Kinetics of HIV-1 CTL epitopes recognized by HLA I alleles in HIV-infected individuals at times near primary infection: the Provir/Latitude45 study.

PubMed

Papuchon, Jennifer; Pinson, Patricia; Guidicelli, Gwenda-Line; Bellecave, Pantxika; Thomas, Réjean; LeBlanc, Roger; Reigadas, Sandrine; Taupin, Jean-Luc; Baril, Jean Guy; Routy, Jean Pierre; Wainberg, Mark; Fleury, Hervé

2014-01-01

In patients responding successfully to ART, the next therapeutic step is viral cure. An interesting strategy is antiviral vaccination, particularly involving CD8 T cell epitopes. However, attempts at vaccination are dependent on the immunogenetic background of individuals. The Provir/Latitude 45 project aims to investigate which CTL epitopes in proviral HIV-1 will be recognized by the immune system when HLA alleles are taken into consideration. A prior study (Papuchon et al, PLoS ONE 2013) showed that chronically-infected patients under successful ART exhibited variations of proviral CTL epitopes compared to a reference viral strain (HXB2) and that a generic vaccine may not be efficient. Here, we investigated viral and/or proviral CTL epitopes at different time points in recently infected individuals of the Canadian primary HIV infection cohort and assessed the affinity of these epitopes for HLA alleles during the study period. An analysis of the results confirms that it is not possible to fully predict which epitopes will be recognized by the HLA alleles of the patients if the reference sequences and epitopes are taken as the basis of simulation. Epitopes may be seen to vary in circulating RNA and proviral DNA. Despite this confirmation, the overall variability of the epitopes was low in these patients who are temporally close to primary infection.

Kinetics of HIV-1 CTL Epitopes Recognized by HLA I Alleles in HIV-Infected Individuals at Times near Primary Infection: The Provir/Latitude45 Study

PubMed Central

Papuchon, Jennifer; Pinson, Patricia; Guidicelli, Gwenda-Line; Bellecave, Pantxika; Thomas, Réjean; LeBlanc, Roger; Reigadas, Sandrine; Taupin, Jean-Luc; Baril, Jean Guy; Routy, Jean Pierre; Wainberg, Mark; Fleury, Hervé

2014-01-01

In patients responding successfully to ART, the next therapeutic step is viral cure. An interesting strategy is antiviral vaccination, particularly involving CD8 T cell epitopes. However, attempts at vaccination are dependent on the immunogenetic background of individuals. The Provir/Latitude 45 project aims to investigate which CTL epitopes in proviral HIV-1 will be recognized by the immune system when HLA alleles are taken into consideration. A prior study (Papuchon et al, PLoS ONE 2013) showed that chronically-infected patients under successful ART exhibited variations of proviral CTL epitopes compared to a reference viral strain (HXB2) and that a generic vaccine may not be efficient. Here, we investigated viral and/or proviral CTL epitopes at different time points in recently infected individuals of the Canadian primary HIV infection cohort and assessed the affinity of these epitopes for HLA alleles during the study period. An analysis of the results confirms that it is not possible to fully predict which epitopes will be recognized by the HLA alleles of the patients if the reference sequences and epitopes are taken as the basis of simulation. Epitopes may be seen to vary in circulating RNA and proviral DNA. Despite this confirmation, the overall variability of the epitopes was low in these patients who are temporally close to primary infection. PMID:24964202

Human T-cell leukemia virus type I (HTLV-1) proviral load and disease progression in asymptomatic HTLV-1 carriers: a nationwide prospective study in Japan.

PubMed

Iwanaga, Masako; Watanabe, Toshiki; Utsunomiya, Atae; Okayama, Akihiko; Uchimaru, Kaoru; Koh, Ki-Ryang; Ogata, Masao; Kikuchi, Hiroshi; Sagara, Yasuko; Uozumi, Kimiharu; Mochizuki, Manabu; Tsukasaki, Kunihiro; Saburi, Yoshio; Yamamura, Masaomi; Tanaka, Junji; Moriuchi, Yukiyoshi; Hino, Shigeo; Kamihira, Shimeru; Yamaguchi, Kazunari

2010-08-26

Definitive risk factors for the development of adult T-cell leukemia (ATL) among asymptomatic human T-cell leukemia virus type I (HTLV-1) carriers remain unclear. Recently, HTLV-1 proviral loads have been evaluated as important predictors of ATL, but a few small prospective studies have been conducted. We prospectively evaluated 1218 asymptomatic HTLV-1 carriers (426 males and 792 females) who were enrolled during 2002 to 2008. The proviral load at enrollment was significantly higher in males than females (median, 2.10 vs 1.39 copies/100 peripheral blood mononuclear cells [PBMCs]; P < .001), in those 40 to 49 and 50 to 59 years of age than that of those 40 years of age and younger (P = .02 and .007, respectively), and in those with a family history of ATL than those without the history (median, 2.32 vs 1.33 copies/100 PBMCs; P = .005). During follow-up, 14 participants progressed to overt ATL. Their baseline proviral load was high (range, 4.17-28.58 copies/100 PBMCs). None developed ATL among those with a baseline proviral load lower than approximately 4 copies. Multivariate Cox analyses indicated that not only a higher proviral load, advanced age, family history of ATL, and first opportunity for HTLV-1 testing during treatment for other diseases were independent risk factors for progression of ATL.

Cattle with the BoLA class II DRB3*0902 allele have significantly lower bovine leukemia proviral loads.

PubMed

Hayashi, Takumi; Mekata, Hirohisa; Sekiguchi, Satoshi; Kirino, Yumi; Mitoma, Shuya; Honkawa, Kazuyuki; Horii, Yoichiro; Norimine, Junzo

2017-09-12

The bovine MHC (BoLA) class II DRB3 alleles are associated with polyclonal expansion of lymphocytes caused by bovine leukemia virus (BLV) infection in cattle. To examine whether the DRB3*0902 allele, one of the resistance-associated alleles, is associated with the proviral load, we measured BLV proviral load of BLV-infected cattle and clarified their DRB3 alleles. Fifty-seven animals with DRB3*0902 were identified out of 835 BLV-infected cattle and had significantly lower proviral load (P<0.000001) compared with the rest of the infected animals, in both Japanese Black and Holstein cattle. This result strongly indicates that the BoLA class II DRA/DRB3*0902 molecule plays an important immunological role in suppressing viral replication, resulting in resistance to the disease progression.

Effect of raltegravir on the total and unintegrated proviral HIV DNA during raltegravir-based HAART.

PubMed

Nicastri, Emanuele; Tommasi, Chiara; Abbate, Isabella; Bonora, Stefano; Tempestilli, Massimo; Bellagamba, Rita; Viscione, Magdalena; Rozera, Gabriella; Gallo, Anna L; Ivanovic, Jelena; Amendola, Alessandra; Pucillo, Leopoldo; Di Perri, Giovanni; Capobianchi, Maria R; Narciso, Pasquale

2011-01-01

Raltegravir is the first approved antiretroviral able to prevent HIV genome integration into the host chromosomes. The aim of the study is to test if raltegravir plasma concentrations can be associated with proviral DNA decline during raltegravir-based salvage therapy. A total of 33 multidrug-resistant HIV-infected patients were enrolled in a longitudinal open-label pilot study and completed a 24-week follow-up. The CD4(+) T-cell count, plasma viral load, proviral HIV DNA and two-long-terminal repeat (2-LTR) circular forms were assessed at baseline, day 14, 30, 60, 90 and 180. The raltegravir trough concentration (C (trough)) was measured by HPLC-ultraviolet and patients were divided into two groups according to the median raltegravir C (trough). The mean±SD values of baseline HIV RNA, CD4(+) T-cell count and HIV DNA were 4.4±0.82 log copies/ml, 256±177 cells/mm(3) , and 2,668±4,721 copies/10(6) peripheral blood mononuclear cells, respectively. Despite a transient increase of total DNA at week 2, a marked proviral DNA decay (P=0.01) with an increase of the 2-LTR unintegrated/total DNA ratio (P=0.06) over time was observed. At univariate analysis, no correlation between raltegravir C(trough) and classical virological parameters was observed. Nevertheless, the decay of proviral HIV DNA was more pronounced in patients displaying C(trough)<158 ng/ml with respect to those with C(trough)>158 ng/ml (P=0.046). Successful raltegravir-based therapy produces a significant decline in proviral DNA and is associated with an increase of the unintegrated/total DNA ratio. Further studies are necessary to define the possible role of pharmacokinetic raltegravir monitoring and the biological meaning of unintegrated proviral DNA. © 2011 International Medical Press

Accelerated appearance of multiple B cell lymphoma types in NFS/N mice congenic for ecotropic murine leukemia viruses.

PubMed

Hartley, J W; Chattopadhyay, S K; Lander, M R; Taddesse-Heath, L; Naghashfar, Z; Morse, H C; Fredrickson, T N

2000-02-01

Spontaneous lymphomas occur at high frequency in NFS x V+ mice, strains congenic for ecotropic murine leukemia virus (MuLV) proviral genes and expressing virus at high titer. In the present study, a total of 703 NFS x V+ lymphomas were studied by histopathology, immunophenotypic analysis, immunoglobulin heavy chain or T cell receptor beta chain rearrangements, and somatic ecotropic MuLV integrations; 90% of the lymphomas tested were of B cell lineage. Low-grade tumors included small lymphocytic, follicular, and splenic marginal zone lymphomas, while high-grade tumors comprised diffuse large-cell (centroblastic and immunoblastic types), splenic marginal zone, and lymphoblastic lymphomas. Comparison of mice of similar genetic background except for presence (NFS x V+) or absence (NFS x V-) of functional ecotropic MuLV genomes showed that NFS x V-clonal lymphomas developed at about one-half the rate of those occurring in NFS x V+ mice, and most were low-grade B cell lymphomas with extended latent periods. In NFS x V+ mice, clonal outgrowth, defined by Ig gene rearrangements, was associated with acquisition of somatic ecotropic proviral integrations, suggesting that, although generation of B cell clones can be virus independent, ecotropic virus may act to increase the rate of generation of clones and speed their evolution to lymphoma. The mechanism remains undefined, because only rare rearrangements were detected in several cellular loci previously associated with MuLV insertional mutagenesis.

A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca).

PubMed

Mayer, Jens; Tsangaras, Kyriakos; Heeger, Felix; Avila-Arcos, María; Stenglein, Mark D; Chen, Wei; Sun, Wei; Mazzoni, Camila J; Osterrieder, Nikolaus; Greenwood, Alex D

2013-08-15

Transcriptome analysis of polar bears (Ursus maritimus) yielded sequences with highest similarity to the human endogenous retrovirus group HERV-K(HML-2). Further analysis of the polar bear draft genome identified an endogenous betaretrovirus group comprising 26 proviral copies and 231 solo LTRs. Molecular dating indicates the group originated before the divergence of bears from a common ancestor but is not present in all carnivores. Closely related sequences were identified in the giant panda (Ailuropoda melanoleuca) and characterized from its genome. We have designated the polar bear and giant panda sequences U. maritimus endogenous retrovirus (UmaERV) and A. melanoleuca endogenous retrovirus (AmeERV), respectively. Phylogenetic analysis demonstrated that the bear virus group is nested within the HERV-K supergroup among bovine and bat endogenous retroviruses suggesting a complex evolutionary history within the HERV-K group. All individual remnants of proviral sequences contain numerous frameshifts and stop codons and thus, the virus is likely non-infectious. Copyright © 2013 Elsevier Inc. All rights reserved.

A novel endogenous betaretrovirus group characterized from polar bears (Ursus maritimus) and giant pandas (Ailuropoda melanoleuca)

PubMed Central

Mayer, Jens; Tsangaras, Kyriakos; Heeger, Felix; Ávila-Arcos, Maria; Stenglein, Mark D.; Chen, Wei; Sun, Wei; Mazzoni, Camila; Osterrieder, Nikolaus; Greenwood, Alex D.

2013-01-01

Transcriptome analysis of polar bears (Ursus maritimus) yielded sequences with highest similarity to the human endogenous retrovirus group HERV-K(HML-2). Further analysis of the polar bear draft genome identified an endogenous betaretrovirus group comprising 26 proviral copies and 231 solo LTRs. Molecular dating indicates the group originated before the divergence of bears from a common ancestor but is not present in all carnivores. Closely related sequences were identified in the giant panda (Ailuropoda melanoleuca) and characterized from its genome. We have designated the polar bear and giant panda sequences Ursus maritimus endogenous retrovirus (UmaERV) and Ailuropoda melanoleuca endogenous retrovirus (AmeERV), respectively. Phylogenetic analysis demonstrated that the bear virus group is nested within the HERV-K supergroup among bovine and bat endogenous retroviruses suggesting a complex evolutionary history within the HERV-K group. All individual remnants of proviral sequences contain numerous frameshifts and stop codons and thus, the virus is likely non-infectious. PMID:23725819

PCR-in situ hybridization detection of human T-cell lymphotropic virus type 1 (HTLV-1) tax proviral DNA in peripheral blood lymphocytes of patients with HTLV-1-associated neurologic disease.

PubMed Central

Levin, M C; Fox, R J; Lehky, T; Walter, M; Fox, C H; Flerlage, N; Bamford, R; Jacobson, S

1996-01-01

PCR-in situ hybridization (PCR-ISH) was developed and utilized to determine the distribution of human T-cell lymphotropic virus type 1 (HTLV-1) tax proviral DNA in peripheral blood lymphocytes (PBL) from patients with HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). PCR-ISH of HTLV-1 tax DNA in PBL from patients with HAM/TSP revealed that 1 in 5,000 to 1 in 10,000 PBL contained virus. PCR-ISH was sensitive, because a positive signal was consistently demonstrated from the HTLV-1-infected cell lines HUT-102 (which contains four to six copies of HTLV-1 proviral DNA per cell) and MT-1 (which contains one to three copies of HTLV-1 proviral DNA per cell). Also, intracellular amplification by PCR-ISH significantly increased sensitivity compared with conventional ISH and was shown to be specific for HTLV-1 tax DNA. These results are in contrast to solution-phase PCR amplification in which greater than 1% of cells were estimated to be infected. The discordance between these results is discussed and may indicate that more than one copy of HTLV-1 tax proviral DNA is present in an individual PBL. PMID:8551632

Low proviral small ruminant lentivirus load as biomarker of natural restriction in goats.

PubMed

Crespo, Helena; Bertolotti, Luigi; Proffiti, Margherita; Cascio, Paolo; Cerruti, Fulvia; Acutis, Pier Luigi; de Andrés, Damián; Reina, Ramsés; Rosati, Sergio

2016-08-30

Small ruminant lentiviruses (SRLV) globally affect welfare and production of sheep and goats and are mainly controlled through elimination of infected animals, independently of the viral kinetics within the single animal. Control programs are based on highly sensitive serological tests, however the existence of low antibody responders leads to the permanent presence of seronegative infected animals in the flock, thus perpetuating the infection. On the other hand, long-term non-progressors show a detectable antibody response not indicative of a shedding animal, suggesting immune contention of infection. In this study, we analyse two goat populations within the same herd, harbouring low or high proviral SRLV loads respectively, both showing a robust antibody response. In vivo findings were confirmed in vitro since fibroblastic cell lines obtained from one high and one low proviral load representative goats, showed respectively a high and a faint production of virus upon infection with reference and field circulating SRLV strains. Differences in virus production were relieved when strain CAEV-Co was used for experimental infection. We analysed LTR promoter activity, proviral load, entry step and production of virus and viral proteins. Intriguingly, proteasomal activity was higher in fibroblasts from low proviral load animals and proteasome inhibition increased viral production in both cell lines, suggesting the implication of active proteasome-dependent restriction factors. Among them, we analysed relative expression and sequences of TRIM5α, APOBEC3 (Z1, Z2, Z3 and Z2-Z3) and BST-2 (Tetherin) and found a global antiviral status in low proviral carriers that may confer protection against viral shedding and disease onset. Copyright © 2016 Elsevier B.V. All rights reserved.

A universal real-time PCR assay for the quantification of group-M HIV-1 proviral load.

PubMed

Malnati, Mauro S; Scarlatti, Gabriella; Gatto, Francesca; Salvatori, Francesca; Cassina, Giulia; Rutigliano, Teresa; Volpi, Rosy; Lusso, Paolo

2008-01-01

Quantification of human immunodeficiency virus type-1 (HIV-1) proviral DNA is increasingly used to measure the HIV-1 cellular reservoirs, a helpful marker to evaluate the efficacy of antiretroviral therapeutic regimens in HIV-1-infected individuals. Furthermore, the proviral DNA load represents a specific marker for the early diagnosis of perinatal HIV-1 infection and might be predictive of HIV-1 disease progression independently of plasma HIV-1 RNA levels and CD4(+) T-cell counts. The high degree of genetic variability of HIV-1 poses a serious challenge for the design of a universal quantitative assay capable of detecting all the genetic subtypes within the main (M) HIV-1 group with similar efficiency. Here, we describe a highly sensitive real-time PCR protocol that allows for the correct quantification of virtually all group-M HIV-1 strains with a higher degree of accuracy compared with other methods. The protocol involves three stages, namely DNA extraction/lysis, cellular DNA quantification and HIV-1 proviral load assessment. Owing to the robustness of the PCR design, this assay can be performed on crude cellular extracts, and therefore it may be suitable for the routine analysis of clinical samples even in developing countries. An accurate quantification of the HIV-1 proviral load can be achieved within 1 d from blood withdrawal.

Cis-drivers and trans-drivers of bovine leukemia virus oncogenesis.

PubMed

Safari, Roghaiyeh; Hamaidia, Malik; de Brogniez, Alix; Gillet, Nicolas; Willems, Luc

2017-10-01

The bovine leukemia virus (BLV) is a retrovirus inducing an asymptomatic and persistent infection in ruminants and leading in a minority of cases to the accumulation of B-lymphocytes (lymphocytosis, leukemia or lymphoma). Although the mechanisms of oncogenesis are still largely unknown, there is clear experimental evidence showing that BLV infection drastically modifies the pattern of gene expression of the host cell. This alteration of the transcriptome in infected B-lymphocytes results first, from a direct activity of viral proteins (i.e. transactivation of gene promoters, protein-protein interactions), second, from insertional mutagenesis by proviral integration (cis-activation) and third, from gene silencing by microRNAs. Expression of viral proteins stimulates a vigorous immune response that indirectly modifies gene transcription in other cell types (e.g. cytotoxic T-cells, auxiliary T-cells, macrophages). In principle, insertional mutagenesis and microRNA-associated RNA interference can modify the cell fate without inducing an antiviral immunity. Despite a tight control by the immune response, the permanent attempts of the virus to replicate ultimately induce mutations in the infected cell. Accumulation of these genomic lesions and Darwinian selection of tumor clones are predicted to lead to cancer. Copyright © 2017 Elsevier B.V. All rights reserved.

CMV-promoter driven codon-optimized expression alters the assembly type and morphology of a reconstituted HERV-K(HML-2).

PubMed

Hohn, Oliver; Hanke, Kirsten; Lausch, Veronika; Zimmermann, Anja; Mostafa, Saeed; Bannert, Norbert

2014-11-11

The HERV-K(HML-2) family contains the most recently integrated and best preserved endogenized proviral sequences in the human genome. All known elements have nevertheless been subjected to mutations or deletions that render expressed particles non-infectious. Moreover, these post-insertional mutations hamper the analysis of the general biological properties of this ancient virus family. The expression of consensus sequences and sequences of elements with reverted post-insertional mutations has therefore been very instrumental in overcoming this limitation. We investigated the particle morphology of a recently reconstituted HERV-K113 element termed oriHERV-K113 using thin-section electron microscopy (EM) and could demonstrate that strong overexpression by substitution of the 5'LTR for a CMV promoter and partial codon optimization altered the virus assembly type and morphology. This included a conversion from the regular C-type to an A-type morphology with a mass of cytoplasmic immature cores tethered to the cell membrane and the membranes of vesicles. Overexpression permitted the release and maturation of virions but reduced the envelope content. A weaker boost of virus expression by Staufen-1 was not sufficient to induce these morphological alterations.

CMV-Promoter Driven Codon-Optimized Expression Alters the Assembly Type and Morphology of a Reconstituted HERV-K(HML-2)

PubMed Central

Hohn, Oliver; Hanke, Kirsten; Lausch, Veronika; Zimmermann, Anja; Mostafa, Saeed; Bannert, Norbert

2014-01-01

The HERV-K(HML-2) family contains the most recently integrated and best preserved endogenized proviral sequences in the human genome. All known elements have nevertheless been subjected to mutations or deletions that render expressed particles non-infectious. Moreover, these post-insertional mutations hamper the analysis of the general biological properties of this ancient virus family. The expression of consensus sequences and sequences of elements with reverted post-insertional mutations has therefore been very instrumental in overcoming this limitation. We investigated the particle morphology of a recently reconstituted HERV-K113 element termed oriHERV-K113 using thin-section electron microscopy (EM) and could demonstrate that strong overexpression by substitution of the 5'LTR for a CMV promoter and partial codon optimization altered the virus assembly type and morphology. This included a conversion from the regular C-type to an A-type morphology with a mass of cytoplasmic immature cores tethered to the cell membrane and the membranes of vesicles. Overexpression permitted the release and maturation of virions but reduced the envelope content. A weaker boost of virus expression by Staufen-1 was not sufficient to induce these morphological alterations. PMID:25393897

Clinical Outcomes of Virologically-Suppressed Patients with Pre-existing HIV-1 Drug Resistance Mutations Switching to Rilpivirine/Emtricitabine/Tenofovir Disoproxil Fumarate in the SPIRIT Study.

PubMed

Porter, Danielle P; Toma, Jonathan; Tan, Yuping; Solberg, Owen; Cai, Suqin; Kulkarni, Rima; Andreatta, Kristen; Lie, Yolanda; Chuck, Susan K; Palella, Frank; Miller, Michael D; White, Kirsten L

2016-02-01

Antiretroviral regimen switching may be considered for HIV-1-infected, virologically-suppressed patients to enable treatment simplification or improve tolerability, but should be guided by knowledge of pre-existing drug resistance. The current study examined the impact of pre-existing drug resistance mutations on virologic outcomes among virologically-suppressed patients switching to Rilpivirine (RPV)/emtricitabine (FTC)/tenofovir disoproxil fumarate (TDF). SPIRIT was a phase 3b study evaluating the safety and efficacy of switching to RPV/FTC/TDF in virologically-suppressed HIV-1-infected patients. Pre-existing drug resistance at baseline was determined by proviral DNA genotyping for 51 RPV/FTC/TDF-treated patients with known mutations by historical RNA genotype and matched controls and compared with clinical outcome at Week 48. Drug resistance mutations in protease or reverse transcriptase were detected in 62.7% of patients by historical RNA genotype and in 68.6% by proviral DNA genotyping at baseline. Proviral DNA sequencing detected 89% of occurrences of NRTI and NNRTI resistance-associated mutations reported by historical genotype. Mutations potentially affecting RPV activity, including E138A/G/K/Q, Y181C, and H221Y, were detected in isolates from 11 patients by one or both assays. None of the patients with single mutants had virologic failure through Week 48. One patient with pre-existing Y181Y/C and M184I by proviral DNA genotyping experienced virologic failure. Nineteen patients with K103N present by historical genotype were confirmed by proviral DNA sequencing and 18/19 remained virologically-suppressed. Virologic success rates were high among virologically-suppressed patients with pre-existing NRTI and NNRTI resistance-associated mutations who switched to RPV/FTC/TDF in the SPIRIT study. While plasma RNA genotyping remains preferred, proviral DNA genotyping may provide additional value in virologically-suppressed patients for whom historical resistance data are unavailable.

Rev-binding aptamer and CMV promoter act as decoys to inhibit HIV replication.

PubMed

Konopka, K; Lee, N S; Rossi, J; Düzgüneş, N

2000-09-19

We examined whether the antiviral effect of an HIV-1 Rev-binding aptamer [RBE(apt)] could be enhanced by a ribozyme directed against the HIV-1 env gene, and whether the antiviral activity was affected by different promoters. The efficacy of the aptamer and ribozyme DNAs was tested in HeLa cells co-transfected with the HIV-1 proviral clones, HXBDeltaBgl or pNL4-3, using transferrin-lipoplexes. The RBE(apt) and anti-env ribozyme genes were inserted into the pTZU6+27 plasmid, or constructed under the control of the human cytomegalovirus (CMV) or Rous sarcoma virus (RSV) promoters. The parental vector plasmids were used as controls. Co-transfection of the pTZU6+27 RBE(apt) plasmid with HXBDeltaBgl, or pNL4-3, at a weight ratio of 5:1, inhibited p24 production by 70 and 45%, respectively. The RSV RBE(apt) plasmid co-transfected with either HIV clone, at the same weight ratio, reduced viral production by 88%. The addition of the anti-env ribozyme to the RSV RBE(apt) did not enhance its antiviral activity. When the constructs were under the control of the CMV promoter, the expression of the HIV plasmids was very low and was independent of the presence of the RBE(apt). Thus, the effect of the RBE(apt) was strongly dependent on the promoter of the tested construct. The anti-HIV activity of the CMV RBE(apt) construct was non-specific, because co-transfection with either pCMV. SPORT-betagal or pCMVlacZ significantly suppressed HIV production from the HIV proviral clones. The reduction in p24 could not be attributed to the non-specific toxicity of the transfection procedure. Transfection of acutely HIV-infected HeLa-CD4 cells with pCMV.SPORT-betagal reduced the p24 level by 35%, while the expression of the U6 RBE(apt) did not affect p24 production. The suppression of HIV production from the HIV proviral clones by the CMV promoter constructs in the co-transfection assays may be explained by competition for transcription factors (TFs) between HIV and CMV promoters. This observation points to the potential for misleading results in co-transfections involving CMV constructs and HIV.

HIV Type 1 (HIV-1) Proviral Reservoirs Decay Continuously Under Sustained Virologic Control in HIV-1–Infected Children Who Received Early Treatment

PubMed Central

Luzuriaga, Katherine; Tabak, Barbara; Garber, Manuel; Chen, Ya Hui; Ziemniak, Carrie; McManus, Margaret M.; Murray, Danielle; Strain, Matthew C.; Richman, Douglas D.; Chun, Tae-Wook; Cunningham, Coleen K.; Persaud, Deborah

2014-01-01

Background. Early initiation of combination antiretroviral therapy (cART) to human immunodeficiency virus type 1 (HIV-1)–infected infants controls HIV-1 replication and reduces mortality. Methods. Plasma viremia (lower limit of detection, <2 copies/mL), T-cell activation, HIV-1–specific immune responses, and the persistence of cells carrying replication-competent virus were quantified during long-term effective combination antiretroviral therapy (cART) in 4 perinatally HIV-1–infected youth who received treatment early (the ET group) and 4 who received treatment late (the LT group). Decay in peripheral blood mononuclear cell (PBMC) proviral DNA levels was also measured over time in the ET youth. Results. Plasma viremia was not detected in any ET youth but was detected in all LT youth (median, 8 copies/mL; P = .03). PBMC proviral load was significantly lower in ET youth (median, 7 copies per million PBMCs) than in LT youth (median, 181 copies; P = .03). Replication-competent virus was recovered from all LT youth but only 1 ET youth. Decay in proviral DNA was noted in all 4 ET youth in association with limited T-cell activation and with absent to minimal HIV-1–specific immune responses. Conclusions. Initiation of early effective cART during infancy significantly limits circulating levels of proviral and replication-competent HIV-1 and promotes continuous decay of viral reservoirs. Continued cART with reduction in HIV-1 reservoirs over time may facilitate HIV-1 eradication strategies. PMID:24850788

The Human Immunodeficiency Virus 1 ASP RNA promotes viral latency by recruiting the Polycomb Repressor Complex 2 and promoting nucleosome assembly

PubMed Central

Zapata, Juan C.; Campilongo, Federica; Barclay, Robert A.; DeMarino, Catherine; Iglesias-Ussel, Maria D.; Kashanchi, Fatah; Romerio, Fabio

2017-01-01

Various epigenetic marks at the HIV-1 5′LTR suppress proviral expression and promote latency. Cellular antisense transcripts known as long noncoding RNAs (lncRNAs) recruit the polycomb repressor complex 2 (PRC2) to gene promoters, which catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), thus promoting nucleosome assembly and suppressing gene expression. We found that an HIV-1 antisense transcript expressed from the 3′LTR and encoding the antisense protein ASP promotes proviral latency. Expression of ASP RNA reduced HIV-1 replication in Jurkat cells. Moreover, ASP RNA expression promoted the establishment and maintenance of HIV-1 latency in Jurkat E4 cells. We show that this transcript interacts with and recruits PRC2 to the HIV-1 5′LTR, increasing accumulation of the suppressive epigenetic mark H3K27me3, while reducing RNA Polymerase II and thus proviral transcription. Altogether, our results suggest that the HIV-1 ASP transcript promotes epigenetic silencing of the HIV-1 5′LTR and proviral latency through the PRC2 pathway. PMID:28340355

The Human Immunodeficiency Virus 1 ASP RNA promotes viral latency by recruiting the Polycomb Repressor Complex 2 and promoting nucleosome assembly.

PubMed

Zapata, Juan C; Campilongo, Federica; Barclay, Robert A; DeMarino, Catherine; Iglesias-Ussel, Maria D; Kashanchi, Fatah; Romerio, Fabio

2017-06-01

Various epigenetic marks at the HIV-1 5'LTR suppress proviral expression and promote latency. Cellular antisense transcripts known as long noncoding RNAs (lncRNAs) recruit the polycomb repressor complex 2 (PRC2) to gene promoters, which catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), thus promoting nucleosome assembly and suppressing gene expression. We found that an HIV-1 antisense transcript expressed from the 3'LTR and encoding the antisense protein ASP promotes proviral latency. Expression of ASP RNA reduced HIV-1 replication in Jurkat cells. Moreover, ASP RNA expression promoted the establishment and maintenance of HIV-1 latency in Jurkat E4 cells. We show that this transcript interacts with and recruits PRC2 to the HIV-1 5'LTR, increasing accumulation of the suppressive epigenetic mark H3K27me3, while reducing RNA Polymerase II and thus proviral transcription. Altogether, our results suggest that the HIV-1 ASP transcript promotes epigenetic silencing of the HIV-1 5'LTR and proviral latency through the PRC2 pathway. Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.

Cytotoxic chemotherapy and the evolution of cellular and viral resistance to antiretroviral therapy in HIV- infected individuals with lymphoma.

PubMed

McFaul, Katie; Liptrott, Neill; Cox, Alison; Martin, Phillip; Egan, Deirdre; Owen, Andrew; Kelly, Sarah; Karolia, Zeenat; Shaw, Kate; Bower, Mark; Boffito, Marta

2016-09-01

The use of combination antiretroviral therapy (cART) and cytotoxic chemotherapy for HIV-associated lymphoma runs the risks of inducing HIV drug resistance. This study examined two possible mechanisms: altered expression of membrane drug transporter protein (MTP) and acquisition of mutations in pro-viral DNA. Expression levels of MTP and pro-viral DNA resistance mutation analysis were performed on peripheral blood mononuclear cells (PBMC) before, during, and after chemotherapy. Twenty nine patients completed the three time point estimations. There were no significant variations before, during, and after chemotherapy in the expression of four MTPs: ABCB1, ABCC1, ABCC2, and SLCO3A1 (OATP3A1). Pro-viral DNA sequencing revealed that only one patient developed a new nucleos/tide reverse transcriptase inhibitor-associated mutation (184V) during the course of the study, giving a mutation rate of 0.0027 per person per year. In conclusion, concomitant administration of cytotoxic chemotherapy and cART does not induce expression of MTP. Furthermore, no significant changes in viral resistance were observed pre- and post-chemotherapy, suggesting mutagenic cytotoxic chemotherapy seems not to induce mutations in HIV pro-viral DNA.

Nucleotide sequence analysis establishes the role of endogenous murine leukemia virus DNA segments in formation of recombinant mink cell focus-forming murine leukemia viruses.

PubMed Central

Khan, A S

1984-01-01

The sequence of 363 nucleotides near the 3' end of the pol gene and 564 nucleotides from the 5' terminus of the env gene in an endogenous murine leukemia viral (MuLV) DNA segment, cloned from AKR/J mouse DNA and designated as A-12, was obtained. For comparison, the nucleotide sequence in an analogous portion of AKR mink cell focus-forming (MCF) 247 MuLV provirus was also determined. Sequence features unique to MCF247 MuLV DNA in the 3' pol and 5' env regions were identified by comparison with nucleotide sequences in analogous regions of NFS -Th-1 xenotropic and AKR ecotropic MuLV proviruses. These included (i) an insertion of 12 base pairs encoding four amino acids located 60 base pairs from the 3' terminus of the pol gene and immediately preceding the env gene, (ii) the deletion of 12 base pairs (encoding four amino acids) and the insertion of 3 base pairs (encoding one amino acid) in the 5' portion of the env gene, and (iii) single base substitutions resulting in 2 MCF247 -specific amino acids in the 3' pol and 23 in the 5' env regions. Nucleotide sequence comparison involving the 3' pol and 5' env regions of AKR MCF247 , NFS xenotropic, and AKR ecotropic MuLV proviruses with the cloned endogenous MuLV DNA indicated that MCF247 proviral DNA sequences were conserved in the cloned endogenous MuLV proviral segment. In fact, total nucleotide sequence identity existed between the endogenous MuLV DNA and the MCF247 MuLV provirus in the 3' portion of the pol gene. In the 5' env region, only 4 of 564 nucleotides were different, resulting in three amino acid changes between AKR MCF247 MuLV DNA and the endogenous MuLV DNA present in clone A-12. In addition, nucleotide sequence comparison indicated that Moloney-and Friend-MCF MuLVs were also highly related in the 3' pol and 5' env regions to the cloned endogenous MuLV DNA. These results establish the role of endogenous MuLV DNA segments in generation of recombinant MCF viruses. PMID:6328017

Protocol for the use of a rapid real-time PCR method for the detection of HIV-1 proviral DNA using double-stranded primer.

PubMed

Pau, Chou-Pong; Wells, Susan K; Granade, Timothy C

2012-01-01

This chapter describes a real-time PCR method for the detection of HIV-1 proviral DNA in whole blood samples using a novel double-stranded primer system. The assay utilizes a simple commercially available DNA extraction method and a rapid and easy-to-perform real-time PCR protocol to consistently detect a minimum of four copies of HIV-1 group M proviral DNA in as little as 90 min after sample (whole blood) collection. Co-amplification of the human RNase P gene serves as an internal control to monitor the efficiency of both the DNA extraction and amplification. Once the assay is validated properly, it may be suitable as an alternative confirmation test for HIV-1 infections in a variety of HIV testing venues including the mother-to-child transmission testing sites, clinics, and diagnostic testing centers.

A human genome-wide loss-of-function screen identifies effective chikungunya antiviral drugs

PubMed Central

Karlas, Alexander; Berre, Stefano; Couderc, Thérèse; Varjak, Margus; Braun, Peter; Meyer, Michael; Gangneux, Nicolas; Karo-Astover, Liis; Weege, Friderike; Raftery, Martin; Schönrich, Günther; Klemm, Uwe; Wurzlbauer, Anne; Bracher, Franz; Merits, Andres; Meyer, Thomas F.; Lecuit, Marc

2016-01-01

Chikungunya virus (CHIKV) is a globally spreading alphavirus against which there is no commercially available vaccine or therapy. Here we use a genome-wide siRNA screen to identify 156 proviral and 41 antiviral host factors affecting CHIKV replication. We analyse the cellular pathways in which human proviral genes are involved and identify druggable targets. Twenty-one small-molecule inhibitors, some of which are FDA approved, targeting six proviral factors or pathways, have high antiviral activity in vitro, with low toxicity. Three identified inhibitors have prophylactic antiviral effects in mouse models of chikungunya infection. Two of them, the calmodulin inhibitor pimozide and the fatty acid synthesis inhibitor TOFA, have a therapeutic effect in vivo when combined. These results demonstrate the value of loss-of-function screening and pathway analysis for the rational identification of small molecules with therapeutic potential and pave the way for the development of new, host-directed, antiviral agents. PMID:27177310

A human genome-wide loss-of-function screen identifies effective chikungunya antiviral drugs.

PubMed

Karlas, Alexander; Berre, Stefano; Couderc, Thérèse; Varjak, Margus; Braun, Peter; Meyer, Michael; Gangneux, Nicolas; Karo-Astover, Liis; Weege, Friderike; Raftery, Martin; Schönrich, Günther; Klemm, Uwe; Wurzlbauer, Anne; Bracher, Franz; Merits, Andres; Meyer, Thomas F; Lecuit, Marc

2016-05-12

Chikungunya virus (CHIKV) is a globally spreading alphavirus against which there is no commercially available vaccine or therapy. Here we use a genome-wide siRNA screen to identify 156 proviral and 41 antiviral host factors affecting CHIKV replication. We analyse the cellular pathways in which human proviral genes are involved and identify druggable targets. Twenty-one small-molecule inhibitors, some of which are FDA approved, targeting six proviral factors or pathways, have high antiviral activity in vitro, with low toxicity. Three identified inhibitors have prophylactic antiviral effects in mouse models of chikungunya infection. Two of them, the calmodulin inhibitor pimozide and the fatty acid synthesis inhibitor TOFA, have a therapeutic effect in vivo when combined. These results demonstrate the value of loss-of-function screening and pathway analysis for the rational identification of small molecules with therapeutic potential and pave the way for the development of new, host-directed, antiviral agents.

In vitro modeling of HIV proviral activity in microglia.

PubMed

Campbell, Lee A; Richie, Christopher T; Zhang, Yajun; Heathward, Emily J; Coke, Lamarque M; Park, Emily Y; Harvey, Brandon K

2017-12-01

Microglia, the resident macrophages of the brain, play a key role in the pathogenesis of HIV-associated neurocognitive disorders (HAND) due to their productive infection by HIV. This results in the release of neurotoxic viral proteins and pro-inflammatory compounds which negatively affect the functionality of surrounding neurons. Because models of HIV infection within the brain are limited, we aimed to create a novel microglia cell line with an integrated HIV provirus capable of recreating several hallmarks of HIV infection. We utilized clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing technology and integrated a modified HIV provirus into CHME-5 immortalized microglia to create HIV-NanoLuc CHME-5. In the modified provirus, the Gag-Pol region is replaced with the coding region for NanoLuciferase (NanoLuc), which allows for the rapid assay of HIV long terminal repeat activity using a luminescent substrate, while still containing the necessary genetic material to produce established neurotoxic viral proteins (e.g. tat, nef, gp120). We confirmed that HIV-NanoLuc CHME-5 microglia express NanoLuc, along with the HIV viral protein Nef. We subsequently exposed these cells to a battery of experiments to modulate the activity of the provirus. Proviral activity was enhanced by treating the cells with pro-inflammatory factors lipopolysaccharide (LPS) and tumor necrosis factor alpha and by overexpressing the viral regulatory protein Tat. Conversely, genetic modification of the toll-like receptor-4 gene by CRISPR/Cas9 reduced LPS-mediated proviral activation, and pharmacological application of NF-κB inhibitor sulfasalazine similarly diminished proviral activity. Overall, these data suggest that HIV-NanoLuc CHME-5 may be a useful tool in the study of HIV-mediated neuropathology and proviral regulation. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Low-level viremia and proviral DNA impede immune reconstitution in HIV-1-infected patients receiving highly active antiretroviral therapy.

PubMed

Ostrowski, Sisse R; Katzenstein, Terese L; Thim, Per T; Pedersen, Bente K; Gerstoft, Jan; Ullum, Henrik

2005-02-01

Immunological and virological consequences of low-level viremia in human immunodeficiency virus (HIV) type 1-infected patients receiving highly active antiretroviral therapy (HAART) remain to be determined. For 24 months, 101 HAART-treated, HIV-1-infected patients with HIV RNA levels 20 copies/mL at >/=1 visit (dVL patients) (median increase, 81 copies/mL [interquartile range, 37-480 copies/mL]). dVL patients had higher concentrations of CD8 cells, activated and memory T cells, and proviral DNA, compared with uVL patients (P<.05). A higher HIV RNA level was independently associated with reduced CD4 gain (P<.001). A higher HIV RNA level also was associated with increases in activated CD8(+)CD38(+) and CD8(+)HLA-DR(+) cells (P<.05), and a higher level of activated CD8(+)CD38(+) cells was independently associated with reduced CD4 gain (P<.05). A higher proviral DNA level was associated with increases in CD4(+)CD45RA(-)CD28(-) effector cells and reductions in naive CD4(+)CD45RA(+)CD62L(+) and CD8(+)CD45RA(+)CD62L(+) cells (P<.05). Higher levels of activated CD4(+)HLA-DR(+) and early differentiated CD4(+)CD45RA(-)CD28(+) cells predicted increased risk of subsequent detectable viremia in patients with undetectable HIV RNA (P<.05). These findings indicate that low-level viremia and proviral DNA are intimately associated with the immunological and virological equilibrium in patients receiving HAART.

Genetic characterization of the HIV-1 reservoir after Vacc-4x and romidepsin therapy in HIV-1 infected individuals.

PubMed

Winckelmann, Anni; Morcilla, Vincent; Shao, Wei; Schleimann, Mariane H; Højen, Jesper F; Schlub, Timothy E; Denton, Paul W; Østergaard, Lars; Søgaard, Ole S; Tolstrup, Martin; Palmer, Sarah

2018-05-11

Therapeutic HIV-1 immunization followed by latency reversal has been suggested as a strategy to eradicate HIV-1. Here we investigate the phylogenetic composition of the HIV-1 regions targeted by the therapeutic HIV-1 peptide vaccine Vacc-4x in participants in a clinical trial. Seventeen participants on suppressive antiretroviral therapy were vaccinated with six doses of Vacc-4x followed by three doses of romidepsin. Seven study participants were selected for sequencing analysis. All participants underwent an analytical treatment interruption. Single-genome/proviral sequencing of the p24-RT region was performed to genetically characterize proviral DNA, cell-associated (CA) RNA and outgrowth viruses during therapy as well as plasma HIV-1 RNA during an analytical treatment interruption. There were no changes in CA HIV-1 RNA (P = 0.83) and DNA (P = 0.09) diversity over the course of the study and no difference between CA HIV-1 RNA and DNA diversity (P = 0.32). Only one participant showed signs of potential vaccine-related selection in the rebounding plasma virus. In five of seven participants, we identified HLA-specific CTL epitopes containing non-silent mutations in 100% of the sequences. We detected no evidence of selective immune pressure reflected in proviral diversity or by occurrence of specific mutation in the vaccine-targeted epitopes. Pre-existing CTL epitope mutations may affect the potency of this therapeutic vaccine. This highlights the challenges of developing effective HIV-1 therapeutic vaccines.This is an open access article distributed under the terms of the Creative Commons Attribution-Non Commercial-No Derivatives License 4.0 (CCBY-NC-ND), where it is permissible to download and share the work provided it is properly cited. The work cannot be changed in any way or used commercially without permission from the journal. http://creativecommons.org/licenses/by-nc-nd/4.0.

Potential Links between Hepadnavirus and Bornavirus Sequences in the Host Genome and Cancer.

PubMed

Honda, Tomoyuki

2017-01-01

Various viruses leave their sequences in the host genomes during infection. Such events occur mainly in retrovirus infection but also sometimes in DNA and non-retroviral RNA virus infections. If viral sequences are integrated into the genomes of germ line cells, the sequences can become inherited as endogenous viral elements (EVEs). The integration events of viral sequences may have oncogenic potential. Because proviral integrations of some retroviruses and/or reactivation of endogenous retroviruses are closely linked to cancers, viral insertions related to non-retroviral viruses also possibly contribute to cancer development. This article focuses on genomic viral sequences derived from two non-retroviral viruses, whose endogenization is already reported, and discusses their possible contributions to cancer. Viral insertions of hepatitis B virus play roles in the development of hepatocellular carcinoma. Endogenous bornavirus-like elements, the only non-retroviral RNA virus-related EVEs found in the human genome, may also be involved in cancer formation. In addition, the possible contribution of the interactions between viruses and retrotransposons, which seem to be a major driving force for generating EVEs related to non-retroviral RNA viruses, to cancers will be discussed. Future studies regarding the possible links described here may open a new avenue for the development of novel therapeutics for tumor virus-related cancers and/or provide novel insights into EVE functions.

Provirus Integration at the 3 Region of N‐myc in Cell Lines Established from Thymic Lymphomas Spontaneously Formed in AKR Mice and a [(BALB/c × B6)F1AKR] Bone Marrow Chimera

PubMed Central

Yano, Yoko; Kobayashi, Seiichi; Yasumizu, Ryoji; Tamaki, Junko; Kubo, Mitsumasa; Sasaki, Akio; Hasan, Shahid; Okuyama, Harue; Inaba, Muneo; Ikehara, Susumu; Hiai, Hiroshi; Kakinuma, Mitsuaki

1991-01-01

Among 18 thymic leukemia cell lines which have been established from spontaneous thymic lym‐phomas in AKR mice as well as in bone marrow chimeras which were constructed by transplanting allogeneic bone marrow cells into irradiated AKR mice, three proviral integration sites were identified; near c‐myc, N‐myc and pim‐l loci. No integration site specific for chimeric leukemia cell lines was found. In three thymic leukemia cell lines which contained rearranged N‐myc, genes, insertions of long terminal repeats (LTRs) of murine leukemia viruses were detected at 18 or 20 bp downstream of the translational termination codon. These results demonstrate that the 3’region of the N‐myc gene is one of the integration targets for murine leukemia viruses in spontaneous thymic lymphomas. In these three cell lines, N‐myc mRNA was stably transcribed and transcription of c‐myc mRNA was down‐regulated. The integrated murine leukemia viruses in AKR thymic leukemia were most likely AKV, though the DNA sequence of the LTR inserted in the genome of a leukemic cell line from [(BALB/c × B6)F1‐AKR], CAK20, was different from LTRs of murine leukemia viruses so far reported. PMID:1900822

Survey of feline leukemia virus and feline coronaviruses in captive neotropical wild felids from Southern Brazil.

PubMed

Guimaraes, Ana M S; Brandão, Paulo E; de Moraes, Wanderlei; Cubas, Zalmir S; Santos, Leonilda C; Villarreal, Laura Y B; Robes, Rogério R; Coelho, Fabiana M; Resende, Mauricio; Santos, Renata C F; Oliveira, Rosangela C; Yamaguti, Mauricio; Marques, Lucas M; Neto, Renata L; Buzinhani, Melissa; Marques, Regina; Messick, Joanne B; Biondo, Alexander W; Timenetsky, Jorge

2009-06-01

A total of 57 captive neotropical felids (one Leopardus geoffroyi, 14 Leopardus pardalis, 17 Leopardus wiedii, 22 Leopardus tigrinus, and three Puma yagouaroundi) from the Itaipu Binacional Wildlife Research Center (Refúgio Bela Vista, Southern Brazil) were anesthetized for blood collection. Feces samples were available for 44 animals, including one L. geoffroyi, eight L. pardalis, 14 L. wiedii, 20 L. tigrinus, and one P. yagouaroundi. Total DNA and RNA were extracted from blood and feces, respectively, using commercial kits. Blood DNA samples were evaluated by polymerase chain reaction (PCR) for feline leukemia virus (FeLV) proviral DNA, whereas reverse transcriptase-PCR was run on fecal samples for detection of coronavirus RNA. None of the samples were positive for coronaviruses. A male L. pardalis and a female L. tigrinus were positive for FeLV proviral DNA, and identities of PCR products were confirmed by sequencing. This is the first evidence of FeLV proviral DNA in these species in Southern Brazil.

Identification of full-length proviral DNA of porcine endogenous retrovirus from Chinese Wuzhishan miniature pigs inbred.

PubMed

Ma, Yuyuan; Lv, Maomin; Xu, Shu; Wu, Jianmin; Tian, Kegong; Zhang, Jingang

2010-07-01

Existence of porcine endogenous retrovirus (PERV) hinders pigs to be used in clinical xenotransplantation to alleviate the shortage of human transplants. Chinese miniature pigs are potential organ donors for xenotransplantation in China. However, so far, an adequate level of information on the molecular characteristics of PERV from Chinese miniature pigs has not been available. We described here the cloning and characterization of full-length proviral DNA of PERV from Chinese Wuzhishan miniature pigs inbred (WZSP). Full-length nucleotide sequences of PERV-WZSP and other PERVs were aligned and phylogenetic tree was constructed from deduced amino-acid sequences of env. The results demonstrated that the full-length proviral DNA of PERV-WZSP belongs to gammaretrovirus and shares high similarity with other PERVs. Sequence analysis also suggested that different patterns of LTR existed in the same porcine germ line and partial PERV-C sequence may recombine with PERV-A sequence in LTR. (c) 2008 Elsevier Ltd. All rights reserved.

ATM supports gammaherpesvirus replication by attenuating type I interferon pathway.

PubMed

Darrah, Eric J; Stoltz, Kyle P; Ledwith, Mitchell; Tarakanova, Vera L

2017-10-01

Ataxia-Telangiectasia mutated (ATM) kinase participates in multiple networks, including DNA damage response, oxidative stress, and mitophagy. ATM also supports replication of diverse DNA and RNA viruses. Gammaherpesviruses are prevalent cancer-associated viruses that benefit from ATM expression during replication. This proviral role of ATM had been ascribed to its signaling within the DNA damage response network; other functions of ATM have not been considered. In this study increased type I interferon (IFN) responses were observed in ATM deficient gammaherpesvirus-infected macrophages. Using a mouse model that combines ATM and type I IFN receptor deficiencies we show that increased type I IFN response in the absence of ATM fully accounts for the proviral role of ATM during gammaherpesvirus replication. Further, increased type I IFN response rendered ATM deficient macrophages more susceptible to antiviral effects of type II IFN. This study identifies attenuation of type I IFN responses as the primary mechanism underlying proviral function of ATM during gammaherpesvirus infection. Copyright © 2017 Elsevier Inc. All rights reserved.

Direct non-productive HIV-1 infection in a T-cell line is driven by cellular activation state and NFκB

PubMed Central

2014-01-01

Background Molecular latency allows HIV-1 to persist in resting memory CD4+ T-cells as transcriptionally silent provirus integrated into host chromosomal DNA. Multiple transcriptional regulatory mechanisms for HIV-1 latency have been described in the context of progressive epigenetic silencing and maintenance. However, our understanding of the determinants critical for the establishment of latency in newly infected cells is limited. Results In this study, we used a recently described, doubly fluorescent HIV-1 latency model to dissect the role of proviral integration sites and cellular activation state on direct non-productive infections at the single cell level. Proviral integration site mapping of infected Jurkat T-cells revealed that productively and non-productively infected cells are indistinguishable in terms of genomic landmarks, surrounding epigenetic landscapes, and proviral orientation relative to host genes. However, direct non-productive infections were inversely correlated with both cellular activation state and NFκB activity. Furthermore, modulating NFκB with either small molecules or by conditional overexpression of NFκB subunits was sufficient to alter the propensity of HIV-1 to directly enter a non-productive latent state in newly infected cells. Importantly, this modulatory effect was limited to a short time window post-infection. Conclusions Taken together, our data suggest that cellular activation state and NFκB activity during the time of infection, but not the site of proviral integration, are important regulators of direct HIV-1 non-productive infections. PMID:24502247

In vivo analysis of replication and immunogenicity of proviral clones of human T-lymphotropic virus type 1 with selective envelope surface-unit mutations

PubMed Central

Silverman, Lee R.; Phipps, Andrew J.; Montgomery, Andy; Fernandez, Soledad; Tsukahara, Tomonori; Ratner, Lee; Lairmore, Michael D.

2005-01-01

Human T-cell leukemia virus type 1 (HTLV-1) is the causative agent of adult T-cell lymphoma/leukemia (ATL). The HTLV-1 envelope gene exhibits limited variability when examined from infected individuals, but has not been tested using infectious clones of the virus in animal models. In vitro assays indicate that HTLV-1 envelope (Env) Ser75Ile, Asn95Asp, and Asn195Asp surface unit (SU) mutants are able to replicate in and immortalize lymphocytes. Herein, we examined the effects of these Env mutants in rabbits inoculated with HTLV-1 immortalized ACH.75, ACH.95, or ACH.195 cell lines (expressing full-length molecular clones with the SU mutations) or the ACH.1 cell line (expressing wild-type SU). All rabbits became infected, and the fidelity of the mutations was maintained throughout the 8-week study. However, SU point mutations resulted in decreased antibody responses to viral group-associated antigen (Gag) and Env antigens. ACH.195 rabbits had a selective decreased antibody response to SU, and one ACH.195 rabbit had an antibody response to both HTLV-1 and HTLV-2 SUs. Some mutant inoculation groups had altered proviral loads. However, peripheral-blood mononuclear cell (PBMC) proviral loads did not correlate with antibody responses. Our data are the first to demonstrate that mutations in critical determinants of HTLV-1 Env SU altered antibody responses and proviral loads, but do not prevent viral replication in vivo. PMID:16046523

Improved detection of CXCR4-using HIV by V3 genotyping: application of population-based and "deep" sequencing to plasma RNA and proviral DNA.

PubMed

Swenson, Luke C; Moores, Andrew; Low, Andrew J; Thielen, Alexander; Dong, Winnie; Woods, Conan; Jensen, Mark A; Wynhoven, Brian; Chan, Dennison; Glascock, Christopher; Harrigan, P Richard

2010-08-01

Tropism testing should rule out CXCR4-using HIV before treatment with CCR5 antagonists. Currently, the recombinant phenotypic Trofile assay (Monogram) is most widely utilized; however, genotypic tests may represent alternative methods. Independent triplicate amplifications of the HIV gp120 V3 region were made from either plasma HIV RNA or proviral DNA. These underwent standard, population-based sequencing with an ABI3730 (RNA n = 63; DNA n = 40), or "deep" sequencing with a Roche/454 Genome Sequencer-FLX (RNA n = 12; DNA n = 12). Position-specific scoring matrices (PSSMX4/R5) (-6.96 cutoff) and geno2pheno[coreceptor] (5% false-positive rate) inferred tropism from V3 sequence. These methods were then independently validated with a separate, blinded dataset (n = 278) of screening samples from the maraviroc MOTIVATE trials. Standard sequencing of HIV RNA with PSSM yielded 69% sensitivity and 91% specificity, relative to Trofile. The validation dataset gave 75% sensitivity and 83% specificity. Proviral DNA plus PSSM gave 77% sensitivity and 71% specificity. "Deep" sequencing of HIV RNA detected >2% inferred-CXCR4-using virus in 8/8 samples called non-R5 by Trofile, and <2% in 4/4 samples called R5. Triplicate analyses of V3 standard sequence data detect greater proportions of CXCR4-using samples than previously achieved. Sequencing proviral DNA and "deep" V3 sequencing may also be useful tools for assessing tropism.

Characterization of proviruses cloned from mink cell focus-forming virus-infected cellular DNA.

PubMed Central

Khan, A S; Repaske, R; Garon, C F; Chan, H W; Rowe, W P; Martin, M A

1982-01-01

Two proviruses were cloned from EcoRI-digested DNA extracted from mink cells chronically infected with AKR mink cell focus-forming (MCF) 247 murine leukemia virus (MuLV), using a lambda phage host vector system. One cloned MuLV DNA fragment (designated MCF 1) contained sequences extending 6.8 kilobases from an EcoRI restriction site in the 5' long terminal repeat (LTR) to an EcoRI site located in the envelope (env) region and was indistinguishable by restriction endonuclease mapping for 5.1 kilobases (except for the EcoRI site in the LTR) from the 5' end of AKR ecotropic proviral DNA. The DNA segment extending from 5.1 to 6.8 kilobases contained several restriction sites that were not present in the AKR ecotropic provirus. A 0.5-kilobase DNA segment located at the 3' end of MCF 1 DNA contained sequences which hybridized to a xenotropic env-specific DNA probe but not to labeled ecotropic env-specific DNA. This dual character of MCF 1 proviral DNA was also confirmed by analyzing heteroduplex molecules by electron microscopy. The second cloned proviral DNA (designated MCF 2) was a 6.9-kilobase EcoRI DNA fragment which contained LTR sequences at each end and a 2.0-kilobase deletion encompassing most of the env region. The MCF 2 proviral DNA proved to be a useful reagent for detecting LTRs electron microscopically due to the presence of nonoverlapping, terminally located LTR sequences which effected its circularization with DNAs containing homologous LTR sequences. Nucleotide sequence analysis demonstrated the presence of a 104-base-pair direct repeat in the LTR of MCF 2 DNA. In contrast, only a single copy of the reiterated component of the direct repeat was present in MCF 1 DNA. Images PMID:6281459

Identification of TL-Om1, an Adult T-Cell Leukemia (ATL) Cell Line, as Reference Material for Quantitative PCR for Human T-Lymphotropic Virus 1

PubMed Central

Okuma, Kazu; Yamagishi, Makoto; Yamochi, Tadanori; Firouzi, Sanaz; Momose, Haruka; Mizukami, Takuo; Takizawa, Kazuya; Araki, Kumiko; Sugamura, Kazuo; Yamaguchi, Kazunari; Watanabe, Toshiki

2014-01-01

Quantitative PCR (qPCR) for human T-lymphotropic virus 1 (HTLV-1) is useful for measuring the amount of integrated HTLV-1 proviral DNA in peripheral blood mononuclear cells. Many laboratories in Japan have developed different HTLV-1 qPCR methods. However, when six independent laboratories analyzed the proviral load of the same samples, there was a 5-fold difference in their results. To standardize HTLV-1 qPCR, preparation of a well-defined reference material is needed. We analyzed the integrated HTLV-1 genome and the internal control (IC) genes of TL-Om1, a cell line derived from adult T-cell leukemia, to confirm its suitability as a reference material for HTLV-1 qPCR. Fluorescent in situ hybridization (FISH) showed that HTLV-1 provirus was monoclonally integrated in chromosome 1 at the site of 1p13 in the TL-Om1 genome. HTLV-1 proviral genome was not transferred from TL-Om1 to an uninfected T-cell line, suggesting that the HTLV-1 proviral copy number in TL-Om1 cells is stable. To determine the copy number of HTLV-1 provirus and IC genes in TL-Om1 cells, we used FISH, digital PCR, and qPCR. HTLV-1 copy numbers obtained by these three methods were similar, suggesting that their results were accurate. Also, the ratio of the copy number of HTLV-1 provirus to one of the IC genes, RNase P, was consistent for all three methods. These findings indicate that TL-Om1 cells are an appropriate reference material for HTLV-1 qPCR. PMID:25502533

Prevalence of koala retrovirus in geographically diverse populations in Australia.

PubMed

Simmons, G S; Young, P R; Hanger, J J; Jones, K; Clarke, D; McKee, J J; Meers, J

2012-10-01

To determine the prevalence of koala retrovirus (KoRV) in selected koala populations and to estimate proviral copy number in a subset of koalas. Blood or tissue samples from 708 koalas in Queensland, New South Wales, Victoria and South Australia were tested for KoRV pol provirus gene using standard polymerase chain reaction (PCR), nested PCR and real-time PCR (qPCR). Prevalence of KoRV provirus-positive koalas was 100% in four regions of Queensland and New South Wales, 72.2% in mainland Victoria, 26.6% on four Victorian islands and 14.8% on Kangaroo Island, South Australia. Estimated proviral copy number per cell in four groups of koalas from Queensland and Victoria showed marked variation, ranging from a mean of 165 copies per cell in the Queensland group to 1.29 × 10(-4) copies per cell in one group of Victorian koalas. The higher prevalence of KoRV-positive koalas in the north of Australia and high proviral loads in Queensland koalas may indicate KoRV entered and became endogenous in the north and is spreading southwards. It is also possible there are genetic differences between koalas in northern and southern Australia that affect susceptibility to KoRV infection or endogenisation, or that environmental factors affecting transmission in northern states are absent or uncommon in southern regions. Although further studies are required, the finding of proviral copy numbers orders of magnitude lower than what would be expected for the presence of a single copy in every cell for many Victorian animals suggests that KoRV is not endogenous in these animals and likely reflects ongoing exogenous infection. © 2012 The Authors. Australian Veterinary Journal © 2012 Australian Veterinary Association.

Standardization of Quantitative PCR for Human T-Cell Leukemia Virus Type 1 in Japan: a Collaborative Study

PubMed Central

Okuma, Kazu; Yamochi, Tadanori; Sato, Tomoo; Sasaki, Daisuke; Hasegawa, Hiroo; Umeki, Kazumi; Kubota, Ryuji; Sobata, Rieko; Matsumoto, Chieko; Kaneko, Noriaki; Naruse, Isao; Yamagishi, Makoto; Nakashima, Makoto; Momose, Haruka; Araki, Kumiko; Mizukami, Takuo; Mizusawa, Saeko; Okada, Yoshiaki; Ochiai, Masaki; Utsunomiya, Atae; Koh, Ki-Ryang; Ogata, Masao; Nosaka, Kisato; Uchimaru, Kaoru; Iwanaga, Masako; Sagara, Yasuko; Yamano, Yoshihisa; Satake, Masahiro; Okayama, Akihiko; Mochizuki, Manabu; Izumo, Shuji; Saito, Shigeru; Itabashi, Kazuo; Kamihira, Shimeru; Yamaguchi, Kazunari; Watanabe, Toshiki

2015-01-01

Quantitative PCR (qPCR) analysis of human T-cell leukemia virus type 1 (HTLV-1) was used to assess the amount of HTLV-1 provirus DNA integrated into the genomic DNA of host blood cells. Accumulating evidence indicates that a high proviral load is one of the risk factors for the development of adult T-cell leukemia/lymphoma and HTLV-1-associated myelopathy/tropical spastic paraparesis. However, interlaboratory variability in qPCR results makes it difficult to assess the differences in reported proviral loads between laboratories. To remedy this situation, we attempted to minimize discrepancies between laboratories through standardization of HTLV-1 qPCR in a collaborative study. TL-Om1 cells that harbor the HTLV-1 provirus were serially diluted with peripheral blood mononuclear cells to prepare a candidate standard. By statistically evaluating the proviral loads of the standard and those determined using in-house qPCR methods at each laboratory, we determined the relative ratios of the measured values in the laboratories to the theoretical values of the TL-Om1 standard. The relative ratios of the laboratories ranged from 0.84 to 4.45. Next, we corrected the proviral loads of the clinical samples from HTLV-1 carriers using the relative ratio. As expected, the overall differences between the laboratories were reduced by half, from 7.4-fold to 3.8-fold on average, after applying the correction. HTLV-1 qPCR can be standardized using TL-Om1 cells as a standard and by determining the relative ratio of the measured to the theoretical standard values in each laboratory. PMID:26292315

Standardization of Quantitative PCR for Human T-Cell Leukemia Virus Type 1 in Japan: a Collaborative Study.

PubMed

Kuramitsu, Madoka; Okuma, Kazu; Yamochi, Tadanori; Sato, Tomoo; Sasaki, Daisuke; Hasegawa, Hiroo; Umeki, Kazumi; Kubota, Ryuji; Sobata, Rieko; Matsumoto, Chieko; Kaneko, Noriaki; Naruse, Isao; Yamagishi, Makoto; Nakashima, Makoto; Momose, Haruka; Araki, Kumiko; Mizukami, Takuo; Mizusawa, Saeko; Okada, Yoshiaki; Ochiai, Masaki; Utsunomiya, Atae; Koh, Ki-Ryang; Ogata, Masao; Nosaka, Kisato; Uchimaru, Kaoru; Iwanaga, Masako; Sagara, Yasuko; Yamano, Yoshihisa; Satake, Masahiro; Okayama, Akihiko; Mochizuki, Manabu; Izumo, Shuji; Saito, Shigeru; Itabashi, Kazuo; Kamihira, Shimeru; Yamaguchi, Kazunari; Watanabe, Toshiki; Hamaguchi, Isao

2015-11-01

Quantitative PCR (qPCR) analysis of human T-cell leukemia virus type 1 (HTLV-1) was used to assess the amount of HTLV-1 provirus DNA integrated into the genomic DNA of host blood cells. Accumulating evidence indicates that a high proviral load is one of the risk factors for the development of adult T-cell leukemia/lymphoma and HTLV-1-associated myelopathy/tropical spastic paraparesis. However, interlaboratory variability in qPCR results makes it difficult to assess the differences in reported proviral loads between laboratories. To remedy this situation, we attempted to minimize discrepancies between laboratories through standardization of HTLV-1 qPCR in a collaborative study. TL-Om1 cells that harbor the HTLV-1 provirus were serially diluted with peripheral blood mononuclear cells to prepare a candidate standard. By statistically evaluating the proviral loads of the standard and those determined using in-house qPCR methods at each laboratory, we determined the relative ratios of the measured values in the laboratories to the theoretical values of the TL-Om1 standard. The relative ratios of the laboratories ranged from 0.84 to 4.45. Next, we corrected the proviral loads of the clinical samples from HTLV-1 carriers using the relative ratio. As expected, the overall differences between the laboratories were reduced by half, from 7.4-fold to 3.8-fold on average, after applying the correction. HTLV-1 qPCR can be standardized using TL-Om1 cells as a standard and by determining the relative ratio of the measured to the theoretical standard values in each laboratory. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

CD4 is expressed on a heterogeneous subset of hematopoietic progenitors, which persistently harbor CXCR4 and CCR5-tropic HIV proviral genomes in vivo.

PubMed

Sebastian, Nadia T; Zaikos, Thomas D; Terry, Valeri; Taschuk, Frances; McNamara, Lucy A; Onafuwa-Nuga, Adewunmi; Yucha, Ryan; Signer, Robert A J; Riddell, James; Bixby, Dale; Markowitz, Norman; Morrison, Sean J; Collins, Kathleen L

2017-07-01

Latent HIV infection of long-lived cells is a barrier to viral clearance. Hematopoietic stem and progenitor cells are a heterogeneous population of cells, some of which are long-lived. CXCR4-tropic HIVs infect a broad range of HSPC subtypes, including hematopoietic stem cells, which are multi-potent and long-lived. However, CCR5-tropic HIV infection is limited to more differentiated progenitor cells with life spans that are less well understood. Consistent with emerging data that restricted progenitor cells can be long-lived, we detected persistent HIV in restricted HSPC populations from optimally treated people. Further, genotypic and phenotypic analysis of amplified env alleles from donor samples indicated that both CXCR4- and CCR5-tropic viruses persisted in HSPCs. RNA profiling confirmed expression of HIV receptor RNA in a pattern that was consistent with in vitro and in vivo results. In addition, we characterized a CD4high HSPC sub-population that was preferentially targeted by a variety of CXCR4- and CCR5-tropic HIVs in vitro. Finally, we present strong evidence that HIV proviral genomes of both tropisms can be transmitted to CD4-negative daughter cells of multiple lineages in vivo. In some cases, the transmitted proviral genomes contained signature deletions that inactivated the virus, eliminating the possibility that coincidental infection explains the results. These data support a model in which both stem and non-stem cell progenitors serve as persistent reservoirs for CXCR4- and CCR5-tropic HIV proviral genomes that can be passed to daughter cells.

HIV proviral DNA associated with decreased neuropsychological function.

PubMed

Shiramizu, Bruce; Paul, Robert; Williams, Andrew; Shikuma, Cecilia; Watters, Michael; Grove, John; Valcour, Victor

2007-01-01

The authors previously found a strong association between elevated HIV proviral DNA (HIV DNA) and a diagnosis of HIV-1-associated dementia (HAD) vs. normal cognition. It is unclear whether HIV DNA globally affects the diagnosis of HAD or whether the effect is limited to individual neuropsychological deficits. This exploratory study examined baseline HIV DNA and its association with individual neuropsychological deficits. HIV DNA was significantly associated with baseline neuropsychological deficits independent of age, ethnicity, IQ, and plasma HIV-1 RNA levels. However, HIV DNA did not predict future changes in neuropsychological deficits. The data suggest that HIV DNA and neuropsychological deficits may co-vary over time.

Dynamics of Viral and Proviral Loads of Feline Immunodeficiency Virus within the Feline Central Nervous System during the Acute Phase following Intravenous Infection

PubMed Central

Ryan, G.; Klein, D.; Knapp, E.; Hosie, M. J.; Grimes, T.; Mabruk, M. J. E. M. F.; Jarrett, O.; Callanan, J. J.

2003-01-01

Animal models of human immunodeficiency virus 1, such as feline immunodeficiency virus (FIV), provide the opportunities to dissect the mechanisms of early interactions of the virus with the central nervous system (CNS). The aims of the present study were to evaluate viral loads within CNS, cerebrospinal fluid (CSF), ocular fluid, and the plasma of cats in the first 23 weeks after intravenous inoculation with FIVGL8. Proviral loads were also determined within peripheral blood mononuclear cells (PBMCs) and brain tissue. In this acute phase of infection, virus entered the brain in the majority of animals. Virus distribution was initially in a random fashion, with more diffuse brain involvement as infection progressed. Virus in the CSF was predictive of brain parenchymal infection. While the peak of virus production in blood coincided with proliferation within brain, more sustained production appeared to continue in brain tissue. In contrast, proviral loads in the brain decreased to undetectable levels in the presence of a strengthening PBMC load. A final observation in this study was that there was no direct correlation between viral loads in regions of brain or ocular tissue and the presence of histopathology. PMID:12805447

Hybridization capture reveals evolution and conservation across the entire Koala retrovirus genome.

PubMed

Tsangaras, Kyriakos; Siracusa, Matthew C; Nikolaidis, Nikolas; Ishida, Yasuko; Cui, Pin; Vielgrader, Hanna; Helgen, Kristofer M; Roca, Alfred L; Greenwood, Alex D

2014-01-01

The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin.

Hybridization Capture Reveals Evolution and Conservation across the Entire Koala Retrovirus Genome

PubMed Central

Ishida, Yasuko; Cui, Pin; Vielgrader, Hanna; Helgen, Kristofer M.; Roca, Alfred L.; Greenwood, Alex D.

2014-01-01

The koala retrovirus (KoRV) is the only retrovirus known to be in the midst of invading the germ line of its host species. Hybridization capture and next generation sequencing were used on modern and museum DNA samples of koala (Phascolarctos cinereus) to examine ca. 130 years of evolution across the full KoRV genome. Overall, the entire proviral genome appeared to be conserved across time in sequence, protein structure and transcriptional binding sites. A total of 138 polymorphisms were detected, of which 72 were found in more than one individual. At every polymorphic site in the museum koalas, one of the character states matched that of modern KoRV. Among non-synonymous polymorphisms, radical substitutions involving large physiochemical differences between amino acids were elevated in env, potentially reflecting anti-viral immune pressure or avoidance of receptor interference. Polymorphisms were not detected within two functional regions believed to affect infectivity. Host sequences flanking proviral integration sites were also captured; with few proviral loci shared among koalas. Recently described variants of KoRV, designated KoRV-B and KoRV-J, were not detected in museum samples, suggesting that these variants may be of recent origin. PMID:24752422

A simple and rapid DNA extraction method from whole blood for highly sensitive detection and quantitation of HIV-1 proviral DNA by real-time PCR.

PubMed

McFall, Sally M; Wagner, Robin L; Jangam, Sujit R; Yamada, Douglas H; Hardie, Diana; Kelso, David M

2015-03-01

Early diagnosis and access to treatment for infants with human immunodeficiency virus-1 (HIV-1) is critical to reduce infant mortality. The lack of simple point-of-care tests impedes the timely initiation of antiretroviral therapy. The development of FINA, filtration isolation of nucleic acids, a novel DNA extraction method that can be performed by clinic personnel in less than 2 min has been reported previously. In this report, significant improvements in the DNA extraction and amplification methods are detailed that allow sensitive quantitation of as little as 10 copies of HIV-1 proviral DNA and detection of 3 copies extracted from 100 μl of whole blood. An internal control to detect PCR inhibition was also incorporated. In a preliminary field evaluation of 61 South African infants, the FINA test demonstrated 100% sensitivity and specificity. The proviral copy number of the infant specimens was quantified, and it was established that 100 microliters of whole blood is required for sensitive diagnosis of infants. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Contribution of type W human endogenous retroviruses to the human genome: characterization of HERV-W proviral insertions and processed pseudogenes.

PubMed

Grandi, Nicole; Cadeddu, Marta; Blomberg, Jonas; Tramontano, Enzo

2016-09-09

Human endogenous retroviruses (HERVs) are ancient sequences integrated in the germ line cells and vertically transmitted through the offspring constituting about 8 % of our genome. In time, HERVs accumulated mutations that compromised their coding capacity. A prominent exception is HERV-W locus 7q21.2, producing a functional Env protein (Syncytin-1) coopted for placental syncytiotrophoblast formation. While expression of HERV-W sequences has been investigated for their correlation to disease, an exhaustive description of the group composition and characteristics is still not available and current HERV-W group information derive from studies published a few years ago that, of course, used the rough assemblies of the human genome available at that time. This hampers the comparison and correlation with current human genome assemblies. In the present work we identified and described in detail the distribution and genetic composition of 213 HERV-W elements. The bioinformatics analysis led to the characterization of several previously unreported features and provided a phylogenetic classification of two main subgroups with different age and structural characteristics. New facts on HERV-W genomic context of insertion and co-localization with sequences putatively involved in disease development are also reported. The present work is a detailed overview of the HERV-W contribution to the human genome and provides a robust genetic background useful to clarify HERV-W role in pathologies with poorly understood etiology, representing, to our knowledge, the most complete and exhaustive HERV-W dataset up to date.

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution.

PubMed

Hayward, Alexander; Cornwallis, Charlie K; Jern, Patric

2015-01-13

Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host-retrovirus interactions. Here we use recent technological advances to infer broad patterns in retroviral diversity, evolution, and host-virus relationships by using a large-scale phylogenomic approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA copy into the host cell genome to produce new viruses. ERVs are provirus insertions in germline cells that are inherited down the host lineage and consequently present a record of past host-viral associations. By mining ERVs from 65 host genomes sampled across vertebrate diversity, we uncover a great diversity of ERVs, indicating that retroviral sequences are much more prevalent and widespread across vertebrates than previously appreciated. The majority of ERV clades that we recover do not contain known retroviruses, implying either that retroviral lineages are highly transient over evolutionary time or that a considerable number of retroviruses remain to be identified. By characterizing the distribution of ERVs, we show that no major vertebrate lineage has escaped retroviral activity and that retroviruses are extreme host generalists, having an unprecedented ability for rampant host switching among distantly related vertebrates. In addition, we examine whether the distribution of ERVs can be explained by host factors predicted to influence viral transmission and find that internal fertilization has a pronounced effect on retroviral colonization of host genomes. By capturing the mode and pattern of retroviral evolution and contrasting ERV diversity with known retroviral diversity, our study provides a cohesive framework to understand host-virus coevolution better.

Pan-vertebrate comparative genomics unmasks retrovirus macroevolution

PubMed Central

Hayward, Alexander; Cornwallis, Charlie K.; Jern, Patric

2015-01-01

Although extensive research has demonstrated host-retrovirus microevolutionary dynamics, it has been difficult to gain a deeper understanding of the macroevolutionary patterns of host–retrovirus interactions. Here we use recent technological advances to infer broad patterns in retroviral diversity, evolution, and host–virus relationships by using a large-scale phylogenomic approach using endogenous retroviruses (ERVs). Retroviruses insert a proviral DNA copy into the host cell genome to produce new viruses. ERVs are provirus insertions in germline cells that are inherited down the host lineage and consequently present a record of past host–viral associations. By mining ERVs from 65 host genomes sampled across vertebrate diversity, we uncover a great diversity of ERVs, indicating that retroviral sequences are much more prevalent and widespread across vertebrates than previously appreciated. The majority of ERV clades that we recover do not contain known retroviruses, implying either that retroviral lineages are highly transient over evolutionary time or that a considerable number of retroviruses remain to be identified. By characterizing the distribution of ERVs, we show that no major vertebrate lineage has escaped retroviral activity and that retroviruses are extreme host generalists, having an unprecedented ability for rampant host switching among distantly related vertebrates. In addition, we examine whether the distribution of ERVs can be explained by host factors predicted to influence viral transmission and find that internal fertilization has a pronounced effect on retroviral colonization of host genomes. By capturing the mode and pattern of retroviral evolution and contrasting ERV diversity with known retroviral diversity, our study provides a cohesive framework to understand host–virus coevolution better. PMID:25535393

Molecular cloning of human T-cell lymphotrophic virus type I-like proviral genome from the peripheral lymphocyte DNA of a patient with chronic neurologic disorders.

PubMed Central

Reddy, E P; Mettus, R V; DeFreitas, E; Wroblewska, Z; Cisco, M; Koprowski, H

1988-01-01

Human T-cell lymphotropic virus type 1 (HTLV-I), the etiologic agent of human T-cell leukemia, has recently been shown to be associated with neurologic disorders such as tropical spastic paraparesis, HTLV-associated myelopathy, and possibly with multiple sclerosis. In this communication, we have examined one specific case of neurologic disorder that can be classified as multiple sclerosis or tropical spastic paraparesis. The patient suffering from chronic neurologic disorder was found to contain antibodies to HTLV-I envelope and gag proteins in his serum and cerebrospinal fluid. Lymphocytes from peripheral blood and cerebrospinal fluid of the patient were shown to express viral RNA sequences by in situ hybridization. Southern blot analysis of the patient lymphocyte DNA revealed the presence of HTLV-I-related sequences. Blot-hybridization analysis of the RNA from fresh peripheral lymphocytes stimulated with interleukin 2 revealed the presence of abundant amounts of genomic viral RNA with little or no subgenomic RNA. We have cloned the proviral genome from the DNA of the peripheral lymphocytes and determined its restriction map. This analysis shows that this proviral genome is very similar if not identical to that of the prototype HTLV-I genome. Images PMID:2897123

T-cell tropism of simian T-cell leukaemia virus type 1 and cytokine profiles in relation to proviral load and immunological changes during chronic infection of naturally infected mandrills (Mandrillus sphinx).

PubMed

Souquière, Sandrine; Mouinga-Ondeme, Augustin; Makuwa, Maria; Beggio, Paola; Radaelli, Antonia; De Giuli Morghen, Carlo; Mortreux, Franck; Kazanji, Mirdad

2009-08-01

Although a wide variety of non-human primates are susceptible to simian T-cell leukaemia virus type 1 (STLV-1), little is known about the virological or molecular determinants of natural STLV-1 infection. We determined STLV-1 virus tropism in vivo and its relation to the immune response by evaluating cytokine production and T-cell subsets in naturally infected and uninfected mandrills. With real-time PCR methods, we found that STLV-1 in mandrills infects both CD4(+) and CD8(+) T cells; however, proviral loads were significantly higher (P = 0.01) in CD4(+) than in CD8(+) cells (mean STLV-1 copies number per 100 cells (+/- SD) was 7.8 +/- 8 in CD4(+) T cells and 3.9 +/- 4.5 in CD8(+) T cells). After culture, STLV-1 provirus was detected in enriched CD4(+) but not in enriched CD8(+) T cells. After 6 months of culture, STLV-1-transformed cell lines expressing CD3(+), CD4(+) and HLADR(+) were established, and STLV-1 proteins and tax/rex mRNA were detected. In STLV-1 infected monkeys, there was a correlation between high proviral load and elevated levels of interleukin (IL)-2, IL-6, IL-10, interferon-gamma and tumour necrosis factor-alpha. The two monkeys with the highest STLV-1 proviral load had activated CD4(+)HLADR(+) and CD8(+)HLADR(+) T-cell subsets and a high percentage of CD25(+) in CD4(+) and CD8(+) T cells. Our study provides the first cellular, immunological and virological characterization of natural STLV-1 infection in mandrills and shows that they are an appropriate animal model for further physiopathological studies of the natural history of human T-cell leukaemia viruses.

High discordance in blood and genital tract HIV-1 drug resistance in Indian women failing first-line therapy.

PubMed

Saravanan, Shanmugam; Gomathi, Selvamurthi; Delong, Allison; Kausalya, Bagavathi; Sivamalar, Sathasivam; Poongulali, Selvamuthu; Brooks, Katherine; Kumarasamy, Nagalingeswaran; Balakrishnan, Pachamuthu; Solomon, Sunil S; Cu-Uvin, Susan; Kantor, Rami

2018-05-24

Examine HIV-1 plasma viral load (PVL) and genital tract (GT) viral load (GVL) and drug resistance in India. At the YRG Centre for AIDS Research and Education, Chennai, we tested: PVL in women on first-line ART for ≥6 months; GVL when PVL >2000 copies/mL; and plasma, genital and proviral reverse transcriptase drug resistance when GVL >2000 copies/mL. Wilcoxon rank-sum and Fisher's exact tests were used to identify failure and resistance associations. Pearson correlations were calculated to evaluate PVL-GVL associations. Inter-compartmental resistance discordance was evaluated using generalized estimating equations. Of 200 women, 37% had detectable (>400 copies/mL) PVL and 31% had PVL >1000 copies/mL. Of women with detectable PVL, 74% had PVL >2000 copies/mL, of which 74% had detectable GVL. Higher PVL was associated with higher GVL. Paired plasma and genital sequences were available for 21 women; mean age of 34 years, median ART duration of 33 months, median CD4 count of 217 cells/mm3, median PVL of 5.4 log10 copies/mL and median GVL of 4.6 log10 copies/mL. Drug resistance was detected in 81%-91% of samples and 67%-76% of samples had dual-class resistance. Complete three-compartment concordance was seen in only 10% of women. GT-proviral discordance was significantly larger than plasma-proviral discordance. GT or proviral mutations discordant from plasma led to clinically relevant resistance in 24% and 30%, respectively. We identified high resistance and high inter-compartmental resistance discordance in Indian women, which might lead to unrecognized resistance transmission and re-emergence compromising treatment outcomes, particularly relevant to countries like India, where sexual HIV transmission is predominant.

Sanger and Next-Generation Sequencing data for characterization of CTL epitopes in archived HIV-1 proviral DNA.

