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1.  The 2008 Retrovirology Prize: Ben Berkhout and his RNA world 
Retrovirology  2008;5:113.
Ben Berkhout wins the 2008 Retrovirology Prize.
doi:10.1186/1742-4690-5-113
PMCID: PMC2615045  PMID: 19077224
2.  Mohmmar Qadaffi, Open Access, and Retrovirology 
Retrovirology  2004;1:24.
Retrovirology has been publishing as an Open Access online journal for approximately six months. In this editorial, I review the reasons for and the advantages of Open Access publishing, update our progress to date, and summarize where we intend to go with this journal.
doi:10.1186/1742-4690-1-24
PMCID: PMC516792  PMID: 15347421
3.  Cellular RNA helicases and HIV-1: Insights from genome-wide, proteomic, and molecular studies 
Virus research  2012;171(2):357-365.
RNA helicases are ubiquitous in plants and animals and function in many cellular processes. Retroviruses, such as human immunodeficiency virus (HIV-1), encode no RNA helicases in their genomes and utilize host cellular RNA helicases at various stages of their life cycle. Here, we briefly summarize the roles RNA helicases play in HIV-1 replication that have been identified recently, in part, through genome-wide screenings, proteomics, and molecular studies. Some of these helicases augment virus propagation while others apparently participate in antiviral defenses against viral replication.
doi:10.1016/j.virusres.2012.06.022
PMCID: PMC3493675  PMID: 22814432
RNA helicases; Human Immunodeficiency virus type 1 (HIV-1); DEAD-Box domain; antiviral
4.  Long non-coding RNAs (lncRNAs) and viral infections 
In this review, we focus on the roles of lncRNAs, including cellular and viral lncRNAs, in virus replication in infected cells. We survey the interactions and functions of several cellular lncRNAs such as XIST, HOTAIR, NEAT1, BIC and several virus encoded lncRNAs.
doi:10.1016/j.biomed.2013.01.001
PMCID: PMC3641704  PMID: 23645970
lncRNAs; virus
5.  The Cellular Autophagy Pathway Modulates Human T-Cell Leukemia Virus Type 1 Replication 
Journal of Virology  2013;87(3):1699-1707.
Autophagy, a general homeostatic process for degradation of cytosolic proteins or organelles, has been reported to modulate the replication of many viruses. The role of autophagy in human T-cell leukemia virus type 1 (HTLV-1) replication has, however, been uncharacterized. Here, we report that HTLV-1 infection increases the accumulation of autophagosomes and that this accumulation increases HTLV-1 production. We found that the HTLV-1 Tax protein increases cellular autophagosome accumulation by acting to block the fusion of autophagosomes to lysosomes, preventing the degradation of the former by the latter. Interestingly, the inhibition of cellular autophagosome-lysosome fusion using bafilomycin A increased the stability of the Tax protein, suggesting that cellular degradation of Tax occurs in part through autophagy. Our current findings indicate that by interrupting the cell's autophagic process, Tax exerts a positive feedback on its own stability.
doi:10.1128/JVI.02147-12
PMCID: PMC3554132  PMID: 23175371
6.  Accumulation of the Inner Nuclear Envelope Protein Sun1 is Pathogenic in Progeric and Dystrophic Laminopathies 
Cell  2012;149(3):565-577.
SUMMARY
Human LMNA gene mutations result in laminopathies that include Emery-Dreifuss Muscular Dystrophy (AD-EDMD) and Hutchinson-Gilford Progeria, the premature aging syndrome (HGPS). The Lmna null (Lmna−/−) and progeroid LmnaΔ9 mutant mice are models for AD-EDMD and HGPS respectively. Both animals develop severe tissue pathologies with abbreviated life spans. Like HGPS cells, Lmna−/− and LmnaΔ9 fibroblasts have typically misshapen nuclei. Unexpectedly, Lmna−/− or LmnaΔ9 mice that are also deficient for the inner nuclear membrane protein Sun1 show markedly reduced tissue pathologies and enhanced longevity. Concordantly, reduction of SUN1 over-accumulation in LMNA mutant fibroblasts and in HGPS cells corrected nuclear defects and cellular senescence. Collectively, these findings implicate Sun1 protein accumulation as a common pathogenic event in Lmna−/−, LmnaΔ9, and HGPS disorders.
doi:10.1016/j.cell.2012.01.059
PMCID: PMC3340584  PMID: 22541428
7.  NEAT1 Long Noncoding RNA and Paraspeckle Bodies Modulate HIV-1 Posttranscriptional Expression 
mBio  2013;4(1):e00596-12.
