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Endogenous Retroviruses: Thierry Heidmann wins the 2009 Retrovirology prize
Ali Saib, Monsef Benkirane
Retrovirology , 2009, DOI: 10.1186/1742-4690-6-108
Abstract: In 2005, thanks to the generosity of the Ming K. Jeang Foundation, the Retrovirology prize was inaugurated. A goal of the Retrovirology Prize is to identify an outstanding mid-career scientist who is close to the peak of his/her productivity and who is expected to have many future years of high achievement. Previous winners of the Retrovirology Prize include Stephen Goff [1], Joseph Sodroski [2], Karen Beemon [3] and Ben Berkhout [4].For 2009, the Editors of Retrovirology have selected Thierry Heidmann (Figure 1) as the recipient of the Retrovirology Prize.TH heads a CNRS laboratory at Université Paris-Sud and Institut Gustave Roussy in Villejuif, in the southern suburbs of Paris. With a strong background in physics and mathematics, he was interested in the early 1980's in linking these disciplines of science with biology, more precisely with neurobiology and the science of complex neuronal networks. To fulfil his aspiration, Thierry entered Jean-Pierre Changeux's lab at the Pasteur Institute to start a PhD on the newly discovered acetylcholine receptor. This exciting experience led Thierry to turn to more applied science, following a profound will to slowly but surely shift from studying the physical sciences to studying the biological sciences! After his PhD, Thierry focused on transposable elements and retrotransposons. The question he asked at that time was simple: how to be able to monitor the transposition of these mobile elements in a mammal where genetic approaches to detect transposition were both poorly efficient and time consuming. He then decided to devise a system that could detect retrotransposition of any element whose mobilization includes a reverse transcription step, no matter where the reverse transcribed, transposed element would target and integrate. This search resulted in 1988 in the generation of the first indicator gene for retrotransposition. This was his first step in the field, but a decisive one. Since then, his laboratory has focused on
Small non-coding RNAs, mammalian cells, and viruses: regulatory interactions?
Man Yeung, Monsef Benkirane, Kuan-Teh Jeang
Retrovirology , 2007, DOI: 10.1186/1742-4690-4-74
Abstract: Plant and animal genomes have thousands of genes that encode non-protein-coding (nc) RNAs. While recent attention has focused significantly on small interfering RNAs (siRNAs) and micro RNAs (miRNAs), ncRNAs also include rRNA, tRNA, small nuclear (sn) RNA, small nucleolar (sno) RNAs, and some of the lesser-known RNAs such as vault RNAs, Y RNAs, rasi-RNAs and piRNAs [reviewed in [1]]. It is now recognized that only 2% of the human genome encodes for protein-coding RNAs while 60 to 70% of our DNA is transcribed into ncRNAs [2,3]. Hence, despite accumulating research on siRNA, miRNA and piRNA, we are likely at the tip of the iceberg in our understanding about functions and regulatory roles served by ncRNAs in cellular metabolism, pathogenesis and host-pathogen interaction.A key biological process served by small ncRNAs is a phenomenon termed RNA interference (RNAi). Recent reviews have reprised the discovery of RNAi and summarized the current state of knowledge about this process [4,5]. In brief, a central tenet of RNAi posits that small guide RNAs recruit, in a sequence-complementary manner, a multi-protein complex composed in part of RNA-binding proteins to RNA targets. This large multi-protein RNAi complex has been shown to include members of the Argonaute ribonuclease III protein family; and depending on biological context, the complex has been found to effect post-transcriptional gene silencing (PTGS), transcriptional gene silencing (TGS), and/or co-transcriptional gene silencing (CTGS) (Fig. 1, top).Conventional wisdom suggests that biological processes are balanced by two principles, yin and yang, which oppose one another in their actions to confer equilibrium. For example, the cell-proliferative effects of oncogenes are countered by commensurate provocations of cellular senescence and apoptosis [6-8]. Moreover, frequently, potent transcriptional activators are also equally strong repressors [9,10]. Indeed, recent developments raise that the yin (negative) of RNA
Changes in microRNA expression profiles in HIV-1-transfected human cells
Man Lung Yeung, Yamina Bennasser, Timothy G Myers, Guojian Jiang, Monsef Benkirane, Kuan-Teh Jeang
Retrovirology , 2005, DOI: 10.1186/1742-4690-2-81