PubMed

Tumiotto, Camille; Riviere, Lionel; Bellecave, Pantxika; Recordon-Pinson, Patricia; Vilain-Parce, Alice; Guidicelli, Gwenda-Line; Fleury, Hervé

2017-01-01

One of the strategies for curing viral HIV-1 is a therapeutic vaccine involving the stimulation of cytotoxic CD8-positive T cells (CTL) that are Human Leucocyte Antigen (HLA)-restricted. The lack of efficiency of previous vaccination strategies may have been due to the immunogenic peptides used, which could be different from a patient's virus epitopes and lead to a poor CTL response. To counteract this lack of specificity, conserved epitopes must be targeted. One alternative is to gather as many data as possible from a large number of patients on their HIV-1 proviral archived epitope variants, taking into account their genetic background to select the best presented CTL epitopes. In order to process big data generated by Next-Generation Sequencing (NGS) of the DNA of HIV-infected patients, we have developed a software package called TutuGenetics. This tool combines an alignment derived either from Sanger or NGS files, HLA typing, target gene and a CTL epitope list as input files. It allows automatic translation after correction of the alignment obtained between the HxB2 reference and the reads, followed by automatic calculation of the MHC IC50 value for each epitope variant and the HLA allele of the patient by using NetMHCpan 3.0, resulting in a csv file as output result. We validated this new tool by comparing Sanger and NGS (454, Roche) sequences obtained from the proviral DNA of patients at success of ART included in the Provir Latitude 45 study and showed a 90% correlation between the quantitative results of NGS and Sanger. This automated analysis combined with complementary samples should yield more data regarding the archived CTL epitopes according to the patients' HLA alleles and will be useful for screening epitopes that in theory are presented efficiently to the HLA groove, thus constituting promising immunogenic peptides for a therapeutic vaccine.

[The recent advances of HAM/TSP research].

PubMed

Osame, M

1999-12-01

The ninth international conference on HTLVs and related disorders was held on April 5-9, 1999 at Kagoshima, Japan under the conference chairperson, Dr. Mitsuhiro Osame. In this meeting, world-wide epidemiological data on HTLV-I carriers, ATL patients, and HAM/TSP patients were summarized as shown in the table. The total number of them was supposed to be more than 2.2 millions, 1,200, and 3,000, respectively. To elucidate the localization of HTLV-I proviral DNA directly, double staining using immunohistochemistry and PCR in situ hybridization in the spinal cords of HAM/TSP patients were performed. HTLV-I proviral DNA was localized only to OPD 4-positive cells (Matsuoka et al, 1998). The localization of HTLV-I messenger RNA was the same (Moritoyo et al, 1996). A novel technique to detect HTLV-I tax protein was also developed. In HAM/TSP patients, 0.04-1.16% of the CSF cells and 0.02-0.54% of PBMCs were positive for HTLV-I tax protein (Moritoyo et al, 1999). It was also hypothesized that HLA alleles control HTLV-I proviral load and thus influence susceptibility to HAM/TSP. Two hundred and thirty-two cases of HAM/TSP were compared with 201 randomly selected HTLV-I seropositive asymptomatic blood donors. It was shown that, after infection with HTLV-I, the class I allele HLA-A*02 halves the odds of HAM/TSP (p < 0.0001), preventing 28% of potential cases of HAM/TSP. Furthermore, HLA-A*02 positive healthy HTLV-I carriers have a proviral load one-third that (p = 0.0114) of HLA-A*02 negative HTLV-I carriers. An association of HLA-DRB1*0101 with disease susceptibility was also identified, which doubled the odds of HAM/TSP in the absence of the protective effect of HLA-A*02 (Jeffery and Usuku et al, 1999).

Possible roles of HIV-1 nucleocapsid protein in the specificity of proviral DNA synthesis and in its variability.

PubMed

Lapadat-Tapolsky, M; Gabus, C; Rau, M; Darlix, J L

1997-05-02

Retroviral nucleocapsid (NC) protein is an integral part of the virion nucleocapsid where it coats the dimeric RNA genome. Due to its nucleic acid binding and annealing activities, NC protein directs the annealing of the tRNA primer to the primer binding site and greatly facilitates minus strand DNA elongation and transfer while protecting the nucleic acids against nuclease degradation. To understand the role of NCp7 in viral DNA synthesis, we examined the influence of NCp7 on self-primed versus primer-specific reverse transcription. The results show that HIV-1 NCp7 can extensively inhibit self-primed reverse transcription of viral and cellular RNAs while promoting primer-specific synthesis of proviral DNA. The role of NCp7 vis-a-vis the presence of mutations in the viral DNA during minus strand elongation was examined. NCp7 maximized the annealing between a cDNA(-) primer containing one to five consecutive errors and an RNA representing the 3' end of the genome. The ability of reverse transcriptase (RT) in the presence of NCp7 to subsequently extend the mutated primers depended upon the position of the mismatch within the primer:template complex. When the mutations were at the polymerisation site, primer extension by RT in the presence of NCp7 was very high, about 40% for one mismatch and 3% for five consecutive mismatches. Mutations within the DNA primer or at its 5' end had little effect on the extension of viral DNA by RT. Taken together these results indicate that NCp7 plays major roles in proviral DNA synthesis within the virion core due to its ability to promote prime-specific proviral DNA synthesis while concurrently inhibiting non-specific reverse transcription of viral and cellular RNAs. Moreover, the observation that NCp7 enhances the incorporation of mutations during minus strand DNA elongation favours the notion that NCp7 is a factor contributing to the high mutation rate of HIV-1.

Loss of retrovirus production in JB/RH melanoma cells transfected with H-2Kb and TAP-1 genes.

PubMed

Li, M; Xu, F; Muller, J; Huang, X; Hearing, V J; Gorelik, E

1999-01-20

JB/RH1 melanoma cells, as well as other melanomas of C57BL/6 mice (B16 and JB/MS), express a common melanoma-associated antigen (MAA) encoded by an ecotropic melanoma-associated retrovirus (MelARV). JB/RH1 cells do not express the H-2Kb molecules due to down-regulation of the H-2Kb and TAP-1 genes. When JB/RH1 cells were transfected with the H-2Kb and cotransfected with the TAP-1 gene, it resulted in the appearance of H-2Kb molecules and an increase in their immunogenicity, albeit they lost expression of retrovirus-encoded MAA recognized by MM2-9B6 mAb. Loss of MAA was found to result from a complete and stable elimination of ecotropic MelARV production in the H-2Kb/TAP-1-transfected JB/RH1 cells. Northern blot analysis showed no differences in ecotropic retroviral messages in MelARV-producing and -nonproducing melanoma cells, suggesting that loss of MelARV production was not due to down-regulation of MelARV transcription. Southern blot analysis revealed several rearrangements in the proviral DNA of H-2Kb-positive JB/RH1 melanoma cells. Sequence analysis of the ecotropic proviral DNA from these cells showed numerous nucleotide substitutions, some of which resulted in the appearance of a novel intraviral PstI restriction site and the loss of a HindIII restriction site in the pol region. PCR amplification of the proviral DNAs indicates that an ecotropic provirus found in the H-2Kb-positive cells is novel and does not preexist in the parental H-2Kb-negative melanoma cells. Conversely, the ecotropic provirus of the parental JB/RH1 cells was not amplifable from the H-2Kb-positive cells. Our data indicate that stable loss of retroviral production in the H-2Kb/TAP-1-transfected melanoma cells is probably due to the induction of recombination between a productive ecotropic MelARV and a defective nonecotropic provirus leading to the generation of a defective ecotropic provirus and the loss of MelARV production and expression of the retrovirus-encoded MAA. Copyright 1999 Academic Press.

Endogenous avian leukosis viral loci in the Red Jungle Fowl genome assembly.

PubMed

Benkel, Bernhard; Rutherford, Katherine

2014-12-01

The current build (galGal4) of the genome of the ancestor of the modern chicken, the Red Jungle Fowl, contains a single endogenous avian leukosis viral element (ALVE) on chromosome 1 (designated RSV-LTR; family ERVK). The assembly shows the ALVE provirus juxtaposed with a member of a second family of avian endogenous retroviruses (designated GGERV20; family ERVL); however, the status of the 3' end of the ALVE element as well as its flanking region remain unclear due to a gap in the reference genome sequence. In this study, we filled the gap in the assembly using a combination of long-range PCR (LR-PCR) and a short contig present in the unassembled portion of the reference genome database. Our results demonstrate that the ALVE element (ALVE-JFevB) is inserted into the putative envelope region of a GGERV20 element, roughly 1 kbp from its 3' end, and that ALVE-JFevB is complete, and depending on its expression status, potentially capable of directing the production of virus. Moreover, the unassembled portion of the genome database contains junction fragments for a second, previously characterized endogenous proviral element, ALVE-6. ©2014 Poultry Science Association Inc.

Foamy Virus Vector Carries a Strong Insulator in Its Long Terminal Repeat Which Reduces Its Genotoxic Potential

PubMed Central

2017-01-01

ABSTRACT Strong viral enhancers in gammaretrovirus vectors have caused cellular proto-oncogene activation and leukemia, necessitating the use of cellular promoters in “enhancerless” self-inactivating integrating vectors. However, cellular promoters result in relatively low transgene expression, often leading to inadequate disease phenotype correction. Vectors derived from foamy virus, a nonpathogenic retrovirus, show higher preference for nongenic integrations than gammaretroviruses/lentiviruses and preferential integration near transcriptional start sites, like gammaretroviruses. We found that strong viral enhancers/promoters placed in foamy viral vectors caused extremely low immortalization of primary mouse hematopoietic stem/progenitor cells compared to analogous gammaretrovirus/lentivirus vectors carrying the same enhancers/promoters, an effect not explained solely by foamy virus' modest insertional site preference for nongenic regions compared to gammaretrovirus/lentivirus vectors. Using CRISPR/Cas9-mediated targeted insertion of analogous proviral sequences into the LMO2 gene and then measuring LMO2 expression, we demonstrate a sequence-specific effect of foamy virus, independent of insertional bias, contributing to reduced genotoxicity. We show that this effect is mediated by a 36-bp insulator located in the foamy virus long terminal repeat (LTR) that has high-affinity binding to the CCCTC-binding factor. Using our LMO2 activation assay, LMO2 expression was significantly increased when this insulator was removed from foamy virus and significantly reduced when the insulator was inserted into the lentiviral LTR. Our results elucidate a mechanism underlying the low genotoxicity of foamy virus, identify a novel insulator, and support the use of foamy virus as a vector for gene therapy, especially when strong enhancers/promoters are required. IMPORTANCE Understanding the genotoxic potential of viral vectors is important in designing safe and efficacious vectors for gene therapy. Self-inactivating vectors devoid of viral long-terminal-repeat enhancers have proven safe; however, transgene expression from cellular promoters is often insufficient for full phenotypic correction. Foamy virus is an attractive vector for gene therapy. We found foamy virus vectors to be remarkably less genotoxic, well below what was expected from their integration site preferences. We demonstrate that the foamy virus long terminal repeats contain an insulator element that binds CCCTC-binding factor and reduces its insertional genotoxicity. Our study elucidates a mechanism behind the low genotoxic potential of foamy virus, identifies a unique insulator, and supports the use of foamy virus as a vector for gene therapy. PMID:29046446

Stable integration of recombinant adeno-associated virus vector genomes after transduction of murine hematopoietic stem cells.

PubMed

Han, Zongchao; Zhong, Li; Maina, Njeri; Hu, Zhongbo; Li, Xiaomiao; Chouthai, Nitin S; Bischof, Daniela; Weigel-Van Aken, Kirsten A; Slayton, William B; Yoder, Mervin C; Srivastava, Arun

2008-03-01

We previously reported that among single-stranded adeno-associated virus (ssAAV) vectors, serotypes 1 through 5, ssAAV1 is the most efficient in transducing murine hematopoietic stem cells (HSCs), but viral second-strand DNA synthesis remains a rate-limiting step. Subsequently, using double-stranded, self-complementary AAV (scAAV) vectors, serotypes 7 through 10, we observed that scAAV7 vectors also transduce murine HSCs efficiently. In the present study, we used scAAV1 and scAAV7 shuttle vectors to transduce HSCs in a murine bone marrow serial transplant model in vivo, which allowed examination of the AAV proviral integration pattern in the mouse genome, as well as recovery and nucleotide sequence analyses of AAV-HSC DNA junction fragments. The proviral genomes were stably integrated, and integration sites were localized to different mouse chromosomes. None of the integration sites was found to be in a transcribed gene, or near a cellular oncogene. None of the animals, monitored for up to 1 year, exhibited pathological abnormalities. Thus, AAV proviral integration-induced risk of oncogenesis was not found in our study, which provides functional confirmation of stable transduction of self-renewing multipotential HSCs by scAAV vectors as well as promise for the use of these vectors in the potential treatment of disorders of the hematopoietic system.

Ultrasonic airborne insertion loss measurements at normal incidence (L).

PubMed

Farley, Jayrin; Anderson, Brian E

2010-12-01

Transmission loss and insertion loss measurements of building materials at audible frequencies are commonly made using plane wave tubes or as a panel between reverberant rooms. These measurements provide information for noise isolation control in architectural acoustics and in product development. Airborne ultrasonic sound transmission through common building materials has not been fully explored. Technologies and products that utilize ultrasonic frequencies are becoming increasingly more common, hence the need to conduct such measurements. This letter presents preliminary measurements of the ultrasonic insertion loss levels for common building materials over a frequency range of 28-90 kHz using continuous-wave excitation.

The site of antiviral action of 3-nitrosobenzamide on the infectivity process of human immunodeficiency virus in human lymphocytes.

PubMed Central

Rice, W G; Schaeffer, C A; Graham, L; Bu, M; McDougal, J S; Orloff, S L; Villinger, F; Young, M; Oroszlan, S; Fesen, M R

1993-01-01

The C-nitroso compound 3-nitrosobenzamide, which has been shown to remove zinc from the retroviral-type zinc finger of p7NC nucleocapsid proteins, inhibits acute infection of human immunodeficiency virus type 1 in cultured human lymphocytes. The attachment of the virus to lymphocytes and the activities of critical viral enzymes, such as reverse transcriptase, protease, and integrase, are not affected by 3-nitrosobenzamide. However, the process of reverse transcription to form proviral DNA is effectively abolished by the drug, identifying the mode of action of 3-nitrosobenzamide as interrupting the role of p7NC in accurate proviral DNA synthesis during the infectious phase of the virus life cycle. Images Fig. 3 Fig. 4 PMID:7692451

Comparative Efficacy of Feline Leukemia Virus (FeLV) Inactivated Whole-Virus Vaccine and Canarypox Virus-Vectored Vaccine during Virulent FeLV Challenge and Immunosuppression.

PubMed

Patel, M; Carritt, K; Lane, J; Jayappa, H; Stahl, M; Bourgeois, M

2015-07-01

Four vaccines for feline leukemia virus (FeLV) are available in the United States. This study's purpose was to compare the efficacy of Nobivac feline 2-FeLV (an inactivated, adjuvanted whole-virus vaccine) and PureVax recombinant FeLV (a live, canarypox virus-vectored vaccine) following FeLV challenge. Cats were vaccinated at 9 and 12 weeks with Nobivac feline 2-FeLV (group A, n = 11) or PureVax recombinant FeLV (group B, n = 10). Group C (n = 11) comprised unvaccinated controls. At 3 months postvaccination, cats were immunosuppressed and challenged with FeLV-A/61E. The outcomes measured were persistent antigenemia at 12 weeks postchallenge (PC) and proviral DNA and viral RNA at 3 to 9 weeks PC. Persistent antigenemia was observed in 0 of 11 cats in group A, 5 of 10 cats in group B, and 10 of 11 cats in group C. Group A was significantly protected compared to those in groups B (P < 0.013) and C (P < 0.0001). No difference was found between groups B and C (P > 0.063). The preventable fraction was 100% for group A and 45% for group B. At 9 weeks PC, proviral DNA and viral RNA were detected 1 of 11 cats in group A, 6 of 10 cats in group B, and 9 of 11 cats in group C. Nucleic acid loads were significantly lower in group A than in group C (P < 0.01). Group A had significantly lower proviral DNA loads than group B at weeks 6 to 9 (P < 0.02). The viral RNA loads were significantly lower in group A than in group B at weeks 7 to 9 (P < 0.01). The results demonstrate that Nobivac feline 2-FeLV-vaccinated cats were fully protected against persistent antigenemia and had significantly smaller amounts of proviral DNA and plasma viral RNA loads than PureVax recombinant FeLV-vaccinated cats and unvaccinated controls. Copyright © 2015, Patel et al.

2B4 expression on natural killer cells increases in HIV-1 infected patients followed prospectively during highly active antiretroviral therapy

PubMed Central

Ostrowski, S R; Ullum, H; Pedersen, B K; Gerstoft, J; Katzenstein, T L

2005-01-01

Human immunodeficiency virus (HIV)-1 infection influences natural killer (NK) cell expression of inhibitory NK receptors and activating natural cytotoxicity receptors. It is unknown whether expression of the co-stimulatory NK cell receptor 2B4 (CD244) on NK cells and CD3+ CD8+ cells are affected by highly active antiretroviral therapy (HAART), low-level viraemia, proviral-DNA or immune activation in HIV-1 infected patients. A total of 101 HAART-treated HIV-1 infected patients with ≤ 200 HIV-RNA copies/ml were followed prospectively for 24 months. HIV-RNA was investigated 3-monthly and 2B4 expression on CD3− CD16+ NK cells and CD3+ CD8+ cells, proviral-DNA and plasma soluble tumour necrosis factor receptor (sTNFr)-II were investigated 6-monthly. For comparison, 2B4 expression was investigated in 20 healthy individuals. The concentration of 2B4+ NK cells was initially reduced in HIV-1 infected patients (P < 0·001) but increased to a normal level during the 24 months’ follow-up. The concentration of CD3+ CD8+ 2B4+ cells in HIV-1 infected patients was normal and did not change during follow-up. The relative fluorescence intensity (RFI) of 2B4 increased on both NK cells and CD3+ CD8+ cells during follow-up (both P < 0·001). Higher levels of proviral-DNA carrying cells and plasma sTNFrII were associated with reductions in the concentration of 2B4+ NK cells (all P < 0·05). HIV-RNA had no effect on 2B4 expression on NK cells or CD3+ CD8+ cells. These findings demonstrate that the concentration of 2B4+ NK cells normalizes during long-term HAART in HIV-1 infected patients. The finding that proviral-DNA and sTNFrII were associated negatively with the concentration of 2B4+ NK cells suggests that immune activation in HIV-1 infected patients receiving HAART influences the target cell recognition by NK cells. PMID:16045743

2B4 expression on natural killer cells increases in HIV-1 infected patients followed prospectively during highly active antiretroviral therapy.

PubMed

Ostrowski, S R; Ullum, H; Pedersen, B K; Gerstoft, J; Katzenstein, T L

2005-09-01

Human immunodeficiency virus (HIV)-1 infection influences natural killer (NK) cell expression of inhibitory NK receptors and activating natural cytotoxicity receptors. It is unknown whether expression of the co-stimulatory NK cell receptor 2B4 (CD244) on NK cells and CD3+ CD8+ cells are affected by highly active antiretroviral therapy (HAART), low-level viraemia, proviral-DNA or immune activation in HIV-1 infected patients. A total of 101 HAART-treated HIV-1 infected patients with < or = 200 HIV-RNA copies/ml were followed prospectively for 24 months. HIV-RNA was investigated 3-monthly and 2B4 expression on CD3- CD16+ NK cells and CD3+ CD8+ cells, proviral-DNA and plasma soluble tumour necrosis factor receptor (sTNFr)-II were investigated 6-monthly. For comparison, 2B4 expression was investigated in 20 healthy individuals. The concentration of 2B4+ NK cells was initially reduced in HIV-1 infected patients (P < 0.001) but increased to a normal level during the 24 months' follow-up. The concentration of CD3+ CD8+ 2B4+ cells in HIV-1 infected patients was normal and did not change during follow-up. The relative fluorescence intensity (RFI) of 2B4 increased on both NK cells and CD3+ CD8+ cells during follow-up (both P < 0.001). Higher levels of proviral-DNA carrying cells and plasma sTNFrII were associated with reductions in the concentration of 2B4+ NK cells (all P < 0.05). HIV-RNA had no effect on 2B4 expression on NK cells or CD3+ CD8+ cells. These findings demonstrate that the concentration of 2B4+ NK cells normalizes during long-term HAART in HIV-1 infected patients. The finding that proviral-DNA and sTNFrII were associated negatively with the concentration of 2B4+ NK cells suggests that immune activation in HIV-1 infected patients receiving HAART influences the target cell recognition by NK cells.

Genotypic tropism testing of proviral DNA to guide maraviroc initiation in aviraemic subjects: 48-week analysis of results from the PROTEST study.

PubMed

Poveda, E; Hernández-Quero, J; Pérez-Elías, M J; Ribas, M A; Martínez-Madrid, O J; Flores, J; Navarro, J; Gutiérrez, F; García-Deltoro, M; Imaz, A; Ocampo, A; Artero, A; Blanco, F; Bernal, E; Pasquau, J; Mínguez-Gallego, C; Pérez, N; Aiestaran, A; García, F; Paredes, R

2017-08-01

Maraviroc (MVC) is a suitable drug for aviraemic subjects on antiretroviral treatment (ART) developing toxicity. Its prescription requires prior tropism testing. It is unknown if proviral DNA genotypic tropism testing is reliable for guiding MVC initiation in aviraemic subjects, so this study was carried out to address this issue. PROTEST was a phase 4, prospective, single-arm clinical trial carried out in 24 HIV care centres in Spain. MVC-naïve HIV-1-infected patients with HIV-1 RNA < 50 copies/mL on stable ART during the previous 6 months who required an ART change because of toxicity and who had R5 HIV, as determined by proviral DNA genotypic tropism testing, initiated MVC with two nucleoside reverse transcriptase inhibitors (NRTIs) and were followed for 48 weeks. Virological failure was defined as two consecutive viral load measurements > 50 copies/mL. Tropism results were available for 141 of 175 (80.6%) subjects screened: 60% had R5 and 85% of these (n = 74) were finally included in the study. Previous ART included protease inhibitors (PIs) in 62% of subjects, nonnucleoside reverse transcriptase inhibitors (NNRTIs) in 36%, and integrase inhibitors (INIs) in 2%. Main reasons for treatment change were dyslipidaemia (42%), gastrointestinal symptoms (22%) and liver toxicity (15%). MVC was given alongside tenofovir (TDF)/emtricitabine (FTC) (54%) and abacavir (ABC)/lamivudine (3TC) (40%) in most patients. Eighty-four per cent of patients maintained a viral load < 50 copies/mL to week 48, whereas 16% discontinued treatment: two withdrew informed consent, one had an R5 to X4 shift between screening and baseline, one was lost to follow-up, one developed an adverse event (rash), two died from non-study-related causes, and five developed protocol-defined virological failure. Initiation of MVC plus two NRTIs in aviraemic subjects based on genotypic tropism testing of proviral HIV-1 DNA is associated with low rates of virological failure for up to 1 year. © 2016 British HIV Association.

Analysis of HTLV-1 proviral load (PVL) and antibody detected with various kinds of tests in Japanese blood donors to understand the relationship between PVL and antibody level and to gain insights toward better antibody testing.

PubMed

Matsumoto, Chieko; Sagara, Yasuko; Sobata, Rieko; Inoue, Yukiko; Morita, Maiko; Uchida, Shigeharu; Kiyokawa, Hiroyuki; Satake, Masahiro; Tadokoro, Kenji

2017-08-01

Adult T-cell leukemia/lymphoma (ATL) occurs in approximately 5% of individuals infected with human T-cell leukemia virus type 1 (HTLV-1). A high proviral load (PVL; more than four copies per 100 peripheral blood mononuclear cells (PBMCs) or 1.6 copies per 100 blood leukocytes) and being male are risk factors for ATL development. Whether anti-HTLV-1 antibody level is related to such risk is unknown. Here, PVL and antibody levels were examined using real-time PCR and other tests in 600 HTLV-1 positive screened Japanese blood donors to understand the relationship between PVL and antibody level in asymptomatic carriers and to gain insights toward better antibody testing for HTLV-1 infection. The 430 donors in whom proviral DNA was detected were considered as true positives for HTLV-1 infection. Among donors aged 40 years or older, more males than females had a PVL corresponding to more than 1.6% infected leukocytes, and an antibody titer below the median (P = 0.0018). In antibody tests using an HTLV-1 positive cell line or Env antigens there was a large discrepancy in antibody titer among 13 provirus-positive samples, probably suggesting that antibody-based screening tests should incorporate multiple HTLV-1 antigens, such as Gag and Env antigens. © 2017 Wiley Periodicals, Inc.

Virological and immunological outcome of treatment interruption in HIV-1-infected subjects vaccinated with MVA-B

PubMed Central

Noguera-Julian, Marc; Bellido, Rocío; Puertas, Maria C.; Carrillo, Jorge; Rodriguez, C.; Perez-Alvarez, Núria; Cobarsí, Patricia; Gomez, Carmen E.; Esteban, Mariano; Jímenez, Jose Luis; García, Felipe; Blanco, Julià; Martinez-Picado, Javier; Paredes, Roger

2017-01-01

The most relevant endpoint in therapeutic HIV vaccination is the assessment of time to viral rebound or duration of sustained control of low-level viremia upon cART treatment cessation. Structured treatment interruptions (STI) are however not without risk to the patient and reliable predictors of viral rebound/control after therapeutic HIV-1 vaccination are urgently needed to ensure patient safety and guide therapeutic vaccine development. Here, we integrated immunological and virological parameters together with viral rebound dynamics after STI in a phase I therapeutic vaccine trial of a polyvalent MVA-B vaccine candidate to define predictors of viral control. Clinical parameters, proviral DNA, host HLA genetics and measures of humoral and cellular immunity were evaluated. A sieve effect analysis was conducted comparing pre-treatment viral sequences to breakthrough viruses after STI. Our results show that a reduced proviral HIV-1 DNA at study entry was independently associated with two virological parameters, delayed HIV-1 RNA rebound (p = 0.029) and lower peak viremia after treatment cessation (p = 0.019). Reduced peak viremia was also positively correlated with a decreased number of HLA class I allele associated polymorphisms in Gag sequences in the rebounding virus population (p = 0.012). Our findings suggest that proviral DNA levels and the number of HLA-associated Gag polymorphisms may have an impact on the clinical outcome of STI. Incorporation of these parameters in future therapeutic vaccine trials may guide refined immunogen design and help conduct safer STI approaches. PMID:28953921

Vaccination of rhesus macaques with a vif-deleted simian immunodeficiency virus proviral DNA vaccine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sparger, Ellen E.; Dubie, Robert A.; Shacklett, Barbara L.

2008-05-10

Studies in non-human primates, with simian immunodeficiency virus (SIV) and simian/human immunodeficiency virus (SHIV) have demonstrated that live-attenuated viral vaccines are highly effective; however these vaccine viruses maintain a low level of pathogenicity. Lentivirus attenuation associated with deletion of the viral vif gene carries a significantly reduced risk for pathogenicity, while retaining the potential for virus replication of low magnitude in the host. This report describes a vif-deleted simian immunodeficiency virus (SIV)mac239 provirus that was tested as an attenuated proviral DNA vaccine by inoculation of female rhesus macaques. SIV-specific interferon-{gamma} enzyme-linked immunospot responses of low magnitude were observed after immunizationmore » with plasmid containing the vif-deleted SIV provirus. However, vaccinated animals displayed strong sustained virus-specific T cell proliferative responses and increasing antiviral antibody titers. These immune responses suggested either persistent vaccine plasmid expression or low level replication of vif-deleted SIV in the host. Immunized and unvaccinated macaques received a single high dose vaginal challenge with pathogenic SIVmac251. A transient suppression of challenge virus load and a greater median survival time was observed for vaccinated animals. However, virus loads for vaccinated and unvaccinated macaques were comparable by twenty weeks after challenge and overall survival curves for the two groups were not significantly different. Thus, a vif-deleted SIVmac239 proviral DNA vaccine is immunogenic and capable of inducing a transient suppression of pathogenic challenge virus, despite severe attenuation of the vaccine virus.« less

Concealed Accessory Pathways with a Single Ventricular and Two Discrete Atrial Insertion Sites.

PubMed

Kipp, Ryan T; Abu Sham'a, Raed; Hiroyuki, Ito; Han, Frederick T; Refaat, Marwan; Hsu, Jonathan C; Field, Michael E; Kopp, Douglas E; Marcus, Gregory M; Scheinman, Melvin M; Hoffmayer, Kurt S

2017-03-01

Atrioventricular reciprocating tachycardia (AVRT) utilizing a concealed accessory pathway is common. It is well appreciated that some patients may have multiple accessory pathways with separate atrial and ventricular insertion sites. We present three cases of AVRT utilizing concealed pathways with evidence that each utilizing a single ventricular insertion and two discrete atrial insertion sites. In case one, two discrete atrial insertion sites were mapped in two separate procedures, and only during the second ablation was the Kent potential identified. Ablation of the Kent potential at this site remote from the two atrial insertion sites resulted in the termination of the retrograde conduction in both pathways. Case two presented with supraventricular tachycardia (SVT) with alternating eccentric atrial activation patterns without alteration in the tachycardia cycle length. The two distinct atrial insertion sites during orthodromic AVRT and ventricular pacing were targeted and each of the two atrial insertion sites were successfully mapped and ablated. In case three, retrograde decremental conduction utilizing both atrial insertion sites was identified prior to ablation. After mapping and ablation of the first discrete atrial insertion site, tachycardia persisted utilizing the second atrial insertion site. Only after ablation of the second atrial insertion site was SVT noninducible, and VA conduction was no longer present. Concealed retrograde accessory pathways with discrete atrial insertion sites may have a common ventricular insertion site. Identification and ablation of the ventricular insertion site or the separate discrete atrial insertion sites result in successful treatment. © 2017 Wiley Periodicals, Inc.

Landscape of Insertion Polymorphisms in the Human Genome

PubMed Central

Onozawa, Masahiro; Goldberg, Liat; Aplan, Peter D.

2015-01-01

Nucleotide substitutions, small (<50 bp) insertions or deletions (indels), and large (>50 bp) deletions are well-known causes of genetic variation within the human genome. We recently reported a previously unrecognized form of polymorphic insertions, termed templated sequence insertion polymorphism (TSIP), in which the inserted sequence was templated from a distant genomic region, and was inserted in the genome through reverse transcription of an RNA intermediate. TSIPs can be grouped into two classes based on nucleotide sequence features at the insertion junctions; class 1 TSIPs show target site duplication, polyadenylation, and preference for insertion at a 5′-TTTT/A-3′ sequence, suggesting a LINE-1 based insertion mechanism, whereas class 2 TSIPs show features consistent with repair of a DNA double strand break by nonhomologous end joining. To gain a more complete picture of TSIPs throughout the human population, we evaluated whole-genome sequence from 52 individuals, and identified 171 TSIPs. Most individuals had 25–30 TSIPs, and common (present in >20% of individuals) TSIPs were found in individuals throughout the world, whereas rare TSIPs tended to cluster in specific geographic regions. The number of rare TSIPs was greater than the number of common TSIPs, suggesting that TSIP generation is an ongoing process. Intriguingly, mitochondrial sequences were a frequent template for class 2 insertions, used more commonly than any nuclear chromosome. Similar to single nucleotide polymorphisms and indels, we suspect that these TSIPs may be important for the generation of human diversity and genetic diseases, and can be useful in tracking historical migration of populations. PMID:25745018

Exposure of cats to low doses of FeLV: seroconversion as the sole parameter of infection

PubMed Central

Major, Andrea; Cattori, Valentino; Boenzli, Eva; Riond, Barbara; Ossent, Peter; Meli, Marina Luisa; Hofmann-Lehmann, Regina; Lutz, Hans

2009-01-01

In felids, feline leukemia virus (FeLV) infection results in a variety of outcomes that range from abortive (virus readily eliminated and never detectable) to progressive infection (persistent viremia and viral shedding). Recently, a novel outcome was postulated for low FeLV infectious doses. Naïve cats exposed to faeces of persistently infected cats seroconverted, indicating infection, but remained negative for provirus and p27 antigen in blood. FeLV provirus was found in some tissues but not in the bone marrow, infection of which is usually considered a necessary stage for disease progression. To investigate the impact of low FeLV doses on young cats and to test the hypothesis that low dose exposure may lead to an unknown pathogenesis of infection without involvement of the bone marrow, 21 cats were infected oronasally with variable viral doses. Blood p27, proviral and viral loads were followed until week 20 post-infection. Tissue proviral loads were determined as well. The immune response was monitored by measuring FeLV whole virus and p45 antibodies; and feline oncornavirus-associated cell membrane antigen (FOCMA) assay. One cat showed regressive infection (transient antigenemia, persistent provirus-positivity, and seroconversion) with provirus only found in some organs at sacrifice. In 7 of the 20 remaining cats FOCMA assay positivity was the only sign of infection, while all other tests were negative. Overall, the results show that FeLV low dose exposure can result in seroconversion during a presumed abortive infection. Therefore, commonly used detection methods do not detect all FeLV-infected animals, possibly leading to an underestimation of the prevalence of infection. PMID:19861115

Concise classification of the genomic porcine endogenous retroviral gamma1 load to defined lineages.

PubMed

Klymiuk, Nikolai; Wolf, Eckhard; Aigner, Bernhard

2008-02-05

We investigated the infection history of porcine endogenous retroviruses (PERV) gamma1 by analyzing published env and LTR sequences. PERV sequences from various breeds, porcine cell lines and infected human primary cells were included in the study. We identified a considerable number of retroviral lineages indicating multiple independent colonization events of the porcine genome. A recent boost of the proviral load in an isolated pig herd and exclusive occurrence of distinct lineages in single studies indicated the ongoing colonization of the porcine genome with endogenous retroviruses. Retroviral recombination between co-packaged genomes was a general factor for PERV gamma1 diversity which indicated the simultaneous expression of different proviral loci over a period of time. In total, our detailed description of endogenous retroviral lineages is the prerequisite for breeding approaches to minimize the infectious potential of porcine tissues for the subsequent use in xenotransplantation.

In Vivo Hypermutation of Xenotropic Murine Leukemia Virus-Related Virus DNA in Peripheral Blood Mononuclear Cells of Rhesus Macaque by APOBEC3 Proteins

PubMed Central

Zhang, Ao; Bogerd, Hal; Villinger, Francois; Gupta, Jaydip Das; Dong, Beihua; Klein, Eric A.; Hackett, John; Schochetman, Gerald; Cullen, Bryan R.; Silverman, Robert H.

2011-01-01

The gammaretrovirus, xenotropic murine leukemia virus-related virus (XMRV), replicates to high titers in some human cell lines and is able to infect non-human primates. To determine whether APOBEC3 (A3) proteins restrict XMRV infections in a non-human primate model, we sequenced proviral DNA from peripheral blood mononuclear cells of XMRV-infected rhesus macaques. Hypermutation characteristic of A3DE, A3F and A3G activities was observed in the XMRV proviral sequences in vivo. Furthermore, expression of rhesus A3DE, A3F, or A3G in human cells inhibited XMRV infection and caused hypermutation of XMRV DNA. These studies show that some rhesus A3 isoforms are highly effective against XMRV in the blood of a non-human primate model of infection and in cultured human cells. PMID:21982221

ATM facilitates mouse gammaherpesvirus reactivation from myeloid cells during chronic infection

PubMed Central

Kulinski, Joseph M.; Darrah, Eric J.; Broniowska, Katarzyna A.; Mboko, Wadzanai P.; Mounce, Bryan C.; Malherbe, Laurent P.; Corbett, John A; Gauld, Stephen B.; Tarakanova, Vera L.

2015-01-01

Gammaherpesviruses are cancer-associated pathogens that establish life-long infection in most adults. Insufficiency of Ataxia-Telangiectasia mutated (ATM) kinase leads to a poor control of chronic gammaherpesvirus infection via an unknown mechanism that likely involves a suboptimal antiviral response. In contrast to the phenotype in the intact host, ATM facilitates gammaherpesvirus reactivation and replication in vitro. We hypothesized that ATM mediates both pro- and antiviral activities to regulate chronic gammaherpesvirus infection in an immunocompetent host. To test the proposed proviral activity of ATM in vivo, we generated mice with ATM deficiency limited to myeloid cells. Myeloid-specific ATM deficiency attenuated gammaherpesvirus infection during the establishment of viral latency. The results of our study uncover a proviral role of ATM in the context of gammaherpesvirus infection in vivo and support a model where ATM combines pro- and antiviral functions to facilitate both gammaherpesvirus-specific T cell immune response and viral reactivation in vivo. PMID:26001649

Evaluation of the hybrid-L24 electrode using microcomputed tomography.

PubMed

Driscoll, Colin L W; Carlson, Matthew L; Fama, Anthony F; Lane, John I

2011-07-01

To compare electrode array position, and depth of insertion of the Cochlear Hybrid-L24 electrode array following traditional cochleostomy and round window (RW) insertion. Prospective cadaveric temporal bone study. Ten cadaveric temporal bones were implanted with the Hybrid-L24 electrode array; half were introduced through a RW approach, whereas the other half were inserted through a traditional scala tympani cochleostomy. A micro-CT scanner was then used to evaluate electrode position, intracochlear trauma, and depth of insertion. All electrodes were inserted into the scala tympani without significant resistance. No electrodes demonstrated tip fold-over or through-fracturing of the osseous spiral lamina, basilar membrane, or spiral ligament. The average angular depth of insertion for all 10 electrodes was 252.4°. Compared to cochleostomy insertions, electrodes inserted through the RW more commonly acquired a proximal perimodiolar orientation, followed a more predictable course, and less commonly contacted critical soft tissue structures. The results of this study demonstrate that the Hybrid-L24 electrode can be successfully inserted using a RW or traditional cochleostomy technique with minimal intracochlear trauma. Our data also suggests that with this model, RW insertions may provide particular advantages with respect to hearing preservation over the traditional cochleostomy approach. Copyright © 2011 The American Laryngological, Rhinological, and Otological Society, Inc.

Delayed seroconversion and rapid onset of lymphoproliferative disease after transmission of human T-cell lymphotropic virus type 1 from a multiorgan donor.

PubMed

Glowacka, Ilona; Korn, Klaus; Potthoff, Sebastian A; Lehmann, Ulrich; Kreipe, Hans H; Ivens, Katrin; Barg-Hock, Hannelore; Schulz, Thomas F; Heim, Albert

2013-11-01

Human T-cell lymphotropic virus type 1 (HTLV-1) screening of blood and organ donors is not mandatory in Germany because of its low prevalence (about 7/100 000). An HTLV-1 transmission event caused by a multiple organ donor was investigated. Validity of diagnostic procedures and HTLV-1 disease association in immunosuppressed organ recipients were analyzed. Two screening immunoassays and an immunoblot (confirmatory assay) were used for detection of HLTV-1/2 antibodies. Proviral DNA was quantified in blood and biopsies of organ recipients by HTLV-1 real-time polymerase chain reaction (PCR). Proviral HTLV-1-DNA was detected in all blood samples of 3 organ recipients (1-100 copies/10(2) cells), but seroconversion was delayed for up to 2 years in screening assays and >6 years in the confirmatory assay. In 2 of 3 organ recipients, a cutaneous T-cell lymphoma was diagnosed 2 and 3 years after infection, respectively. Proviral HTLV-1 DNA concentration was almost 100 copies/10(2) cells in cutaneous lymphoma biopsies whereas in biopsies of other tissues ≤3.0 copies/10(2) cells were found. The third organ recipient did not suffer from lymphoma, but detailed clinical data on this patient were not available to us. Biopsy results support an etiological role for HTLV-1 in these cases of primary cutaneous T-cell lymphoma after solid organ transplant. HTLV-1-associated lymphoma can arise quickly in immunocompromised transplant recipients. The diagnosis of potentially HTLV-1-associated disease in organ recipients may require PCR because of delayed seroconversion.

Number and location of mouse mammary tumor virus proviral DNA in mouse DNA of normal tissue and of mammary tumors.

PubMed Central

Groner, B; Hynes, N E

1980-01-01

The Southern DNA filter transfer technique was used to characterize the genomic location of the mouse mammary tumor proviral DNA in different inbred strains of mice. Two of the strains (C3H and CBA) arose from a cross of a Bagg albino (BALB/c) mouse and a DBA mouse. The mouse mammary tumor virus-containing restriction enzyme DNA fragments of these strains had similar patterns, suggesting that the proviruses of these mice are in similar genomic locations. Conversely, the pattern arising from the DNA of the GR mouse, a strain genetically unrelated to the others, appeared different, suggesting that its mouse mammary tumor proviruses are located in different genomic sites. The structure of another gene, that coding for beta-globin, was also compared. The mice strains which we studied can be categorized into two classes, expressing either one or two beta-globin proteins. The macroenvironment of the beta-globin gene appeared similar among the mice strains belonging to one genetic class. Female mice of the C3H strain exogenously transmit mouse mammary tumor virus via the milk, and their offspring have a high incidence of mammary tumor occurrence. DNA isolated from individual mammary tumors taken from C3H mice or from BALB/c mice foster nursed on C3H mothers was analyzed by the DNA filter transfer technique. Additional mouse mammary tumor virus-containing fragments were found in the DNA isolated from each mammary tumor. These proviral sequences were integrated into different genomic sites in each tumor. Images PMID:6245257

Proviral Features of Human T Cell Leukemia Virus Type 1 in Carriers with Indeterminate Western Blot Analysis Results

PubMed Central

Sekizuka, Tsuyoshi; Yamochi, Tadanori; Firouzi, Sanaz; Sato, Tomoo; Umeki, Kazumi; Sasaki, Daisuke; Hasegawa, Hiroo; Kubota, Ryuji; Sobata, Rieko; Matsumoto, Chieko; Kaneko, Noriaki; Momose, Haruka; Araki, Kumiko; Saito, Masumichi; Nosaka, Kisato; Utsunomiya, Atae; Koh, Ki-Ryang; Ogata, Masao; Uchimaru, Kaoru; Iwanaga, Masako; Sagara, Yasuko; Yamano, Yoshihisa; Okayama, Akihiko; Miura, Kiyonori; Satake, Masahiro; Saito, Shigeru; Itabashi, Kazuo; Yamaguchi, Kazunari; Kuroda, Makoto; Watanabe, Toshiki; Okuma, Kazu

2017-01-01

ABSTRACT Western blotting (WB) for human T cell leukemia virus type 1 (HTLV-1) is performed to confirm anti-HTLV-1 antibodies detected at the initial screening of blood donors and in pregnant women. However, the frequent occurrence of indeterminate results is a problem with this test. We therefore assessed the cause of indeterminate WB results by analyzing HTLV-1 provirus genomic sequences. A quantitative PCR assay measuring HTLV-1 provirus in WB-indeterminate samples revealed that the median proviral load was approximately 100-fold lower than that of WB-positive samples (0.01 versus 0.71 copy/100 cells). Phylogenic analysis of the complete HTLV-1 genomes of WB-indeterminate samples did not identify any specific phylogenetic groups. When we analyzed the nucleotide changes in 19 HTLV-1 isolates from WB-indeterminate samples, we identified 135 single nucleotide substitutions, composed of four types, G to A (29%), C to T (19%), T to C (19%), and A to G (16%). In the most frequent G-to-A substitution, 64% occurred at GG dinucleotides, indicating that APOBEC3G is responsible for mutagenesis in WB-indeterminate samples. Moreover, interestingly, five WB-indeterminate isolates had nonsense mutations in Pol and/or Tax, Env, p12, and p30. These findings suggest that WB-indeterminate carriers have low production of viral antigens because of a combination of a low proviral load and mutations in the provirus, which may interfere with host recognition of HTLV-1 antigens. PMID:28701419

Proviral Features of Human T Cell Leukemia Virus Type 1 in Carriers with Indeterminate Western Blot Analysis Results.

PubMed

Kuramitsu, Madoka; Sekizuka, Tsuyoshi; Yamochi, Tadanori; Firouzi, Sanaz; Sato, Tomoo; Umeki, Kazumi; Sasaki, Daisuke; Hasegawa, Hiroo; Kubota, Ryuji; Sobata, Rieko; Matsumoto, Chieko; Kaneko, Noriaki; Momose, Haruka; Araki, Kumiko; Saito, Masumichi; Nosaka, Kisato; Utsunomiya, Atae; Koh, Ki-Ryang; Ogata, Masao; Uchimaru, Kaoru; Iwanaga, Masako; Sagara, Yasuko; Yamano, Yoshihisa; Okayama, Akihiko; Miura, Kiyonori; Satake, Masahiro; Saito, Shigeru; Itabashi, Kazuo; Yamaguchi, Kazunari; Kuroda, Makoto; Watanabe, Toshiki; Okuma, Kazu; Hamaguchi, Isao

2017-09-01

Western blotting (WB) for human T cell leukemia virus type 1 (HTLV-1) is performed to confirm anti-HTLV-1 antibodies detected at the initial screening of blood donors and in pregnant women. However, the frequent occurrence of indeterminate results is a problem with this test. We therefore assessed the cause of indeterminate WB results by analyzing HTLV-1 provirus genomic sequences. A quantitative PCR assay measuring HTLV-1 provirus in WB-indeterminate samples revealed that the median proviral load was approximately 100-fold lower than that of WB-positive samples (0.01 versus 0.71 copy/100 cells). Phylogenic analysis of the complete HTLV-1 genomes of WB-indeterminate samples did not identify any specific phylogenetic groups. When we analyzed the nucleotide changes in 19 HTLV-1 isolates from WB-indeterminate samples, we identified 135 single nucleotide substitutions, composed of four types, G to A (29%), C to T (19%), T to C (19%), and A to G (16%). In the most frequent G-to-A substitution, 64% occurred at GG dinucleotides, indicating that APOBEC3G is responsible for mutagenesis in WB-indeterminate samples. Moreover, interestingly, five WB-indeterminate isolates had nonsense mutations in Pol and/or Tax, Env, p12, and p30. These findings suggest that WB-indeterminate carriers have low production of viral antigens because of a combination of a low proviral load and mutations in the provirus, which may interfere with host recognition of HTLV-1 antigens. Copyright © 2017 American Society for Microbiology.

Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART.

PubMed

Wiegand, Ann; Spindler, Jonathan; Hong, Feiyu F; Shao, Wei; Cyktor, Joshua C; Cillo, Anthony R; Halvas, Elias K; Coffin, John M; Mellors, John W; Kearney, Mary F

2017-05-02

Little is known about the fraction of human immunodeficiency virus type 1 (HIV-1) proviruses that express unspliced viral RNA in vivo or about the levels of HIV RNA expression within single infected cells. We developed a sensitive cell-associated HIV RNA and DNA single-genome sequencing (CARD-SGS) method to investigate fractional proviral expression of HIV RNA (1.3-kb fragment of p6, protease, and reverse transcriptase) and the levels of HIV RNA in single HIV-infected cells from blood samples obtained from individuals with viremia or individuals on long-term suppressive antiretroviral therapy (ART). Spiking experiments show that the CARD-SGS method can detect a single cell expressing HIV RNA. Applying CARD-SGS to blood mononuclear cells in six samples from four HIV-infected donors (one with viremia and not on ART and three with viremia suppressed on ART) revealed that an average of 7% of proviruses (range: 2-18%) expressed HIV RNA. Levels of expression varied from one to 62 HIV RNA molecules per cell (median of 1). CARD-SGS also revealed the frequent expression of identical HIV RNA sequences across multiple single cells and across multiple time points in donors on suppressive ART consistent with constitutive expression of HIV RNA in infected cell clones. Defective proviruses were found to express HIV RNA at levels similar to those proviruses that had no obvious defects. CARD-SGS is a useful tool to characterize fractional proviral expression in single infected cells that persist despite ART and to assess the impact of experimental interventions on proviral populations and their expression.

Rapid, Point-of-Care Extraction of Human Immunodeficiency Virus Type 1 Proviral DNA from Whole Blood for Detection by Real-Time PCR ▿

PubMed Central

Jangam, Sujit R.; Yamada, Douglas H.; McFall, Sally M.; Kelso, David M.

2009-01-01

PCR detection of human immunodeficiency virus type 1 (HIV-1) proviral DNA is the method recommended for use for the diagnosis of HIV-1 infection in infants in limited-resource settings. Currently, testing must be performed in central laboratories, which are usually located some distance from health care facilities. While the collection and transportation of samples, such as dried blood spots, has improved test accessibility, the results are often not returned for several weeks. To enable PCR to be performed at the point of care while the mothers wait, we have developed a vertical filtration method that uses a separation membrane and an absorbent pad to extract cellular DNA from whole blood in less than 2 min. Cells are trapped in the separation membrane as the specimen is collected, and then a lysis buffer is added. The membrane retains the DNA, while the buffer washes away PCR inhibitors, which get wicked into the absorbent blotter pad. The membrane containing the entrapped DNA is then added to the PCR mixture without further purification. The method demonstrates a high degree of reproducibility and analytical sensitivity and allows the quantification of as few as 20 copies of HIV-1 proviral DNA from 100 μl of blood. In a blinded study with 182 longitudinal samples from infants (ages, 0 to 72 weeks) obtained from the Women and Infants Transmission Study, our assay demonstrated a sensitivity of 99% and a specificity of 100%. PMID:19644129

Retroviral DNA--the silent winner: blood transfusion containing latent feline leukemia provirus causes infection and disease in naïve recipient cats.

PubMed

Nesina, Stefanie; Katrin Helfer-Hungerbuehler, A; Riond, Barbara; Boretti, Felicitas S; Willi, Barbara; Meli, Marina L; Grest, Paula; Hofmann-Lehmann, Regina

2015-12-21

The feline leukemia virus (FeLV) is a gamma-retrovirus of domestic cats that was discovered half a century ago. Cats that are infected with FeLV may develop a progressive infection resulting in persistent viremia, immunodeficiency, tumors, anemia and death. A significant number of cats mount a protective immune response that suppresses viremia; these cats develop a regressive infection characterized by the absence of viral replication and the presence of low levels of proviral DNA. The biological importance of these latter provirus carriers is largely unknown. Here, we demonstrate that ten cats that received a transfusion of blood from aviremic provirus carriers developed active FeLV infections, some with a progressive outcome and the development of fatal FeLV-associated disease. The infection outcome, disease spectrum and evolution into FeLV-C in one cat mirrored those of natural infection. Two cats developed persistent antigenemia; six cats were transiently antigenemic. Reactivation of infection occurred in some cats. One recipient developed non-regenerative anemia associated with FeLV-C, and four others developed a T-cell lymphoma, one with secondary lymphoblastic leukemia. Five of the ten recipient cats received provirus-positive aviremic blood, whereas the other five received provirus- and viral RNA-positive but aviremic blood. Notably, the cats that received blood containing only proviral DNA exhibited a later onset but graver outcome of FeLV infection than the cats that were transfused with blood containing proviral DNA and viral RNA. Leukocyte counts and cytokine analyses indicated that the immune system of the latter cats reacted quicker and more efficiently. Our results underline the biological and epidemiological relevance of FeLV provirus carriers and the risk of inadvertent FeLV transmission via blood transfusion and demonstrate the replication capacity of proviral DNA if uncontrolled by the immune system. Our results have implications not only for veterinary medicine, such as the requirement for testing blood donors and blood products for FeLV provirus by sensitive polymerase chain reaction, but are also of general interest by revealing the importance of latent retroviral DNA in infected hosts. When aiming to eliminate a retroviral infection from a population, provirus carriers must be considered.

RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences

PubMed Central

Sperber, Göran; Lövgren, Anders; Eriksson, Nils-Einar; Benachenhou, Farid; Blomberg, Jonas

2009-01-01

Background The rapid accumulation of genomic information in databases necessitates rapid and specific algorithms for extracting biologically meaningful information. More or less complete retroviral sequences, also called proviral or endogenous retroviral sequences; ERVs, constitutes at least 5% of vertebrate genomes. After infecting the host, these retroviruses have integrated in germ line cells, and have then been carried in genomes for at least several 100 million years. A better understanding of structure and function of these sequences can have profound biological and medical consequences. Methods RetroTector© (ReTe) is a platform-independent Java program for identification and characterization of proviral sequences in vertebrate genomes. The full ReTe requires a local installation with a MySQL database. Although not overly complicated, the installation may take some time. A "light" version of ReTe, (RetroTector online; ROL) which does not require specific installation procedures is provided, via the World Wide Web. Results ROL was implemented under the Batchelor web interface (A Lövgren et al). It allows both GenBank accession number, file and FASTA cut-and-paste admission of sequences (5 to 10 000 kilobases). Up to ten submissions can be done simultaneously, allowing batch analysis of <= 100 Megabases. Jobs are shown in an IP-number specific list. Results are text files, and can be viewed with the program, RetroTectorViewer.jar (at the same site), which has the full graphical capabilities of the basic ReTe program. A detailed analysis of any retroviral sequences found in the submitted sequence is graphically presented, exportable in standard formats. With the current server, a complete analysis of a 1 Megabase sequence is complete in 10 minutes. It is possible to mask nonretroviral repetitive sequences in the submitted sequence, using host genome specific "brooms", which increase specificity. Discussion Proviral sequences can be hard to recognize, especially if the integration occurred many million years ago. Precise delineation of LTR, gag, pro, pol and env can be difficult, requiring manual work. ROL is a way of simplifying these tasks. Conclusion ROL provides 1. annotation and presentation of known retroviral sequences, 2. detection of proviral chains in unknown genomic sequences, with up to 100 Mbase per submission. PMID:19534753

RetroTector online, a rational tool for analysis of retroviral elements in small and medium size vertebrate genomic sequences.

PubMed

Sperber, Göran; Lövgren, Anders; Eriksson, Nils-Einar; Benachenhou, Farid; Blomberg, Jonas

2009-06-16

The rapid accumulation of genomic information in databases necessitates rapid and specific algorithms for extracting biologically meaningful information. More or less complete retroviral sequences, also called proviral or endogenous retroviral sequences; ERVs, constitutes at least 5% of vertebrate genomes. After infecting the host, these retroviruses have integrated in germ line cells, and have then been carried in genomes for at least several 100 million years. A better understanding of structure and function of these sequences can have profound biological and medical consequences. RetroTector (ReTe) is a platform-independent Java program for identification and characterization of proviral sequences in vertebrate genomes. The full ReTe requires a local installation with a MySQL database. Although not overly complicated, the installation may take some time. A "light" version of ReTe, (RetroTector online; ROL) which does not require specific installation procedures is provided, via the World Wide Web. ROL http://www.fysiologi.neuro.uu.se/jbgs/ was implemented under the Batchelor web interface (A Lövgren et al). It allows both GenBank accession number, file and FASTA cut-and-paste admission of sequences (5 to 10,000 kilobases). Up to ten submissions can be done simultaneously, allowing batch analysis of

Human T-cell lymphotropic virus type 1 subtype C molecular variants among indigenous australians: new insights into the molecular epidemiology of HTLV-1 in Australo-Melanesia.

PubMed

Cassar, Olivier; Einsiedel, Lloyd; Afonso, Philippe V; Gessain, Antoine

2013-01-01

HTLV-1 infection is endemic among people of Melanesian descent in Papua New Guinea, the Solomon Islands and Vanuatu. Molecular studies reveal that these Melanesian strains belong to the highly divergent HTLV-1c subtype. In Australia, HTLV-1 is also endemic among the Indigenous people of central Australia; however, the molecular epidemiology of HTLV-1 infection in this population remains poorly documented. Studying a series of 23 HTLV-1 strains from Indigenous residents of central Australia, we analyzed coding (gag, pol, env, tax) and non-coding (LTR) genomic proviral regions. Four complete HTLV-1 proviral sequences were also characterized. Phylogenetic analyses implemented with both Neighbor-Joining and Maximum Likelihood methods revealed that all proviral strains belong to the HTLV-1c subtype with a high genetic diversity, which varied with the geographic origin of the infected individuals. Two distinct Australians clades were found, the first including strains derived from most patients whose origins are in the North, and the second comprising a majority of those from the South of central Australia. Time divergence estimation suggests that the speciation of these two Australian clades probably occurred 9,120 years ago (38,000-4,500). The HTLV-1c subtype is endemic to central Australia where the Indigenous population is infected with diverse subtype c variants. At least two Australian clades exist, which cluster according to the geographic origin of the human hosts. These molecular variants are probably of very ancient origin. Further studies could provide new insights into the evolution and modes of dissemination of these retrovirus variants and the associated ancient migration events through which early human settlement of Australia and Melanesia was achieved.

New insights into prevalence, genetic diversity, and proviral load of human T-cell leukemia virus types 1 and 2 in pregnant women in Gabon in equatorial central Africa.

PubMed

Etenna, Sonia Lekana-Douki; Caron, Mélanie; Besson, Guillaume; Makuwa, Maria; Gessain, Antoine; Mahé, Antoine; Kazanji, Mirdad

2008-11-01

Human T-cell leukemia virus type 1 (HTLV-1) is highly endemic in areas of central Africa; mother-to-child transmission and sexual transmission are considered to be the predominant routes. To determine the prevalence and subtypes of HTLV-1/2 in pregnant women in Gabon, we conducted an epidemiological survey in the five main cities of the country. In 907 samples, the HTLV-1 seroprevalence was 2.1%, which is lower than that previously reported. Only one case of HTLV-2 infection was found. The HTLV-1 seroprevalence increased with age and differed between regions (P

Telomere Length, Proviral Load and Neurologic Impairment in HTLV-1 and HTLV-2-Infected Subjects.

PubMed

Usadi, Benjamin; Bruhn, Roberta; Lin, Jue; Lee, Tzong-Hae; Blackburn, Elizabeth; Murphy, Edward L

2016-08-11

Short or damaged telomeres have been implicated in degenerative conditions. We hypothesized that analysis of telomere length (TL) in human T-cell lymphotropic virus (HTLV) infection and HTLV-associated neuropathy might provide clues to the etiology of HTLV-associated disease and viral dynamics. A subset of 45 human T-cell lymphotropic virus type 1 (HTLV-1), 45 human T-cell lymphotropic virus type 2 (HTLV-2), and 45 seronegative subjects was selected from the larger HTLV Outcomes Study (HOST) cohort, matched on age, sex and race/ethnicity. Telomere-to-single-copy gene (T/S) ratio (a measure of TL) and HTLV-1 and HTLV-2 proviral loads were measured in peripheral blood mononuclear cells (PBMCs) using quantitative PCR (qPCR). Vibration sensation measured by tuning fork during neurologic examinations performed as part of the HOST study allowed for an assessment of peripheral neuropathy. TL was compared between groups using t-tests, linear and logistic regression. Mean T/S ratio was 1.02 ± 0.16 in HTLV-1, 1.03 ± 0.17 in HTLV-2 and 0.99 ± 0.18 in HTLV seronegative subjects (p = 0.322). TL was not associated with HTLV-1 or -2 proviral load. Shorter TL was significantly associated with impaired vibration sense in the HTLV-2 positive group only. Overall, we found no evidence that telomere length was affected by chronic HTLV-1 and HTLV-2 infection. That TL was only associated with peripheral neuropathy in the HTLV-2-positive group is intriguing, but should be interpreted cautiously. Studies with larger sample size and telomere length measurement in lymphocyte subsets may clarify the relationship between TL and HTLV-infection.

Screening for prolonged incubation of HTLV-I infection in British and Jamaican relatives of British patients with tropical spastic paraparesis.

PubMed Central

Cruickshank, J K; Richardson, J H; Morgan, O S; Porter, J; Klenerman, P; Knight, J; Newell, A L; Rudge, P; Dalgleish, A G

1990-01-01

OBJECTIVE--To compare the prevalence of antibody to and proviral DNA of the retrovirus HTLV-I in relatives of 11 British patients with tropical spastic paraparesis who had migrated from Jamaica before they developed symptoms, and to examine factors possibly related to transmission of HTLV-I. DESIGN--Migrant, family study. Antibody state was determined by several methods and confirmed by western blotting; the polymerase chain reaction was used to detect proviral DNA. SETTING--Britain and Jamaica. SUBJECTS--All available first degree relatives: those born and still resident in Jamaica (group 1); those born in Jamaica who migrated to Britain (group 2); and index patients' children who were born and resident in Britain (group 3). All had been breast fed and none had had blood transfusions. RESULTS--Of the 66 living relatives, 60 were traced. Seroprevalence among those born in Jamaica (irrespective of current residence) was 22% (10/46; 95% confidence limits 9 to 34%) compared with zero among British born offspring (0/14) and was higher in group 2 at 33% (7/21; 12 to 55%) than in group 1 at 12% (3/25; 0 to 25%). (Patients in group 1 had the greatest mean age.) Proviral DNA was not detected in any subject negative for HTLV-I antibody, making prolonged viral incubation in those negative for the antibody unlikely. CONCLUSION--In this sample factors related to place of birth and early residence were more important in transmission of HTLV-I than maternal or age effects. In areas with a low to moderate prevalence policies of preventing mothers who are carriers of the virus from breast feeding would be premature. PMID:2106960

HTLV-1 proviral load in cerebrospinal fluid may not be a good marker to differentiate asymptomatic carriers with high proviral load in blood from HAM/TSP patients.

PubMed

Martins, Marina Lobato; de Freitas Carneiro-Proietti, Anna Bárbara; Nicolato, Rodrigo; de Miranda, Débora Marques; Romanelli, Luiz Cláudio Ferreira

2018-03-27

An elevated human T cell leukemia virus type 1 (HTLV-1) proviral load (PVL) is an important risk factor for HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), although there is a considerable frequency of asymptomatic carriers (AC) with high PVL in blood. Our objective was to evaluate whether PVL quantified in cerebrospinal fluid (CSF) is helpful to distinguish AC from HAM when AC have high PVL in blood (AC H ). AC H (n = 7) were characterized to have high PVL in blood by quantification of samples collected over time (mean 7 years). HAM patients (n = 14) also had analyzed blood samples collected at different times (mean 9 years). Comparing paired CSF and blood samples of each individual, CSF PVL mean was 4.7-fold higher than blood PVL in the AC H group and 10.8-fold in the HAM group. CSF PVL was significantly greater than blood PVL in the HAM group (p = 0.004), but not in the AC H group. Important to highlight, CSF PVL was not significantly different between the AC H and the HAM groups. These results suggested that significantly higher PVL in CSF than in blood is a hallmark of HAM/TSP patients, but this is also true for asymptomatic carriers with high PVL in blood, thus reducing its usefulness as a marker for HAM/TSP. A greater number of AC H should be analyzed, but whether they will eventually develop HAM/TSP or why they have not developed the disease are still questions to be clarified. Longitudinal studies are necessary to answer these questions.

Evolution of Specific Antibodies and Proviral DNA in Milk of Small Ruminants Infected by Small Ruminant Lentivirus

PubMed Central

Barquero, Nuria; Gomez-Lucia, Esperanza; Arjona, Alvaro; Toural, Cristina; las Heras, Alfonso; Fernández-Garayzabal, José F.; Domenech, Ana

2013-01-01

The diagnosis of Small Ruminant Lentivirus (SRLV) is based on clinical signs, pathological lesions and laboratory testing. No standard reference test for the diagnosis of maedi visna has been validated up to the present, and it is puzzling that tests which detect antibodies against the virus and tests which detect the proviral genome may render opposite results. The aim of this study was to evaluate the presence in milk throughout a lactation period of specific antibodies by ELISA and of SRLV proviral DNA by a PCR of the highly conserved pol region. A six-month study was conducted with the milk of 28 ewes and 31 goats intensively reared. The percentage of animals with antibodies against SRLV increased throughout the study period. Seroprevalence in sheep was 28% at the beginning of the study and by the end it had increased up to 52.4%. In goats, initial seroprevalence of 5.6% increased to 16%. The percentage of PCR positive ewes was stable throughout the study period. Of the positive sheep, 21.4% were PCR-positive before antibodies could be detected and most of them became PCR-negative shortly after the first detection of antibodies. This might suggest that antibodies have a neutralizing effect. In addition, an equal percentage of sheep were always PCR-negative but either became ELISA-positive or was always ELISA-positive, which might support this hypothesis. On the other hand, the PCR results in goats did not follow any pattern and oscillated between 35.3% and 55.6% depending on the month. Most goats positive by PCR failed to develop antibodies in the 6 months tested. We may conclude that the infection and the antibody response to it follow a different trend in sheep and goats. PMID:24153063

Single-cell analysis of HIV-1 transcriptional activity reveals expression of proviruses in expanded clones during ART

PubMed Central

Wiegand, Ann; Spindler, Jonathan; Hong, Feiyu F.; Shao, Wei; Cyktor, Joshua C.; Cillo, Anthony R.; Halvas, Elias K.; Coffin, John M.; Mellors, John W.; Kearney, Mary F.

2017-01-01

Little is known about the fraction of human immunodeficiency virus type 1 (HIV-1) proviruses that express unspliced viral RNA in vivo or about the levels of HIV RNA expression within single infected cells. We developed a sensitive cell-associated HIV RNA and DNA single-genome sequencing (CARD-SGS) method to investigate fractional proviral expression of HIV RNA (1.3-kb fragment of p6, protease, and reverse transcriptase) and the levels of HIV RNA in single HIV-infected cells from blood samples obtained from individuals with viremia or individuals on long-term suppressive antiretroviral therapy (ART). Spiking experiments show that the CARD-SGS method can detect a single cell expressing HIV RNA. Applying CARD-SGS to blood mononuclear cells in six samples from four HIV-infected donors (one with viremia and not on ART and three with viremia suppressed on ART) revealed that an average of 7% of proviruses (range: 2–18%) expressed HIV RNA. Levels of expression varied from one to 62 HIV RNA molecules per cell (median of 1). CARD-SGS also revealed the frequent expression of identical HIV RNA sequences across multiple single cells and across multiple time points in donors on suppressive ART consistent with constitutive expression of HIV RNA in infected cell clones. Defective proviruses were found to express HIV RNA at levels similar to those proviruses that had no obvious defects. CARD-SGS is a useful tool to characterize fractional proviral expression in single infected cells that persist despite ART and to assess the impact of experimental interventions on proviral populations and their expression. PMID:28416661

Utilization of a DNA enzyme immunoassay for the detection of proviral DNA of human immunodeficiency virus type 1 by polymerase chain reaction.

PubMed

Zella, D; Cavicchini, A; Cattaneo, E; Cimarelli, A; Bertazzoni, U

1995-02-01

The detection of proviral DNA by Polymerase Chain Reaction (PCR) is regarded as an important tool in the diagnosis of HIV-1 infection, specially among adults at risk of AIDS and children born to seropositive mothers. However, application of PCR in routine testing is hampered by the need to use radioactive probes. In this study, a non-radioactive test based on a microtiter plate (DNA Enzyme ImmunoAssay, DEIA) was used for the detection of proviral sequences of HIV-1 in peripheral blood cells of different patients. The results of the PCR-DEIA assay were compared to those obtained by liquid hybridization (PCR-LH), virus isolation (VI) and Western blot (WB). The study population included 92 patients belonging to three different groups: seropositive subjects with a well-defined clinical status and WB profile; adults at risk of infection with negative or indeterminate WB; children born to seropositive mothers with still unestablished HIV-1 infection. In the seropositive subjects, both PCR-LH and PCR-DEIA confirmed infection and gave the same results as WB. In adults at risk of infection, PCR with both methods anticipated the seroconversion in one patient with indeterminate WB and confirmed the absence of infection among seronegative and other indeterminate patients. In children born to seropositive mothers, both PCR systems as well as VI permitted an early diagnosis of infection, as confirmed by the clinical follow-up. This study has shown that in subjects at risk of AIDS and in children born to seropositive mothers, the non-isotopic DEIA method presents the same sensitivity and specificity for the detection of HIV-1 infection as the radioactive procedure. The DEIA method appears to be particularly useful for the detection of PCR products in routine diagnostic analyses.

High level of APOBEC3F/3G editing in HIV-2 DNA vif and pol sequences from antiretroviral-naive patients.

PubMed

Bertine, Mélanie; Charpentier, Charlotte; Visseaux, Benoit; Storto, Alexandre; Collin, Gilles; Larrouy, Lucile; Damond, Florence; Matheron, Sophie; Brun-Vézinet, Françoise; Descamps, Diane

2015-04-24

In HIV-1, hypermutation introduced by APOBEC3F/3G cytidine deaminase activity leads to defective viruses. In-vivo impact of APOBEC3F/3G editing on HIV-2 sequences remains unknown. The objective of this study was to assess the level of APOBEC3F/3G editing in HIV-2-infected antiretroviral-naive patients. Direct sequencing of vif and pol regions was performed on HIV-2 proviral DNA from antiretroviral-naive patients included in the French Agence Nationale de Recherches sur le SIDA et les hépatites virales CO5 HIV-2 cohort. Hypermutated sequences were identified using Hypermut2.0 program. HIV-1 proviral sequences from Genbank were also assessed. Among 82 antiretroviral-naive HIV-2-infected patients assessed, 15 (28.8%) and five (16.7%) displayed Vif proviral defective sequences in HIV-2 groups A and B, respectively. A lower proportion of defective sequences was observed in protease-reverse transcriptase region. A higher median number of G-to-A mutations was observed in HIV-2 group B than in group A, both in Vif and protease-reverse transcriptase regions (P = 0.02 and P = 0.006, respectively). Compared with HIV-1 Vif sequences, a higher number of Vif defective sequences was observed in HIV-2 group A (P = 0.00001) and group B sequences (P = 0.013). We showed for the first time a high level of APOBEC3F/3G editing in HIV-2 sequences from antiretroviral-naive patients. Our study reported a group effect with a significantly higher level of APOBEC3F/3G editing in HIV-2 group B than in group A sequences.

Complications Related to Insertion and Use of Central Venous Catheters (CVC).

PubMed

Hodzic, Samir; Golic, Darko; Smajic, Jasmina; Sijercic, Selma; Umihanic, Sekib; Umihanic, Sefika

2014-10-01

Central Venous Catheters (CVC) are essential in everyday medical practice, especially in treating patients in intensive care units (ICU). The application of these catheters is accompanied with the risk of complications, such as the complications caused during the CVC insertion, infections at the location of the insertion, and complications during the use of the catheter, sepsis and other metastatic infections. This study is a retrospective-prospective and it was implemented in the period 1(st) January 2011- 31(st) December 2012. It included 108 examinees with CVC placed for more than 7 days. The most common complications occurring in more than 2 attempts of CVC applications are: hearth arrhythmias in both groups in 12 cases, 7 in multi-lumen (12.72%) and 5 in mono-lumen ones (9.43%). Artery puncture occurs in both groups in 7 cases, 5 in multi-lumen (9.09%) and 2 in mono-lumen ones (3.77%). Hematoma occurred in both groups in 4 cases, 3 in multi-lumen CVCs (5.45%) and 1 in mono-lumen ones (1.88%). The most common complication in multi-lumen catheters was heart arrhythmia, in 20 cases (36.37%). The most common complications in mono-lumen CVCs was hearth arrhythmias, in 20 cases as extrasystoles and they were registered in 16 catheter insertions (30.18%). Out of total number of catheters of both groups, out of 108 catheters the complications during insertion occurred in 49 catheters (45.40%). The most common complications in both groups were heart arrhythmias, artery punctures and hematomas at the place of catheter insertion.

[Reducing the Incidence of Phlebitis Related to Intravenous Injection in Pediatric Patients].

PubMed

Cho, Yen-Hua; Yen, Li-Ling; Yu, Kai-Ling; Chang, Chun-Chu; Chen, Hsuen-Ling

2015-06-01

Peripheral venous catheter (PVC) is commonly used to provide nutrition and medicine to pediatric inpatients. Phlebitis is a common side effect of PVC insertion. Over 90% of pediatric patients in the paedi-atric medical ward at the Chang Gung Memorial Hospital (CGMH) receive PVC insertion, with an incident rate of phlebitis of 5.07%. Common cause factors of phlebitis are: insufficient sterilization time, inappropriate methods used to fix the PVC, the use of fixtures that loosen easily, high re-fix rates, and inadequate wound care after catheter removal. The purpose of this project was to reduce the incidence rate of PVC-insertion-related phlebitis in children from 5.07% to 2.5%. A one-week clinical observation identified the re-inserting / re-fixing of existing PVCs as the principal cause of phlebitis in the CGMH paediatric ward. Therefore, the researchers modified the catheter care bundle based on a review of the literature and the suggestions of clinical pediatric experts. Modifications included applying 2% chlorhexidine to sterilize the insertion site; using a new, non-woven fabric splint to fix the PVC site; providing cartoon-themed waterproof dressings for the first bath after the removal of the PVC; and setting standard operating procedures (SOPs) for PVC insertion and catheter removal. After applying these modifications, the incident rate of phlebitis in children with PVC insertions decreased from 5.07% to 2.08%. The application of 2% chlorhexidine reduces the waiting time for sterilization; the purpose-designed splint strengthens the fixation of the PVC; and the development of the SOPs for PVC insertion and post-removal catheter care reduces the risk of phlebitis. The combination of these strategies effectively reduces the incidence of phlebitis and improves the nursing care quality.

ATM facilitates mouse gammaherpesvirus reactivation from myeloid cells during chronic infection.

PubMed

Kulinski, Joseph M; Darrah, Eric J; Broniowska, Katarzyna A; Mboko, Wadzanai P; Mounce, Bryan C; Malherbe, Laurent P; Corbett, John A; Gauld, Stephen B; Tarakanova, Vera L

2015-09-01

Gammaherpesviruses are cancer-associated pathogens that establish life-long infection in most adults. Insufficiency of Ataxia-Telangiectasia mutated (ATM) kinase leads to a poor control of chronic gammaherpesvirus infection via an unknown mechanism that likely involves a suboptimal antiviral response. In contrast to the phenotype in the intact host, ATM facilitates gammaherpesvirus reactivation and replication in vitro. We hypothesized that ATM mediates both pro- and antiviral activities to regulate chronic gammaherpesvirus infection in an immunocompetent host. To test the proposed proviral activity of ATM in vivo, we generated mice with ATM deficiency limited to myeloid cells. Myeloid-specific ATM deficiency attenuated gammaherpesvirus infection during the establishment of viral latency. The results of our study uncover a proviral role of ATM in the context of gammaherpesvirus infection in vivo and support a model where ATM combines pro- and antiviral functions to facilitate both gammaherpesvirus-specific T cell immune response and viral reactivation in vivo. Copyright © 2015 Elsevier Inc. All rights reserved.

Rapid detection of HIV-1 proviral DNA for early infant diagnosis using recombinase polymerase amplification.

PubMed

Boyle, David S; Lehman, Dara A; Lillis, Lorraine; Peterson, Dylan; Singhal, Mitra; Armes, Niall; Parker, Mathew; Piepenburg, Olaf; Overbaugh, Julie

2013-04-02

Early diagnosis and treatment of human immunodeficiency virus type 1 (HIV-1) infection in infants can greatly reduce mortality rates. However, current infant HIV-1 diagnostics cannot reliably be performed at the point of care, often delaying treatment and compromising its efficacy. Recombinase polymerase amplification (RPA) is a novel technology that is ideal for an HIV-1 diagnostic, as it amplifies target DNA in <20 min at a constant temperature, without the need for complex thermocycling equipment. Here we tested 63 HIV-1-specific primer and probe combinations and identified two RPA assays that target distinct regions of the HIV-1 genome (long terminal repeat [LTR] and pol) and can reliably detect 3 copies of proviral DNA by the use of fluorescence detection and lateral-flow strip detection. These pol and LTR primers amplified 98.6% and 93%, respectively, of the diverse HIV-1 variants tested. This is the first example of an isothermal assay that consistently detects all of the major HIV-1 global subtypes.

Staphylococcus aureus infections following knee and hip prosthesis insertion procedures.

PubMed

Arduino, Jean Marie; Kaye, Keith S; Reed, Shelby D; Peter, Senaka A; Sexton, Daniel J; Chen, Luke F; Hardy, N Chantelle; Tong, Steven Yc; Smugar, Steven S; Fowler, Vance G; Anderson, Deverick J

2015-01-01

Staphylococcus aureus is the most common and most important pathogen following knee and hip arthroplasty procedures. Understanding the epidemiology of invasive S. aureus infections is important to quantify this serious complication. This nested retrospective cohort analysis included adult patients who had undergone insertion of knee or hip prostheses with clean or clean-contaminated wound class at 11 hospitals between 2003-2006. Invasive S. aureus infections, non-superficial incisional surgical site infections (SSIs) and blood stream infections (BSIs), were prospectively identified following each procedure. Prevalence rates, per 100 procedures, were estimated. 13,719 prosthetic knee (62%) and hip (38%) insertion procedures were performed. Of 92 invasive S. aureus infections identified, SSIs were more common (80%) than SSI and BSI (10%) or BSI alone (10%). The rate of invasive S. aureus infection/100 procedures was 0.57 [95% CI: 0.43-0.73] for knee insertion and 0.83 [95% CI: 0.61-1.08] for hip insertion. More than half (53%) were methicillin-resistant. Median time-to-onset of infection was 34 and 26 days for knee and hip insertion, respectively. Infection was associated with higher National Healthcare Safety Network risk index (p ≤ 0.0001). Post-operative invasive S. aureus infections were rare, but difficult-to-treat methicillin-resistant infections were relatively common. Optimizing preventative efforts may greatly reduce the healthcare burden associated with S. aureus infections.

A novel gammaretroviral shuttle vector insertional mutagenesis screen identifies SHARPIN as a breast cancer metastasis gene and prognostic biomarker.

PubMed

Bii, Victor M; Rae, Dustin T; Trobridge, Grant D

2015-11-24

Breast cancer (BC) is the second leading cause of malignancy among U.S. women. Metastasis results in a poor prognosis and increased mortality, but the molecular mechanisms by which metastatic tumors occur are not well understood. Identifying the genes that drive the metastatic process could provide targets for improved therapy and biomarkers to improve BC patient outcomes. Using a forward mutagenesis screen, BC cells mutagenized with a replication-incompetent gammaretroviral vector (γRV) were xenotransplanted into the mammary fat pad of immunodeficient mice. In this approach the vector provirus dysregulates nearby genes, providing a selective advantage to transduced cells to form metastases. Metastatic tumors were analyzed for proviral integration sites to identify nearby candidate metastasis genes. The γRV has a transgene cassette that allows for rescue in bacteria and rapid identification of vector integration sites. Using this approach, we identified the previously described metastasis gene WWTR1 (TAZ), and three other novel candidate metastasis genes including SHARPIN. SHARPIN was independently validated in vivo as a BC metastasis gene. Analysis of patient data showed that SHARPIN expression predicts metastasis-free survival after adjuvant therapy. Our approach has broad potential to identify genes involved in oncogenic processes for BC and other cancers. We show here it can identify both known (WWTR1) and novel (SHARPIN) BC metastasis genes.

Expanding possibilities for intervention against small ruminant lentiviruses through genetic marker-assisted selective breeding

USDA-ARS?s Scientific Manuscript database

Small ruminant lentiviruses include members that infect sheep (ovine lentivirus [OvLV]; also known as ovine progressive pneumonia virus/maedi-visna virus) and goats (caprine arthritis encephalitis virus [CAEV]). Breed differences in seroprevalence and proviral concentration of OvLV had suggested a s...

Peripherally inserted central catheters in the neonatal period.

PubMed

Uygun, Ibrahim; Okur, Mehmet Hanifi; Otcu, Selcuk; Ozturk, Hayrettin

2011-10-01

Peripherally inserted central catheters (PICC) have been extensively used in neonates. However, insertion of these thinnest catheters is a very delicate procedure associated with a high failure rate. In our Neonatal Surgical Intensive Care Unit, we developed a very easy new PICC insertion and evaluated the neonates treated with PICCs which were inserted by using our technique as well as catheter features such as success rate, number of insertion attempts, reason for removal and complications. Information was retrospectively collected on all 40 PICCs inserted at Kutahya Evliya Celebi Goverment Hospital and Dicle University Hospital during a 6-years period from September 2004 to September 2010. A total of 40 PICCs were inserted in 37 patients (26, 70% males, 11, 30% females) by using new technique. The median age of patients was 8.3 days (range 1 to 66 days) and the median weight of patients was 2365 g (range 600 to 5000 g). The vein most commonly accessed was long saphenous vein (85%). The length of PICCs in the body was 19.6 cm (range 5 cm to 30 cm). The tip was located in a central vein in all patients. Surgical abdomen was the most common cause for PICC insertion (38%). Duration of catheterization was 7.7±5.6 days (1-F 5.5 days, 2-F 8.6 days). Almost all of the PICCs were inserted successfully (40/42, success rate 95%) and in the first venipucture (36/42, 86%). Completion of therapy and removed after death were achieved with 87% of PICCs. Three minor complications were noted. Minor bleeding in the insertion site which was stopped via compression occurred in two neonates. Major complication was not seen. No deaths were directly attributed to PICCs use. The new insertion technique of the neonatal peripherally inserted central catheters may be one of the easiest and safest techniques, in comparison to previous techniques reported in the literature.

Retroviral insertions in the VISION database identify molecular pathways in mouse lymphoid leukemia and lymphoma

PubMed Central

Weiser, Keith C.; Liu, Bin; Hansen, Gwenn M.; Skapura, Darlene; Hentges, Kathryn E.; Yarlagadda, Sujatha; Morse III, Herbert C.

2007-01-01

AKXD recombinant inbred (RI) strains develop a variety of leukemias and lymphomas due to somatically acquired insertions of retroviral DNA into the genome of hematopoetic cells that can mutate cellular proto-oncogenes and tumor suppressor genes. We generated a new set of tumors from nine AKXD RI strains selected for their propensity to develop B-cell tumors, the most common type of human hematopoietic cancers. We employed a PCR technique called viral insertion site amplification (VISA) to rapidly isolate genomic sequence at the site of provirus insertion. Here we describe 550 VISA sequence tags (VSTs) that identify 74 common insertion sites (CISs), of which 21 have not been identified previously. Several suspected proto-oncogenes and tumor suppressor genes lie near CISs, providing supportive evidence for their roles in cancer. Furthermore, numerous previously uncharacterized genes lie near CISs, providing a pool of candidate disease genes for future research. Pathway analysis of candidate genes identified several signaling pathways as common and powerful routes to blood cancer, including Notch, E-protein, NFκB, and Ras signaling. Misregulation of several Notch signaling genes was confirmed by quantitative RT-PCR. Our data suggest that analyses of insertional mutagenesis on a single genetic background are biased toward the identification of cooperating mutations. This tumor collection represents the most comprehensive study of the genetics of B-cell leukemia and lymphoma development in mice. We have deposited the VST sequences, CISs in a genome viewer, histopathology, and molecular tumor typing data in a public web database called VISION (Viral Insertion Sites Identifying Oncogenes), which is located at http://www.mouse-genome.bcm.tmc.edu/vision. PMID:17926094

Retroviral insertions in the VISION database identify molecular pathways in mouse lymphoid leukemia and lymphoma.