ABSTRACT
Most of the human genome is transcribed into protein-noncoding RNAs (ncRNAs), including small ncRNAs and long ncRNAs (lncRNAs). Over the past decade, rapidly emerging evidence has increasingly supported the view that lncRNAs serve key regulatory and functional roles in mammal cells. HIV-1 replication relies on various cell functions. To date, while the involvement of host protein factors and microRNAs (miRNAs) in the HIV-1 life cycle has been extensively studied, the relationship between lncRNAs and HIV-1 remains uncharacterized. Here, we have profiled 83 disease-related lncRNAs in HIV-1-infected T cells. We found NEAT1 to be one of several lncRNAs whose expression is changed by HIV-1 infection, and we have characterized its role in HIV-1 replication. We report here that the knockdown of NEAT1 enhances virus production through increased nucleus-to-cytoplasm export of Rev-dependent instability element (INS)-containing HIV-1 mRNAs.
IMPORTANCE
Long protein-noncoding RNAs (lncRNAs) play roles in regulating gene expression and modulating protein activities. There is emerging evidence that lncRNAs are involved in the replication of viruses. To our knowledge, this report is the first to characterize a role contributed by an lncRNA, NEAT1, to HIV-1 replication. NEAT1 is essential for the integrity of the nuclear paraspeckle substructure. Based on our findings from NEAT1 knockdown, we have identified the nuclear paraspeckle body as another important subcellular organelle for HIV-1 replication.
doi:10.1128/mBio.00596-12
PMCID: PMC3560530  PMID: 23362321
8.  A method to study the role of DDX3 RNA helicase in HIV-1 
Viral replication requires the use of host cell proteins and enzymes. Many viruses utilize viral helicases at various stages of their life cycle; these viruses have evolved to encode directly helicase or helicase-like proteins. In contrast, the genomes of retroviruses are devoid of viral helicases. Human immunodeficiency virus (HIV-1) has adopted the ability to use one or more cellular RNA helicases for its replicative life cycle. In this chapter, we briefly summarize the approach for assaying the RNA unwinding activity of RNA helicasesd and measurement of the effect helicase inhibitors on HIV-1 replication.
doi:10.1007/978-1-60327-355-8_20
PMCID: PMC3535447  PMID: 20225157
RNA helicases; Human immunodeficiency virus type 1 (HIV-1); DEAD-Box domain; DDX3
9.  Highlights, predictions, and changes 
Retrovirology  2012;9:96.
Recent literature highlights at Retrovirology are described. Predictions are made regarding “hot” retrovirology research trends for the coming year based on recent journal access statistics. Changes in Retrovirology editor and the frequency of the Retrovirology Prize are announced.
doi:10.1186/1742-4690-9-96
PMCID: PMC3511057  PMID: 23153244
10.  Human T cell leukemia virus type 1 (HTLV-1) and leukemic transformation: viral infectivity, Tax, HBZ, and therapy 
Oncogene  2010;30(12):1379-1389.
The human T – cell leukemia virus type 1 (HTLV-1) was the first retrovirus discovered to be causative of a human cancer, Adult T-cell leukemia (ATL). The transforming entity of HTLV-1 has been attributed to the virally-encoded oncoprotein, Tax. Unlike the v-onc proteins encoded by other oncogenic animal retroviruses that transform cells, Tax does not originate from a c-onc counterpart. In this article, we review progress in our understanding of HTLV-1 infectivity, cellular transformation, anti-sense transcription, and therapy, thirty years after the original discovery of this virus.
doi:10.1038/onc.2010.537
PMCID: PMC3413891  PMID: 21119600
human T-cell leukemia virus type 1 (HTLV-1); adult T cell leukemia (ATL); Tax; HTLV-1 bZIP factor (HBZ); aneuploidy
11.  Rev-ing up post-transcriptional HIV-1 RNA expression 
RNA Biology  2011;8(2):195-199.