Abstract: MicroRNAs (miRNAs) are small RNAs of 18–25 nucleotides (nt) in length that are involved in the regulation of a variety of biological processes including developmental timing, signal transduction, apoptosis, cell proliferation and tumorigenesis [1-3]. Recent studies indicate that cellular miRNAs can variably inhibit [4] or promote [5] viral replication. Viruses, on the other hand, seem to have developed strategies which include virus-encoded RNAi suppressors [6-12] and/or virus-encoded miRNAs [13-19]. Mechanistically, a current view is that miRNAs function to silence gene expression through imperfect base-pairing with cognate transcripts. Since RNA silencing mediated by miRNA does not require perfect sequence complementarity, one miRNA can target multiply different mRNAs [20]. It is conceivable that viruses may seek to alter cellular miRNA expression in ways that benefit viral replication. Extant findings support such a notion since several viruses have been found to encode RNAi suppressors which could function to influence the cell's overall miRNA milieu [6-12].For HIV-1, it has been proposed, based on in vitro assays, that Tat can partially repress the processing activity of Dicer [21]. Because Dicer is involved in the maturation of cellular miRNAs, we wondered how miRNA profiles in human cells that express HIV-1 proteins might differ from counterpart cells that do not express viral genes. To ask if HIV-1 alters the expression of host miRNAs, we employed a high throughput microarray approach to quantify changes in miRNA expression. We used a platform based on the RNA-primed Array-based Klenow Enzyme (RAKE) assay. RAKE originally described by Nelson and colleagues is a microarray assay which uses on-slide enzymatic reactions and primer extension [22]. We printed specific DNA oligonucleotide probes which contain three distinct elements onto a microarray glass slide (Fig 1A). The three different elements include a 5' linker containing a constant nucleotide sequence wi
The Tudor Domain Protein Spindlin1 Is Involved in Intrinsic Antiviral Defense against Incoming Hepatitis B Virus and Herpes Simplex Virus Type 1
Aurélie Ducroux,Shirine Benhenda,Lise Rivière,O. John Semmes,Monsef Benkirane,Christine Neuveut
PLOS Pathogens , 2014, DOI: doi/10.1371/journal.ppat.1004343
Abstract: Hepatitis B virus infection (HBV) is a major risk factor for the development of hepatocellular carcinoma. HBV replicates from a covalently closed circular DNA (cccDNA) that remains as an episome within the nucleus of infected cells and serves as a template for the transcription of HBV RNAs. The regulatory protein HBx has been shown to be essential for cccDNA transcription in the context of infection. Here we identified Spindlin1, a cellular Tudor-domain protein, as an HBx interacting partner. We further demonstrated that Spindlin1 is recruited to the cccDNA and inhibits its transcription in the context of infection. Spindlin1 knockdown induced an increase in HBV transcription and in histone H4K4 trimethylation at the cccDNA, suggesting that Spindlin1 impacts on epigenetic regulation. Spindlin1-induced transcriptional inhibition was greater for the HBV virus deficient for the expression of HBx than for the HBV WT virus, suggesting that HBx counteracts Spindlin1 repression. Importantly, we showed that the repressive role of Spindlin1 is not limited to HBV transcription but also extends to other DNA virus that replicate within the nucleus such as Herpes Simplex Virus type 1 (HSV-1). Taken together our results identify Spindlin1 as a critical component of the intrinsic antiviral defense and shed new light on the function of HBx in HBV infection.
Hyperthermia Stimulates HIV-1 Replication
Ferdinand Roesch,Oussama Meziane,Anna Kula,Sébastien Nisole,Fran?oise Porrot,Ian Anderson,Fabrizio Mammano,Ariberto Fassati,Alessandro Marcello,Monsef Benkirane,Olivier Schwartz
PLOS Pathogens , 2012, DOI: 10.1371/journal.ppat.1002792
Abstract: HIV-infected individuals may experience fever episodes. Fever is an elevation of the body temperature accompanied by inflammation. It is usually beneficial for the host through enhancement of immunological defenses. In cultures, transient non-physiological heat shock (42–45°C) and Heat Shock Proteins (HSPs) modulate HIV-1 replication, through poorly defined mechanisms. The effect of physiological hyperthermia (38–40°C) on HIV-1 infection has not been extensively investigated. Here, we show that culturing primary CD4+ T lymphocytes and cell lines at a fever-like temperature (39.5°C) increased the efficiency of HIV-1 replication by 2 to 7 fold. Hyperthermia did not facilitate viral entry nor reverse transcription, but increased Tat transactivation of the LTR viral promoter. Hyperthermia also boosted HIV-1 reactivation in a model of latently-infected cells. By imaging HIV-1 transcription, we further show that Hsp90 co-localized with actively transcribing provirus, and this phenomenon was enhanced at 39.5°C. The Hsp90 inhibitor 17-AAG abrogated the increase of HIV-1 replication in hyperthermic cells. Altogether, our results indicate that fever may directly stimulate HIV-1 replication, in a process involving Hsp90 and facilitation of Tat-mediated LTR activity.