PubMed

Weiser, Keith C; Liu, Bin; Hansen, Gwenn M; Skapura, Darlene; Hentges, Kathryn E; Yarlagadda, Sujatha; Morse Iii, Herbert C; Justice, Monica J

2007-10-01

AKXD recombinant inbred (RI) strains develop a variety of leukemias and lymphomas due to somatically acquired insertions of retroviral DNA into the genome of hematopoetic cells that can mutate cellular proto-oncogenes and tumor suppressor genes. We generated a new set of tumors from nine AKXD RI strains selected for their propensity to develop B-cell tumors, the most common type of human hematopoietic cancers. We employed a PCR technique called viral insertion site amplification (VISA) to rapidly isolate genomic sequence at the site of provirus insertion. Here we describe 550 VISA sequence tags (VSTs) that identify 74 common insertion sites (CISs), of which 21 have not been identified previously. Several suspected proto-oncogenes and tumor suppressor genes lie near CISs, providing supportive evidence for their roles in cancer. Furthermore, numerous previously uncharacterized genes lie near CISs, providing a pool of candidate disease genes for future research. Pathway analysis of candidate genes identified several signaling pathways as common and powerful routes to blood cancer, including Notch, E-protein, NFkappaB, and Ras signaling. Misregulation of several Notch signaling genes was confirmed by quantitative RT-PCR. Our data suggest that analyses of insertional mutagenesis on a single genetic background are biased toward the identification of cooperating mutations. This tumor collection represents the most comprehensive study of the genetics of B-cell leukemia and lymphoma development in mice. We have deposited the VST sequences, CISs in a genome viewer, histopathology, and molecular tumor typing data in a public web database called VISION (Viral Insertion Sites Identifying Oncogenes), which is located at http://www.mouse-genome.bcm.tmc.edu/vision .

Chromosomal localization of Emv-16 and Emv-17, two closely linked ecotropic proviruses of RF/J mice.

PubMed Central

Buchberg, A M; Taylor, B A; Jenkins, N A; Copeland, N G

1986-01-01

Emv-16 and Emv-17, the two closely linked ecotropic proviral loci of RF/J mice, have been mapped to chromosome 1 between leaden, ln, and the mouse engrailed homeo-box locus, En-1, by using recombinant inbred strains and conventional backcross analysis. Images PMID:2878091

Influenza vaccination of HIV-1-positive and HIV-1-negative former intravenous drug users.

PubMed

Amendola, A; Boschini, A; Colzani, D; Anselmi, G; Oltolina, A; Zucconi, R; Begnini, M; Besana, S; Tanzi, E; Zanetti, A R

2001-12-01

The immunogenicity of an anti-influenza vaccine was assessed in 409 former intravenous drug user volunteers and its effect on the levels of HIV-1 RNA, proviral DNA and on CD4+ lymphocyte counts in a subset HIV-1-positive subjects was measured. HIV-1-positive individuals (n = 72) were divided into three groups on the basis of their CD4+ lymphocyte counts, while the 337 HIV-1-negative participants were allocated into group four. Haemagglutination inhibiting (HI) responses varied from 45.8 to 70% in the HIV-1-positive subjects and were significantly higher in group four (80.7% responses to the H1N1 strain, 81.6% to the H3N2 strain, and 83% to the B strain). The percentage of subjects with HI protective antibody titres (> or = 1:40) increased significantly after vaccination, especially in HIV-1 uninfected subjects. Immunization caused no significant changes in CD4+ counts and in neither plasma HIV-1 RNA nor proviral DNA levels. Therefore, vaccination against influenza may benefit persons infected by HIV-1. Copyright 2001 Wiley-Liss, Inc.

Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome

PubMed Central

De Nicola, Beatrice; Lech, Christopher J.; Heddi, Brahim; Regmi, Sagar; Frasson, Ilaria; Perrone, Rosalba; Richter, Sara N.; Phan, Anh Tuân

2016-01-01

The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics. PMID:27298260

Cross-subtype Detection of HIV-1 Using Reverse Transcription and Recombinase Polymerase Amplification

PubMed Central

Lillis, Lorraine; Lehman, Dara A.; Siverson, Joshua B.; Weis, Julie; Cantera, Jason; Parker, Mathew; Piepenburg, Olaf; Overbaugh, Julie; Boyle, David S.

2016-01-01

A low complexity diagnostic test that rapidly and reliably detects HIV infection in infants at the point of care could facilitate early treatment, improving outcomes. However, many infant HIV diagnostics can only be performed in laboratory settings. Recombinase polymerase amplification (RPA) is an isothermal amplification technology that can rapidly amplify proviral DNA from multiple subtypes of HIV-1 in under twenty minutes without complex equipment. In this study we added reverse transcription (RT) to RPA to allow detection of both HIV-1 RNA and DNA. We show that this RT-RPA HIV-1 assay has a limit of detection of 10 to 30 copies of an exact sequence matched DNA or RNA, respectively. In addition, at 100 copies of RNA or DNA, the assay detected 171 of 175 (97.7 %) sequence variants that represent all the major subtypes and recombinant forms of HIV-1 Groups M and O. This data suggests that the application of RT-RPA for the combined detection of HIV-1 viral RNA and proviral DNA may prove a highly sensitive tool for rapid and accurate diagnosis of infant HIV. PMID:26821087

Multiple independent insertions of 5S rRNA genes in the spliced-leader gene family of trypanosome species.

PubMed

Beauparlant, Marc A; Drouin, Guy

2014-02-01

Analyses of the 5S rRNA genes found in the spliced-leader (SL) gene repeat units of numerous trypanosome species suggest that such linkages were not inherited from a common ancestor, but were the result of independent 5S rRNA gene insertions. In trypanosomes, 5S rRNA genes are found either in the tandemly repeated units coding for SL genes or in independent tandemly repeated units. Given that trypanosome species where 5S rRNA genes are within the tandemly repeated units coding for SL genes are phylogenetically related, one might hypothesize that this arrangement is the result of an ancestral insertion of 5S rRNA genes into the tandemly repeated SL gene family of trypanosomes. Here, we use the types of 5S rRNA genes found associated with SL genes, the flanking regions of the inserted 5S rRNA genes and the position of these insertions to show that most of the 5S rRNA genes found within SL gene repeat units of trypanosome species were not acquired from a common ancestor but are the results of independent insertions. These multiple 5S rRNA genes insertion events in trypanosomes are likely the result of frequent founder events in different hosts and/or geographical locations in species having short generation times.

Post-transplantation HTLV-1 myelopathy in three recipients from a single donor.

PubMed

Zarranz Imirizaldu, J J; Gomez Esteban, J C; Rouco Axpe, I; Perez Concha, T; Velasco Juanes, F; Allue Susaeta, I; Corral Carranceja, J M

2003-08-01

This paper reports for the first time three cases of infection by HTLV-I via organ transplantation; all the organs coming from the same asymptomatic infected donor. The need is considered for the implementation of compulsory screenings for HTLV antibodies on organ donors and on blood banks. The determination of antibodies for HTLV-I/II on samples of serum and cerebral spinal fluid from the patients and the donor was performed by enzyme immunoassay and western blot. Analysis of proviral DNA was performed by polymerase chain reaction. To detect changes in the sequence of amino acids, the tax gene was sequentiated, amplified, and compared with ATK prototype stocks. Spinal cord magnetic resonance imaging, cerebral spinal fluid, and somatosensory evoked potential studies were carried out in all patients. All three transplanted patients developed a myelopathy within a very short period of time. In all three patients and donor the virus belonged to the Cosmopolitan A subtype. The homology of HTLV-I sequences recovered from the patients and donor was 100% in all four cases. Proviral load was high in all three patients. The factors that certainly contributed to the infection in the first place, and the development of the disease later, were on the one hand the high proviral load and their immunosuppressed condition, and on the other the virus genotype, which proved to be an aggressive variant. However, the analysis of the histocompatibility antigen showed that two of the patients carried an haplotype that has been associated with a lower risk of developing this disease. It is argued that, although in Spain and other European countries there is not compulsory screening for HTLV antibodies because of the studies that show a low seroprevalence, in view of the cases here reported, and to avoid the serious consequences that such infection has on transplanted patients, compulsory screenings, both on organ donors and on blood banks, should be implemented.

Tax secretion from peripheral blood mononuclear cells and Tax detection in plasma of patients with human T-lymphotropic virus-type 1-associated myelopathy/tropical spastic paraparesis and asymptomatic carriers.

PubMed

Medina, Fernando; Quintremil, Sebastián; Alberti, Carolina; Godoy, Fabián; Pando, María E; Bustamante, Andrés; Barriga, Andrés; Cartier, Luis; Puente, Javier; Tanaka, Yuetsu; Valenzuela, María A; Ramírez, Eugenio

2016-03-01

Human T-lymphotropic virus-type 1 (HTLV-1) is the etiologic agent of the neurologic disease HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Tax viral protein plays a critical role in viral pathogenesis. Previous studies suggested that extracellular Tax might involve cytokine-like extracellular effects. We evaluated Tax secretion in 18 h-ex vivo peripheral blood mononuclear cells (PBMCs) cultures from 15 HAM/TSP patients and 15 asymptomatic carriers. Futhermore, Tax plasma level was evaluated from other 12 HAM/TSP patients and 10 asymptomatic carriers. Proviral load and mRNA encoding Tax were quantified by PCR and real-time RT-PCR, respectively. Intracellular Tax in CD4(+)CD25(+) cells occurred in 100% and 86.7% of HAM/TSP patients and asymptomatic carriers, respectively. Percentage of CD4(+)CD25(+) Tax+, proviral load and mRNA encoding Tax were significantly higher in HAM/TSP patients. Western blot analyses showed higher secretion levels of ubiquitinated Tax in HAM/TSP patients than in asymptomatic carriers. In HTLV-1-infected subjects, Western blot of plasma Tax showed higher levels in HAM/TSP patients than in asymptomatic carriers, whereas no Tax was found in non-infected subjects. Immunoprecipitated plasma Tax resolved on SDS-PAGE gave two major bands of 57 and 48 kDa allowing identification of Tax and Ubiquitin peptides by mass spectrometry. Relative percentage of either CD4(+)CD25(+) Tax+ cells, or Tax protein released from PBMCs, or plasma Tax, correlates neither with tax mRNA nor with proviral load. This fact could be explained by a complex regulation of Tax expression. Tax secreted from PBMCs or present in plasma could potentially become a biomarker to distinguish between HAM/TSP patients and asymptomatic carriers. © 2015 Wiley Periodicals, Inc.

A systematic evaluation of expression of HERV-W elements; influence of genomic context, viral structure and orientation

PubMed Central

2011-01-01

Background One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this family has also been associated with human disease such as multiple sclerosis (MS) and schizophrenia. It is not known whether this broad expression of HERV-W elements represents transcriptional leakage or specific transcription initiated from the retroviral promoter in the long terminal repeat (LTR) region. Therefore, potential influences of genomic context, structure and orientation on the expression levels of individual HERV-W elements in normal human tissues were systematically investigated. Results Whereas intronic HERV-W elements with a pseudogene structure exhibited a strong anti-sense orientation bias, intronic elements with a proviral structure and solo LTRs did not. Although a highly variable expression across tissues and elements was observed, systematic effects of context, structure and orientation were also observed. Elements located in intronic regions appeared to be expressed at higher levels than elements located in intergenic regions. Intronic elements with proviral structures were expressed at higher levels than those elements bearing hallmarks of processed pseudogenes or solo LTRs. Relative to their corresponding genes, intronic elements integrated on the sense strand appeared to be transcribed at higher levels than those integrated on the anti-sense strand. Moreover, the expression of proviral elements appeared to be independent from that of their corresponding genes. Conclusions Intronic HERV-W provirus integrations on the sense strand appear to have elicited a weaker negative selection than pseudogene integrations of transcripts from such elements. Our current findings suggest that the previously observed diversified and tissue-specific expression of elements in the HERV-W family is the result of both directed transcription (involving both the LTR and internal sequence) and leaky transcription of HERV-W elements in normal human tissues. PMID:21226900

Development of neurologic diseases in a patient with primate T lymphotropic virus type 1 (PTLV-1).

PubMed

Enose-Akahata, Yoshimi; Caruso, Breanna; Haner, Benjamin; Charlip, Emily; Nair, Govind; Massoud, Raya; Billioux, Bridgette J; Ohayon, Joan; Switzer, William M; Jacobson, Steven

2016-08-12

Virus transmission from various wild and domestic animals contributes to an increased risk of emerging infectious diseases in human populations. HTLV-1 is a human retrovirus associated with acute T-cell leukemia and HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). HTLV-1 originated from ancient zoonotic transmission from nonhuman primates, although cases of zoonotic infections continue to occur. Similar to HTLV-1, the simian counterpart, STLV-1, causes chronic infection and leukemia and lymphoma in naturally infected monkeys, and combined are called primate T-lymphotropic viruses (PTLV-1). However, other clinical syndromes typically seen in humans such as a chronic progressive myelopathy have not been observed in nonhuman primates. Little is known about the development of neurologic and inflammatory diseases in human populations infected with STLV-1-like viruses following nonhuman primate exposure. We performed detailed laboratory analyses on an HTLV-1 seropositive patient with typical HAM/TSP who was born in Liberia and now resides in the United States. Using a novel droplet digital PCR for the detection of the HTLV-1 tax gene, the proviral load in PBMC and cerebrospinal fluid cells was 12.98 and 51.68 %, respectively; however, we observed a distinct difference in fluorescence amplitude of the positive droplet population suggesting possible mutations in proviral DNA. A complete PTLV-1 proviral genome was amplified from the patient's PBMC DNA using an overlapping PCR strategy. Phylogenetic analysis of the envelope and LTR sequences showed the virus was highly related to PTLV-1 from sooty mangabey monkeys (smm) and humans exposed via nonhuman primates in West Africa. These results demonstrate the patient is infected with a simian variant of PTLV-1, suggesting for the first time that PTLV-1smm infection in humans may be associated with a chronic progressive neurologic disease.

Hepatic expression of proteasome subunit alpha type-6 is upregulated during viral hepatitis and putatively regulates the expression of ISG15 ubiquitin-like modifier, a proviral host gene in hepatitis C virus infection.

PubMed

Broering, R; Trippler, M; Werner, M; Real, C I; Megger, D A; Bracht, T; Schweinsberg, V; Sitek, B; Eisenacher, M; Meyer, H E; Baba, H A; Weber, F; Hoffmann, A-C; Gerken, G; Schlaak, J F

2016-05-01

The interferon-stimulated gene 15 (ISG15) plays an important role in the pathogenesis of hepatitis C virus (HCV) infection. ISG15-regulated proteins have previously been identified that putatively affect this proviral interaction. The present observational study aimed to elucidate the relation between ISG15 and these host factors during HCV infection. Transcriptomic and proteomic analyses were performed using liver samples of HCV-infected (n = 54) and uninfected (n = 10) or HBV-infected controls (n = 23). Primary human hepatocytes (PHH) were treated with Toll-like receptor ligands, interferons and kinase inhibitors. Expression of ISG15 and proteasome subunit alpha type-6 (PSMA6) was suppressed in subgenomic HCV replicon cell lines using specific siRNAs. Comparison of hepatic expression patterns revealed significantly increased signals for ISG15, IFIT1, HNRNPK and PSMA6 on the protein level as well as ISG15, IFIT1 and PSMA6 on the mRNA level in HCV-infected patients. In contrast to interferon-stimulated genes, PSMA6 expression occurred independent of HCV load and genotype. In PHH, the expression of ISG15 and PSMA6 was distinctly induced by poly(I:C), depending on IRF3 activation or PI3K/AKT signalling, respectively. Suppression of PSMA6 in HCV replicon cells led to significant induction of ISG15 expression, thus combined knock-down of both genes abrogated the antiviral effect induced by the separate suppression of ISG15. These data indicate that hepatic expression of PSMA6, which is upregulated during viral hepatitis, likely depends on TLR3 activation. PSMA6 affects the expression of immunoregulatory ISG15, a proviral factor in the pathogenesis of HCV infection. Therefore, the proteasome might be involved in the enigmatic interaction between ISG15 and HCV. © 2016 John Wiley & Sons Ltd.

Posterior medial meniscus-femoral insertion into the anterior cruciate ligament. A case report.

PubMed

Bhargava, A; Ferrari, D A

1998-03-01

Medial meniscal anomalies are rare. The anterior horn insertion into the anterior cruciate ligament is the most common. In the course of an arthroscopy for torn lateral meniscus, an anomalous band in continuity with the posterior horn of the medial meniscus was observed to insert into the anterior cruciate ligament. Although the tibial portion of the anterior cruciate was redundant, the anomalous band provided tension to the anterior cruciate ligament and a negative pivot shift. A previously unreported posterior medial meniscal femoral insertion is described.

Use of biliary stent in laparoscopic common bile duct exploration.

PubMed

Lyon, Matthew; Menon, Seema; Jain, Abhiney; Kumar, Harish

2015-05-01

It is well supported in the literature that laparoscopic common bile duct exploration (LCBDE) for choledocholithiasis has equal efficacy when compared to ERCP followed by laparoscopic cholecystectomy. Decompression after supra-duodenal choledochotomy is common practice as it reduced the risk of bile leaks. We conducted a prospective non-randomized study to compare outcomes and length of stay in patients undergoing biliary stent insertion versus T-tube drainage following LCBDE via choledochotomy. The study involved 116 patients with choledocholithiasis who underwent LCBDE and decompression of the biliary system by either ante-grade biliary stent or T-tube insertion. A 7 French straight/duodenal curve biliary Diagmed™ stent (9-11 cm) was placed in 82 patients (Biliary Stent Group). T-tube insertion was used for 34 patients (T-tube group). The length of hospital stay and complications for the selected patients were recorded. All trans-cystic common bile duct explorations were excluded from the study. The mean hospital stay for patients who underwent ante-grade biliary stent or T-tube insertion after LBCDE were 1 and 3.4 days, respectively. This is a statistically significant result with a p value of less than 0.001. Of the T-tube group, two patients required laparoscopic washout due to bile leaks, one had ongoing biliary stasis and one reported ongoing pain whilst the T-tube was in situ. A complication rate of 11.2%, this was a significant finding. There were no complications or concerns reported for the Biliary Stent Group. Our results show that there is a significant reduction in length of hospital stay and morbidity for patients that have ante-grade biliary stent decompression of the CBD post laparoscopic choledochotomy when compared T-tube drainage. This implies that ante-grade biliary stent insertion is likely to reduce costs and increase overall patient satisfaction. We support the use of ante-grade biliary stent insertion during LCBDE when primary closure is not preferred.

SUN2 Modulates HIV-1 Infection and Latency through Association with Lamin A/C To Maintain the Repressive Chromatin.

PubMed

Sun, Wei-Wei; Jiao, Shi; Sun, Li; Zhou, Zhaocai; Jin, Xia; Wang, Jian-Hua

2018-05-01

The postintegrational latency of HIV-1 is characterized by reversible silencing of long terminal repeat (LTR)-driven transcription of the HIV genome. It is known that the formation of repressive chromatin at the 5'-LTR of HIV-1 proviral DNA impedes viral transcription by blocking the recruitment of positive transcription factors. How the repressive chromatin is formed and modulated during HIV-1 infection remains elusive. Elucidation of which chromatin reassembly factor mediates the reorganization of chromatin is likely to facilitate the understanding of the host's modulation of HIV-1 transcription and latency. Here we revealed that "Sad1 and UNC84 domain containing 2" (SUN2), an inner nuclear membrane protein, maintained the repressive chromatin and inhibited HIV LTR-driven transcription of proviral DNA through an association with lamin A/C. Specifically, lamin A/C tethered SUN2 to the nucleosomes 1 and 2 of the HIV-1 5'-LTR to block the initiation and elongation of HIV-1 transcription. SUN2 knockdown converted chromatin to an active form and thus enhanced the phosphorylation of RNA polymerase II and its recruitment to the 5'-LTR HIV-1 proviral DNA, leading to reactivation of HIV-1 from latency. Conversely, the exogenous factors such as tumor necrosis factor alpha (TNF-α) induced reactivation, and the replication of HIV-1 led to the disassociation between SUN2 and lamin A/C, suggesting that disruption of the association between SUN2 and lamin A/C to convert the repressive chromatin to the active form might be a prerequisite for the initiation of HIV-1 transcription and replication. Together, our findings indicate that SUN2 is a novel chromatin reassembly factor that helps to maintain chromatin in a repressive state and consequently inhibits HIV-1 transcription. IMPORTANCE Despite the successful use of scores of antiretroviral drugs, HIV latency poses a major impediment to virus eradication. Elucidation of the mechanism of latency facilitates the discovery of new therapeutic strategies. It has been known that the formation of repressive chromatin at the 5'-LTR of HIV-1 proviral DNA impedes viral transcription and maintains viral latency, but how the repressive chromatin is formed and modulated during HIV-1 infection remains elusive. In this study, we performed in-depth virological and cell biological studies and discovered that an inner nuclear membrane protein, SUN2, is a novel chromatin reassembly factor that maintains repressive chromatin and thus modulates HIV-1 transcription and latency: therefore, targeting SUN2 may lead to new strategies for HIV cure. Copyright © 2018 Sun et al.

Pressure-relieving properties of various shoe inserts in older people with plantar heel pain.

PubMed

Bonanno, Daniel R; Landorf, Karl B; Menz, Hylton B

2011-03-01

Plantar heel pain is one of the most common musculoskeletal conditions affecting the foot and it is commonly experienced by older adults. Contoured foot orthoses and some heel inserts have been found to be effective for plantar heel pain, however the mechanism by which they achieve their effects is largely unknown. The aim of this study was to investigate the effects of foot orthoses and heel inserts on plantar pressures in older adults with plantar heel pain. Thirty-six adults aged over 65 years with plantar heel pain participated in the study. Using the in-shoe Pedar(®) system, plantar pressure data were recorded while participants walked along an 8 m walkway wearing a standardised shoe and 4 different shoe inserts. The shoe inserts consisted of a silicon heel cup, a soft foam heel pad, a heel lift and a prefabricated foot orthosis. Data were collected for the heel, midfoot and forefoot. Statistically significant attenuation of heel peak plantar pressure was provided by 3 of the 4 shoe inserts. The greatest reduction was achieved by the prefabricated foot orthosis, which provided a fivefold reduction compared to the next most effective insert. The contoured nature of the prefabricated foot orthosis allowed for an increase in midfoot contact area, resulting in a greater redistribution of force. The prefabricated foot orthosis was also the only shoe insert that did not increase forefoot pressure. The findings from this study indicate that of the shoe inserts tested, the contoured prefabricated foot orthosis is the most effective at reducing pressure under the heel in older people with heel pain. Copyright © 2010 Elsevier B.V. All rights reserved.

A practical review of the muscles of facial mimicry with special emphasis on the superficial musculoaponeurotic system.

PubMed

Hutto, Justin R; Vattoth, Surjith

2015-01-01

In this article, we elaborate a practical approach to superficial facial anatomy enabling easy identification of the facial mimic muscles by classifying them according to their shared common insertion sites. The facial mimic muscles are often difficult to identify on imaging. By tracing them from their common group insertion sites back to their individual origins as well as understanding key anatomic relationships, radiologists can more accurately identify these muscles.

3D-QSAR and virtual screening studies of thiazolidine-2,4-dione analogs: Validation of experimental inhibitory potencies towards PIM-1 kinase

NASA Astrophysics Data System (ADS)

Asati, Vivek; Bharti, Sanjay Kumar; Budhwani, Ashok Kumar

2017-04-01

The proviral insertion site in moloney murine leukemia virus (PIM) is a family of serine/threonine kinase of Ca2+-calmodulin-dependent protein kinase (CAMK) group which is responsible for the activation and regulation of cellular transcription and translation. The three isoforms of PIM kinase (PIM-1, PIM-2 and PIM-3) share high homology and functional idleness are widely expressed and involved in a variety of biological processes including cell survival, proliferation, differentiation and apoptosis. Altered expression of PIM-1 kinase correlated with hematologic malignancies and solid tumors. In the present study, atom-based 3D-QSAR, docking and virtual screening studies have been performed on a series of thiazolidine-2,4-dione derivatives as PIM-1 kinase inhibitors. 3D-QSAR and docking approach has shortlisted the most active thiazolidine-2,4-dione derivatives such as 28, 31, 33 and 35 with the incorporation of more than one structural feature in a single molecule. External validations by various parameters and molecular docking studies at the active site of PIM-1 kinase have proved the reliability of the developed 3D-QSAR model. The generated pharmacophore (AADHR.33) from 3D-QSAR study was used for screening of drug like compounds from ZINC database, where ZINC15056464 and ZINC83292944 showed potential binding affinities at the active site amino acid residues (LYS67, GLU171, ASP128 and ASP186) of PIM-1 kinase.

Recent Amplification of the Kangaroo Endogenous Retrovirus, KERV, Limited to the Centromere▿

PubMed Central

Ferreri, Gianni C.; Brown, Judith D.; Obergfell, Craig; Jue, Nathaniel; Finn, Caitlin E.; O'Neill, Michael J.; O'Neill, Rachel J.

2011-01-01

Mammalian retrotransposons, transposable elements that are processed through an RNA intermediate, are categorized as short interspersed elements (SINEs), long interspersed elements (LINEs), and long terminal repeat (LTR) retroelements, which include endogenous retroviruses. The ability of transposable elements to autonomously amplify led to their initial characterization as selfish or junk DNA; however, it is now known that they may acquire specific cellular functions in a genome and are implicated in host defense mechanisms as well as in genome evolution. Interactions between classes of transposable elements may exert a markedly different and potentially more significant effect on a genome than interactions between members of a single class of transposable elements. We examined the genomic structure and evolution of the kangaroo endogenous retrovirus (KERV) in the marsupial genus Macropus. The complete proviral structure of the kangaroo endogenous retrovirus, phylogenetic relationship among relative retroviruses, and expression of this virus in both Macropus rufogriseus and M. eugenii are presented for the first time. In addition, we show the relative copy number and distribution of the kangaroo endogenous retrovirus in the Macropus genus. Our data indicate that amplification of the kangaroo endogenous retrovirus occurred in a lineage-specific fashion, is restricted to the centromeres, and is not correlated with LINE depletion. Finally, analysis of KERV long terminal repeat sequences using massively parallel sequencing indicates that the recent amplification in M. rufogriseus is likely due to duplications and concerted evolution rather than a high number of independent insertion events. PMID:21389136

Systematic Functional Characterization of Resistance to PI3K Inhibition in Breast Cancer.

PubMed

Le, Xiuning; Antony, Rajee; Razavi, Pedram; Treacy, Daniel J; Luo, Flora; Ghandi, Mahmoud; Castel, Pau; Scaltriti, Maurizio; Baselga, Jose; Garraway, Levi A

2016-10-01

PIK3CA (which encodes the PI3K alpha isoform) is the most frequently mutated oncogene in breast cancer. Small-molecule PI3K inhibitors have shown promise in clinical trials; however, intrinsic and acquired resistance limits their utility. We used a systematic gain-of-function approach to identify genes whose upregulation confers resistance to the PI3K inhibitor BYL719 in breast cancer cells. Among the validated resistance genes, Proviral Insertion site in Murine leukemia virus (PIM) kinases conferred resistance by maintaining downstream PI3K effector activation in an AKT-independent manner. Concurrent pharmacologic inhibition of PIM and PI3K overcame this resistance mechanism. We also observed increased PIM expression and activity in a subset of breast cancer biopsies with clinical resistance to PI3K inhibitors. PIM1 overexpression was mutually exclusive with PIK3CA mutation in treatment-naïve breast cancers, suggesting downstream functional redundancy. Together, these results offer new insights into resistance to PI3K inhibitors and support clinical studies of combined PIM/PI3K inhibition in a subset of PIK3CA-mutant cancers. PIM kinase overexpression confers resistance to small-molecule PI3K inhibitors. Combined inhibition of PIM and PI3K may therefore be warranted in a subset of breast cancers. Cancer Discov; 6(10); 1134-47. ©2016 AACR.This article is highlighted in the In This Issue feature, p. 1069. ©2016 American Association for Cancer Research.

Temperature Rise in Kirschner Wires Inserted Using Two Drilling Methods: Forward and Oscillation.

PubMed

Anderson, Scott Richard; Inceoglu, Serkan; Wongworawat, Montri D

2017-05-01

Kirschner wires (K-wires) are commonly used in orthopedic surgery. However, the loosening of the pins can lead to delayed or improper healing or infection. Wire loosening can occur by thermal necrosis that occurs due to heat produced during wire insertion. Although the parameters that affect temperature rise in cortical bone during wire insertion and drilling have been studied, the effect of drilling mode (oscillation versus forward) is unknown. The purpose of this study was to compare the temperature changes occurring in cortical bone during wire insertions by oscillating and forward drills. Our hypothesis is that oscillation drilling would produce less heat compared with forward drilling in K-wire insertion with 2 commonly used wire diameters. We drilled K-wires in a pig metacarpal model and measured the temperature rise between forward and oscillation drilling modes using diamond-tipped 0.062- and 0.045-inch-diameter K-wires. There were 20 holes drilled for each group (n = 20). The average temperature rise using the 0.062-inch K-wire under forward and oscillation insertion was 14.0 ± 5.5°C and 8.8 ± 2.6°C, respectively. For the 0.045-inch K-wire, under forward and oscillation insertion, the average temperature rise was 11.4 ± 2.6°C and 7.1 ± 1.9°C, respectively. The effects of the drilling mode and wire diameter on temperature rise were significant ( P < .05). In conclusion, the oscillation of K-wires during insertion causes a lower temperature rise when compared with forward drilling.

Intranasal anatomy of the nasolacrimal sac in endoscopic dacryocystorhinostomy.

PubMed

Wormald, P J; Kew, J; Van Hasselt, A

2000-09-01

Intranasal surface anatomy is fundamental to the technique of endoscopic dacryocystorhinostomy. In the current literature the lacrimal sac is described as being situated anterior to the anterior end of the middle turbinate with between 0% and 20% of the sac above the insertion of the middle turbinate on the lateral nasal wall (the axilla of the middle turbinate). The aim of this study was to use CT dacryocystograms (DCGs) and CT scans to establish the relationship of the lacrimal sac to the lateral nasal wall. Forty-seven individual lacrimal sacs were measured in relation to the common canaliculus, and 76 were measured in relation to the insertion of the middle turbinate. Measurements taken from the long axis of the sac showed the mean height of the sac above the middle turbinate insertion was 8.8 mm (SD = 0.2, 95% CI = 1.3) and below it was 4.1 mm (SD = 2.3, 95% CI = 1.1). The average measurement of the sac above the com-mon canaliculus on CT DCGs was 5.3 mm (SD = 1.7, 95% CI = 0.56), whereas the average measurement below the common canaliculus was 7.7 mm (SD = 2, 95% CI = 1.3) (n = 47 CT DCGs). The findings in this study show that a major portion of the sac is locat-ed above the insertion of the anterior end of the middle turbinate and, in addition, that a significant part of the sac lies above the entry point of the common canaliculus. Knowledge of these findings can ensure that the sac is adequately exposed during dacryocystorhinostomy by removal of sufficient bone and mucosa above the anterior insertion of the middle turbinate.

Mutations in Ovis aries TMEM154 are associated with lower small ruminant lentivirus proviral concentration in one sheep flock

USDA-ARS?s Scientific Manuscript database

Small ruminant lentivirus (SRLV), also called ovine progressive pneumonia virus or maedi-visna, is present in 24% of U.S. sheep. Like human immunodeficiency virus, SRLV is a macrophage-tropic lentivirus that causes lifelong infection. The production impacts from SRLV are due to a range of disease sy...

Fabrication of robust tooling for mass production of polymeric microfluidic devices

NASA Astrophysics Data System (ADS)

Fu, G.; Tor, S. B.; Loh, N. H.; Hardt, D. E.

2010-08-01

Polymer microfluidic devices are gaining popularity for bio-applications. In both commonly used methods for the fabrication of polymer microfluidic devices, i.e. injection molding and hot-embossing, the quality of a mold insert is of high importance. Micro powder injection molding (μPIM) provides a suitable option for metal mold insert fabrication. In this paper, two mold inserts with micro-features of different patterns and sizes were produced using 316L stainless steel powder and an in-house binder system. The mold inserts were successfully used to produce cyclic olefin copolymer (COC, trade name TOPAS) micromixer plates with micro-channels of widths 100 µm and 50 µm. Compared with CNC-machined hot work steel mold inserts, the quality of the micro-channels is better as far as geometrical quality and dimensional tolerance are concerned. However, surface finish and flatness of the μPIM mold inserts are inferior to those of CNC-machined mold inserts.

Simian immunodeficiency viruses from African green monkeys display unusual genetic diversity.

PubMed Central

Johnson, P R; Fomsgaard, A; Allan, J; Gravell, M; London, W T; Olmsted, R A; Hirsch, V M

1990-01-01

African green monkeys are asymptomatic carriers of simian immunodeficiency viruses (SIV), commonly called SIVagm. As many as 50% of African green monkeys in the wild may be SIV seropositive. This high seroprevalence rate and the potential for genetic variation of lentiviruses suggested to us that African green monkeys may harbor widely differing genotypes of SIVagm. To investigate this hypothesis, we determined the entire nucleotide sequence of an infectious proviral molecular clone of SIVagm (155-4) and partial sequences (long terminal repeat and Gag) of three other distinct SIVagm isolates (90, gri-1, and ver-1). Comparisons among the SIVagm isolates revealed extreme diversity at the nucleotide and amino acid levels. Long terminal repeat nucleotide sequences varied up to 35% and Gag protein sequences varied up to 30%. The variability among SIVagm isolates exceeded the variability among any other group of primate lentiviruses. Our data suggest that SIVagm has been in the African green monkey population for a long time and may be the oldest primate lentivirus group in existence. PMID:2304139

Study to Expand Simulation Cockpit Displays of Advanced Sensors

DTIC Science & Technology

1981-03-01

common source is being used for multiple sensor types). If inde- pendent displays and controls are desired then two independent video sources or sensor...line is inserted in each gap, the result is the familiar 211 in- terlace. If two lines are inserted, the result is 31l interlace, and so on. The total...symbol generators. If these systems are oper- ating at various scan rates and if a common display device, such as a multifunction display (MFD) is to

Visual attention distracter insertion for improved EEG rapid serial visual presentation (RSVP) target stimuli detection

NASA Astrophysics Data System (ADS)

Khosla, Deepak; Huber, David J.; Martin, Kevin

2017-05-01

This paper† describes a technique in which we improve upon the prior performance of the Rapid Serial Visual Presentation (RSVP) EEG paradigm for image classification though the insertion of visual attention distracters and overall sequence reordering based upon the expected ratio of rare to common "events" in the environment and operational context. Inserting distracter images maintains the ratio of common events to rare events at an ideal level, maximizing the rare event detection via P300 EEG response to the RSVP stimuli. The method has two steps: first, we compute the optimal number of distracters needed for an RSVP stimuli based on the desired sequence length and expected number of targets and insert the distracters into the RSVP sequence, and then we reorder the RSVP sequence to maximize P300 detection. We show that by reducing the ratio of target events to nontarget events using this method, we can allow RSVP sequences with more targets without sacrificing area under the ROC curve (azimuth).

Mobile-bearing knees reduce rotational asymmetric wear.

PubMed

Ho, Fang-Yuan; Ma, Hon-Ming; Liau, Jiann-Jong; Yeh, Chuan-Ren; Huang, Chun-Hsiung

2007-09-01

Polyethylene wear of bearing components is the most common long-term complication in total knee arthroplasty. One would anticipate differing kinematics would generate different wear patterns (including wear type, degree, and symmetry) on the articulating surface of mobile-bearing and fixed-bearing inserts. Because mobile-bearing designs facilitate movement of the insert relative to the tray when the knee rotates, we hypothesized mobile-bearing designs would reduce the incidence of rotational asymmetric wear. We examined 51 worn tibial inserts, including 15 from mobile-bearing rotating-platform posterior-cruciate-sacrificing dished prostheses and 36 from fixed-bearing posterior-cruciate-retaining flat prostheses, which were retrieved at revision surgery with an average implantation time of 115 months. We divided wear types into low-grade wear (burnishing, abrasion, and cold flow) and high-grade wear (scratching, pitting, metal embedding, and delamination) to assess wear degree of polyethylene. To assess symmetry of wear, the insert surface was divided into medial and lateral sides and each side was further divided into three equal zones along the anteroposterior direction. Low-grade wear was more common in mobile-bearing knees, whereas high-grade wear was more common in fixed-bearing knees. We identified no internal/external rotational asymmetric wear or anteroposterior asymmetric wear in mobile-bearing knees.

Shock-absorbing effect of shoe insert materials commonly used in management of lower extremity disorders.

PubMed

Shiba, N; Kitaoka, H B; Cahalan, T D; Chao, E Y

1995-01-01

The efficacy of 3 shock-absorbing materials was compared by determining impact characteristics with a drop test method and also by testing the effect of each material when used as a shoe insert in 16 asymptomatic subjects. Peak vertical ground reaction force (F1, F2, F3) and temporal force factors (T1, T2, T3) were obtained with a force plate at a high-frequency sampling rate. Impact force, impact time, impact slope, and impact energy were determined. A standard weight was dropped from 3 heights on each material covering the force plate while reduction of peak force was compared. Impact force was attenuated most effectively by Insert 3 (polymeric foam rubber) and averaged 11% less than that in shoes without inserts. Impact time was increased for all 3 inserts. Impact slope and impact energy were reduced significantly in Insert 3. There was a significant difference in peak vertical force F1 for all 3 inserts, in vertical force F2 for Insert 2 (viscoelastic polymeric material), and in vertical force F3 for Insert 2. Drop-test studies showed that at all ball heights, the highest mean peak force was observed consistently in Insert 2.

Transcriptional regulation of latent feline immunodeficiency virus in peripheral CD4+ T-lymphocytes.

PubMed

McDonnel, Samantha J; Sparger, Ellen E; Luciw, Paul A; Murphy, Brian G

2012-05-01

Feline immunodeficiency virus (FIV), the lentivirus of domestic cats responsible for feline AIDS, establishes a latent infection in peripheral blood CD4+ T-cells approximately eight months after experimental inoculation. In this study, cats experimentally infected with the FIV-C strain in the asymptomatic phase demonstrated an estimated viral load of 1 infected cell per approximately 10(3) CD4+ T-cells, with about 1 copy of viral DNA per cell. Approximately 1 in 10 proviral copies was capable of transcription in the asymptomatic phase. The latent FIV proviral promoter was associated with deacetylated, methylated histones, which is consistent with a condensed chromatin structure. In contrast, the transcriptionally active FIV promoter was associated with histone acetylation and demethylation. In addition, RNA polymerase II appeared to be paused on the latent viral promoter, and short promoter-proximal transcripts were detected. Our findings for the FIV promoter in infected cats are similar to results obtained in studies of human immunodeficiency virus (HIV)-1 latent proviruses in cell culture in vitro studies. Thus, the FIV/cat model may offer insights into in vivo mechanisms of HIV latency and provides a unique opportunity to test novel therapeutic interventions aimed at eradicating latent virus.

Localization of HTLV-I tax proviral DNA in mononuclear cells.

PubMed

Zucker-Franklin, Dorothea; Pancake, Bette A; Najfeld, Vesna

2003-01-01

The tax sequence of HTLV-I is demonstrable in the skin and blood mononuclear cells of patients with mycosis fungoides, as well as in the mononuclear leukocytes of some healthy blood donors, but was not demonstrable when PCR/Southern analyses were carried out on preparations of high-molecular-weight genomic DNA. Therefore, it was postulated that tax DNA may not be integrated. To investigate this possibility fluorescence in situ hybridization was carried out on cells arrested in metaphase, using a probe containing the HTLV-I tax proviral DNA full-length open reading frame coding sequence. While metaphases prepared from C91PL cells, a cell line infected with HTLV-I, showed an abundance of chromosome-associated as well as extra-chromosomal signals, metaphases prepared with blood mononuclear cells from healthy tax sequence positive donors did not reveal any tax DNA associated with chromosomes. Such signals were readily detected extra-chromosomally. Although it has been demonstrated that transactivation of genes by gene products encoded by extra-chromosomal DNA may have nosocomial implications, whether transactivation by p40 tax generated from extra-chromosomal tax sequences is responsible for the development of neoplasia remains to be investigated.

Lack of evidence to support the association of a single IL28B genotype SNP rs12979860 with the HTLV-1 clinical outcomes and proviral load

PubMed Central

2012-01-01

Background The Interleukin 28B (IL28B) rs12979860 polymorphisms was recently reported to be associated with the human T-cell leukemia virus type 1 (HTLV-1) proviral load (PvL) and the development of the HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). Methods In an attempt to examine this hypothesis, we assessed the association of the rs12979860 genotypes with HTLV-1 PvL levels and clinical status in 112 unrelated Brazilian subjects (81 HTLV-1 asymptomatic carriers, 24 individuals with HAM/TSP and 7 with Adult T cell Leukemia/Lymphoma (ATLL)). Results All 112 samples were successfully genotyped and their PvLs compared. Neither the homozygote TT nor the heterozygote CT mutations nor the combination genotypes (TT/CT) were associated with a greater PvL. We also observed no significant difference in allele distribution between asymptomatic carriers and patients with HTLV-1 associated HAM/TSP. Conclusions Our study failed to support the previously reported positive association between the IL28B rs12979860 polymorphisms and an increased risk of developing HAM/TSP in the Brazilian population. PMID:23259930

Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome.

PubMed

De Nicola, Beatrice; Lech, Christopher J; Heddi, Brahim; Regmi, Sagar; Frasson, Ilaria; Perrone, Rosalba; Richter, Sara N; Phan, Anh Tuân

2016-07-27

The long terminal repeat (LTR) of the proviral human immunodeficiency virus (HIV)-1 genome is integral to virus transcription and host cell infection. The guanine-rich U3 region within the LTR promoter, previously shown to form G-quadruplex structures, represents an attractive target to inhibit HIV transcription and replication. In this work, we report the structure of a biologically relevant G-quadruplex within the LTR promoter region of HIV-1. The guanine-rich sequence designated LTR-IV forms a well-defined structure in physiological cationic solution. The nuclear magnetic resonance (NMR) structure of this sequence reveals a parallel-stranded G-quadruplex containing a single-nucleotide thymine bulge, which participates in a conserved stacking interaction with a neighboring single-nucleotide adenine loop. Transcription analysis in a HIV-1 replication competent cell indicates that the LTR-IV region may act as a modulator of G-quadruplex formation in the LTR promoter. Consequently, the LTR-IV G-quadruplex structure presented within this work could represent a valuable target for the design of HIV therapeutics. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

RAB1A promotes Vaccinia virus replication by facilitating the production of intracellular enveloped virions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pechenick Jowers, Tali; Featherstone, Rebecca J.; Reynolds, Danielle K.

2015-01-15

Vaccinia virus (VACV) is a large double-stranded DNA virus with a complex cytoplasmic replication cycle that exploits numerous cellular proteins. This work characterises the role of a proviral cellular protein, the small GTPase RAB1A, in VACV replication. Using siRNA, we identified RAB1A as required for the production of extracellular enveloped virions (EEVs), but not intracellular mature virions (IMVs). Immunofluorescence and electron microscopy further refined the role of RAB1A as facilitating the wrapping of IMVs to become intracellular enveloped virions (IEVs). This is consistent with the known function of RAB1A in maintenance of ER to Golgi transport. VACV can therefore bemore » added to the growing list of viruses which require RAB1A for optimal replication, highlighting this protein as a broadly proviral host factor. - Highlights: • Characterisation of the role of the small GTPase RAB1A in VACV replication. • RAB1A is not required for production of the primary virion form (IMV). • RAB1A is required for production of processed virion forms (IEVs, CEVs and EEVs). • Consistent with known role of RAB1A in ER to Golgi transport.« less

Cross-subtype detection of HIV-1 using reverse transcription and recombinase polymerase amplification.

PubMed

Lillis, Lorraine; Lehman, Dara A; Siverson, Joshua B; Weis, Julie; Cantera, Jason; Parker, Mathew; Piepenburg, Olaf; Overbaugh, Julie; Boyle, David S

2016-04-01

A low complexity diagnostic test that rapidly and reliably detects HIV infection in infants at the point of care could facilitate early treatment, improving outcomes. However, many infant HIV diagnostics can only be performed in laboratory settings. Recombinase polymerase amplification (RPA) is an isothermal amplification technology that can rapidly amplify proviral DNA from multiple subtypes of HIV-1 in under twenty minutes without complex equipment. In this study we added reverse transcription (RT) to RPA to allow detection of both HIV-1 RNA and DNA. We show that this RT-RPA HIV-1 assay has a limit of detection of 10-30 copies of an exact sequence matched DNA or RNA, respectively. In addition, at 100 copies of RNA or DNA, the assay detected 171 of 175 (97.7%) sequence variants that represent all the major subtypes and recombinant forms of HIV-1 Groups M and O. This data suggests that the application of RT-RPA for the combined detection of HIV-1 viral RNA and proviral DNA may prove a highly sensitive tool for rapid and accurate diagnosis of infant HIV. Copyright © 2016 Elsevier B.V. All rights reserved.

Lateral Intercondylar Ridge: Is it a reliable landmark for femoral ACL insertion?: An anatomical study.

PubMed

Bhattacharyya, Rahul; Ker, Andrew; Fogg, Quentin; Spencer, Simon J; Joseph, Jibu

2018-02-01

Incorrect femoral tunnel placement is the most common cause of graft failure during Anterior Cruciate Ligament (ACL) Reconstruction. A reliable landmark can minimize errors. To identify whether the Lateral Intercondylar Ridge (LIR) is a consistent anatomical structure and define its relationship with the femoral ACL insertion. Phase 1: we studied 23 femoral dry bone specimens macroscopically. Using a digital microscribe, the medial surface of the lateral femoral condyle was reconstructed (3D) to evaluate whether there was an identifiable bony ridge. Phase 2: 7 cadaveric specimens with intact soft tissues were dissected to identify the femoral ACL insertion. A 3D reconstruction of the femoral ACL insertion and the surface allowed us to define the relationship between the LIR and the ACL insertion. All specimens had a defined LIR on the medial surface of the lateral femoral condyle. The ridge was consistently located just anterior to the femoral ACL insertion. The ACL footprint was present in the depression between the ridge and the Inferior Articular Cartilage Margin (IACM). The mean distance from the midpoint of the IACM to the LIR was 10.1 mm. This is the first study to use the microscribe to digitally reconstruct the medial surface of the lateral femoral condyle. It shows that the LIR is a consistent anatomical structure that defines the anterior margin of the femoral ACL insertion, which guides femoral tunnel placement. Our findings support the ruler technique, which is a commonly used method for anatomic single bundle ACL reconstruction. Crown Copyright © 2017. Published by Elsevier Ltd. All rights reserved.

Analysis of proviral integration in human mammary epithelial cell lines immortalized by retroviral infection with a temperature-sensitive SV40 T-antigen construct.

PubMed

Stamps, A C; Davies, S C; Burman, J; O'Hare, M J

1994-06-15

A panel of eight conditionally immortal lines derived by infection of human breast epithelial cells with an amphotropic retrovirus transducing a ts mutant of SV40 large T-antigen was analyzed with respect to individual retroviral integration patterns. Each line contained multiple integration sites which were clonal and stable over extended passage. Similar integration patterns were observed between individual lines arising separately from the same stock of pre-immortal cells, suggesting a common progenitor. Retroviral integration analysis of pre-immortal cells at different stages of pre-crisis growth showed changes indicative of a progressive transition from polyclonality to clonality as the cells approached crisis. Each of the immortal lines contained a sub-set of the integration sites of their pre-immortal progenitors, with individual combinations and copy numbers of sites. Since all the cell lines appeared to originate from single foci in separate flasks, it is likely that each set arose from a common clone of pre-immortal cells as the result of separate genetic events. There was no evidence from this analysis to suggest that specific integration sites played any part either in the selection of pre-crisis clones or in the subsequent establishment of immortal lines.

Histopathology of tympanic membranes from patients with ventilation tubes.

PubMed

Oktay, Mehmet Faruk; Tansuker, Hasan Deniz; Fukushima, Hisaki; Paparella, Michael M; Schachern, Patricia A; Cureoglu, Sebahattin

2018-06-01

To evaluate the histopathologic changes in tympanic membranes (TMs) with ventilation tubes (VTs). In this retrospective human temporal bone study our overall study group included 4 subgroups of TMs from deceased donors as follows: 24 with a history of VT insertion for chronic otitis media with effusion (COME-VT); 5 with a history of VT insertion for Meniere's disease (MD-VT); 33 without a history of VT insertion for chronic otitis media with effusion (COME); and 14 without a history of VT insertion for Meniere's disease (MD). We classified the extent of migration of the outer keratinized squamous epithelium onto the inner surface of TM perforations and noted the presence and location of tympanosclerosis, of atrophy, of perforation, and/or of cholesteatoma formation. Tympanosclerosis occurred in 14/24 TMs in the COME-VT subgroup; 2/5, MD-VT; 7/33, COME; and 0/14, MD. The VT insertion site was mostly in the anteroinferior (63%) quadrant of the TM; tympanosclerosis occurred more frequently in the posteroinferior (42%) and posterosuperior (33%) quadrants. We found no significant correlation between the location of tympanosclerosis and the VT insertion site (P>0.05). Atrophy occurred in 7/24 TMs in the COME-VT subgroup; 3/5, MD-VT; 8/33, COME; and 2/14, MD. We found no significant correlation between the location of atrophy and the VT insertion site; however, atrophy was located mostly in the anteroinferior quadrant (one of the most common VT insertion sites) of the TM. Regarding the ingrowth of keratinized epithelium, the mucocutanous junction was detected at any point at the inner surface of the TM in 50% of the specimens. We observed intratympanic cholesteatoma formation in 2/24 TMs in the COME-VT subgroup. TM changes due to VT insertion are more common than previously realized. Meticulous otomicroscopic evaluation of the TM is necessary during tympanomastoidectomies in order to prevent the intratympanic inclusion pearls and squamous epithelial ingrowth to prevent any further cholesteatoma formation. Copyright © 2017. Published by Elsevier B.V.

Identification of Interleukin-27 (IL-27)/IL-27 Receptor Subunit Alpha as a Critical Immune Axis for In Vivo HIV Control.

PubMed

Ruiz-Riol, M; Berdnik, D; Llano, A; Mothe, B; Gálvez, C; Pérez-Álvarez, S; Oriol-Tordera, B; Olvera, A; Silva-Arrieta, S; Meulbroek, M; Pujol, F; Coll, J; Martinez-Picado, J; Ganoza, C; Sanchez, J; Gómez, G; Wyss-Coray, T; Brander, C

2017-08-15

Intact and broad immune cell effector functions and specific individual cytokines have been linked to HIV disease outcome, but their relative contribution to HIV control remains unclear. We asked whether the proteome of secreted cytokines and signaling factors in peripheral blood can be used to discover specific pathways critical for host viral control. A custom glass-based microarray, able to measure >600 plasma proteins involved in cell-to-cell communication, was used to measure plasma protein profiles in 96 HIV-infected, treatment-naive individuals with high (>50,000) or low (<10,000 HIV RNA copies/ml) viral loads. Univariate and regression model analysis demonstrate that plasma levels of soluble interleukin-27 (IL-27) are significantly elevated in individuals with high plasma viremia ( P < 0.0001) and are positively correlated with proviral HIV-DNA copy numbers in peripheral blood mononuclear cells (PBMC) (Rho = 0.4011; P = 0.0027). Moreover, soluble IL-27 plasma levels are negatively associated with the breadth and magnitude of the total virus-specific T-cell responses and directly with plasma levels of molecules involved in Wnt/β-catenin signaling. In addition to IL-27, gene expression levels of the specific IL-27 receptor ( IL27RA ) in PBMC correlated directly with both plasma viral load (Rho = 0.3531; P = 0.0218) and the proviral copy number in the peripheral blood as an indirect measure of partial viral reservoir (Rho = 0.4580; P = 0.0030). These results were validated in unrelated cohorts of early infected subjects as well as subjects before and after initiation of antiretroviral treatment, and they identify IL-27 and its specific receptor as a critical immune axis for the antiviral immune response and as robust correlates of viral load and proviral reservoir size in PBMC. IMPORTANCE The detailed knowledge of immune mechanisms that contribute to HIV control is a prerequisite for the design of effective treatment strategies to achieve HIV cure. Cells communicate with each other by secreting signaling proteins, and the blood is a key conduit for transporting such factors. Investigating the communication factors promoting effective immune responses and having potentially antiviral functions against HIV using a novel focused omics approach ("communicome") has the potential to significantly improve our knowledge of effective host immunity and accelerate the HIV cure agenda. Including 140 subjects with variable viral loads and measuring the plasma levels of >600 soluble proteins, our data highlight the importance of Th17 cells and Wnt/β-catenin signaling in HIV control and especially identify the IL-27/IL-27 receptor subunit alpha (IL-27RA) axis as a predictor of plasma viral load and proviral copy number in the peripheral blood. These data may provide important guidance to therapeutic approaches in the HIV cure agenda. Copyright © 2017 Ruiz-Riol et al.

Teaching Advanced SQL Skills: Text Bulk Loading

ERIC Educational Resources Information Center

Olsen, David; Hauser, Karina

2007-01-01

Studies show that advanced database skills are important for students to be prepared for today's highly competitive job market. A common task for database administrators is to insert a large amount of data into a database. This paper illustrates how an up-to-date, advanced database topic, namely bulk insert, can be incorporated into a database…

Unexpected dramatic increase in CD4+ cell count in a patient with AIDS after enfuvirtide treatment despite persistent viremia and resistance mutations.

PubMed

Soria, Alessandro; Cavarelli, Mariangela; Sala, Stefania; Alessandrini, Anna Ida; Scarlatti, Gabriella; Lazzarin, Adriano; Castagna, Antonella

2008-06-01

An unexpected dramatic immune recovery was observed in a patient with full-blown AIDS receiving enfuvirtide-based antiretroviral therapy after multiple treatment failures. A complex interplay of viral and host factors, including the control of X4 viruses and proviral burden, may favor immune restoration with HIV neutralizing activity, despite persistent viremia.

IUD knowledge and experience among family medicine residents.

PubMed

Schubert, Finn D; Herbitter, Cara; Fletcher, Jason; Gold, Marji

2015-06-01

The intrauterine device (IUD) is a highly effective contraceptive method with few contraindications; however, clinician lack of training in insertion and misconceptions about IUD risks are barriers to utilization. Previous research has shown gaps in IUD training in family medicine residency programs. An online survey addressing experience with IUD insertion, knowledge of patient eligibility and IUD risks, and intent to insert IUDs in practice was circulated to residents at 15 US family medicine residency programs. Programs were eligible to participate if they were receiving funding to enhance training in family planning and abortion care and interested in additional support to enhance IUD training. The overall response rate for the surveys was 76.1% (332/436). Experience with the levonorgestrel intrauterine system was more common than with the copper IUD. Residents performed well on knowledge questions, but many would not insert in common patient scenarios in which insertion was not contraindicated, including a history of sexually transmitted infection in the past 6 months (48.2% would not insert), a history of ectopic pregnancy (37.0%), no pap smear in the past year (30.7%), or if the patient was not in a monogamous relationship (29.2%). The vast majority of residents (88.7%) reported that they were likely or very likely to provide IUDs in their future family medicine practice. Although residents overwhelmingly expressed interest in providing IUDs after residency, our results suggest that additional clinical and didactic training is needed, particularly interventions targeted at dispelling misconceptions about patient eligibility for IUDs.

Characterization of simian T-cell leukemia virus type 1 in naturally infected Japanese macaques as a model of HTLV-1 infection

PubMed Central

2013-01-01

Background Human T-cell leukemia virus type 1 (HTLV-1) causes chronic infection leading to development of adult T-cell leukemia (ATL) and inflammatory diseases. Non-human primates infected with simian T-cell leukemia virus type 1 (STLV-1) are considered to constitute a suitable animal model for HTLV-1 research. However, the function of the regulatory and accessory genes of STLV-1 has not been analyzed in detail. In this study, STLV-1 in naturally infected Japanese macaques was analyzed. Results We identified spliced transcripts of STLV-1 corresponding to HTLV-1 tax and HTLV-1 bZIP factor (HBZ). STLV-1 Tax activated the NFAT, AP-1 and NF-κB signaling pathways, whereas STLV-1 bZIP factor (SBZ) suppressed them. Conversely, SBZ enhanced TGF-β signaling and induced Foxp3 expression. Furthermore, STLV-1 Tax activated the canonical Wnt pathway while SBZ suppressed it. STLV-1 Tax enhanced the viral promoter activity while SBZ suppressed its activation. Then we addressed the clonal proliferation of STLV-1+ cells by massively sequencing the provirus integration sites. Some clones proliferated distinctively in monkeys with higher STLV-1 proviral loads. Notably, one of the monkeys surveyed in this study developed T-cell lymphoma in the brain; STLV-1 provirus was integrated in the lymphoma cell genome. When anti-CCR4 antibody, mogamulizumab, was administered into STLV-1-infected monkeys, the proviral load decreased dramatically within 2 weeks. We observed that some abundant clones recovered after discontinuation of mogamulizumab administration. Conclusions STLV-1 Tax and SBZ have functions similar to those of their counterparts in HTLV-1. This study demonstrates that Japanese macaques naturally infected with STLV-1 resemble HTLV-1 carriers and are a suitable model for the investigation of persistent HTLV-1 infection and asymptomatic HTLV-1 carrier state. Using these animals, we verified that mogamulizumab, which is currently used as a drug for relapsed ATL, is also effective in reducing the proviral load in asymptomatic individuals. PMID:24156738

Single-cell heterogeneity and cell-cycle-related viral gene bursts in the human leukaemia virus HTLV-1

PubMed Central

Billman, Martin R; Rueda, David; Bangham, Charles R M

2017-01-01

Background: The human leukaemia virus HTLV-1 expresses essential accessory genes that manipulate the expression, splicing and transport of viral mRNAs.  Two of these genes, tax and hbz, also promote proliferation of the infected cell, and both genes are thought to contribute to oncogenesis in adult T-cell leukaemia/lymphoma.  The regulation of HTLV-1 proviral latency is not understood.  tax, on the proviral plus strand, is usually silent in freshly-isolated cells, whereas the minus-strand-encoded hbz gene is persistently expressed at a low level.  However, the persistently activated host immune response to Tax indicates frequent expression of tax in vivo.  Methods: We used single-molecule RNA-FISH to quantify the expression of HTLV-1 transcripts at the single-cell level in a total of >19,000 cells from five T-cell clones, naturally infected with HTLV-1, isolated by limiting dilution from peripheral blood of HTLV-1-infected subjects.  Results: We found strong heterogeneity both within and between clones in the expression of the proviral plus-strand (detected by hybridization to the tax gene) and the minus-strand ( hbz gene). Both genes are transcribed in bursts; tax expression is enhanced in the absence of hbz, while hbz expression increased in cells with high tax expression. Surprisingly, we found that hbz expression is strongly associated with the S and G 2/M phases of the cell cycle, independent of tax expression.  Contrary to current belief, hbz is not expressed in all cells at all times, even within one clone.  In hbz-positive cells, the abundance of hbz transcripts showed a very strong positive linear correlation with nuclear volume. Conclusions: The occurrence of intense, intermittent plus-strand gene bursts in independent primary HTLV-1-infected T-cell clones from unrelated individuals strongly suggests that the HTLV-1 plus-strand is expressed in bursts in vivo.  Our results offer an explanation for the paradoxical correlations observed between the host immune response and HTLV-1 transcription. PMID:29062917

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome

PubMed Central

Konkel, Miriam K.; Batzer, Mark A.

2010-01-01

It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified as the cause of genetic disorders, including cancer predisposition. Cancer cells are notorious for their genomic instability, and often show genomic rearrangements at the microscopic and submicroscopic level to which transposable elements (TEs) contribute. Here, we review the role of TEs in genome instability, with particular focus on non-LTR retrotransposons. Currently, three non-LTR retrotransposon families – long interspersed element 1 (L1), SVA (short interspersed element (SINE-R), variable number of tandem repeats (VNTR), and Alu), and Alu (a SINE) elements – mobilize in the human genome, and cause genomic instability through both insertion- and post-insertion-based mutagenesis. Due to the abundance and high sequence identity of TEs, they frequently mislead the homologous recombination repair pathway into non-allelic homologous recombination, causing deletions, duplications, and inversions. While less comprehensively studied, non-LTR retrotransposon insertions and TE-mediated rearrangements are probably more common in cancer cells than in healthy tissue. This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development. PMID:20307669

Biliary and pancreatic stenting: Devices and insertion techniques in therapeutic endoscopic retrograde cholangiopancreatography and endoscopic ultrasonography

PubMed Central

Mangiavillano, Benedetto; Pagano, Nico; Baron, Todd H; Arena, Monica; Iabichino, Giuseppe; Consolo, Pierluigi; Opocher, Enrico; Luigiano, Carmelo

2016-01-01

Stents are tubular devices made of plastic or metal. Endoscopic stenting is the most common treatment for obstruction of the common bile duct or of the main pancreatic duct, but also employed for the treatment of bilio-pancreatic leakages, for preventing post- endoscopic retrograde cholangiopancreatography pancreatitis and to drain the gallbladder and pancreatic fluid collections. Recent progresses in techniques of stent insertion and metal stent design are represented by new, fully-covered lumen apposing metal stents. These stents are specifically designed for transmural drainage, with a saddle-shape design and bilateral flanges, to provide lumen-to-lumen anchoring, reducing the risk of migration and leakage. This review is an update of the technique of stent insertion and metal stent deployment, of the most recent data available on stent types and characteristics and the new applications for biliopancreatic stents. PMID:26862364

The ATRX cDNA is prone to bacterial IS10 element insertions that alter its structure.

PubMed

Valle-García, David; Griffiths, Lyra M; Dyer, Michael A; Bernstein, Emily; Recillas-Targa, Félix

2014-01-01

The SWI/SNF-like chromatin-remodeling protein ATRX has emerged as a key factor in the regulation of α-globin gene expression, incorporation of histone variants into the chromatin template and, more recently, as a frequently mutated gene across a wide spectrum of cancers. Therefore, the availability of a functional ATRX cDNA for expression studies is a valuable tool for the scientific community. We have identified two independent transposon insertions of a bacterial IS10 element into exon 8 of ATRX isoform 2 coding sequence in two different plasmids derived from a single source. We demonstrate that these insertion events are common and there is an insertion hotspot within the ATRX cDNA. Such IS10 insertions produce a truncated form of ATRX, which significantly compromises its nuclear localization. In turn, we describe ways to prevent IS10 insertion during propagation and cloning of ATRX-containing vectors, including optimal growth conditions, bacterial strains, and suggested sequencing strategies. Finally, we have generated an insertion-free plasmid that is available to the community for expression studies of ATRX.

Anatomic variations found on dissection of depressor septi nasi muscles in cadavers.

PubMed

Ebrahimi, Ali; Nejadsarvari, Nasrin; Motamedi, Mohammad Hosein Kalantar; Rezaee, Maryam; Koushki, Ehsan Shams

2012-01-01

To define variations of the depressor septi muscle in Iranians; to provide guidance for modification of this muscle during rhinoplasty in patients with an active muscle and short upper lip; and to correlate our findings with our clinical experience to develop the applied algorithms. This study was conducted by dissecting 82 depressor septi nasi muscles in 41 Iranian cadavers. Origin and insertion points of each muscle were studied. Three variations were found in muscle insertion points: periosteal, orbicularis oris, and floating. Forty-four percent of the muscles were inserted into the periosteum of the maxilla (n = 36); 39% of muscles were inserted into the orbicularis oris muscle (n = 32); and 17% were diminutive or floating (n = 14). Periosteal insertion was thicker and stronger than the other variations. In all cadavers, the origin of the muscle was medial crus of alar cartilage and caudal of the nasal septum. This cadaveric dissection showed that the percentage of depressor septi muscle insertions is not similar to that found in other surveys. In this study, periosteal insertion of the depressor septi muscle was the most common variation.

Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses.

PubMed

Willemsen, Anouk; Carrasco, José L; Elena, Santiago F; Zwart, Mark P

2018-05-10

Horizontal gene transfer is common among viruses, while they also have highly compact genomes and tend to lose artificial genomic insertions rapidly. Understanding the stability of genomic insertions in viral genomes is therefore relevant for explaining and predicting their evolutionary patterns. Here, we revisit a large body of experimental research on a plant RNA virus, tobacco etch potyvirus (TEV), to identify the patterns underlying the stability of a range of homologous and heterologous insertions in the viral genome. We obtained a wide range of estimates for the recombination rate-the rate at which deletions removing the insertion occur-and these appeared to be independent of the type of insertion and its location. Of the factors we considered, recombination rate was the best predictor of insertion stability, although we could not identify the specific sequence characteristics that would help predict insertion instability. We also considered experimentally the possibility that functional insertions lead to higher mutational robustness through increased redundancy. However, our observations suggest that both functional and non-functional increases in genome size decreased the mutational robustness. Our results therefore demonstrate the importance of recombination rates for predicting the long-term stability and evolution of viral RNA genomes and suggest that there are unexpected drawbacks to increases in genome size for mutational robustness.

Informed peg-in-hole insertion using optical sensors

NASA Astrophysics Data System (ADS)

Paulos, Eric; Canny, John F.

1993-08-01

Peg-in-hole insertion is not only a longstanding problem in robotics but the most common automated mechanical assembly task. In this paper we present a high precision, self-calibrating peg-in-hole insertion strategy using several very simple, inexpensive, and accurate optical sensors. The self-calibrating feature allows us to achieve successful dead-reckoning insertions with tolerances of 25 microns without any accurate initial position information for the robot, pegs, or holes. The program we implemented works for any cylindrical peg, and the sensing steps do not depend on the peg diameter, which the program does not know. The key to the strategy is the use of a fixed sensor to localize both a mobile sensor and the peg, while the mobile sensor localizes the hole. Our strategy is extremely fast, localizing pegs as they are in route to their insertion location without pausing. The result is that insertion times are dominated by the transport time between pick and place operations.

An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data.

PubMed

Tsangaras, Kyriakos; Mayer, Jens; Alquezar-Planas, David E; Greenwood, Alex D

2015-11-24

Transcriptome analysis of polar bear (Ursus maritimus) tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV). Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs) of a newly described endogenous retrovirus were characterized from the polar bear draft genome sequence. Closely related sequences were identified by PCR analysis of brown bear (Ursus arctos) and black bear (Ursus americanus) but were absent in non-Ursinae bear species. The virus was therefore designated UrsusERV. Two distinct groups of LTRs were observed including a recombinant ERV that contained one LTR belonging to each group indicating that genomic invasions by at least two UrsusERV variants have recently occurred. Age estimates based on proviral LTR divergence and conservation of integration sites among ursids suggest the viral group is only a few million years old. The youngest provirus was polar bear specific, had intact open reading frames (ORFs) and could potentially encode functional proteins. Phylogenetic analyses of UrsusERV consensus protein sequences suggest that it is part of a pig, gibbon and koala retrovirus clade. The young age estimates and lineage specificity of the virus suggests UrsusERV is a recent cross species transmission from an unknown reservoir and places the viral group among the youngest of ERVs identified in mammals.

Proviral Latency, Persistent Human Immunodeficiency Virus Infection, and the Development of Latency Reversing Agents

PubMed Central

Archin, Nancie M.

2017-01-01

Abstract Quiescent proviral genomes that persist during human immunodeficiency virus type 1 (HIV-1) infection despite effective antiretroviral therapy (ART) can fuel rebound viremia after ART interruption and is a central obstacle to the cure of HIV infection. The induction of quiescent provirus is the goal of a new class of potential therapeutics, latency reversing agents (LRAs). The discovery, development, and testing of HIV LRAs is a key part of current efforts to develop latency reversal and viral clearance strategies to eradicate established HIV infection. The development of LRAs is burdened by many uncertainties that make drug discovery difficult. The biology of HIV latency is complex and incompletely understood. Potential targets for LRAs are host factors, and the potential toxicities of host-directed therapies in individuals that are otherwise clinically stable may be unacceptable. Assays to measure latency reversal and assess the effectiveness of potential therapeutics are complex and incompletely validated. Despite these obstacles, novel LRAs are under development and beginning to enter combination testing with viral clearance strategies. It is hoped that the steady advances in the development of LRAs now being paired with emerging immunotherapeutics to clear persistently infected cells will soon allow measurable clinical advances toward an HIV cure. PMID:28520964

Evaluation of viremia, proviral load and cytokine profile in naturally feline immunodeficiency virus infected cats treated with two different protocols of recombinant feline interferon omega.

PubMed

Leal, Rodolfo O; Gil, Solange; Duarte, Ana; McGahie, David; Sepúlveda, Nuno; Niza, Maria M R E; Tavares, Luís

2015-04-01

This study assesses viremia, provirus and blood cytokine profile in naturally FIV-infected cats treated with two distinct protocols of interferon omega (rFeIFN-ω). Samples from FIV-cats previously submitted to two single-arm studies were used: 7/18 received the licensed/subcutaneous protocol (SC) while 11/18 were treated orally (PO). Viremia, provirus and blood mRNA expression of interleukin (IL)-1, IL-4, IL-6, IL-10, IL-12p40, Interferon-γ and Tumor Necrosis Factor-α were monitored by Real-Time qPCR. Concurrent plasma levels of IL-6, IL-12p40 and IL-4 were assessed by ELISA. IL-6 plasma levels decreased in the SC group (p = 0.031). IL-6 mRNA expression (p = 0.037) decreased in the PO group, albeit not sufficiently to change concurrent plasma levels. Neither viremia nor other measured cytokines changed with therapy. Proviral load increased in the SC group (p = 0.031), which can be justified by a clinically irrelevant increase of lymphocyte count. Independently of the protocol, rFeIFN-ω seems to act on innate immunity by reducing pro-inflammatory stimulus. Copyright © 2015 Elsevier Ltd. All rights reserved.

A contaminant-free assessment of Endogenous Retroviral RNA in human plasma

PubMed Central

Karamitros, Timokratis; Paraskevis, Dimitrios; Hatzakis, Angelos; Psichogiou, Mina; Elefsiniotis, Ioannis; Hurst, Tara; Geretti, Anna-Maria; Beloukas, Apostolos; Frater, John; Klenerman, Paul; Katzourakis, Aris; Magiorkinis, Gkikas

2016-01-01

Endogenous retroviruses (ERVs) comprise 6–8% of the human genome. HERVs are silenced in most normal tissues, up-regulated in stem cells and in placenta but also in cancer and HIV-1 infection. Crucially, there are conflicting reports on detecting HERV RNA in non-cellular clinical samples such as plasma that suggest the study of HERV RNA can be daunting. Indeed, we find that the use of real-time PCR in a quality assured clinical laboratory setting can be sensitive to low-level proviral contamination. We developed a mathematical model for low-level contamination that allowed us to design a laboratory protocol and standard operating procedures for robust measurement of HERV RNA. We focus on one family, HERV-K HML-2 (HK2) that has been most recently active even though they invaded our ancestral genomes almost 30 millions ago. We extensively validated our experimental design on a model cell culture system showing high sensitivity and specificity, totally eliminating the proviral contamination. We then tested 236 plasma samples from patients infected with HIV-1, HCV or HBV and found them to be negative. The study of HERV RNA for human translational studies should be performed with extensively validated protocols and standard operating procedures to control the widespread low-level human DNA contamination. PMID:27640347

Zinc finger nuclease: a new approach for excising HIV-1 proviral DNA from infected human T cells.

PubMed

Qu, Xiying; Wang, Pengfei; Ding, Donglin; Wang, Xiaohui; Zhang, Gongmin; Zhou, Xin; Liu, Lin; Zhu, Xiaoli; Zeng, Hanxian; Zhu, Huanzhang

2014-09-01

A major reason that Acquired Immune Deficiency Syndrome (AIDS) cannot be completely cured is the human immunodeficiency virus 1 (HIV-1) provirus integrated into the human genome. Though existing therapies can inhibit replication of HIV-1, they cannot eradicate it. A molecular therapy gains popularity due to its specifically targeting to HIV-1 infected cells and effectively removing the HIV-1, regardless of viral genes being active or dormant. Now, we propose a new method which can excellently delete the HIV provirus from the infected human T cell genome. First, we designed zinc-finger nucleases (ZFNs) that target a sequence within the long terminal repeat (LTR) U3 region that is highly conserved in whole clade. Then, we screened out one pair of ZFN and named it as ZFN-U3. We discovered that ZFN-U3 can exactly target and eliminate the full-length HIV-1 proviral DNA after the infected human cell lines treated with it, and the frequency of its excision was about 30 % without cytotoxicity. These results prove that ZFN-U3 can efficiently excise integrated HIV-1 from the human genome in infected cells. This method to delete full length HIV-1 in human genome can therefore provide a novel approach to cure HIV-infected individuals in the future.

An Evolutionarily Young Polar Bear (Ursus maritimus) Endogenous Retrovirus Identified from Next Generation Sequence Data

PubMed Central

Tsangaras, Kyriakos; Mayer, Jens; Alquezar-Planas, David E.; Greenwood, Alex D.

2015-01-01

Transcriptome analysis of polar bear (Ursus maritimus) tissues identified sequences with similarity to Porcine Endogenous Retroviruses (PERV). Based on these sequences, four proviral copies and 15 solo long terminal repeats (LTRs) of a newly described endogenous retrovirus were characterized from the polar bear draft genome sequence. Closely related sequences were identified by PCR analysis of brown bear (Ursus arctos) and black bear (Ursus americanus) but were absent in non-Ursinae bear species. The virus was therefore designated UrsusERV. Two distinct groups of LTRs were observed including a recombinant ERV that contained one LTR belonging to each group indicating that genomic invasions by at least two UrsusERV variants have recently occurred. Age estimates based on proviral LTR divergence and conservation of integration sites among ursids suggest the viral group is only a few million years old. The youngest provirus was polar bear specific, had intact open reading frames (ORFs) and could potentially encode functional proteins. Phylogenetic analyses of UrsusERV consensus protein sequences suggest that it is part of a pig, gibbon and koala retrovirus clade. The young age estimates and lineage specificity of the virus suggests UrsusERV is a recent cross species transmission from an unknown reservoir and places the viral group among the youngest of ERVs identified in mammals. PMID:26610552

Prime-boost vaccination using DNA and whole inactivated virus vaccines provides limited protection against virulent feline immunodeficiency virus.

PubMed

Dunham, Stephen P; Bruce, Jennifer; Klein, Dieter; Flynn, J Norman; Golder, Matthew C; MacDonald, Susan; Jarrett, Oswald; Neil, James C

2006-11-30

Protection against feline immunodeficiency virus (FIV) has been achieved using a variety of vaccines notably whole inactivated virus (WIV) and DNA. However protection against more virulent isolates, typical of those encountered in natural infections, has been difficult to achieve. In an attempt to improve protection against virulent FIV(GL8), we combined both DNA and WIV vaccines in a "prime-boost" approach. Thirty cats were divided into four groups receiving vaccinations and one unvaccinated control group. Following viral challenge, two vaccinated animals, one receiving DNA alone and one the prime-boost vaccine remained free of viraemia, whilst all controls became viraemic. Animals vaccinated with WIV showed apparent early enhancement of infection at 2 weeks post challenge (pc) with higher plasma viral RNA loads than control animals or cats immunised with DNA alone. Despite this, animals vaccinated with WIV or DNA alone showed significantly lower proviral loads in peripheral blood mononuclear cells and mesenteric lymph node cells, whilst those receiving the DNA-WIV prime-boost vaccine showed significantly lower proviral loads in PBMC, than control animals, at 35 weeks pc. Therefore both DNA and WIV vaccines conferred limited protection against viral challenge but the combination of WIV and DNA in a prime-boost approach appeared to offer no significant advantage over either vaccine alone.

Hot topic: Bovine leukemia virus (BLV)-infected cows with low proviral load are not a source of infection for BLV-free cattle.

PubMed

Juliarena, Marcela A; Barrios, Clarisa N; Ceriani, M Carolina; Esteban, Eduardo N

2016-06-01

The bovine leukemia virus (BLV) causes leukemia or lymphoma in cattle. Although most BLV-infected animals do not develop the disease, they maintain the transmission chain of BLV at the herd level. As a feasible approach to control the virus, selection of cattle carrying the BoLA-DRB3*0902 allele has been proposed, as this allele is strongly associated with a BLV infection profile or the low proviral load (LPL) phenotype. To test whether these cattle affect the BLV transmission chain under natural conditions, selected BLV-infected LPL-BoLA-DRB3*0902 heterozygous cows were incorporated into a BLV-negative dairy herd. An average ratio of 5.4 (range 4.17-6.37) BLV-negative cows per BLV-infected cow was maintained during the 20mo of the experiment, and no BLV-negative cattle became infected. The BLV incidence rate in this herd was thus zero, whereas BLV incidence rates in different local herds varied from 0.06 to 0.17 cases per 100 cattle-days. This finding strongly suggests that LPL-BoLA-DRB3*0902 cattle disrupted the BLV-transmission chain in the study period. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Urethral Foreign Bodies: Clinical Presentation and Management.

PubMed

Palmer, Cristina J; Houlihan, Matthew; Psutka, Sarah P; Ellis, K Alexandria; Vidal, Patricia; Hollowell, Courtney M P

2016-11-01

To review a single institution's 15-year experience with urethral foreign bodies, including evaluation, clinical findings, and treatment. In total, 27 patients comprising 35 episodes of inserted urethral foreign bodies were reviewed at Cook County Hospital between 2000 and 2015. Retrospective chart review was performed to describe the clinical presentation, rationale for insertion, management, recidivism, and sequelae. Median patient age was 26 (range 12-60). Twenty-six patients (97 %) were male, 1 was female (3%). Items inserted included pieces of plastic forks, spoons, metal screws and aluminum, pieces of cardboard or paper, staples, writing utensils such as pens and pencils, as well as coaxial cable and spray foam sealant. Reported reasons for insertion were self-stimulation, erectile enhancement, and attention seeking. Presenting symptoms included dysuria, gross hematuria, urinary retention, urinary tract infection, and penile discharge. The most common technique for removal was manual extraction with extrinsic pressure (n = 19, 54%). Other methods include endoscopic retrieval (n = 8, 23%), open cystotomy (n = 1, 3%), and voiding to expel the foreign body (n = 7, 20%). Postremoval complications included urinary tract infection (n = 7), sepsis (n = 4), urethral false passage (n = 5), laceration (n = 5), and stricture (n = 1). We present the largest single-institutional series of urethral foreign bodies to date. Urethral foreign body insertion is a relatively rare occurrence and, commonly, is a recurrent behavior. Urethral trauma related to foreign body insertion is associated with significant risk of infection and urethral injury with long-term sequelae. Copyright © 2016 Elsevier Inc. All rights reserved.

A mobile threat to genome stability: The impact of non-LTR retrotransposons upon the human genome.

PubMed

Konkel, Miriam K; Batzer, Mark A

2010-08-01

It is now commonly agreed that the human genome is not the stable entity originally presumed. Deletions, duplications, inversions, and insertions are common, and contribute significantly to genomic structural variations (SVs). Their collective impact generates much of the inter-individual genomic diversity observed among humans. Not only do these variations change the structure of the genome; they may also have functional implications, e.g. altered gene expression. Some SVs have been identified as the cause of genetic disorders, including cancer predisposition. Cancer cells are notorious for their genomic instability, and often show genomic rearrangements at the microscopic and submicroscopic level to which transposable elements (TEs) contribute. Here, we review the role of TEs in genome instability, with particular focus on non-LTR retrotransposons. Currently, three non-LTR retrotransposon families - long interspersed element 1 (L1), SVA (short interspersed element (SINE-R), variable number of tandem repeats (VNTR), and Alu), and Alu (a SINE) elements - mobilize in the human genome, and cause genomic instability through both insertion- and post-insertion-based mutagenesis. Due to the abundance and high sequence identity of TEs, they frequently mislead the homologous recombination repair pathway into non-allelic homologous recombination, causing deletions, duplications, and inversions. While less comprehensively studied, non-LTR retrotransposon insertions and TE-mediated rearrangements are probably more common in cancer cells than in healthy tissue. This may be at least partially attributed to the commonly seen global hypomethylation as well as general epigenetic dysfunction of cancer cells. Where possible, we provide examples that impact cancer predisposition and/or development. Copyright © 2010 Elsevier Ltd. All rights reserved.

The incidence of blood contamination of lead unit dose containers with and without single-use protective inserts used with commercially prepared radiopharmaceutical unit doses.

PubMed

Pickett, M W; Kosegi, J E; Thomas, K S; Waterstram-Rich, K M

1998-09-01

This investigation evaluated the effectiveness of disposable plastic inserts in radiopharmaceutical unit dose lead containers (pigs) in preventing the distribution of doses in blood-contaminated containers. Technologists commonly dispose of the syringes by placing them into the lead pigs, leaving the needles uncapped. This process raises the question of unsuspected blood contamination of these pigs. Consequently, the distribution of commercially prepared radiopharmaceutical doses in reusable lead pigs may result in radiopharmaceutical doses being distributed in containers that are contaminated with blood. Using a simple chemical wipe test designed to determine the presence or absence of blood contamination, 618 pigs from commercial radiopharmacies throughout the U.S. were tested for contamination. The inside of the pigs and inserts, if present, were wiped before and after dose administration. Of the pigs tested, 292 came from radiopharmacies that used a protective, disposable plastic insert inside the pig, and 326 came from radiopharmacies that did not use an insert. Of those pigs without the protective disposable inserts, 39.3% arrived in the nuclear medicine department in pigs contaminated with blood. Of those pigs with inserts, 1% arrived with blood-contaminated inserts. After dose administration, 46.3% of the pigs without inserts were contaminated with blood and 3% of the protective inserts were contaminated. The proper use of disposable plastic inserts reduces the possibility of distributing radiopharmaceutical unit doses in containers contaminated with blood.

Current microbiology of percutaneous endoscopic gastrostomy tube (PEG tube) insertion site infections in patients with cancer.

PubMed

Rolston, Kenneth V I; Mihu, Coralia; Tarrand, Jeffrey J

2011-08-01

Percutaneous endoscopic gastrostomy (PEG) is frequently used to provide enteral access in cancer patients who are unable to swallow. Infection is an important complication in this setting. Current microbiological data are needed to guide infection prevention and treatment strategies. The microbiological records of our institution (a 550-bed comprehensive cancer center) were retrospectively reviewed over an 8-month study period in order to identify patients who developed PEG tube insertion site infections, and review their microbiological details and susceptibility/resistance data. Fifty-eight episodes of PEG tube insertion site infections were identified. Of these, 31 (53%) were monomicrobial, and the rest were polymicrobial. The most common organisms isolated were Candida species, Staphylococcus aureus, and Pseudomonas aeruginosa. All infections were local (cellulitis, complicated skin, and skin structure infections including abdominal wall abscess) with no cases of concomitant bacteremia being documented. Most of the organisms isolated were susceptible to commonly used antimicrobial agents, although some quinolone-resistant and some multidrug-resistant organisms were isolated. This retrospective study provides descriptive data regarding PEG tube insertion site infections. These data have helped us update institutional guidelines for infection prevention and treatment as part of our focus on antimicrobial stewardship.