The post-transcriptional export of spliced and unspliced HIV-1 (human immunodeficiency virus type 1) RNAs from the nucleus to the cytoplasm is a complex process. Part of the complexity arises from the fact that eukaryotic cells normally retain unspliced RNAs in the nucleus preventing their exit into the cytoplasm. HIV-1 has evolved a protein, Rev, that participates in the export of unspliced/partially spliced viral RNAs from the nucleus. It has been documented that several cellular factors cooperate in trans with Rev, and certain cis-RNA motifs/features are important for transcripts to be recognized by Rev and its co-factors. Here, the post-transcriptional activities of Rev are discussed in the context of a recent finding that an RNA cap methyltransferase contributes to the expression of unspliced/partially spliced HIV-1 transcripts.
doi:10.4161/rna.8.2.14803
PMCID: PMC3127099  PMID: 21358275
PIMT; TGS1; HIV-1; Rev; CRM1; RNA export
12.  Reflections on Searching for a Postdoctoral Position: Three Points to Ponder 
Choosing the right laboratory in which to do postdoctoral training is perhaps one of the most important decisions that a scientist makes in his or her career. Does one choose a laboratory based on the research topic or the research style of the mentor? Does one choose a large laboratory or a small one? How does one fit the selection of a postdoctoral laboratory into the context of one’s long-range career goals? Here, I briefly discuss three points worth considering in seeking a research laboratory for postdoctoral training after the completion of a graduate degree.
PMCID: PMC3178847  PMID: 21966035
education; postdoctoral training; mentoring
13.  Viral transformation and aneuploidy 
Human tumor viruses are associated with a variety of human malignancies, and it is estimated that 15% of all human cancers have a viral etiology. An abnormality in chromosomal ploidy or aneuploidy is a hallmark of cancers. In normal cells, euploidy is governed by several factors including an intact spindle assembly checkpoint (SAC), accurate centrosome duplication, and proper cytokinesis. Viral oncoproteins are suggested to perturb the cellular machineries for chromosomal segregation creating aneuploidy which can lead to the malignant transformation of infected cells. Here we review in brief some of the mechanisms employed by viruses that can cause cellular aneuploidy.
doi:10.1002/em.20480
PMCID: PMC2760603  PMID: 19326462
Spindle assembly checkpoint; centrosome; aneuploidy; human T-cell leukemia virus type I (HTLV-I); Tax
14.  Human T cell leukemia virus type 1 (HTLV-1) and oncogene or oncomiR addiction? 
Oncotarget  2010;1(6):453-456.
The mechanism of HTLV-1 transformation of cells to Adult T cell leukemia (ATL) remains not fully understood. Currently, the viral Tax oncoprotein is known to be required to initiate transformation. Emerging evidence suggests that Tax is not needed to maintain the transformed ATL phenotype. Recent studies have shown that HTLV-1 transformed cells show deregulated expression of cellular microRNAs (miRNAs). Here we discuss the possibility that early ATL cells are Tax-oncogeneaddicted while late ATL cells are oncogenic microRNA (oncomiR) – addicted. The potential utility of interrupting oncomiR addiction as a cancer treatment is broached.
PMCID: PMC3058865  PMID: 21311101
HTLV; ATL; MicroRNAs; Leukemia; oncogene
15.  The importance of individualized article-specific metrics for evaluating research productivity 
Retrovirology  2009;6:82.
This editorial discusses the rationale for using article-specific rather than journal-specific metrics for evaluating highly published authors.
doi:10.1186/1742-4690-6-82
PMCID: PMC2757017  PMID: 19758447
16.  H-index, mentoring-index, highly-cited and highly-accessed: how to evaluate scientists? 
Retrovirology  2008;5:106.
How best to evaluate scientists within a peer group is a difficult task. This editorial discusses the use of the H-index and total citations. It also raises the consideration of a mentoring-index and the value of understanding the frequency that a published paper is accessed by readers.
doi:10.1186/1742-4690-5-106
PMCID: PMC2607307  PMID: 19032780
17.  Jacov Tal (1940 – 2005): remembrances of a friend 
Retrovirology  2005;2:12.
