A systematic analysis of host factors reveals a Med23-interferon-λ regulatory axis against herpes simplex virus type 1 replication

Herpes simplex virus type 1 (HSV-1) is a neurotropic virus causing vesicular oral or genital skin lesions, meningitis and other diseases particularly harmful in immunocompromised individuals. To comprehensively investigate the complex interaction between HSV-1 and its host we combined two genome-scale screens for host factors (HFs) involved in virus replication. A yeast two-hybrid screen for protein interactions and a RNA interference (RNAi) screen with a druggable genome small interfering RNA (siRNA) library confirmed existing and identified novel HFs which functionally influence HSV-1 infection. Bioinformatic analyses found the 358 HFs were enriched for several pathways and multi-protein complexes. Of particular interest was the identification of Med23 as a strongly anti-viral component of the largely pro-viral Mediator complex, which links specific transcription factors to RNA polymerase II. The anti-viral effect of Med23 on HSV-1 replication was confirmed in gain-of-function gene overexpression experiments, and this inhibitory effect was specific to HSV-1, as a range of other viruses including Vaccinia virus and Semliki Forest virus were unaffected by Med23 depletion. We found Med23 significantly upregulated expression of the type III interferon family (IFN-λ) at the mRNA and protein level by directly interacting with the transcription factor IRF7. The synergistic effect of Med23 and IRF7 on IFN-λ induction suggests this is the major transcription factor for IFN-λ expression. Genotypic analysis of patients suffering recurrent orofacial HSV-1 outbreaks, previously shown to be deficient in IFN-λ secretion, found a significant correlation with a single nucleotide polymorphism in the IFN-λ3 (IL28b) promoter strongly linked to Hepatitis C disease and treatment outcome. This paper describes a link between Med23 and IFN-λ, provides evidence for the crucial role of IFN-λ in HSV-1 immune control, and highlights the power of integrative genome-scale approaches to identify HFs critical for disease progression and outcome

Presence of functionally active protease-activated receptors 1 and 2 in myenteric glia

Protease-activated receptors (PARs) belong to the family of membrane receptors coupled to G-proteins; their presence is reported in a wide variety of cells. The object of this study was to demonstrate the presence of PAR-1 and PAR-2 in myenteric glia of the guinea pig, and to elucidate the cellular mechanisms that are triggered upon receptor activation. Thrombin and PAR-1 agonist peptide (PARP-1) activate PAR-1 with a maximum mean ± SEM change in intracellular calcium concentration with respect to basal level (δ[Ca 2+ ] i ) of 183 ± 18 nm and 169 ± 6 nm, respectively. Trypsin and PAR-2 agonist peptide (PARP-2) activate PAR-2 with a maximum δ[Ca 2+ ] i of 364 ± 28 nm and 239 ± 19 nm, respectively. Inhibition of phospholipase C by U73312 (1 µm) decreased the δ[Ca 2+ ] i due to PAR-1 activation from 167 ± 10 nm to 87 ± 6 nm. The PAR-2-mediated δ[Ca 2+ ] i decreased from 193 ± 10 nm to 124 ± 8 nm when phospholipase C activity was inhibited. Blockade of sphingosine kinase with dimethylsphingosine (1 µm) decreased the δ[Ca 2+ ] i due to PAR-2 activation from 149 ± 19 nm to 67 ± 1 nm, but did not influence the PAR-1-mediated δ[Ca 2+ ] i . PAR-1 and PAR-2 were localized in myenteric glia by immunolabeling. Our results indicate that PAR-1 and PAR-2 are present in myenteric glia of the guinea pig, and their activation leads to increases in intracellular calcium via different signal transduction mechanisms that involve activation of phospholipase C and sphingosine kinase.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66037/1/j.1471-4159.2002.01119.x.pd

Basic Biomedical Sciences and the Future of Medical Education: Implications for Internal Medicine

The academic model of medical education in the United States is facing substantial challenges. Apprenticeship experiences with clinical faculty are increasingly important in most medical schools and residency programs. This trend threatens to separate clinical education from the scientific foundations of medical practice. Paradoxically, this devaluation of biomedical science is occurring as the ability to use new discoveries to rationalize clinical decision making is rapidly expanding. Understanding the scientific foundations of medical practice and the ability to apply them in the care of patients separates the physician from other health care professionals. The de-emphasis of biomedical science in medical education poses particular dangers for the future of internal medicine as the satisfaction derived from the application of science to the solving of a clinical problem has been a central attraction of the specialty. Internists should be engaged in the ongoing discussions of medical education reform and provide a strong voice in support of rigorous scientific training for the profession