Soft Tissue Phantoms for Realistic Needle Insertion: A Comparative Study.

PubMed

Leibinger, Alexander; Forte, Antonio E; Tan, Zhengchu; Oldfield, Matthew J; Beyrau, Frank; Dini, Daniele; Rodriguez Y Baena, Ferdinando

2016-08-01

Phantoms are common substitutes for soft tissues in biomechanical research and are usually tuned to match tissue properties using standard testing protocols at small strains. However, the response due to complex tool-tissue interactions can differ depending on the phantom and no comprehensive comparative study has been published to date, which could aid researchers to select suitable materials. In this work, gelatin, a common phantom in literature, and a composite hydrogel developed at Imperial College, were matched for mechanical stiffness to porcine brain, and the interactions during needle insertions within them were analyzed. Specifically, we examined insertion forces for brain and the phantoms; we also measured displacements and strains within the phantoms via a laser-based image correlation technique in combination with fluorescent beads. It is shown that the insertion forces for gelatin and brain agree closely, but that the composite hydrogel better mimics the viscous nature of soft tissue. Both materials match different characteristics of brain, but neither of them is a perfect substitute. Thus, when selecting a phantom material, both the soft tissue properties and the complex tool-tissue interactions arising during tissue manipulation should be taken into consideration. These conclusions are presented in tabular form to aid future selection.

The evaluation of lateral pterygoid muscle pathologic changes and insertion patterns in temporomandibular joints with or without disc displacement using magnetic resonance imaging.

PubMed

Imanimoghaddam, M; Madani, A S; Hashemi, E M

2013-09-01

Temporomandibular joint (TMJ) disc displacement is a common disorder in patients with internal derangement. Certain anatomic features of TMJ may make the patient prone to this condition, namely lateral pterygoid muscle (LPM) insertion variations. The aim of this study was to investigate LPM attachments and their relationships with disc displacement and subsequent pathologic changes. A total of 26 patients with clinical temporomandibular disorders (TMDs) and a control group of 14 unaffected individuals were studied. Magnetic resonance images (MRIs) were taken to evaluate LPM insertion patterns, superior LPM head pathologic changes, and relative disc to condyle position. Data registration and analysis were done using SPSS v. 16.0. The most common variation (type I) was shown to be the superior head with two bundles, one attached to the disc and another to the condyle. No significant relationship between LPM insertion type and disc displacement or pathologic changes of the muscle was found. However, a link between disc displacement and muscle pathologic changes was established (P=0.001). Copyright © 2013 International Association of Oral and Maxillofacial Surgeons. Published by Elsevier Ltd. All rights reserved.

Molecular Studies of HTLV-1 in a Newly Recognized High Risk Population (AIDS).

DTIC Science & Technology

1992-06-16

proviral DNA from preipheral blood mononuclear cells DNA . Overall rate of infection if 12% for Jews arriving from Khurusan-North-Eastern Iran. No...to policies of applicable Federal Law 45 CFR 46. .1 ) In conducting research utilizing recombinant DNA technology,theestigator(s) adhered to current...clustering and outbreaks of HD suggest possible viral ethiology (11-13). The increasingly frequent reports of Epstein Bar Virus ( EBV ) genome detection

Design and implementation of an external quality assessment program for HIV viral load measurements using dried blood spots.

PubMed

Prach, Lisa M; Puren, Adrian; Lippman, Sheri A; Carmona, Sergio; Stephenson, Sophie; Cutler, Ewalde; Barnhart, Scott; Liegler, Teri

2015-03-01

An external quality assurance program was developed for HIV-1 RNA viral load measurements taken from dried blood spots using a reference panel and field-collected specimens. The program demonstrated that accurate and reproducible quantitation can be obtained from field-collected specimens. Residual proviral DNA may confound interpretation in virologically suppressed subjects. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Readability assessment of package inserts of biological medicinal products from the European medicines agency website.

PubMed

Piñero-López, Ma Ángeles; Modamio, Pilar; Lastra, Cecilia F; Mariño, Eduardo L

2014-07-01

Package inserts that accompany medicines are a common source of information aimed at patients and should match patient abilities in terms of readability. Our objective was to determine the degree of readability of the package inserts for biological medicinal products commercially available in 2007 and compare them with the readability of the same package inserts in 2010. A total of 33 package inserts were selected and classified into five groups according to the type of medicine: monoclonal antibody-based products, cytokines, therapeutic enzymes, recombinant blood factors and other blood-related products, and recombinant hormones. The package inserts were downloaded from the European Medicines Agency website in 2007 and 2010. Readability was evaluated for the entire text of five of the six sections of the package inserts and for the 'Annex' when there was one. Three readability formulas were used: SMOG (Simple Measure of Gobbledygook) grade, Flesh-Kincaid grade level, and Szigriszt's perspicuity index. No significant differences were found between the readability results for the 2007 package inserts and those from 2010 according to any of the three readability indices studied (p>0.05). However, there were significant differences (p<0.05) between the readability scores of the sections of the package inserts in both 2007 and 2010. The readability of the package inserts was above the recommended sixth grade reading level (ages 11-12) and may lead to difficulties of understanding for people with limited literacy. All the sections should be easy to read and, therefore, the readability of the medicine package inserts studied should be improved.

Human lamina cribrosa insertion and age.

PubMed

Sigal, Ian A; Flanagan, John G; Lathrop, Kira L; Tertinegg, Inka; Bilonick, Richard

2012-10-03

To test the hypothesis that in healthy human eyes the lamina cribrosa (LC) insertion into the pia mater increases with age. The optic nerve heads (ONHs) of donor eyes fixed at either 5 or 50 mm Hg of IOP were sectioned, stained, and imaged under bright- and dark-field conditions. A 3-dimensional (3D) model of each ONH was reconstructed. From the 3D models we measured the area of LC insertion into the peripapillary scleral flange and into the pia, and computed the total area of insertion and fraction of LC inserting into the pia. Linear mixed effect models were used to determine if the measurements were associated with age or IOP. We analyzed 21 eyes from 11 individuals between 47 and 91 years old. The LC inserted into the pia in all eyes. The fraction of LC inserting into the pia (2.2%-29.6%) had a significant decrease with age (P = 0.049), which resulted from a nonsignificant increase in the total area of LC insertion (P = 0.41) and a nonsignificant decrease in the area of LC insertion into the pia (P = 0.55). None of the measures was associated with fixation IOP (P values 0.44-0.81). Differences between fellow eyes were smaller than differences between unrelated eyes. The LC insertion into the pia mater is common in middle-aged and older eyes, and does not increase with age. The biomechanical and vascular implications of the LC insertion into the pia mater are not well understood and should be investigated further.

Human Lamina Cribrosa Insertion and Age

PubMed Central

Sigal, Ian A.; Flanagan, John G.; Lathrop, Kira L.; Tertinegg, Inka; Bilonick, Richard

2012-01-01

Purpose. To test the hypothesis that in healthy human eyes the lamina cribrosa (LC) insertion into the pia mater increases with age. Methods. The optic nerve heads (ONHs) of donor eyes fixed at either 5 or 50 mm Hg of IOP were sectioned, stained, and imaged under bright- and dark-field conditions. A 3-dimensional (3D) model of each ONH was reconstructed. From the 3D models we measured the area of LC insertion into the peripapillary scleral flange and into the pia, and computed the total area of insertion and fraction of LC inserting into the pia. Linear mixed effect models were used to determine if the measurements were associated with age or IOP. Results. We analyzed 21 eyes from 11 individuals between 47 and 91 years old. The LC inserted into the pia in all eyes. The fraction of LC inserting into the pia (2.2%–29.6%) had a significant decrease with age (P = 0.049), which resulted from a nonsignificant increase in the total area of LC insertion (P = 0.41) and a nonsignificant decrease in the area of LC insertion into the pia (P = 0.55). None of the measures was associated with fixation IOP (P values 0.44–0.81). Differences between fellow eyes were smaller than differences between unrelated eyes. Conclusions. The LC insertion into the pia mater is common in middle-aged and older eyes, and does not increase with age. The biomechanical and vascular implications of the LC insertion into the pia mater are not well understood and should be investigated further. PMID:22956611

Risk of venous thromboembolism in hospitalized patients with peripherally inserted central catheters.

PubMed

Lobo, Bob L; Vaidean, Georgeta; Broyles, Joyce; Reaves, Anne B; Shorr, Ronald I

2009-09-01

Peripherally inserted central catheters (PICC) are increasingly used in hospitalized patients. The benefit can be offset by complications such as upper extremity deep vein thrombosis (UEDVT). Retrospective study of patients who received a PICC while hospitalized at the Methodist University Hospital (MUH) in Memphis, TN. All adult consecutive patients who had PICCs inserted during the study period and who did not have a UEDVT at the time of PICC insertion were included in the study. A UEDVT was defined as a symptomatic event in the ipsilateral extremity, leading to the performance of duplex ultrasonography, which confirmed the diagnosis of UEDVT. Pulmonary embolism (PE) was defined as a symptomatic event prompting the performance of ventilation-perfusion lung scan or spiral computed tomography (CT). Among 777 patients, 38 patients experienced 1 or more venous thromboembolisms (VTEs), yielding an incidence of 4.89%. A total of 7444 PICC-days were recorded for 777 patients. This yields a rate of 5.10 VTEs/1000 PICC-days. Compared to patients whose PICC was inserted in the SVC, patients whose PICC was in another location had an increased risk (odds ratio = 2.61 [95% CI = 1.28-5.35]) of VTE. PICC related VTE was significantly more common among patients with a past history of VTE (odds ratio = 10.83 [95% CI = 4.89-23.95]). About 5% of patients undergoing PICC placement in acute care hospitals will develop thromboembolic complications. Thromboembolic complications were especially common among persons with a past history of VTE. Catheter tip location at the time of insertion may be an important modifiable risk factor. Copyright 2009 Society of Hospital Medicine.

A randomized non-crossover study comparing the ProSeal and Classic laryngeal mask airway in anaesthetized children.

PubMed

Lopez-Gil, M; Brimacombe, J; Garcia, G

2005-12-01

We tested the hypothesis that ease of insertion, oropharyngeal leak pressure, fibreoptic position, gastric insufflation, and the frequency of mucosal trauma differ between the ProSeal laryngeal mask airway (PLMA) and the classic laryngeal mask airway (cLMA) in anaesthetized children. For the PLMA, we also assessed the ease of gastric tube placement via the PLMA drain tube and measure residual gastric volume. 240 consecutive ASA I-III children aged 1-16 yr were randomized for airway management with the ProSeal or cLMA. The time taken to provide an effective airway, the number of insertion attempts, fibreoptic position of the airway tube and frequency of mucosal trauma were similar, but oropharyngeal leak pressure was higher (33 vs 26 cm H(2)O, P<0.0001) and gastric insufflation less common (0 vs 6%, P<0.01) for the PLMA. Gastric tube insertion was successful at the first attempt in 106 of 120, and at the second attempt in 14 of 120. The mean (sd; range) value for residual gastric volume was 2.2 (5.9; 0-30) ml. There were no differences in performance among sizes for the PLMA and the cLMA. We conclude that ease of insertion, fibreoptic position, and frequency of mucosal trauma are similar for the PLMA and cLMA in children, but oropharyngeal leak pressure is higher and gastric insufflation less common for the PLMA. Gastric tube insertion has a high success rate, provided the PLMA is correctly positioned.

The zebrafish spiel-ohne-grenzen (spg) gene encodes the POU domain protein Pou2 related to mammalian Oct4 and is essential for formation of the midbrain and hindbrain, and for pre-gastrula morphogenesis.

PubMed

Burgess, Shawn; Reim, Gerlinde; Chen, Wenbiao; Hopkins, Nancy; Brand, Michael

2002-02-01

In early embryonic development, the brain is divided into three main regions along the anteroposterior axis: the forebrain, midbrain and hindbrain. Through retroviral insertional mutagenesis and chemical mutagenesis experiments in zebrafish, we have isolated mutations that cause abnormal hindbrain organization and a failure of the midbrain-hindbrain boundary (MHB) to form, a region that acts as an organizer for the adjacent brain regions. The mutations fail to complement the spiel-ohne-grenzen (spg) mutation, which causes a similar phenotype, but for which the affected gene is unknown. We show through genetic mapping, cloning of the proviral insertion site and allele sequencing that spg mutations disrupt pou2, a gene encoding the Pou2 transcription factor. Based on chromosomal synteny, phylogenetic sequence comparison, and expression and functional data, we suggest that pou2 is the zebrafish ortholog of mouse Oct3/Oct4 and human POU5F1. For the mammalian genes, a function in brain development has so far not been described. In the absence of functional pou2, expression of markers for the midbrain, MHB and the hindbrain primordium (pax2.1, wnt1, krox20) are severely reduced, correlating with the neuroectoderm-specific expression phase of pou2. Injection of pou2 mRNA restores these defects in spg mutant embryos, but does not activate these markers ectopically, demonstrating a permissive role for pou2. Injections of pou2-morpholinos phenocopy the spg phenotype at low concentration, further proving that spg encodes pou2. Two observations suggest that pou2 has an additional earlier function: higher pou2-morpholino concentrations specifically cause a pre-gastrula arrest of cell division and morphogenesis, and expression of pou2 mRNA itself is reduced in spg-homozygous embryos at this stage. These experiments suggest two roles for pou2. Initially, Pou2 functions during early proliferation and morphogenesis of the blastomeres, similar to Oct3/4 in mammals during formation of the inner cell mass. During zebrafish brain formation, Pou2 then functions a second time to activate gene expression in the midbrain and hindbrain primordium, which is reflected at later stages in the specific lack in spg embryos of the MHB and associated defects in the mid- and hindbrain.

Incorporation of excess wild-type and mutant tRNA(3Lys) into human immunodeficiency virus type 1.

PubMed Central

Huang, Y; Mak, J; Cao, Q; Li, Z; Wainberg, M A; Kleiman, L

1994-01-01

Human immunodeficiency virus (HIV) particles produced in COS-7 cells transfected with HIV type 1 (HIV-1) proviral DNA contain 8 molecules of tRNA(3Lys) per 2 molecules of genomic RNA and 12 molecules of tRNA1,2Lys per 2 molecules of genomic RNA. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a human tRNA3Lys gene, there is a large increase in the amount of cytoplasmic tRNA3Lys per microgram of total cellular RNA, and the tRNA3Lys content in the virus increases from 8 to 17 molecules per 2 molecules of genomic RNA. However, the total number of tRNALys molecules per 2 molecules of genomic RNA remains constant at 20; i.e., the viral tRNA1,2Lys content decreases from 12 to 3 molecules per 2 molecules of genomic RNA. All detectable tRNA3Lys is aminoacylated in the cytoplasm of infected cells and deacylated in the virus. When COS-7 cells are transfected with a plasmid containing both HIV-1 proviral DNA and a mutant amber suppressor tRNA3Lys gene (in which the anticodon is changed from TTT to CTA), there is also a large increase in the relative concentration of cytoplasmic tRNA3Lys, and the tRNA3Lys content in the virus increases from 8 to 15 molecules per 2 molecules of genomic RNA, with a decrease in viral tRNA1,2Lys from 12 to 5 molecules per 2 molecules of genomic RNA. Thus, the total number of molecules of tRNALys in the virion remains at 20. The alteration of the anticodon has little effect on the viral packaging of this mutant tRNA in spite of the fact that it no longer contains the modified base mcm 5s2U at position 34, and its ability to be aminoacylated is significantly impaired compared with that of wild-type tRNA3Lys. Viral particles which have incorporated either excess wild-type tRNA3Lys or mutant suppressor tRNA3Lys show no differences in viral infectivity compared with wild-type HIV-1. Images PMID:7966556

A Study of Use of “PORT” Catheter in Patients with Cancer: A Single-Center Experience

PubMed Central

Madabhavi, Irappa; Patel, Apurva; Sarkar, Malay; Anand, Asha; Panchal, Harsha; Parikh, Sonia

2017-01-01

Background: Effective and reliable venous access is one of the cornerstones of modern medical therapy in oncology. Materials and methods: This is a prospective observational study, which collected data of patients who require “PORT” catheter insertion for any cancer, at a tertiary care oncology hospital in Ahmadabad, Gujarat, India, during a 2-year period. Aims and objectives: The main objective of this study was to study the various complications and outcomes related to “PORT” catheters. Results: “PORT” catheter was inserted in 100 patients and was most commonly used in solid malignancies (n = 86, 86%), followed by hematologic malignancies (n = 14, 14%). Among the solid malignancies, breast cancer (38, 38%) was the most common underlying disease, whereas among the hematologic malignancies, acute lymphoblastic leukemia (6, 6%) was the most common underlying disease for “PORT” catheter insertion. Chemotherapy was started on the first day of “PORT” catheter in 74% of patients in the “PORT” study group. The various complications developed in the “PORT” study group in the descending order are as follows: 4 patients (4%) developed early infection (⩽30 days after “PORT” placement), 4 (4%) late infection (⩾30 days after “PORT” placement), 4 (4%) bloodstream infection, 2 (2%) local skin infection at the “PORT” insertion site, 2 (2%) dislodgment of the “PORT” catheter, 2 (2%) fracture of the “PORT” catheter, and 1 recurrent pleural effusion. One patient (1%) developed thrombosis as the complication of “PORT” catheter insertion. Conclusions: The most disturbing aspect of treatment for a patient with cancer is multiple painful venipunctures made for administration of cytotoxic agents, antibiotics, blood products, and nutritional supplements. The focus of this prospective observational research is to study the various underlying diseases for which “PORT” catheter is needed in different solid and hematologic malignancies and the various complications and outcomes in pediatric and adult patients with cancer. PMID:28469510

Discovery of a novel retrovirus sequence in an Australian native rodent (Melomys burtoni): a putative link between gibbon ape leukemia virus and koala retrovirus.

PubMed

Simmons, Greg; Clarke, Daniel; McKee, Jeff; Young, Paul; Meers, Joanne

2014-01-01

Gibbon ape leukaemia virus (GALV) and koala retrovirus (KoRV) share a remarkably close sequence identity despite the fact that they occur in distantly related mammals on different continents. It has previously been suggested that infection of their respective hosts may have occurred as a result of a species jump from another, as yet unidentified vertebrate host. To investigate possible sources of these retroviruses in the Australian context, DNA samples were obtained from 42 vertebrate species and screened using PCR in order to detect proviral sequences closely related to KoRV and GALV. Four proviral partial sequences totalling 2880 bases which share a strong similarity with KoRV and GALV were detected in DNA from a native Australian rodent, the grassland melomys, Melomys burtoni. We have designated this novel gammaretrovirus Melomys burtoni retrovirus (MbRV). The concatenated nucleotide sequence of MbRV shares 93% identity with the corresponding sequence from GALV-SEATO and 83% identity with KoRV. The geographic ranges of the grassland melomys and of the koala partially overlap. Thus a species jump by MbRV from melomys to koalas is conceivable. However the genus Melomys does not occur in mainland South East Asia and so it appears most likely that another as yet unidentified host was the source of GALV.

hnRNP K Coordinates Transcriptional Silencing by SETDB1 in Embryonic Stem Cells

PubMed Central

Thompson, Peter J.; Dulberg, Vered; Moon, Kyung-Mee; Foster, Leonard J.; Chen, Carol; Karimi, Mohammad M.; Lorincz, Matthew C.

2015-01-01

Retrotransposition of endogenous retroviruses (ERVs) poses a substantial threat to genome stability. Transcriptional silencing of a subset of these parasitic elements in early mouse embryonic and germ cell development is dependent upon the lysine methyltransferase SETDB1, which deposits H3K9 trimethylation (H3K9me3) and the co-repressor KAP1, which binds SETDB1 when SUMOylated. Here we identified the transcription co-factor hnRNP K as a novel binding partner of the SETDB1/KAP1 complex in mouse embryonic stem cells (mESCs) and show that hnRNP K is required for ERV silencing. RNAi-mediated knockdown of hnRNP K led to depletion of H3K9me3 at ERVs, concomitant with de-repression of proviral reporter constructs and specific ERV subfamilies, as well as a cohort of germline-specific genes directly targeted by SETDB1. While hnRNP K recruitment to ERVs is dependent upon KAP1, SETDB1 binding at these elements requires hnRNP K. Furthermore, an intact SUMO conjugation pathway is necessary for SETDB1 recruitment to proviral chromatin and depletion of hnRNP K resulted in reduced SUMOylation at ERVs. Taken together, these findings reveal a novel regulatory hierarchy governing SETDB1 recruitment and in turn, transcriptional silencing in mESCs. PMID:25611934

Insertion Loss of Personal Protective Clothing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shull D.J.; Biesel, V.B.; Cunefare, K.A.

1999-05-13

'The use of personal protective clothing that covers the head is a common practice in many industries. Such personal protective clothing will impact the sound pressure level and the frequency content of sounds to which the wearer will be exposed. The use of such clothing, then, may impact speech and alarm audibility. A measure of the impact of such clothing is its insertion loss. Insertion loss measurements were performed on four types of personal protective clothing in use by Westinghouse Savannah River Company personnel which utilize cloth and plastic hood configurations to protect the head. All clothing configurations tested atmore » least partially cover the ears. The measurements revealed that insertion loss of the items tested was notable at frequencies above 1000 Hz only and was a function of material stiffness and acoustic flanking paths to the ear. Further, an estimate of the clothing''s noise reduction rating reveals poor performance in that regard, even though the insertion loss of the test articles was significant at frequencies at and above 1000 Hz.'« less

Active role of a human genomic insert in replication of a yeast artificial chromosome.

PubMed

van Brabant, A J; Fangman, W L; Brewer, B J

1999-06-01

Yeast artificial chromosomes (YACs) are a common tool for cloning eukaryotic DNA. The manner by which large pieces of foreign DNA are assimilated by yeast cells into a functional chromosome is poorly understood, as is the reason why some of them are stably maintained and some are not. We examined the replication of a stable YAC containing a 240-kb insert of DNA from the human T-cell receptor beta locus. The human insert contains multiple sites that serve as origins of replication. The activity of these origins appears to require the yeast ARS consensus sequence and, as with yeast origins, additional flanking sequences. In addition, the origins in the human insert exhibit a spacing, a range of activation efficiencies, and a variation in times of activation during S phase similar to those found for normal yeast chromosomes. We propose that an appropriate combination of replication origin density, activation times, and initiation efficiencies is necessary for the successful maintenance of YAC inserts.

Alu element insertion in PKLR gene as a novel cause of pyruvate kinase deficiency in Middle Eastern patients.

PubMed

Lesmana, Harry; Dyer, Lisa; Li, Xia; Denton, James; Griffiths, Jenna; Chonat, Satheesh; Seu, Katie G; Heeney, Matthew M; Zhang, Kejian; Hopkin, Robert J; Kalfa, Theodosia A

2018-03-01

Pyruvate kinase deficiency (PKD) is the most frequent red blood cell enzyme abnormality of the glycolytic pathway and the most common cause of hereditary nonspherocytic hemolytic anemia. Over 250 PKLR-gene mutations have been described, including missense/nonsense, splicing and regulatory mutations, small insertions, small and gross deletions, causing PKD and hemolytic anemia of variable severity. Alu retrotransposons are the most abundant mobile DNA sequences in the human genome, contributing to almost 11% of its mass. Alu insertions have been associated with a number of human diseases either by disrupting a coding region or a splice signal. Here, we report on two unrelated Middle Eastern patients, both born from consanguineous parents, with transfusion-dependent hemolytic anemia, where sequence analysis revealed a homozygous insertion of AluYb9 within exon 6 of the PKLR gene, causing precipitous decrease of PKLR RNA levels. This Alu element insertion consists a previously unrecognized mechanism underlying pathogenesis of PKD. © 2017 Wiley Periodicals, Inc.

The retrovirus HTLV-1 inserts an ectopic CTCF-binding site into the human genome.

PubMed

Satou, Yorifumi; Miyazato, Paola; Ishihara, Ko; Yaguchi, Hiroko; Melamed, Anat; Miura, Michi; Fukuda, Asami; Nosaka, Kisato; Watanabe, Takehisa; Rowan, Aileen G; Nakao, Mitsuyoshi; Bangham, Charles R M

2016-03-15

Human T-lymphotropic virus type 1 (HTLV-1) is a retrovirus that causes malignant and inflammatory diseases in ∼10% of infected people. A typical host has between 10(4) and 10(5) clones of HTLV-1-infected T lymphocytes, each clone distinguished by the genomic integration site of the single-copy HTLV-1 provirus. The HTLV-1 bZIP (HBZ) factor gene is constitutively expressed from the minus strand of the provirus, whereas plus-strand expression, required for viral propagation to uninfected cells, is suppressed or intermittent in vivo, allowing escape from host immune surveillance. It remains unknown what regulates this pattern of proviral transcription and latency. Here, we show that CTCF, a key regulator of chromatin structure and function, binds to the provirus at a sharp border in epigenetic modifications in the pX region of the HTLV-1 provirus in T cells naturally infected with HTLV-1. CTCF is a zinc-finger protein that binds to an insulator region in genomic DNA and plays a fundamental role in controlling higher order chromatin structure and gene expression in vertebrate cells. We show that CTCF bound to HTLV-1 acts as an enhancer blocker, regulates HTLV-1 mRNA splicing, and forms long-distance interactions with flanking host chromatin. CTCF-binding sites (CTCF-BSs) have been propagated throughout the genome by transposons in certain primate lineages, but CTCF binding has not previously been described in present-day exogenous retroviruses. The presence of an ectopic CTCF-BS introduced by the retrovirus in tens of thousands of genomic locations has the potential to cause widespread abnormalities in host cell chromatin structure and gene expression.

Retroviral mutation rates and A-to-G hypermutations during different stages of retroviral replication.

PubMed Central

Kim, T; Mudry, R A; Rexrode, C A; Pathak, V K

1996-01-01

Retroviruses mutate at a high rate in vivo during viral replication. Mutations may occur during proviral transcription by RNA polymerase II, during minus-strand DNA synthesis (RNA template) by viral reverse transcriptase, or during plus-strand DNA synthesis (DNA template) by reverse transcriptase. To determine the contributions of different stages of replication to the retroviral mutation rates, we developed a spleen necrosis virus-based in vivo system to selectively identify mutations occurring during the early stage (RNA transcription plus minus-strand synthesis) and the late stage (plus-strand synthesis plus DNA repair). A lacZalpha reporter gene was inserted into the long terminal repeat (LTR) of a spleen necrosis virus shuttle vector, and proviruses were recovered from infected cells as plasmids containing either one or both LTRs. Plasmids containing both LTRs generated a mutant phenotype only if the lacZalpha genes in both LTRs were mutated, which is most likely to occur during the early stage. Mutant phenotypes were identified from plasmids containing one LTR regardless of the stage at which the mutations occurred. Thus, mutant frequencies obtained after recovery of plasmids containing both LTRs or one LTR provided early-stage and total mutation rates, respectively. Analysis of 56,409 proviruses suggested that the retroviral mutation rates during the early and late stages of replication were equal or within twofold of each other. In addition, two mutants with A-to-G hypermutations were discovered, suggesting a role for mammalian double-stranded RNA adenosine deaminase enzyme in retroviral mutations. These experiments provide a system to selectively identify mutations in the early stage of retroviral replication and to provide upper and lower limits to the in vivo mutation rates during minus-strand and plus-strand synthesis, respectively. PMID:8892879

The FACT Complex Promotes Avian Leukosis Virus DNA Integration.

PubMed

Winans, Shelby; Larue, Ross C; Abraham, Carly M; Shkriabai, Nikolozi; Skopp, Amelie; Winkler, Duane; Kvaratskhelia, Mamuka; Beemon, Karen L

2017-04-01

All retroviruses need to integrate a DNA copy of their genome into the host chromatin. Cellular proteins regulating and targeting lentiviral and gammaretroviral integration in infected cells have been discovered, but the factors that mediate alpharetroviral avian leukosis virus (ALV) integration are unknown. In this study, we have identified the FACT protein complex, which consists of SSRP1 and Spt16, as a principal cellular binding partner of ALV integrase (IN). Biochemical experiments with purified recombinant proteins show that SSRP1 and Spt16 are able to individually bind ALV IN, but only the FACT complex effectively stimulates ALV integration activity in vitro Likewise, in infected cells, the FACT complex promotes ALV integration activity, with proviral integration frequency varying directly with cellular expression levels of the FACT complex. An increase in 2-long-terminal-repeat (2-LTR) circles in the depleted FACT complex cell line indicates that this complex regulates the ALV life cycle at the level of integration. This regulation is shown to be specific to ALV, as disruption of the FACT complex did not inhibit either lentiviral or gammaretroviral integration in infected cells. IMPORTANCE The majority of human gene therapy approaches utilize HIV-1- or murine leukemia virus (MLV)-based vectors, which preferentially integrate near genes and regulatory regions; thus, insertional mutagenesis is a substantial risk. In contrast, ALV integrates more randomly throughout the genome, which decreases the risks of deleterious integration. Understanding how ALV integration is regulated could facilitate the development of ALV-based vectors for use in human gene therapy. Here we show that the FACT complex directly binds and regulates ALV integration efficiency in vitro and in infected cells. Copyright © 2017 American Society for Microbiology.

[Analysis of Alu-insertion polymorphism in three subethnic groups of Kalmyks].

PubMed

Khusainova, R I; Balinova, N V; Kutuev, I A; Spitsina, N Kh; Akhmetova, V L; Valiev, R R; Spitsyn, V A; Khusnutdinova, E K

2009-03-01

Eight Alu insertions at the NBC27, TPA25, NBC148, NBC123, ACE, APOA1, NBC51, and PV92 locus were examined in three subethnic groups of Kalmyks (Torgouds, Derbets, and Buzava). In general, the pattern of allele frequencies in Kalmyks was consistent with that in Asian populations of the world, and was similar to the Alu insertion frequencies pattern in Turkic populations of the Volga--Ural region and Central Asia. Pairwise comparisons of three subpopulations of Kalmyks with respect to the frequency distributions of eight Alu insertions revealed the differences between the groups examined. The coefficient of gene differentiation, F(st), constituted 1.37%, pointing to the common origin of the groups of interest, as well as to the uniformity of the gene pools of subethnic groups of Kalmyks examined.

Anatomical Footprint of the Tibialis Anterior Tendon: Surgical Implications for Foot and Ankle Reconstructions.

PubMed

Willegger, Madeleine; Seyidova, Nargiz; Schuh, Reinhard; Windhager, Reinhard; Hirtler, Lena

2017-01-01

This study aimed to analyze precisely the dimensions, shapes, and variations of the insertional footprints of the tibialis anterior tendon (TAT) at the medial cuneiform (MC) and first metatarsal (MT1) base. Forty-one formalin-fixed human cadaveric specimens were dissected. After preparation of the TAT footprint, standardized photographs were made and the following parameters were evaluated: the footprint length, width, area of insertion, dorsoplantar location, shape, and additional tendon slips. Twenty feet (48.8%) showed an equal insertion at the MC and MT1, another 20 feet (48.8%) had a wide insertion at the MC and a narrow insertion at the MT1, and 1 foot (2.4%) demonstrated a narrow insertion at the MC and a wide insertion at the MT1. Additional tendon slips inserting at the metatarsal shaft were found in two feet (4.8%). Regarding the dorsoplantar orientation, the footprints were located medial in 29 feet (70.7%) and medioplantar in 12 feet (29.3%). The most common shape at the MT1 base was the crescent type (75.6%) and the oval type at the MC (58.5%). The present study provided more detailed data on the dimensions and morphologic types of the tibialis anterior tendon footprint. The established anatomical data may allow for a safer surgical preparation and a more anatomical reconstruction.

An audit of the complications of intercostal chest drain insertion in a high volume trauma service in South Africa

PubMed Central

Oosthuizen, GV; Sartorius, B; Keene, C; Clarke, DL

2014-01-01

Introduction Intercostal chest drain (ICD) insertion is a commonly performed procedure in trauma and may be associated with significant morbidity. Methods This was a retrospective review of ICD complications in a major trauma service in South Africa over a four-year period from January 2010 to December 2013. Results A total of 1,050 ICDs were inserted in 1,006 patients, of which 91% were male. The median patient age was 24 years (interquartile range [IQR]: 20–29 years). There were 962 patients with unilateral ICDs and 44 with bilateral ICDs. Seventy-five per cent (758/1,006) sustained penetrating trauma and the remaining 25% (248/1006) sustained blunt trauma. Indications for ICD insertion were: haemopneumothorax (n=338), haemothorax (n=314), simple pneumothorax (n=265), tension pneumothorax (n=79) and open pneumothorax (n=54). Overall, 203 ICDs (19%) were associated with complications: 18% (36/203) were kinked, 18% (36/203) were inserted subcutaneously, 13% (27/203) were too shallow and in 7% (14/203) there was inadequate fixation resulting in dislodgement. Four patients (2%) sustained visceral injuries and two sustained vascular injuries. Forty-one per cent (83/203) were inserted outside the ‘triangle of safety’ but without visceral or vascular injuries. One patient had the ICD inserted on the wrong side. Junior doctors inserted 798 ICDs (76%) while senior doctors inserted 252 (24%). Junior doctors had a significantly higher complication rate (24%) compared with senior doctors (5%) (p<0.001). There was no mortality as a direct result of ICD insertion. Conclusions ICD insertion is associated with a high rate of complications. These complications are significantly higher when junior doctors perform the procedure. A multifaceted quality improvement programme is needed to improve the situation. PMID:25350185

An audit of the complications of intercostal chest drain insertion in a high volume trauma service in South Africa.

PubMed

Kong, V Y; Oosthuizen, G V; Sartorius, B; Keene, C; Clarke, D L

2014-11-01

Intercostal chest drain (ICD) insertion is a commonly performed procedure in trauma and may be associated with significant morbidity. This was a retrospective review of ICD complications in a major trauma service in South Africa over a four-year period from January 2010 to December 2013. A total of 1,050 ICDs were inserted in 1,006 patients, of which 91% were male. The median patient age was 24 years (interquartile range [IQR]: 20-29 years). There were 962 patients with unilateral ICDs and 44 with bilateral ICDs. Seventy-five per cent (758/1,006) sustained penetrating trauma and the remaining 25% (248/1006) sustained blunt trauma. Indications for ICD insertion were: haemopneumothorax (n=338), haemothorax (n=314), simple pneumothorax (n=265), tension pneumothorax (n=79) and open pneumothorax (n=54). Overall, 203 ICDs (19%) were associated with complications: 18% (36/203) were kinked, 18% (36/203) were inserted subcutaneously, 13% (27/203) were too shallow and in 7% (14/203) there was inadequate fixation resulting in dislodgement. Four patients (2%) sustained visceral injuries and two sustained vascular injuries. Forty-one per cent (83/203) were inserted outside the 'triangle of safety' but without visceral or vascular injuries. One patient had the ICD inserted on the wrong side. Junior doctors inserted 798 ICDs (76%) while senior doctors inserted 252 (24%). Junior doctors had a significantly higher complication rate (24%) compared with senior doctors (5%) (p<0.001). There was no mortality as a direct result of ICD insertion. Conclusions ICD insertion is associated with a high rate of complications. These complications are significantly higher when junior doctors perform the procedure. A multifaceted quality improvement programme is needed to improve the situation.

Predicting the failure of retrograde ureteral stent insertion for managing malignant ureteral obstruction in outpatients

PubMed Central

WANG, JIN-YOU; ZHANG, HAI-LIANG; ZHU, YAO; QIN, XIAO-JIAN; DAI, BO; YE, DING-WEI

2016-01-01

Malignant ureteral obstruction (MUO) is an unpropitious sign that is commonly observed in patients with advanced incurable cancer. The present study aimed to evaluate predictive factors for the failure of retrograde ureteral stent insertion in the management of MUO in outpatients. A total of 164 patients with MUO were retrospectively assessed in this study. Clinical factors, including age, gender, type of malignancy, level of obstruction, cause of obstruction, pre-operative creatinine level, degree of hydronephrosis, condition of the contralateral ureter, prior radiotherapy, Eastern Cooperative Oncology Group performance status (ECOG PS), bladder wall invasion and technical failure, were recorded for each case. Univariate and multivariate logistic regression analyses were used to investigate the risk factors for predicting the failure of retrograde ureteral stent insertion. In total, 38 out of 164 patients experienced bilateral obstruction, therefore, a total of 202 ureteral units were available for data analysis. The rate of insertion failure in MUO was 34.65%. Multivariate analyses identified ECOG PS, degree of hydronephrosis and bladder wall invasion as independent predictors for insertion failure. Overall, the present study found that rate of retrograde ureteral stent insertion failure is high in outpatients with MUO, and that ECOG PS, degree of hydronephrosis and bladder invasion are potential independent predictors of insertion failure. PMID:26870299

Does insertion of intramuscular electromyographic electrodes alter motor behavior during locomotion?

PubMed

Armour Smith, Jo; Kulig, Kornelia

2015-06-01

Intramuscular electromyography (EMG) is commonly used to quantify activity in the trunk musculature. However, it is unclear if the discomfort or fear of pain associated with insertion of intramuscular EMG electrodes results in altered motor behavior. This study examined whether intramuscular EMG affects locomotor speed and trunk motion, and examined the anticipated and actual pain associated with electrode insertion in healthy individuals and individuals with a history of low back pain (LBP). Before and after insertion of intramuscular electrodes into the lumbar and thoracic paraspinals, participants performed multiple repetitions of a walking turn at self-selected and controlled average speed. Low levels of anticipated and actual pain were reported in both groups. Self-selected locomotor speed was significantly increased following insertion of the electrodes. At the controlled speed, the amplitude of sagittal plane lumbo-pelvic motion decreased significantly post-insertion, but the extent of this change was the same in both groups. Lumbo-pelvic motion in the frontal and axial planes and thoraco-lumbar motion in all planes were not affected by the insertions. This study demonstrates that intramuscular EMG is an appropriate methodology to selectively quantify the activation patterns of the individual muscles in the paraspinal group, both in healthy individuals and individuals with a history of LBP. Copyright © 2015 Elsevier Ltd. All rights reserved.

Management of subcalcaneal pain and Achilles tendonitis with heel inserts

PubMed Central

Maclellan, G. E.; Vyvyan, Barbara

1981-01-01

Soft tissue symptoms in the leg due to sporting activity are commonly associated with the force of heel strike. Conventional training shoes compromise between comfort and performance; few models are suitably designed for both considerations. Using a visco-elastic polymer insert the symptoms of heel pain and Achilles tendonitis have been largely or completely abolished in a preliminary study. Imagesp117-ap117-bp117-cp118-a PMID:7272653

A comparison of buffered lidocaine versus ELA-Max before peripheral intravenous catheter insertions in children.

PubMed

Luhmann, Janet; Hurt, Sarah; Shootman, Mario; Kennedy, Robert

2004-03-01

Peripheral intravenous catheter (PIV) insertion is a common, painful experience for many children in the pediatric emergency department. Although local anesthetics such as injected buffered lidocaine have been shown to be effective at reducing pain and anxiety associated with PIV insertion, they are not routinely used. ELA-Max, a topical local anesthetic, has the advantage of needle-free administration but has not been compared with buffered lidocaine for PIV insertion. To compare the reduction of pain and anxiety during PIV insertion provided by subcutaneous buffered 1% lidocaine or topical ELA-Max in children. A randomized trial in children 4 to 17 years old undergoing PIV insertion with 22-gauge catheters was conducted. Children received either buffered lidocaine or ELA-Max. Buffered lidocaine was administered by using 30-gauge needles to inject 0.1 to 0.2 mL subcutaneously just before PIV insertion. ELA-Max was applied to the skin and occluded with Tegaderm 30 minutes before PIV insertion. Self-reported Visual Analog Scale (VAS) questionnaires (rating on a scale of 1-10; 1 = no pain, anxiety) were completed by patients and their parents before PIV insertion to assess baseline perceptions about pain and anxiety associated with PIV insertion and immediately after PIV insertion to assess pain and anxiety associated with the experience. After PIV insertion, the nurse who inserted the PIV also completed a VAS questionnaire assessing technical difficulty and satisfaction with the local anesthesia. A blinded observer also completed a VAS questionnaire to assess pain and anxiety associated with the PIV insertion. Data were analyzed by using chi2 and t tests. Sixty-nine subjects were enrolled, and questionnaires were competed by all (mean age: 12.1 +/- 4.5 years; 61% female). There were no differences for buffered lidocaine and ELA-Max groups in age, gender, race, prior IV experience, or baseline pain and anxiety. There were no significant differences between buffered lidocaine and ELA-Max in mean pain and anxiety after PIV insertion by patient, parent, and blinded observer ratings. Nurse ratings of technical difficulty, number of PIV-insertion attempts, and satisfaction with local anesthesia also were not significantly different for buffered lidocaine and ELA-Max groups. ELA-Max provided similar pain and anxiety reduction during PIV insertion in children compared with injected buffered lidocaine. Technical difficulty and satisfaction by nurses inserting the PIV also were similar.

Six- and twelve-month documented removal rates among women electing postpartum inpatient compared to delayed or interval contraceptive implant insertions after Medicaid payment reform.

PubMed

Crockett, Amy H; Pickell, Lesley Bundon; Heberlein, Emily C; Billings, Deborah L; Mills, Benjie

2017-01-01

This study aims to document 6- and 12-month removal rates for women receiving the contraceptive implant inpatient postpartum versus those receiving the same contraceptive method during an outpatient visit, in a setting where postpartum inpatient long-acting reversible contraceptive (LARC) services (devices plus provider insertion costs) are reimbursed by Medicaid. We conducted a retrospective cohort study among Medicaid-enrolled women using medical record review for all women receiving the etonogestrel implant between July 1, 2007 and June 30, 2014. We compared the percentage of women with the implant removed at 6 and 12 months as well as reasons for early removal, for inpatient postpartum implant insertions vs. delayed postpartum or interval outpatient implant insertions. A total of 4% of women (34/776 insertions) had documented implant removal within 6 months post-insertion, with no difference between postpartum inpatient and outpatient (delayed postpartum or interval). A total of 12% (62/518 insertions) of women had documented implant removal within 12 months. A lower percentage of women with postpartum inpatient insertions had the implant removed at 12 months post-insertion, compared to outpatient insertions (7% vs. 14%, p=.04). After controlling for age, parity, race and body mass index, women with postpartum inpatient insertions were less likely to have the implant removed within 12 months (OR=0.44, 95% CI 0.20-0.97). The most commonly stated reason for removal was abnormal uterine bleeding, regardless of insertion timing. In a setting with a Medicaid policy that covers postpartum inpatient LARC insertion, a low percentage of women who received an implant immediately postpartum had it removed within 1 year of insertion. A Medicaid payment policy that removes institutional barriers to offering postpartum inpatient contraceptive implants to women free-of-charge may facilitate meeting women's desires and intentions to delay subsequent pregnancy, as evidenced by low removal rates up to 12 months post-insertion. Further research with women is needed to assess how these services meet their postpartum contraceptive needs and desires to postpone or prevent subsequent pregnancy. Copyright © 2016 Elsevier Inc. All rights reserved.

Roles of Pro-viral Host Factors in Mosquito-Borne Flavivirus Infections.

PubMed

Campos, Rafael K; Garcia-Blanco, Mariano A; Bradrick, Shelton S

2017-07-09

Identification and analysis of viral host factors is a growing area of research which aims to understand the how viruses molecularly interface with the host cell. Investigations into flavivirus-host interactions has led to new discoveries in viral and cell biology, and will potentially bolster strategies to control the important diseases caused by these pathogens. Here, we address the current knowledge of prominent host factors required for the flavivirus life-cycle and mechanisms by which they promote infection.

HangOut: generating clean PSI-BLAST profiles for domains with long insertions.

PubMed

Kim, Bong-Hyun; Cong, Qian; Grishin, Nick V

2010-06-15

Profile-based similarity search is an essential step in structure-function studies of proteins. However, inclusion of non-homologous sequence segments into a profile causes its corruption and results in false positives. Profile corruption is common in multidomain proteins, and single domains with long insertions are a significant source of errors. We developed a procedure (HangOut) that, for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles. HangOut is implemented in Python 2.3 and runs on all Unix-compatible platforms. The source code is available under the GNU GPL license at http://prodata.swmed.edu/HangOut/. Supplementary data are available at Bioinformatics online.

Avulsion fracture of an ossified pes anserinus tendon post-lateral patellar dislocation.

PubMed

Albtoush, Omar M; Taib, Abtehag A; Horger, Marius; Springer, Fabian

2018-05-01

The pes anserinus is a common tendon comprising the tendinous insertions of the sartorius, gracilis, and semitendinosus muscles. It inserts at the anteromedial aspect of the tibia and plays a significant role in stabilization of the medial side of the knee joint. The current article presents a case with recurrent lateral patellar dislocations causing chronic stress along the medial knee stabilizers and consecutive enthesophyte formation at the insertion of the pes anserinus tendon that showed a transverse fracture upon a subsequent incident of traumatic lateral patellar dislocation. Avulsion injuries of the pes anserinus tendon are rarely encountered, and to our knowledge, association with recurrent lateral patellar dislocations has not been described before.

A sticky situation: management of spray polyurethane foam insulation in body orifices.

PubMed

Sowerby, Robert J; Sowerby, Leigh J; Vinden, Chris

2011-11-01

Spray polyurethane foam insulation is commonly used in the construction industry to fill gaps, seal, and insulate. We present three cases of intentional spray foam insertion in body orifices and discuss the management of such situations in the emergency department. This series includes a case of oral foam insertion used in a suicide attempt by suffocation and two cases of rectal insertion. All of these cases had potential long-term consequences; one was life-threatening. To our knowledge, this is the first published report on the medical management and removal of foam insulation from body orifices. In all three cases, the foam insulation material was successfully removed after allowing the material to harden.

Development of a virtual reality haptic Veress needle insertion simulator for surgical skills training.

PubMed

Okrainec, A; Farcas, M; Henao, O; Choy, I; Green, J; Fotoohi, M; Leslie, R; Wight, D; Karam, P; Gonzalez, N; Apkarian, J

2009-01-01

The Veress needle is the most commonly used technique for creating the pneumoperitoneum at the start of a laparoscopic surgical procedure. Inserting the Veress needle correctly is crucial since errors can cause significant harm to patients. Unfortunately, this technique can be difficult to teach since surgeons rely heavily on tactile feedback while advancing the needle through the various layers of the abdominal wall. This critical step in laparoscopy, therefore, can be challenging for novice trainees to learn without adequate opportunities to practice in a safe environment with no risk of injury to patients. To address this issue, we have successfully developed a prototype of a virtual reality haptic needle insertion simulator using the tactile feedback of 22 surgeons to set realistic haptic parameters. A survey of these surgeons concluded that our device appeared and felt realistic, and could potentially be a useful tool for teaching the proper technique of Veress needle insertion.

Target-matched insertion gain derived from three different hearing aid selection procedures.

PubMed

Punch, J L; Shovels, A H; Dickinson, W W; Calder, J H; Snead, C

1995-11-01

Three hearing aid selection procedures were compared to determine if any one was superior in producing prescribed real-ear insertion gain. For each of three subject groups, 12 in-the-ear style hearing aids with Class D circuitry and similar dispenser controls were ordered from one of three manufacturers. Subject groups were classified based on the type of information included on the hearing aid order form: (1) the subject's audiogram, (2) a three-part matrix specifying the desired maximum output, full-on gain, and frequency response slope of the hearing aid, or (3) the desired 2-cc coupler full-in grain of the hearing aid, based on real-ear coupler difference (RECD) measurements. Following electroacoustic adjustments aimed at approximating a commonly used target insertion gain formula, results revealed no significant differences among any of the three selection procedures with respect to obtaining acceptable insertion gain values.

CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles.

PubMed

Lemos, Brenda R; Kaplan, Adam C; Bae, Ji Eun; Ferrazzoli, Alexander E; Kuo, James; Anand, Ranjith P; Waterman, David P; Haber, James E

2018-02-27

Harnessing CRISPR-Cas9 technology provides an unprecedented ability to modify genomic loci via DNA double-strand break (DSB) induction and repair. We analyzed nonhomologous end-joining (NHEJ) repair induced by Cas9 in budding yeast and found that the orientation of binding of Cas9 and its guide RNA (gRNA) profoundly influences the pattern of insertion/deletions (indels) at the site of cleavage. A common indel created by Cas9 is a 1-bp (+1) insertion that appears to result from Cas9 creating a 1-nt 5' overhang that is filled in by a DNA polymerase and ligated. The origin of +1 insertions was investigated by using two gRNAs with PAM sequences located on opposite DNA strands but designed to cleave the same sequence. These templated +1 insertions are dependent on the X-family DNA polymerase, Pol4. Deleting Pol4 also eliminated +2 and +3 insertions, which are biased toward homonucleotide insertions. Using inverted PAM sequences, we also found significant differences in overall NHEJ efficiency and repair profiles, suggesting that the binding of the Cas9:gRNA complex influences subsequent NHEJ processing. As with events induced by the site-specific HO endonuclease, CRISPR-Cas9-mediated NHEJ repair depends on the Ku heterodimer and DNA ligase 4. Cas9 events are highly dependent on the Mre11-Rad50-Xrs2 complex, independent of Mre11's nuclease activity. Inspection of the outcomes of a large number of Cas9 cleavage events in mammalian cells reveals a similar templated origin of +1 insertions in human cells, but also a significant frequency of similarly templated +2 insertions.

Safe percutaneous suprapubic catheterisation.

PubMed

Goyal, N K; Goel, A; Sankhwar, S N

2012-11-01

We describe our technique of percutaneous suprapubic catheter insertion with special reference to steps that help to avoid common complications of haematuria and catheter misplacement. The procedure is performed using a stainless steel reusable trocar under local infiltrative anaesthesia, usually at the bedside. After clinical confirmation of a full bladder, the trocar is advanced into the bladder through a skin incision. Once the bladder is entered, the obturator is removed and the assistant inserts a Foley catheter followed by rapid balloon inflation. Slight traction is applied to the catheter for about five minutes. Patients with previous lower abdominal surgery, an inadequately distended bladder or acute pelvic trauma do not undergo suprapubic catheterisation using this method. The procedure was performed in 72 men (mean age: 42.4 years, range: 18-78 years) with urinary retention with a palpable bladder. The average duration of the procedure was less than five minutes. No complications were noted in any of the patients. Trocar suprapubic catheter insertion is a safe and effective bedside procedure for emergency bladder drainage and can be performed by resident surgeons. The common complications associated with the procedure can be avoided with a few careful steps.

Intercostal drainage tube or intracardiac drainage tube?

PubMed

Anitha, N; Kamath, S Ganesh; Khymdeit, Edison; Prabhu, Manjunath

2016-01-01

Although insertion of chest drain tubes is a common medical practice, there are risks associated with this procedure, especially when inexperienced physicians perform it. Wrong insertion of the tube has been known to cause morbidity and occasional mortality. We report a case where the left ventricle was accidentally punctured leading to near-exsanguination. This report is to highlight the need for experienced physicians to supervise the procedure and train the younger physician in the safe performance of the procedure.

IS1598 (IsPg4) distributed to abscess-forming strains of Porphyromonas gingivalis may enhance virulence through upregulation of nrdD-like gene expression.

PubMed

Sonoi, Norihiro; Maeda, Hiroshi; Murauchi, Toshimitsu; Yamamoto, Tadashi; Omori, Kazuhiro; Kokeguchi, Susumu; Naruishi, Koji; Takashiba, Shogo

2018-01-01

An insertion sequence, IS1598 (IsPg4) has been found in virulent strains of Porphyromonas gingivalis in a murine abscess model. The present study was performed to investigate the effects of genetic rearrangements by IS1598 on the phenotypic characteristics of the virulent strains. For this purpose, we searched for a common insertion site of IS1598 among the virulent strains. Through cloning and database search, a common insertion site was identified beside an nrdD-like gene in the virulent FDC 381, W83 and W50 strains. In this region, predicted promoters of the nrdD-like gene and IS1598 are located in tandem, and accumulation of nrdD-like gene mRNA was 5-fold higher in virulent strains (W83, W50, FDC 381) than avirulent strains (ATCC33277, SU63, SUNY1021, ESO59 without IS1598). The role of the nrdD-like gene in virulence of P. gingivalis was investigated by constructing a nrdD-deficient mutant. In the murine abscess model, the parental W83 strain produced necrotic abscesses, while the nrdD-deficient mutant had almost lost this ability. Insertion of IS1598 into the nrdD-like gene promoter region may be related to the phenotypic differences in virulence among P. gingivalis strains through upregulation of the expression of this gene.

Tibial interface wear in retrieved total knee components and correlations with modular insert motion.

PubMed

Rao, Anand R; Engh, Gerard A; Collier, Matthew B; Lounici, Smain

2002-10-01

Wear occurring at the interface between the polyethylene insert and metal baseplate of a modular tibial component has become an increasingly common finding at the time of revision total knee arthroplasty. Although this so-called backside wear on retrieved polyethylene inserts has been evaluated in prior studies, wear on retrieved metal baseplates has not been described, to our knowledge. The purposes of the present study were to characterize backside wear on retrieved polyethylene inserts and on the mating surfaces of their corresponding baseplates and to investigate if there is a relationship between backside wear and relative motion of the modular elements. Twenty-nine retrieved modular tibial components of twelve fixed-bearing designs were analyzed in vitro with regard to backside wear and relative motion between the polyethylene insert and the metal baseplate. We graded the backside of each polyethylene insert and the mating surface of the metal baseplate for wear with use of a scoring system that consisted of three modes of wear and three levels of severity of wear. Relative motion between the insert and the baseplate was measured in the transverse plane with use of a mechanical testing machine. These measurements were used to compute the insert motion index, which served to quantify unrestricted motion of the insert with respect to the baseplate. The mean insert motion index for the tibial components was 416 micro m (range, 104 micro m to 760 micro m). On a wear-grading scale ranging from 0 to 54 (with 0 indicating no wear), the mean backside wear score was 30 (range, 12 to 48) for the inserts and 28 (range, 7 to 51) for the baseplates. Insert motion was positively correlated with backside polyethylene wear (p = 0.003) and baseplate wear (p < 0.001). Baseplate wear was strongly correlated with backside polyethylene wear (p < 0.001). Backside wear was correlated with the relative motion between the polyethylene insert and the metal baseplate. New locking mechanism designs directed toward better methods of securing the polyethylene insert to the tibial tray are needed to minimize the generation of particulate wear debris at the modular interface.

L1 Retrotransposon Heterogeneity in Ovarian Tumor Cell Evolution.

PubMed

Nguyen, Thu H M; Carreira, Patricia E; Sanchez-Luque, Francisco J; Schauer, Stephanie N; Fagg, Allister C; Richardson, Sandra R; Davies, Claire M; Jesuadian, J Samuel; Kempen, Marie-Jeanne H C; Troskie, Robin-Lee; James, Cini; Beaven, Elizabeth A; Wallis, Tristan P; Coward, Jermaine I G; Chetty, Naven P; Crandon, Alexander J; Venter, Deon J; Armes, Jane E; Perrin, Lewis C; Hooper, John D; Ewing, Adam D; Upton, Kyle R; Faulkner, Geoffrey J

2018-06-26

LINE-1 (L1) retrotransposons are a source of insertional mutagenesis in tumor cells. However, the clinical significance of L1 mobilization during tumorigenesis remains unclear. Here, we applied retrotransposon capture sequencing (RC-seq) to multiple single-cell clones isolated from five ovarian cancer cell lines and HeLa cells and detected endogenous L1 retrotransposition in vitro. We then applied RC-seq to ovarian tumor and matched blood samples from 19 patients and identified 88 tumor-specific L1 insertions. In one tumor, an intronic de novo L1 insertion supplied a novel cis-enhancer to the putative chemoresistance gene STC1. Notably, the tumor subclone carrying the STC1 L1 mutation increased in prevalence after chemotherapy, further increasing STC1 expression. We also identified hypomethylated donor L1s responsible for new L1 insertions in tumors and cultivated cancer cells. These congruent in vitro and in vivo results highlight L1 insertional mutagenesis as a common component of ovarian tumorigenesis and cancer genome heterogeneity. Copyright © 2018 The Author(s). Published by Elsevier Inc. All rights reserved.

Effects of insertion speed and trocar stiffness on the accuracy of needle position for brachytherapy

DOE Office of Scientific and Technical Information (OSTI.GOV)

McGill, Carl S.; Schwartz, Jonathon A.; Moore, Jason Z.

2012-04-15

Purpose: In prostate brachytherapy, accurate positioning of the needle tip to place radioactive seeds at its target site is critical for successful radiation treatment. During the procedure, needle deflection leads to seed misplacement and suboptimal radiation dose to cancerous cells. In practice, radiation oncologists commonly use high-speed hand needle insertion to minimize displacement of the prostate as well as the needle deflection. Effects of speed during needle insertion and stiffness of trocar (a solid rod inside the hollow cannula) on needle deflection are studied. Methods: Needle insertion experiments into phantom were performed using a 2{sup 2} factorial design (2 parametersmore » at 2 levels), with each condition having replicates. Analysis of the deflection data included calculating the average, standard deviation, and analysis of variance (ANOVA) to find significant single and two-way interaction factors. Results: The stiffer tungsten carbide trocar is effective in reducing the average and standard deviation of needle deflection. The fast insertion speed together with the stiffer trocar generated the smallest average and standard deviation for needle deflection for almost all cases. Conclusions: The combination of stiff tungsten carbide trocar and fast needle insertion speed are important to decreasing needle deflection. The knowledge gained from this study can be used to improve the accuracy of needle insertion during brachytherapy procedures.« less

Pancreatic stent insertion after an unintentional guidewire cannulation of the pancreatic duct during ERCP.

PubMed

García-Cano, Jesús; Viñuelas Chicano, Miriam; Del Moral Martínez, María; Muñiz Muñoz, Marta; Murillo Matamoros, Claudio; Suárez Matías, Miguel; Valiente González, Laura; Martínez Pérez, Teresa; Martínez Fernández, Raquel; Gómez Ruiz, Carmen Julia; Pérez García, José Ignacio; Morillas Ariño, Julia

2018-04-24

the guidewire (GW) may enter the pancreatic duct during common bile duct (CBD) cannulation attempts in endoscopic retrograde cholangiopancreatography (ERCP). After GW passage into the pancreas, the most effective maneuver for CBD cannulation and pancreatitis prevention has not been determined. to study CBD cannulation and post-ERCP pancreatitis rates when a pancreatic stent is inserted after an unintentional GW cannulation of the pancreatic duct. a retrospective analysis of patients undergoing ERCP for biliary drainage that were included prospectively into a database. After unintentional GW cannulation of the pancreatic duct, a straight 5-Fr and 4-cm long plastic stent was inserted. The stents had no internal flaps to facilitate expulsion. CBD cannulation attempts were made above the stent. A pancreatic sphincterotomy was performed in patients older than 60 years before stent insertion. a total of 46 pancreatic stents were inserted during 154 ERCP (29.8%) procedures. In the stent group, CBD cannulation was accomplished in 44/46 (95.6%) subjects. A total of 21/46 (45.6%) pancreatic sphincterotomies were performed. Only 1/46 (2.17%) mild pancreatitis cases were observed and most stents were spontaneously expelled. in this study, the CBD was eventually reached with the insertion of a plastic pancreatic stent after an unintentional GW passage into the pancreatic duct while attempting a CBD cannulation. No adverse events were observed following pancreatic stent insertion.

Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals.

PubMed

Clarridge, Katherine E; Blazkova, Jana; Einkauf, Kevin; Petrone, Mary; Refsland, Eric W; Justement, J Shawn; Shi, Victoria; Huiting, Erin D; Seamon, Catherine A; Lee, Guinevere Q; Yu, Xu G; Moir, Susan; Sneller, Michael C; Lichterfeld, Mathias; Chun, Tae-Wook

2018-01-01

Therapeutic strategies aimed at achieving antiretroviral therapy (ART)-free HIV remission in infected individuals are under active investigation. Considering the vast majority of HIV-infected individuals experience plasma viral rebound upon cessation of therapy, clinical trials evaluating the efficacy of curative strategies would likely require inclusion of ART interruption. However, it is unclear what impact short-term analytical treatment interruption (ATI) and subsequent reinitiation of ART have on immunologic and virologic parameters of HIV-infected individuals. Here, we show a significant increase of HIV burden in the CD4+ T cells of infected individuals during ATI that was correlated with the level of plasma viral rebound. However, the size of the HIV reservoirs as well as immune parameters, including markers of exhaustion and activation, returned to pre-ATI levels 6-12 months after the study participants resumed ART. Of note, the proportions of near full-length, genome-intact and structurally defective HIV proviral DNA sequences were similar prior to ATI and following reinitiation of ART. In addition, there was no evidence of emergence of antiretroviral drug resistance mutations within intact HIV proviral DNA sequences following reinitiation of ART. These data demonstrate that short-term ATI does not necessarily lead to expansion of the persistent HIV reservoir nor irreparable damages to the immune system in the peripheral blood, warranting the inclusion of ATI in future clinical trials evaluating curative strategies.

Effect of analytical treatment interruption and reinitiation of antiretroviral therapy on HIV reservoirs and immunologic parameters in infected individuals

PubMed Central

Petrone, Mary; Justement, J. Shawn; Shi, Victoria; Huiting, Erin D.; Yu, Xu G.; Moir, Susan; Sneller, Michael C.; Lichterfeld, Mathias

2018-01-01

Therapeutic strategies aimed at achieving antiretroviral therapy (ART)-free HIV remission in infected individuals are under active investigation. Considering the vast majority of HIV-infected individuals experience plasma viral rebound upon cessation of therapy, clinical trials evaluating the efficacy of curative strategies would likely require inclusion of ART interruption. However, it is unclear what impact short-term analytical treatment interruption (ATI) and subsequent reinitiation of ART have on immunologic and virologic parameters of HIV-infected individuals. Here, we show a significant increase of HIV burden in the CD4+ T cells of infected individuals during ATI that was correlated with the level of plasma viral rebound. However, the size of the HIV reservoirs as well as immune parameters, including markers of exhaustion and activation, returned to pre-ATI levels 6–12 months after the study participants resumed ART. Of note, the proportions of near full-length, genome-intact and structurally defective HIV proviral DNA sequences were similar prior to ATI and following reinitiation of ART. In addition, there was no evidence of emergence of antiretroviral drug resistance mutations within intact HIV proviral DNA sequences following reinitiation of ART. These data demonstrate that short-term ATI does not necessarily lead to expansion of the persistent HIV reservoir nor irreparable damages to the immune system in the peripheral blood, warranting the inclusion of ATI in future clinical trials evaluating curative strategies. PMID:29324842

Cocaine modulates HIV-1 integration in primary CD4+ T cells: implications in HIV-1 pathogenesis in drug-abusing patients

PubMed Central

Addai, Amma B.; Pandhare, Jui; Paromov, Victor; Mantri, Chinmay K.; Pratap, Siddharth; Dash, Chandravanu

2015-01-01

Epidemiologic studies suggest that cocaine abuse worsens HIV-1 disease progression. Increased viral load has been suggested to play a key role for the accelerated HIV disease among cocaine-abusing patients. The goal of this study was to investigate whether cocaine enhances proviral DNA integration as a mechanism to increase viral load. We infected CD4+ T cells that are the primary targets of HIV-1 in vivo and treated the cells with physiologically relevant concentrations of cocaine (1 µM–100 µM). Proviral DNA integration in the host genome was measured by nested qPCR. Our results illustrated that cocaine from 1 µM through 50 µM increased HIV-1 integration in CD4+ T cells in a dose-dependent manner. As integration can be modulated by several early postentry steps of HIV-1 infection, we examined the direct effects of cocaine on viral integration by in vitro integration assays by use of HIV-1 PICs. Our data illustrated that cocaine directly increases viral DNA integration. Furthermore, our MS analysis showed that cocaine is able to enter CD4+ T cells and localize to the nucleus-. In summary, our data provide strong evidence that cocaine can increase HIV-1 integration in CD4+ T cells. Therefore, we hypothesize that increased HIV-1 integration is a novel mechanism by which cocaine enhances viral load and worsens disease progression in drug-abusing HIV-1 patients. PMID:25691383

The prion protein has RNA binding and chaperoning properties characteristic of nucleocapsid protein NCP7 of HIV-1.

PubMed

Gabus, C; Derrington, E; Leblanc, P; Chnaiderman, J; Dormont, D; Swietnicki, W; Morillas, M; Surewicz, W K; Marc, D; Nandi, P; Darlix, J L

2001-06-01

Transmissible spongiform encephalopathies are fatal neurodegenerative diseases associated with the accumulation of a protease-resistant form of the prion protein (PrP). Although PrP is conserved in vertebrates, its function remains to be identified. In vitro PrP binds large nucleic acids causing the formation of nucleoprotein complexes resembling human immunodeficiency virus type 1 (HIV-1) nucleocapsid-RNA complexes and in vivo MuLV replication accelerates the scrapie infectious process, suggesting possible interactions between retroviruses and PrP. Retroviruses, including HIV-1 encode a major nucleic acid binding protein (NC protein) found within the virus where 2000 NC protein molecules coat the dimeric genome. NC is required in virus assembly and infection to chaperone RNA dimerization and packaging and in proviral DNA synthesis by reverse transcriptase (RT). In HIV-1, 5'-leader RNA/NC interactions appear to control these viral processes. This prompted us to compare and contrast the interactions of human and ovine PrP and HIV-1 NCp7 with HIV-1 5'-leader RNA. Results show that PrP has properties characteristic of NCp7 with respect to viral RNA dimerization and proviral DNA synthesis by RT. The NC-like properties of huPrP map to the N-terminal region of huPrP. Interestingly, PrP localizes in the membrane and cytoplasm of PrP-expressing cells. These findings suggest that PrP is a multifunctional protein possibly participating in nucleic acid metabolism.

Chromosomal Distribution of Endogenous Jaagsiekte Sheep Retrovirus Proviral Sequences in the Sheep Genome

PubMed Central

Carlson, Jonathan; Lyon, Monique; Bishop, Jeanette; Vaiman, Anne; Cribiu, Edmond; Mornex, Jean-François; Brown, Susan; Knudson, Dennis; DeMartini, James; Leroux, Caroline

2003-01-01

A family of endogenous retroviruses (enJSRV) closely related to Jaagsiekte sheep retrovirus (JSRV) is ubiquitous in domestic and wild sheep and goats. Southern blot hybridization studies indicate that there is little active replication or movement of the enJSRV proviruses in these species. Two approaches were used to investigate the distribution of proviral loci in the sheep genome. Fluorescence in situ hybridization (FISH) to metaphase chromosome spreads using viral DNA probes was used to detect loci on chromosomes. Hybridization signals were reproducibly detected on seven sheep chromosomes and eight goat chromosomes in seven cell lines. In addition, a panel of 30 sheep-hamster hybrid cell lines, each of which carries one or more sheep chromosomes and which collectively contain the whole sheep genome, was examined for enJSRV sequences. DNA from each of the lines was used as a template for PCR with JSRV gag-specific primers. A PCR product was amplified from 27 of the hybrid lines, indicating that JSRV gag sequences are found on at least 15 of the 28 sheep chromosomes, including those identified by FISH. Thus, enJSRV proviruses are essentially randomly distributed among the chromosomes of sheep and goats. FISH and/or Southern blot hybridization on DNA from several of the sheep-hamster hybrid cell lines suggests that loci containing multiple copies of enJSRV are present on chromosomes 6 and 9. The origin and functional significance of these arrays is not known. PMID:12915578

Genome editing strategies: potential tools for eradicating HIV-1/AIDS

PubMed Central

Khalili, Kamel; Gordon, Jennifer; Cosentino, Laura; Hu, Wenhui

2015-01-01

Current therapy for controlling HIV-1 infection and preventing AIDS progression has profoundly decreased viral replication in cells susceptible to HIV-1 infection, but it does not eliminate the low level of viral replication in latently infected cells which contain integrated copies of HIV-1 proviral DNA. There is an urgent need for the development of HIV-1 genome eradication strategies that will lead to a permanent or “sterile” cure of HIV-1/AIDS. In the past few years, novel nuclease-initiated genome editing tools have been developing rapidly, including ZFNs, TALENs, and the CRISPR/Cas9 system. These surgical knives, which can excise any genome, provide a great opportunity to eradicate the HIV-1 genome by targeting highly conserved regions of the HIV-1 long terminal repeats or essential viral genes. Given the time consuming and costly engineering of target-specific ZFNs and TALENs, the RNA-guided endonuclease Cas9 technology has emerged as a simpler and more versatile technology to allow permanent removal of integrated HIV-1 proviral DNA in eukaryotic cells, and hopefully animal models or human patients. The major unmet challenges of this approach at present include inefficient nuclease gene delivery, potential off-target cleavage, and cell-specific genome targeting. Nanoparticle or lentivirus-mediated delivery of next generation Cas9 technologies including nickase or RNA-guided FokI nuclease (RFN) will further improve the potential for genome editing to become a promising approach for curing HIV-1/AIDS. PMID:25716921

Sequence editing by Apolipoprotein B RNA-editing catalytic component-B and epidemiological surveillance of transmitted HIV-1 drug resistance

PubMed Central

Gifford, Robert J.; Rhee, Soo-Yon; Eriksson, Nicolas; Liu, Tommy F.; Kiuchi, Mark; Das, Amar K.; Shafer, Robert W.

2008-01-01

Design Promiscuous guanine (G) to adenine (A) substitutions catalysed by apolipoprotein B RNA-editing catalytic component (APOBEC) enzymes are observed in a proportion of HIV-1 sequences in vivo and can introduce artifacts into some genetic analyses. The potential impact of undetected lethal editing on genotypic estimation of transmitted drug resistance was assessed. Methods Classifiers of lethal, APOBEC-mediated editing were developed by analysis of lentiviral pol gene sequence variation and evaluated using control sets of HIV-1 sequences. The potential impact of sequence editing on genotypic estimation of drug resistance was assessed in sets of sequences obtained from 77 studies of 25 or more therapy-naive individuals, using mixture modelling approaches to determine the maximum likelihood classification of sequences as lethally edited as opposed to viable. Results Analysis of 6437 protease and reverse transcriptase sequences from therapy-naive individuals using a novel classifier of lethal, APOBEC3G-mediated sequence editing, the polypeptide-like 3G (APOBEC3G)-mediated defectives (A3GD) index’, detected lethal editing in association with spurious ‘transmitted drug resistance’ in nearly 3% of proviral sequences obtained from whole blood and 0.2% of samples obtained from plasma. Conclusion Screening for lethally edited sequences in datasets containing a proportion of proviral DNA, such as those likely to be obtained for epidemiological surveillance of transmitted drug resistance in the developing world, can eliminate rare but potentially significant errors in genotypic estimation of transmitted drug resistance. PMID:18356601

Risk factors for central line-associated bloodstream infection in pediatric oncology patients with a totally implantable venous access port: A cohort study.

PubMed

Viana Taveira, Michelle Ribeiro; Lima, Luciana Santana; de Araújo, Cláudia Corrêa; de Mello, Maria Júlia Gonçalves

2017-02-01

Totally implantable venous access ports (TIVAPs) are used for prolonged central venous access, allowing the infusion of chemotherapy and other fluids and improving the quality of life of children with cancer. TIVAPs were developed to reduce the infection rates associated with central venous catheters; however, infectious events remain common and have not been fully investigated in pediatric oncology patients. A retrospective cohort was formed to investigate risk factors for central line-associated bloodstream infection (CLABSI) in pediatric cancer patients. Sociodemographic, clinical, and TIVAP insertion-related variables were evaluated, with the endpoint being the first CLABSI. A Kaplan-Meier analysis was performed to determine CLABSI-free catheter survival. Overall, 188 children were evaluated over 77,541 catheter days, with 94 being diagnosed with CLABSI (50%). Although coagulase-negative staphylococci were the pathogens most commonly isolated, Gram-negative microorganisms (46.8%) were also prevalent. In the multivariate analysis, factors that increased the risk for CLABSI were TIVAP insertion prior to chemotherapy (risk ratio [RR] = 1.56; P < 0.01), white blood cell count less than 1,000 mm -3 on the day of implantation (RR = 1.64; P < 0.01), and chronic malnutrition (RR = 1.41; P < 0.05). Median time without CLABSI following TIVAP insertion was 74.5 days. Risk factors for CLABSI in pediatric cancer patients with a TIVAP may be related to the severity of the child's condition at catheter insertion. Insertion of the catheter before chemotherapy and unfavorable conditions such as malnutrition and bone marrow aplasia can increase the risk of CLABSI. Protocols must be revised and surveillance increased over the first 10 weeks of treatment. © 2016 Wiley Periodicals, Inc.

Post-procedural Care in Interventional Radiology: What Every Interventional Radiologist Should Know-Part II: Catheter Care and Management of Common Systemic Post-procedural Complications.

PubMed

Taslakian, Bedros; Sridhar, Divya

2017-09-01

Interventional radiology (IR) has evolved into a full-fledged clinical specialty with attendant comprehensive patient care responsibilities. Providing excellent and thorough clinical care is as essential to the practice of IR as achieving technical success in procedures. Basic clinical skills that every interventional radiologist should learn include routine management of percutaneously inserted drainage and vascular catheters and rapid effective management of common systemic post-procedural complications. A structured approach to post-procedural care, including routine follow-up and early identification and management of complications, facilitates efficient and thorough management with an emphasis on quality and patient safety. The aim of this second part, in conjunction with part 1, is to complete the comprehensive review of post-procedural care in patients undergoing interventional radiology procedures. We discuss common problems encountered after insertion of drainage and vascular catheters and describe effective methods of troubleshooting these problems. Commonly encountered systemic complications in IR are described, and ways for immediate identification and management of these complications are provided.

Development of a clinical prediction rule to improve peripheral intravenous cannulae first attempt success in the emergency department and reduce post insertion failure rates: the Vascular Access Decisions in the Emergency Room (VADER) study protocol

PubMed Central

Carr, Peter J; Rippey, James C R; Cooke, Marie L; Bharat, Chrianna; Murray, Kevin; Higgins, Niall S; Foale, Aileen; Rickard, Claire M

2016-01-01

Introduction Peripheral intravenous cannula (PIVC) insertion is one of the most common clinical interventions performed in emergency care worldwide. However, factors associated with successful PIVC placement and maintenance are not well understood. This study seeks to determine the predictors of first time PIVC insertion success in emergency department (ED) and identify the rationale for removal of the ED inserted PIVC in patients admitted to the hospital ward. Reducing failed insertion attempts and improving peripheral intravenous cannulation practice could lead to better staff and patient experiences, as well as improving hospital efficiency. Methods and analysis We propose an observational cohort study of PIVC insertions in a patient population presenting to ED, with follow-up observation of the PIVC in subsequent admissions to the hospital ward. We will collect specific PIVC observational data such as; clinician factors, patient factors, device information and clinical practice variables. Trained researchers will gather ED PIVC insertion data to identify predictors of insertion success. In those admitted from the ED, we will determine the dwell time of the ED-inserted PIVC. Multivariate regression analyses will be used to identify factors associated with insertions success and PIVC failure and standard statistical validation techniques will be used to create and assess the effectiveness of a clinical predication rule. Ethics and dissemination The findings of our study will provide new evidence to improve insertion success rates in the ED setting and identify strategies to reduce premature device failure for patients admitted to hospital wards. Results will unravel a complexity of factors that contribute to unsuccessful PIVC attempts such as patient and clinician factors along with the products, technologies and infusates used. Trial registration number ACTRN12615000588594; Pre-results. PMID:26868942

Development of a clinical prediction rule to improve peripheral intravenous cannulae first attempt success in the emergency department and reduce post insertion failure rates: the Vascular Access Decisions in the Emergency Room (VADER) study protocol.

PubMed

Carr, Peter J; Rippey, James C R; Cooke, Marie L; Bharat, Chrianna; Murray, Kevin; Higgins, Niall S; Foale, Aileen; Rickard, Claire M

2016-02-11

Peripheral intravenous cannula (PIVC) insertion is one of the most common clinical interventions performed in emergency care worldwide. However, factors associated with successful PIVC placement and maintenance are not well understood. This study seeks to determine the predictors of first time PIVC insertion success in emergency department (ED) and identify the rationale for removal of the ED inserted PIVC in patients admitted to the hospital ward. Reducing failed insertion attempts and improving peripheral intravenous cannulation practice could lead to better staff and patient experiences, as well as improving hospital efficiency. We propose an observational cohort study of PIVC insertions in a patient population presenting to ED, with follow-up observation of the PIVC in subsequent admissions to the hospital ward. We will collect specific PIVC observational data such as; clinician factors, patient factors, device information and clinical practice variables. Trained researchers will gather ED PIVC insertion data to identify predictors of insertion success. In those admitted from the ED, we will determine the dwell time of the ED-inserted PIVC. Multivariate regression analyses will be used to identify factors associated with insertions success and PIVC failure and standard statistical validation techniques will be used to create and assess the effectiveness of a clinical predication rule. The findings of our study will provide new evidence to improve insertion success rates in the ED setting and identify strategies to reduce premature device failure for patients admitted to hospital wards. Results will unravel a complexity of factors that contribute to unsuccessful PIVC attempts such as patient and clinician factors along with the products, technologies and infusates used. ACTRN12615000588594; Pre-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Pediatric Enteric Feeding Techniques: Insertion, Maintenance, and Management of Problems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nijs, Els L. F., E-mail: nijs@email.chop.ed; Cahill, Anne Marie, E-mail: cahill@email.chop.ed

Enteral feeding is considered a widespread, well-accepted means of delivering nutrition to adults and children who are unable to consume food by mouth or who need support in maintaining adequate nutrition for a variety of reasons, including acute and chronic disease states. Delivery of enteral feeding to nutritionally deprived patients may be achieved by several means. In this article, the indications and insertion of enteral access in children will be reviewed. In addition, common complications and management of problems will be discussed.

Molecular Characteristics of the Mycobacterium tuberculosis LAM-RUS Family Prevalent in Central Russia▿ †

PubMed Central

Dubiley, Svetlana; Kirillov, Eugene; Ignatova, Anna; Stepanshina, Valentina; Shemyakin, Igor

2007-01-01

We analyzed IS6110-associated polymorphisms in the phospholipase C genes of 107 isolates of Mycobacterium tuberculosis selected to be representative of isolates circulating in central Russia. We found that the majority of Latin American-Mediterranean family strains contained an insertion in a unique position in the plcA gene, suggesting a common ancestor. This insertion can serve as a specific genetic marker for this group, which we designate the LAM-RUS family. PMID:17942651

Z-2 Threaded Insert Design and Testing Abstract

NASA Technical Reports Server (NTRS)

Rhodes, RIchard; Graziosi, Dave; Jones, Bobby; Ferl, Jinny; Scarborough, Steve; Sweeney, Mitch

2016-01-01

The Z-2 Prototype Planetary Extravehicular Space Suit Assembly is a continuation of NASA's Z series of spacesuits. The Z-2 is another step in the NASA's technology development roadmap leading to human exploration of the Martian surface. To meet a more challenging set of requirements than previous suit systems standard design features, such as threaded inserts, have been re-analyzed and improved. NASA's Z-2 prototype space suit contains several components fabricated from an advanced hybrid composite laminate consisting of IM10 carbon fiber and fiber glass. One requirement NASA levied on the suit composites was the ability to have removable, replaceable helicoil inserts to which other suit components would be fastened. An approach utilizing bonded in inserts with helicoils inside of them was implemented. The design of the interface flanges of the composites allowed some of the inserts to be a "T" style insert that was installed through the entire thickness of the laminate. The flange portion of the insert provides a mechanical lock as a redundancy to the adhesive aiding in the pullout load that the insert can withstand. In some locations it was not possible to utilize at "T" style insert and a blind insert was used instead. These inserts rely completely on the bond strength of the adhesive to resist pullout. It was determined during the design of the suit that the inserts did not need to withstand loads induced from pressure cycling but instead tension induced from torqueing the screws to bolt on hardware which creates a much higher stress on them. Bolt tension is determined by dividing the torque on the screw by a k value multiplied by the thread diameter of the bolt. The k value is a factor that accounts for friction in the system. A common value used for k for a non-lubricated screw is 0.2. The k value can go down by as much as 0.1 if the screw is lubricated which means for the same torque, a much larger tension could be placed on the bolt and insert. This paper summarizes testing that was performed to determine a k value for helicoil inserts in the Z2 suit and how the insert design was modified to resist a higher pull out tension.

Association between latent proviral characteristics and immune activation in antiretrovirus-treated human immunodeficiency virus type 1-infected adults.

PubMed

Liang, Emily C; Sceats, Lindsay; Bayless, Nicholas L; Strauss-Albee, Dara M; Kubo, Jessica; Grant, Philip M; Furman, David; Desai, Manisha; Katzenstein, David A; Davis, Mark M; Zolopa, Andrew R; Blish, Catherine A

2014-08-01

Generalized immune activation during HIV infection is associated with an increased risk of cardiovascular disease, neurocognitive disease, osteoporosis, metabolic disorders, and physical frailty. The mechanisms driving this immune activation are poorly understood, particularly for individuals effectively treated with antiretroviral medications. We hypothesized that viral characteristics such as sequence diversity may play a role in driving HIV-associated immune activation. We therefore sequenced proviral DNA isolated from peripheral blood mononuclear cells from HIV-infected individuals on fully suppressive antiretroviral therapy. We performed phylogenetic analyses, calculated viral diversity and divergence in the env and pol genes, and determined coreceptor tropism and the frequency of drug resistance mutations. Comprehensive immune profiling included quantification of immune cell subsets, plasma cytokine levels, and intracellular signaling responses in T cells, B cells, and monocytes. These antiretroviral therapy-treated HIV-infected individuals exhibited a wide range of diversity and divergence in both env and pol genes. However, proviral diversity and divergence in env and pol, coreceptor tropism, and the level of drug resistance did not significantly correlate with markers of immune activation. A clinical history of virologic failure was also not significantly associated with levels of immune activation, indicating that a history of virologic failure does not inexorably lead to increased immune activation as long as suppressive antiretroviral medications are provided. Overall, this study demonstrates that latent viral diversity is unlikely to be a major driver of persistent HIV-associated immune activation. Chronic immune activation, which is associated with cardiovascular disease, neurologic disease, and early aging, is likely to be a major driver of morbidity and mortality in HIV-infected individuals. Although treatment of HIV with antiretroviral medications decreases the level of immune activation, levels do not return to normal. The factors driving this persistent immune activation, particularly during effective treatment, are poorly understood. In this study, we investigated whether characteristics of the latent, integrated HIV provirus that persists during treatment are associated with immune activation. We found no relationship between latent viral characteristics and immune activation in treated individuals, indicating that qualities of the provirus are unlikely to be a major driver of persistent inflammation. We also found that individuals who had previously failed treatment but were currently effectively treated did not have significantly increased levels of immune activation, providing hope that past treatment failures do not have a lifelong "legacy" impact. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Evaluation of a new mid-scala cochlear implant electrode using microcomputed tomography.