An obituary commemorates the life and works of Jacov Tal.
doi:10.1186/1742-4690-2-12
PMCID: PMC550676  PMID: 15725354
18.  Reciprocal functional pseudotyping of HIV-1 and HTLV-1 viral genomes by the heterologous counterpart envelope proteins 
Virology  2013;443(1):106-112.
HIV-1 and HTLV-1 can infect CD4+ T cells and can co-infect the same individual. In principle, it is possible that both viruses can infect the same CD4+ T cells in dually infected persons. Currently, how efficiently HTLV-1 and HIV-1 co-infects the same cell and the full extent of their biological interactions are not well-understood. Here, we report evidence confirming that both viruses can infect the same cells and that HTLV-1 envelope (Env) can pseudotype HIV-1 viral particles and HIV-1 envelope (Env) can pseudotype HTLV-1 virions to mediate subsequent infections of substrate cells. We also show that the construction of a chimeric HTLV-1 molecular clone carrying the HIV-1 Env in place of its HTLV-1 counterpart results in a replication competent moiety. These findings raise new implications of viral complementation and assortment between HIV-1 and HTLV-1 in dually infected persons.
doi:10.1016/j.virol.2013.04.027
PMCID: PMC3728900  PMID: 23747197
HIV-1; HTLV-1; Pseudotyping; Chimera
19.  Ring finger protein 39 genetic variants associate with HIV-1 plasma viral loads and its replication in cell culture 
Cell & Bioscience  2014;4:40.
Background
The human immunodeficiency virus (HIV-1) exploits host proteins to complete its life cycle. Genome-wide siRNA approaches suggested that host proteins affect HIV-1 replication. However, the results barely overlapped. RING finger protein 39 (RNF39) has been identified from genome-wide association studies. However, its function during HIV-1 replication remains unclear.
Methods and results
We investigated the relationship between common RNF39 genetic variants and HIV-1 viral loads. The effect of RNF39 protein knockdown or overexpression on HIV-1 replication was then investigated in different cell lines. Two genetic variants were associated with HIV-1 viral loads. Patients with the ht1-GG/GG haplotype presented lower RNF39 expression levels and lower HIV-1 viral load. RNF39 knockdown inhibited HIV-1 expression.
Conclusions
RNF39 protein may be involved in HIV-1 replication as observed in genetic studies on patients with HIV-1 and in in vitro cell cultures.
doi:10.1186/2045-3701-4-40
PMCID: PMC4131809  PMID: 25126410
HIV-1 viral load; RNF39; Single nucleotide polymorphism; Viral replication
20.  Activation of HIV-1 from Latent Infection via Synergy of RUNX1 Inhibitor Ro5-3335 and SAHA 
PLoS Pathogens  2014;10(3):e1003997.
A major barrier to the elimination of HIV-1 infection is the presence of a pool of long-lived, latently infected CD4+ memory T-cells. The search for treatments to re-activate latent HIV to aid in clearance is hindered by the incomplete understanding of the mechanisms that lead to transcriptional silencing of viral gene expression in host cells. Here we identify a previously unknown role for RUNX1 in HIV-1 transcriptional latency. The RUNX proteins, in combination with the co-factor CBF-β, are critical transcriptional regulators in T-cells. RUNX1 strongly modulates CD4 expression and contributes to CD4+ T-cell function. We show that RUNX1 can bind DNA sequences within the HIV-1 LTR and that this binding represses transcription. Using patient samples we show a negative correlation between RUNX1 expression and viral load. Furthermore, we find that pharmacologic inhibition of RUNX1 by a small molecule inhibitor, Ro5-3335, synergizes with the histone deacetylase (HDAC) inhibitor SAHA (Vorinostat) to enhance the activation of latent HIV-1 in both cell lines and PBMCs from patients. Our findings indicate that RUNX1 and CBF-β cooperate in cells to modulate HIV-1 replication, identifying for the first time RUNX1 as a cellular factor involved in HIV-1 latency. This work highlights the therapeutic potential of inhibitors of RUNX1 to re-activate virus and aid in clearance of HIV-1.