Potential role of levocarnitine supplementation for the treatment of chemotherapy-induced fatigue in non-anaemic cancer patients

Ifosfamide and cisplatin cause urinary loss of carnitine, which is a fundamental molecule for energy production in mammalian cells. We investigated whether restoration of the carnitine pool might improve chemotherapy-induced fatigue in non-anaemic cancer patients. Consecutive patients with low plasma carnitine levels who experienced fatigue during chemotherapy were considered eligible for study entry. Patients were excluded if they had anaemia or other conditions thought to be causing asthenia. Fatigue was assessed by the Functional Assessment of Cancer Therapy-Fatigue quality of life questionnaire. Treatment consisted of oral levocarnitine 4 g daily, for 7 days. Fifty patients were enrolled; chemotherapy was cisplatin-based in 44 patients and ifosfamide-based in six patients. In the whole group, baseline mean Functional Assessment of Cancer Therapy-Fatigue score was 19.7 (±6.4; standard deviation) and the mean plasma carnitine value was 20.9 μM (±6.8; standard deviation). After 1 week, fatigue ameliorated in 45 patients and the mean Functional Assessment of Cancer Therapy-Fatigue score was 34.9 (±5.4; standard deviation) (P<.001). All patients achieved normal plasma carnitine levels. Patients maintained the improved Functional Assessment of Cancer Therapy-Fatigue score until the next cycle of chemotherapy. In selected patients, levocarnitine supplementation may be effective in alleviating chemotherapy-induced fatigue. This compound deserves further investigations in a randomised, placebo-controlled study

Variability in a dominant block to SIV early reverse transcription in rhesus monkey cells predicts in vivo viral replication and time to death

While it has long been appreciated that there is considerable variability in host containment of HIV/SIV replication, the determinants of that variability are not fully understood. Previous studies demonstrated that the degree of permissivity of a macaque's peripheral blood mononuclear cells (PBMC) for infection with simian immunodeficiency virus (SIV) in vitro predicted that animal's peak plasma virus RNA levels following SIV infection in vivo. The present study was conducted to define the mechanisms underlying the variable intrinsic susceptibility of rhesus monkey PBMC to SIVsmE660 infection. In a cohort of 15 unrelated Indian-origin rhesus monkeys, infectability of PBMC of individual animals with SIVsmE660, as defined by tissue culture infectious dose (TCID50), varied by more than 3 logs and was a stable phenotype over time. Susceptibility of a monkey's PBMC to wild type SIVsmE660 infection correlated with the susceptibility of that monkey's PBMC to infection with VSV-G pseudotyped SIVsm543-GFP. Moreover, the permissivity of an individual monkey's PBMC for infection with this construct correlated with the permissivity of a B-lymphoblastoid cell line (B-LCL) generated from PBMC of the same animal. We found that the degree of intrinsic resistance of monkey B-LCL correlated with the copy number of early reverse transcription (ERT) SIV DNA. The resistance of monkey B-LCL to SIVsmE660 replication could be abrogated by preincubation of cells with the SIV virus-like particles (VLPs) and SIV resistance phenotype could be transferred to a SIV susceptible B-LCL through cell fusion. Finally, we observed a positive correlation between susceptibility of monkey B-LCL to SIV infection with a VSV-G pseudotyped SIV-GFP construct in vitro and both the peak plasma virus RNA levels in vivo and time to death following wild type SIV infection. These findings suggest that a dominant early RT restricting factor that can be saturated by SIV capsid may contribute to the variable resistance to SIV infection in rhesus monkey B-LCL and that this differential intrinsic susceptibility contributes to the clinical outcome of an SIV infection

Ferromanganese nodules and micro-hardgrounds associated with the Cadiz Contourite Channel (NE Atlantic): Palaeoenvironmental records of fluid venting and bottom currents