PubMed

Frisch, Christopher D; Carlson, Matthew L; Lane, John I; Driscoll, Colin L W

2015-12-01

To investigate electrode position, depth of insertion, and electrode contact using an electrode array with a mid-scala design following round window (RW) and cochleostomy insertion. Eight fresh-frozen cadaveric bones were implanted; half via a RW approach and half through an anteroinferior cochleostomy using a styleted mid-scala electrode design. Microcomputed tomography was used to acquire oblique coronal and oblique axial reformations. Individual electrode positions along each array, insertional depth, and electrode contact were determined using National Institutes of Health Image J software. All electrodes were inserted without significant resistance. The average angular depth of insertion was 436.5° for the RW group and 422.7° for the cochleostomy group. All electrodes acquired a perimodiolar position in the proximal segment and a lateral wall position at the basal turn, regardless of approach. Electrodes distal to the basal turn demonstrated a variable location, with 78% mid scala. One cochleostomy array fractured through the interscalar partition (ISP), acquiring a scala vestibuli position. The odds ratio for either abutting the modiolus, ISP, lateral wall or floor, or fracturing through the ISP were 2.7 times more likely following a cochleostomy insertion (P = .032). The styleted mid-scala electrode design acquires a proximal perimodiolar position, a lateral wall location, as it traverses the basal turn, and most commonly a mid-scala position in the distal array. Interscalar excursion occurred in one of the cochleostomy insertions. Cochleostomy insertion is more likely to result in ultimate final electrode position adjacent to critical intracochlear structures. NA. © 2015 The American Laryngological, Rhinological and Otological Society, Inc.

Infections and foreign bodies in ENT.

PubMed

Kullar, Peter; Yates, Philip D

2012-10-30

Infections play a major role in the practice of ENT. Microbial penetration into tissues of the head and neck can initiate a focal reaction causing superficial self-resolving infections. However, some of these have the potential to develop into life-threatening disease. We provide an overview of the most common ENT infections with focus on the presentation, diagnosis and management. Foreign bodies of the ear, nose and throat are a common presentation to primary and emergency care. Most commonly these are seen in children and include plastic toys, beads and foodstuffs inserted into the ears and nose. Diagnosis is often delayed as insertion is usually not witnessed. In exceptional cases airway foreign bodies can present as a life-threatening emergency. Removal of foreign bodies can usually be achieved by a skilled practitioner with minimal complications. Methods of removal include suction catheters, syringing, and use of instrumentation. In adults, the treatment of oesophageal food bolus obstruction may require a combination of medical and surgical intervention.

Bilateral Pneumothoraces in a Trauma Patient After Dobhoff Tube Insertion.

PubMed

Abidali, Ali; Mangram, Alicia; Shirah, Gina R; Wilson, Whitney; Abidali, Ahmed; Moeser, Phillip; Dzandu, James K

2018-03-05

BACKGROUND Dobhoff tube insertion is a common procedure used in the clinical setting to deliver enteral nutrition. Although it is often viewed as an innocuous bedside procedure, there are risks for numerous complications such as tracheobronchial insertion, which could lead to deleterious consequences. We present to our knowledge the first reported case of bilateral pneumothoraces caused by the insertion of a Dobhoff tube. In addition, we also discuss common pitfalls for confirming the positioning of Dobhoff tubes, as well as risk factors that can predispose a patient to improper tube placement. CASE REPORT We present the case of a 74-year-old male patient with multiple orthopedic injuries following an auto-pedestrian collision. Five attempts were made to place a Dobhoff tube to maintain enteral nutrition. Follow-up abdominal x-ray revealed displacement of the Dobhoff tube in the left pleural space. After removal of the tube, a follow-up chest x-ray revealed iatrogenic bilateral pneumothoraces. Acute hypoxemic respiratory failure ensued; therefore, bilateral chest tubes were placed. Over the next three weeks, the patient's respiratory status improved and both chest tubes were removed. The patient was eventually discharged to a skilled nursing facility. CONCLUSIONS Improper placement of Dobhoff tubes can lead to rare complications such as bilateral pneumothoraces. This unique case report of bilateral pneumothoraces after Dobhoff tube placement emphasizes the necessity of using proper diagnostic techniques for verifying proper tube placement, as well as understanding the risk factors that predispose a patient to a malpositioned tube.

Genes and Gene Therapy

MedlinePlus

... a child can have a genetic disorder. Gene therapy is an experimental technique that uses genes to ... prevent disease. The most common form of gene therapy involves inserting a normal gene to replace an ...

Avian sarcoma virus 17 carries the jun oncogene.

PubMed Central

Maki, Y; Bos, T J; Davis, C; Starbuck, M; Vogt, P K

1987-01-01

Biologically active molecular clones of avian sarcoma virus 17 (ASV 17) contain a replication-defective proviral genome of 3.5 kilobases (kb). The genome retains partial gag and env sequences, which flank a cell-derived putative oncogene of 0.93 kb, termed jun. The jun gene lacks preserved coding domains of tyrosine-specific protein kinases. It also shows no significant nucleic acid homology with other known oncogenes. The probable transformation-specific protein in ASV 17-transformed cells is a 55-kDa gag-jun fusion product. Images PMID:3033666

When and why a colonoscopist should discontinue colonoscopy by himself?

PubMed

Gan, Tao; Yang, Jin-Lin; Wu, Jun-Chao; Wang, Yi-Ping; Yang, Li

2015-07-07

To investigate when and why a colonoscopist should discontinue incomplete colonoscopy by himself. In this cross-sectional study, 517 difficult colonoscope insertions (Grade C, Kudo's difficulty classification) screened from 37800 colonoscopy insertions were collected from April 2004 to June 2014 by three 4(th)-level (Kudo's classification) colonoscopists. The following common factors for the incomplete insertion were excluded: structural obstruction of the colon or rectum, insufficient colon cleansing, discontinuation due to patient's discomfort or pain, severe colon disease with a perforation risk (e.g., severe ischemic colonopathy). All the excluded patients were re-scheduled if permission was obtained from the patients whose intubation had failed. If the repeat intubations were still a failure because of the difficult operative techniques, those patients were also included in this study. The patient's age, sex, anesthesia and colonoscope type were recorded before colonoscopy. During the colonoscopic examination, the influencing factors of fixation, tortuosity, laxity and redundancy of the colon were assessed, and the insertion time (> 10 min or ≤ 10 min) were registered. The insertion time was analyzed by t-test, and other factors were analyzed by univariate and multivariate logistic regression. Three hundred and twenty-two (62.3%) of the 517 insertions were complete in the colonoscope insertion into the ileocecum, but 195 (37.7%) failed in the insertion. Fixation, tortuosity, laxity or redundancy occurred during the colonoscopic examination. Multivariate logistic regression analysis revealed that fixation (OR = 0.06, 95%CI: 0.03-0.16, P < 0.001) and tortuosity (OR = 0.04, 95%CI: 0.02-0.08, P < 0.001) were significantly related to the insertion into the ileocecum in the left hemicolon; multivariate logistic regression analysis also revealed that fixation (OR = 0.16, 95%CI: 0.06-0.39, P < 0.001), tortuosity (OR 0.23, 95%CI: 0.13-0.43, P < 0.001), redundancy (OR = 0.12, 95%CI: 0.05-0.26, P < 0.001) and sex (OR = 0.35, 95%CI: 0.20-0.63, P < 0.001) were significantly related to the insertion into the ileocecum in the right hemicolon. Prolonged insertion time (> 10 min) was an unfavorable factor for the insertion into the ileocecum. Colonoscopy should be discontinued if freedom of the colonoscope body's insertion and rotation is completely lost, and the insertion time is prolonged over 30 min.

Z-2 Threaded Insert Design and Testing

NASA Technical Reports Server (NTRS)

Ross, Amy; Rhodes, Richard; Jones, Robert J.; Graziosi, David; Ferl, Jinny; Sweeny, Mitch; Scarborough, Stephen

2016-01-01

NASA's Z-2 prototype space suit contains several components fabricated from an advanced hybrid composite laminate consisting of IM10 carbon fiber and fiber glass. One requirement was to have removable, replaceable helicoil inserts to which other suit components would be fastened. An approach utilizing bonded in inserts with helicoils inside of them was implemented. During initial assembly, cracking sounds were heard followed by the lifting of one of the blind inserts out of its hole when the screws were torqued. A failure investigation was initiated to understand the mechanism of the failure. Ultimately, it was determined that the pre-tension caused by torqueing the fasteners is a much larger force than induced from the pressure loads of the suit which was not considered in the insert design. Bolt tension is determined by dividing the torque on the screw by a k value multiplied by the thread diameter of the bolt. The k value is a factor that accounts for friction in the system. A common value used for k for a non-lubricated screw is 0.2. The k value can go down by as much as 0.1 if the screw is lubricated which means for the same torque, a much larger tension could be placed on the bolt and insert. This paper summarizes the failure investigation that was performed to identify the root cause of the suit failure and details how the insert design was modified to resist a higher pull out tension.

A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

NASA Astrophysics Data System (ADS)

Nguyen, Trong-Nghia; Putikam, Raghunath; Lin, M. C.

2015-03-01

We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH2OO and anti/syn-CH3C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH2OO and anti-CH3C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH3C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C-H bonds. For syn-CH3C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH3 group by the terminal O atom producing CH2C(H)O-OH. At 298 K, the intramolecular insertion process in CH2OO was found to be 600 times faster than the commonly assumed ring-closing reaction.

Practice patterns of retrievable inferior vena cava filters and predictors of filter retrieval in patients with pulmonary embolism.

PubMed

Kang, Jieun; Ko, Heung-Kyu; Shin, Ji Hoon; Ko, Gi-Young; Jo, Kyung-Wook; Huh, Jin Won; Oh, Yeon-Mok; Lee, Sang-Do; Lee, Jae Seung

2017-12-01

Retrievable inferior vena cava (IVC) filters are increasingly used in patients with venous thromboembolism (VTE) who have contraindications to anticoagulant therapy. However, previous studies have shown that many retrievable filters are left permanently in patients. This study aimed to identify the common indications for IVC filter insertion, the filter retrieval rate, and the predictive factors for filter retrieval attempts. To this end, a retrospective cohort study was performed at a tertiary care center in South Korea between January 2010 and May 2016. Electronic medical charts were reviewed for patients with pulmonary embolism (PE) who underwent IVC filter insertion. A total of 439 cases were reviewed. The most common indication for filter insertion was a preoperative/procedural aim, followed by extensive iliofemoral deep vein thrombosis (DVT). Retrieval of the IVC filter was attempted in 44.9% of patients. The retrieval success rate was 93.9%. History of cerebral hemorrhage, malignancy, and admission to a nonsurgical department were the significant predictive factors of a lower retrieval attempt rate in multivariate analysis. With the increased use of IVC filters, more issues should be addressed before placing a filter and physicians should attempt to improve the filter retrieval rate.

Permanent stenting in "unextractable" common bile duct stones in high risk patients. A prospective randomized study comparing two different stents.

PubMed

Pisello, Franco; Geraci, Girolamo; Li Volsi, Francesco; Modica, Giuseppe; Sciumè, Carmelo

2008-11-01

Endoscopic sphincterotomy (ES) and stone extraction is the treatment of choice for bile duct stones. Therefore, if ES and conventional stone extraction fail, further treatment is mandatory. Insertion of a biliary endoprosthesis is an effective option. We treated 30 high-risk patients (17 women and 13 men, mean age 82 years) affected by difficult common bile duct stones. The patients were randomly assigned preoperatively using closed envelopes (blind randomization) into two groups to receive insertion of polyethylene or hydrophilic hydromer-coated polyurethane stent, respectively. Follow-up was achieved by contacting referring physicians and patient's relatives. Biliary drainage was established in all patients. Early minor complications occurred in 28%. In all these patients, the stent was a definitive measure. Median follow-up was 38 months. Late complications occurred in 34%. Cholangitis was the most frequent. During follow up, 11 patients died, two as result of a biliary-related cause. No statistically significant difference was observed on different stents patency. Endoprosthesis insertion as a permanent therapy is an effective alternative to surgery or dissolution therapy. Therefore, biliary stenting should preferably be restricted to high-risk patients unfit for operative treatment and with a short life expectancy.

Safe percutaneous suprapubic catheterisation

PubMed Central

Goyal, NK; Goel, A; Sankhwar, SN

2012-01-01

INTRODUCTION We describe our technique of percutaneous suprapubic catheter insertion with special reference to steps that help to avoid common complications of haematuria and catheter misplacement. METHODS The procedure is performed using a stainless steel reusable trocar under local infiltrative anaesthesia, usually at the bedside. After clinical confirmation of a full bladder, the trocar is advanced into the bladder through a skin incision. Once the bladder is entered, the obturator is removed and the assistant inserts a Foley catheter followed by rapid balloon inflation. Slight traction is applied to the catheter for about five minutes. Patients with previous lower abdominal surgery, an inadequately distended bladder or acute pelvic trauma do not undergo suprapubic catheterisation using this method. RESULTS The procedure was performed in 72 men (mean age: 42.4 years, range: 18–78 years) with urinary retention with a palpable bladder. The average duration of the procedure was less than five minutes. No complications were noted in any of the patients. CONCLUSIONS Trocar suprapubic catheter insertion is a safe and effective bedside procedure for emergency bladder drainage and can be performed by resident surgeons. The common complications associated with the procedure can be avoided with a few careful steps. PMID:23131233

Predeployment validation of fault-tolerant systems through software-implemented fault insertion

NASA Technical Reports Server (NTRS)

Czeck, Edward W.; Siewiorek, Daniel P.; Segall, Zary Z.

1989-01-01

Fault injection-based automated testing (FIAT) environment, which can be used to experimentally characterize and evaluate distributed realtime systems under fault-free and faulted conditions is described. A survey is presented of validation methodologies. The need for fault insertion based on validation methodologies is demonstrated. The origins and models of faults, and motivation for the FIAT concept are reviewed. FIAT employs a validation methodology which builds confidence in the system through first providing a baseline of fault-free performance data and then characterizing the behavior of the system with faults present. Fault insertion is accomplished through software and allows faults or the manifestation of faults to be inserted by either seeding faults into memory or triggering error detection mechanisms. FIAT is capable of emulating a variety of fault-tolerant strategies and architectures, can monitor system activity, and can automatically orchestrate experiments involving insertion of faults. There is a common system interface which allows ease of use to decrease experiment development and run time. Fault models chosen for experiments on FIAT have generated system responses which parallel those observed in real systems under faulty conditions. These capabilities are shown by two example experiments each using a different fault-tolerance strategy.

Vaginal inserts based on chitosan and carboxymethylcellulose complexes for local delivery of chlorhexidine: preparation, characterization and antimicrobial activity.

PubMed

Bigucci, Federica; Abruzzo, Angela; Vitali, Beatrice; Saladini, Bruno; Cerchiara, Teresa; Gallucci, Maria Caterina; Luppi, Barbara

2015-01-30

The aim of this work was to prepare vaginal inserts based on chitosan/carboxymethylcellulose polyelectrolyte complexes for local delivery of chlorhexidine digluconate. Complexes were prepared with different chitosan/carboxymethylcellulose molar ratios at a pH value close to pKa interval of the polymers and were characterized in terms of physico-chemical properties, complexation yield and drug loading. Then complexes were used to prepare inserts as vaginal dosage forms and their physical handling, morphology, water-uptake ability and drug release properties as well as antimicrobial activity toward Candida albicans and Escherichia coli were evaluated. Results confirmed the ionic interaction between chitosan and carboxymethylcellulose and the influence of the charge amount on the complexation yield. Complexes were characterized by high values of drug loading and showed increasing water-uptake ability with the increase of carboxymethylcellulose amount. The selection of appropriate chitosan/carboxymethylcellulose molar ratios allowed to obtain cone-like shaped solid inserts, easy to handle and able to hydrate releasing the drug over time. Finally, the formulated inserts showed antimicrobial activity against common pathogens responsible for vaginal infections. Copyright © 2014 Elsevier B.V. All rights reserved.

Endoscopic Dacrocystorhinostomy in Lacrimal Canalicular Trauma

PubMed Central

Khan, Humayun A; Bayat, Aredeshir; De Carpentier, JP

2007-01-01

A case is presented where the common insertion of the upper and lower canaliculus of the lacrimal sac was repaired using endoscopic dacrocystorhinostomy (DCR) techniques, with silicone stenting and securing of stents intranasally. PMID:17316509

Testicular Prostheses: Development and Modern Usage

PubMed Central

Bodiwala, D; Summerton, DJ; Terry, TR

2007-01-01

INTRODUCTION Testicular prostheses produced from various materials have been in use since 1941. The absence of a testicle has been shown to be a psychologically traumatic experience for males of all ages. The indications for insertion of a prosthesis include absence or following orchidectomy from a number of causes such as malignancy, torsion and orchitis. The most common substance used around the world in the manufacture of these implants is silicone; however, in the US, this material is currently banned because of theoretical health risks. This has led to the development of saline-filled prostheses as an alternative. PATIENTS AND METHODS A Medline search was carried out on all articles on testicular prosthesis between 1966 and 2006. CONCLUSIONS This review highlights the controversies regarding prosthetic materials, the complications of insertion and the potential benefits of this commonly performed procedure. PMID:17535609

Retained rectal foreign body with rectal perforation; a complication of the traditional management of haemorrhoids: a case report.

PubMed

Olaoye, Iyiade Olatunde; Adensina, Micheal Dapo

2013-10-01

Retained rectal foreign bodies are most commonly seen in homosexuals and after assault. A few have been reported after self-treatment of anorectal conditions and prostatic massage. Harmful traditional medical practices have been reported in many communities in Africa but therapeutic anal insertion of foreign bodies for the management of haemorrhoids is rare. We present a patient with features of peritonitis following insertion of a wine bottle into his rectum in an attempt to manage his prolapsed haemorrhoids.

A Very Long Foreign Body in the Bladder

PubMed Central

Imai, Atsushi; Suzuki, Yuichiro; Hashimoto, Yasuhiro; Sasaki, Atsushi; Saitoh, Hisao; Ohyama, Chikara

2011-01-01

In the urinary tract, foreign body is most commonly found in the urinary bladder. But it is anatomically very difficult for a man to self-insert a long object into the urinary bladder. Here we report a case of a 49-year-old Japanese man who has inserted a 140-cm vinyl tube in the bladder for masturbation. He could not retrieve it, and the bladder foreign body remained in this position for about two years. He was referred to our hospital and open surgery was performed. PMID:21687624

Specific insertions of zinc finger domains into Gag-Pol yield engineered retroviral vectors with selective integration properties

PubMed Central

Lim, Kwang-il; Klimczak, Ryan; Yu, Julie H.; Schaffer, David V.

2010-01-01

Retroviral vectors offer benefits of efficient delivery and stable gene expression; however, their clinical use raises the concerns of insertional mutagenesis and potential oncogenesis due to genomic integration preferences in transcriptional start sites (TSS). We have shifted the integration preferences of retroviral vectors by generating a library of viral variants with a DNA-binding domain inserted at random positions throughout murine leukemia virus Gag-Pol, then selecting for variants that are viable and exhibit altered integration properties. We found seven permissive zinc finger domain (ZFD) insertion sites throughout Gag-Pol, including within p12, reverse transcriptase, and integrase. Comprehensive genome integration analysis showed that several ZFD insertions yielded retroviral vector variants with shifted integration patterns that did not favor TSS. Furthermore, integration site analysis revealed selective integration for numerous mutants. For example, two retroviral variants with a given ZFD at appropriate positions in Gag-Pol strikingly integrated primarily into four common sites out of 3.1 × 109 possible human genome locations (P = 4.6 × 10-29). Our findings demonstrate that insertion of DNA-binding motifs into multiple locations in Gag-Pol can make considerable progress toward engineering safer retroviral vectors that integrate into a significantly narrowed pool of sites on human genome and overcome the preference for TSS. PMID:20616052

Organ-specific SPECT activity calibration using 3D printed phantoms for molecular radiotherapy dosimetry.

PubMed

Robinson, Andrew P; Tipping, Jill; Cullen, David M; Hamilton, David; Brown, Richard; Flynn, Alex; Oldfield, Christopher; Page, Emma; Price, Emlyn; Smith, Andrew; Snee, Richard

2016-12-01

Patient-specific absorbed dose calculations for molecular radiotherapy require accurate activity quantification. This is commonly derived from Single-Photon Emission Computed Tomography (SPECT) imaging using a calibration factor relating detected counts to known activity in a phantom insert. A series of phantom inserts, based on the mathematical models underlying many clinical dosimetry calculations, have been produced using 3D printing techniques. SPECT/CT data for the phantom inserts has been used to calculate new organ-specific calibration factors for (99m) Tc and (177)Lu. The measured calibration factors are compared to predicted values from calculations using a Gaussian kernel. Measured SPECT calibration factors for 3D printed organs display a clear dependence on organ shape for (99m) Tc and (177)Lu. The observed variation in calibration factor is reproduced using Gaussian kernel-based calculation over two orders of magnitude change in insert volume for (99m) Tc and (177)Lu. These new organ-specific calibration factors show a 24, 11 and 8 % reduction in absorbed dose for the liver, spleen and kidneys, respectively. Non-spherical calibration factors from 3D printed phantom inserts can significantly improve the accuracy of whole organ activity quantification for molecular radiotherapy, providing a crucial step towards individualised activity quantification and patient-specific dosimetry. 3D printed inserts are found to provide a cost effective and efficient way for clinical centres to access more realistic phantom data.

Lysenin Toxin Membrane Insertion Is pH-Dependent but Independent of Neighboring Lysenins.

PubMed

Munguira, Ignacio L B; Takahashi, Hirohide; Casuso, Ignacio; Scheuring, Simon

2017-11-07

Pore-forming toxins form a family of proteins that act as virulence factors of pathogenic bacteria, but similar proteins are found in all kingdoms of life, including the vertebrate immune system. They are secreted as soluble monomers that oligomerize on target membranes in the so-called prepore state; after activation, they insert into the membrane and adopt the pore state. Lysenin is a pore-forming toxin from the earthworm Eisenida foetida, of which both the soluble and membrane-inserted structures are solved. However, the activation and membrane-insertion mechanisms have remained elusive. Here, we used high-speed atomic force microscopy to directly visualize the membrane-insertion mechanism. Changing the environmental pH from pH 7.5 to below pH 6.0 favored membrane insertion. We detected a short α-helix in the soluble structure that comprised three glutamic acids (Glu92, Glu94, and Glu97) that we hypothesized may represent a pH-sensor (as in similar toxins, e.g., Listeriolysin). Mutant lysenin still can form pores, but mutating these glutamic acids to glutamines rendered the toxin pH-insensitive. On the other hand, toxins in the pore state did not favor insertion of neighboring prepores; indeed, pore insertion breaks the hexagonal ordered domains of prepores and separates from neighboring molecules in the membrane. pH-dependent activation of toxins may represent a common feature of pore-forming toxins. High-speed atomic force microscopy with single-molecule resolution at high temporal resolution and the possibility of exchanging buffers during the experiments presents itself as a unique tool for the study of toxin-state conversion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Persistence of Penaeus stylirostris densovirus delays mortality caused by white spot syndrome virus infection in black tiger shrimp (Penaeus monodon)

PubMed Central

2013-01-01

Background Persistent infection of Penaeus stylirostris densovirus (PstDNV) (also called IHHNV) and its non-infectious inserts in the black tiger shrimp, Penaeus monodon (P. monodon) genome are commonly found without apparent disease. Here, we introduced the method of multiplex PCR in order to differentiate shrimp with viral inserts from ones with the infectious virus. The method allowed us to study the effect of pre-infection of IHHNV, in comparison to IHHNV inserts, on WSSV resistance in P. monodon. Results A multiplex PCR system was developed to amplify the entire IHHNV genome, ensuring the accurate diagnosis. Field samples containing IHHNV DNA templates as low as 20 pg or equivalent 150 viral copies can be detected by this method. By challenging the two groups of diagnosed shrimp with WSSV, we found that shrimp with IHHNV infection and those with viral inserts responded to WSSV differently. Considering cumulative mortality, average time to death of shrimp in IHHNV-infected group (day 14) was significantly delayed relative to that (day 10) of IHHNV-inserted group. Real-time PCR analysis of WSSV copy number indicated the lower amount of WSSV in the IHHNV-infected group than the virus-inserted group. The ratio of IHHNV: WSSV copy number in all determined IHHNV-infected samples ranged from approximately 4 to 300-fold. Conclusion The multiplex PCR assay developed herein proved optimal for convenient differentiation of shrimp specimens with real IHHNV infection and those with insert types. Diagnosed shrimp were also found to exhibit different WSSV tolerance. After exposed to WSSV, the naturally pre-infected IHHNV P. monodon were less susceptible to WSSV and, consequently, survived longer than the IHHNV-inserted shrimp. PMID:23414329

Amphiphilic interactions of ionic liquids with lipid biomembranes: a molecular simulation study.

PubMed

Yoo, Brian; Shah, Jindal K; Zhu, Yingxi; Maginn, Edward J

2014-11-21

Current bottlenecks in the large-scale commercial use of many ionic liquids (ILs) include their high costs, low biodegradability, and often unknown toxicities. As a proactive effort to better understand the molecular mechanisms of ionic liquid toxicities, the work herein presents a comprehensive molecular simulation study on the interactions of 1-n-alkyl-3-methylimidazolium-based ILs with a phosphatidylcholine (PC) lipid bilayer. We explore the effects of increasing alkyl chain length (n = 4, 8, and 12) in the cation and anion hydrophobicity on the interactions with the lipid bilayer. Bulk atomistic molecular dynamics (MD) simulations performed at millimolar (mM) IL concentrations show spontaneous insertion of cations into the lipid bilayer regardless of the alkyl chain length and a favorable orientational preference once a cation is inserted. Cations also exhibit the ability to "flip" inside the lipid bilayer (as is common for amphiphiles) if partially inserted with an unfavorable orientation. Moreover, structural analysis of the lipid bilayer show that cationic insertion induces roughening of the bilayer surface, which may be a precursor to bilayer disruption. To overcome the limitation in the timescale of our simulations, free energies for a single IL cation and anion insertion have been determined based on potential of mean force calculations. These results show a decrease in free energy in response to both short and long alkyl chain IL cation insertion, and likewise for a single hydrophobic anion insertion, but an increase in free energy for the insertion of a hydrophilic chloride anion. Both bulk MD simulations and free energy calculations suggest that toxicity mechanisms toward biological systems are likely caused by ILs behaving as ionic surfactants. [Yoo et al., Soft Matter, 2014].

Selective Regulation of Human Immunodeficiency Virus-Infected CD4+ Lymphocytes by a Synthetic Immunomodulator Leads to Potent Virus Suppression In Vitro and in hu-PBL-SCID Mice

PubMed Central

Bahr, George M.; Darcissac, Edith C. A.; Castéran, Nathalie; Amiel, Corinne; Cocude, Cécile; Truong, Marie-José; Dewulf, Joëlle; Capron, André; Mouton, Yves

2001-01-01

We have previously observed that the synthetic immunomodulator Murabutide inhibits human immunodeficiency virus type 1 (HIV-1) replication at multiple levels in macrophages and dendritic cells. The present study was designed to profile the activity of Murabutide on CD8-depleted phytohemagglutinin-activated lymphocytes from HIV-1-infected subjects and on the outcome of HIV-1 infection in severe combined immunodeficiency mice reconstituted with human peripheral blood leukocytes (hu-PBL-SCID mice). Maintaining cultures of CD8-depleted blasts from 36 patients in the presence of Murabutide produced dramatically reduced levels of viral p24 protein in the supernatants. This activity correlated with reduced viral transcripts and proviral DNA, was evident in cultures harboring R5, X4-R5, or X4 HIV-1 isolates, was not linked to inhibition of cellular DNA synthesis, and did not correlate with β-chemokine release. Moreover, c-myc mRNA expression was down-regulated in Murabutide-treated cells, suggesting potential interference of the immunomodulator with the nuclear transport of viral preintegration complexes. On the other hand, daily treatment of HIV-1-infected hu-PBL-SCID mice with Murabutide significantly reduced the viral loads in plasma and the proviral DNA content in human peritoneal cells. These results are the first to demonstrate that a clinically acceptable synthetic immunomodulator with an ability to enhance the host's nonspecific immune defense mechanisms against infections can directly regulate cellular factors in infected lymphocytes, leading to controlled HIV-1 replication. PMID:11435574

Evaluation of the role of TAX, HBZ, and HTLV-1 proviral load on the survival of ATLL patients.

PubMed

Akbarin, Mohammad Mehdi; Shirdel, Abbas; Bari, Alireza; Mohaddes, Seyedeh Tahereh; Rafatpanah, Houshang; Karimani, Ehsan Ghayour; Etminani, Kobra; Golabpour, Amin; Torshizi, Reza

2017-06-01

Adult T-cell leukemia/lymphoma (ATLL) is an aggressive malignancy with very poor prognosis and short survival, caused by the human T-lymphotropic virus type-1 (HTLV-1). The HTLV-1 biomarkers trans-activator x (TAX) and HTLV-1 basic leucine zipper factor (HBZ) are main oncogenes and life-threatening elements. This study aimed to assess the role of the TAX and HBZ genes and HTLV-1 proviral load (PVL) in the survival of patients with ATLL. Forty-three HTLV-1-infected individuals, including 18 asymptomatic carriers (AC) and 25 ATLL patients (ATLL), were evaluated between 2011 and 2015. The mRNA expression of TAX and HBZ and the HTLV-1 PVL were measured by quantitative PCR. Significant differences in the mean expression levels of TAX and HBZ were observed between the two study groups (ATLL and AC, P =0.014 and P =0.000, respectively). In addition, the ATLL group showed a significantly higher PVL than AC ( P =0.000). There was a significant negative relationship between PVL and survival among all study groups ( P =0.047). The HTLV-1 PVL and expression of TAX and HBZ were higher in the ATLL group than in the AC group. Moreover, a higher PVL was associated with shorter survival time among all ATLL subjects. Therefore, measurement of PVL, TAX , and HBZ may be beneficial for monitoring and predicting HTLV-1-infection outcomes, and PVL may be useful for prognosis assessment of ATLL patients. This research demonstrates the possible correlation between these virological markers and survival in ATLL patients.

Molecular characterization of a novel gammaretrovirus in killer whales (Orcinus orca).

PubMed

Lamere, Sarah A; St Leger, Judy A; Schrenzel, Mark D; Anthony, Simon J; Rideout, Bruce A; Salomon, Daniel R

2009-12-01

There are currently no published data documenting the presence of retroviruses in cetaceans, though the occurrences of cancers and immunodeficiency states suggest the potential. We examined tissues from adult killer whales and detected a novel gammaretrovirus by degenerate PCR. Reverse transcription-PCR also demonstrated tissue and serum expression of retroviral mRNA. The full-length sequence of the provirus was obtained by PCR, and a TaqMan-based copy number assay did not demonstrate evidence of productive infection. PCR on blood samples from 11 healthy captive killer whales and tissues from 3 free-ranging animals detected the proviral DNA in all tissues examined from all animals. A survey of multiple cetacean species by PCR for gag, pol, and env sequences showed homologs of this virus in the DNA of eight species of delphinids, pygmy and dwarf sperm whales, and harbor porpoises, but not in beluga or fin whales. Analysis of the bottlenose dolphin genome revealed two full-length proviral sequences with 97.4% and 96.9% nucleotide identity to the killer whale gammaretrovirus. The results of single-cell PCR on killer whale sperm and Southern blotting are also consistent with the conclusion that the provirus is endogenous. We suggest that this gammaretrovirus entered the delphinoid ancestor's genome before the divergence of modern dolphins or that an exogenous variant existed following divergence that was ultimately endogenized. However, the transcriptional activity demonstrated in tissues and the nearly intact viral genome suggest a more recent integration into the killer whale genome, favoring the latter hypothesis. The proposed name for this retrovirus is killer whale endogenous retrovirus.

Reexamination of human T cell lymphotropic virus (HTLV-I/II) prevalence.

PubMed

Zucker-Franklin, D; Pancake, B A; Marmor, M; Legler, P M

1997-06-10

In the United States, blood donors are being screened for infection with human T cell lymphotropic viruses I and II (HTLV-I/II) by serologic means, which detect antibodies to the structural proteins of these viruses. Because patients with mycosis fungoides (MF) usually do not have such antibodies even though their cells harbor HTLV-I Tax and/or pol proviral sequences, it was questioned whether the prevalence of HTLV infection among healthy blood donors may also be underestimated by current means of testing. To examine this possibility, a study on specimens of relatives of mycosis fungoides patients (MFR) was begun. In addition, to collect data more expeditiously, a cohort of former injection drug users (IDUs) was tested by routine serologic methods, as well as by PCR/Southern blot analysis for Tax, pol, and gag proviral sequences and Western blot analysis for antibodies to the Tax gene product. To date, 6/8 MFRs and 42/81 (51.8%) of HIV-negative IDUs proved to be positive for HTLV, whereas routine serology identified none of the MFR and only 18/81 (22.2%) of the IDUs. Among the latter test subjects, the incidence of HTLV-I also proved to be 10 times higher than expected. Therefore, it is likely that among healthy blood donors infection with HTLV-I/II is more prevalent than is currently assumed. Since Tax is the transforming sequence of HTLV-I/II, testing for Tax sequences and antibodies to its gene product may be desirable in blood transfusion and tissue donor facilities.

Reexamination of human T cell lymphotropic virus (HTLV-I/II) prevalence

PubMed Central

Zucker-Franklin, Dorothea; Pancake, Bette A.; Marmor, Michael; Legler, Patricia M.

1997-01-01

In the United States, blood donors are being screened for infection with human T cell lymphotropic viruses I and II (HTLV-I/II) by serologic means, which detect antibodies to the structural proteins of these viruses. Because patients with mycosis fungoides (MF) usually do not have such antibodies even though their cells harbor HTLV-I Tax and/or pol proviral sequences, it was questioned whether the prevalence of HTLV infection among healthy blood donors may also be underestimated by current means of testing. To examine this possibility, a study on specimens of relatives of mycosis fungoides patients (MFR) was begun. In addition, to collect data more expeditiously, a cohort of former injection drug users (IDUs) was tested by routine serologic methods, as well as by PCR/Southern blot analysis for Tax, pol, and gag proviral sequences and Western blot analysis for antibodies to the Tax gene product. To date, 6/8 MFRs and 42/81 (51.8%) of HIV-negative IDUs proved to be positive for HTLV, whereas routine serology identified none of the MFR and only 18/81 (22.2%) of the IDUs. Among the latter test subjects, the incidence of HTLV-I also proved to be 10 times higher than expected. Therefore, it is likely that among healthy blood donors infection with HTLV-I/II is more prevalent than is currently assumed. Since Tax is the transforming sequence of HTLV-I/II, testing for Tax sequences and antibodies to its gene product may be desirable in blood transfusion and tissue donor facilities. PMID:9177230

Germ line insertion of mtDNA at the breakpoint junction of a reciprocal constitutional translocation.

PubMed

Willett-Brozick, J E; Savul, S A; Richey, L E; Baysal, B E

2001-08-01

Constitutional chromosomal translocations are relatively common causes of human morbidity, yet the DNA double-strand break (DSB) repair mechanisms that generate them are incompletely understood. We cloned, sequenced and analyzed the breakpoint junctions of a familial constitutional reciprocal translocation t(9;11)(p24;q23). Within the 10-kb region flanking the breakpoints, chromosome 11 had 25% repeat elements, whereas chromosome 9 had 98% repeats, 95% of which were L1-type LINE elements. The breakpoints occurred within an L1-type repeat element at 9p24 and at the 3'-end of an Alu sequence at 11q23. At the breakpoint junction of derivative chromosome 9, we discovered an unusually large 41-bp insertion, which showed 100% identity to 12S mitochondrial DNA (mtDNA) between nucleotides 896 and 936 of the mtDNA sequence. Analysis of the human genome failed to show the preexistence of the inserted sequence at normal chromosomes 9 and 11 breakpoint junctions or elsewhere in the genome, strongly suggesting that the insertion was derived from human mtDNA and captured into the junction during the DSB repair process. To our knowledge, these findings represent the first observation of spontaneous germ line insertion of modern human mtDNA sequences and suggest that DSB repair may play a role in inter-organellar gene transfer in vivo. Our findings also provide evidence for a previously unrecognized insertional mechanism in human, by which non-mobile extra-chromosomal fragments can be inserted into the genome at DSB repair junctions.

Quantifying electrical impacts on redundant wire insertion in 7nm unidirectional designs

NASA Astrophysics Data System (ADS)

Mohyeldin, Ahmed; Schroeder, Uwe Paul; Srinivasan, Ramya; Narisetty, Haritez; Malik, Shobhit; Madhavan, Sriram

2017-04-01

In nano-meter scale Integrated Circuits, via fails due to random defects is a well-known yield detractor, and via redundancy insertion is a common method to help enhance semiconductors yield. For the case of Self Aligned Double Patterning (SADP), which might require unidirectional design layers as in the case of some advanced technology nodes, the conventional methods of inserting redundant vias don't work any longer. This is because adding redundant vias conventionally requires adding metal shapes in the non-preferred direction, which will violate the SADP design constraints in that case. Therefore, such metal layers fabricated using unidirectional SADP require an alternative method for providing the needed redundancy. This paper proposes a post-layout Design for Manufacturability (DFM) redundancy insertion method tailored for the design requirements introduced by unidirectional metal layers. The proposed method adds redundant wires in the preferred direction - after searching for nearby vacant routing tracks - in order to provide redundant paths for electrical signals. This method opportunistically adds robustness against failures due to silicon defects without impacting area or incurring new design rule violations. Implementation details of this redundancy insertion method will be explained in this paper. One known challenge with similar DFM layout fixing methods is the possible introduction of undesired electrical impact, causing other unintentional failures in design functionality. In this paper, a study is presented to quantify the electrical impacts of such redundancy insertion scheme and to examine if that electrical impact can be tolerated. The paper will show results to evaluate DFM insertion rates and corresponding electrical impact for a given design utilization and maximum inserted wire length. Parasitic extraction and static timing analysis results will be presented. A typical digital design implemented using GLOBALFOUNDRIES 7nm technology is used for demonstration. The provided results can help evaluate such extensive DFM insertion method from an electrical standpoint. Furthermore, the results could provide guidance on how to implement the proposed method of adding electrical redundancy such that intolerable electrical impacts could be avoided.

Semi-Automatic Electronic Stent Register: a novel approach to preventing ureteric stents lost to follow up.

PubMed

Macneil, James W H; Michail, Peter; Patel, Manish I; Ashbourne, Julie; Bariol, Simon V; Ende, David A; Hossack, Tania A; Lau, Howard; Wang, Audrey C; Brooks, Andrew J

2017-10-01

Ureteric stents are indispensable tools in modern urology; however, the risk of them not being followed-up once inserted poses medical and medico-legal risks. Stent registers are a common solution to mitigate this risk; however, manual registers are logistically challenging, especially for busy units. Western Sydney Local Health District developed a novel Semi-Automatic Electronic Stent Register (SAESR) utilizing billing information to track stent insertions. To determine the utility of this system, an audit was conducted comparing the 6 months before the introduction of the register to the first 6 months of the register. In the first 6 months of the register, 457 stents were inserted. At the time of writing, two of these are severely delayed for removal, representing a rate of 0.4%. In the 6 months immediately preceding the introduction of the register, 497 stents were inserted, and six were either missed completely or severely delayed in their removal, representing a rate of 1.2%. A non-inferiority analysis found this to be no worse than the results achieved before the introduction of the register. The SAESR allowed us to improve upon our better than expected rate of stents lost to follow up or severely delayed. We demonstrated non-inferiority in the rate of lost or severely delayed stents, and a number of other advantages including savings in personnel costs. The semi-automatic register represents an effective way of reducing the risk associated with a common urological procedure. We believe that this methodology could be implemented elsewhere. © 2017 Royal Australasian College of Surgeons.

Genome-wide screening identifies a KCNIP1 copy number variant as a genetic predictor for atrial fibrillation

PubMed Central

Tsai, Chia-Ti; Hsieh, Chia-Shan; Chang, Sheng-Nan; Chuang, Eric Y.; Ueng, Kwo-Chang; Tsai, Chin-Feng; Lin, Tsung-Hsien; Wu, Cho-Kai; Lee, Jen-Kuang; Lin, Lian-Yu; Wang, Yi-Chih; Yu, Chih-Chieh; Lai, Ling-Ping; Tseng, Chuen-Den; Hwang, Juey-Jen; Chiang, Fu-Tien; Lin, Jiunn-Lee

2016-01-01

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. Previous genome-wide association studies had identified single-nucleotide polymorphisms in several genomic regions to be associated with AF. In human genome, copy number variations (CNVs) are known to contribute to disease susceptibility. Using a genome-wide multistage approach to identify AF susceptibility CNVs, we here show a common 4,470-bp diallelic CNV in the first intron of potassium interacting channel 1 gene (KCNIP1) is strongly associated with AF in Taiwanese populations (odds ratio=2.27 for insertion allele; P=6.23 × 10−24). KCNIP1 insertion is associated with higher KCNIP1 mRNA expression. KCNIP1-encoded protein potassium interacting channel 1 (KCHIP1) is physically associated with potassium Kv channels and modulates atrial transient outward current in cardiac myocytes. Overexpression of KCNIP1 results in inducible AF in zebrafish. In conclusions, a common CNV in KCNIP1 gene is a genetic predictor of AF risk possibly pointing to a functional pathway. PMID:26831368

A Rare Case of Port-a-Cath Migration into the Mediastinum.

PubMed

Shah, B K; Srijan Tandukar, S; Shrestha, S; Sanchirico, P

2014-07-03

Port-a-cath is commonly used in patients who require frequent administration of intravenous medications. We describe a rare case of port-a-cath migration into the mediastinum 16 months after its insertion.

Radiological assessment of placement of the hysteroscopically inserted Essure permanent birth control device.

PubMed

Lorente Ramos, R M; Azpeitia Armán, J; Aparicio Rodríguez-Miñón, P; Salazar Arquero, F J; Albillos Merino, J C

2015-01-01

Essure is a permanent birth control device that is inserted through the cervix by hysteroscopy. The device is placed in the fallopian tubes, where it causes occlusion by stimulating fibrosis. Patients can be followed up with plain-film X-rays, hysterosalpingography, and ultrasonography, although the devices can also be identified incidentally on CT and MRI. The follow-up of Essure is based on checking the criteria for appropriate positioning and correct functioning (tubal occlusion) and on diagnosing complications. The most common complications are perforation, migration (toward the uterine or peritoneal cavity), and occlusion failure. In hysterosalpingography, vascular intravasation is the most common cause of diagnostic error. Radiologists need to know how to recognize the device on different imaging techniques, how to check that it is correctly placed and functioning, and how to diagnose complications. Copyright © 2014 SERAM. Published by Elsevier España, S.L.U. All rights reserved.

MMTV insertional mutagenesis identifies genes, gene families and pathways involved in mammary cancer.

PubMed

Theodorou, Vassiliki; Kimm, Melanie A; Boer, Mandy; Wessels, Lodewyk; Theelen, Wendy; Jonkers, Jos; Hilkens, John

2007-06-01

We performed a high-throughput retroviral insertional mutagenesis screen in mouse mammary tumor virus (MMTV)-induced mammary tumors and identified 33 common insertion sites, of which 17 genes were previously not known to be associated with mammary cancer and 13 had not previously been linked to cancer in general. Although members of the Wnt and fibroblast growth factors (Fgf) families were frequently tagged, our exhaustive screening for MMTV insertion sites uncovered a new repertoire of candidate breast cancer oncogenes. We validated one of these genes, Rspo3, as an oncogene by overexpression in a p53-deficient mammary epithelial cell line. The human orthologs of the candidate oncogenes were frequently deregulated in human breast cancers and associated with several tumor parameters. Computational analysis of all MMTV-tagged genes uncovered specific gene families not previously associated with cancer and showed a significant overrepresentation of protein domains and signaling pathways mainly associated with development and growth factor signaling. Comparison of all tagged genes in MMTV and Moloney murine leukemia virus-induced malignancies showed that both viruses target mostly different genes that act predominantly in distinct pathways.

A Simulation-Based Blended Curriculum for Short Peripheral Intravenous Catheter Insertion: An Industry-Practice Collaboration.

PubMed

Glover, Kevin R; Stahl, Brian R; Murray, Connie; LeClair, Matthew; Gallucci, Susan; King, Mary Anne; Labrozzi, Laura J; Schuster, Catherine; Keleekai, Nowai L

2017-09-01

Despite peripheral intravenous catheter (PIVC) insertion being a commonly performed skill, practicing nurses may receive little substantive education, training, or opportunities to practice this skill at a competent level. This article describes a collaboration between private industry and a hospital to modify, implement, and evaluate a simulation-based blended PIVC insertion continuing education program for staff nurses. Included is an overview of the practical and theoretical rationale for the initial development of the curriculum to address an identified PIVC insertion education gap, the collaborative modification and implementation of the program, and an evaluation of the program. The curriculum combined self-paced e-learning and classroom-based deliberate practice with simulation tools of varying fidelity in a peer-to-peer learning environment. Given the mutual challenges of resource allocation in industry training and clinical nursing education departments, interprofessional partnerships may be an effective option for sharing instructional knowledge and resources to promote innovation and improve patient care. J Contin Educ Nurs. 2017;48(9):397-406. Copyright 2017, SLACK Incorporated.

A novel and facile decay path of Criegee intermediates by intramolecular insertion reactions via roaming transition states

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nguyen, Trong-Nghia; Department of Physical Chemistry, Hanoi University of Science and Technology, Hanoi; Putikam, Raghunath

2015-03-28

We have discovered a new and highly competitive product channel in the unimolecular decay process for small Criegee intermediates, CH{sub 2}OO and anti/syn-CH{sub 3}C(H)OO, occurring by intramolecular insertion reactions via a roaming-like transition state (TS) based on quantum-chemical calculations. Our results show that in the decomposition of CH{sub 2}OO and anti-CH{sub 3}C(H)OO, the predominant paths directly produce cis-HC(O)OH and syn-CH{sub 3}C(O)OH acids with >110 kcal/mol exothermicities via loose roaming-like insertion TSs involving the terminal O atom and the neighboring C–H bonds. For syn-CH{sub 3}C(H)OO, the major decomposition channel occurs by abstraction of a H atom from the CH{sub 3} groupmore » by the terminal O atom producing CH{sub 2}C(H)O–OH. At 298 K, the intramolecular insertion process in CH{sub 2}OO was found to be 600 times faster than the commonly assumed ring-closing reaction.« less

Posology of insulins: A review of standard textbooks and product inserts.

PubMed

Bhutani, Garima; Kalra, Sanjay

2015-01-01

The study is aimed to assess whether the information contained in standard pharmacology, endocrinology, and diabetology textbooks regarding timings of administration, frequency and dose of various insulins is adequate and also to see whether the information contained in these texts is concordant with product inserts. Four standard textbooks of pharmacology, two of diabetology and three of endocrinology were assessed for the published information regarding dose, timing, and frequency of insulin administration. The product inserts of commonly available insulins in India were also studied for the same. Various omissions and disparities could be seen in the coverage of insulins in standard textbooks. Posology information about premixed insulins and basal insulins have been omitted by the majority of the textbooks. Details about dose, frequency and timings of ultra-short acting insulins have also not been covered by all textbooks. Some discrepancies regarding prescribing information was also noted in product inserts, especially in case of newer insulins. Thus, this article stresses upon the need of a uniform source of information for providing adequate and standardized knowledge regarding timing, frequency, and dose of insulins.

Comprehensive Antiretroviral Restriction Factor Profiling Reveals the Evolutionary Imprint of the ex Vivo and in Vivo IFN-β Response in HTLV-1-Associated Neuroinflammation.

PubMed

Leal, Fabio E; Menezes, Soraya Maria; Costa, Emanuela A S; Brailey, Phillip M; Gama, Lucio; Segurado, Aluisio C; Kallas, Esper G; Nixon, Douglas F; Dierckx, Tim; Khouri, Ricardo; Vercauteren, Jurgen; Galvão-Castro, Bernardo; Saraiva Raposo, Rui Andre; Van Weyenbergh, Johan

2018-01-01

HTLV-1-Associated Myelopathy (HAM/TSP) is a progressive neuroinflammatory disorder for which no disease-modifying treatment exists. Modest clinical benefit from type I interferons (IFN-α/β) in HAM/TSP contrasts with its recently identified IFN-inducible gene signature. In addition, IFN-α treatment in vivo decreases proviral load and immune activation in HAM/TSP, whereas IFN-β therapy decreases tax mRNA and lymphoproliferation. We hypothesize this "IFN paradox" in HAM/TSP might be explained by both cell type- and gene-specific effects of type I IFN in HTLV-1-associated pathogenesis. Therefore, we analyzed ex vivo transcriptomes of CD4 + T cells, PBMCs and whole blood in healthy controls, HTLV-1-infected individuals, and HAM/TSP patients. First, we used a targeted approach, simultaneously quantifying HTLV-1 mRNA (HBZ, Tax), proviral load and 42 host genes with known antiretroviral (anti-HIV) activity in purified CD4 + T cells. This revealed two major clusters ("antiviral/protective" vs. "proviral/deleterious"), as evidenced by significant negative (TRIM5/TRIM22/BST2) vs. positive correlation (ISG15/PAF1/CDKN1A) with HTLV-1 viral markers and clinical status. Surprisingly, we found a significant inversion of antiretroviral activity of host restriction factors, as evidenced by opposite correlation to in vivo HIV-1 vs. HTLV-1 RNA levels. The anti-HTLV-1 effect of antiviral cluster genes was significantly correlated to their adaptive chimp/human evolution score, for both Tax mRNA and PVL. Six genes of the proposed antiviral cluster underwent lentivirus-driven purifying selection during primate evolution (TRIM5/TRIM22/BST2/APOBEC3F-G-H), underscoring the cross-retroviral evolutionary imprint. Secondly, we examined the genome-wide type I IFN response in HAM/TSP patients, following short-term ex vivo culture of PBMCs with either IFN-α or IFN-β. Microarray analysis evidenced 12 antiretroviral genes (including TRIM5α/TRIM22/BST2) were significantly up-regulated by IFN-β, but not IFN-α, in HAM/TSP. This was paralleled by a significant decrease in lymphoproliferation by IFN-β, but not IFN-α treatment. Finally, using published ex vivo whole blood transcriptomic data of independent cohorts, we validated the significant positive correlation between TRIM5, TRIM22, and BST2 in HTLV-1-infected individuals and HAM/TSP patients, which was independent of the HAM/TSP disease signature. In conclusion, our results provide ex vivo mechanistic evidence for the observed immunovirological effect of in vivo IFN-β treatment in HAM/TSP, reconcile an apparent IFN paradox in HTLV-1 research and identify biomarkers/targets for a precision medicine approach.

Comprehensive Antiretroviral Restriction Factor Profiling Reveals the Evolutionary Imprint of the ex Vivo and in Vivo IFN-β Response in HTLV-1-Associated Neuroinflammation

PubMed Central

Leal, Fabio E.; Menezes, Soraya Maria; Costa, Emanuela A. S.; Brailey, Phillip M.; Gama, Lucio; Segurado, Aluisio C.; Kallas, Esper G.; Nixon, Douglas F.; Dierckx, Tim; Khouri, Ricardo; Vercauteren, Jurgen; Galvão-Castro, Bernardo; Saraiva Raposo, Rui Andre; Van Weyenbergh, Johan

2018-01-01

HTLV-1-Associated Myelopathy (HAM/TSP) is a progressive neuroinflammatory disorder for which no disease-modifying treatment exists. Modest clinical benefit from type I interferons (IFN-α/β) in HAM/TSP contrasts with its recently identified IFN-inducible gene signature. In addition, IFN-α treatment in vivo decreases proviral load and immune activation in HAM/TSP, whereas IFN-β therapy decreases tax mRNA and lymphoproliferation. We hypothesize this “IFN paradox” in HAM/TSP might be explained by both cell type- and gene-specific effects of type I IFN in HTLV-1-associated pathogenesis. Therefore, we analyzed ex vivo transcriptomes of CD4+ T cells, PBMCs and whole blood in healthy controls, HTLV-1-infected individuals, and HAM/TSP patients. First, we used a targeted approach, simultaneously quantifying HTLV-1 mRNA (HBZ, Tax), proviral load and 42 host genes with known antiretroviral (anti-HIV) activity in purified CD4+ T cells. This revealed two major clusters (“antiviral/protective” vs. “proviral/deleterious”), as evidenced by significant negative (TRIM5/TRIM22/BST2) vs. positive correlation (ISG15/PAF1/CDKN1A) with HTLV-1 viral markers and clinical status. Surprisingly, we found a significant inversion of antiretroviral activity of host restriction factors, as evidenced by opposite correlation to in vivo HIV-1 vs. HTLV-1 RNA levels. The anti-HTLV-1 effect of antiviral cluster genes was significantly correlated to their adaptive chimp/human evolution score, for both Tax mRNA and PVL. Six genes of the proposed antiviral cluster underwent lentivirus-driven purifying selection during primate evolution (TRIM5/TRIM22/BST2/APOBEC3F-G-H), underscoring the cross-retroviral evolutionary imprint. Secondly, we examined the genome-wide type I IFN response in HAM/TSP patients, following short-term ex vivo culture of PBMCs with either IFN-α or IFN-β. Microarray analysis evidenced 12 antiretroviral genes (including TRIM5α/TRIM22/BST2) were significantly up-regulated by IFN-β, but not IFN-α, in HAM/TSP. This was paralleled by a significant decrease in lymphoproliferation by IFN-β, but not IFN-α treatment. Finally, using published ex vivo whole blood transcriptomic data of independent cohorts, we validated the significant positive correlation between TRIM5, TRIM22, and BST2 in HTLV-1-infected individuals and HAM/TSP patients, which was independent of the HAM/TSP disease signature. In conclusion, our results provide ex vivo mechanistic evidence for the observed immunovirological effect of in vivo IFN-β treatment in HAM/TSP, reconcile an apparent IFN paradox in HTLV-1 research and identify biomarkers/targets for a precision medicine approach. PMID:29872426

Prevalence and risk factors for cats testing positive for feline immunodeficiency virus and feline leukaemia virus infection in cats entering an animal shelter in New Zealand.

PubMed

Gates, M C; Vigeant, S; Dale, A

2017-11-01

AIMS To estimate the prevalence of cats testing positive for antibodies to feline immunodeficiency virus (FIV) and feline leukaemia virus (FeLV) antigens in domestic cats entering a New Zealand animal shelter, based on a commercial point-of-care ELISA, to identify risk factors associated with cats testing positive, and to compare the results obtained from the ELISA with those obtained using PCR-based testing. METHOD A cross-sectional study was performed on 388 cats entering the Royal New Zealand Society for the Prevention of Cruelty to Animals animal shelter in Auckland, New Zealand between 7 February 2014 and 30 May 2014. Whole blood samples were collected from each cat and tested for FIV antibody and FeLV antigen using a commercial point-of-care ELISA. Information on the signalment and health status of the cat at the time of entry was also recorded. Blood and saliva samples from a subset of cats were tested for FIV and FeLV proviral DNA using a real-time PCR assay. RESULTS Of the 388 cats in the study sample, 146 (37.6%) had been relinquished by owners, 237 (62.4%) were strays, and 5 (1.3%) were of unknown origin. Overall, 53/388 (13.7%) cats tested positive for FIV antibodies and 4/388 (1.0%) were positive for FeLV antigen. Stray cats had a higher FIV seroprevalence than relinquished cats (42/237 (17.8%) vs. 11/146 (7.5%); p=0.008). Of 53 cats that were FIV-seropositive, 51 (96%) tested positive for FIV proviral DNA using PCR testing of blood. Of these 51 cats, 28 (55%) were positive by PCR testing of saliva. Of the four cats that were FeLV antigen-positive by ELISA, two (50%) were positive for FeLV proviral DNA by PCR testing of blood. The odds of a cat being seropositive for FIV were greater for intact compared to desexed cats (OR=3.3; 95% CI=1.6-7.4) and for male compared to female cats (OR=6.5; 95% CI=3.2-14.0). CONCLUSIONS AND CLINICAL RELEVANCE The seroprevalence for FIV was 14% among cats entering an animal shelter in Auckland, whereas the prevalence of FeLV antigen-positive cats was only 1%. These findings suggest differences in the transmission dynamics of each virus in free-roaming cat populations in New Zealand. Our study also highlights the potential role of desexing cats in reducing transmission of FIV. However, further data from first-opinion veterinary practices are required to confirm that these findings may be generalised to the wider domestic cat population in New Zealand.

A virtual reality based simulator for learning nasogastric tube placement.

PubMed

Choi, Kup-Sze; He, Xuejian; Chiang, Vico Chung-Lim; Deng, Zhaohong

2015-02-01

Nasogastric tube (NGT) placement is a common clinical procedure where a plastic tube is inserted into the stomach through the nostril for feeding or drainage. However, the placement is a blind process in which the tube may be mistakenly inserted into other locations, leading to unexpected complications or fatal incidents. The placement techniques are conventionally acquired by practising on unrealistic rubber mannequins or on humans. In this paper, a virtual reality based training simulation system is proposed to facilitate the training of NGT placement. It focuses on the simulation of tube insertion and the rendering of the feedback forces with a haptic device. A hybrid force model is developed to compute the forces analytically or numerically under different conditions, including the situations when the patient is swallowing or when the tube is buckled at the nostril. To ensure real-time interactive simulations, an offline simulation approach is adopted to obtain the relationship between the insertion depth and insertion force using a non-linear finite element method. The offline dataset is then used to generate real-time feedback forces by interpolation. The virtual training process is logged quantitatively with metrics that can be used for assessing objective performance and tracking progress. The system has been evaluated by nursing professionals. They found that the haptic feeling produced by the simulated forces is similar to their experience during real NGT insertion. The proposed system provides a new educational tool to enhance conventional training in NGT placement. Copyright © 2014 Elsevier Ltd. All rights reserved.

Nephric duct insertion is a crucial step in urinary tract maturation that is regulated by a Gata3-Raldh2-Ret molecular network in mice.

PubMed

Chia, Ian; Grote, David; Marcotte, Michael; Batourina, Ekaterina; Mendelsohn, Cathy; Bouchard, Maxime

2011-05-01

Urinary tract development depends on a complex series of events in which the ureter moves from its initial branch point on the nephric duct (ND) to its final insertion site in the cloaca (the primitive bladder and urethra). Defects in this maturation process can result in malpositioned ureters and hydronephrosis, a common cause of renal disease in children. Here, we report that insertion of the ND into the cloaca is an unrecognized but crucial step that is required for proper positioning of the ureter and that depends on Ret signaling. Analysis of Ret mutant mice at birth reveals hydronephrosis and defective ureter maturation, abnormalities that our results suggest are caused, at least in part, by delayed insertion of the ND. We find a similar set of malformations in mutants lacking either Gata3 or Raldh2. We show that these factors act in parallel to regulate ND insertion via Ret. Morphological analysis of ND extension in wild-type embryos reveals elaborate cellular protrusions at ND tips that are not detected in Ret, Gata3 or Raldh2 mutant embryos, suggesting that these protrusions may normally be important for fusion with the cloaca. Together, our studies reveal a novel Ret-dependent event, ND insertion, that, when abnormal, can cause obstruction and hydronephrosis at birth; whether ND defects underlie similar types of urinary tract abnormalities in humans is an interesting possibility.

Clostridium perfringens type A–E toxin plasmids

PubMed Central

Freedman, John C.; Theoret, James R.; Wisniewski, Jessica A.; Uzal, Francisco A.; Rood, Julian I.; McClane, Bruce A.

2014-01-01

Clostridium perfringens relies upon plasmid-encoded toxin genes to cause intestinal infections. These toxin genes are associated with insertion sequences that may facilitate their mobilization and transfer, giving rise to new toxin plasmids with common backbones. Most toxin plasmids carry a transfer of clostridial plasmids locus mediating conjugation, which likely explains the presence of similar toxin plasmids in otherwise unrelated C. perfringens strains. The association of many toxin genes with insertion sequences and conjugative plasmids provides virulence flexibility when causing intestinal infections. However, incompatibility issues apparently limit the number of toxin plasmids maintained by a single cell. PMID:25283728

A Rare Case of Port-a-Cath Migration into the Mediastinum

PubMed Central

Shah, BK; Tandukar, S Srijan; Shrestha, S; Sanchirico, P

2014-01-01

ABSTRACT Port-a-cath is commonly used in patients who require frequent administration of intravenous medications. We describe a rare case of port-a-cath migration into the mediastinum 16 months after its insertion. PMID:25803390

Impact of the excision of an ancient repeat insertion on Rickettsia conorii guanylate kinase activity.

PubMed

Abergel, Chantal; Blanc, Guillaume; Monchois, Vincent; Renesto, Patricia; Sigoillot, Cécile; Ogata, Hiroyuki; Raoult, Didier; Claverie, Jean-Michel

2006-11-01

The genomic sequencing of Rickettsia conorii revealed a new family of Rickettsia-specific palindromic elements (RPEs) capable of in-frame insertion in preexisting open reading frames (ORFs). Many of these altered ORFs correspond to proteins with well-characterized or essential functions in other microorganisms. Previous experiments indicated that RPE-containing genes are normally transcribed and that no excision of the repeat occurs at the mRNA level. Using mass spectrometry, we now confirmed the retention of the RPE-derived amino acid residues in 4 proteins successfully expressed in Escherichia coli, raising the general question of the consequences of this common insertion event on the fitness of Rickettsia enzymes. The predicted guanylate kinase activity of the R. conorii gmk gene product was measured both on the RPE-containing and RPE-excised recombinant proteins. We show that the 2 proteins are active but exhibit substantial differences in their affinity for adenosine triphosphate, guanosine monophosphate, and catalytic constants. The distribution of the RPEgmk insert among Rickettsia species indicates that the insertion event is ancient and occurred after the divergence of Rickettsia felis and R. conorii but before that of Rickettsia helvetica and R. conorii. We found no evidence that the gmk gene fixed adaptive changes to compensate the RPE peptide insertion. Furthermore, the analysis of the rates of divergence in 23 RPE-containing genes indicates that coding RPE repeats tend to evolve under weak selective constraint, at a rate similar to intergenic noncoding RPE sequences. Altogether, these results suggest that the insertion of RPE-encoded "selfish peptides," although respecting the original fold and activity of the host proteins, might be slightly detrimental to the enzyme efficiency within limits tolerable for slow-growing intracellular parasites such as Rickettsia.

Variation in the shape of the tibial insertion site of the anterior cruciate ligament: classification is required.

PubMed

Guenther, Daniel; Irarrázaval, Sebastian; Nishizawa, Yuichiro; Vernacchia, Cara; Thorhauer, Eric; Musahl, Volker; Irrgang, James J; Fu, Freddie H

2017-08-01

To propose a classification system for the shape of the tibial insertion site (TIS) of the anterior cruciate ligament (ACL) and to demonstrate the intra- and inter-rater agreement of this system. Due to variation in shape and size, different surgical approaches may be feasible to improve reconstruction of the TIS. One hundred patients with a mean age of 26 ± 11 years were included. The ACL was cut arthroscopically at the base of the tibial insertion site. Arthroscopic images were taken from the lateral and medial portal. Images were de-identified and duplicated. Two blinded observers classified the tibial insertion site according to a classification system. The tibial insertion site was classified as type I (elliptical) in 51 knees (51 %), type II (triangular) in 33 knees (33 %) and type III (C-shaped) in 16 knees (16 %). There was good agreement between raters when viewing the insertion site from the lateral portal (κ = 0.65) as well as from the medial portal (κ = 0.66). Intra-rater reliability was good to excellent. Agreement in the description of the insertion site between the medial and lateral portals was good for rater 1 and good for rater 2 (κ = 0.74 and 0.77, respectively). There is variation in the shape of the ACL TIS. The classification system is a repeatable and reliable tool to summarize the shape of the TIS using three common patterns. For clinical relevance, different shapes may require different types of reconstruction to ensure proper footprint restoration. Consideration of the individual TIS shape is required to prevent iatrogenic damage of adjacent structures like the menisci. III.

Prospective short-term feasibility study of perioperative suprapubic catheters in laparoscopic colectomy.

PubMed

Nagao, Sayaka; Saida, Yoshihisa; Enomoto, Toshiyuki; Takahashi, Asako; Higuchi, Tadashi; Moriyama, Hodaka; Niituma, Toru; Watanabe, Manabu; Asai, Koji; Kusachi, Shinya

2018-05-16

Here we report a prospective study on whether a temporary suprapubic catheter (SPC) can be safely inserted as a substitute for transurethral balloon catheterization during laparoscopy-assisted colectomy. Our subjects included 52 cases who gave informed consent to have an SPC inserted. These subjects were selected from cases who underwent laparoscopy-assisted surgery for primary colorectal cancer from October 2014 to August 2015. An SPC was inserted into 45 of the original 52 cases. The median surgical duration was 220 min (range, 11-438 min), and the SPC insertion was performed at a median of 133 min (range, 9-384 min) after the start of surgery. Insertion required a median duration of 116 s. In one case (2.2%), the bladder was perforated by the paracentesis needle, and in two cases (4.4%), hematuria was observed at the time of insertion; however, surgery was completed without any incident in these three cases. Six of the remaining 42 cases (13.3%) demonstrated neither micturition desire nor independent urination on the day the catheter was clamped. In these cases, the clamp was released two to four times, and draining of an average of 586-mL urine, micturition desire, and independent urination were confirmed 2-4 days later. Transurethral balloon catheterization is a simple procedure that is commonly used on surgical patients, but it can cause pain, discomfort, and infection. In contrast, SPC insertion is a procedure that avoids crossing the urethra and its associated disadvantages. Here we were able to demonstrate that the procedure can be safely used in laparoscopic surgery patients. © 2018 Japan Society for Endoscopic Surgery, Asia Endosurgery Task Force and John Wiley & Sons Australia, Ltd.

Two measures of performance in a peg-in-hole manipulation task with force feedback

NASA Technical Reports Server (NTRS)

Hill, J. W.

1977-01-01

The results are described from two manipulators on a peg-in-hole task, which is part of a continued effort to develop models for human performance with remote manipulators. Task difficulty is varied by changing the diameter of the peg to be inserted in a 50 mm diameter hole. An automatic measuring system records the distance between the tool being held by the manipulator and the receptacle into which it is to be inserted. The data from repeated insertions are processed by computer to determine task times, accumulated distances, and trajectories. Experiments with both the MA-11 cable-connected master-slave manipulator common to hot cell work and the MA-23 servo-controlled manipulator (with and without force feedback) are described. Comparison of these results with previous results of the Ames Manipulator shows that force feedback provides a consistent advantage.

Cholorhexidine, octenidine or povidone iodine for catheter related infections: A randomized controlled trial.

PubMed

Bilir, Ayten; Yelken, Birgül; Erkan, Ayse

2013-06-01

Protection of the catheter site by antimicrobial agents is one of the most important factors in the prevention of infection. Povidone iodine and chlorhexidine gluconate are the most common used agents for dressing. The purpose of this study was to compare the effects of povidone iodine, chlorhexidine gluconate and octenidine hydrochloride in preventing catheter related infections. Patients were randomized to receive; 4% chlorhexidine gluconate, 10% povidone iodine or octenidine hydrochlorodine for cutaneous antisepsis. Cultures were taken at the site surrounding catheter insertion and at the catheter hub after removal to help identify the source of microorganisms. Catheter related sepsis was 10.5% in the povidone iodine and octenidine hydrochlorodine groups. Catheter related colonization was 26.3% in povidone iodine group and 21.5% in octenidine hydrochlorodine group. 4% chlorhexidine or octenidine hydrochlorodine for cutaneous disinfection before insertion of an intravascular device and for post-insertion site care can reduce the catheter related colonization.

Complete Genome Sequence of a Novel Newcastle Disease Virus Strain Isolated from a Chicken in West Africa

PubMed Central

Kim, Shin-Hee; Nayak, Subhashree; Paldurai, Anandan; Nayak, Baibaswata; Samuel, Arthur; Aplogan, Gilbert L.; Awoume, Kodzo A.; Webby, Richard J.; Ducatez, Mariette F.; Collins, Peter L.

2012-01-01

The complete genome sequence of an African Newcastle disease virus (NDV) strain isolated from a chicken in Togo in 2009 was determined. The genome is 15,198 nucleotides (nt) in length and is classified in genotype VII in the class II cluster. Compared to common vaccine strains, the African strain contains a previously described 6-nt insert in the downstream untranslated region of the N gene and a novel 6-nt insert in the HN-L intergenic region. Genome length differences are a marker of the natural history of NDV. This is the first description of a class II NDV strain with a genome of 15,198 nt and a 6-nt insert in the HN-L intergenic region. Sequence divergence relative to vaccine strains was substantial, likely contributes to outbreaks, and illustrates the continued evolution of new NDV strains in West Africa. PMID:22997417

Gaps in monitoring systems for Implanon NXT services in South Africa: An assessment of 12 facilities in two districts

PubMed

Pillay, D; Morroni, C; Pleaner, M; Adeogba, O; Chersich, M; Naidoo, N; Mullick, S; Rees, H

2017-10-01

Background. Implanon NXT, a long-acting subdermal contraceptive implant, was introduced in South Africa (SA) in early 2014 as part of an expanded contraceptive method mix. After initial high levels of uptake, reports emerged of frequent early removals and declines in use. Monitoring of progress and challenges in implant service delivery could identify aspects of the programme that require strengthening. Objectives. To assess data management and record keeping within implant services at primary care facilities. Methods. We developed a checklist to assess the tools used for monitoring implant services and data reporting to district offices. The checklist was piloted in seven facilities. An additional six high-volume and six low-volume implant insertion clinics in the City of Johannesburg (CoJ), Gauteng Province, and the Dr Kenneth Kaunda District, North West Province, were selected for assessment. Results. All 12 facilities completed a Daily Head Count Register, which tallied the number of clients attending the clinic, but not information about implant use. A more detailed Tick Register recorded services that clinic attendees received, with nine documenting number of implant insertions and six implant removals. A more specific tool, an Insertion Checklist, collected data on insertion procedures and client characteristics, but was only used in CoJ (five of six facilities). Other registers, which were developed de novo by staff at individual facilities, captured more detailed information about insertions and removals, including reasons. Five of six low-volume insertion facilities used these registers, but only three of six high-volume facilities. No facilities used the form specifically developed by the National Department of Health for implant pharmacovigilance. Nine of 12 clinics reported data on numbers of insertions to the district office, six reported removals and none provided data on reasons for removals. Conclusion. For data to inform effective decision-making and quality improvement in implant services in SA, standardised reporting guidelines and data collection tools are needed, reinforced by staff training and quality assessment of data collection. Staff often took the initiative to fill gaps in reporting systems. Current systems are unable to accurately monitor uptake or discontinuation, or identify aspects of services requiring strengthening. Lack of pharmacovigilance data is especially concerning. Deficiencies noted in these monitoring systems may be common to family planning services more broadly, which warrants investigation. Creative Commons Attribution - NonCommercial Works License (CC BY-NC 4.0)

Bilateral Pneumothoraces in a Trauma Patient After Dobhoff Tube Insertion

PubMed Central

Abidali, Ali; Mangram, Alicia; Shirah, Gina R.; Wilson, Whitney; Abidali, Ahmed; Moeser, Phillip; Dzandu, James K.

2018-01-01

Patient: Male, 74 Final Diagnosis: Pneumothorax Symptoms: Hypoxemia • shortness of breath Medication: — Clinical Procedure: — Specialty: Surgery Objective: Diagnostic/therapeutic accidents Background: Dobhoff tube insertion is a common procedure used in the clinical setting to deliver enteral nutrition. Although it is often viewed as an innocuous bedside procedure, there are risks for numerous complications such as tracheobronchial insertion, which could lead to deleterious consequences. We present to our knowledge the first reported case of bilateral pneumothoraces caused by the insertion of a Dobhoff tube. In addition, we also discuss common pitfalls for confirming the positioning of Dobhoff tubes, as well as risk factors that can predispose a patient to improper tube placement. Case Report: We present the case of a 74-year-old male patient with multiple orthopedic injuries following an auto-pedestrian collision. Five attempts were made to place a Dobhoff tube to maintain enteral nutrition. Follow-up abdominal x-ray revealed displacement of the Dobhoff tube in the left pleural space. After removal of the tube, a follow-up chest x-ray revealed iatrogenic bilateral pneumothoraces. Acute hypoxemic respiratory failure ensued; therefore, bilateral chest tubes were placed. Over the next three weeks, the patient’s respiratory status improved and both chest tubes were removed. The patient was eventually discharged to a skilled nursing facility. Conclusions: Improper placement of Dobhoff tubes can lead to rare complications such as bilateral pneumothoraces. This unique case report of bilateral pneumothoraces after Dobhoff tube placement emphasizes the necessity of using proper diagnostic techniques for verifying proper tube placement, as well as understanding the risk factors that predispose a patient to a malpositioned tube. PMID:29503437

Design and evaluation of a computed tomography (CT)-compatible needle insertion device using an electromagnetic tracking system and CT images.

PubMed

Shahriari, Navid; Hekman, Edsko; Oudkerk, Matthijs; Misra, Sarthak

2015-11-01

Percutaneous needle insertion procedures are commonly used for diagnostic and therapeutic purposes. Although current technology allows accurate localization of lesions, they cannot yet be precisely targeted. Lung cancer is the most common cause of cancer-related death, and early detection reduces the mortality rate. Therefore, suspicious lesions are tested for diagnosis by performing needle biopsy. In this paper, we have presented a novel computed tomography (CT)-compatible needle insertion device (NID). The NID is used to steer a flexible needle (φ0.55 mm) with a bevel at the tip in biological tissue. CT images and an electromagnetic (EM) tracking system are used in two separate scenarios to track the needle tip in three-dimensional space during the procedure. Our system uses a control algorithm to steer the needle through a combination of insertion and minimal number of rotations. Noise analysis of CT images has demonstrated the compatibility of the device. The results for three experimental cases (case 1: open-loop control, case 2: closed-loop control using EM tracking system and case 3: closed-loop control using CT images) are presented. Each experimental case is performed five times, and average targeting errors are 2.86 ± 1.14, 1.11 ± 0.14 and 1.94 ± 0.63 mm for case 1, case 2 and case 3, respectively. The achieved results show that our device is CT-compatible and it is able to steer a bevel-tipped needle toward a target. We are able to use intermittent CT images and EM tracking data to control the needle path in a closed-loop manner. These results are promising and suggest that it is possible to accurately target the lesions in real clinical procedures in the future.

Indwelling urinary catheter management and catheter-associated urinary tract infection prevention practices in Nurses Improving Care for Healthsystem Elders hospitals.

PubMed

Fink, Regina; Gilmartin, Heather; Richard, Angela; Capezuti, Elizabeth; Boltz, Marie; Wald, Heidi

2012-10-01

Indwelling urinary catheters (IUCs) are commonly used in hospitalized patients, especially elders. Catheter-associated urinary tract infections (CAUTIs) account for 34% of all health care associated infections in the United States, associated with excess morbidity and health care costs. Adherence to CAUTI prevention practices has not been well described. This study used an electronic survey to examine IUC care practices for CAUTI prevention in 3 areas-(1) equipment and alternatives and insertion and maintenance techniques; (2) personnel, policies, training, and education; and (3) documentation, surveillance, and removal reminders-at 75 acute care hospitals in the Nurses Improving the Care of Healthsystem Elders (NICHE) system. CAUTI prevention practices commonly followed included wearing gloves (97%), handwashing (89%), maintaining a sterile barrier (81%), and using a no-touch insertion technique (73%). Silver-coated catheters were used to varying degrees in 59% of the hospitals; 4% reported never using a catheter-securing device. Urethral meatal care was provided daily by 43% of hospitals and more frequently that that by 41% of hospitals. Nurses were the most frequently reported IUC inserters. Training in aseptic technique and CAUTI prevention at the time of initial nursing hire was provided by 64% of hospitals; however, only 47% annually validated competency in IUC insertion. Systems for IUC removal were implemented in 56% of hospitals. IUC documentation and routine CAUTI surveillance practices varied widely. Although many CAUTI prevention practices at NICHE hospitals are in alignment with evidence-based guidelines, there is room for improvement. Further research is needed to identify the effect of enhanced compliance with CAUTI prevention practices on the prevalence of CAUTI in NICHE hospitals. Copyright © 2012 Association for Professionals in Infection Control and Epidemiology, Inc. Published by Mosby, Inc. All rights reserved.

Safety of achilles detachment and reattachment using a standard midline approach to insertional enthesophytes.

PubMed

McAlister, Jeffrey E; Hyer, Christopher F

2015-01-01

Detachment with reattachment of the Achilles tendon is a common surgery for debridement of retrocalcaneal exostosis, bursitis, and other insertional pathologic entities. The technique involves a midline skin incision on the posterior Achilles to the tendon. The distal Achilles attachment is removed in a U-shaped manner, leaving the medial and lateral flares, but exposing the posterior spur. This midline approach provides excellent exposure and allows for rapid and efficient surgical debridement. The tendon is reapproximated and repaired with a suture anchor to facilitate fixation to the posterior calcaneus. Some surgeons have expressed concerned that the rupture risk could be increased in the postoperative period using this technique. The present study was a retrospective medical record review of 98 patients (100 feet) who had undergone a midline approach with Achilles reattachment after insertional Achilles debridement during a 3-year period. The demographic and comorbidity data were collected and analyzed. The outcome measures were postoperative rupture and the need for revision surgery. The mean age was 51.9 years, and the patients included 59 females (60.2%) and 39 males (39.8%). The complications included 4 rupture or avulsion revisions (4.0%) and 2 recurrent pain and tendinitis revisions (2.0%). The most common repeat repair procedure included hardware removal and a flexor hallucis longus transfer or augmentation. Nine patients (9.0%) had wound complications, 7 (77.8%) of which necessitated incision and drainage. The midline approach with Achilles detachment and reattachment is a safe and effective method of surgical treatment of insertional Achilles pathologic entities. The low reoperation rate of 4.0% will allow foot and ankle surgeons to safely rely on this approach. Copyright © 2015 American College of Foot and Ankle Surgeons. Published by Elsevier Inc. All rights reserved.

Flow cytometric detection of human immunodeficiency virus type 1 proviral DNA by the polymerase chain reaction incorporating digoxigenin- or fluorescein-labeled dUTP

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Gang; Olson, J.C.; Pu, R.

1995-10-01

Serological assays are routinely used in the laboratory diagnosis of human immunodeficiency virus type-1 (HrV-1) infection, but the polymerase chain reaction (PCR) is ultimately the most sensitive and direct method for establishing definitive diagnosis. As an alternative to the conventional radioactive PCR procedure we have developed and evaluated a pair of rapid nonradioisotopic flow cytometric detection methods. Using heminested PCR we directly incorporated fluorescein-12-dUTP (fluo-dUTP) or digoxigenin-11-dUTP (dig-dUTP) into the PCR-amplicons. The labeled amplicons were hybridized with biotinylated antisense and sense probes, followed by capture of the hybrid DNA using streptavidin-coated beads which were finally analyzed in a flow cytometermore » by (1) direct detection of the fluorescence intensity of the amplicons incorporating fluo-dUTP and (2) immunodetection of the amplicons incorporating dig-dUTP by anti-digoxigenin IgG labeled with fluorescein isothiocyanate (FITC). Although both assays were functionally comparable with radiolabeled probe in reliably detecting as low as five copies of HIV-1 proviral DNA sequences, the immunodetection of dig-dUTP consistently yielded higher mean channel fluorescence and gave a stable signal over an extended period of 12-14 weeks. In testing a panel of 20 pedigreed PBMC specimens from blood donors with or without HIV-1 infection, the results of both flow cytometric assays were identical with those of the conventional radioactive procedure. Therefore, we conclude that the dig-dUTP incorporation in amplicons, hybridization with a pair of sense-antisense biotinylated probes and immunodetection of hybrids by flow cytometric analyses is the nonisotopic method of choice for PCR-diagnosis of HIV-1 infection. 21 refs., 2 figs., 4 tabs.« less

Potent and reversible lentiviral vector restriction in murine induced pluripotent stem cells.

PubMed

Geis, Franziska K; Galla, Melanie; Hoffmann, Dirk; Kuehle, Johannes; Zychlinski, Daniela; Maetzig, Tobias; Schott, Juliane W; Schwarzer, Adrian; Goffinet, Christine; Goff, Stephen P; Schambach, Axel

2017-05-31

Retroviral vectors are derived from wild-type retroviruses, can be used to study retrovirus-host interactions and are effective tools in gene and cell therapy. However, numerous cell types are resistant or less permissive to retrovirus infection due to the presence of active defense mechanisms, or the absence of important cellular host co-factors. In contrast to multipotent stem cells, pluripotent stem cells (PSC) have potential to differentiate into all three germ layers. Much remains to be elucidated in the field of anti-viral immunity in stem cells, especially in PSC. In this study, we report that transduction with HIV-1-based, lentiviral vectors (LV) is impaired in murine PSC. Analyses of early retroviral events in induced pluripotent stem cells (iPSC) revealed that the restriction is independent of envelope choice and does not affect reverse transcription, but perturbs nuclear entry and proviral integration. Proteasomal inhibition by MG132 could not circumvent the restriction. However, prevention of cyclophilin A (CypA) binding to the HIV-1 capsid via use of either a CypA inhibitor (cyclosporine A) or CypA-independent capsid mutants improved transduction. In addition, application of higher vector doses also increased transduction. Our data revealed a CypA mediated restriction in iPSC, which was acquired during reprogramming, associated with pluripotency and relieved upon subsequent differentiation. We showed that murine PSC and iPSC are less susceptible to LV. The block observed in iPSC was CypA-dependent and resulted in reduced nuclear entry of viral DNA and proviral integration. Our study helps to improve transduction of murine pluripotent cells with HIV-1-based vectors and contributes to our understanding of retrovirus-host interactions in PSC.