Author Summary
Since it was first discovered in the early 1980s, Human Immunodeficiency Virus 1 (HIV-1), the causative agent of Acquired Immunodeficiency Syndrome (AIDS), has been the focus of intense research. In untreated individuals, the number of CD4+ T-cells in the blood slowly drops over time and the patient eventually succumbs to an opportunistic infection. Although current therapies are capable of managing the virus; they do not represent a true cure. As a retrovirus, HIV-1 incorporates itself into the host genome and survives in the long-lived population of memory T-cells found in the human host. In this study, we examine the roll of a T-cell specific transcription factor (RUNX1) in the control of HIV-1 replication. Through various molecular studies, we show that RUNX1 represses HIV-1 replication in T-cells. By examining samples from patients with HIV-1, we are able to show a negative correlation between viral replication and RUNX1 expression. Finally, we show that an inhibitor of RUNX1 synergizes with Vorinostat, a current lead compound in the quest to re-active HIV-1 and purge the latent pool.
doi:10.1371/journal.ppat.1003997
PMCID: PMC3961356  PMID: 24651404
21.  Analysis of Meiosis in SUN1 Deficient Mice Reveals a Distinct Role of SUN2 in Mammalian Meiotic LINC Complex Formation and Function 
PLoS Genetics  2014;10(2):e1004099.
LINC complexes are evolutionarily conserved nuclear envelope bridges, composed of SUN (Sad-1/UNC-84) and KASH (Klarsicht/ANC-1/Syne/homology) domain proteins. They are crucial for nuclear positioning and nuclear shape determination, and also mediate nuclear envelope (NE) attachment of meiotic telomeres, essential for driving homolog synapsis and recombination. In mice, SUN1 and SUN2 are the only SUN domain proteins expressed during meiosis, sharing their localization with meiosis-specific KASH5. Recent studies have shown that loss of SUN1 severely interferes with meiotic processes. Absence of SUN1 provokes defective telomere attachment and causes infertility. Here, we report that meiotic telomere attachment is not entirely lost in mice deficient for SUN1, but numerous telomeres are still attached to the NE through SUN2/KASH5-LINC complexes. In Sun1−/− meiocytes attached telomeres retained the capacity to form bouquet-like clusters. Furthermore, we could detect significant numbers of late meiotic recombination events in Sun1−/− mice. Together, this indicates that even in the absence of SUN1 telomere attachment and their movement within the nuclear envelope per se can be functional.
Author Summary
Correct genome haploidization during meiosis requires tightly regulated chromosome movements that follow a highly conserved choreography during prophase I. Errors in these movements cause subsequent meiotic defects, which typically lead to infertility. At the beginning of meiotic prophase, chromosome ends are tethered to the nuclear envelope (NE). This attachment of telomeres appears to be mediated by well-conserved membrane spanning protein complexes within the NE (LINC complexes). In mouse meiosis, the two main LINC components SUN1 and SUN2 were independently described to localize at the sites of telomere attachment. While SUN1 has been demonstrated to be critical for meiotic telomere attachment, the precise role of SUN2 in this context, however, has been discussed controversially in the field. Our current study was targeted to determine the factual capacity of SUN2 in telomere attachment and chromosome movements in SUN1 deficient mice. Remarkably, although telomere attachment is impaired in the absence of SUN1, we could find a yet undescribed SUN1-independent telomere attachment, which presumably is mediated by SUN2 and KASH5. This SUN2 mediated telomere attachment is stable throughout prophase I and functional in moving telomeres within the NE. Thus, our results clearly indicate that SUN1 and SUN2, at least partially, fulfill redundant meiotic functions.
doi:10.1371/journal.pgen.1004099
PMCID: PMC3937131  PMID: 24586178
23.  Association between GRIN3A Gene Polymorphism in Kawasaki Disease and Coronary Artery Aneurysms in Taiwanese Children 
PLoS ONE  2013;8(11):e81384.