Ferromanganese nodule fields and hardgrounds have recently been discovered in the Cadiz Contourite Channel in the Gulf of Cadiz (850–1000 m). This channel is part of a large contourite depositional system generated by the Mediterranean Outflow Water. Ferromanganese deposits linked to contourites are interesting tools for palaeoenviromental studies and show an increasing economic interest as potential mineral resources for base and strategic metals. We present a complete characterisation of these deposits based on submarine photographs and geophysical, petrographic, mineralogical and geochemical data. The genesis and growth of ferromanganese deposits, strongly enriched in Fe vs. Mn (av. 39% vs. 6%) in this contourite depositional system result from the combination of hydrogenetic and diagenetic processes. The interaction of the Mediterranean Outflow Water with the continental margin has led to the formation of Late Pleistocene–Holocene ferromanganese mineral deposits, in parallel to the evolution of the contourite depositional system triggered by climatic and tectonic events. The diagenetic growth was fuelled by the anaerobic oxidation of thermogenic hydrocarbons (δ13CPDB=−20 to −37‰) and organic matter within the channel floor sediments, promoting the formation of Fe–Mn carbonate nodules. High 87Sr/86Sr isotopic values (up to 0.70993±0.00025) observed in the inner parts of nodules are related to the influence of radiogenic fluids fuelled by deep-seated fluid venting across the fault systems in the diapirs below the Cadiz Contourite Channel. Erosive action of the Mediterranean Outflow Water undercurrent could have exhumed the Fe–Mn carbonate nodules, especially in the glacial periods, when the lower core of the undercurrent was more active in the study area. The growth rate determined by 230Thexcess/232Th was 113±11 mm/Ma, supporting the hypothesis that the growth of the nodules records palaeoenvironmental changes during the last 70 ka. Ca-rich layers in the nodules could point to the interaction between the Mediterranean Outflow Water and the North Atlantic Deep Water during the Heinrich events. Siderite–rhodochrosite nodules exposed to the oxidising seabottom waters were replaced by Fe–Mn oxyhydroxides. Slow hydrogenetic growth of goethite from the seawaters is observed in the outermost parts of the exhumed nodules and hardgrounds, which show imprints of the Mediterranean Outflow Water with low 87Sr/86Sr isotopic values (down to 0.70693±0.00081). We propose a new genetic and evolutionary model for ferromanganese oxide nodules derived from ferromanganese carbonate nodules formed on continental margins above the carbonate compensation depth and dominated by hydrocarbon seepage structures and strong erosive action of bottom currents. We also compare and discuss the generation of ferromanganese deposits in the Cadiz Contourite Channel with that in other locations and suggest that our model can be applied to ferromanganiferous deposits in other contouritic systems affected by fluid venting

Host sequence motifs shared by HIV predict response to antiretroviral therapy

<p>Abstract</p> <p>Background</p> <p>The HIV viral genome mutates at a high rate and poses a significant long term health risk even in the presence of combination antiretroviral therapy. Current methods for predicting a patient's response to therapy rely on site-directed mutagenesis experiments and <it>in vitro </it>resistance assays. In this bioinformatics study we treat response to antiretroviral therapy as a two-body problem: response to therapy is considered to be a function of both the host and pathogen proteomes. We set out to identify potential responders based on the presence or absence of host protein and DNA motifs on the HIV proteome.</p> <p>Results</p> <p>An alignment of thousands of HIV-1 sequences attested to extensive variation in nucleotide sequence but also showed conservation of eukaryotic short linear motifs on the protein coding regions. The reduction in viral load of patients in the Stanford HIV Drug Resistance Database exhibited a bimodal distribution after 24 weeks of antiretroviral therapy, with 2,000 copies/ml cutoff. Similarly, patients allocated into responder/non-responder categories based on consistent viral load reduction during a 24 week period showed clear separation. In both cases of phenotype identification, a set of features composed of short linear motifs in the reverse transcriptase region of HIV sequence accurately predicted a patient's response to therapy. Motifs that overlap resistance sites were highly predictive of responder identification in single drug regimens but these features lost importance in defining responders in multi-drug therapies.</p> <p>Conclusion</p> <p>HIV sequence mutates in a way that preferentially preserves peptide sequence motifs that are also found in the human proteome. The presence and absence of such motifs at specific regions of the HIV sequence is highly predictive of response to therapy. Some of these predictive motifs overlap with known HIV-1 resistance sites. These motifs are well established in bioinformatics databases and hence do not require identification via <it>in vitro </it>mutation experiments.</p

siRNA Screening of a Targeted Library of DNA Repair Factors in HIV Infection Reveals a Role for Base Excision Repair in HIV Integration

Host DNA repair enzymes have long been assumed to play a role in HIV replication, and many different DNA repair factors have been associated with HIV. In order to identify DNA repair pathways required for HIV infection, we conducted a targeted siRNA screen using 232 siRNA pools for genes associated with DNA repair. Mapping the genes targeted by effective siRNA pools to well-defined DNA repair pathways revealed that many of the siRNAs targeting enzymes associated with the short patch base excision repair (BER) pathway reduced HIV infection. For six siRNA pools targeting BER enzymes, the negative effect of mRNA knockdown was rescued by expression of the corresponding cDNA, validating the importance of the gene in HIV replication. Additionally, mouse embryo fibroblasts (MEFs) lacking expression of specific BER enzymes had decreased transduction by HIV-based retroviral vectors. Examining the role BER enzymes play in HIV infection suggests a role for the BER pathway in HIV integration