Genotypes of JC virus, DNA of cytomegalovirus, and proviral DNA of human immunodeficiency virus in eyes of acquired immunodeficiency syndrome patients.

PubMed

Eberwein, Philipp; Hansen, Lutz L; Agostini, Hansjürgen T

2005-02-01

JC virus (JCV) is a human polyomavirus that exists in at least eight different genotypes as a result of coevolution with different human populations all over the world. Well adapted to its host, it usually persists in the kidneys and possibly the brain. If the host becomes immunodeficient, JCV can cause the fatal demyelinating disease progressive multifocal leukoencephalopathy (PML). There is increasing evidence that JCV is transactivated by cytomegalovirus (CMV) and the human immunodeficiency virus (HIV). Both CMV and HIV can infect the retina of acquired immunodeficiency syndrome (AIDS) patients, causing severe necrosis in the case of CMV retinitis or a mild HIV-associated vasculopathy, with bleeding and cotton wool spots. The authors therefore investigated by polymerase chain reaction (PCR) whether DNA of these three viruses was detectable in paraffin-embedded eyes of AIDS patients with a clinical history of CMV retinitis. From a total of 65 eyes, JCV was detected in 21 (32%). Thirty-six (55%) were positive for CMV and 6 (9%) for proviral DNA of HIV. JCV and CMV were found in 13 eyes, JCV and HIV in 3 eyes, CMV and HIV in 1 eye, and DNA from all three viruses in 1 eye. The JCV genotypes were types 1A, 2A, 2E, 3, and 4. In 21 eyes of patients without AIDS, only one sample was JCV positive. In conclusion, JCV DNA can be detected in ocular tissue of AIDS patients at a significantly higher level than in eyes of nonimmunosuppressed patients. Further investigations will help to decide if JCV contributes to the retinopathy caused by CMV and HIV.

Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration

DOE PAGES

Cardozo, Erwing Fabian; Andrade, Adriana; Mellors, John W.; ...

2017-07-05

The kinetics of HIV-1 decay under treatment depends on the class of antiretrovirals used. Mathematical models are useful to interpret the different profiles, providing quantitative information about the kinetics of virus replication and the cell populations contributing to viral decay. We modeled proviral integration in short- and long-lived infected cells to compare viral kinetics under treatment with and without the integrase inhibitor raltegravir (RAL). We fitted the model to data obtained from participants treated with RAL-containing regimes or with a four-drug regimen of protease and reverse transcriptase inhibitors. Our model explains the existence and quantifies the three phases of HIV-1more » RNA decay in RAL-based regimens vs. the two phases observed in therapies without RAL. Our findings indicate that HIV-1 infection is mostly sustained by short-lived infected cells with fast integration and a short viral production period, and by long-lived infected cells with slow integration but an equally short viral production period. We propose that these cells represent activated and resting infected CD4+ T-cells, respectively, and estimate that infection of resting cells represent ~4% of productive reverse transcription events in chronic infection. RAL reveals the kinetics of proviral integration, showing that in short-lived cells the pre-integration population has a half-life of ~7 hours, whereas in long-lived cells this half-life is ~6 weeks. We also show that the efficacy of RAL can be estimated by the difference in viral load at the start of the second phase in protocols with and without RAL. Altogether, we provide a mechanistic model of viral infection that parsimoniously explains the kinetics of viral load decline under multiple classes of antiretrovirals.« less

Neurologic Disease in Captive Lions (Panthera leo) with Low-Titer Lion Lentivirus Infection▿

PubMed Central

Brennan, Greg; Podell, Michael D.; Wack, Raymund; Kraft, Susan; Troyer, Jennifer L.; Bielefeldt-Ohmann, Helle; VandeWoude, Sue

2006-01-01

Lion lentivirus (LLV; also known as feline immunodeficiency virus of lion, Panthera leo [FIVPle]) is present in free-ranging and captive lion populations at a seroprevalence of up to 100%; however, clinical signs are rarely reported. LLV displays up to 25% interclade sequence diversity, suggesting that it has been in the lion population for some time and may be significantly host adapted. Three captive lions diagnosed with LLV infection displayed lymphocyte subset alterations and progressive behavioral, locomotor, and neuroanatomic abnormalities. No evidence of infection with other potential neuropathogens was found. Antemortem electrodiagnostics and radiologic imaging indicated a diagnosis consistent with lentiviral neuropathy. PCR was used to determine a partial lentiviral genomic sequence and to quantify the proviral burden in eight postmortem tissue specimens. Phylogenetic analysis demonstrated that the virus was consistent with the LLV detected in other captive and free-ranging lions. Despite progressive neurologic signs, the proviral load in tissues, including several regions of the brain, was low; furthermore, gross and histopathologic changes in the brain were minimal. These findings suggest that the symptoms in these animals resulted from nonspecific encephalopathy, similar to human immunodeficiency virus, FIV, and simian immunodeficiency virus (SIV) neuropathies, rather than a direct effect of active viral replication. The association of neuropathy and lymphocyte subset alterations with chronic LLV infection suggests that long-term LLV infection can have detrimental effects for the host, including death. This is similar to reports of aged sootey mangabeys dying from diseases typically associated with end-stage SIV infection and indicates areas for further research of lentiviral infections of seemingly adapted natural hosts, including mechanisms of host control and viral adaptation. PMID:17005739

Neurologic disease in captive lions (Panthera leo) with low-titer lion lentivirus infection.

PubMed

Brennan, Greg; Podell, Michael D; Wack, Raymund; Kraft, Susan; Troyer, Jennifer L; Bielefeldt-Ohmann, Helle; VandeWoude, Sue

2006-12-01

Lion lentivirus (LLV; also known as feline immunodeficiency virus of lion, Panthera leo [FIVPle]) is present in free-ranging and captive lion populations at a seroprevalence of up to 100%; however, clinical signs are rarely reported. LLV displays up to 25% interclade sequence diversity, suggesting that it has been in the lion population for some time and may be significantly host adapted. Three captive lions diagnosed with LLV infection displayed lymphocyte subset alterations and progressive behavioral, locomotor, and neuroanatomic abnormalities. No evidence of infection with other potential neuropathogens was found. Antemortem electrodiagnostics and radiologic imaging indicated a diagnosis consistent with lentiviral neuropathy. PCR was used to determine a partial lentiviral genomic sequence and to quantify the proviral burden in eight postmortem tissue specimens. Phylogenetic analysis demonstrated that the virus was consistent with the LLV detected in other captive and free-ranging lions. Despite progressive neurologic signs, the proviral load in tissues, including several regions of the brain, was low; furthermore, gross and histopathologic changes in the brain were minimal. These findings suggest that the symptoms in these animals resulted from nonspecific encephalopathy, similar to human immunodeficiency virus, FIV, and simian immunodeficiency virus (SIV) neuropathies, rather than a direct effect of active viral replication. The association of neuropathy and lymphocyte subset alterations with chronic LLV infection suggests that long-term LLV infection can have detrimental effects for the host, including death. This is similar to reports of aged sootey mangabeys dying from diseases typically associated with end-stage SIV infection and indicates areas for further research of lentiviral infections of seemingly adapted natural hosts, including mechanisms of host control and viral adaptation.

Treatment with integrase inhibitor suggests a new interpretation of HIV RNA decay curves that reveals a subset of cells with slow integration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cardozo, Erwing Fabian; Andrade, Adriana; Mellors, John W.

The kinetics of HIV-1 decay under treatment depends on the class of antiretrovirals used. Mathematical models are useful to interpret the different profiles, providing quantitative information about the kinetics of virus replication and the cell populations contributing to viral decay. We modeled proviral integration in short- and long-lived infected cells to compare viral kinetics under treatment with and without the integrase inhibitor raltegravir (RAL). We fitted the model to data obtained from participants treated with RAL-containing regimes or with a four-drug regimen of protease and reverse transcriptase inhibitors. Our model explains the existence and quantifies the three phases of HIV-1more » RNA decay in RAL-based regimens vs. the two phases observed in therapies without RAL. Our findings indicate that HIV-1 infection is mostly sustained by short-lived infected cells with fast integration and a short viral production period, and by long-lived infected cells with slow integration but an equally short viral production period. We propose that these cells represent activated and resting infected CD4+ T-cells, respectively, and estimate that infection of resting cells represent ~4% of productive reverse transcription events in chronic infection. RAL reveals the kinetics of proviral integration, showing that in short-lived cells the pre-integration population has a half-life of ~7 hours, whereas in long-lived cells this half-life is ~6 weeks. We also show that the efficacy of RAL can be estimated by the difference in viral load at the start of the second phase in protocols with and without RAL. Altogether, we provide a mechanistic model of viral infection that parsimoniously explains the kinetics of viral load decline under multiple classes of antiretrovirals.« less

High Prevalence of HTLV-1 Infection among Japanese Immigrants in Non-endemic Area of Brazil

PubMed Central

Bandeira, Larissa M.; Uehara, Silvia N. O.; Asato, Marcel A.; Aguena, Gabriela S.; Maedo, Cristiane M.; Benites, Nikolas H.; Puga, Marco A. M.; Rezende, Grazielli R.; Finotti, Carolina M.; Cesar, Gabriela A.; Tanaka, Tayana S. O.; Castro, Vivianne O. L.; Otsuki, Koko; Vicente, Ana C. P.; Fernandes, Carlos E.; Motta-Castro, Ana R. C.

2015-01-01

Background Human T-lymphotropic virus type 1 (HTLV-1) has worldwide distribution and is considered endemic in many world regions, including southwestern Japan and Brazil. Japanese immigrants and their descendants have a high risk of acquiring this infection due to intense population exchange between Brazil and Japan. Objective This cross-sectional study aimed to estimate the prevalence of HTLV, analyze the main risk factors associated with this infection, identify the main circulating types and subtypes of HTLV in Japanese immigrants and descendants living in Campo Grande-MS (Middle-West Brazil), as well as analyze the phylogenetic relationship among isolates of HTLV. Study Design A total of 219 individuals were interviewed and submitted to blood collection. All collected blood samples were submitted for detection of anti-HTLV-1/2 using the immunoassay ELISA and confirmed by immunoblot method. The proviral DNA of the 14 samples HTLV- 1 positive were genotyped by nucleotide sequencing. Results The overall prevalence of HTLV-1 was 6.8% (IC 95%: 3,5-10,2). Descriptive analysis of behavioral risk factors showed statistical association between HTLV-1 and age greater than or equal to 45 years. The proviral DNA of HTLV-1 was detected in all HTLV-1 positive samples. Of these, 14 were sequenced and classified as Cosmopolitan subtype, and 50% (7/14) belonged to subgroup A (transcontinental) and 50% (7/14) to the subgroup B (Japanese). Conclusion The high prevalence of HTLV-1 found evidence of the importance of early diagnosis and counseling of individuals infected with HTLV-1 for the control and prevention of the spread of this infection among Japanese immigrants and their descendants in Central Brazil. PMID:25886507

HTLV-1 Tax-Specific CTL Epitope-Pulsed Dendritic Cell Therapy Reduces Proviral Load in Infected Rats with Immune Tolerance against Tax.

PubMed

Ando, Satomi; Hasegawa, Atsuhiko; Murakami, Yuji; Zeng, Na; Takatsuka, Natsuko; Maeda, Yasuhiro; Masuda, Takao; Suehiro, Youko; Kannagi, Mari

2017-02-01

Adult T cell leukemia/lymphoma (ATL), a CD4 + T cell malignancy with a poor prognosis, is caused by human T cell leukemia virus type 1 (HTLV-1) infection. High proviral load (PVL) is a risk factor for the progression to ATL. We previously reported that some asymptomatic carriers had severely reduced functions of CTLs against HTLV-1 Tax, the major target Ag. Furthermore, the CTL responses tended to be inversely correlated with PVL, suggesting that weak HTLV-1-specific CTL responses may be involved in the elevation of PVL. Our previous animal studies indicated that oral HTLV-1 infection, the major route of infection, caused persistent infection with higher PVL in rats compared with other routes. In this study, we found that Tax-specific CD8 + T cells were present, but not functional, in orally infected rats as observed in some human asymptomatic carriers. Even in the infected rats with immune unresponsiveness against Tax, Tax-specific CTL epitope-pulsed dendritic cell (DC) therapy reduced the PVL and induced Tax-specific CD8 + T cells capable of proliferating and producing IFN-γ. Furthermore, we found that monocyte-derived DCs from most infected individuals still had the capacity to stimulate CMV-specific autologous CTLs in vitro, indicating that DC therapy may be applicable to most infected individuals. These data suggest that peptide-pulsed DC immunotherapy will be useful to induce functional HTLV-1-specific CTLs and decrease PVL in infected individuals with high PVL and impaired HTLV-1-specific CTL responses, thereby reducing the risk of the development of ATL. Copyright © 2017 by The American Association of Immunologists, Inc.

Use of the bovine leukaemia virus LTR U3 promoter for expressing antisense antiviral RNAs and competitive inhibition of viral infection in cell culture.

PubMed

Shayakhmetov, D; Kovalenko, D; Yurov, G; Borisenko, A; Tikchonenko, T

1997-08-01

Use of viral inducible promoters which can be activated by virus-specific transactivator proteins to drive expression of antisense (as)RNA genes appears to be an attractive approach to inhibit virus infections in vivo. To this end, we have constructed an asRNA gene expressed from the bovine leukaemia virus (BLV) U3 promoter that is complementary to the R-U5 region of the BLV genome. This is the region that is most susceptible to inhibition by asRNA. With plasmid pLU, which expresses the asRNA gene under the control of the BLV U3 promoter, 75% inhibition of virus replication was attained in CC81 cells (the molar ratio of pLU DNA over BLV proviral DNA in the transfection mixture was 5:1). Plasmid pLT, which contains only the BLV U3 promoter without any asRNA-coding region, also efficiently (up to 60%) inhibited virus replication when cotransfected with BLV proviral DNA at a ratio of 20:1. It was suggested that competition between functional and 'empty' viral promoters for the viral transactivator protein p38tax could account for this inhibition. An immunoblotting assay showed that in the presence of nuclear extracts from CC81 cells exogenous BLV p38tax specifically associates with its responsive sequence located in the BLV U3 promoter. Moreover, the additional expression of p38tax in CC81 cells abolishes the inhibitory effect of the empty viral promoter. These observations suggest a new mechanism of BLV inhibition caused, most probably, by sequestering of the viral transactivator protein.

Effect of vitamin supplements on HIV shedding in breast milk.

PubMed

Villamor, Eduardo; Koulinska, Irene N; Aboud, Said; Murrin, Clare; Bosch, Ronald J; Manji, Karim P; Fawzi, Wafaie W

2010-10-01

Supplementation in lactating HIV-1-infected women with preformed vitamin A and β-carotene (VA/BC) increases the risk of mother-to-child transmission of HIV through breastfeeding. Identifying a biological mechanism to explain this unexpected finding would lend support to a causal effect. The aim of the study was to evaluate the effect of VA/BC or multivitamin (B complex, vitamin C, and vitamin E) supplementation of HIV-infected women on HIV shedding in breast milk during the first 2 y postpartum. We quantified viral (cell-free) and proviral (cell-associated) HIV loads in breast-milk samples collected ≤15 d after delivery and every 3 mo thereafter from 594 Tanzanian HIV-1-infected women who participated in a randomized trial. Women received 1 of the following 4 daily oral regimens in a 2 × 2 factorial fashion during pregnancy and throughout the first 2 y postpartum: multivitamin, VA/BC, multivitamin including VA/BC, or placebo. The proportion of breast-milk samples with detectable viral load was significantly higher in women who received VA/BC (51.3%) than in women who were not assigned to VA/BC (44.8%; P = 0.02). The effect was apparent ≥6 mo postpartum (relative risk: 1.34; 95% CI: 1.04, 1.73). No associations with proviral load were observed. The multivitamin had no effects. In observational analyses, β-carotene but not retinol breast-milk concentrations were significantly associated with an increased viral load in milk. VA/BC supplementation in lactating women increases the HIV load in breast milk. This finding contributes to explaining the adverse effect of VA/BC on mother-to-child transmission. β-Carotene appears to have an effect on breast-milk viral load, independent of preformed vitamin A. This trial was registered at clinicaltrials.gov as NCT00197756.

Occurrence of Phlebitis: A Systematic Review and Meta-analysis.

PubMed

Chang, Wen P; Peng, Yu X

Peripheral venous catheters (PVCs) are commonly used in clinical practice. However, varying degrees of phlebitis often occur in patients receiving intravenous injections. The relevant literature suggests that phlebitis occurrence is highly associated with the catheter gauge, insertion site, and catheterization duration. Nevertheless, no meta-analysis has been performed on the influence of these three factors on the occurrence of phlebitis. The objective of this study was to determine whether any significant differences exist in the occurrence of phlebitis between catheters of 20 gauge or smaller and those larger than 20 gauge, between catheters inserted in the antecubital fossa and those inserted in other locations on the upper limbs, or between catheters inserted for more than 96 hours and those inserted for 96 hours or less. Using a systematic approach, we searched for literature published between 2006 and 2017 in the Cumulative Index to Nursing and Allied Health Literature (CINAHL), PubMed, ProQuest, and Cochrane Library databases. We used Comprehensive Meta-analysis Version 2 to perform our meta-analysis. After the screening and review processes, we identified 17 studies that met our selection conditions. Among these studies, 14 contained complete data for meta-analysis. These studies involved 4,343 patients and 5,846 PVCs. Regarding the overall effect size in the meta-analysis, the results of the forest plot comparing catheters of 20 gauge or smaller and those larger than 20 gauge presented a risk ratio (RR) of 0.88 (95% confidence interval [0.67, 1.17], p = .380), indicating no statistically significant difference in the occurrence of phlebitis between catheters of the aforementioned gauges. The results of the forest plot comparing catheters inserted in the antecubital fossa and those inserted in other locations on the upper limbs presented an RR of 1.05 (95% confidence interval [0.82, 1.34], p = .696), indicating no statistically significant difference in the occurrence of phlebitis between catheters inserted in the aforementioned locations. The results of the forest plot comparing catheters inserted for more than 96 hours and those inserted for 96 hours or less presented an RR of 1.13 (95% confidence interval [0.49, 2.61], p = .779), indicating no statistically significant difference in the occurrence of phlebitis between catheters inserted for the aforementioned durations. The empirical results of this meta-analysis can serve as a reference for hospital management for selecting the PVC gauge, insertion site, and catheterization duration. In addition to the three factors that we analyzed, whether any other factors influence the occurrence of phlebitis in patients with catheter implantation is worth investigating in future research.

Vaginal Practices among Women at High Risk of HIV Infection in Uganda and Tanzania: Recorded Behaviour from a Daily Pictorial Diary

PubMed Central

Francis, Suzanna C.; Baisley, Kathy; Lees, Shelley S.; Andrew, Bahati; Zalwango, Flavia; Seeley, Janet; Vandepitte, Judith; Ao, Trong T.; van de Wijgert, Janneke; Watson-Jones, Deborah; Kapiga, Saidi; Grosskurth, Heiner; Hayes, Richard J.

2013-01-01

Background Intravaginal practices (IVP) are highly prevalent in sub-Saharan African and have been implicated as risk factors for HIV acquisition. However, types of IVP vary between populations, and detailed information on IVP among women at risk for HIV in different populations is needed. We investigated IVP among women who practice transactional sex in two populations: semi-urban, facility workers in Tanzania who engage in opportunistic sex work; and urban, self-identified sex workers and bar workers in Uganda. The aim of the study was to describe and compare IVP using a daily pictorial diary. Methodology/Principal Findings Two hundred women were recruited from a HIV prevention intervention feasibility study in Kampala, Uganda and in North-West Tanzania. Women were given diaries to record IVP daily for six weeks. Baseline data showed that Ugandan participants had more lifetime partners and transactional sex than Tanzanian participants. Results from the diary showed that 96% of Tanzanian participants and 100% of Ugandan participants reported intravaginal cleansing during the six week study period. The most common types of cleansing were with water only or water and soap. In both countries, intravaginal insertion (e.g. with herbs) was less common than cleansing, but insertion was practiced by more participants in Uganda (46%) than in Tanzania (10%). In Uganda, participants also reported more frequent sex, and more insertion related to sex. In both populations, cleansing was more often reported on days with reported sex and during menstruation, and in Uganda, when participants experienced vaginal discomfort. Participants were more likely to cleanse after sex if they reported no condom use. Conclusions While intravaginal cleansing was commonly practiced in both cohorts, there was higher frequency of cleansing and insertion in Uganda. Differences in IVP were likely to reflect differences in sexual behaviour between populations, and may warrant different approaches to interventions targeting IVP. Vaginal practices among women at high risk in Uganda and Tanzania: recorded behaviour from a daily pictorial diary. PMID:23555618

Folding and insertion thermodynamics of the transmembrane WALP peptide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de; Bennett, W. F. Drew; Pfaendtner, Jim

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA){sub n} (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of meanmore » force characterizing the peptide’s insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.« less

Folding and insertion thermodynamics of the transmembrane WALP peptide

NASA Astrophysics Data System (ADS)

Bereau, Tristan; Bennett, W. F. Drew; Pfaendtner, Jim; Deserno, Markus; Karttunen, Mikko

2015-12-01

The anchor of most integral membrane proteins consists of one or several helices spanning the lipid bilayer. The WALP peptide, GWW(LA)n (L)WWA, is a common model helix to study the fundamentals of protein insertion and folding, as well as helix-helix association in the membrane. Its structural properties have been illuminated in a large number of experimental and simulation studies. In this combined coarse-grained and atomistic simulation study, we probe the thermodynamics of a single WALP peptide, focusing on both the insertion across the water-membrane interface, as well as folding in both water and a membrane. The potential of mean force characterizing the peptide's insertion into the membrane shows qualitatively similar behavior across peptides and three force fields. However, the Martini force field exhibits a pronounced secondary minimum for an adsorbed interfacial state, which may even become the global minimum—in contrast to both atomistic simulations and the alternative PLUM force field. Even though the two coarse-grained models reproduce the free energy of insertion of individual amino acids side chains, they both underestimate its corresponding value for the full peptide (as compared with atomistic simulations), hinting at cooperative physics beyond the residue level. Folding of WALP in the two environments indicates the helix as the most stable structure, though with different relative stabilities and chain-length dependence.

Standardized, Interdepartmental, Simulation-Based Central Line Insertion Course Closes an Educational Gap and Improves Intern Comfort with the Procedure.

PubMed

Grudziak, Joanna; Herndon, Blair; Dancel, Ria D; Arora, Harendra; Tignanelli, Christopher J; Phillips, Michael R; Crowner, Jason R; True, Nicholas A; Kiser, Andy C; Brown, Rebecca F; Goodell, Harry P; Murty, Neil; Meyers, Michael O; Montgomery, Sean P

2017-06-01

Central line placement is a common procedure, routinely performed by junior residents in medical and surgical departments. Before this project, no standardized instructional course on the insertion of central lines existed at our institution, and few interns had received formal ultrasound training. Interns from five departments participated in a simulation-based central line insertion course. Intern familiarity with the procedure and with ultrasound, as well as their prior experience with line placement and their level of comfort, was assessed. Of the 99 interns in participating departments, 45 per cent had been trained as of October 2015. Forty-one per cent were female. The majority (59.5%) had no prior formal ultrasound training, and 46.0 per cent had never placed a line as primary operator. Scores increased significantly, from a precourse score mean of 13.7 to a postcourse score mean of 16.1, P < 0.001. All three of the self-reported measures of comfort with ultrasound also improved significantly. All interns reported the course was "very much" helpful, and 100 per cent reported they felt "somewhat" or "much" more comfortable with the procedure after attendance. To our knowledge, this is the first hospital-wide, standardized, simulation-based central line insertion course in the United States. Preliminary results indicate overwhelming satisfaction with the course, better ultrasound preparedness, and improved comfort with central line insertion.

Sensitivity for Diagnosing Group A Streptococcal Pharyngitis from Manufacturers is 10% Higher than Reported in Peer-Reviewed Publications.

PubMed

Vachhani, Raj; Patel, Toral; Centor, Robert M; Estrada, Carlos A

2017-01-01

Meta-analyses based on peer-reviewed publications report a sensitivity of approximately 85% for rapid antigen streptococcus tests to diagnose group A streptococcal (GAS) pharyngitis. Because these meta-analyses excluded package inserts, we examined the test characteristics of rapid antigen streptococcal tests and molecular methods that manufacturers report in their package inserts. We included tests available in the US market (Food and Drug Administration, period searched 1993-2015) and used package insert data to calculate pooled sensitivity and specificity. To examine quality, we used the Quality Assessment of Diagnostic Accuracy Studies-2. We excluded 26 tests having different trade names but identical methods and data. The study design was prospective in 41.7% (10 of 24). The pooled sensitivity of the most commonly used method, lateral flow/immunochromatographic, was 95% (95% confidence interval [CI] 94-96) and the pooled specificity was 98% (96-98); 7108 patients. The pooled sensitivity of the polymerase chain reaction or molecular methods was 98% (95% CI 96-98) and the pooled specificity was 96% (95% CI 95-97); 5685 patients. Package inserts include sponsored studies that overestimate the sensitivity of rapid tests to diagnose GAS pharyngitis by approximately 10%. Physicians should understand that package inserts overestimate diagnostic test utility; a negative test cannot be used to exclude GAS pharyngitis.

Comparison between gastrostomy feeding and self-expandable metal stent insertion for patients with esophageal cancer and dysphagia.

PubMed

Min, Yang Won; Jang, Eun Young; Jung, Ji Hey; Lee, Hyuk; Min, Byung-Hoon; Lee, Jun Haeng; Rhee, Poong-Lyul; Kim, Jae J

2017-01-01

Self-expandable metal stent (SEMS) insertion and percutaneous gastrostomy (PG) feeding are commonly used for patients with esophageal cancer and dysphagia. This study aimed to compare outcomes between SEMS insertion and PG feeding for them. We retrospectively analyzed 308 patients with esophageal cancer who underwent fully covered SEMS insertion (stent group) or PG (gastrostomy group) for dysphagia due to tumor. Patients with other causes of dysphagia, such as radiation-induced or postoperative stricture, were excluded from the study. Clinical outcomes were compared between the two groups, including overall survival and need for additional intervention and postprocedural nutritional status. At baseline, the stent group (n = 169) had more stage IV patients, less cervical cancers, and received radiotherapy and esophagectomy less often than the gastrostomy group (n = 64). The Kaplan-Meier curves showed higher overall survival in the gastrostomy group than in the stent group. Multivariate analysis revealed that PG was associated with better survival compared with SEMS insertion (hazard ratio 0.541, 95% confidence interval 0.346-0.848, p = 0.007). In addition, the gastrostomy group needed additional intervention less often (3.1% vs. 21.9%, p < 0.001) and experienced less decrease in serum albumin levels (-0.15 ± 0.56 g/dL vs. -0.39 ± 0.58 g/dL, p = 0.011) than the stent group after procedure. Our data suggested that, compared with SEMS insertion, PG is associated with better overall survival in patients with esophageal cancer and dysphagia. Stabilized nutritional status by PG may play a role in improving patient survival.

Barriers and Facilitators to Central Venous Catheter Insertion: A Qualitative Study.

PubMed

Cameron, Kenzie A; Cohen, Elaine R; Hertz, Joelle R; Wayne, Diane B; Mitra, Debi; Barsuk, Jeffrey H

2018-03-14

The aims of the study were to identify perceived barriers and facilitators to central venous catheter (CVC) insertion among healthcare providers and to understand the extent to which an existing Simulation-Based Mastery Learning (SBML) program may address barriers and leverage facilitators. Providers participating in a CVC insertion SBML train-the-trainer program, in addition to intensive care unit nurse managers, were purposively sampled from Veterans Administration Medical Centers located in geographically diverse areas. We conducted semistructured interviews to assess perceptions of barriers and facilitators to CVC insertion. Deidentified transcripts were analyzed using a grounded theory approach and the constant comparative method. We subsequently mapped identified barriers and facilitators to our SBML curriculum to determine whether or not the curriculum addresses these factors. We interviewed 28 providers at six Veterans Administration Medical Centers, identifying the following five overarching factors of perceived barriers to CVC insertion: (1) equipment, (2) personnel/staff, (3) setting or organizational context, (4) patient or provider, and (5) time-related barriers. Three overarching factors of facilitators emerged: (1) equipment, (2) personnel, and (3) setting or organizational context facilitators. The SBML curriculum seems to address most identified barriers, while leveraging many facilitators; building on the commonly identified facilitator of nursing staff contribution by expanding the curriculum to explicitly include nurse involvement could improve team efficiency and organizational culture of safety. Many identified facilitators (e.g., ability to use ultrasound, personnel confidence/competence) were also identified as barriers. Evidence-based SBML programs have the potential to amplify these facilitators while addressing the barriers by providing an opportunity to practice and master CVC insertion skills.

The Alphabet Soup of HIV Reservoir Markers.

PubMed

Sharaf, Radwa R; Li, Jonathan Z

2017-04-01

Despite the success of antiretroviral therapy in suppressing HIV, life-long therapy is required to avoid HIV reactivation from long-lived viral reservoirs. Currently, there is intense interest in searching for therapeutic interventions that can purge the viral reservoir to achieve complete remission in HIV patients off antiretroviral therapy. The evaluation of such interventions relies on our ability to accurately and precisely measure the true size of the viral reservoir. In this review, we assess the most commonly used HIV reservoir assays, as a clear understanding of the strengths and weaknesses of each is vital for the accurate interpretation of results and for the development of improved assays. The quantification of intracellular or plasma HIV RNA or DNA levels remains the most commonly used tests for the characterization of the viral reservoir. While cost-effective and high-throughput, these assays are not able to differentiate between replication-competent or defective fractions or quantify the number of infected cells. Viral outgrowth assays provide a lower bound for the fraction of cells that can produce infectious virus, but these assays are laborious, expensive and substantially underestimate the potential reservoir of replication-competent provirus. Newer assays are now available that seek to overcome some of these problems, including full-length proviral sequencing, inducible HIV RNA assays, ultrasensitive p24 assays and murine adoptive transfer techniques. The development and evaluation of strategies for HIV remission rely upon our ability to accurately and precisely quantify the size of the remaining viral reservoir. At this time, all current HIV reservoir assays have drawbacks such that combinations of assays are generally needed to gain a more comprehensive view of the viral reservoir. The development of novel, rapid, high-throughput assays that can sensitively quantify the levels of the replication-competent HIV reservoir is still needed.

[Intrauterine device: about a rare complication and literature review].

PubMed

Kallat, Adil; Ibrahimi, Ahmed; Fahsi, Otheman; El Sayegh, Hachem; Iken, Ali; Benslimane, Lounis; Nouini, Yassine

2017-01-01

The intrauterine device (IUD) is the most common contraceptive method used in the world. Transuterine migration is a rare complication, accounting for 1/350 - 1/10000 insertions in the literature. We report the case of a 40-year old patient, who had had an IUD insertion 12-year before, presenting with pelvic and right lower back pain associated with intermittent hematuria and burning during urination. Radiological assessment showed calcific deposits on intra bladder IUD. The patient underwent cystostomy, without any difficulty, allowing stone and IUD extraction. A urinary catheter was left in place for 5 days and then withdrawn. The postoperative course was uneventful.

Modeling crack growth during Li insertion in storage particles using a fracture phase field approach

NASA Astrophysics Data System (ADS)

Klinsmann, Markus; Rosato, Daniele; Kamlah, Marc; McMeeking, Robert M.

2016-07-01

Fracture of storage particles is considered to be one of the major reasons for capacity fade and increasing power loss in many commercial lithium ion batteries. The appearance of fracture and cracks in the particles is commonly ascribed to mechanical stress, which evolves from inhomogeneous swelling and shrinkage of the material when lithium is inserted or extracted. Here, a coupled model of lithium diffusion, mechanical stress and crack growth using a phase field method is applied to investigate how the formation of cracks depends on the size of the particle and the presence or absence of an initial crack, as well as the applied flux at the boundary. The model shows great versatility in that it is free of constraints with respect to particle geometry, dimension or crack path and allows simultaneous observation of the evolution of lithium diffusion and crack growth. In this work, we focus on the insertion process. In particular, we demonstrate the presence of intricate fracture phenomena, such as, crack branching or complete breakage of storage particles within just a single half cycle of lithium insertion, a phenomenon that was only speculated about before.

The Application of Coconut Fiber as Dissipative Silencer

NASA Astrophysics Data System (ADS)

Madlan, M. A.; Ghazali, M. I.; Zaman, I.; Kasron, M. Z.; Ying, T. C.

2017-01-01

Heat ventilation air conditioning system (HVAC) is one of the ducting systems that broadly applied in the building. There are HVAC silencers in the market, however the sound absorptive material commonly used is mineral wool. In this research study, a sound absorptive material made of coconut fiber was tested to identify its performance as a potential replacement of green material for ducting silencer. The experiment was carried out in a testing apparatus that follows the BS EN ISO 11691:2009 standard. Different configurations of sound absorptive material and contents of coconut fiber were investigated in the study. The trend of insertion loss at 1/3 octave frequency was identified where at frequency below 3000Hz, the insertion loss of dissipative silencer is observed high at certain frequency with a very narrow range. At 3000Hz, the insertion loss of 4dB to 6dB is constant until 4000Hz and drops until 5000Hz before it increases again steadily up to 13dB at 10000Hz. A similar trend was observed for different configuration of sound absorptive material. Despite the configuration different, the outcome shows that the insertion loss is increasing with higher content of coconut fiber.

Does Needle Rotation Improve Lesion Targeting?

PubMed Central

Badaan, Shadi; Petrisor, Doru; Kim, Chunwoo; Mozer, Pierre; Mazilu, Dumitru; Gruionu, Lucian; Patriciu, Alex; Cleary, Kevin; Stoianovici, Dan

2011-01-01

Background Image-guided robots are manipulators that operate based on medical images. Perhaps the most common class of image-guided robots are robots for needle interventions. Typically, these robots actively position and/or orient a needle guide, but needle insertion is still done by the physician. While this arrangement may have safety advantages and keep the physician in control of needle insertion, actuated needle drivers can incorporate other useful features. Methods We first present a new needle driver that can actively insert and rotate a needle. With this device we investigate the use of needle rotation in controlled in-vitro experiments performed with a specially developed revolving needle driver. Results These experiments show that needle rotation can improve targeting and may reduce errors by as much as 70%. Conclusion The new needle driver provides a unique kinematic architecture that enables insertion with a compact mechanism. Perhaps the most interesting conclusion of the study is that lesions of soft tissue organs may not be perfectly targeted with a needle without using special techniques, either manually or with a robotic device. The results of this study show that needle rotation may be an effective method of reducing targeting errors. PMID:21360796

Inter- and Intraspecific Variations in the Pectoral Muscles of Common Chimpanzees (Pan troglodytes), Bonobos (Pan paniscus), and Humans (Homo sapiens).

PubMed

Potau, J M; Arias-Martorell, J; Bello-Hellegouarch, G; Casado, A; Pastor, J F; de Paz, F; Diogo, R

2018-01-01

We have analyzed anatomic variations in the pectoralis major and pectoralis minor muscles of common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) and compared them to anatomic variations in these muscles in humans (Homo sapiens) . We have macroscopically dissected these muscles in six adult Pan troglodytes , five Pan paniscus of ages ranging from fetus to adult, and five adult Homo sapiens . Although Pan troglodytes are thought to lack a separate pectoralis abdominis muscle, we have identified this muscle in three of the Pan troglodytes ; none of the Pan paniscus , however, had this muscle. We have also found deep supernumerary fascicles in the pectoralis major of two Pan troglodytes and all five Pan paniscus . In all six Pan troglodytes , the pectoralis minor was inserted at the supraspinatus tendon, while, in Pan paniscus and Homo sapiens , it was inserted at the coracoid process of the scapula. Some of the anatomic features and variations of these muscles in common chimpanzees and bonobos are similar to those found in humans, therefore enhancing our knowledge of primate comparative anatomy and evolution and also shedding light on several clinical issues.

Inter- and Intraspecific Variations in the Pectoral Muscles of Common Chimpanzees (Pan troglodytes), Bonobos (Pan paniscus), and Humans (Homo sapiens)

PubMed Central

Arias-Martorell, J.; Bello-Hellegouarch, G.; Casado, A.; Pastor, J. F.; de Paz, F.; Diogo, R.

2018-01-01

We have analyzed anatomic variations in the pectoralis major and pectoralis minor muscles of common chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) and compared them to anatomic variations in these muscles in humans (Homo sapiens). We have macroscopically dissected these muscles in six adult Pan troglodytes, five Pan paniscus of ages ranging from fetus to adult, and five adult Homo sapiens. Although Pan troglodytes are thought to lack a separate pectoralis abdominis muscle, we have identified this muscle in three of the Pan troglodytes; none of the Pan paniscus, however, had this muscle. We have also found deep supernumerary fascicles in the pectoralis major of two Pan troglodytes and all five Pan paniscus. In all six Pan troglodytes, the pectoralis minor was inserted at the supraspinatus tendon, while, in Pan paniscus and Homo sapiens, it was inserted at the coracoid process of the scapula. Some of the anatomic features and variations of these muscles in common chimpanzees and bonobos are similar to those found in humans, therefore enhancing our knowledge of primate comparative anatomy and evolution and also shedding light on several clinical issues. PMID:29581990

Carcinoids of the common bile duct: a case report and literature review

PubMed Central

Ross, Alison C.; Hurley, James B.; Hay, W. Bruce; Rusnak, Conrad H.; Petrunia, Denis M.

1999-01-01

Carcinoids of the extrahepatic bile ducts and particularly the common bile duct are extremely rare. A 65-year-old woman presented with obstructive jaundice. Laboratory and imaging studies gave results that were consistent with an obstructing lesion in the common bile duct. In this case, a stent was inserted initially to decompress the bile ducts. Subsequently a laparotomy and pancreaticoduodenectomy were performed and a tissue diagnosis of carcinoid of the common bile duct was made. The patient was well with no evidence of recurrence 17 months postoperatively. The authors believe this is the 19th reported case of an extrahepatic bile duct carcinoid. PMID:10071590

Diagnosis of feline leukaemia virus infection by semi-quantitative real-time polymerase chain reaction.

PubMed

Pinches, Mark D G; Helps, Christopher R; Gruffydd-Jones, Tim J; Egan, Kathy; Jarrett, Oswald; Tasker, Séverine

2007-02-01

In this paper the design and use of a semi-quantitative real-time polymerase chain reaction assay (RT-PCR) for feline leukaemia virus (FeLV) provirus is described. Its performance is evaluated against established methods of FeLV diagnosis, including virus isolation and enzyme-linked immunoassay (ELISA) in a population of naturally infected cats. The RT-PCR assay is found to have both a high sensitivity (0.92) and specificity (0.99) when examined by expectation maximisation methods and is also able to detect a large number of cats with low FeLV proviral loads that were negative by other conventional test methods.

Modelling the role of Tax expression in HTLV-I persistence in vivo.

PubMed

Li, Michael Y; Lim, Aaron G

2011-12-01

Human T-lymphotropic virus type I (HTLV-I) is a persistent human retrovirus characterized by life-long infection and risk of developing HAM/TSP, a progressive neurological and inflammatory disease, and adult T-cell leukemia (ATL). Chronically infected individuals often harbor high proviral loads despite maintaining a persistently activated immune response. Based on a new hypothesis for the persistence of HTLV-I infection, a three-dimensional compartmental model is constructed that describes the dynamic interactions among latently infected target cells, target-cell activation, and immune responses to HTLV-I, with an emphasis on understanding the role of Tax expression in the persistence of HTLV-I.

PEG tube insertion -- discharge

MedlinePlus

... be treated with medicine. Caring for the PEG-tube Site Drainage from around the PEG tube is common for the first 1 or 2 ... cotton swab or gauze. Try to remove any drainage or crusting on the skin and tube. Be gentle. If you used soap, gently clean ...

Thinking outside the shunt-sterile CSF malabsorption in pilocytic astrocytomas: case series and review of the literature.

PubMed

Johnson, J A; O'Halloran, P J; Crimmins, D; Caird, J

2016-11-01

Ventriculoperitoneal (VP) shunt insertion is the most common cerebrospinal fluid (CSF) diversionary procedure used for the treatment of chronic hydrocephalus. Sterile CSF ascites is a rare complication of VP shunt insertion. This can arise from either an overproduction of CSF or inadequate filtration of CSF at the level of the peritoneum. By either mechanism, the development of CSF ascites requires an intact VP shunt. The authors discuss two paediatric cases diagnosed with suprasellar pilocytic astrocytomas treated with platinum-based chemotherapy, who subsequently developed sterile CSF ascites. We review the literature with regard to CSF malabsorption and discuss it as a contributing factor to shunt malfunction. CSF malabsorption with resultant ascites is a rare complication of VP shunting with many etiologies. Two common predisposing factors included the use of platinum-based chemotherapeutic agents, as well as the specific neuropathology. Further analysis of these two entities is needed in order to elucidate their role in contributing to the development of CSF ascites in this patient cohort.

Partner-Level Factors Associated with Insertive and Receptive Condomless Anal Intercourse Among Transgender Women in Lima, Peru.

PubMed

Satcher, Milan F; Segura, Eddy R; Silva-Santisteban, Alfonso; Sanchez, Jorge; Lama, Javier R; Clark, Jesse L

2017-08-01

Condomless anal intercourse among transgender women (TW) in Peru has been shown to vary by the type of partner involved (e.g. primary vs. casual vs. transactional sex partner), but no previous studies have explored variations in partner-level patterns of condom use according to type of anal intercourse. We evaluated the relationship between partnership characteristics and condom use during insertive (IAI) versus receptive anal intercourse (RAI) among TW with recent, non-female partners. Condomless IAI was more common with transactional and casual sex partners and by TW who self-reported HIV-uninfected serostatus (p < 0.05), alcohol use disorders, or substance use before sex. Condomless RAI was more common with primary partners and by TW who described their HIV serostatus as unknown (p < 0.05). Examining partner-level differences between condomless IAI and RAI reveals distinct patterns of HIV/STI risk among TW, suggesting a need for HIV prevention strategies tailored to the specific contexts of partners, practices, and networks.

Characteristics and pathogenesis of facial nerve stimulation after cochlear implant surgeries: A single-center retrospective analysis from 1,151 patients.

PubMed

Kim, Y R; Yoo, M H; Lee, J Y; Yang, C J; Park, J W; Kang, B C; Kang, W S; Ahn, J H; Chung, J W; Park, H J

2018-05-29

Incidence of facial nerve stimulation (FNS) was 2.8% (32 out of 1151) and higher in ears with cochlear anomaly (6.4%, 25 out of 391) than without cochlear anomaly (0.9%, 7 out of 760). FNS occurred at various current levels and locations of electrodes by different mechanisms related to incomplete insertion of electrodes, cochleo-facial dehiscence, and types of cochlear anomalies. FNS at apical electrodes related to cochleo-facial dehiscence with low current levels, and FNS at basal electrodes with high current levels and partial insertion of electrodes. FNS at most electrodes with high current levels was the most common type in patients with a common cavity or narrowing of the bony cochlear nerve canal. Understanding the mechanisms of FNS might provide insight for preventing FNS when performing CI surgeries. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Molecular Surveillance for Lymphoproliferative Disease Virus in Wild Turkeys (Meleagris gallopavo) from the Eastern United States.

PubMed

Thomas, Jesse M; Allison, Andrew B; Holmes, Edward C; Phillips, Jamie E; Bunting, Elizabeth M; Yabsley, Michael J; Brown, Justin D

2015-01-01

Lymphoproliferative disease virus (LPDV) is a poorly understood, oncogenic avian retrovirus of domestic turkeys that has historically been restricted to Europe and Israel. However, a recent study reported LPDV in multiple wild turkey diagnostic cases from throughout the eastern United States of America (USA). To better understand the distribution of LPDV in the eastern USA, we surveyed 1,164 reportedly asymptomatic hunter-harvested wild turkeys from 17 states for the presence of LPDV proviral DNA by PCR. In total, 564/1,164 (47%) turkeys were positive for LPDV. Wild turkeys from each state had a relatively high prevalence of LPDV, although statewide prevalence varied from 26 to 83%. Phylogenetic analysis revealed two major clades of LPDV in the USA, although one was at a low frequency suggesting restricted transmission, as well as significant clustering by state of isolation. To determine the best tissue to target for diagnostic purposes, liver, spleen, and bone marrow were tested from a subset of 15 hunter-harvested wild turkeys and 20 wild turkey diagnostic cases. Overall, bone marrow provided the highest level of detection for both hunter-harvested turkeys and diagnostic cases. The sensitivity of LPDV detection between tissues was not significantly different for diagnostic cases, but was for hunter-harvested birds. These results indicate that LPDV infection is common and widespread in wild turkey populations throughout the eastern USA, even without overt signs of disease.

A Kinome-Wide Small Interfering RNA Screen Identifies Proviral and Antiviral Host Factors in Severe Acute Respiratory Syndrome Coronavirus Replication, Including Double-Stranded RNA-Activated Protein Kinase and Early Secretory Pathway Proteins

PubMed Central

de Wilde, Adriaan H.; Wannee, Kazimier F.; Scholte, Florine E. M.; Goeman, Jelle J.; ten Dijke, Peter; Snijder, Eric J.

2015-01-01

ABSTRACT To identify host factors relevant for severe acute respiratory syndrome-coronavirus (SARS-CoV) replication, we performed a small interfering RNA (siRNA) library screen targeting the human kinome. Protein kinases are key regulators of many cellular functions, and the systematic knockdown of their expression should provide a broad perspective on factors and pathways promoting or antagonizing coronavirus replication. In addition to 40 proteins that promote SARS-CoV replication, our study identified 90 factors exhibiting an antiviral effect. Pathway analysis grouped subsets of these factors in specific cellular processes, including the innate immune response and the metabolism of complex lipids, which appear to play a role in SARS-CoV infection. Several factors were selected for in-depth validation in follow-up experiments. In cells depleted for the β2 subunit of the coatomer protein complex (COPB2), the strongest proviral hit, we observed reduced SARS-CoV protein expression and a >2-log reduction in virus yield. Knockdown of the COPB2-related proteins COPB1 and Golgi-specific brefeldin A-resistant guanine nucleotide exchange factor 1 (GBF1) also suggested that COPI-coated vesicles and/or the early secretory pathway are important for SARS-CoV replication. Depletion of the antiviral double-stranded RNA-activated protein kinase (PKR) enhanced virus replication in the primary screen, and validation experiments confirmed increased SARS-CoV protein expression and virus production upon PKR depletion. In addition, cyclin-dependent kinase 6 (CDK6) was identified as a novel antiviral host factor in SARS-CoV replication. The inventory of pro- and antiviral host factors and pathways described here substantiates and expands our understanding of SARS-CoV replication and may contribute to the identification of novel targets for antiviral therapy. IMPORTANCE Replication of all viruses, including SARS-CoV, depends on and is influenced by cellular pathways. Although substantial progress has been made in dissecting the coronavirus replicative cycle, our understanding of the host factors that stimulate (proviral factors) or restrict (antiviral factors) infection remains far from complete. To study the role of host proteins in SARS-CoV infection, we set out to systematically identify kinase-regulated processes that influence virus replication. Protein kinases are key regulators in signal transduction, controlling a wide variety of cellular processes, and many of them are targets of approved drugs and other compounds. Our screen identified a variety of hits and will form the basis for more detailed follow-up studies that should contribute to a better understanding of SARS-CoV replication and coronavirus-host interactions in general. The identified factors could be interesting targets for the development of host-directed antiviral therapy to treat infections with SARS-CoV or other pathogenic coronaviruses. PMID:26041291

A simple, efficient resistance soldering apparatus

NASA Technical Reports Server (NTRS)

Vermillion, C. M.

1972-01-01

Multiple resistance soldering device for attaching electric leads to multiple terminal block connectors uses power source with one terminal connected to working probe, and other terminal attached to connector carrying common pins for lead insertion. Mating of male and female connectors solders each lead to individual cup pin.

What to Do If Your Child Feels Lousy.

ERIC Educational Resources Information Center

Parish, Lawrence C.

1991-01-01

Describes head, body, and crab lice so parents can recognize and respond to the problem in their children, noting that head lice are common in grade school children. The article includes an insert that describes 10 steps in recognizing signs of lice and providing treatment. (SM)

Comparison between gastrostomy feeding and self-expandable metal stent insertion for patients with esophageal cancer and dysphagia

PubMed Central

Jung, Ji Hey; Lee, Hyuk; Min, Byung-Hoon; Lee, Jun Haeng; Rhee, Poong-Lyul; Kim, Jae J.

2017-01-01

Background Self-expandable metal stent (SEMS) insertion and percutaneous gastrostomy (PG) feeding are commonly used for patients with esophageal cancer and dysphagia. This study aimed to compare outcomes between SEMS insertion and PG feeding for them. Methods We retrospectively analyzed 308 patients with esophageal cancer who underwent fully covered SEMS insertion (stent group) or PG (gastrostomy group) for dysphagia due to tumor. Patients with other causes of dysphagia, such as radiation-induced or postoperative stricture, were excluded from the study. Clinical outcomes were compared between the two groups, including overall survival and need for additional intervention and postprocedural nutritional status. Results At baseline, the stent group (n = 169) had more stage IV patients, less cervical cancers, and received radiotherapy and esophagectomy less often than the gastrostomy group (n = 64). The Kaplan-Meier curves showed higher overall survival in the gastrostomy group than in the stent group. Multivariate analysis revealed that PG was associated with better survival compared with SEMS insertion (hazard ratio 0.541, 95% confidence interval 0.346–0.848, p = 0.007). In addition, the gastrostomy group needed additional intervention less often (3.1% vs. 21.9%, p < 0.001) and experienced less decrease in serum albumin levels (-0.15 ± 0.56 g/dL vs. -0.39 ± 0.58 g/dL, p = 0.011) than the stent group after procedure. Conclusions Our data suggested that, compared with SEMS insertion, PG is associated with better overall survival in patients with esophageal cancer and dysphagia. Stabilized nutritional status by PG may play a role in improving patient survival. PMID:28632744

A procedure to estimate the origins and the insertions of the knee ligaments from computed tomography images.

PubMed

Ascani, Daniele; Mazzà, Claudia; De Lollis, Angelo; Bernardoni, Massimiliano; Viceconti, Marco

2015-01-21

The estimation of the origin and insertion of the four knee ligaments is crucial for individualised dynamic modelling of the knee. Commonly this information is obtained ex vivo or from high resolution MRI, which is not always available. Aim of this work is to devise a method to estimate the origins and insertions from computed tomography (CT) images. A reference registration atlas was created using a set of 16 bone landmarks visible in CT and eight origins and insertions estimated from MRI and in vitro data available in the literature for three knees. This atlas can be registered to the set of bone landmarks palpated on any given CT using an affine transformation. The resulting orientation and translation matrices and scaling factors can be used to find also the ligament origin and insertions. This procedure was validated on seven pathological knees for which both CT and MRI of the knee region were available, using a proprietary software tool (NMSBuilder, SCS srl, Italy). To assess the procedure reproducibility and repeatability, four different operators performed the landmarks palpation on all seven patients. The average difference between the values predicted by registration on the CT scan and those estimated on the MRI was 2.1±1.2 mm for the femur and 2.7±1.0 mm for the tibia, respectively. The procedure is highly repeatable, with no significant differences observed within or between the operators (p>0.1) and allows to estimate origins and insertions of the knee ligaments from a CT scan with the same level of accuracy obtainable with MRI. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison of Children's Venipuncture Fear and Pain: Randomized Controlled Trial of EMLA® and J-Tip Needleless Injection System®.

PubMed

Stoltz, Petronella; Manworren, Renee C B

Needle procedures, like venipuncture and intravenous (IV) catheter insertion, are recognized as a common cause of pain and fear for children in hospitals and emergency departments. The purpose of this study was to compare children's self-reported pain and fear related to IV insertion with administration of either the topical local anesthetic EMLA® or 1% buffered lidocaine delivered with the J-Tip Needleless Injection System® (J-Tip®). In this prospective, randomized trial, 150 consecutive pediatric patients 8 to 18years of age undergoing IV insertion were randomly assigned 1:1 to treatment group. Participants self-reported procedural pain using a Visual Analog Scale, and procedural fear using the Children's Fear Scale. Procedural pain scores were significantly lower in the EMLA® group (mean score 1.63+1.659) vs. the J-Tip® group (2.99±2.586; p<0.001). Post-procedure fear scores were significantly lower than pre-procedure fear scores in both treatment groups (p<0.002), but there was no difference in fear scores between the two treatment groups (p=0.314). EMLA® provided superior pain relief for IV insertion compared to J-Tip®. Although EMLA® use resulted in lower self-reported pain scores compared to J-Tip®, pain scores for both treatments were low and fear scores did not differ. When IV insertion can be delayed for 60-90min, EMLA® should be used. When a delay is contraindicated, J-Tip® may be a reasonable alternative to minimize procedural pain of IV insertion. Copyright © 2017 Elsevier Inc. All rights reserved.

Evolutionary force of AT-rich repeats to trap genomic and episomal DNAs into the rice genome: lessons from endogenous pararetrovirus.

PubMed

Liu, Ruifang; Koyanagi, Kanako O; Chen, Sunlu; Kishima, Yuji

2012-12-01

In plant genomes, the incorporation of DNA segments is not a common method of artificial gene transfer. Nevertheless, various segments of pararetroviruses have been found in plant genomes in recent decades. The rice genome contains a number of segments of endogenous rice tungro bacilliform virus-like sequences (ERTBVs), many of which are present between AT dinucleotide repeats (ATrs). Comparison of genomic sequences between two closely related rice subspecies, japonica and indica, allowed us to verify the preferential insertion of ERTBVs into ATrs. In addition to ERTBVs, the comparative analyses showed that ATrs occasionally incorporate repeat sequences including transposable elements, and a wide range of other sequences. Besides the known genomic sequences, the insertion sequences also represented DNAs of unclear origins together with ERTBVs, suggesting that ATrs have integrated episomal DNAs that would have been suspended in the nucleus. Such insertion DNAs might be trapped by ATrs in the genome in a host-dependent manner. Conversely, other simple mono- and dinucleotide sequence repeats (SSR) were less frequently involved in insertion events relative to ATrs. Therefore, ATrs could be regarded as hot spots of double-strand breaks that induce non-homologous end joining. The insertions within ATrs occasionally generated new gene-related sequences or involved structural modifications of existing genes. Likewise, in a comparison between Arabidopsis thaliana and Arabidopsis lyrata, the insertions preferred ATrs to other SSRs. Therefore ATrs in plant genomes could be considered as genomic dumping sites that have trapped various DNA molecules and may have exerted a powerful evolutionary force. © 2012 The Authors. The Plant Journal © 2012 Blackwell Publishing Ltd.

Correlation between extension-block K-wire insertion angle and postoperative extension loss in mallet finger fracture.

PubMed

Lee, S K; Kim, Y H; Moon, K H; Choy, W S

2018-02-01

Extension-block pinning represents a simple and reliable surgical technique. Although this procedure is commonly performed successfully, some patients develop postoperative extension loss. To date, the relationship between extension-block Kirschner wire (K-wire) insertion angle and postoperative extension loss in mallet finger fracture remains unclear. We aimed to clarify this relationship and further evaluate how various operative and non-operative factors affect postoperative extension loss after extension-block pinning for mallet finger fracture. A retrospective study was conducted to investigate a relationship between extension block K-wire insertion angle and postoperative extension loss. The inclusion criteria were: (1) a dorsal intra-articular fracture fragment involving 30% of the base of the distal phalanx with or without volar subluxation of the distal phalanx; and (2) <3 weeks delay from the injury without treatment. Extension-block K-wire insertion angle and fixation angle of the distal interphalangeal (DIP) joint were assessed using lateral radiograph at immediate postoperative time. Postoperative extension loss was assessed by using lateral radiograph at latest follow-up. Extension-block K-wire insertion angle was defined as the acute angle between extension block K-wire and longitudinal axis of middle phalangeal head. DIP joint fixation angle was defined as the acute angle between the distal phalanx and middle phalanx longitudinal axes. Seventy-five patients were included. The correlation analysis revealed that extension-block K-wire insertion angle had a negative correlation with postoperative extension loss, whereas fracture size and time to operation had a positive correlation (correlation coefficient for extension block K-wire angle: -0.66, facture size: +0.67, time to operation: +0.60). When stratifying patients in terms of negative and positive fixation angle of the DIP joint, the independent t-test showed that mean postoperative extension loss is -3.67° and +4.54° (DIP joint fixation angles of <0° and ≥0°, respectively, P=0.024). When stratifying patients in terms of extension-block K-wire insertion angle (30°, 30°-40°, >40°), ANOVA showed significantly less postoperative extension loss for higher insertion angles (>40°) than for medium insertion angles (30°-40°). Mean postoperative extension loss difference between higher insertion angle (>40°) and medium insertion angle (30°-40°) was 11° (P=0.002). Using an insertion angle of the extension-block K-wire of 40°-45° and a slightly hyperextended position of the DIP joint may help reducing postoperative extension loss. Therapeutic level III. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

R Vasquez-Del Carpio; T Silverstein; S Lone

Exposure of DNA to UV radiation causes covalent linkages between adjacent pyrimidines. The most common lesion found in DNA from these UV-induced linkages is the cis-syn cyclobutane pyrimidine dimer. Human DNA polymerase {Kappa} (Pol{Kappa}), a member of the Y-family of DNA polymerases, is unable to insert nucleotides opposite the 3'T of a cis-syn T-T dimer, but it can efficiently extend from a nucleotide inserted opposite the 3'T of the dimer by another DNA polymerase. We present here the structure of human Pol{Kappa} in the act of inserting a nucleotide opposite the 5'T of the cis-syn T-T dimer. The structure revealsmore » a constrained active-site cleft that is unable to accommodate the 3'T of a cis-syn T-T dimer but is remarkably well adapted to accommodate the 5'T via Watson-Crick base pairing, in accord with a proposed role for Pol{Kappa} in the extension reaction opposite from cyclobutane pyrimidine dimers in vivo.« less

Objective evaluation of insert material for diabetic and athletic footwear.

PubMed

Brodsky, J W; Kourosh, S; Stills, M; Mooney, V

1988-12-01

Five of the most commonly used materials for shoe inserts (soft Plastazote, medium Pelite, PPT, Spenco, and Sorbothane) were objectively evaluated in the laboratory to characterize their behavior in the following three specific functions that correspond to clinical use: (1) the effect on the materials of repeated compression. (2) the effect of a combination of repetitive shear and compression. (3) the force-distribution (force-attenuation) properties of these materials, both when new and after repeated compression. The last function represents a model for relief of pressure beneath plantar bony prominences, a topic of special concern for the insensitive foot. All materials were effective in reducing transmitted force over the simulated bony prominence with a rank order of effectiveness. Other factors considered were: amount and rate of permanent deformation offset by considerations of enhanced moldability when comparing the neoprene and urethane materials with the polyethylene foams. The ideal insert represents a combination of material to achieve both durability and moldability.

Antigenic Diversity of the Plasmodium vivax Circumsporozoite Protein in Parasite Isolates of Western Colombia

PubMed Central

Hernández-Martínez, Miguel Ángel; Escalante, Ananías A.; Arévalo-Herrera, Myriam; Herrera, Sócrates

2011-01-01

Circumsporozoite (CS) protein is a malaria antigen involved in sporozoite invasion of hepatocytes, and thus considered to have good vaccine potential. We evaluated the polymorphism of the Plasmodium vivax CS gene in 24 parasite isolates collected from malaria-endemic areas of Colombia. We sequenced 27 alleles, most of which (25/27) corresponded to the VK247 genotype and the remainder to the VK210 type. All VK247 alleles presented a mutation (Gly → Asn) at position 28 in the N-terminal region, whereas the C-terminal presented three insertions: the ANKKAGDAG, which is common in all VK247 isolates; 12 alleles presented the insertion GAGGQAAGGNAANKKAGDAG; and 5 alleles presented the insertion GGNAGGNA. Both repeat regions were polymorphic in gene sequence and size. Sequences coding for B-, T-CD4+, and T-CD8+ cell epitopes were found to be conserved. This study confirms the high polymorphism of the repeat domain and the highly conserved nature of the flanking regions. PMID:21292878

LAPAROSCOPY AFTER PREVIOUS LAPAROTOMY

PubMed Central

Godinjak, Zulfo; Idrizbegović, Edin; Begić, Kerim

2006-01-01

Following the abdominal surgery, extensive adhesions often occur and they can cause difficulties during laparoscopic operations. However, previous laparotomy is not considered to be a contraindication for lap-aroscopy. The aim of this study is to present that an insertion of Veres needle in the region of umbilicus is a safe method for creating a pneumoperitoneum for laparoscopic operations after previous laparotomy. In the last three years, we have performed 144 laparoscopic operations in patients that previously underwent one or two laparotomies. Pathology of digestive system, genital organs, Cesarean Section or abdominal war injuries were the most common causes of previous laparotomy. During those operations or during entering into abdominal cavity we have not experienced any complications, while in 7 patients we performed conversion to laparotomy following the diagnostic laparoscopy. In all patients an insertion of Veres needle and trocar insertion in the umbilical region was performed, namely a technique of closed laparoscopy. Not even in one patient adhesions in the region of umbilicus were found, and no abdominal organs were injured. PMID:17177649

Cholorhexidine, octenidine or povidone iodine for catheter related infections: A randomized controlled trial

PubMed Central

Bilir, Ayten; Yelken, Birgül; Erkan, Ayse

2013-01-01

Background: Protection of the catheter site by antimicrobial agents is one of the most important factors in the prevention of infection. Povidone iodine and chlorhexidine gluconate are the most common used agents for dressing. The purpose of this study was to compare the effects of povidone iodine, chlorhexidine gluconate and octenidine hydrochloride in preventing catheter related infections. Materials and Methods: Patients were randomized to receive; 4% chlorhexidine gluconate, 10% povidone iodine or octenidine hydrochlorodine for cutaneous antisepsis. Cultures were taken at the site surrounding catheter insertion and at the catheter hub after removal to help identify the source of microorganisms. Results: Catheter related sepsis was 10.5% in the povidone iodine and octenidine hydrochlorodine groups. Catheter related colonization was 26.3% in povidone iodine group and 21.5% in octenidine hydrochlorodine group. Conclusion: 4% chlorhexidine or octenidine hydrochlorodine for cutaneous disinfection before insertion of an intravascular device and for post-insertion site care can reduce the catheter related colonization. PMID:24250702

Surgical anatomy of latissimus dorsi muscle in transfers about the shoulder.

PubMed

Goldberg, Benjamin A; Elhassan, Bassem; Marciniak, Steven; Dunn, Jonathan H

2009-03-01

Transfer of the latissimus dorsi to the greater tuberosity has been used successfully in the treatment of massive rotator-cuff deficiency. For safe release and transfer of the tendon, the variations in the tendinous insertions of the latissimus dorsi and teres major onto the humerus need to be understood. In anatomical dissection of 12 cadavers, mean width of the latissimus tendon was 3.3 cm at its insertion, and mean length was 7.3 cm. In all specimens, there were fascial connections between the latissimus and teres major and between the latissimus and the long head of the triceps. There were 3 insertion patterns of the latissimus dorsi tendon onto the humerus with respect to the tendon of the teres major: completely separate (8 cadavers), loosely bound (3 cadavers), and completely joined (1 cadaver). If the latissimus dorsi were being transferred in the last type, the teres major would need to be transferred with the latissimus dorsi as a common musculotendinous unit.

Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes.

PubMed

Cianciulli, Antonia; Calvello, Rosa; Panaro, Maria A

2015-04-01

In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor. Copyright © 2015 Elsevier Ltd. All rights reserved.

Incomplete Lineage Sorting and Hybridization Statistics for Large-Scale Retroposon Insertion Data

PubMed Central

Kuritzin, Andrej; Kischka, Tabea

2016-01-01

Ancient retroposon insertions can be used as virtually homoplasy-free markers to reconstruct the phylogenetic history of species. Inherited, orthologous insertions in related species offer reliable signals of a common origin of the given species. One prerequisite for such a phylogenetically informative insertion is that the inserted element was fixed in the ancestral population before speciation; if not, polymorphically inserted elements may lead to random distributions of presence/absence states during speciation and possibly to apparently conflicting reconstructions of their ancestry. Fortunately, such misleading fixed cases are relatively rare but nevertheless, need to be considered. Here, we present novel, comprehensive statistical models applicable for (1) analyzing any pattern of rare genomic changes, (2) testing and differentiating conflicting phylogenetic reconstructions based on rare genomic changes caused by incomplete lineage sorting or/and ancestral hybridization, and (3) differentiating between search strategies involving genome information from one or several lineages. When the new statistics are applied, in non-conflicting cases a minimum of three elements present in both of two species and absent in a third group are considered significant support (p<0.05) for the branching of the third from the other two, if all three of the given species are screened equally for genome or experimental data. Five elements are necessary for significant support (p<0.05) if a diagnostic locus derived from only one of three species is screened, and no conflicting markers are detected. Most potentially conflicting patterns can be evaluated for their significance and ancestral hybridization can be distinguished from incomplete lineage sorting by considering symmetric or asymmetric distribution of rare genomic changes among possible tree configurations. Additionally, we provide an R-application to make the new KKSC insertion significance test available for the scientific community at http://retrogenomics.uni-muenster.de:3838/KKSC_significance_test/. PMID:26967525

The "bench-presser's shoulder": an overuse insertional tendinopathy of the pectoralis minor muscle.

PubMed

Bhatia, Deepak N; de Beer, Joe F; van Rooyen, Karin S; Lam, Francis; du Toit, Donald F

2007-08-01

Tendinopathies of the rotator cuff muscles, biceps tendon and pectoralis major muscle are common causes of shoulder pain in athletes. Overuse insertional tendinopathy of pectoralis minor is a previously undescribed cause of shoulder pain in weightlifters/sportsmen. To describe the clinical features, diagnostic tests and results of an overuse insertional tendinopathy of the pectoralis minor muscle. To also present a new technique of ultrasonographic evaluation and injection of the pectoralis minor muscle/tendon based on use of standard anatomical landmarks (subscapularis, coracoid process and axillary artery) as stepwise reference points for ultrasonographic orientation. Between 2005 and 2006, seven sportsmen presenting with this condition were diagnosed and treated at the Cape Shoulder Institute, Cape Town, South Africa. In five patients, the initiating and aggravating factor was performance of the bench-press exercise (hence the term "bench-presser's shoulder"). Medial juxta-coracoid tenderness, a painful active-contraction test and bench-press manoeuvre, and decrease in pain after ultrasound-guided injection of a local anaesthetic agent into the enthesis, in the absence of any other clinically/radiologically apparent pathology, were diagnostic of pectoralis minor insertional tendinopathy. All seven patients were successfully treated with a single ultrasound-guided injection of a corticosteroid into the enthesis of pectoralis minor followed by a period of rest and stretching exercises. This study describes the clinical features and management of pectoralis minor insertional tendinopathy, secondary to the bench-press type of weightlifting. A new pain site-based classification of shoulder pathology in weightlifters is suggested.

Genome-Wide Transposon Mutagenesis in Pathogenic Leptospira Species▿ ‡

PubMed Central

Murray, Gerald L.; Morel, Viviane; Cerqueira, Gustavo M.; Croda, Julio; Srikram, Amporn; Henry, Rebekah; Ko, Albert I.; Dellagostin, Odir A.; Bulach, Dieter M.; Sermswan, Rasana W.; Adler, Ben; Picardeau, Mathieu

2009-01-01

Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner-based transposon Himar1 to generate the first defined mutants in L. interrogans. In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans. This library provides a valuable resource for the study of gene function in L. interrogans. Combined with the genome sequences of L. interrogans, this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans. PMID:19047402

Genome-wide transposon mutagenesis in pathogenic Leptospira species.

PubMed

Murray, Gerald L; Morel, Viviane; Cerqueira, Gustavo M; Croda, Julio; Srikram, Amporn; Henry, Rebekah; Ko, Albert I; Dellagostin, Odir A; Bulach, Dieter M; Sermswan, Rasana W; Adler, Ben; Picardeau, Mathieu

2009-02-01

Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner-based transposon Himar1 to generate the first defined mutants in L. interrogans. In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans. This library provides a valuable resource for the study of gene function in L. interrogans. Combined with the genome sequences of L. interrogans, this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans.

Foreign bodies in the urinary bladder and their management: a Pakistani experience.

PubMed

Mannan, A; Anwar, S; Qayyum, A; Tasneem, R A

2011-01-01

This was a retrospective study conducted to assess the nature, presentation, mode of insertion, diagnosis and management of foreign bodies in the urinary bladder. Between January 1998 and December 2007, 20 patients with foreign bodies in their urinary bladder were treated at our centre. The records of these patients were reviewed and analysed for their symptoms, mode of insertion, diagnosis, management and complications. A total of 20 foreign bodies were recovered from the urinary bladders during the study period. These included JJ stents with calculi, intrauterine contraceptive devices with stones, a rubber stick, ribbon gauze, encrusted pieces of Foley catheter, proline thread with calculus, a suture needle, broken cold knives, the ceramic beak of a paediatric resectoscope, a knotted suprapubic tube, a hair clip, a nail, an electrical wire and a hairpin. The common presenting features were dysuria and haematuria. The diagnosis was established radiologically in most of the cases. The circumstances of insertion were variable; iatrogenic in 16 (80.0 percent) cases, sexual stimulation in two (10.0 percent), accidental insertion by a child in one (5.0 percent) and physical torture in one (5.0 percent). 17 (85.0 percent) foreign bodies were recovered endoscopically, and cystolithotomy was required in three (15.0 percent) patients. The instances of foreign bodies in the urinary bladder are uncommon. A diagnosis is usually made radiologically. Iatrogenic foreign bodies were found to be the most frequent type of insertion encountered. Endoscopic retrieval is usually successful, with minimal morbidity.

Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum

PubMed Central

Griffiths, Emma; Gupta, Radhey S.

2004-01-01

The Deinococcus-Thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16S rRNA trees. No unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. In this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the Deinococcus-Thermus phylum but are not found in any other group of bacteria. The identified signatures include a 7-amino-acid (aa) insert in threonyl-tRNA synthetase, 1- and 3-aa inserts in the RNA polymerase β′ subunit, a 5-aa deletion in signal recognition particle (Ffh/SR54), a 2-aa insert in major sigma factor 70 (σ70), a 2-aa insert in seryl-tRNA synthetase (SerRS), a 1-aa insert in ribosomal protein L1, and a 2-aa insert in UvrA homologs. By using PCR primers for conserved regions, fragments of these genes were amplified from a number of Deinococcus-Thermus species, and all such fragments (except SerRS in Deinococcus proteolyticus) were found to contain the indicated signatures. The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group. The signature in SerRS, which is absent in D. proteolyticus, was likely introduced after the branching of this species. Phylogenetic studies as well as the nature of the inserts in some of these proteins (viz., σ70 and SerRS) also support a sister group relationship between the Thermus and the Meiothermus genera. The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group. PMID:15126471

A Case for Inserting Community into Public School Curriculum

ERIC Educational Resources Information Center

Theobald, Paul

2006-01-01

This essay contends that there are fundamental connections between a nation's political arrangements and its educational efforts on behalf of youth. Though the common school architects of the nineteenth century recognized these connections, they were profoundly forgotten in a later Darwinian milieu that suggested--our allegiance to democracy…

Innovative Orientation Leads to Improved Success in Online Courses

ERIC Educational Resources Information Center

Taylor, Jean M.; Dunn, Margie; Winn, Sandra K.

2015-01-01

A team of instructional designers, educators, and the School of Liberal Arts (SLA) academic program coordinator from a nonprofit online college, collaborated on producing short voice-over videos with interactive elements that address the most common technology frustrations of beginning students. These videos were inserted into the "Start…

Spotted Wing Drosophila, Sparganothis phenology and a new look at the BugFloods

USDA-ARS?s Scientific Manuscript database

Drosophila suzukii, commonly known as spotted wing drosophila (SWD), does not readily oviposit in cranberries. Following multiple replicated trials using ripe, under-ripe, and over-ripe organic Wisconsin cranberries, SWD females would not (or could not) insert eggs into under-ripe or ripe cranberrie...

AN EVALUATION OF ELECTRODE INSERTION TECHNIQUES FOR MEASUREMENT OF REDOX POTENTIAL IN ESTUARINE SEDIMENTS

EPA Science Inventory

Eh measurements by electrodes are commonly used to characterize redox status of sediments in freshwater, marine and estuarine studies, due to the relative ease and rapidity of data collection. In our studies of fine-grained estuarine seabeds, we observed that Eh values measured i...

Water penetration of grommets: an in vitro study.

PubMed

Ibrahim, Yousef; Fram, Paul; Hughes, Gavin; Phillips, Pete; Owens, David

2017-10-01

The insertion of grommets has been one of the most common procedures carried out by ENT surgeons for patients with persistent middle ear fluid. There has always been apprehension at the use of grommets by patients undertaking swimming or other water sports due to concerns of grommet penetration by water into the middle ear. Despite this, no common consensus exists amongst otolaryngologists regarding post-operative advice following grommet insertion. Most studies focus on surface swimming and do not consider other activities such as diving that patients may undertake. This study aimed to determine the hydrostatic head required for water to pass through a grommet using different water-based solutions. These were selected to simulate conditions such as swimming and showering or bathing. An improved model of a grommeted middle ear (based on previous work by Ricks et al.) was constructed using two 5-ml plastic syringes, latex (from a surgical glove), two rubber neoprene membranes and a Shah Ventilation Tube (1.14 mm). Different water solutions were added to the system and the hydrostatic head measured using digital calipers. The results revealed that the hydrostatic head required to penetrate a grommet is lowest using soapy water and highest with distilled water. The differences between chlorinated water and 3% saline were not significant. We hope that this study can be used in conjunction with previous work to better prepare the ENT surgeon in giving suitable post-operative advice following grommet insertion.

Assessing nursing students' knowledge and skills in performing venepuncture and inserting peripheral venous catheters.

PubMed

Ahlin, C; Klang-Söderkvist, B; Johansson, E; Björkholm, M; Löfmark, A

2017-03-01

Venepuncture and the insertion of peripheral venous catheters are common tasks in health care, and training in these procedures is included in nursing programmes. Evidence of nursing students' knowledge and skills in these procedures is limited. The main aim of this study was to assess nursing students' knowledge and skills when performing venepuncture and inserting peripheral venous catheters. Potential associations between level of knowledge and skills, self-training, self-efficacy, and demographic characteristics were also investigated. The assessment was performed by lecturers at a university college in Sweden using the two previously tested instruments "Assess Venepuncture" and "Assess Peripheral Venous Catheter Insertion". Between 81% and 100% of steps were carried out correctly by the students. The step with the highest rating was "Uses gloves", and lowest rating was 'Informs the patients about the possibility of obtaining local anaesthesia'. Significant correlations between degree of self-training and correct performance were found in the group of students who registered their self-training. No associations between demographic characteristics and correct performances were found. Assessing that students have achieved adequate levels of knowledge and skills in these procedures at different levels of the nursing education is of importance to prevent complications and support patient safety. Copyright © 2017 Elsevier Ltd. All rights reserved.

Modeling and Control of Needles with Torsional Friction

PubMed Central

Reed, Kyle B.; Okamura, Allison M.; Cowan, Noah J.

2010-01-01

A flexible needle can be accurately steered by robotically controlling the bevel tip orientation as the needle is inserted into tissue. Friction between the long, flexible needle shaft and the tissue can cause a significant discrepancy between the orientation of the needle tip and the orientation of the base where the needle angle is controlled. Our experiments show that several common phantom tissues used in needle steering experiments impart substantial friction forces to the needle shaft, resulting in a lag of over 45° for a 10 cm insertion depth in some phantoms; clinical studies report torques large enough to cause similar errors during needle insertions. Such angle discrepancies will result in poor performance or failure of path planners and image-guided controllers, since the needles used in percutaneous procedures are too small for state-of-the-art imaging to accurately measure the tip angle. To compensate for the angle discrepancy, we develop an estimator using a mechanics-based model of the rotational dynamics of a needle being inserted into tissue. Compared to controllers that assume a rigid needle in a frictionless environment, our estimator-based controller improves the tip angle convergence time by nearly 50% and reduces the path deviation of the needle by 70%. PMID:19695979

Does Bedside Sonography Effectively Identify Nasogastric Tube Placements in Pediatric Critical Care Patients?

PubMed

Atalay, Yunus Oktay; Aydin, Ramazan; Ertugrul, Omer; Gul, Selim Baris; Polat, Ahmet Veysel; Paksu, Muhammet Sukru

2016-12-01

A nasogastric tube (NGT) insertion is a common procedure in intensive care units, with some serious complications that result from the malposition of the NGT tip. This pilot study was designed to investigate the efficiency of ultrasound in verifying correct NGT placement and to compare these results with radiographic findings. This was a single-center, double-blind prospective study of patients who had received an NGT in the pediatric critical care unit. Twenty-one patients aged 1 month to 18 years were included in this study. All NGTs were inserted by the same critical care physician. After insertion, the physician first confirmed NGT placement by the auscultation of the epigastrium following the insufflation of air. Confirmation was supplemented with an abdominal radiograph. A radiologist who was unaware of the radiographic findings performed bedside sonography on all patients and verified the location of the NGTs. The findings from these 2 physicians were then compared. NGTs were inserted without any complications, and none of the NGTs were positioned in the respiratory tract in any of the patients. All NGT tips were visualized by radiography and sonography with a sensitivity of 100%. Bedside sonography performed by a radiologist is an effective and sensitive diagnostic procedure for confirming the correct NGT position in patients in the pediatric critical care unit.

Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma.

PubMed

Doucet-O'Hare, Tara T; Sharma, Reema; Rodić, Nemanja; Anders, Robert A; Burns, Kathleen H; Kazazian, Haig H

2016-09-01

Squamous cell carcinoma of the esophagus (SCC) is the most common form of esophageal cancer in the world and is typically diagnosed at an advanced stage when successful treatment is challenging. Understanding the mutational profile of this cancer may identify new treatment strategies. Because somatic retrotransposition has been shown in tumors of the gastrointestinal system, we focused on LINE-1 (L1) mobilization as a source of genetic instability in this cancer. We hypothesized that retrotransposition is ongoing in SCC patients. The expression of L1 encoded proteins is necessary for retrotransposition to occur; therefore, we evaluated the expression of L1 open reading frame 1 protein (ORF1p). Using immunohistochemistry, we detected ORF1p expression in all four SCC cases evaluated. Using L1-seq, we identified and validated 74 somatic insertions in eight tumors of the nine evaluated. Of these, 12 insertions appeared to be somatic, not genetically inherited, and sub-clonal (i.e., present in less than one copy per genome equivalent) in the adjacent normal esophagus (NE), while clonal in the tumor. Our results indicate that L1 retrotransposition is active in SCC of the esophagus and that insertion events are present in histologically NE that expands clonally in the subsequent tumor. © 2016 WILEY PERIODICALS, INC.

Physical mapping of complex genomes

DOEpatents

Evans, G.A.

1993-06-15

A method for the simultaneous identification of overlapping cosmid clones among multiple cosmid clones and the use of the method for mapping complex genomes are provided. A library of cosmid clones that contains the DNA to be mapped is constructed and arranged in a manner such that individual clones can be identified and replicas of the arranged clones prepared. In preferred embodiments, the clones are arranged in a two dimensional matrix. In such embodiments, the cosmid clones in a row are pooled, mixed probes complementary to the ends of the DNA inserts in the pooled clones are synthesized, hybridized to a first replica of the library. Hybridizing clones, which include the pooled row, are identified. A second portion of clones is prepared by pooling cosmid clones that correspond to a column in the matrix. The second pool thereby includes one clone from the first portion pooled clones. This common clone is located on the replica at the intersection of the column and row. Mixed probes complementary to the ends of the DNA inserts in the second pooled portion of clones are prepared and hybridized to a second replica of the library. The hybridization pattern on the first and second replicas of the library are compared and cross-hybridizing clones, other than the clones in the pooled column and row, that hybridize to identical clones in the first and second replicas are identified. These clones necessarily include DNA inserts that overlap with the DNA insert in the common clone located at the intersection of the pooled row and pooled column. The DNA in the entire library may be mapped by pooling the clones in each of the rows and columns of the matrix, preparing mixed end-specific probes and hybridizing the probes from each row or column to a replica of the library. Since all clones in the library are located at the intersection of a column and a row, the overlapping clones for all clones in the library may be identified and a physical map constructed.

Childhood-onset HAM/TSP with progressive cognitive impairment.

PubMed

Zorzi, Giovanna; Mancuso, Roberta; Nardocci, Nardo; Farina, Laura; Guerini, Franca Rosa; Ferrante, Pasquale

2010-04-01

HTLV-I associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a chronic myelopathy, usually with adult-onset. Very few cases of childhood-onset have been described, most presenting with progressive paraparesis and sphincteric disturbances as in the adult form. Here we report a young male with childhood-onset of HAM/TSP and progressive cognitive and behavioral disturbances. A serological screening revealed HTLV-I infection, confirmed by Western Immunoblotting analysis. Molecular characterization of amplified HTLV-I proviral DNA has been performed both in the patient and his mother by LTR sequence analysis, and HLA genotype inheritance was evaluated. Our case indicates the possibility that cognitive dysfunctions may be one manifestation of HTLV-I infection in childhood.

Space Telecommunications Radio System (STRS) Architecture Standard. Release 1.02.1

NASA Technical Reports Server (NTRS)

Reinhart, Richard C.; Kacpura, Thomas J.; Handler, Louis M.; Hall, C. Steve; Mortensen, Dale J.; Johnson, Sandra K.; Briones, Janette C.; Nappier, Jennifer M.; Downey, Joseph A.; Lux, James P.

2012-01-01

This document contains the NASA architecture standard for software defined radios used in space- and ground-based platforms to enable commonality among radio developments to enhance capability and services while reducing mission and programmatic risk. Transceivers (or transponders) with functionality primarily defined in software (e.g., firmware) have the ability to change their functional behavior through software alone. This radio architecture standard offers value by employing common waveform software interfaces, method of instantiation, operation, and testing among different compliant hardware and software products. These common interfaces within the architecture abstract application software from the underlying hardware to enable technology insertion independently at either the software or hardware layer.