Suppression of HIV-1 replication by microRNA effectors
Christine Chable-Bessia, Oussama Meziane, Daniel Latreille, Robinson Triboulet, Alessia Zamborlini, Alexandre Wagschal, Jean-Marc Jacquet, Jacques Reynes, Yves Levy, Ali Saib, Yamina Bennasser, Monsef Benkirane
Retrovirology , 2009, DOI: 10.1186/1742-4690-6-26
Abstract: RNA silencing (RNAi) is a new gene regulatory mechanism conserved from plants to humans. RNAi mediators are small non-coding RNAs (sncRNAs) that function through sequence specific mRNA targeting to either induce their degradation and/or inhibit translation [1,2]. In mammals, RNAi is mediated by different classes of small non-coding RNAs including piRNAs, microRNAs and siRNAs [3-5]. MicroRNAs are produced from a primary transcript (pri-miRNA) which is processed in the nucleus by the microprocessor complex containing RNase Drosha and DGCR8. The resulting product or pre-miRNA is exported to the cytoplasm through the exportin-5 pathway. Cytoplasmic pre-miRNA is processed by typeIII RNase Dicer to miRNA/miRNA* duplex of 19 to 25 nucleotides. miRNA/miRNA* is incorporated into the RNA-Induced Silencing Complex (RISC) where miRNA* is degraded while miRNA serves as a guide for mRNA targeting [2]. Key components of miRISC are proteins of the Argonaute family (Ago1 to Ago4) that are required for miRNA-mediated silencing [6,7]. To ensure mRNA translational inhibition and decay, miRISC, loaded with miRNA and its mRNA targets, associate with proteins involved in mRNA processing [2]. A key factor in this process is the GW182 protein that interacts directly with Argonaute1 (Ago1) [8], and the human homologs of GW182 that interact with Ago1–4 [9]. GW182 orchestrates both mRNA decapping, through the recruitment of p54/RCK that regulates the activity of the decapping enzymes DCP1/DCP2 [10], and mRNA deadenylation by recruiting the CCR4-NOT1 complex [11]. mRNA decapping and deadenylation leads to mRNA decay through the action of XRN1, a 5'-3' exonuclease [10]. Interestingly, RNAi effectors, including miRNAs and their target mRNAs, Ago proteins, GW182, RCK/p54, LSm-1 and DCP proteins co-localize in cytoplasmic structures called GW-bodies or P-bodies suggesting that miRNA-mediated silencing occurs at these sites [11-15]. Emerging evidence suggests that miRNA-mediated gene regulation serv
Role of SAMHD1 nuclear localization in restriction of HIV-1 and SIVmac
Alberto Brandariz-Nu?ez, Jose Carlos Valle-Casuso, Tommy E White, Nadine Laguette, Monsef Benkirane, Jurgen Brojatsch, Felipe Diaz-Griffero
Retrovirology , 2012, DOI: 10.1186/1742-4690-9-49
Abstract: Here, we identified the nuclear localization signal (NLS) of SAMHD1, and studied its contribution to restriction of HIV-1 and SIVmac. By studying the cellular distribution of different SAMHD1 variants, we mapped the nuclear localization of SAMHD1 to residues 11KRPR14. Mutagenesis of these residues changed the cellular distribution of SAMHD1 from the nucleus to the cytoplasm. SAMHD1 mutants that lost nuclear localization restricted HIV-1 and SIV as potently as the wild type protein. Interestingly, SAMHD1 mutants that localized to the cytoplasm were not degraded by nuclear Vpx alleles. Therefore, nuclear Vpx alleles require nuclear localization of SAMHD1 in order to induce its degradation. In agreement, SIVmac viruses encoding Vpx did not overcome the restriction imposed by the cytoplasmic variants of SAMHD1.We mapped the NLS of SAMHD1 to residues 11KRPR14 and studied the contribution of SAMHD1 nuclear localization to restriction of HIV-1 and SIV. These experiments demonstrate that cytoplasmic variants of SAMHD1 potently block lentiviral infection and are resistant to Vpx-mediated degradation. The nuclear Vpx alleles studied here are only capable of degrading a nuclearly localized SAMHD1 suggesting that Vpx-mediated degradation of SAMHD1 is initiated in the nucleus.