Kawasaki disease (KD) is pediatric systemic vasculitis with the classic complication of coronary artery aneurysm (CAA). It is the leading cause of acquired cardiovascular diseases in children. Some severe cases present with multi-organ involvement or neurological dysfunction. To identify the role of the glutamate receptor, ionotropic, N-methyl-d-aspartate 3A (GRIN3A) in KD, we investigated genetic variations in GRIN3A in a Taiwanese cohort of 262 KD patients (76 with and 186 without CAA complications). We used univariate and multivariate regression analyses to identify the associations between clinical characteristics and GRIN3A genetic variations in KD. According to univariate regression analysis, CAA formation in KD was significantly associated with fever duration (p < 0.0001), first Intravenous immunoglobulin (IVIG) used (days after day one of fever) (p < 0.0001), and the GRIN3A (rs7849782) genetic variant (p < 0.001). KD patients with GG+GC genotype showed a lower rate of developing CAA (GG+GC genotype: odds ratio = 0.26; 95% CI = 0.14–0.46). Significant associations were identified between KD with CAA complication and the GRIN3A (rs7849782) genetic variant by using multivariate regression analysis. Specifically, significant correlations were observed between KD with CAA complications and the presence of GG+GC genotypes for the GRIN3A rs7849782 single-nucleotide polymorphism (full model: odds ratio = 0.25; 95% CI = 0.14–0.46). Our results suggest that a polymorphism of the GRIN3A gene may play a role in KD pathogenesis.
doi:10.1371/journal.pone.0081384
PMCID: PMC3838481  PMID: 24278430
24.  Sorting nexin 24 genetic variation associates with coronary artery aneurysm severity in Kawasaki disease patients 
Cell & Bioscience  2013;3:44.
Background
The sorting nexin (SNX) family is involved in endocytosis and protein trafficking and plays multiple roles in various diseases. The role of SNX proteins in Kawasaki disease (KD) is not known. We attempted to test whether genetic SNX variation associates with the risk of coronary artery aneurysm (CAA) formation in KD.
Methods and results
Chi-square tests were used to identify SNX24 genetic variants associated with KD susceptibility and CAA formation in KD; models were adjusted for fever duration and time of first administration of intravenous immunoglobulin. We obtained clinical characteristics and genotypes from KD patients (76 with CAA and 186 without CAA) in a population-based retrospective KD cohort study (n = 262). Clinical and genetic factors were associated with CAA formation in KD. In addition, endothelial cell inflammation was evaluated. Significant correlation was observed between KD with CAA complications and the rs28891 single-nucleotide polymorphism in SNX24. Patients with CC + CT genotypes had lesser CAA complications. In lipopolysaccharide-treated human umbilical vein endothelial cells, siRNA knockdown of SNX24 significantly decreased gene expression of the proinflammatory cytokines IL-1 beta, IL-6, and IL-8.
Conclusions
Polymorphisms in SNX24 may be used as genetic markers for the diagnosis and prognosis of CAA formation in KD.
doi:10.1186/2045-3701-3-44
PMCID: PMC4176999  PMID: 24268062
Kawasaki disease; Coronary artery aneurysm; Sorting nexin 24; Polymorphism
25.  Commensal Microbiota Contributes to Chronic Endocarditis in TAX1BP1 Deficient Mice 
PLoS ONE  2013;8(9):e73205.
Tax1-binding protein 1 (Tax1bp1) negatively regulates NF-κB by editing the ubiquitylation of target molecules by its catalytic partner A20. Genetically engineered TAX1BP1-deficient (KO) mice develop age-dependent inflammatory constitutions in multiple organs manifested as valvulitis or dermatitis and succumb to premature death. Laser capture dissection and gene expression microarray analysis on the mitral valves of TAX1BP1-KO mice (8 and 16 week old) revealed 588 gene transcription alterations from the wild type. SAA3 (serum amyloid A3), CHI3L1, HP, IL1B and SPP1/OPN were induced 1,180-, 361-, 187-, 122- and 101-fold respectively. WIF1 (Wnt inhibitory factor 1) exhibited 11-fold reduction. Intense Saa3 staining and significant I-κBα reduction were reconfirmed and massive infiltration of inflammatory lymphocytes and edema formation were seen in the area. Antibiotics-induced ‘germ free’ status or the additional MyD88 deficiency significantly ameliorated TAX1BP1-KO mice's inflammatory lesions. These pathological conditions, as we named ‘pseudo-infective endocarditis’ were boosted by the commensal microbiota who are usually harmless by their nature. This experimental outcome raises a novel mechanistic linkage between endothelial inflammation caused by the ubiquitin remodeling immune regulators and fatal cardiac dysfunction.
doi:10.1371/journal.pone.0073205
PMCID: PMC3785488  PMID: 24086273

Results 1-25 (120)