Sidewall penetrator for oil wells

NASA Technical Reports Server (NTRS)

Collins, E. R., Jr.

1981-01-01

Penetrator bores horizontal holes in well casing to increase trapped oil drainage. Several penetrators operated by common drive are inserted into well at once. Shaft, made from spiraling cable, rotates and thrusts simultaneously through rigid curvilinear guide tube forcing bit through casing into strata. Device pierces more deeply than armor-piercing bullets and shaped explosive charges.

Affectibility in Educational Technologies: A Socio-Technical Perspective for Design

ERIC Educational Resources Information Center

Hayashi, Elaine C. S.; Baranauskas, M. Cecilia C.

2013-01-01

Digital artifacts have the potential for augmenting the interest of students and the quality of learning environments. However, it is still common to find technology being inserted in learning settings without a closer connection to the learners' contemporary world. In this paper we report on results of a qualitative research conducted to address…

A novel misoprostol delivery system for induction of labor: clinical utility and patient considerations.

PubMed

Stephenson, Megan L; Wing, Deborah A

2015-01-01

Induction of labor is one of the most commonly performed obstetric procedures and will likely become more common as the reproductive population in developed nations changes. As the proportion of women undergoing induction grows, there is a constant search for more efficacious ways to induce labor while maintaining fetal and maternal safety as well as patient satisfaction. With almost half of induced labors requiring cervical ripening, methods for achieving active labor and vaginal delivery are constantly being investigated. Prostaglandins have been shown to be effective induction agents, and specifically vaginal misoprostol, used off-label, have been widely utilized to initiate cervical ripening and active labor. The challenge is to administer this medication accurately while maintaining the ability to discontinue the medication when needed. The misoprostol vaginal insert initiates cervical ripening utilizing a delivery system that controls medication release and can be rapidly removed. This paper reviews the design, development, and clinical utility of the misoprostol vaginal insert for induction of labor as well as patient considerations related to the delivery system.

Response to crizotinib in a non-small-cell lung cancer patient harboring an EML4-ALK fusion with an atypical LTBP1 insertion.

PubMed

Aguado, Cristina; Gil, Maria-de-Los-Llanos; Yeste, Zaira; Giménez-Capitán, Ana; Teixidó, Cristina; Karachaliou, Niki; Viteri, Santiago; Rosell, Rafael; Molina-Vila, Miguel A

2018-01-01

Fusion of the anaplastic lymphoma receptor tyrosine kinase gene ( ALK ) with the echinoderm microtubule-associated protein 4 gene ( EML4 ) is the second most common actionable alteration in non-small-cell lung cancer, with a frequency of 5%. Here, we present a case of an EML4-ALK-positive patient with an atypical in-frame insertion from the LTBP1 gene in the canonical junction of variant 1 . The patient was a 39-year-old never-smoker female diagnosed with Stage IV lung adenocarcinoma. A core biopsy was negative for EGFR and KRAS mutations but positive for ALK immunohistochemistry and fluorescence in situ hybridization. When submitted to nCounter, the sample showed a 3'/5' imbalance indicative of an ALK rearrangement, but failed to give a positive signal for any of the variants tested. Finally, a band with a molecular weight higher than expected appeared after reverse transcriptase-polymerase chain reaction analysis. When Sanger sequencing was performed, the band revealed an atypical EML4-ALK fusion gene with an in-frame 129 bp insertion. A 115 bp segment of the insertion corresponded to an intronic region of LTBP1 , a gene located in the short arm of chromosome 2, between ALK and EML4 . The patient received crizotinib and showed a good therapeutic response that is still ongoing after 12 months. Our result suggests that short in-frame insertions of other genes in the EML4-ALK junction do not affect the sensitivity of the EML4-ALK fusion protein to crizotinib.

Vascular nursing experience, practice knowledge, and beliefs: Results from the Michigan PICC1 survey.

PubMed

Chopra, Vineet; Kuhn, Latoya; Ratz, David; Flanders, Scott A; Krein, Sarah L

2016-04-01

Peripherally inserted central catheters (PICCs) are increasingly used in hospitalized patients. Yet, little is known about the vascular access nurses who often place them. We conducted a Web-based survey to assess vascular access nursing experience, practice, knowledge, and beliefs related to PICC insertion and care in 47 Michigan hospitals. The response rate was 81% (172 received invitations, 140 completed the survey). More than half of all respondents (58%) reported placing PICCs for ≥5 years, and 23% had obtained dedicated vascular access certification. The most common reported indications for PICC insertion included intravenous antibiotics, difficult venous access, and chemotherapy. Many respondents (46%) reported placing a PICC in a patient receiving dialysis; however, 91% of these respondents reported receiving approval from nephrology prior to insertion. Almost all respondents (91%) used ultrasound to find a suitable vein for PICC insertion, and 76% used electrocardiography guidance to place PICCs. PICC occlusion was reported as the most frequently encountered complication, followed by device migration and deep vein thrombosis. Although 94% of respondents noted that their hospitals tracked the number of PICCs placed, only 40% reported tracking duration of PICC use. Relatedly, 30% of nurses reported that their hospitals had a written policy to evaluate PICC necessity or appropriateness. This survey of vascular nursing experiences highlights opportunities to improve practices such as avoiding PICC use in dialysis, better tracking of PICC dwell times, and necessity. Hospitalists may use these data to inform clinical practice, appropriateness, and safety of PICCs in hospitalized patients. © 2015 Society of Hospital Medicine.

Molecular Dynamics Simulations and Structural Analysis to Decipher Functional Impact of a Twenty Residue Insert in the Ternary Complex of Mus musculus TdT Isoform

PubMed Central

Mutt, Eshita; Sowdhamini, Ramanathan

2016-01-01

Insertions/deletions are common evolutionary tools employed to alter the structural and functional repertoire of protein domains. An insert situated proximal to the active site or ligand binding site frequently impacts protein function; however, the effect of distal indels on protein activity and/or stability are often not studied. In this paper, we have investigated a distal insert, which influences the function and stability of a unique DNA polymerase, called terminal deoxynucleotidyl transferase (TdT). TdT (EC:2.7.7.31) is a monomeric 58 kDa protein belonging to family X of eukaryotic DNA polymerases and known for its role in V(D)J recombination as well as in non-homologous end-joining (NHEJ) pathways. Two murine isoforms of TdT, with a length difference of twenty residues and having different biochemical properties, have been studied. All-atom molecular dynamics simulations at different temperatures and interaction network analyses were performed on the short and long-length isoforms. We observed conformational changes in the regions distal to the insert position (thumb subdomain) in the longer isoform, which indirectly affects the activity and stability of the enzyme through a mediating loop (Loop1). A structural rationale could be provided to explain the reduced polymerization rate as well as increased thermosensitivity of the longer isoform caused by peripherally located length variations within a DNA polymerase. These observations increase our understanding of the roles of length variants in introducing functional diversity in protein families in general. PMID:27311013

Arched needle technique for inferior alveolar mandibular nerve block.

PubMed

Chakranarayan, Ashish; Mukherjee, B

2013-03-01

One of the most commonly used local anesthetic techniques in dentistry is the Fischer's technique for the inferior alveolar nerve block. Incidentally this technique also suffers the maximum failure rate of approximately 35-45%. We studied a method of inferior alveolar nerve block by injecting a local anesthetic solution into the pterygomandibular space by arching and changing the approach angle of the conventional technique and estimated its efficacy. The needle after the initial insertion is arched and inserted in a manner that it approaches the medial surface of the ramus at an angle almost perpendicular to it. The technique was applied to 100 patients for mandibular molar extraction and the anesthetic effects were assessed. A success rate of 98% was obtained.

Alu polymorphic insertions reveal genetic structure of north Indian populations.

PubMed

Tripathi, Manorama; Tripathi, Piyush; Chauhan, Ugam Kumari; Herrera, Rene J; Agrawal, Suraksha

2008-10-01

The Indian subcontinent is characterized by the ancestral and cultural diversity of its people. Genetic input from several unique source populations and from the unique social architecture provided by the caste system has shaped the current genetic landscape of India. In the present study 200 individuals each from three upper-caste and four middle-caste Hindu groups and from two Muslim populations in North India were examined for 10 polymorphic Alu insertions (PAIs). The investigated PAIs exhibit high levels of polymorphism and average heterozygosity. Limited interpopulation variance and genetic flow in the present study suggest admixture. The results of this study demonstrate that, contrary to common belief, the caste system has not provided an impermeable barrier to genetic exchange among Indian groups.

Insertion torque recordings for the diagnosis of contact between orthodontic mini-implants and dental roots: protocol for a systematic review.

PubMed

Meursinge Reynders, Reint; Ladu, Luisa; Ronchi, Laura; Di Girolamo, Nicola; de Lange, Jan; Roberts, Nia; Plüddemann, Annette

2015-04-02

Hitting a dental root during the insertion of orthodontic mini-implants (OMIs) is a common adverse effect of this intervention. This condition can permanently damage these structures and can cause implant instability. Increased torque levels (index test) recorded during the insertion of OMIs may provide a more accurate and immediate diagnosis of implant-root contact (target condition) than radiographic imaging (reference standard). An accurate index test could reduce or eliminate X-ray exposure. These issues, the common use of OMIs, the high prevalence of the target condition, and because most OMIs are placed between roots warrant a systematic review. We will assess 1) the diagnostic accuracy and the adverse effects of the index test, 2) whether OMIs with root contact have higher insertion torque values than those without, and 3) whether intermediate torque values have clinical diagnostic utility. The Preferred Reporting Items for Systematic review and Meta-Analysis Protocols (PRISMA-P) 2015 statement was used as a the guideline for reporting this protocol. Inserting implants deliberately into dental roots of human participants would not be approved by ethical review boards and adverse effects of interventions are generally underreported. We will therefore apply broad spectrum eligibility criteria, which will include clinical, animal and cadaver models. Not including these models could slow down knowledge translation. Both randomized and non-randomized research studies will be included. Comparisons of interest and subgroups are pre-specified. We will conduct searches in MEDLINE and more than 40 other electronic databases. We will search the grey literature and reference lists and hand-search ten journals. All methodological procedures will be conducted by three reviewers. Study selection, data extraction and analyses, and protocols for contacting authors and resolving conflicts between reviewers are described. Designed specific risk of bias tools will be tailored to the research question. Different research models will be analysed separately. Parameters for exploring statistical heterogeneity and conducting meta-analyses are pre-specified. The quality of evidence for outcomes will be assessed through the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach. The findings of this systematic review will be useful for patients, clinicians, researchers, guideline developers, policymakers, and surgical companies.

Complications and management of forgotten long-term biliary stents.

PubMed

Sohn, Se Hoon; Park, Jae Hyun; Kim, Kook Hyun; Kim, Tae Nyeun

2017-01-28

To evaluate complications and management outcomes of retained long-term plastic biliary stents. Endoscopic plastic biliary stent placement was performed in 802 patients at Yeungnam University Hospital between January 2000 and December 2014. Follow-up loss with a subsequently forgotten stent for more than 12 mo occurred in 38 patients. We retrospectively examined the cause of biliary stent insertion, status of stents, complications associated with biliary stents and management outcomes of long-term plastic biliary stents. Continuous variables were analyzed using the t test. Observed frequencies in subsets of the study population were compared using Fisher's exact test and χ 2 tests. Statistical significance was defined as P < 0.05 (two-tailed). Mean age of patients was 73.7 ± 12 years and male-to-female ratio was 2.2:1. Indications of plastic biliary stent insertion were bile duct stones (63.2%, 24/38) and benign bile duct stricture (52.6%, 20/38). Mean duration of retained plastic stent was 22.6 ± 12.2 mo, and in 10 cases (26.3%), stents were retained for more than 24 mo. Common bile duct (CBD) stones or sludge were found in most cases (92.1%, 35/38). The most common complication was acute cholangitis (94.7%, 36/38). Stent removal by endoscopic approach was successfully performed in 92.1% (35/38) of the cases. In 3 cases, an additional plastic stent was inserted alongside the previous stent due to failure of the stent removal. Endoscopic removal of bile duct stones was successful in 73.7% (28/38) of the cases. When patients were divided into two groups by duration of stent placement (12 to 24 mo vs over 24 mo), there were no differences in the development of cholangitis, presence of biliary stones, and success rate of endoscopic removal of stones and biliary stents. The most common complication of retained long-term plastic biliary stents was acute cholangitis associated with CBD stones. Endoscopic management was successfully performed in most cases.

[Application of right jugular vessels to build extracorporeal membrane oxygenation for treating the critically ill children].

PubMed

Yan, X G; Lu, Z J; Zheng, J C; Zhang, W W; Lu, G P; Jia, B

2016-07-01

To summarize the experience in applying a technique of inserting a cannula through right internal jugular vein and common carotid artery to build extracorporeal membrane oxygenation (ECMO) for critically ill children. The data of critically ill patients received ECMO support through right internal jugular vein and common carotid artery between December 2011 and December 2015 from Children's Hospital of Fudan University were analyzed retrospectively.The data included diagnosis, age, body weight, time of cannula and ECMO running, complication and prognosis. In total 28 patients received ECMO support, 3 patients of post-cardiac surgery with transthoracic cannula were excluded.Twenty-five patients inserted cannula through neck vessels were enrolled, 15 boys and 10 girls, the median age was 1.8 years (range, 1 d-13 years), the median weight was 12.0 (2.8-50.0) kg.All the cannula sites were right internal jugular vein and right common carotid artery, before cannula use 5 patients had been inserted central vein tube and 3 patients with blood filter tube in right internal jugular vein, in one case cannula was applied during cardiopulmonary resuscitation.V-A ECMO had been built for all the cases successfully, the median operation time was (45±26) min.The pump flow was 80-150 ml/(kg·min), the median duration of ECMO support was 153(14-567) h. Sixteen (64%) patients weaned off ECMO successfully, 15(60%) survived to hospital discharge.About the complication of cannula, six patients developed cannula site bleeding, and two patients required re-fixation of cannula, one patient's external jugular vein had been hurt and sutured for bleeding. Application of right jugular vessels to build ECMO is easy and safe for treating the sick children. The skill should be proficient to assure ECMO run and reduce the complications.

T-cell receptor signaling enhances transcriptional elongation from latent HIV proviruses by activating P-TEFb through an ERK-dependent pathway.

PubMed

Kim, Young Kyeung; Mbonye, Uri; Hokello, Joseph; Karn, Jonathan

2011-07-29

Latent human immunodeficiency virus (HIV) proviruses are thought to be primarily reactivated in vivo through stimulation of the T-cell receptor (TCR). Activation of the TCR induces multiple signal transduction pathways, leading to the ordered nuclear migration of the HIV transcription initiation factors NF-κB (nuclear factor κB) and NFAT (nuclear factor of activated T-cells), as well as potential effects on HIV transcriptional elongation. We have monitored the kinetics of proviral reactivation using chromatin immunoprecipitation assays to measure changes in the distribution of RNA polymerase II in the HIV provirus. Surprisingly, in contrast to TNF-α (tumor necrosis factor α) activation, where early transcription elongation is highly restricted due to rate-limiting concentrations of Tat, efficient and sustained HIV elongation and positive transcription elongation factor b (P-TEFb) recruitment are detected immediately after the activation of latent proviruses through the TCR. Inhibition of NFAT activation by cyclosporine had no effect on either HIV transcription initiation or elongation. However, examination of P-TEFb complexes by gel-filtration chromatography showed that TCR signaling led to the rapid dissociation of the large inactive P-TEFb:7SK RNP (small nuclear RNA 7SK ribonucleoprotein) complex and the release of active low-molecular-weight P-TEFb complexes. Both P-TEFb recruitment to the HIV long terminal repeat and enhanced HIV processivity were blocked by the ERK (extracellular-signal-regulated kinase) inhibitor U0126, but not by AKT (serine/threonine protein kinase Akt) and PI3K (phosphatidylinositol 3-kinase) inhibitors. In contrast to treatment with HMBA (hexamethylene bisacetamide) and DRB (5,6-dichlorobenzimidazole 1-β-ribofuranoside), which disrupt the large 7SK RNP complex but do not stimulate early HIV elongation, TCR signaling provides the first example of a physiological pathway that can shift the balance between the inactive P-TEFb pool and the active P-TEFb pool and thereby stimulate proviral reactivation. Copyright © 2011 Elsevier Ltd. All rights reserved.

BOLA-DRB3 gene polymorphisms influence bovine leukaemia virus infection levels in Holstein and Holstein × Jersey crossbreed dairy cattle.

PubMed

Carignano, H A; Beribe, M J; Caffaro, M E; Amadio, A; Nani, J P; Gutierrez, G; Alvarez, I; Trono, K; Miretti, M M; Poli, M A

2017-08-01

Bovine leukemia virus (BLV) infections, causing persistent lymphocytosis and lethal lymphosarcoma in cattle, have reached high endemicity on dairy farms. We observed extensive inter-individual variation in the level of infection (LI) by assessing differences in proviral load in peripheral blood. This phenotypic variation appears to be determined by host genetics variants, especially those located in the BoLA-DRB3 MHCII molecule. We performed an association study using sequencing-based typed BOLA-DRB3 alleles from over 800 Holstein and Holstein × Jersey cows considering LI in vivo and accounting for filial relationships. The DBR3*0902 allele was associated with a low level of infection (LLI) (<1% of circulating infected B-cells), whereas the DRB3*1001 and DRB3*1201 alleles were related to a high level of infection (HLI). We found evidence that 13 polymorphic positions located in the pockets of the peptide-binding cleft of the BOLA-DRB3 alleles were associated with LI. DRB3*0902 had unique haplotypes for each of the pockets: Ser 13 -Glu 70 -Arg 71 -Glu 74 (pocket 4), Ser 11 -Ser 30 (pocket 6), Glu 28 -Trp 61 -Arg 71 (pocket 7) and Asn 37 -Asp 57 (pocket 9), and all of them were significantly associated with LLI. Conversely, Lys 13 -Arg 70 -Ala 71 -Ala 74 and Ser 13 -Arg 70 -Ala 71 -Ala 74 , corresponding to the DRB3*1001 and *1201 alleles respectively, were associated with HLI. We showed that the specific amino acid pattern in the DRB3*0902 peptide-binding cleft may be related to the set point of a very low proviral load level in adult cows. Moreover, we identified two BOLA-DRB3 alleles associated with a HLI, which is compatible with a highly contagious profile. © 2017 Stichting International Foundation for Animal Genetics.

Integration of Myeloblastosis Associated Virus proviral sequences occurs in the vicinity of genes encoding signaling proteins and regulators of cell proliferation

PubMed Central

Li, Chang Long; Coullin, Philippe; Bernheim, Alain; Joliot, Véronique; Auffray, Charles; Zoroob, Rima; Perbal, Bernard

2006-01-01

Aims Myeloblastosis Associated Virus type 1 (N) [MAV 1(N)] induces specifically nephroblastomas in 8–10 weeks when injected to newborn chicken. The MAV-induced nephroblastomas constitute a unique animal model of the pediatric Wilms' tumor. We have made use of three independent nephroblastomas that represent increasing tumor grades, to identify the host DNA regions in which MAV proviral sequences were integrated. METHODS Cellular sequences localized next to MAV-integration sites in the tumor DNAs were used to screen a Bacterial Artificial Chromosomes (BACs) library and isolate BACs containing about 150 kilobases of normal DNA corresponding to MAV integration regions (MIRs). These BACs were mapped on the chicken chromosomes by Fluorescent In Situ Hybridization (FISH) and used for molecular studies. Results The different MAV integration sites that were conserved after tumor cell selection identify genes involved in the control of cell signaling and proliferation. Syntenic fragments in human DNA contain genes whose products have been involved in normal and pathological kidney development, and several oncogenes responsible for tumorigenesis in human. Conclusion The identification of putative target genes for MAV provides important clues for the understanding of the MAV pathogenic potential. These studies identified ADAMTS1 as a gene upregulated in MAV-induced nephroblastoma and established that ccn3/nov is not a preferential site of integration for MAV as previously thought. The present results support our hypothesis that the highly efficient and specific MAV-induced tumorigenesis results from the alteration of multiple target genes in differentiating blastemal cells, some of which are required for the progression to highly aggressive stages. This study reinforces our previous conclusions that the MAV-induced nephroblastoma constitutes an excellent model in which to characterize new potential oncogenes and tumor suppressors involved in the establishment and maintenance of tumors. PMID:16403231

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 cAMP-responsive element (CRE)-binding protein/CRE modulator/activation transcription factor binding.

PubMed

Pierard, Valérie; Guiguen, Allan; Colin, Laurence; Wijmeersch, Gaëlle; Vanhulle, Caroline; Van Driessche, Benoît; Dekoninck, Ann; Blazkova, Jana; Cardona, Christelle; Merimi, Makram; Vierendeel, Valérie; Calomme, Claire; Nguyên, Thi Liên-Anh; Nuttinck, Michèle; Twizere, Jean-Claude; Kettmann, Richard; Portetelle, Daniel; Burny, Arsène; Hirsch, Ivan; Rohr, Olivier; Van Lint, Carine

2010-06-18

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.

Higher HTLV-1c proviral loads are associated with blood stream infections in an Indigenous Australian population.

PubMed

Einsiedel, Lloyd; Cassar, Olivier; Spelman, Tim; Joseph, Sheela; Gessain, Antoine

2016-05-01

An association between blood stream infections (BSI) and HTLV-1 seropositivity in Indigenous Australians might result from HTLV-1 mediated inflammation and parasite coinfections that provide portals of entry for bacteria. To determine whether BSI risk increases with HTLV-1c proviral load (PVL) and to identify the pathogens responsible in the context of HTLV-1 related conditions. Indigenous adults admitted to Alice Springs Hospital, central Australia, were recruited as cases or controls according to whether they had a BSI. Clinical data were extracted from case notes and the hospital pathology database. HTLV-1 serology and PVL assays were then performed and risk factors for BSI were determined for HTLV-1 infected subjects. Risk factors were compared between 44 cases and 30 controls who were HTLV-1 Western blot positive. In a multivariable model, high HTLV-1c PVL was predictive of BSI during the study period (OR, 9.10; 95% CI, 2.40-34.4). Median (IQR) HTLV-1c PVL (copies per 100 PBL) was 39-fold higher for patients recording any BSI (0.116 (0.009, 0.277)) relative to those who had no BSI (0.003 (0.000, 0.067))(p=0.0007). Mean (SD) PVL for subjects with no BSI (n=27), 1 BSI (n=37) and ≥2 BSI (n=10) during the study period were 0.120 (0.301), 0.271 (0.622) and 0.500 (0.654) copies per 100 PBL, respectively (p=0.0007). Five BSI were associated with possible complications of HTLV-1; strongyloidiasis (3), infective dermatitis (1), HTLV-1 associated bronchiectasis (1). Higher HTLV-1c PVL predicts BSI risk; however; most BSI were not associated with recognised complications of HTLV-1 infection. Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Long-term follow-up of HTLV-1 proviral load in asymptomatic carriers and in incident cases of HAM/TSP: what is its relevance as a prognostic marker for neurologic disease?

PubMed

Martins, Marina Lobato; Guimarães, Jacqueline Cronemberger; Ribas, João Gabriel; Romanelli, Luiz Cláudio Ferreira; de Freitas Carneiro-Proietti, Anna Bárbara

2017-02-01

HTLV-1 proviral load (pvl) is an important risk marker for HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), but its value as prognostic marker is not well defined. Long-term prospective cohort studies are necessary to clarify this question. Here, we analyzed HTLV-1 pvl in the peripheral blood of 82 asymptomatic carriers (AC; 351 samples), 12 HAM/TSP patients (HAM; 46 samples), and six incident cases of HAM/TSP (iHAM), with serial samples collected before (n = 10) and after (n = 20) the disease onset. The mean interval of follow-up was 10 years in the AC group and 8 years in HAM and iHAM groups. pvl was not significantly different between the first and last measurements in the three groups, but there was a trend to decrease over time. Coefficient of variation of pvl was significantly lower in the AC group than in HAM (p = 0.015) and iHAM (p = 0.022) patients. AC and HAM individuals showed a significant and strong positive correlation between the first and last measurements of pvl, but not iHAM subjects. All individuals who developed HAM/TSP during the follow-up had high pvl level (>1 %) before the onset of disease, but a typical increase in pvl was not observed in that period. The data suggest that there is a trend to reach an equilibrium plateau of pvl over time, characteristic of each individual. A significant rate of AC keeps high pvl levels for a long time without developing clinical symptoms associated to HTLV-1 infection. Thus, serial quantification of pvl in the peripheral blood does not seem to be a good prognostic marker for HAM/TSP.

Hepatitis C Virus Core Protein Promotes miR-122 Destabilization by Inhibiting GLD-2

PubMed Central

Kim, Geon-Woo; Lee, Seung-Hoon; Cho, Hee; Kim, Minwoo; Shin, Eui-Cheol; Oh, Jong-Won

2016-01-01

The liver-specific microRNA miR-122, which has essential roles in liver development and metabolism, is a key proviral factor for hepatitis C virus (HCV). Despite its crucial role in the liver and HCV life cycle, little is known about the molecular mechanism of miR-122 expression regulation by HCV infection. Here, we show that the HCV core protein downregulates the abundance of miR-122 by promoting its destabilization via the inhibition of GLD-2, a non-canonical cytoplasmic poly(A) polymerase. The decrease in miR-122 expression resulted in the dysregulation of the known functions of miR-122, including its proviral activity for HCV. By high-throughput sequencing of small RNAs from human liver biopsies, we found that the 22-nucleotide (nt) prototype miR-122 is modified at its 3′ end by 3′-terminal non-templated and templated nucleotide additions. Remarkably, the proportion of miR-122 isomers bearing a single nucleotide tail of any ribonucleotide decreased in liver specimens from patients with HCV. We found that these single-nucleotide-tailed miR-122 isomers display increased miRNA activity and stability over the 22-nt prototype miR-122 and that the 3′-terminal extension is catalyzed by the unique terminal nucleotidyl transferase activity of GLD-2, which is capable of adding any single ribonucleotide without preference of adenylate to the miR-122 3′ end. The HCV core protein specifically inhibited GLD-2, and its interaction with GLD-2 in the cytoplasm was found to be responsible for miR-122 downregulation. Collectively, our results provide new insights into the regulatory role of the HCV core protein in controlling viral RNA abundance and miR-122 functions through miR-122 stability modulation. PMID:27366906

HIV-1 induction-maintenance at the lymph node level: the "Apollo-97" Study.

PubMed

Lafeuillade, A; Poggi, C; Chadapaud, S; Hittinger, G; Chouraqui, M; Delbeke, E

2001-10-01

To assess the effects of five-drug combination therapy on HIV-1 load in lymph nodes and subsequent maintenance with four and three drugs. Ten pharmacotherapeutically naive patients received a combination of zidovudine, lamivudine, didanosine, ritonavir, and saquinavir for 24 weeks, then zidovudine, lamivudine, didanosine, and saquinavir for the next 24 weeks, and finally zidovudine, lamivudine, and saquinavir for the last 24 weeks. HIV-1 RNA in lymph nodes was measured using quantitative polymerase chain reaction (PCR) at baseline, after 12, 24, 48, and 78 weeks. Plasma HIV-1 RNA, proviral DNA in peripheral blood mononuclear cells (PBMCs), circulating lymphocyte subsets, and protease inhibitor levels in blood were also regularly measured. Genotypic resistance was assessed in the different compartments in 2 patients who were failed by therapy. HIV-1 RNA decreased in lymph nodes in 9 patients and was stable in 1 despite initial control of plasma replication <20 copies/ml in each patient. Lymph node levels rebounded in 1 patient at week 72 as a result of lack of adherence and remained stable in the 8 others despite maintenance regimens. This represents a mean drop of -3.17 log in lymph nodes for the 8 patients maintaining undetectable viremia at 72 weeks. In the patient with stable lymph node viral RNA, selection of the M184V mutation was demonstrated at this level before detection in plasma and low blood saquinavir levels were found throughout the study. Continuous improvements in immune parameters were observed in all cases, although PBMC proviral DNA levels either showed a continuous decrease or stabilized to a plateau. More complex regimens do not perform better in lymph nodes than classic triple therapy. The persistence of HIV-1 RNA in lymph nodes could be related with cellular resistance mechanisms rather than an insufficient potency of the regimens.

Effect of vitamin supplements on HIV shedding in breast milk123

PubMed Central

Koulinska, Irene N; Aboud, Said; Murrin, Clare; Bosch, Ronald J; Manji, Karim P; Fawzi, Wafaie W

2010-01-01

Background: Supplementation in lactating HIV-1–infected women with preformed vitamin A and β-carotene (VA/BC) increases the risk of mother-to-child transmission of HIV through breastfeeding. Identifying a biological mechanism to explain this unexpected finding would lend support to a causal effect. Objective: The aim of the study was to evaluate the effect of VA/BC or multivitamin (B complex, vitamin C, and vitamin E) supplementation of HIV-infected women on HIV shedding in breast milk during the first 2 y postpartum. Design: We quantified viral (cell-free) and proviral (cell-associated) HIV loads in breast-milk samples collected ≤15 d after delivery and every 3 mo thereafter from 594 Tanzanian HIV-1–infected women who participated in a randomized trial. Women received 1 of the following 4 daily oral regimens in a 2 × 2 factorial fashion during pregnancy and throughout the first 2 y postpartum: multivitamin, VA/BC, multivitamin including VA/BC, or placebo. Results: The proportion of breast-milk samples with detectable viral load was significantly higher in women who received VA/BC (51.3%) than in women who were not assigned to VA/BC (44.8%; P = 0.02). The effect was apparent ≥6 mo postpartum (relative risk: 1.34; 95% CI: 1.04, 1.73). No associations with proviral load were observed. The multivitamin had no effects. In observational analyses, β-carotene but not retinol breast-milk concentrations were significantly associated with an increased viral load in milk. Conclusions: VA/BC supplementation in lactating women increases the HIV load in breast milk. This finding contributes to explaining the adverse effect of VA/BC on mother-to-child transmission. β-Carotene appears to have an effect on breast-milk viral load, independent of preformed vitamin A. This trial was registered at clinicaltrials.gov as NCT00197756. PMID:20739426

Development of a recombinase polymerase amplification lateral flow dipstick (RPA-LFD) for the field diagnosis of caprine arthritis-encephalitis virus (CAEV) infection.

PubMed

Tu, Po-An; Shiu, Jia-Shian; Lee, Shu-Hwae; Pang, Victor Fei; Wang, De-Chi; Wang, Pei-Hwa

2017-05-01

Caprine arthritis-encephalitis (CAE) in goats is a complex disease syndrome caused by a lentivirus. This persistent viral infection results in arthritis in adult goats and encephalitis in lambs. The prognosis for the encephalitic form is normally poor, and this form of the disease has caused substantial economic losses for goat farmers. Hence, a more efficient detection platform based on recombinase polymerase amplification (RPA) and a lateral flow dipstick (LFD) was developed in the present study for detecting the proviral DNA of caprine arthritis-encephalitis virus (CAEV). Under the optimal incubation conditions, specifically, 30min at 37°C for RPA followed by 5min at room temperature for LFD, the assay was found to be sensitive to a lower limit of 80pg of total DNA and 10 copies of plasmid DNA. Furthermore, there was no cross-reaction with other tested viruses, including goat pox virus and bovine leukemia virus. Given its simplicity and portability, this RPA-LFD protocol can serve as an alternative tool to ELISA for the primary screening of CAEV, one that is suitable for both laboratory and field application. When the RPA-LFD was applied in parallel with serological ELISA for the detection of CAEV in field samples, the RPA-LFD assay exhibited a higher sensitivity than the traditional method, and 82% of the 200 samples collected in Taiwan were found to be positive. To our knowledge, this is the first report providing evidence to support the use of an RPA-LFD assay as a specific and sensitive platform for detecting CAEV proviral DNA in goats in a faster manner, one that is also applicable for on-site utilization at farms and that should be useful in both eradication programs and epidemiological studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Transgenic breeding of anti-Bombyx mori L. nuclear polyhedrosis virus silkworm Bombyx mori.

PubMed

Yang, Huijuan; Fan, Wei; Wei, Hao; Zhang, Jinwei; Zhou, Zhonghua; Li, Jianying; Lin, Jianrong; Ding, Nong; Zhong, Boxiong

2008-10-01

Silkworm strains resistant to Bombyx mori L. nuclear polyhedrosis virus were obtained through transgenic experiments. piggyBac transposon with an A3 promoter were randomly inserted into the silkworm, driving the enhanced green fluorescent protein (EGFP) reporter gene into the silkworm genome. Polymerase chain reaction results verified the insertion of the extraneous EGFP gene, and fluorescence microscopy showed that the EGFP was expressed in the midgut tissue. The morbidity ratio of the nuclear polyhedrosis decreased from 90% in the original silkworm strain to 66.7% in the transgenic silkworm strain. Compared with the resistance to the Bombyx mori L. nuclear polyhedrosis virus in the Qiufeng strain, which is commonly used in the production, there was an increase of 33 centesimal points in the transgenic silkworms. The antivirotic character in the Chunhua x Qiuyue strain, which was bred from a different transgenic family, was about 10 centesimal points higher than that in the Qiufeng x Baiyu, another crossbreed used in production. Our results indicated a good application value of the transposon-inserted mutation in the breeding of anti-BmNPV silkworm strain.

An Incremental High-Utility Mining Algorithm with Transaction Insertion

PubMed Central

Gan, Wensheng; Zhang, Binbin

2015-01-01

Association-rule mining is commonly used to discover useful and meaningful patterns from a very large database. It only considers the occurrence frequencies of items to reveal the relationships among itemsets. Traditional association-rule mining is, however, not suitable in real-world applications since the purchased items from a customer may have various factors, such as profit or quantity. High-utility mining was designed to solve the limitations of association-rule mining by considering both the quantity and profit measures. Most algorithms of high-utility mining are designed to handle the static database. Fewer researches handle the dynamic high-utility mining with transaction insertion, thus requiring the computations of database rescan and combination explosion of pattern-growth mechanism. In this paper, an efficient incremental algorithm with transaction insertion is designed to reduce computations without candidate generation based on the utility-list structures. The enumeration tree and the relationships between 2-itemsets are also adopted in the proposed algorithm to speed up the computations. Several experiments are conducted to show the performance of the proposed algorithm in terms of runtime, memory consumption, and number of generated patterns. PMID:25811038

Diagnostic Lumbar Puncture

PubMed Central

Doherty, Carolynne M; Forbes, Raeburn B

2014-01-01

Diagnostic Lumbar Puncture is one of the most commonly performed invasive tests in clinical medicine. Evaluation of an acute headache and investigation of inflammatory or infectious disease of the nervous system are the most common indications. Serious complications are rare, and correct technique will minimise diagnostic error and maximise patient comfort. We review the technique of diagnostic Lumbar Puncture including anatomy, needle selection, needle insertion, measurement of opening pressure, Cerebrospinal Fluid (CSF) specimen handling and after care. We also make some quality improvement suggestions for those designing services incorporating diagnostic Lumbar Puncture. PMID:25075138

Microorganisms present on peripheral intravenous needleless connectors in the clinical environment.

PubMed

Slater, Karen; Cooke, Marie; Whitby, Michael; Fullerton, Fiona; Douglas, Joel; Hay, Jennine; Rickard, Claire

2017-08-01

The aim of this study was to quantify culturable microorganisms on needleless connectors (NCs) attached to peripheral intravenous catheters in hospitalized adult medical patients. Half (50%) of 40 NCs were contaminated with microorganisms commonly found on the skin or mouth. Staphylococcus capitis and Staphylococcus epidermidis were most commonly isolated. Emergency department insertion and higher patient dependency were statistically associated with positive NC microorganism growth. These results reaffirm the need for NC decontamination prior to access. Crown Copyright © 2017. Published by Elsevier Inc. All rights reserved.

[Data Mining-revealed Characteristics of Clinical Application of Scalp Acupuncture].

PubMed

Wang, Qiong; Xing, Hai-Jiao; Bao, Na; Kong, Ling-Juan; Jia, Ye-Juan; Yang, Ke; Sun, Yan-Hui; Wang, Jian-Ling; Shi, Jing; Li, Xiao-Feng; Xu, Jing; Zhang, Xuan-Ping; Zhang, Xin; Jia, Chun-Sheng; Li, Ren-Ling

2018-03-25

To explore the regularity and characteristics of clinical application of scalp acupuncture therapy for different types of clinical conditions so as to provide a reference for clinical practice. In the present study, "head acupuncture" and"scalp acupuncture" were used as the keywords to search papers and academic dissertations having definite standards for diagnosis and therapeutic effect assessment and published in journals and academic conferences collected in database China National Knowledge Internet(CNKI) from January 1 of 1959 to December 31 of 2016, followed by constructing a database after sorting, screening, recording, extracting, and statistical analysis by using a computer. Then, the data mining was conducted for summarizing the indications of disease categories, involved medical departments, needle-insertion methods, needle manipulation techniques, academic schools, and clinical efficacy of scalp acupuncture therapy. As a result, a total of 587 papers met our including criteria were analyzed. The scalp acupuncture therapy was widely employed in the treatment of various clinical conditions of different departments, with the application frequency being the internal medicine (438 times), surgery (75 times), pediatrics (44 times), etc. Of the indicated 102 types of clinical problems, 55 belong to the internal medicine, constituting of 53.92%, particularly the cerebral apoplexy and its sequelae with the top application frequency being 102 and 115 times, respectively. In terms of needle inserting methods mentioned in partial papers (most papers do not mention), fingernail-pressing-aided needle insertion, needle-twirling insertion, fingers-squeezed-needle insertion, particularly the swiftly rotating needle insertion and rapid needle-propelling insertion were most commonly used.Regarding the needle manipulation method, rapid needle twirling technique was frequently employed, usually at a frequency of approximately 200 times per min. In regard to the academic schools, JIAO Shun-fa's scalp acupuncture system was most frequently used, followed by the international standardized scalp acupuncture. The therapeutic effect of scalp acupuncture is effective in the treatment of different conditions of various departments, especially those of the dermatology and gynecology. Scalp acupuncture has superiority in the treatment disorders of the internal medicine and has been demonstrated to have positive effects for many types of problems, particularly for apoplexy and its sequelae. Rapid needle-propelling insertion and rapid needle-twirling technique are often employed.

The insertion of self expanding metal stents with flexible bronchoscopy under sedation for malignant tracheobronchial stenosis: a single-center retrospective analysis.

PubMed

McGrath, Emmet E; Warriner, David; Anderson, Paul

2012-02-01

To describe a 10-year experience of inserting Ultraflex™ self-expanding metal stents (SEMS) under sedation using flexible bronchoscopy for the treatment of malignant tracheobronchial stenosis in a tertiary referral centre. Medical notes were retrospectively reviewed for all patients who underwent SEMS insertion between 1999 and 2009. A data analysis of 68 patients who had Ultraflex™ SEMS inserted under sedation was completed. Thirty three males and 35 females with a mean age of 67.9 years (range 35-94) presented with features including dyspnea/respiratory distress (39 patients), stridor (16 patients) and hemoptysis/dyspnea (13 patients). Etiology of stenosis included lung cancer (46 patients) esophageal cancer (14 patients) and other malignancies (8 patients). Mean dose of midazolam administered was 5mg (range 0-10mg). The trachea was the most common site of stent insertion followed by the right and left main bronchus, respectively. Adjuvant laser therapy was applied at some stage in 31% of all cases, and chemotherapy and/or radiotherapy was administered to at least 64% of patients with malignant disease. Hemoptysis and stent migration were the most frequent complications (5 and 4 patients, respectively). The mean survival time of stented non-small cell lung cancer (NSCLC) patients was 214 days (range 5-1233) and that of esophageal malignancy was 70 days (range 12-249). Mean pack-year history of individuals with lung cancer requiring stent insertion was 37 (range 2-100). Ultraflex stents offer a safe and effective therapy for patients who are inoperable or unresectable that otherwise would have no alternative therapy. It has an immediate beneficial effect upon patients, not only through symptom relief but, in some, through prolongation of life. Survival data is no worse than other studies using different varieties of stents and insertion techniques indicating its longer-term efficacy. Moreover, this report highlights the feasibility of performing this procedure successfully in a respiratory unit, without the need for general anesthesia. Copyright © 2011 SEPAR. Published by Elsevier Espana. All rights reserved.

Effectiveness of the levonorgestrel-releasing intrauterine system in the treatment of adenomyosis diagnosed and monitored by magnetic resonance imaging.

PubMed

Bragheto, Aristides M; Caserta, Nelson; Bahamondes, Luis; Petta, Carlos A

2007-09-01

This study was conducted to evaluate the effect of the levonorgestrel-releasing intrauterine system (LNG-IUS) on adenomyotic lesions diagnosed and monitored by magnetic resonance imaging (MRI). LNG-IUS was inserted during menstrual bleeding in 29 women, 24 to 46 years of age, with MRI-diagnosed adenomyosis associated with menorrhagia and dysmenorrhea. Clinical evaluations were carried out at baseline and at 3 and 6 months postinsertion. MRI was performed at baseline and at 6 months postinsertion and was used to calculate junctional zone thickness (in mm), to define the junctional zone borders, to identify the presence of high-signal foci on T(2)-weighted images and to calculate uterine volume (in mL). A significant reduction of 24.2% in junctional zone thickness was observed (p<.0001); however, no significant decrease in uterine volume was observed (142.6 mL vs. 136.4 mL; p=.2077) between baseline and the 6-month evaluation. A significant decrease in pain score was observed at 3 and 6 months after insertion (p<.0001); however, six women continued to report pain scores >3 at 6 months of observation. At 3 months of use, the most common bleeding pattern was spotting, and at 6 months of observation, oligomenorrhea was the most common pattern observed, although spotting was present in one third of the women. The insertion of an LNG-IUS led to a reduction in pain and abnormal bleeding associated with adenomyosis. MRI was useful for monitoring response of adenomyotic lesions to the LNG-IUS.

Rectal suppository insertion: the reliability of the evidence as a basis for nursing practice.

PubMed

Bradshaw, Ann; Price, Lynda

2007-01-01

This paper considers the correct method for inserting a rectal suppository, both as a medication and also to achieve bowel evacuation. The aim is to find out whether the correct method is blunt end or pointed end foremost. It follows from a question raised by a third year student nurse. In the classroom, she had been taught that the correct method for the administration of a suppository for systemic absorption was to insert it blunt end foremost into the rectum. However, if the suppository was to be used for evacuant purposes, it should be given pointed end foremost. In clinical practice, however, she was told the suppository should always be inserted pointed end foremost in all cases, whatever the purpose. This article seeks to clarify the dilemma by examining the sources of evidence underpinning different methods for inserting a rectal suppository. Hence, the literature on the insertion of rectal suppositories was gathered as systematically as possible from medical journals and textbooks, nursing journals and textbooks and manufacturers' information to patients. Having gathered the literature, this was examined, appraised and critically analysed for rigour, coherence and reliability. The review of the literature appears to show that evidence adduced for inserting the suppository blunt end foremost derives from one study published in the Lancet in 1991, which challenged 'commonsense'. There did not appear to be other, more recent research. On the other hand, manufacturers' information to patients states generally that the suppository should be inserted pointed end foremost. This has direct relevance for the administration of suppositories and also raises questions as to how research may become integrated into healthcare practice without adequate justification. An article published in the Lancet in 1991 has had a fundamental effect on nursing practice, but has not been subject to scrutiny. The advice given in this Lancet article differs from that currently given by most manufacturers of suppositories, which involves the terms of their product licence. Hence, there is a potential for problems with legal liability should an untoward event arise. Inserting rectal suppositories, whether as a medication or to achieve bowel evacuation, is a very common healthcare practice. Currently, there is inconsistency and discrepancy in the correct method for this procedure in both nursing education and practice. This paper examines the reliability of existing evidence and shows the need for further work in order to provide a reliable evidence base for this commonplace clinical procedure.

Electron Transfer Governed Crystal Transformation of Tungsten Trioxide upon Li Ions Intercalation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Zhiguo; He, Yang; Gu, Meng

2016-09-21

Reversible insertion/extraction of ions into a host lattice constitutes the fundamental operating principle of rechargeable battery and electrochromic materials. It is far more commonly observed that insertion of ions into a host lattice can lead to structural evolution of the host lattice, and for the most cases such a lattice evolution is subtle. However, it has never been clear as what kind of factors to control such a lattice structural evolution. Based on tungsten trioxide (WO3) model crystal, we use in situ transmission electron microscopy (TEM) and first principles calculation to explore the nature of Li ions intercalation induced crystalmore » symmetry evolution of WO3. We discovered that Li insertion into the octahedral cavity of WO3 lattice will lead to a low to high symmetry transition, featuring a sequential monoclinic→tetragonal→cubic phase transition. The first principle calculation reveals that the phase transition is essentially governed by the electron transfer from Li to the WO6 octahedrons, which effectively leads to the weakening the W-O bond and modifying system band structure, resulting in an insulator to metal transition. The observation of the electronic effect on crystal symmetry and conductivity is significant, providing deep insights on the intercalation reactions in secondary rechargeable ion batteries and the approach for tailoring the functionalities of material based on insertion of ions in the lattice.« less

Interrogation of electrical connector faults using miniaturized UWB sources

NASA Astrophysics Data System (ADS)

Tokgöz, Çaǧata; Dardona, Sameh

2017-01-01

A diagnostic method for the detection, identification, and characterization of precursors of faults due to partial insertion of pin-socket contacts within electrical connectors commonly used in avionics systems is presented. It is demonstrated that a miniaturized ultrawideband (UWB) source and a minispectrum analyzer can be employed to measure resonant frequency shifts in connector S parameters as a small and low-cost alternative to a large and expensive network analyzer. The transfer function of an electrical connector is represented as a ratio of the spectra measured using the spectrum analyzer with and without the connector. Alternatively, the transfer function is derived in terms of the connector S parameters and the reflection coefficients at both ports of the connector. The transfer function data obtained using this derivation agreed well with its representation as a measured spectral ratio. The derivation enabled the extraction of the connector S parameters from the measured transfer function data as a function of the insertion depth of a pin-socket contact within the connector. In comparison with the S parameters measured directly using a network analyzer at multiple insertion depths, the S parameters extracted from the measured transfer function showed consistent and reliable representation of the electrical connector fault. The results demonstrate the potential of integrating a low-cost miniaturized UWB device into a connector harness for real-time detection of precursors to partially inserted connector faults.

Percutaneous transfemoral repositioning of malpositioned central venous catheters.

PubMed

Hartnell, G G; Roizental, M

1995-04-01

Central venous catheters inserted by blind surgical placement may not advance into a satisfactory position and may require repositioning. Malpositioning via surgical insertion is common in patients in whom central venous catheters have previously been placed, as these patients are more likely to have central venous thrombosis and distortion of central venous anatomy. This is less of a problem when catheter placement is guided by imaging; however, even when insertion is satisfactory, central venous catheters may become displaced spontaneously after insertion (Fig. 1). Repositioning can be effected by direct manipulation using guidewires or tip-deflecting wires [1, 2], by manipulation via a transfemoral venous approach [3-5], and by injection of contrast material or saline [6]. Limitations of the direct approach include (1) the number and type of maneuvers that can be performed to effect repositioning when anatomy is distorted, (2) difficulty in accessing the catheter, and (3) the risk of introducing infection. Moreover, these patients are often immunosuppressed, and there is a risk of introducing infection by exposing and directly manipulating the venous catheter. Vigorous injection of contrast material or saline may be unsuccessful for the same reasons: It seldom exerts sufficient force to reposition large-caliber central venous catheters and may cause vessel damage or rupture if injection is made into a small or thrombosed vessel. We illustrate several alternative methods for catheter repositioning via a transfemoral venous approach.

Highly efficient CRISPR/HDR-mediated knock-in for mouse embryonic stem cells and zygotes.

PubMed

Wang, Bangmei; Li, Kunyu; Wang, Amy; Reiser, Michelle; Saunders, Thom; Lockey, Richard F; Wang, Jia-Wang

2015-10-01

The clustered regularly interspaced short palindromic repeat (CRISPR) gene editing technique, based on the non-homologous end-joining (NHEJ) repair pathway, has been used to generate gene knock-outs with variable sizes of small insertion/deletions with high efficiency. More precise genome editing, either the insertion or deletion of a desired fragment, can be done by combining the homology-directed-repair (HDR) pathway with CRISPR cleavage. However, HDR-mediated gene knock-in experiments are typically inefficient, and there have been no reports of successful gene knock-in with DNA fragments larger than 4 kb. Here, we describe the targeted insertion of large DNA fragments (7.4 and 5.8 kb) into the genomes of mouse embryonic stem (ES) cells and zygotes, respectively, using the CRISPR/HDR technique without NHEJ inhibitors. Our data show that CRISPR/HDR without NHEJ inhibitors can result in highly efficient gene knock-in, equivalent to CRISPR/HDR with NHEJ inhibitors. Although NHEJ is the dominant repair pathway associated with CRISPR-mediated double-strand breaks (DSBs), and biallelic gene knock-ins are common, NHEJ and biallelic gene knock-ins were not detected. Our results demonstrate that efficient targeted insertion of large DNA fragments without NHEJ inhibitors is possible, a result that should stimulate interest in understanding the mechanisms of high efficiency CRISPR targeting in general.

Sequence variations of the partially dominant DELLA gene Rht-B1c in wheat and their functional impacts

PubMed Central

Ma, Zhengqiang

2013-01-01

Rht-B1c, allelic to the DELLA protein-encoding gene Rht-B1a, is a natural mutation documented in common wheat (Triticum aestivum). It confers variation to a number of traits related to cell and plant morphology, seed dormancy, and photosynthesis. The present study was conducted to examine the sequence variations of Rht-B1c and their functional impacts. The results showed that Rht-B1c was partially dominant or co-dominant for plant height, and exhibited an increased dwarfing effect. At the sequence level, Rht-B1c differed from Rht-B1a by one 2kb Veju retrotransposon insertion, three coding region single nucleotide polymorphisms (SNPs), one 197bp insertion, and four SNPs in the 1kb upstream sequence. Haplotype investigations, association analyses, transient expression assays, and expression profiling showed that the Veju insertion was primarily responsible for the extreme dwarfing effect. It was found that the Veju insertion changed processing of the Rht-B1c transcripts and resulted in DELLA motif primary structure disruption. Expression assays showed that Rht-B1c caused reduction of total Rht-1 transcript levels, and up-regulation of GATA-like transcription factors and genes positively regulated by these factors, suggesting that one way in which Rht-1 proteins affect plant growth and development is through GATA-like transcription factor regulation. PMID:23918966

Evaluation of torque maintenance of abutment and cylinder screws with Morse taper implants.

PubMed

Ferreira, Mayara Barbosa; Delben, Juliana Aparecida; Barão, Valentim Adelino Ricardo; Faverani, Leonardo Perez; Dos Santos, Paulo Henrique; Assunção, Wirley Gonçalves

2012-11-01

The screw loosening of implant-supported prostheses is a common mechanical failure and is related to several factors as insertion torque and preload. The aim of this study was to evaluate the torque maintenance of retention screws of tapered abutments and cylinders of Morse taper implants submitted to retightening and detorque measurements. Two groups were obtained (n = 12): group I-tapered abutment connected to the implant with titanium retention screw and group II-cylinder with metallic base connected to tapered abutment with titanium retention screw. The detorque values were measured by an analogic torque gauge after 3 minutes of torque insertion. The detorque was measured 10 times for each retention screw of groups I and II, totalizing 120 detorque measurements in each group. Data were submitted to ANOVA and Fisher exact test (P < 0.05). Both groups presented reduced detorque value (P < 0.05) in comparison to the insertion torque in all measurement periods. There was a statistically significant difference (P < 0.05) between the detorque values of the first measurement and the other measurement periods for the abutment screw. However, there was no statistically significant difference (P > 0.05) for the detorque values of all measurement periods for the cylinder screw. In conclusion, the abutment and cylinder screws exhibited torque loss after insertion, which indicates the need for retightening during function of the implant-supported prostheses.

Impact of the Central Polypurine Tract on the Kinetics of Human Immunodeficiency Virus Type 1 Vector Transduction

PubMed Central

Van Maele, Bénédicte; De Rijck, Jan; De Clercq, Erik; Debyser, Zeger

2003-01-01

Lentiviral vectors derived from human immunodeficiency virus type 1 (HIV-1) show great promise as gene carriers for future gene therapy. Insertion of a fragment containing the central polypurine tract (cPPT) in HIV-1 vector constructs is known to enhance transduction efficiency drastically, reportedly by facilitating the nuclear import of HIV-1 cDNA through a central DNA flap. We have studied the impact of the cPPT on the kinetics of HIV-1 vector transduction by real-time PCR. The kinetics of total HIV-1 DNA, two-long-terminal-repeat (2-LTR) circles, and, by an Alu-PCR, integrated proviral DNA were monitored. About 6 to 12 h after transduction, the total HIV-1 DNA reached a maximum level, followed by a steep decrease. The 2-LTR circles peaked after 24 to 48 h and were diluted upon cell division. Integration of HIV-1 DNA was first detected at 12 h postinfection. When HIV-1 vectors that contained the cPPT were used, DNA synthesis was similar but a threefold higher amount of 2-LTR circles was detected, confirming the impact on nuclear import. Moreover, a 10-fold increase in the amount of integrated DNA was observed in the presence of the cPPT. Only in the absence of the cPPT was a saturation in 2-LTR circle formation seen at a high multiplicity of infection, suggesting a role for the cPPT in overcoming a barrier to the nuclear import of HIV-1 DNA. A major effect of the central DNA flap on the juxtaposition of both LTRs is unlikely, since transduction with HIV-1 vectors containing ectopic cPPT fragments resulted in increased amounts of 2-LTR circles as well as integrated DNA. Inhibitors of transduction by cPPT-containing HIV vectors were also studied by real-time PCR. The reverse transcriptase inhibitor azidothymidine (AZT) and the nonnucleoside reverse transcriptase inhibitor α-APA clearly inhibited viral DNA synthesis, whereas integrase inhibitors such as the diketo acid L-708,906 and the pyranodipyrimidine V-165 specifically inhibited integration. PMID:12663775

Antiretroviral Agents Effectively Block HIV Replication after Cell-to-Cell Transfer

PubMed Central

Permanyer, Marc; Ballana, Ester; Ruiz, Alba; Badia, Roger; Riveira-Munoz, Eva; Gonzalo, Encarna; Clotet, Bonaventura

2012-01-01

Cell-to-cell transmission of HIV has been proposed as a mechanism contributing to virus escape to the action of antiretrovirals and a mode of HIV persistence during antiretroviral therapy. Here, cocultures of infected HIV-1 cells with primary CD4+ T cells or lymphoid cells were used to evaluate virus transmission and the effect of known antiretrovirals. Transfer of HIV antigen from infected to uninfected cells was resistant to the reverse transcriptase inhibitors (RTIs) zidovudine (AZT) and tenofovir, but was blocked by the attachment inhibitor IgGb12. However, quantitative measurement of viral DNA production demonstrated that all anti-HIV agents blocked virus replication with similar potency to cell-free virus infections. Cell-free and cell-associated infections were equally sensitive to inhibition of viral replication when HIV-1 long terminal repeat (LTR)-driven green fluorescent protein (GFP) expression in target cells was measured. However, detection of GFP by flow cytometry may incorrectly estimate the efficacy of antiretrovirals in cell-associated virus transmission, due to replication-independent Tat-mediated LTR transactivation as a consequence of cell-to-cell events that did not occur in short-term (48-h) cell-free virus infections. In conclusion, common markers of virus replication may not accurately correlate and measure infectivity or drug efficacy in cell-to-cell virus transmission. When accurately quantified, active drugs blocked proviral DNA and virus replication in cell-to-cell transmission, recapitulating the efficacy of antiretrovirals in cell-free virus infections and in vivo. PMID:22696642

Determining the feline immunodeficiency virus (FIV) status of FIV-vaccinated cats using point-of-care antibody kits.

PubMed

Westman, Mark E; Malik, Richard; Hall, Evelyn; Sheehy, Paul A; Norris, Jacqueline M

2015-10-01

This study challenges the commonly held view that the feline immunodeficiency virus (FIV) infection status of FIV-vaccinated cats cannot be determined using point-of-care antibody test kits due to indistinguishable antibody production in FIV-vaccinated and naturally FIV-infected cats. The performance of three commercially available point-of-care antibody test kits was compared in a mixed population of FIV-vaccinated (n=119) and FIV-unvaccinated (n=239) cats in Australia. FIV infection status was assigned by considering the results of all antibody kits in concert with results from a commercially available PCR assay (FIV RealPCR™). Two lateral flow immunochromatography test kits (Witness FeLV/FIV; Anigen Rapid FIV/FeLV) had excellent overall sensitivity (100%; 100%) and specificity (98%; 100%) and could discern the true FIV infection status of cats, irrespective of FIV vaccination history. The lateral flow ELISA test kit (SNAP FIV/FeLV Combo) could not determine if antibodies detected were due to previous FIV vaccination, natural FIV infection, or both. The sensitivity and specificity of FIV RealPCR™ for detection of viral and proviral nucleic acid was 92% and 99%, respectively. These results will potentially change the way veterinary practitioners screen for FIV in jurisdictions where FIV vaccination is practiced, especially in shelter scenarios where the feasibility of mass screening is impacted by the cost of testing. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Selection for avian leukosis virus integration sites determines the clonal progression of B-cell lymphomas

PubMed Central

Malhotra, Sanandan; Justice, James; Morgan, Robin

2017-01-01

Avian leukosis virus (ALV) is a simple retrovirus that causes a wide range of tumors in chickens, the most common of which are B-cell lymphomas. The viral genome integrates into the host genome and uses its strong promoter and enhancer sequences to alter the expression of nearby genes, frequently inducing tumors. In this study, we compare the preferences for ALV integration sites in cultured cells and in tumors, by analysis of over 87,000 unique integration sites. In tissue culture we observed integration was relatively random with slight preferences for genes, transcription start sites and CpG islands. We also observed a preference for integrations in or near expressed and spliced genes. The integration pattern in cultured cells changed over the course of selection for oncogenic characteristics in tumors. In comparison to tissue culture, ALV integrations are more highly selected for proximity to transcription start sites in tumors. There is also a significant selection of ALV integrations away from CpG islands in the highly clonally expanded cells in tumors. Additionally, we utilized a high throughput method to quantify the magnitude of clonality in different stages of tumorigenesis. An ALV-induced tumor carries between 700 and 3000 unique integrations, with an average of 2.3 to 4 copies of proviral DNA per infected cell. We observed increasing tumor clonality during progression of B-cell lymphomas and identified gene players (especially TERT and MYB) and biological processes involved in tumor progression. PMID:29099869

Population dynamics of rhesus macaques and associated foamy virus in Bangladesh

PubMed Central

Feeroz, Mostafa M; Soliven, Khanh; Small, Christopher T; Engel, Gregory A; Andreina Pacheco, M; Yee, JoAnn L; Wang, Xiaoxing; Kamrul Hasan, M; Oh, Gunwha; Levine, Kathryn L; Rabiul Alam, SM; Craig, Karen L; Jackson, Dana L; Lee, Eun-Gyung; Barry, Peter A; Lerche, Nicholas W; Escalante, Ananias A; Matsen IV, Frederick A; Linial, Maxine L; Jones-Engel, Lisa

2013-01-01

Foamy viruses are complex retroviruses that have been shown to be transmitted from nonhuman primates to humans. In Bangladesh, infection with simian foamy virus (SFV) is ubiquitous among rhesus macaques, which come into contact with humans in diverse locations and contexts throughout the country. We analyzed microsatellite DNA from 126 macaques at six sites in Bangladesh in order to characterize geographic patterns of macaque population structure. We also included in this study 38 macaques owned by nomadic people who train them to perform for audiences. PCR was used to analyze a portion of the proviral gag gene from all SFV-positive macaques, and multiple clones were sequenced. Phylogenetic analysis was used to infer long-term patterns of viral transmission. Analyses of SFV gag gene sequences indicated that macaque populations from different areas harbor genetically distinct strains of SFV, suggesting that geographic features such as forest cover play a role in determining the dispersal of macaques and SFV. We also found evidence suggesting that humans traveling the region with performing macaques likely play a role in the translocation of macaques and SFV. Our studies found that individual animals can harbor more than one strain of SFV and that presence of more than one SFV strain is more common among older animals. Some macaques are infected with SFV that appears to be recombinant. These findings paint a more detailed picture of how geographic and sociocultural factors influence the spectrum of simian-borne retroviruses. PMID:26038465

Differences in crestal bone-to-implant contact following an under-drilling compared to an over-drilling protocol. A study in the rabbit tibia.

PubMed

Cohen, Omer; Ormianer, Zeev; Tal, Haim; Rothamel, Daniel; Weinreb, Miron; Moses, Ofer

2016-12-01

The objective of this study is to compare bone-to-implant contact (BIC) between implants inserted at high torque due to under-drilling of the crestal bone to those inserted at low torque due to over-drilling of the crestal bone. Forty implants with diameters of 3.75 mm (group A) or 3.55 mm (group B) were inserted in the proximal tibiae of NZW rabbits in two separate surgeries on day 0 or 21. Osteotomy of the crestal bone was finalized with a 3.65-mm drill. In group A, implants were inserted at torque ≥35 Ncm (under-drilling) and in group B with torque <10 Ncm (over-drilling). Implants and their surrounding bone were retrieved on day 42, thus creating 3- and 6-week observation periods, processed for non-decalcified histology and stained with toluidine blue. Crestal BIC (c-BIC) and total BIC (t-BIC) were measured. Wilcoxon test was used to evaluate differences between groups. Three weeks post-surgery, the mean c-BIC in group A was 16.3 ± 3.3 vs 31.5 ± 3.4 % in group B (P < 0.05). At 6 weeks, a similar trend was observed (group A: 28.7 ± 3.6 %; group B: 38.4 ± 4.9 %) (P > 0.05). No differences in t-BIC were noted at 3 weeks and at 6 weeks between the groups. Insertion of implants with an over-drilling protocol of the crestal aspect of the osteotomy resulted in increased short-term crestal bone-to-implant contact. Insertion of implants with a high torque following an under-drilling protocol, commonly used for immediate loading, may reduce crestal bone-to-implant contact at early healing stages.

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bhaway, Sarang M.; Qiang, Zhe; Xia, Yanfeng

Emergent lithium-ion (Li +) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li +, but in many cases these nanostructures evolve during electrochemical charging–discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporousmore » NiCo 2O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge–discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Anodes with larger ordered mesopores (17–28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. Furthermore, this preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; but, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge–discharge cycles leads to capacity decay in battery performance. We translate these multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge–discharge cycles.« less

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes

DOE PAGES

Bhaway, Sarang M.; Qiang, Zhe; Xia, Yanfeng; ...

2017-02-07

Emergent lithium-ion (Li +) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li +, but in many cases these nanostructures evolve during electrochemical charging–discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporousmore » NiCo 2O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge–discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Anodes with larger ordered mesopores (17–28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. Furthermore, this preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; but, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge–discharge cycles leads to capacity decay in battery performance. We translate these multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge–discharge cycles.« less

Structural and Kinetic Analysis of Nucleoside Triphosphate Incorporation Opposite an Abasic Site by Human Translesion DNA Polymerase η

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patra, Amritaj; Zhang, Qianqian; Lei, Li

2015-02-09

The most prevalent lesion in DNA is an abasic site resulting from glycolytic cleavage of a base. In a number of cellular studies, abasic sites preferentially code for dATP insertion (the “A rule”). In some cases frameshifts are also common. X-ray structures with abasic sites in oligonucleotides have been reported for several microbial and human DNA polymerases (pols), e.g. Dpo4, RB69, KlenTaq, yeast pol ι, human (h) pol ι, and human pol β. We reported previously that hpol η is a major pol involved in abasic site bypass (Choi, J.-Y., Lim, S., Kim, E. J., Jo, A., and Guengerich, F.more » P. (2010 J. Mol. Biol. 404, 34–44). hpol η inserted all four dNTPs in steady-state and pre-steady-state assays, preferentially inserting A and G. In LC-MS analysis of primer-template pairs, A and G were inserted but little C or T was inserted. Frameshifts were observed when an appropriate pyrimidine was positioned 5' to the abasic site in the template. In x-ray structures of hpol η with a non-hydrolyzable analog of dATP or dGTP opposite an abasic site, H-bonding was observed between the phosphate 5' to the abasic site and water H-bonded to N1 and N6 of A and N1 and O6 of G nucleoside triphosphate analogs, offering an explanation for what appears to be a “purine rule.” A structure was also obtained for an A inserted and bonded in the primer opposite the abasic site, but it did not pair with a 5' T in the template. Finally, we conclude that hpol η, a major copying enzyme with abasic sites, follows a purine rule, which can also lead to frameshifts. The phenomenon can be explained with H-bonds.« less

Operando Grazing Incidence Small-Angle X-ray Scattering/X-ray Diffraction of Model Ordered Mesoporous Lithium-Ion Battery Anodes.

PubMed

Bhaway, Sarang M; Qiang, Zhe; Xia, Yanfeng; Xia, Xuhui; Lee, Byeongdu; Yager, Kevin G; Zhang, Lihua; Kisslinger, Kim; Chen, Yu-Ming; Liu, Kewei; Zhu, Yu; Vogt, Bryan D

2017-02-28

Emergent lithium-ion (Li + ) batteries commonly rely on nanostructuring of the active electrode materials to decrease the Li + ion diffusion path length and to accommodate the strains associated with the insertion and de-insertion of Li + , but in many cases these nanostructures evolve during electrochemical charging-discharging. This change in the nanostructure can adversely impact performance, and challenges remain regarding how to control these changes from the perspective of morphological design. In order to address these questions, operando grazing-incidence small-angle X-ray scattering and X-ray diffraction (GISAXS/GIXD) were used to assess the structural evolution of a family of model ordered mesoporous NiCo 2 O 4 anode films during battery operation. The pore dimensions were systematically varied and appear to impact the stability of the ordered nanostructure during the cycling. For the anodes with small mesopores (≈9 nm), the ordered nanostructure collapses during the first two charge-discharge cycles, as determined from GISAXS. This collapse is accompanied by irreversible Li-ion insertion within the oxide framework, determined from GIXD and irreversible capacity loss. Conversely, anodes with larger ordered mesopores (17-28 nm) mostly maintained their nanostructure through the first two cycles with reversible Li-ion insertion. During the second cycle, there was a small additional deformation of the mesostructure. This preservation of the ordered structure lead to significant improvement in capacity retention during these first two cycles; however, a gradual loss in the ordered nanostructure from continuing deformation of the ordered structure during additional charge-discharge cycles leads to capacity decay in battery performance. These multiscale operando measurements provide insight into how changes at the atomic scale (lithium insertion and de-insertion) are translated to the nanostructure during battery operation. Moreover, small changes in the nanostructure can build up to significant morphological transformations that adversely impact battery performance through multiple charge-discharge cycles.

A single codon insertion in PICALM is associated with development of familial subvalvular aortic stenosis in Newfoundland dogs

USDA-ARS?s Scientific Manuscript database

Familial subvalvular aortic stenosis (SAS) is one of the most common congenital heart defects in dogs and is an inherited defect of Newfoundlands, golden retrievers and human children. Although SAS is known to be inherited, specific genes involved in Newfoundlands with SAS have not been defined. We ...

Can One Take the Logarithm or the Sine of a Dimensioned Quantity or a Unit? Dimensional Analysis Involving Transcendental Functions

ERIC Educational Resources Information Center

Matta, Cherif F.; Massa, Lou; Gubskaya, Anna V.; Knoll, Eva

2011-01-01

The fate of dimensions of dimensioned quantities that are inserted into the argument of transcendental functions such as logarithms, exponentiation, trigonometric, and hyperbolic functions is discussed. Emphasis is placed on common misconceptions that are not often systematically examined in undergraduate courses of physical sciences. The argument…

Young Adults' Linguistic Manipulation of English in Bangla in Bangladesh

ERIC Educational Resources Information Center

Sultana, Shaila

2014-01-01

It is commonly assumed in the print media that bilingual young adults in Bangladesh are subjugated by the colonial legacy of English and they are "polluting" Bangla, the national language of Bangladesh, by their indiscriminate insertion of English in it. However, this ethnographic study on a group of young adults in a university in…

Child Development and Structural Variation in the Human Genome

ERIC Educational Resources Information Center

Zhang, Ying; Haraksingh, Rajini; Grubert, Fabian; Abyzov, Alexej; Gerstein, Mark; Weissman, Sherman; Urban, Alexander E.

2013-01-01

Structural variation of the human genome sequence is the insertion, deletion, or rearrangement of stretches of DNA sequence sized from around 1,000 to millions of base pairs. Over the past few years, structural variation has been shown to be far more common in human genomes than previously thought. Very little is currently known about the effects…

Extravasation injuries.

PubMed

Chiu, Kenneth; Tindholdt, Tyge Tind; Tønseth, Kim Alexander

2016-02-09

It is common for an intravascular catheter to be inserted to administer various types of therapy. Extravasation occurs frequently, and in the most severe cases plastic surgeons are often summoned to assess the extent of the injury and the possibility for reconstruction. The Department of Plastic and Reconstructive Surgery at Oslo University Hospital assesses approximately 15 severe cases of this type each year.

Inserting Mastered Targets during Error Correction When Teaching Skills to Children with Autism

ERIC Educational Resources Information Center

Plaisance, Lauren; Lerman, Dorothea C.; Laudont, Courtney; Wu, Wai-Ling

2016-01-01

Research has identified a variety of effective approaches for responding to errors during discrete-trial training. In one commonly used method, the therapist delivers a prompt contingent on the occurrence of an incorrect response and then re-presents the trial so that the learner has an opportunity to perform the correct response independently.…

THE EFFECT OF A TARGETED KNOCKOUT MUTATION ON THE TRANSCRIPTIONAL PROFILE OF THE KIDNEY IN TSC2 MUTANT (EKER) RATS.

EPA Science Inventory

Renal cell carcinoma (RCC) is the most common tumor of the adult kidney, accounting for up to 80% of malignant renal neoplasms. Hereditary RCC in the Eker rat, which bear a number of cellular, molecular and phenotypic similarities to human RCC, results from an inherited insertion...

Exploring the Mathematics of Bouncing Balls

ERIC Educational Resources Information Center

Vinogradova, Natalya; Blaine, Larry G.

2010-01-01

A common textbook problem asks students to calculate the total distance traveled by a bouncing ball, from its initial release until it comes to rest, under the assumption that the height of each bounce is some fixed proportion "r" of the height of the previous bounce. The solution is found by inserting information about "r" and the height from…

Comparing Labor Insertion of Graduates from Two Areas of Knowledge in Three Mexican Localities

ERIC Educational Resources Information Center

Leal, Marco Aurelio Navarro; Roux, Ruth

2015-01-01

Engineering programs are commonly supported by higher education policy and planning initiatives on the grounds of a supposed saturation of the labor market by other types of educational programs. However, labor market saturation is dependent on the economic characteristics and the sociocultural capital of specific locations. The aims of this study…

Treatment of gallbladder stone with common bile duct stones in the laparoscopic era.

PubMed

Zhang, Wei-jie; Xu, Gui-fang; Huang, Qin; Luo, Kun-lun; Dong, Zhi-tao; Li, Jie-ming; Wu, Guo-zhong; Guan, Wen-xian

2015-01-26

Laparoscopic common bile duct exploration (LCBDE) for stone can be carried out by either laparoscopic transcystic stone extraction (LTSE) or laparoscopic choledochotomy (LC). It remains unknown as to which approach is optimal for management of gallbladder stone with common bile duct stones (CBDS) in Chinese patients. From May 2000 to February 2009, we prospective treated 346 consecutive patients with gallbladder stones and CBDS with laparoscopic cholecystectomy and LCBDE. Intraoperative findings, postoperative complications, postoperative hospital stay and costs were analyzed. Because of LCBDE failure,16 cases (4.6%) required open surgery. Of 330 successful LCBDE-treated patients, 237 underwent LTSE and 93 required LC. No mortality occurred in either group. The bile duct stone clearance rate was similar in both groups. Patients in the LTSE group were significantly younger and had fewer complications with smaller, fewer stones, shorter operative time and postoperative hospital stays, and lower costs, compared to those in the LC group. Compared with patients with T-tube insertion, patients in the LC group with primary closure had shorter operative time, shorter postoperative hospital stay, and lower costs. In cases requiring LCBDE, LTSE should be the first choice, whereas LC may be restricted to large, multiple stones. LC with primary closure without external drainage of the CBDS is as effective and safe as the T-tube insertion approach.

Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product

PubMed Central

Dailey, Tamara A.; Gerdes, Svetlana; Jahn, Dieter; O'Brian, Mark R.; Warren, Martin J.

2017-01-01

SUMMARY The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized. PMID:28123057

FELINE IMMUNODEFICIENCY VIRUS (FIV) IN WILD PALLAS’ CATS

PubMed Central

Brown, Meredith A.; Munkhtsog, Bariushaa; Troyer, Jennifer L.; Ross, Steve; Sellers, Rani; Fine, Amanda E.; Swanson, William F.; Roelke, Melody E.; O’Brien1, Stephen J.

2009-01-01

Feline immunodeficiency virus (FIV), a feline lentivirus related to HIV, causes immune dysfunction in domestic and wild cats. The Pallas’ cat is the only species from Asia known to harbor a species-specific strain of FIV designated FIVOma in natural populations. Here, a 25% seroprevalence of FIV is reported from 28 wild Mongolian Pallas’ cats sampled from 2000-2008. Phylogenetic analysis of proviral RT-Pol from eight FIVOma isolates from Mongolia, Russia, China and Kazakhstan reveals a unique monophyletic lineage of the virus within the Pallas’ cat population, most closely related to the African cheetah and leopard FIV strains. Histopathological examination of lymph node and spleen from infected and uninfected Pallas’ cats suggests that FIVOma causes immune depletion in its’ native host. PMID:19926144

Genotyping of feline leukemia virus in Mexican housecats.

PubMed

Ramírez, Hugo; Autran, Marcela; García, M Martha; Carmona, M Ángel; Rodríguez, Cecilia; Martínez, H Alejandro

2016-04-01

Feline leukemia virus (FeLV) is a retrovirus with variable rates of infection globally. DNA was obtained from cats' peripheral blood mononuclear cells, and proviral DNA of pol and env genes was detected using PCR. Seventy-six percent of cats scored positive for FeLV using env-PCR; and 54 %, by pol-PCR. Phylogenetic analysis of both regions identified sequences that correspond to a group that includes endogenous retroviruses. They form an independent branch and, therefore, a new group of endogenous viruses. Cat gender, age, outdoor access, and cohabitation with other cats were found to be significant risk factors associated with the disease. This strongly suggests that these FeLV genotypes are widely distributed in the studied feline population in Mexico.

Preventive and Therapeutic Strategies for Bovine Leukemia Virus: Lessons for HTLV

PubMed Central

Rodríguez, Sabrina M.; Florins, Arnaud; Gillet, Nicolas; de Brogniez, Alix; Sánchez-Alcaraz, María Teresa; Boxus, Mathieu; Boulanger, Fanny; Gutiérrez, Gerónimo; Trono, Karina; Alvarez, Irene; Vagnoni, Lucas; Willems, Luc

2011-01-01

Bovine leukemia virus (BLV) is a retrovirus closely related to the human T-lymphotropic virus type 1 (HTLV-1). BLV is a major animal health problem worldwide causing important economic losses. A series of attempts were developed to reduce prevalence, chiefly by eradication of infected cattle, segregation of BLV-free animals and vaccination. Although having been instrumental in regions such as the EU, these strategies were unsuccessful elsewhere mainly due to economic costs, management restrictions and lack of an efficient vaccine. This review, which summarizes the different attempts previously developed to decrease seroprevalence of BLV, may be informative for management of HTLV-1 infection. We also propose a new approach based on competitive infection with virus deletants aiming at reducing proviral loads. PMID:21994777

Effects of the HEET garment in the prevention of hypothermia in a porcine model.

PubMed

Johnson, Don; Gegel, Brian; Burgert, James; Duncklee, Geoffrey W; Robison, Ricci R; Lewis, Eric J; Crum, Paul M; Kuhns, William; Moore, Daniel; O'Brien, Scott; Elliott, Joel; Washington, Jason; Boyle, John; Seigler, Dale

2010-11-01

Hypothermia is a common battlefield trauma occurrence. This study compared the effectiveness of the hypothermia, environmental, exposure, and trauma (HEET) garment (Trident Industries, Beaufort, SC) with and without thermal inserts with a control group of two wool blankets in the prevention of hypothermia in a treated hypovolemic porcine model. Five female swine (Sus scrofa-Yorkshire cross) were assigned to each of three groups: HEET with thermal inserts (n=5); HEET without thermal inserts (n=5); or control (n=5). After the animals were anesthetized and stabilized for 30 min, the swine were hemorrhaged to a mean arterial pressure (MAP) of 30 mm Hg, simulating a battlefield injury. Hetastarch 6% (500 mL) was rapidly administered, simulating initial field resuscitation. One hour later, the animals' shed blood was reinfused, simulating transfusion at a field medical facility. The investigators moved the animal into a cooler set at 10°C ± 0.5°C. A pulmonary artery catheter was used to monitor core body temperature over a 6-h period. A repeated measures ANOVA and Tukey's post hoc test were used to analyze the data. There was a significant difference between the groups. At the end of 6h, the mean core temperature for the HEET with inserts group was 32.69°C ± 1.5; the HEET without inserts, 31.02°C ± 1.8; and control, 34.78°C ± 1.2 (P<0.05). While all groups became hypothermic, the wool blanket group was most effective in maintaining body temperature closer to normothermia. The HEET garments with and without heaters are ineffective in preventing hypothermia. Copyright © 2010 Elsevier Inc. All rights reserved.

Inserting pedicle screws in the upper thoracic spine without the use of fluoroscopy or image guidance. Is it safe?

PubMed

Schizas, Constantin; Theumann, Nicolas; Kosmopoulos, Victor

2007-05-01

Several studies have looked at accuracy of thoracic pedicle screw placement using fluoroscopy, image guidance, and anatomical landmarks. To our knowledge the upper thoracic spine (T1-T6) has not been specifically studied in the context of screw insertion and placement accuracy without the use of either image guidance or fluoroscopy. Our objective was to study the accuracy of upper thoracic screw placement without the use of fluoroscopy or image guidance, and report on implant related complications. A single surgeon inserted 60 screws in 13 consecutive non-scoliotic spine patients. These were the first 60 screws placed in the high thoracic spine in our institution. The most common diagnosis in our patient population was trauma. All screws were inserted using a modified Roy-Camille technique. Post-operative axial computed tomography (CT) images were obtained for each patient and analyzed by an independent senior radiologist for placement accuracy. Implant related complications were prospectively noted. No pedicle screw misplacement was found in 61.5% of the patients. In the remaining 38.5% of patients some misplacements were noted. Fifty-three screws out of the total 60 implanted were placed correctly within all the pedicle margins. The overall pedicle screw placement accuracy was 88.3% using our modified Roy-Camille technique. Five medial and two lateral violations were noted in the seven misplaced screws. One of the seven misplaced screws was considered to be questionable in terms of pedicle perforation. No implant related complications were noted. We found that inserting pedicle screws in the upper thoracic spine based solely on anatomical landmarks was safe with an accuracy comparable to that of published studies using image-guided navigation at the thoracic level.

The core domain as the force sensor of the yeast mechanosensitive TRP channel.

PubMed

Su, Zhenwei; Anishkin, Andriy; Kung, Ching; Saimi, Yoshiro

2011-12-01

Stretch-activated conductances are commonly encountered in careful electric recordings. Those of known proteins (TRP, MscL, MscS, K(2p), Kv, etc.) all share a core, which houses the ion pathway and the gate, but no recognizable force-sensing domain. Like animal TRPs, the yeast TRPY1 is polymodal, activated by stretch force, Ca(2+), etc. To test whether its S5-S6 core senses the stretch force, we tried to uncouple it from the peripheral domains by strategic peptide insertions to block the covalent core-periphery interactions. Insertion of long unstructured peptides should distort, if not disrupt, protein structures that transmit force. Such insertions between S6 and the C-terminal tail largely removed Ca(2+) activation, showing their effectiveness. However, such insertions as well as those between S5 and the N-terminal region, which includes S1-S4, did not significantly alter mechanosensitivity. Even insertions at both locations flanking the S5-S6 core did not much alter mechanosensitivity. Tryptophan scanning mutations in S5 were also constructed to perturb possible noncovalent core-periphery contacts. The testable tryptophan mutations also have little or no effects on mechanosensitivity. Boltzmann fits of the wild-type force-response curves agree with a structural homology model for a stretch-induced core expansion of ~2 nm(2) upon opening. We hypothesize that membrane tension pulls on S5-S6, expanding the core and opening the TRPY1 gate. The core being the major force sensor offers the simplest, though not the only, explanation of why so many channels of disparate designs are mechanically sensitive. Compared with the bacterial MscL, TRPY1 is much less sensitive to force, befitting a polymodal channel that relies on multiple stimuli.

A randomized, double-blind comparison study of EMLA and ELA-Max for topical anesthesia in children undergoing intravenous insertion.

PubMed

Koh, Jeffrey L; Harrison, Dale; Myers, Robert; Dembinski, Robert; Turner, Helen; McGraw, Terrence

2004-12-01

Topical anesthetics may help reduce discomfort associated with procedures involving needle-puncture, such as intravenous (i.v.) insertions, in children. EMLA cream has become a common, noninvasive therapy for topical anesthesia in children. ELA-Max is a recently introduced topical anesthetic cream marketed as being as effective in producing topical anesthesia after a 30-min application as EMLA is after a 60-min application. The purpose of this research was to compare ELA-Max at 30 min with EMLA at 60 min for providing topical anesthesia for i.v. insertions in children. Sixty children, ages 8-17 years, requiring an i.v. were randomized to receive either the 30 min application of ELA-Max (n = 30) or the 60 min application of EMLA (n = 30). Children rated any pain associated with the i.v. insertion using a 100-mm Visual Analog Scale (VAS). The anesthesiologist assessed the presence of blanching at the site and rated the difficulty of placing the i.v. There was no clinically or statistically significant difference in pain ratings (P = 0.87) between the ELA-Max (mean = 25.7) and the EMLA (mean = 26.8) groups. ELA-Max caused significantly (P = 0.04) less blanching than EMLA, however there was no difference in the anesthesiologists' rating of the difficulty of the i.v. placement between the groups (P = 0.73). Results from this study support the claim that a 30-min application of ELA-Max (with occlusion) is as effective as a 60-min application of EMLA (with occlusion) for producing topical anesthesia for i.v. insertion in children.

