussed.

Psychophysics of a nociceptive test in the mouse: ambient temperature as a key factor for variation.

BackgroundThe mouse is increasingly used in biomedical research, notably in behavioral neurosciences for the development of tests or models of pain. Our goal was to provide the scientific community with an outstanding tool that allows the determination of psychophysical descriptors of a nociceptive reaction, which are inaccessible with conventional methods: namely the true threshold, true latency, conduction velocity of the peripheral fibers that trigger the response and latency of the central decision-making process.Methodology/Principal FindingsBasically, the procedures involved heating of the tail with a CO2 laser, recording of tail temperature with an infrared camera and stopping the heating when the animal reacted. The method is based mainly on the measurement of three observable variables, namely the initial temperature, the heating rate and the temperature reached at the actual moment of the reaction following random variations in noxious radiant heat. The initial temperature of the tail, which itself depends on the ambient temperature, very markedly influenced the behavioral threshold, the behavioral latency and the conduction velocity of the peripheral fibers but not the latency of the central decision-making.Conclusions/SignificanceWe have validated a psychophysical approach to nociceptive reactions for the mouse, which has already been described for rats and Humans. It enables the determination of four variables, which contribute to the overall latency of the response. The usefulness of such an approach was demonstrated by providing new fundamental findings regarding the influence of ambient temperature on nociceptive processes. We conclude by challenging the validity of using as “pain index" the reaction time of a behavioral response to an increasing heat stimulus and emphasize the need for a very careful control of the ambient temperature, as a prevailing environmental source of variation, during any behavioral testing of mice.

Using NetMagic to observe fine-grained per-flow latency measurements

We introduce NetMagic to demonstrate the efficacy of RLI architecture RLI for the fine-grained per-flow latency measurements. In this demo, the main function of RLI is implemented in NetMagic, which is the key component of our experimental network comprising several computers and switches. We are going to show how NetMagic can provide rapid implementation and evaluation of RLI architecture that is difficult with commercial switch or router platforms. In the demo, the estimated fine-grained per-flow latency by RLI is monitored and dynamically presented. Further, the true latency with a resolution of 8ns is also provided by NetMagic for the evaluation. The efficacy of RLI architecture can be observed in a real-time fashion by the difference between estimated latencies and true ones.

Human Bocavirus DNA in Paranasal Sinus Mucosa

Human Bocavirus DNA in Paranasal Sinus Mucosa

In this issue

In this issue

DNA cytosine methylation in the Bovine Leukemia Virus promoter is associated with latency in a Lymphoma-derived B-cell line : potential involvement of direct inhibition of CREB/CREM/ATF binding

Bovine leukemia virus (BLV) proviral latency represents a viral strategy to escape the host immune system and allow tumor development. Besides the previously demonstrated role of histone deacetylation in the epigenetic repression of BLV expression, we showed here that BLV promoter activity was induced by several DNA methylation inhibitors (such as 5-aza-2'-deoxycytidine) and that overexpressed DNMT1 and DNMT3A, but not DNMT3B, down-regulated BLV promoter activity. Importantly, cytosine hypermethylation in the 5'-long terminal repeat (LTR) U3 and R regions was associated with true latency in the lymphoma-derived B-cell line L267 but not with defective latency in YR2 cells. Moreover, the virus-encoded transactivator Tax(BLV) decreased DNA methyltransferase expression levels, which could explain the lower level of cytosine methylation observed in the L267(LTaxSN) 5'-LTR compared with the L267 5'-LTR. Interestingly, DNA methylation inhibitors and Tax(BLV) synergistically activated BLV promoter transcriptional activity in a cAMP-responsive element (CRE)-dependent manner. Mechanistically, methylation at the -154 or -129 CpG position (relative to the transcription start site) impaired in vitro binding of CRE-binding protein (CREB) transcription factors to their respective CRE sites. Methylation at -129 CpG alone was sufficient to decrease BLV promoter-driven reporter gene expression by 2-fold. We demonstrated in vivo the recruitment of CREB/CRE modulator (CREM) and to a lesser extent activating transcription factor-1 (ATF-1) to the hypomethylated CRE region of the YR2 5'-LTR, whereas we detected no CREB/CREM/ATF recruitment to the hypermethylated corresponding region in the L267 cells. Altogether, these findings suggest that site-specific DNA methylation of the BLV promoter represses viral transcription by directly inhibiting transcription factor binding, thereby contributing to true proviral latency.