Antibiotic sensitivity pattern of common bacterial pathogens in NICU and neonatal ward in Hamedan province of Iran  [PDF]
Alireza Monsef, Fatemeh Eghbalian
Health (Health) , 2010, DOI: 10.4236/health.2010.26094
Abstract: Bacterial pathogens and drug resistance are different in hospitals of each country. In this study we determined bacterial path- ogens and drug sensitivity in the neonatal ward and neonatal intensive care unit (NICU) in Ekbatan hospital in Hamedan. This cross-sectional descriptive study was done on 1150 hospitalized neonates in neonatal and NICU wards of Ekbatan hospital of the Hamadan university of medical sciences from September 2004 to September 2006. Blood, cerebrospinal fluid (CSF), urine, stool, eye excretion, synovial fluid, umbilical secretion and ascitic fluid were evaluated. Positive cultures were evaluated for antibiotic resistance with disk diffusion test methed. All of the data in questionnaires was analyzed with SPSS 13. Cultures including blood, urine, CSF , stool, eye excretion, synovial fluid, umbilical secretion and ascitic fluid was done in 417 neonates (833 cultures). These cultures were including: urine, 323 cases (38.8%) blood 293 cases (35.2%), CSF 180 cases (21.6%) , stool 17 cases (2%), eye secretion 16 cases (1.9%) and other secretions (synovial, umbilical, etc) 4 cases (0.5%). The cultures were positive in 105 cases (25.2%). 60 male neonates (57.1%) and 45 female neonates (42.9%) were culture positive. The most common microorganisms were E coli 66.7% (70 cases), Klebsiella 10.5% (11 cases). Drug resistance was high in these microorganisms. The most common microorganisms were Ecoli and klebsiella. Drug resistance was high in the isolated microorganisms.
Does conventional phototherapy have any effect on platelet count in full term neonates with indirect hyperbilirubinemia?  [PDF]
Alireza Monsef, Fatemeh Eghbalian
Health (Health) , 2011, DOI: 10.4236/health.2011.312119
Abstract: This study evaluates the platelet count changes in neonates with hyperbillirubinemia who received phototherapy. In this Prospective Descriptive-cross sectional study 144 full term newborns with indirect hyperbillirubinemia who received phototherapy in neonatal ward of Bessat hospital in Hamedan province of Iran were studied from September 2007 to February 2008 for evaluation the effect of phototherapy on platelet count. The platelet had counted by cell counter and it had controlled by slide platelet counting. The data were analyzed using spss version. 13 and compared with paired-samples T test. 58 neonates (40.3%) were boys and 86 (59.7%) were girls. The mean age of neonates was 7.04 +/– 5.49 days (2 - 29 days). The mean (± SD) platelet counts were 287833.3 + 92332.4 before and 299444.4 + 98565.2 after phototherapy. Analysis of data with paired T test showed significant difference in platelet count before and after phototherapy. Mean platelet count after phototherapy was higher than that before treatment. The study had propounded that mean platelet count increased with extended mean phototherapy time. This study had propounded this hypothesis that phototherapy in full term icteric newborns leads to increased platelet count. It may be due to accelerated platelet turnover in peripheral microvasculature with adequate platelet reserve.
Assessment of the Nutritional Status of the Egyptian Patient with End Stage Liver Disease Prior to Liver Transplantation  [PDF]
Waheed A. Monsef, Ibrahim Mostafa, Doaa Zaky
Open Journal of Gastroenterology (OJGas) , 2014, DOI: 10.4236/ojgas.2014.44024
Abstract: Background and Aim: Patients with advanced liver disease have several risk factors to develop nutritional deficiencies. Accurate nutritional assessment is a real challenge because many of the traditionally measured parameters of nutritional status vary with severity of liver disease independently of nutritional status. The objective of this study was to assess the Egyptian patients with end stage liver disease and to compare different tools used to assess their nutritional status. Patients and Methods: 60 patients were nutritionally assessed by SGA, RFH-SGA anthropometry, handgrip dynamometry and biochemical tests. Clinical variables were cross analyzed with the nutritional assessment methods. Results: Malnutrition ranged from 7% by BMI and 100% by SGA. Agreement among all the methods was low compared with the SGA. Correlation between Malnutrition prevalence and the severity of liver disease was verified using Child-Pugh score more than MELD score. Conclusion: Malnutrition is highly prevalent among the Egyptian patients with end stage liver disease prior to liver transplantation. Although the diagnosis of nutritional status is not easy among this category of patients, it varied according to the method used. Nutritional support should be an important part of the preoperative care of liver transplantation patients.
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