Characteristics Associated With Urethral and Rectal Gonorrhea and Chlamydia Diagnoses in a US National Sample of Gay and Bisexual Men: Results From the One Thousand Strong Panel.

PubMed

Grov, Christian; Cain, Demetria; Rendina, H Jonathan; Ventuneac, Ana; Parsons, Jeffrey T

2016-03-01

Gay and bisexual men are at elevated risk for Neisseria gonorrhoeae and Chlamydia trachomatis (GC/CT). Rectal GC/CT symptoms may be less obvious than urethral, increasing opportunities for undiagnosed rectal GC/CT. A US national sample of 1071 gay and bisexual men completed urethral and rectal GC/CT testing and an online survey. In total, 6.2% were GC/CT positive (5.3% rectal, 1.7% urethral). We calculated adjusted (for education, race, age, relationship status, having health insurance, and income) odds ratios for factors associated with rectal and urethral GC/CT diagnoses. Age was inversely associated with urethral and rectal GC/CT. Compared with white men, Latinos had significantly greater odds of rectal GC/CT. Among men who reported anal sex, those reporting only insertive sex had lower odds of rectal GC/CT than did men who reported both insertive and receptive. There was a positive association between rectal GC/CT and number of male partners (<12 months), the number of anal receptive acts, receptive condomless anal sex (CAS) acts, and insertive CAS acts. Compared with those who had engaged in both insertive and receptive anal sex, those who engaged in only receptive anal sex had lower odds of urethral GC/CT. The number of male partners (<12 months) was associated with increased odds of urethral GC/CT. Rectal GC/CT was more common than urethral and associated with some demographic and behavioral characteristics. Our finding that insertive CAS acts was associated with rectal GC/CT highlights that providers should screen patients for GC/CT via a full range of transmission routes, lest GC/CT go undiagnosed.

Identification of Genes Involved in Biofilm Formation and Respiration via Mini-Himar Transposon Mutagenesis of Geobacter sulfurreducens▿ †

PubMed Central

Rollefson, Janet B.; Levar, Caleb E.; Bond, Daniel R.

2009-01-01

Electron transfer from cells to metals and electrodes by the Fe(III)-reducing anaerobe Geobacter sulfurreducens requires proper expression of redox proteins and attachment mechanisms to interface bacteria with surfaces and neighboring cells. We hypothesized that transposon mutagenesis would complement targeted knockout studies in Geobacter spp. and identify novel genes involved in this process. Escherichia coli mating strains and plasmids were used to develop a conjugation protocol and deliver mini-Himar transposons, creating a library of over 8,000 mutants that was anaerobically arrayed and screened for a range of phenotypes, including auxotrophy for amino acids, inability to reduce Fe(III) citrate, and attachment to surfaces. Following protocol validation, mutants with strong phenotypes were further characterized in a three-electrode system to simultaneously quantify attachment, biofilm development, and respiratory parameters, revealing mutants defective in Fe(III) reduction but unaffected in electron transfer to electrodes (such as an insertion in GSU1330, a putative metal export protein) or defective in electrode reduction but demonstrating wild-type biofilm formation (due to an insertion upstream of the NHL domain protein GSU2505). An insertion in a putative ATP-dependent transporter (GSU1501) eliminated electrode colonization but not Fe(III) citrate reduction. A more complex phenotype was demonstrated by a mutant containing an insertion in a transglutaminase domain protein (GSU3361), which suddenly ceased to respire when biofilms reached approximately 50% of the wild-type levels. As most insertions were not in cytochromes but rather in transporters, two-component signaling proteins, and proteins of unknown function, this collection illustrates how biofilm formation and electron transfer are separate but complementary phenotypes, controlled by multiple loci not commonly studied in Geobacter spp. PMID:19395486

Severe neutropenia at time of port insertion is not a risk factor for catheter-associated infections in children with acute lymphoblastic leukemia.

PubMed

Junqueira, Beatriz L P; Connolly, Bairbre; Abla, Oussama; Tomlinson, George; Amaral, Joao G

2010-09-15

The objective of this study was to determine whether severe neutropenia on the day of port-a-catheter (PORT) insertion was a risk factor for catheter-associated infection (CAI) in children with acute lymphoblastic leukemia (ALL). This was a retrospective study of children with ALL who had a PORT insertion between January 2005 and August 2008. Early (≤ 30 days) and late (>30 days) postprocedure complications were reviewed. The length of follow-up ranged between 7 months and 42 months. In total, 192 PORTs were inserted in 179 children. There were 43 CAIs (22%), and the infection rate was 0.35 per 1000 catheter-days. The CAI rate (15%) in children who had severe neutropenia on the day of the procedure did not differ statistically from the CAI rate (24%) in children who did not have severe neutropenia (P = .137). Conversely, patients with severe neutropenia who had a CAI were more likely to have their PORT removed (P = .019). The most common organisms to cause catheter removal were coagulase-negative Staphylococcus and Staphylococcus aureus. Patients with high-risk ALL had a statistically significant higher incidence of late CAI than patients with standard-risk ALL (P = .012). Age (P = .272), positive blood culture preprocedure (P = 1.0), and dexamethasone use (P = .201) were not risk factors for CAI. Patients who had an early CAI did not have a greater chance of having a late CAI. The catheter infection-free survival rate at 1 year was 88.6%. The current results indicated that severe neutropenia on the day of PORT insertion does not increase the risk of CAI in children with ALL. © 2010 American Cancer Society.

Modified C1 lateral mass screw insertion using a high entry point to avoid postoperative occipital neuralgia.

PubMed

Lee, Sun-Ho; Kim, Eun-Sang; Eoh, Whan

2013-01-01

For the past decade, a screw-rod construct has been used commonly to stabilize the atlantoaxial joint, but the insertion of the screw through the C1 lateral mass (LM) can cause several complications. We evaluated whether using a higher screw entry point for C1 lateral mass (LM) fixation than in the standard procedure could prevent screw-induced occipital neuralgia. We enrolled 12 consecutive patients who underwent bilateral C1 LM fixation, with the modified screw insertion point at the junction of the C1 posterior arch and the midpoint of the posterior inferior portion of the C1 LM. We measured postoperative clinical and radiological parameters and recorded intraoperative complications, postoperative neurological deficits and the occurrence of occipital neuralgia. Postoperative plain radiographs were used to check for malpositioning of the screw or failure of the construct. Four patients underwent atlantoaxial stabilization for a transverse ligament injury or a C1 or C2 fracture, six patients for os odontoideum, and two patients for C2 metastasis. No patient experienced vertebral artery injury or cerebrospinal fluid leak, and all had minimal blood loss. No patient suffered significant occipital neuralgia, although one patient developed mild, transient unilateral neuralgia. There was also no radiographic evidence of construct failure. Twenty screws were positioned correctly through the intended entry points, but three screws were placed inferiorly (that is, below the arch), and one screw was inserted too medially. When performing C1-C2 fixation using the standard (Harms) construct, surgeons should be aware of the possible development of occipital neuralgia. A higher entry point may prevent this complication; therefore, we recommend that the screw should be inserted into the arch of C1 if it can be accommodated. Copyright © 2012 Elsevier Ltd. All rights reserved.

Comparison of Ultra-Conserved Elements in Drosophilids and Vertebrates

PubMed Central

Makunin, Igor V.; Shloma, Viktor V.; Stephen, Stuart J.; Pheasant, Michael; Belyakin, Stepan N.

2013-01-01

Metazoan genomes contain many ultra-conserved elements (UCEs), long sequences identical between distant species. In this study we identified UCEs in drosophilid and vertebrate species with a similar level of phylogenetic divergence measured at protein-coding regions, and demonstrated that both the length and number of UCEs are larger in vertebrates. The proportion of non-exonic UCEs declines in distant drosophilids whilst an opposite trend was observed in vertebrates. We generated a set of 2,126 Sophophora UCEs by merging elements identified in several drosophila species and compared these to the eutherian UCEs identified in placental mammals. In contrast to vertebrates, the Sophophora UCEs are depleted around transcription start sites. Analysis of 52,954 P-element, piggyBac and Minos insertions in the D. melanogaster genome revealed depletion of the P-element and piggyBac insertions in and around the Sophophora UCEs. We examined eleven fly strains with transposon insertions into the intergenic UCEs and identified associated phenotypes in five strains. Four insertions behave as recessive lethals, and in one case we observed a suppression of the marker gene within the transgene, presumably by silenced chromatin around the integration site. To confirm the lethality is caused by integration of transposons we performed a phenotype rescue experiment for two stocks and demonstrated that the excision of the transposons from the intergenic UCEs restores viability. Sequencing of DNA after the transposon excision in one fly strain with the restored viability revealed a 47 bp insertion at the original transposon integration site suggesting that the nature of the mutation is important for the appearance of the phenotype. Our results suggest that the UCEs in flies and vertebrates have both common and distinct features, and demonstrate that a significant proportion of intergenic drosophila UCEs are sensitive to disruption. PMID:24349264

Seven Years of Recording from Monkey Cortex with a Chronically Implanted Multiple Microelectrode

PubMed Central

Krüger, Jürgen; Caruana, Fausto; Volta, Riccardo Dalla; Rizzolatti, Giacomo

2010-01-01

A brush of 64 microwires was chronically implanted in the ventral premotor cortex of a macaque monkey. Contrary to common approaches, the wires were inserted from the white matter side. This approach, by avoiding mechanical pressure on the dura and pia mater during penetration, disturbed only minimally the cortical recording site. With this approach isolated potentials and multiunit activity were recorded for more than 7 years in about one-third of electrodes. The indirect insertion method also provided an excellent stability within each recording session, and in some cases even allowed recording from the same neurons for several years. Histological examination of the implanted brain region shows only a very marginal damage to the recording area. Advantages and problems related to long-term recording are discussed. PMID:20577628

Total Nasal Reconstruction for Extruded, Pending Extrusion and Severely Displaced Silicone Nasal Implants in Asian Patients.

PubMed

Hodgkinson, Darryl J

2017-04-01

The Australian population is 10% of Asian origin, and many of our Asian patients have had nasal augmentation using prosthetic material prior to immigration or as medical tourists back in their country of origin. Insertion of nasal prostheses is the most common way to augment the nasal dorsum in the Asian patient and although there is a trend towards autogenous primary augmentation still, the vast majority of patients seen in clinical practice have had augmentation by the insertion of foreign material generally silicone. Level of Evidence IV This journal requires that authors assign a level of evidence to each article. For a full description of these evidence-based medicine ratings, please refer to the Table of Contents or the online Instructions to Authors www.springer.com/00266 .

pK(a) Values of Titrable Amino Acids at the Water/Membrane Interface.

PubMed

Teixeira, Vitor H; Vila-Viçosa, Diogo; Reis, Pedro B P S; Machuqueiro, Miguel

2016-03-08

Peptides and proteins protonation equilibrium is strongly influenced by its surrounding media. Remarkably, until now, there have been no quantitative and systematic studies reporting the pK(a) shifts in the common titrable amino acids upon lipid membrane insertion. Here, we applied our recently developed CpHMD-L method to calculate the pK(a) values of titrable amino acid residues incorporated in Ala-based pentapeptides at the water/membrane interface. We observed that membrane insertion leads to desolvation and a clear stabilization of the neutral forms, and we quantified the increases/decreases of the pK(a) values in the anionic/cationic residues along the membrane normal. This work highlights the importance of properly modeling the protonation equilibrium in peptides and proteins interacting with membranes using molecular dynamics simulations.

Integrating ethics into technical courses: micro-insertion.

PubMed

Davis, Michael

2006-10-01

Perhaps the most common reason science and engineering faculty give for not including 'ethics' (that is, research ethics, engineering ethics, or some discussion of professional responsibility) in their technical classes is that 'there is no room'. This article 1) describes a technique ('micro-insertion') that introduces ethics (and related topics) into technical courses in small enough units not to push out technical material, 2) explains where this technique might fit into the larger undertaking of integrating ethics into the technical (scientific or engineering) curriculum, and 3) concludes with some quantified evidence (collected over more than a decade) suggesting success. Integrating ethics into science and engineering courses is largely a matter of providing context for what is already being taught, context that also makes the material already being taught seem 'more relevant'.

Packaging double-helical DNA into viral capsids.

PubMed

LaMarque, Jaclyn C; Le, Thuc-Vy L; Harvey, Stephen C

2004-02-15

DNA packaging in bacteriophage P4 has been examined using a molecular mechanics model with a reduced representation containing one pseudoatom per turn of the double helix. The model is a discretized version of an elastic continuum model. The DNA is inserted piecewise into the model capsid, with the structure being reoptimized after each piece is inserted. Various optimization protocols were investigated, and it was found that molecular dynamics at a very low temperature (0.3 K) produces the optimal packaged structure. This structure is a concentric spool, rather than the coaxial spool that has been commonly accepted for so many years. This geometry, which was originally suggested by Hall and Schellman in 1982 (Biopolymers Vol. 21, pp. 2011-2031), produces a lower overall elastic energy than coaxial spooling. Copyright 2003 Wiley Periodicals, Inc.

A rubber tube in the bladder as a complication of autoerotic stimulation of the urethra.

PubMed

Stamatiou, Konstantinos; Moschouris, Hippocrates

2016-10-05

Self-insertion of foreign bodies in the urethra is most commonly associated with sexual or erotic arousal of adolescents with mental health disorders. Rarely it may practiced by healthy adults for masturbation. Migration of foreign bodies used for the abovementioned purpose from the urethra to adjacent organs is a relatively uncommon urologic problem that may cause serious complications which arose tardive. Presentation includes a variety of acute or chronic symptoms that depend of the underlying complications. The method of extraction depends on the shape, size and nature of the object and should be tailored according to the condition of the patient. In the present article we present a case of a rubber tube inserted to the urethra for erotic arousal purposes which migrated to the bladder during masturbation.

Negotiating an Oil and Gas Lease. Teachers Instructional Packet, TIP No. 6, Spring 1985.

ERIC Educational Resources Information Center

Texas A and M Univ., College Station. Texas Real Estate Research Center.

Part of a series of classroom aids designed for real estate instructors, this instructional packet was developed to help real estate students understand the more common provisions and the legal significance of an oil and gas lease, as well as some provisions landowners may wish to insert for personal benefit and protection. Following an evaluation…

MEMS Reliability Assurance Guidelines for Space Applications

NASA Technical Reports Server (NTRS)

Stark, Brian (Editor)

1999-01-01

This guide is a reference for understanding the various aspects of microelectromechanical systems, or MEMS, with an emphasis on device reliability. Material properties, failure mechanisms, processing techniques, device structures, and packaging techniques common to MEMS are addressed in detail. Design and qualification methodologies provide the reader with the means to develop suitable qualification plans for the insertion of MEMS into the space environment.

Advanced Energy Storage and Conversion Devices

DTIC Science & Technology

2008-12-01

determined lithium-ion insertion mechanisms. 3.1 Background and Objectives Polymer electrolyte membrane fuel cells ( PEMFCs ) function by permitting...is one of the most critical components in the polymer electrolyte fuel cells. In recent years, PEMFCs have been identified as promising power...and residual hydrocarbons that are commonly produced by internal combustion engines. PEMFCs , due to their high efficiency and modularity of design

Emergence of a Novel Chimeric Gene Underlying Grain Number in Rice

PubMed Central

Chen, Hao; Tang, Yanyan; Liu, Jianfeng; Tan, Lubin; Jiang, Jiahuan; Wang, Mumu; Zhu, Zuofeng; Sun, Xianyou; Sun, Chuanqing

2017-01-01

Grain number is an important factor in determining grain production of rice (Oryza sativa L.). The molecular genetic basis for grain number is complex. Discovering new genes involved in regulating rice grain number increases our knowledge regarding its molecular mechanisms and aids breeding programs. Here, we identified GRAINS NUMBER 2 (GN2), a novel gene that is responsible for rice grain number, from “Yuanjiang” common wild rice (O. rufipogon Griff.). Transgenic plants overexpressing GN2 showed less grain number, reduced plant height, and later heading date than control plants. Interestingly, GN2 arose through the insertion of a 1094-bp sequence from LOC_Os02g45150 into the third exon of LOC_Os02g56630, and the inserted sequence recruited its nearby sequence to generate the chimeric GN2. The gene structure and expression pattern of GN2 were distinct from those of LOC_Os02g45150 and LOC_Os02g56630. Sequence analysis showed that GN2 may be generated in the natural population of Yuanjiang common wild rice. In this study, we identified a novel functional chimeric gene and also provided information regarding the molecular mechanisms regulating rice grain number. PMID:27986805

Groin Injuries (Athletic Pubalgia) and Return to Play.

PubMed

Elattar, Osama; Choi, Ho-Rim; Dills, Vickie D; Busconi, Brian

2016-07-01

Groin pain is a common entity in athletes involved in sports that require acute cutting, pivoting, or kicking such as soccer and ice hockey. Athletic pubalgia is increasingly recognized as a common cause of chronic groin and adductor pain in athletes. It is considered an overuse injury predisposing to disruption of the rectus tendon insertion to the pubis and weakness of the posterior inguinal wall without a clinically detectable hernia. These patients often require surgical therapy after failure of nonoperative measures. A variety of surgical options have been used, and most patients improve and return to high-level competition. PubMed databases were searched to identify relevant scientific and review articles from January 1920 to January 2015 using the search terms groin pain, sports hernia, athletic pubalgia, adductor strain, osteitis pubis, stress fractures, femoroacetabular impingement, and labral tears. Clinical review. Level 4. Athletic pubalgia is an overuse injury involving a weakness in the rectus abdominis insertion or posterior inguinal wall of the lower abdomen caused by acute or repetitive injury of the structure. A variety of surgical options have been reported with successful outcomes, with high rates of return to the sport in the majority of cases. © 2016 The Author(s).

Design and evaluation of corn starch-bonded Rhizophora spp. particleboard phantoms for SPECT/CT imaging

NASA Astrophysics Data System (ADS)

Hamid, Puteri Nor Khatijah Abd; Yusof, Mohd Fahmi Mohd; Aziz Tajuddin, Abd; Hashim, Rokiah; Zainon, Rafidah

2018-01-01

The aim of this study was to design and evaluate of corn starch-bonded Rhizophora spp. particleboards as phantom for SPECT/CT imaging. The phantom was designed according to the Jaszczak phantom commonly used in SPECT imaging with dimension of 22 cm diameter and 18 cm length. Six inserts with different diameter were made for insertion of vials filled with 1.6 µCi/ml of 99mTc unsealed source. The particleboard phantom was scanned using SPECT/CT imaging protocol. The contrast of each vial for particleboards phantom were calculated based on the ratio of counts in radionuclide volume and phantom background and compared to Perspex® and water phantom. The results showed that contrast values for each vial in particleboard phantomis near to 1.0 and in good agreement with Perspex® and water phantoms as common phantom materials for SPECT/CT. The paired sample t-test result showed no significant difference of contrast values between images in particleboard phantoms and that in water. The overall results showed the potential of corn starch-bonded Rhizophora spp. as phantom for quality control and dosimetry works in SPECT/CT imaging.

Abdominal paracentesis and thoracocentesis.

PubMed

Lee, Ser Yee; Pormento, James G; Koong, Heng Nung

2009-04-01

Abdominal paracentesis and thoracocentesis are common bedside procedures with diagnostic, therapeutic and palliative roles. We describe a useful and familiar a useful and familiar technique with the use of a multiple lumen catheter commonly used for central venous line insertion for drainage of ascites or moderate to large pleural effusions. The use of a multiple lumen catheter allows easier and more rapid aspiration of fluid with a smaller probability of the side holes being blocked as compared to the standard needle or single catheter methods. This is particularly useful in situations where the dedicated commercial kits for thoracocentesis and abdominal paracentesis are not readily available.

Retroviral insertional mutagenesis identifies Zeb2 activation as a novel leukemogenic collaborating event in CALM-AF10 transgenic mice.

PubMed

Caudell, David; Harper, David P; Novak, Rachel L; Pierce, Rachel M; Slape, Christopher; Wolff, Linda; Aplan, Peter D

2010-02-11

The t(10;11) translocation results in a CALM-AF10 fusion gene in a subset of leukemia patients. Expression of a CALM-AF10 transgene results in leukemia, with prolonged latency and incomplete penetrance, suggesting that additional events are necessary for leukemic transformation. CALM-AF10 mice infected with the MOL4070LTR retrovirus developed acute leukemia, and ligation-mediated polymerase chain reaction was used to identify retroviral insertions at 19 common insertion sites, including Zeb2, Nf1, Mn1, Evi1, Ift57, Mpl, Plag1, Kras, Erg, Vav1, and Gata1. A total of 26% (11 of 42) of the mice had retroviral integrations near Zeb2, a transcriptional corepressor leading to overexpression of the Zeb2-transcript. A total of 91% (10 of 11) of mice with Zeb2 insertions developed B-lineage acute lymphoblastic leukemia, suggesting that Zeb2 activation promotes the transformation of CALM-AF10 hematopoietic precursors toward B-lineage leukemias. More than half of the mice with Zeb2 integrations also had Nf1 integrations, suggesting cooperativity among CALM-AF10, Zeb2, and Ras pathway mutations. We searched for Nras, Kras, and Ptpn11 point mutations in the CALM-AF10 leukemic mice. Three mutations were identified, all of which occurred in mice with Zeb2 integrations, consistent with the hypothesis that Zeb2 and Ras pathway activation promotes B-lineage leukemic transformation in concert with CALM-AF10.

Retroviral insertional mutagenesis identifies Zeb2 activation as a novel leukemogenic collaborating event in CALM-AF10 transgenic mice

PubMed Central

Caudell, David; Harper, David P.; Novak, Rachel L.; Pierce, Rachel M.; Slape, Christopher; Wolff, Linda

2010-01-01

The t(10;11) translocation results in a CALM-AF10 fusion gene in a subset of leukemia patients. Expression of a CALM-AF10 transgene results in leukemia, with prolonged latency and incomplete penetrance, suggesting that additional events are necessary for leukemic transformation. CALM-AF10 mice infected with the MOL4070LTR retrovirus developed acute leukemia, and ligation-mediated polymerase chain reaction was used to identify retroviral insertions at 19 common insertion sites, including Zeb2, Nf1, Mn1, Evi1, Ift57, Mpl, Plag1, Kras, Erg, Vav1, and Gata1. A total of 26% (11 of 42) of the mice had retroviral integrations near Zeb2, a transcriptional corepressor leading to overexpression of the Zeb2-transcript. A total of 91% (10 of 11) of mice with Zeb2 insertions developed B-lineage acute lymphoblastic leukemia, suggesting that Zeb2 activation promotes the transformation of CALM-AF10 hematopoietic precursors toward B-lineage leukemias. More than half of the mice with Zeb2 integrations also had Nf1 integrations, suggesting cooperativity among CALM-AF10, Zeb2, and Ras pathway mutations. We searched for Nras, Kras, and Ptpn11 point mutations in the CALM-AF10 leukemic mice. Three mutations were identified, all of which occurred in mice with Zeb2 integrations, consistent with the hypothesis that Zeb2 and Ras pathway activation promotes B-lineage leukemic transformation in concert with CALM-AF10. PMID:20007546

Indications, retrieval rate, and complications of inferior vena cava filters: Single-center experience in Saudi Arabia.

PubMed

Shabib, Abdullah Bin; Alsayed, Fahad; Aldughaythir, Saad; Habeeb, Hanan; Al Tamimi, Sumayyah; Masuadi, Emad; Alzahrani, Mohsen; Alaklabi, Ali; Alotaibi, Azzam; Rajendram, Rajkumar; Almegren, Mosaad

2018-01-01

Inferior vena cava (IVC) filter is indicated in patients with acute venous thromboembolism (VTE) in whom therapeutic anticoagulation is contraindicated. While prophylactic insertion of an IVC filter may be considered for patients at high risk of VTE, there are significant differences between clinical guidelines on the role of IVC filters. These discrepancies have arisen predominantly because of the paucity of data on the efficacy and safety of IVC filters. We, therefore, evaluated the indications for filter insertion, the rate of filter retrieval and complications in patients who received IVC filters at King Abdulaziz Medical City (KAMC), Riyadh, Saudi Arabia. A descriptive, retrospective review of electronic- and paper-based medical records was performed. Consecutive sampling was used to study all adult patients who received an IVC filter at KAMC between 2007 and 2016 and met the inclusion criteria. A total of 382 IVC filters were inserted. 113 patients (30%) had an acute VTE and a contraindication to anticoagulation while 53 patients (14%) received an IVC filter in the absence of VTE (i.e., prophylactic). Only 124 (32.5%) IVC filters were eventually retrieved. The most common reason for nonretrieval was the need for permanent filtration (155, 60%). Thrombotic complications developed in 72 (19%) patients; nine patients had fatal pulmonary embolism. The insertion of IVC filters in this cohort was associated with low retrieval rate and relatively high incidence of thrombotic complications. Follow-up of patients is required to detect IVC filter-related complications and to increase retrieval rate.

Indel PDB: a database of structural insertions and deletions derived from sequence alignments of closely related proteins.

PubMed

Hsing, Michael; Cherkasov, Artem

2008-06-25

Insertions and deletions (indels) represent a common type of sequence variations, which are less studied and pose many important biological questions. Recent research has shown that the presence of sizable indels in protein sequences may be indicative of protein essentiality and their role in protein interaction networks. Examples of utilization of indels for structure-based drug design have also been recently demonstrated. Nonetheless many structural and functional characteristics of indels remain less researched or unknown. We have created a web-based resource, Indel PDB, representing a structural database of insertions/deletions identified from the sequence alignments of highly similar proteins found in the Protein Data Bank (PDB). Indel PDB utilized large amounts of available structural information to characterize 1-, 2- and 3-dimensional features of indel sites. Indel PDB contains 117,266 non-redundant indel sites extracted from 11,294 indel-containing proteins. Unlike loop databases, Indel PDB features more indel sequences with secondary structures including alpha-helices and beta-sheets in addition to loops. The insertion fragments have been characterized by their sequences, lengths, locations, secondary structure composition, solvent accessibility, protein domain association and three dimensional structures. By utilizing the data available in Indel PDB, we have studied and presented here several sequence and structural features of indels. We anticipate that Indel PDB will not only enable future functional studies of indels, but will also assist protein modeling efforts and identification of indel-directed drug binding sites.

Structure, Function, Self-Assembly and Origin of Simple Membrane Proteins

NASA Technical Reports Server (NTRS)

Pohorille, Andrew

2003-01-01

Integral membrane proteins perform such essential cellular functions as transport of ions, nutrients and waste products across cell walls, transduction of environmental signals, regulation of cell fusion, recognition of other cells, energy capture and its conversion into high-energy compounds. In fact, 30-40% of genes in modem organisms codes for membrane proteins. Although contemporary membrane proteins or their functional assemblies can be quite complex, their transmembrane fragments are usually remarkably simple. The most common structural motif for these fragments is a bundle of alpha-helices, but occasionally it could be a beta-barrel. In a series of molecular dynamics computer simulations we investigated self-organizing properties of simple membrane proteins based on these structural motifs. Specifically, we studied folding and insertion into membranes of short, nonpolar or amphiphatic peptides. We also investigated glycophorin A, a peptide that forms sequence-specific dimers, and a transmembrane aggregate of four identical alpha-helices that forms an efficient and selective voltage-gated proton channel was investigated. Many peptides are attracted to water-membrane interfaces. Once at the interface, nonpolar peptides spontaneously fold to a-helices. Whenever the sequence permits, peptides that contain both polar and nonpolar amino also adopt helical structures, in which polar and nonpolar amino acid side chains are immersed in water and membrane, respectively. Specific identity of side chains is less important. Helical peptides at the interface could insert into the membrane and adopt a transmembrane conformation. However, insertion of a single helix is unfavorable because polar groups in the peptide become completely dehydrated upon insertion. The unfavorable free energy of insertion can be regained by spontaneous association of peptides in the membrane. The first step in this process is the formation of dimers, although the most common are aggregates of 4-7 helices. The helices could arrange themselves such that they formed pores capable of transporting ions and small molecules across membranes. Stability of transmembrane aggregates of simple proteins is often only marginal and, therefore, it can be regulated by environmental signals or small sequence modifications in the region of interhelical interactions. A key step in the earliest evolution of membrane proteins was the emergence of selectivity for specific substrates. Many channels could become selective if one or only a few properly chosen amino acids are properly placed along the channel, acting as filters or gates. This is a convenient evolutionary solution because it does not require imposing conditions on the whole sequence.

Automated model-based quantitative analysis of phantoms with spherical inserts in FDG PET scans.

PubMed

Ulrich, Ethan J; Sunderland, John J; Smith, Brian J; Mohiuddin, Imran; Parkhurst, Jessica; Plichta, Kristin A; Buatti, John M; Beichel, Reinhard R

2018-01-01

Quality control plays an increasingly important role in quantitative PET imaging and is typically performed using phantoms. The purpose of this work was to develop and validate a fully automated analysis method for two common PET/CT quality assurance phantoms: the NEMA NU-2 IQ and SNMMI/CTN oncology phantom. The algorithm was designed to only utilize the PET scan to enable the analysis of phantoms with thin-walled inserts. We introduce a model-based method for automated analysis of phantoms with spherical inserts. Models are first constructed for each type of phantom to be analyzed. A robust insert detection algorithm uses the model to locate all inserts inside the phantom. First, candidates for inserts are detected using a scale-space detection approach. Second, candidates are given an initial label using a score-based optimization algorithm. Third, a robust model fitting step aligns the phantom model to the initial labeling and fixes incorrect labels. Finally, the detected insert locations are refined and measurements are taken for each insert and several background regions. In addition, an approach for automated selection of NEMA and CTN phantom models is presented. The method was evaluated on a diverse set of 15 NEMA and 20 CTN phantom PET/CT scans. NEMA phantoms were filled with radioactive tracer solution at 9.7:1 activity ratio over background, and CTN phantoms were filled with 4:1 and 2:1 activity ratio over background. For quantitative evaluation, an independent reference standard was generated by two experts using PET/CT scans of the phantoms. In addition, the automated approach was compared against manual analysis, which represents the current clinical standard approach, of the PET phantom scans by four experts. The automated analysis method successfully detected and measured all inserts in all test phantom scans. It is a deterministic algorithm (zero variability), and the insert detection RMS error (i.e., bias) was 0.97, 1.12, and 1.48 mm for phantom activity ratios 9.7:1, 4:1, and 2:1, respectively. For all phantoms and at all contrast ratios, the average RMS error was found to be significantly lower for the proposed automated method compared to the manual analysis of the phantom scans. The uptake measurements produced by the automated method showed high correlation with the independent reference standard (R 2 ≥ 0.9987). In addition, the average computing time for the automated method was 30.6 s and was found to be significantly lower (P ≪ 0.001) compared to manual analysis (mean: 247.8 s). The proposed automated approach was found to have less error when measured against the independent reference than the manual approach. It can be easily adapted to other phantoms with spherical inserts. In addition, it eliminates inter- and intraoperator variability in PET phantom analysis and is significantly more time efficient, and therefore, represents a promising approach to facilitate and simplify PET standardization and harmonization efforts. © 2017 American Association of Physicists in Medicine.

Fibularis tertius: revisiting the anatomy.

PubMed

Rourke, K; Dafydd, H; Parkin, I G

2007-11-01

Fibularis tertius (FT) may be used during reconstructive surgery and muscle transposition with retention of function. The muscle was examined in both lower limbs of 41 cadavers. Measurements were made of muscle belly length and width, tendon length and width, and the size of the origin on the fibula. Tendon insertion, nerve and blood supplies were also examined. FT was absent in five (6.1%) lower limbs of three (7.3%) subjects. The size of its origin demonstrated inter- and intra-individual variation. FT arose from the distal fibula and on average occupied (28.4 +/- 9.1)% (mean +/- S. D.) of the total shaft length. In all cases the tendon inserted into the dorsal surface of the shafts of both the fourth and fifth metatarsals. A small nerve branch consistently arose from the deep fibular nerve near the origin of extensor digitorum longus. The nerve ran parallel to the length of this muscle, between it and extensor hallucis longus, before piercing FT. Anatomy textbooks describe FT as inserting into the fifth metatarsal only. This study, supported by data from previous reports, suggests that the "textbook" accounts of FT should be updated to record that most commonly its tendon reaches both the fourth and fifth metatarsals.

Efficiency of vibrational sounding in parasitoid host location depends on substrate density.

PubMed

Fischer, S; Samietz, J; Dorn, S

2003-10-01

Parasitoids of concealed hosts have to drill through a substrate with their ovipositor for successful parasitization. Hymenopteran species in this drill-and-sting guild locate immobile pupal hosts by vibrational sounding, i.e., echolocation on solid substrate. Although this host location strategy is assumed to be common among the Orussidae and Ichneumonidae there is no information yet whether it is adapted to characteristics of the host microhabitat. This study examined the effect of substrate density on responsiveness and host location efficiency in two pupal parasitoids, Pimpla turionellae and Xanthopimpla stemmator (Hymenoptera: Ichneumonidae), with different host-niche specialization and corresponding ovipositor morphology. Location and frequency of ovipositor insertions were scored on cylindrical plant stem models of various densities. Substrate density had a significant negative effect on responsiveness, number of ovipositor insertions, and host location precision in both species. The more niche-specific species X. stemmator showed a higher host location precision and insertion activity. We could show that vibrational sounding is obviously adapted to the host microhabitat of the parasitoid species using this host location strategy. We suggest the attenuation of pulses during vibrational sounding as the energetically costly limiting factor for this adaptation.

Miniature ureteroscope tip designs for use in thulium fiber laser lithotripsy

NASA Astrophysics Data System (ADS)

Kennedy, Joshua D.; Wilson, Christopher R.; Irby, Pierce B.; Fried, Nathaniel M.

2017-02-01

A miniature ureteroscope has the potential to eliminate need for full anesthesia and dilation, increase comfort and safety of laser lithotripsy via ureteroscopy, and reduce hospital costs via an office based procedure. A prototype, 4.5 Fr (1.5-mm-OD), five channel ureteroscope tip was developed, housing a 200-μm-ID central channel for insertion of small, 100-μm-core fibers and four surrounding channels, each with 510-μm-ID for instrumentation, irrigation, imaging, and illumination, respectively. Common urological instruments (including fibers, guidewires, and stone baskets) were inserted through tip's working channels to demonstrate feasibility. Low irrigation rates were measured, revealing a need for manual pump-assisted irrigation. Imaging was conducted using 3k, 6k, and 10k pixel miniature flexible endoscopes with 0.4, 0.6, and 0.9 mm outer diameters, respectively. The 3k pixel endoscope with integrated illumination was inserted through the prototype unimpeded, and successfully demonstrated ability to differentiate between hard tissues (e.g. kidney stones) and soft tissues (e.g. ureter wall), for visibility and safety during potential clinical application. Based on both image quality and instrument diameter, the 6k pixel endoscope provided an optimal solution for miniature ureteroscopy.

Operando observations of solid-state electrochemical reactions in Li-ion batteries by spatially resolved TEM EELS and electron holography.

PubMed

Yamamoto, Kazuo; Iriyama, Yasutoshi; Hirayama, Tsukasa

2017-02-08

All-solid-state Li-ion batteries having incombustible solid electrolytes are promising energy storage devices because they have significant advantages in terms of safety, lifetime and energy density. Electrochemical reactions, namely, Li-ion insertion/extraction reactions, commonly occur around the nanometer-scale interfaces between the electrodes and solid electrolytes. Thus, transmission electron microscopy (TEM) is an appropriate technique to directly observe such reactions, providing important information for understanding the fundamental solid-state electrochemistry and improving battery performance. In this review, we introduce two types of TEM techniques for operando observations of battery reactions, spatially resolved electron energy-loss spectroscopy in a TEM mode for direct detection of the Li concentration profiles and electron holography for observing the electric potential changes due to Li-ion insertion/extraction reactions. We visually show how Li-ion insertion/extractions affect the crystal structures, electronic structures, and local electric potential during the charge-discharge processes in these batteries. © The Author 2016. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

PIMMS (Pragmatic Insertional Mutation Mapping System) Laboratory Methodology a Readily Accessible Tool for Identification of Essential Genes in Streptococcus

PubMed Central

Blanchard, Adam M.; Egan, Sharon A.; Emes, Richard D.; Warry, Andrew; Leigh, James A.

2016-01-01

The Pragmatic Insertional Mutation Mapping (PIMMS) laboratory protocol was developed alongside various bioinformatics packages (Blanchard et al., 2015) to enable detection of essential and conditionally essential genes in Streptococcus and related bacteria. This extended the methodology commonly used to locate insertional mutations in individual mutants to the analysis of mutations in populations of bacteria. In Streptococcus uberis, a pyogenic Streptococcus associated with intramammary infection and mastitis in ruminants, the mutagen pGhost9:ISS1 was shown to integrate across the entire genome. Analysis of >80,000 mutations revealed 196 coding sequences, which were not be mutated and a further 67 where mutation only occurred beyond the 90th percentile of the coding sequence. These sequences showed good concordance with sequences within the database of essential genes and typically matched sequences known to be associated with basic cellular functions. Due to the broad utility of this mutagen and the simplicity of the methodology it is anticipated that PIMMS will be of value to a wide range of laboratories in functional genomic analysis of a wide range of Gram positive bacteria (Streptococcus, Enterococcus, and Lactococcus) of medical, veterinary, and industrial significance. PMID:27826289

The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus.

PubMed

Sun, Zhenguo; Ke, Xiquan; Salzberg, Steven L; Kim, Daehwan; Antonescu, Valentin; Cheng, Yulan; Huang, Binbin; Song, Jee Hoon; Abraham, John M; Ibrahim, Sariat; Tian, Hui; Meltzer, Stephen J

2017-05-01

Novel fusion transcripts (FTs) caused by chromosomal rearrangement are common factors in the development of cancers. In the current study, the authors used massively parallel RNA sequencing to identify new FTs in colon cancers. RNA sequencing (RNA-Seq) and TopHat-Fusion were used to identify new FTs in colon cancers. The authors then investigated whether the novel FT nuclear receptor subfamily 5, group A, member 2 (NR5A2)-Kelch-like family member 29 FT (KLHL29FT) was transcribed from a genomic chromosomal rearrangement. Next, the expression of NR5A2-KLHL29FT was measured by quantitative real-time polymerase chain reaction in colon cancers and matched corresponding normal epithelia. The authors identified the FT NR5A2-KLHL29FT in normal and cancerous epithelia. While investigating this transcript, it was unexpectedly found that it was due to an uncharacterized polymorphic germline insertion of the NR5A2 sequence from chromosome 1 into the KLHL29 locus at chromosome 2, rather than a chromosomal rearrangement. This germline insertion, which occurred at a population frequency of 0.40, appeared to bear no relationship to cancer development. Moreover, expression of NR5A2-KLHL29FT was validated in RNA specimens from samples with insertions of NR5A2 at the KLHL29 gene locus, but not from samples without this insertion. It is interesting to note that NR5A2-KLH29FT expression levels were significantly lower in colon cancers than in matched normal colonic epithelia (P =.029), suggesting the potential participation of NR5A2-KLHL29FT in the origin or progression of this tumor type. NR5A2-KLHL29FT was generated from a polymorphism insertion of the NR5A2 sequence into the KLHL29 locus. NR5A2-KLHL29FT may influence the origin or progression of colon cancer. Moreover, researchers should be aware that similar FTs may occur due to transchromosomal insertions that are not correctly annotated in genome databases, especially with current assembly algorithms. Cancer 2017;123:1507-1515. © 2017 American Cancer Society. © 2016 American Cancer Society.

Patterns of nasal foreign body in northeast Malaysia: A five-year experience.

PubMed

Yaroko, A A; Baharudin, A

2015-11-01

The aim of this study was to determine the common presentations and management outcomes in case of nasal foreign body. A retrospective study was carried out over 5 years, from January 2008 to December 2012. The total number of patients was 43; maximum age was 9 years. Patient biodata, clinical presentation, type of foreign body and management outcome were obtained and analyzed from the medical records of the Universiti Sains Malaysia Hospital. Of the total 43 patients, 60.5% were male and 39.5% female. The most frequent age at which nasal foreign bodies were found was 3 years (48.83%) and the least frequent age bracket was 7-9 years (2.33%). Most patients had foul smelling nasal discharge (34.88%) or were asymptomatic (34.88%); the least common presentation was nasal discomfort (2.33%). Seeds (23.26%) were the most common foreign body, followed by rubber and batteries (16.28%). In most cases (58.14%), the foreign body had been inserted into the right nostril; 39.53% were inserted into the left nostril, and 2.33% were bilateral. Foreign bodies were removed under general and local anesthesia in 53.49% and 41.86% of cases respectively; 4.65% were dislodged spontaneously. Nasal foreign bodies are encountered daily in our routine clinical practice in the pediatric age group. General anesthesia is required in uncooperative agitated patients to avoid complications. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Mapping the architecture of the HIV-lTat circuit: A decision-making circuit that lacks bistability and exploits stochastic noise

PubMed Central

Razooky, Brandon S.; Weinberger, Leor S.

2014-01-01

Upon infection of a CD4+ T cell, HIV-l appears to ‘choose’ between two alternate fates: active replication or a long-lived dormant statetermed proviral latency. A transcriptional positive-feedback loop generated by the HIV-l Tat protein appears sufficient to mediate this decision. Here, we describea coupled wet-lab and computational approach that uses mathematical modeling and live-cell time-lapse microscopy to map the architecture of the HIV-l Tat transcriptional regulatorycircuit and generate predictive models of HIV-l latency. This approach provided the first characterization of a ‘decision-making’ circuit that lacks bistability andinstead exploits stochastic fluctuations in cellular molecules (i.e. noise) to generate a decision between an on or off transcriptional state. PMID:21167940

Natural history of the ERVWE1 endogenous retroviral locus

PubMed Central

Bonnaud, Bertrand; Beliaeff, Jean; Bouton, Olivier; Oriol, Guy; Duret, Laurent; Mallet, François

2005-01-01

Background The human HERV-W multicopy family includes a unique proviral locus, termed ERVWE1, whose full-length envelope ORF was preserved through evolution by the action of a selective pressure. The encoded Env protein (Syncytin) is involved in hominoid placental physiology. Results In order to infer the natural history of this domestication process, a comparative genomic analysis of the human 7q21.2 syntenic regions in eutherians was performed. In primates, this region was progressively colonized by LTR-elements, leading to two different evolutionary pathways in Cercopithecidae and Hominidae, a genetic drift versus a domestication, respectively. Conclusion The preservation in Hominoids of a genomic structure consisting in the juxtaposition of a retrotransposon-derived MaLR LTR and the ERVWE1 provirus suggests a functional link between both elements. PMID:16176588

Bovine immunodeficiency-like virus: inactivation in milk by pasteurisation.

PubMed

Venables, C; Lysons, R; Horigan, M; Stagg, D; Dawson, M

1997-03-15

Bioassay was used to determine whether bovine immunodeficiency-like virus (BIV) in milk was inactivated by pasteurisation. Three groups of three calves were inoculated with virus (BIV isolate FL112), milk seeded with virus and milk seeded with virus that had been pasteurised before inoculation, respectively. Seroconversion to BIV was monitored for 12 months by an indirect immunofluorescence assay. The presence of BIV proviral DNA in peripheral blood was determined by a nested polymerase chain reaction (PCR). The animals were euthanized and virus isolation and PCR were attempted on peripheral blood mononunclear cells, prescapular lymph node and spleen. Transmission of BIV was confirmed in the groups that were inoculated with the virus and with the virus in milk, but no evidence of its transmission was demonstrated in the group that received the pasteurised inoculum.

Construction and characterization of a human T-cell lymphotropic virus type 3 infectious molecular clone.

PubMed

Chevalier, Sébastien Alain; Ko, Nga Ling; Calattini, Sara; Mallet, Adeline; Prévost, Marie-Christine; Kehn, Kylene; Brady, John N; Kashanchi, Fatah; Gessain, Antoine; Mahieux, Renaud

2008-07-01

We and others have uncovered the existence of human T-cell lymphotropic virus type 3 (HTLV-3). We have now generated an HTLV-3 proviral clone. We established that gag, env, pol, pro, and tax/rex as well as minus-strand mRNAs are present in cells transfected with the HTLV-3 clone. HTLV-3 p24(gag) protein is detected in the cell culture supernatant. Transfection of 293T-long terminal repeat (LTR)-green fluorescent protein (GFP) cells with the HTLV-3 clone promotes formation of syncytia, a hallmark of Env expression, together with the appearance of fluorescent cells, demonstrating that Tax is expressed. Viral particles are visible by electron microscopy. These particles are infectious, as demonstrated by infection experiments with purified virions.

HIV Tat/P-TEFb Interaction: A Potential Target for Novel Anti-HIV Therapies.

PubMed

Asamitsu, Kaori; Fujinaga, Koh; Okamoto, Takashi

2018-04-17

Transcription is a crucial step in the life cycle of the human immunodeficiency virus type 1 (HIV 1) and is primarily involved in the maintenance of viral latency. Both viral and cellular transcription factors, including transcriptional activators, suppressor proteins and epigenetic factors, are involved in HIV transcription from the proviral DNA integrated within the host cell genome. Among them, the virus-encoded transcriptional activator Tat is the master regulator of HIV transcription. Interestingly, unlike other known transcriptional activators, Tat primarily activates transcriptional elongation and initiation by interacting with the cellular positive transcriptional elongation factor b (P-TEFb). In this review, we describe the molecular mechanism underlying how Tat activates viral transcription through interaction with P-TEFb. We propose a novel therapeutic strategy against HIV replication through blocking Tat action.

Retroviral integration: Site matters

PubMed Central

Demeulemeester, Jonas; De Rijck, Jan

2015-01-01

Here, we review genomic target site selection during retroviral integration as a multistep process in which specific biases are introduced at each level. The first asymmetries are introduced when the virus takes a specific route into the nucleus. Next, by co‐opting distinct host cofactors, the integration machinery is guided to particular chromatin contexts. As the viral integrase captures a local target nucleosome, specific contacts introduce fine‐grained biases in the integration site distribution. In vivo, the established population of proviruses is subject to both positive and negative selection, thereby continuously reshaping the integration site distribution. By affecting stochastic proviral expression as well as the mutagenic potential of the virus, integration site choice may be an inherent part of the evolutionary strategies used by different retroviruses to maximise reproductive success. PMID:26293289

Arterial catheter complications and management problems: observations from AACN's Thunder Project.

PubMed

1993-09-01

Arterial cannulation, while common in critical care, is a procedure with attendant risks of complications. Anecdotal data from the American Association of Critical Care Nurses' Thunder Project provided evidence that catheters, insertion sites, and monitoring systems continue to be sources of complications. The problems have not changed since arterial cannulation began. Line management issues cannot be resolved until low-maintenance systems are developed.

Complications and management of forgotten long-term biliary stents

PubMed Central

Sohn, Se Hoon; Park, Jae Hyun; Kim, Kook Hyun; Kim, Tae Nyeun

2017-01-01

AIM To evaluate complications and management outcomes of retained long-term plastic biliary stents. METHODS Endoscopic plastic biliary stent placement was performed in 802 patients at Yeungnam University Hospital between January 2000 and December 2014. Follow-up loss with a subsequently forgotten stent for more than 12 mo occurred in 38 patients. We retrospectively examined the cause of biliary stent insertion, status of stents, complications associated with biliary stents and management outcomes of long-term plastic biliary stents. Continuous variables were analyzed using the t test. Observed frequencies in subsets of the study population were compared using Fisher’s exact test and χ2 tests. Statistical significance was defined as P < 0.05 (two-tailed). RESULTS Mean age of patients was 73.7 ± 12 years and male-to-female ratio was 2.2:1. Indications of plastic biliary stent insertion were bile duct stones (63.2%, 24/38) and benign bile duct stricture (52.6%, 20/38). Mean duration of retained plastic stent was 22.6 ± 12.2 mo, and in 10 cases (26.3%), stents were retained for more than 24 mo. Common bile duct (CBD) stones or sludge were found in most cases (92.1%, 35/38). The most common complication was acute cholangitis (94.7%, 36/38). Stent removal by endoscopic approach was successfully performed in 92.1% (35/38) of the cases. In 3 cases, an additional plastic stent was inserted alongside the previous stent due to failure of the stent removal. Endoscopic removal of bile duct stones was successful in 73.7% (28/38) of the cases. When patients were divided into two groups by duration of stent placement (12 to 24 mo vs over 24 mo), there were no differences in the development of cholangitis, presence of biliary stones, and success rate of endoscopic removal of stones and biliary stents. CONCLUSION The most common complication of retained long-term plastic biliary stents was acute cholangitis associated with CBD stones. Endoscopic management was successfully performed in most cases. PMID:28216968

Long-term outcome of self expandable metal stents for biliary obstruction in chronic pancreatitis.

PubMed

Waldthaler, Alexander; Schütte, Kerstin; Weigt, Jochen; Kropf, Siegfried; Malfertheiner, Peter; Kahl, Stefan

2013-01-10

Insertion of a self-expandable metal stent is still controversial for treatment of benign common bile duct stenosis but can be a valuable alternative to surgical treatment. Aim of our study was to analyze the efficacy of covered and uncovered self-expandable metal stent in patients with chronic pancreatitis and common bile duct stenosis. Twenty patients with common bile duct stenosis due to alcoholic chronic pancreatitis were retrospective analyzed. All patients had advanced chronic pancreatitis, presenting with calcifications in pancreatic head. Uncovered self-expandable metal stent (uSEMS) were used in 11 patients (3 females, 8 males) while in 9 patients (3 females, 6 males) partially covered self-expandable metal stent (cSEMS) were inserted. All patients treated with self-expandable metal stent had contraindications for surgery. Overall mean follow up time was 155 weeks: 206 (52-412) weeks in uSEMS, and 93 (25-233) weeks in cSEMS, respectively. Stent patency was in mean 118 weeks: 159 (44-412) weeks in uSEMS and 67 (25-150) weeks in cSEMS (P=0.019). In the uSEMS group, reintervention was necessary in 5 patients (45%) due to stent obstruction, whereas in the cSEMS group 4 patients (44%) needed reintervention (2 obstructions, 2 migration). Stent migration is an early complication, compared to obstruction (P<0.05), and in cSEMS obstruction occurred significantly earlier compared to uSEMS (P<0.05). Patency of uSEMS was significantly longer compared to partially cSEMS. Available self-expandable metal stent, unfortunately, do not meet the demands on successful treatment of benign common bile duct stenosis.

Design and fabrication of embedded micro-mirror inserts for out-of-plane coupling in PCB-level optical interconnections

NASA Astrophysics Data System (ADS)

Van Erps, Jurgen; Hendrickx, Nina; Bosman, Erwin; Van Daele, Peter; Debaes, Christof; Thienpont, Hugo

2010-05-01

Optical interconnections have gained interest over the last years, and several approaches have been presented for the integration of optics to the printed circuit board (PCB)-level. The use of a polymer optical waveguide layer appears to be the prevailing solution to route optical signals on the PCB. The most difficult issue is the efficient out-of-plane coupling of light between surface-normal optoelectronic devices (lasers and photodetectors) and PCB-integrated waveguides. The most common approach consists of using 45° reflecting micro-mirrors. The micro-mirror performance significantly affects the total insertion loss of the optical interconnect system, and hence has a crucial role on the system's bit error rate (BER) characteristics. Several technologies have been proposed for the fabrication of 45° reflector micro-mirrors directly into waveguides. Alternatively, it is possible to make use of discrete coupling components which have to be inserted into cavities formed in the PCB-integrated waveguides. In this paper, we present a hybrid approach where we try to combine the advantages of integrated and discrete coupling mirrors, i.e. low coupling loss and maintenance of the planararity of the top surface of the optical layer, allowing the lamination of additional layers or the mounting of optoelectronic devices. The micro-mirror inserts are designed through non-sequential ray tracing simulations, including a tolerance analysis, and subsequently prototyped with Deep Proton Writing (DPW). The DPW prototypes are compatible with mass fabrication at low cost in a wide variety of high-tech plastics. The DPW micro-mirror insert is metallized and inserted in a laser ablated cavity in the optical layer and in a next step covered with cladding material. Surface roughness measurements confirm the excellent quality of the mirror facet. An average mirror loss of 0.35-dB was measured in a receiver scheme, which is the most stringent configuration. Finally, the configuration is robust, since the mirror is embedded and thus protected from environmental contamination, like dust or moisture adsorption, which makes them interesting candidates for out-of-plane coupling in high-end boards.

Biomechanical properties of double- and single-row suture anchor repair for surgical treatment of insertional Achilles tendinopathy.

PubMed

Beitzel, Knut; Mazzocca, Augustus D; Obopilwe, Elifho; Boyle, James W; McWilliam, James; Rincon, Lina; Dhar, Yasmin; Arciero, Robert A; Amendola, Annunziato

2013-07-01

Because of intratendinous ossifications, retrocalcaneal bursitis, or intratendinous necrosis commonly found in insertional tendinosis, it is often necessary to detach the tendon partially or entirely from its tendon-to-bone junction. Double-row repair for insertional Achilles tendinopathy will generate an increased contact area and demonstrate higher biomechanical stability. Controlled laboratory study. Eighteen cadaver Achilles tendons were split longitudinally and detached, exposing the calcaneus; an ostectomy was performed and the tendon was reattached to the calcaneus in 1 of 2 ways: 2 suture anchors (single row) or a 4-anchor (double row) construct. Footprint area measurements over time, displacement after cyclic loading (2000 cycles), and final load to failure were measured. The double-row refixation technique was statistically superior to the single-row technique in footprint area measurement initially and 5 minutes after repair (P = .009 and P = .01, respectively) but not after 24 hours (P = .713). The double-row construct demonstrated significantly improved measures for peak load (433.9 ± 84.3 N vs 212.0 ± 49.7 N; P = .042), load at yield (354.7 ± 106.2 N vs 198.7 ± 39.5 N; P = .01), and slope (51.8 ± 9.9 N/mm vs 66.7 ± 16.2 N/mm; P = .021). Cyclic loading did not demonstrate significant differences between the 2 constructs. Double-row construct for reinsertion of a completely detached Achilles tendon using proximal and distal rows resulted in significantly larger contact area initially and 5 minutes after repair and led to significantly higher peak load to failure on destructive testing. In treatment for insertional Achilles tendinosis, the tendon often has to be detached and anatomically reattached to its insertion at the calcaneus. To our knowledge there is a lack of biomechanical studies supporting either a number or a pattern of suture anchor fixation. Because the stresses going across the insertion site of the Achilles tendon are significant during rehabilitation and weightbearing activities, it is imperative to have a strong construct that allows satisfactory healing during the early postoperative process.

[Multidimensional Strategy Regarding the Reduction of Central-Line Associated Infection in Pediatric Intensive Care].

PubMed

Rodrigues, Jorge; Dias, Andrea; Oliveira, Guiomar; Farela Neves, José

2016-06-01

To determine the central-line associated bloodstream infection rate after implementation of central venous catheter-care practice bundles and guidelines and to compare it with the previous central-line associated bloodstream infection rate. A prospective, longitudinal, observational descriptive study with an exploratory component was performed in a Pediatric Intensive Care Unit during five months. The universe was composed of every child admitted to Pediatric Intensive Care Unit who inserted a central venous catheter. A comparative study with historical controls was performed to evaluate the result of the intervention (group 1 versus group 2). Seventy five children were included, with a median age of 23 months: 22 (29.3%) newborns; 28 (37.3%) with recent surgery and 32 (43.8%) with underlying illness. A total of 105 central venous catheter were inserted, the majority a single central venous catheter (69.3%), with a mean duration of 6.8 ± 6.7 days. The most common type of central venous catheter was the short-term, non-tunneled central venous catheter (45.7%), while the subclavian and brachial flexure veins were the most frequent insertion sites (both 25.7%). There were no cases of central-line associated bloodstream infection reported during this study. Comparing with historical controls (group 1), both groups were similar regarding age, gender, department of origin and place of central venous catheter insertion. In the current study (group 2), the median length of stay was higher, while the mean duration of central venous catheter (excluding peripherally inserted central line) was similar in both groups. There were no statistical differences regarding central venous catheter caliber and number of lumens. Fewer children admitted to Pediatric Intensive Care Unit had central venous catheter inserted in group 2, with no significant difference between single or multiple central venous catheter. After multidimensional strategy implementation there was no reported central-line associated bloodstream infection Conclusions: Efforts must be made to preserve the same degree of multidimensional prevention, in order to confirm the effective reduction of the central-line associated bloodstream infection rate and to allow its maintenance.

Similar Patterns of Infection with Bovine Foamy Virus in Experimentally Inoculated Calves and Sheep

PubMed Central

Hechler, Torsten; Löchelt, Martin; Kuźmak, Jacek

2013-01-01

Foamy viruses (FVs) are the least known retroviruses commonly found in primates, cats, horses, and cattle. Although FVs are considered apathogenic, simian and feline FVs have been shown to be associated with some transient health abnormalities in animal models. Currently, data regarding the course of infection with bovine FV (BFV) are not available. In this study, we conducted experimental infections of natural (cattle) and heterologous (sheep) hosts with the BFV100 isolate and monitored infection patterns in both hosts during the early phase postinoculation as well as after long-term infection. Four calves and six sheep inoculated with BFV100 showed no signs of pathology but developed persistent infection, as confirmed by virus rescue, consistent detection of BFV-specific antibodies, and presence of viral DNA. In both hosts, antibodies against BFV Gag and Bet appeared early after infection and persisted at high and stable levels while seroreactivity toward Env was consistently detectable only in BFV-infected sheep. Interestingly, the BFV proviral DNA load was highest in lung, spleen, and liver and moderate in leukocytes, while salivary glands contained either low or undetectable DNA loads in calves or sheep, respectively. Additionally, comparison of partial BFV sequences from inoculum and infected animals demonstrated very limited changes after long-term infection in the heterologous host, clearly less than those found in BFV field isolates. The persistence of BFV infection in both hosts suggests full replication competence of the BFV100 isolate with no requirement of genetic adaptation for productive replication in the authentic and even in a heterologous host. PMID:23325680

Similar patterns of infection with bovine foamy virus in experimentally inoculated calves and sheep.

PubMed

Materniak, Magdalena; Hechler, Torsten; Löchelt, Martin; Kuzmak, Jacek

2013-03-01

Foamy viruses (FVs) are the least known retroviruses commonly found in primates, cats, horses, and cattle. Although FVs are considered apathogenic, simian and feline FVs have been shown to be associated with some transient health abnormalities in animal models. Currently, data regarding the course of infection with bovine FV (BFV) are not available. In this study, we conducted experimental infections of natural (cattle) and heterologous (sheep) hosts with the BFV(100) isolate and monitored infection patterns in both hosts during the early phase postinoculation as well as after long-term infection. Four calves and six sheep inoculated with BFV(100) showed no signs of pathology but developed persistent infection, as confirmed by virus rescue, consistent detection of BFV-specific antibodies, and presence of viral DNA. In both hosts, antibodies against BFV Gag and Bet appeared early after infection and persisted at high and stable levels while seroreactivity toward Env was consistently detectable only in BFV-infected sheep. Interestingly, the BFV proviral DNA load was highest in lung, spleen, and liver and moderate in leukocytes, while salivary glands contained either low or undetectable DNA loads in calves or sheep, respectively. Additionally, comparison of partial BFV sequences from inoculum and infected animals demonstrated very limited changes after long-term infection in the heterologous host, clearly less than those found in BFV field isolates. The persistence of BFV infection in both hosts suggests full replication competence of the BFV(100) isolate with no requirement of genetic adaptation for productive replication in the authentic and even in a heterologous host.

Reactivation of latent HIV-1 by a wide variety of butyric acid-producing bacteria.

PubMed

Imai, Kenichi; Yamada, Kiyoshi; Tamura, Muneaki; Ochiai, Kuniyasu; Okamoto, Takashi

2012-08-01

Latently infected cells harbor human immunodeficiency virus type 1 (HIV-1) proviral DNA copies integrated in heterochromatin, allowing persistence of transcriptionally silent proviruses. It is widely accepted that hypoacetylation of histone proteins by histone deacetylases (HDACs) is involved in maintaining the HIV-1 latency by repressing viral transcription. HIV-1 replication can be induced from latently infected cells by environmental factors, such as inflammation and co-infection with other microbes. It is known that a bacterial metabolite butyric acid inhibits catalytic action of HDAC and induces transcription of silenced genes including HIV-1 provirus. There are a number of such bacteria in gut, vaginal, and oral cavities that produce butyric acid during their anaerobic glycolysis. Since these organs are known to be the major site of HIV-1 transmission and its replication, we explored a possibility that explosive viral replication in these organs could be ascribable to butyric acid produced from anaerobic resident bacteria. In this study, we demonstrate that the culture supernatant of various bacteria producing butyric acid could greatly reactivate the latently-infected HIV-1. These bacteria include Fusobacterium nucleatum (commonly present in oral cavity, and gut), Clostridium cochlearium, Eubacterium multiforme (gut), and Anaerococcus tetradius (vagina). We also clarified that butyric acid in these culture supernatants could induce histone acetylation and HIV-1 replication by inhibiting HDAC. Our observations indicate that butyric acid-producing bacteria could be involved in AIDS progression by reactivating the latent HIV provirus and, subsequently, by eliminating such bacterial infection may contribute to the prevention of the AIDS development and transmission.

Does Navigation Improve Accuracy of Placement of Pedicle Screws in Single-level Lumbar Degenerative Spondylolisthesis?: A Comparison Between Free-hand and Three-dimensional O-Arm Navigation Techniques.

PubMed

Boon Tow, Benjamin Phak; Yue, Wai Mun; Srivastava, Abhishek; Lai, Jenn Ming; Guo, Chang Ming; Wearn Peng, Benedict Chan; Chen, John L T; Yew, Andy K S; Seng, Chusheng; Tan, Seang Beng

2015-10-01

This was a prospective, nonrandomized study. To assess the accuracy of O-arm navigation-based pedicle screw insertion in lumbar degenerative spondylolisthesis and to compare it with free-hand pedicle screw insertion technique in matched population. O-arm navigation is latest in navigation technology that can provide real-time intraoperative images in 3 dimensions while placing the pedicle screws to improve intraoperative pedicle screw accuracy. Degenerative lumbar spondylolisthesis is a locally unstable pathology and placement of pedicle screws can cause increased rotation and translation of the vertebral body. However, is this motion detected by the tracker placed across the unstable segment, is a matter of debate. Inability to detect these positional changes can lead to pedicle perforation while inserting screws using navigation. No study has evaluated the role of O-arm navigation in this patient population. The study population was divided into 2 groups with 19 patients each, one comprising patients who underwent O-arm navigation-based pedicle screw insertion (group 1) and the other comprising patients who underwent free-hand pedicle screw insertion technique (group 2). A total of 152 pedicle screws were implanted in 38 patients for 1-level instrumented fusion for degenerative lumbar spondylolisthesis. Intraoperative 3-dimensional computed tomography scans using the O-arm were obtained for all patients after insertion of pedicle screws. The images were reviewed intraoperatively and postoperatively for the analysis of pedicle breaches. Assessments in either of the group included (i) accuracy of placement of screws; (ii) the rate and direction of perforation; and (iii) the number of segments the perforated screw was away from the navigation tracker. Mean age of patients in group 1 (O-arm navigation-assisted) was 60 years (SD 11.25; range, 37-73 y), whereas in group 2 (free-hand pedicle screw) was 62 years (SD 18.07; range, 36-90 y). Overall anatomic perforation rate was 12.5% (19/152). Individually, group 1 had 14.47% (11/76) of perforations in comparison with 10.53% (8/76) observed in group 2. The difference was not statistically significant. The lateral margin was the most common site of perforation in both group 1 (64%, 7/11) and group 2 (62.5%, 5/8). Functional perforation rate for the series was 3.3% (5/152), with group 1 having 2.63% (2/76) and group 2 having 3.95% (3/76). The rate of perforation (PR) was significantly higher statistically when the tracker was placed 3 or more [PR 37.5% (6/16)] spinal segments away from instrumented segment compared with when it was placed 1 (0%) or 2 [PR 13.89% (5/36)] spinal segments away. Overall, 11 screws (11/152, 7.24%) had grade 2 perforations and had to be revised. No neurological complications were observed in the series. O-arm navigation does not provide any significant advantage over conventional free-hand pedicle screw insertion technique in patients with single-level degenerative spondylolisthesis. The accuracy is dependent on the distance of the tracker from the level of instrumentation. Lateral perforations are more common because of instability at the instrumented level leading to translation and rotation of the vertebral body while placing pedicle screws leading to preferential lateral trajectory. These lateral perforations could not be prevented by using navigation. However, no significant complications were noted in either technique.

Hot News: Gene Therapy with CRISPR/Cas9 Coming to Age for HIV Cure.

PubMed

Soriano, Vicente

2017-01-01

The huge success of current antiretroviral therapy is mediated by a triple effect: (i) Halting progression to AIDS in infected persons; (ii) reducing the risk of transmission to contacts (treatment as prevention); and (iii) minimizing the risk of HIV acquisition treating uninfected persons at risk (pre-exposure prophylaxis). However, UNAIDS has estimated that only 70% of infected people globally are diagnosed, only 53% are treated, and overall 44% have undetectable viral load, which is the necessary request for ensuring any antiretroviral benefit. Thus, with 37 million people currently living with HIV worldwide and more than 2 million new infections per year, the prospects for global HIV eradication are far on the horizon. Over the past couple of years, rapid development has been seen for technologies enabling modification of gene expression, either by direct inhibition by RNA interference (RNAi) or by genomic modification at DNA level. In particular, genome-editing endonucleases have significantly improved our ability to make precise changes in the DNA of eukaryotic cells. Notably, firstgeneration genome-editing technologies (i.e., ZFNs and TALENs) have been replaced by clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), which work with a short guide RNA (gRNA) to hybridize to a target DNA site and recruit the Cas9 endonuclease. Once integrated into the host genome, HIV gene expression is regulated by the LTR promoter. Hypothetically, gene editing of the HIV promoter might have the potential to deactivate viral transcription by the introduction of mutations or fragment excision. HIV gene therapy progressed very slowly until recent breakthroughs in gene-editing methods using CRISPR/Cas9 (Liao et al. Nat Commun 2015;6:6413). Using a shorter version of the Cas9 endonuclease ensembled into an adenoviral vector, critical segments of thAQ!e viral DNA genome spanning between the LTR and gag regions were successfully removed in HIV transgenic mice. Excision was confirmed in all examined tissues as well as in circulating lymphocytes and resulted in a drastic reduction of HIV-RNA (Kaminski et al. Gene Ther 2016;23:690-5). Moreover, using latently infected CD4+ T lymphocytes from HIV-infected persons, lentiviral-delivered CRISPR/Cas9 precisely removed the entire HIV genome spanning between the 50 and 30 LTRs of integrated HIV proviral DNA (Kaminski et al., Sci Rep 2016;6:22555), providing a proof of concept of the high potential of genome-editing technologies. Before moving to the clinic, the CRISPR/Cas9 technology must solve several major issues in the HIV scenario. First, generation of resistance is a major concern. Mutations may occur surrounding the targeted site and result in the selection of strains that are no longer recognized nor cleaved by CRISPR (Badia et al. Curr Opin Virol 2017;24:46-54). The efficacy of the anti-HIV CRISPR/Cas9 strategy is highly dependent on the gRNA sequence, yet some mutant viral strains show poor or no cleavage at all. Higher CRISPR/Cas9 pressure could delay but not eliminate viral replication when using a combination of distinct gRNAs targeting distinct HIV proviral genes. In this case, although the reading frame may remain unaltered, an accumulation of insertions and/or deletions may occur in the target sequence, rendering new viral strains insensitive to CRISPR/Cas9 cleavage. Finally, double-strand breaks resulting from CRISPR/Cas9 activity and subsequent cellular non-homologous end joining machinery may introduce mutations in sequences that are no longer recognized by the gRNA, and therefore not susceptible to Cas9 cleavage. A second consideration is a need for developing safe and effective mechanisms of delivery. Adenoviral vectors have long been studied in gene therapy and represent an ideal viral vector for transduction at different tissues. However, the packaging size of adenoviral vectors is a limiting factor, especially for CRIPSR/Cas9. Third, HIV has a genome of about 10 kb while a gRNA generally only targets 20 bp of the DNA molecule, which means that there are thousands available targeting sites for the provirus in latently infected cells. To date, there is no platform established solely for gRNA candidate evaluation in HIV provirus eradication. A final consideration is an access to all tissues and cells potentially harboring the HIV provirus, including reservoirs as the central nervous system. In this regard, efforts are being focused in the development of Cas9/gRNA nanoparticle formulations. To overcome these problems, a group in Florida recently developed human transgenic cells that may be used for gene-editing studies and as platform for high-throughput screen of HIV provirus disrupters (Huang et al. Sci Rep 2017;7:5955). Of note, Cas9 protein instead of a Cas9 plasmid was used. Compared to a plasmid introduction, Cas9 protein agents could be easily quantitatively applied and standardized, mimicking better real clinic scenarios. In summary, RNAi-based technologies have widely dominated gene therapy research during the past decade, with overall slow progress. However, the advent of new gene-editing technologies, and especially the CRISPR/Cas9 system, has revolutionized the field. In the HIV context, CRISPR/Cas9 applications might go further than those of RNAi, for example, enabling excision of segments of integrated proviral DNA from latently infected cells and allowing complete provirus elimination, or it may be used to reverse HIV latency. Although important challenges still need to be overcome, a promising pathway to HIV cure seems to have been found.

Rapid and sensitive insulated isothermal PCR for point-of-need feline leukaemia virus detection.

PubMed

Wilkes, Rebecca P; Anis, Eman; Dunbar, Dawn; Lee, Pei-Yu A; Tsai, Yun-Long; Lee, Fu-Chun; Chang, Hsiao-Fen G; Wang, Hwa-Tang T; Graham, Elizabeth M

2018-04-01

Objectives Feline leukaemia virus (FeLV), a gamma retrovirus, causes diseases of the feline haematopoietic system that are invariably fatal. Rapid and accurate testing at the point-of-need (PON) supports prevention of virus spread and management of clinical disease. This study evaluated the performance of an insulated isothermal PCR (iiPCR) that detects proviral DNA, and a reverse transcription (RT)-iiPCR that detects both viral RNA and proviral DNA, for FeLV detection at the PON. Methods Mycoplasma haemofelis, feline coronavirus, feline herpesvirus, feline calicivirus and feline immunodeficiency virus were used to test analytical specificity. In vitro transcribed RNA, artificial plasmid, FeLV strain American Type Culture Collection VR-719 and a clinical FeLV isolate were used in the analytical sensitivity assays. A retrospective study including 116 clinical plasma and serum samples that had been tested with virus isolation, real-time PCR and ELISA, and a prospective study including 150 clinical plasma and serum samples were implemented to evaluate the clinical performances of the iiPCR-based methods for FeLV detection. Results Ninety-five percent assay limit of detection was calculated to be 16 RNA and five DNA copies for the RT-iiPCR, and six DNA copies for the iiPCR. Both reactions had analytical sensitivity comparable to a reference real-time PCR (qPCR) and did not detect five non-target feline pathogens. The clinical performance of the RT-iiPCR and iiPCR had 98.82% agreement (kappa[κ] = 0.97) and 100% agreement (κ = 1.0), respectively, with the qPCR (n = 85). The agreement between an automatic nucleic extraction/RT-iiPCR system and virus isolation to detect FeLV in plasma or serum was 95.69% (κ = 0.95) and 98.67% (κ = 0.85) in a retrospective (n = 116) and a prospective (n = 150) study, respectively. Conclusions and relevance These results suggested that both RT-iiPCR and iiPCR assays can serve as reliable tools for PON FeLV detection.

The effect of HTLV-1 virulence factors (HBZ, Tax, proviral load), HLA class I and plasma neopterin on manifestation of HTLV-1 associated myelopathy tropical spastic paraparesis.

PubMed

Tarokhian, Hanieh; Taghadosi, Mahdi; Rafatpanah, Hushang; Rajaei, Taraneh; Azarpazhooh, Mahmoud Reza; Valizadeh, Narges; Rezaee, S A Rahim

2017-01-15

Previous studies have suggested debatable roles of Tax and HBZ gene expression in the pathogenesis of HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP). In this study, HTLV-1 and host interactions in the manifestation of HAM/TSP were evaluated. A cross-sectional study was conducted on 33 HAM/TSP patients and 38 HTLV-1 asymptomatic carriers (ACs). HTLV-1-Tax, HBZ gene expression, and proviral load (PVL) were assessed using the quantitative real-time PCR (TaqMan), host plasma neopterin level, and HLA-I, and the clinical manifestation were evaluated. The HTLV-1 PVLs in HAM/TSP and ACs were 306±360.741 copies/10 4 PBMCs and 250.98±629.94 copies/10 4 PBMCs, respectively; the PVL was higher in HAM/TSP than that in ACs (p=0.004). HTLV-1 Tax and HBZ expression in HAM/TSP was higher than that in ACs, wherein only the Tax expression was statistically significant (p=0.039). In contrast to Japanese HTLV-1-infected subjects, HLA-A*02, HLA-A*24, HLA-Cw*08, and HLA-B*5401 did not exhibit preventive effects for HAM/TSP manifestation. The plasma neopterin level was significantly higher in HAM/TSPs than that in ACs; furthermore, there was a strong significant correlation between plasma neopterin and PVL (R=0.76, p=0.001). Moreover, there were significant correlation between urinary disturbances and haematological indices, including the RBC count (R=-0.61, p=0.01) and Hematocrit (Ht) index (R=-0.75, p=0.002), and between mobility disturbances with Tax expression (R=-0.58, p=0.02) and WBC counts (R=-0.54, p=0.04), and finally, a significant association was found between the sensory disturbances and PVL (p=0.05). Overall, HTLV-1 PVL and Tax may be the valid predictors of disease development, and the neopterin level may be a valid predictor of disease progression. In addition, Tax and neopterin are more helpful than PVL for the monitoring of HTLV-1-infected patients. Copyright © 2016 Elsevier B.V. All rights reserved.

Human T-lymphotropic virus type-1 p30 alters cell cycle G2 regulation of T lymphocytes to enhance cell survival

PubMed Central

Datta, Antara; Silverman, Lee; Phipps, Andrew J; Hiraragi, Hajime; Ratner, Lee; Lairmore, Michael D

2007-01-01

Background Human T-lymphotropic virus type-1 (HTLV-1) causes adult T-cell leukemia/lymphoma and is linked to a number of lymphocyte-mediated disorders. HTLV-1 contains both regulatory and accessory genes in four pX open reading frames. pX ORF-II encodes two proteins, p13 and p30, whose roles are still being defined in the virus life cycle and in HTLV-1 virus-host cell interactions. Proviral clones of HTLV-1 with pX ORF-II mutations diminish the ability of the virus to maintain viral loads in vivo. p30 expressed exogenously differentially modulates CREB and Tax-responsive element-mediated transcription through its interaction with CREB-binding protein/p300 and while acting as a repressor of many genes including Tax, in part by blocking tax/rex RNA nuclear export, selectively enhances key gene pathways involved in T-cell signaling/activation. Results Herein, we analyzed the role of p30 in cell cycle regulation. Jurkat T-cells transduced with a p30 expressing lentivirus vector accumulated in the G2-M phase of cell cycle. We then analyzed key proteins involved in G2-M checkpoint activation. p30 expression in Jurkat T-cells resulted in an increase in phosphorylation at serine 216 of nuclear cell division cycle 25C (Cdc25C), had enhanced checkpoint kinase 1 (Chk1) serine 345 phosphorylation, reduced expression of polo-like kinase 1 (PLK1), diminished phosphorylation of PLK1 at tyrosine 210 and reduced phosphorylation of Cdc25C at serine 198. Finally, primary human lymphocyte derived cell lines immortalized by a HTLV-1 proviral clone defective in p30 expression were more susceptible to camptothecin induced apoptosis. Collectively these data are consistent with a cell survival role of p30 against genotoxic insults to HTLV-1 infected lymphocytes. Conclusion Collectively, our data are the first to indicate that HTLV-1 p30 expression results in activation of the G2-M cell cycle checkpoint, events that would promote early viral spread and T-cell survival. PMID:17634129

Endoscopic-Assisted Burr Hole Reservoir and Ventricle Catheter Placement.

PubMed

Antes, Sebastian; Tschan, Christoph A; Heckelmann, Michael; Salah, Mohamed; Senger, Sebastian; Linsler, Stefan; Oertel, Joachim

2017-05-01

Accurate positioning of a ventricle catheter is of utmost importance. Various techniques to ensure optimal positioning have been described. Commonly, after catheter placement, additional manipulation is necessary to connect a burr hole reservoir or shunt components. This manipulation can lead to accidental catheter dislocation and should be avoided. Here, we present a new technique that allows direct endoscopic insertion of a burr hole reservoir with an already mounted ventricle catheter. Before insertion, the ventricle catheter was slit at the tip, shortened to the correct length, and connected to the special burr hole reservoir. An intracatheter endoscope was then advanced through the reservoir and the connected catheter. This assemblage allowed using the endoscope as a stylet for shielded ventricular puncture. To confirm correct placement of the ventricle catheter, the endoscope was protruded a few millimeters beyond the catheter tip for inspection. The new technique was applied in 12 procedures. The modified burr hole reservoir was inserted for first-time ventriculoperitoneal shunting (n = 1), cerebrospinal fluid withdrawals and drug administration (n = 2), or different stenting procedures (n = 9). Optimal positioning of the catheter was achieved in 11 of 12 cases. No subcutaneous cerebrospinal fluid collection or fluid leakage through the wound occurred. No parenchymal damage or bleeding appeared. The use of the intracatheter endoscope combined with the modified burr hole reservoir provides a sufficient technique for accurate and safe placement. Connecting the ventricle catheter to the reservoir before the insertion reduces later manipulation and accidental dislocation of the catheter. Copyright © 2017 Elsevier Inc. All rights reserved.

Image-guided Ommaya reservoir insertion for intraventricular chemotherapy: a retrospective series.

PubMed

Lau, Jonathan C; Kosteniuk, Suzanne E; Macdonald, David R; Megyesi, Joseph F

2018-03-01

Ayub Ommaya proposed a surgical technique for subcutaneous reservoir and pump placement in 1963 to allow access to intraventricular cerebrospinal fluid (CSF). Currently, the most common indication for Ommaya reservoir insertion (ORI) in adults is for patients with hematologic or leptomeningeal disorders requiring repeated injection of chemotherapy into the CSF space. Historically, the intraventricular catheter has been inserted blindly based on anatomical landmarks. The purpose of this study was to examine short-term complication rates with ORI with image guidance (IG) and without image guidance (non-IG). We retrospectively evaluated all operative cases of ORI from 2000 to 2014 by the senior author. Patient demographic data, surgical outcomes, and peri-operative complications were collected. Accurate placement and early (30-day) morbidity or mortality were considered primary outcomes. Fifty-five consecutive patients underwent ORI by the senior author over the study period (43.5 ± 16.6 years; 40.0% female). Indications for placement included acute lymphoblastic leukemia, diffuse large B-cell lymphoma, and leptomeningeal carcinomatosis. There were seven (12.7%) total complications: three (37.5%) with no-IG versus four (8.5%) with IG. Catheter malpositions were significantly higher in the non-IG group at 37.5% compared to 2.1%. Catheters were also more likely to require multiple passes with non-IG at 25% compare to 0% with IG. There were no early infections in either group. We demonstrate improved accuracy and decreased complications using an image-guided approach compared with a traditional approach. Our results support routine use of intra-operative image guidance for proximal catheter insertion in elective ORI for intraventricular chemotherapy.

Mobile elements reveal small population size in the ancient ancestors of Homo sapiens.

PubMed

Huff, Chad D; Xing, Jinchuan; Rogers, Alan R; Witherspoon, David; Jorde, Lynn B

2010-02-02

The genealogies of different genetic loci vary in depth. The deeper the genealogy, the greater the chance that it will include a rare event, such as the insertion of a mobile element. Therefore, the genealogy of a region that contains a mobile element is on average older than that of the rest of the genome. In a simple demographic model, the expected time to most recent common ancestor (TMRCA) is doubled if a rare insertion is present. We test this expectation by examining single nucleotide polymorphisms around polymorphic Alu insertions from two completely sequenced human genomes. The estimated TMRCA for regions containing a polymorphic insertion is two times larger than the genomic average (P < <10(-30)), as predicted. Because genealogies that contain polymorphic mobile elements are old, they are shaped largely by the forces of ancient population history and are insensitive to recent demographic events, such as bottlenecks and expansions. Remarkably, the information in just two human DNA sequences provides substantial information about ancient human population size. By comparing the likelihood of various demographic models, we estimate that the effective population size of human ancestors living before 1.2 million years ago was 18,500, and we can reject all models where the ancient effective population size was larger than 26,000. This result implies an unusually small population for a species spread across the entire Old World, particularly in light of the effective population sizes of chimpanzees (21,000) and gorillas (25,000), which each inhabit only one part of a single continent.

Primary implant stability in augmented sinuslift-sites after completed bone regeneration: a randomized controlled clinical study comparing four subantrally inserted biomaterials

PubMed Central

Troedhan, Angelo; Schlichting, Izabela; Kurrek, Andreas; Wainwright, Marcel

2014-01-01

Implant-Insertion-Torque-Value (ITV) proved to be a significant clinical parameter to predict long term implant success-rates and to decide upon immediate loading. The study evaluated ITVs, when four different and commonly used biomaterials were used in sinuslift-procedures compared to natural subantral bone in two-stage-implant-procedures. The tHUCSL-INTRALIFT-method was chosen for sinuslifting in 155 sinuslift-sites for its minimal invasive transcrestal approach and scalable augmentation volume. Four different biomaterials were inserted randomly (easy-graft CRYSTAL n = 38, easy-graft CLASSIC n = 41, NanoBone n = 42, BioOss n = 34), 2 ccm in each case. After a mean healing period of 8,92 months uniform tapered screw Q2-implants were inserted and Drill-Torque-Values (DTV) and ITV were recorded and compared to a group of 36 subantral sites without need of sinuslifting. DTV/ITV were processed for statistics by ANOVA-tests. Mean DTV/ITV obtained in Ncm were: Control Group 10,2/22,2, Bio-Oss 12,7/26,2, NanoBone 17,5/33,3, easy-graft CLASSIC 20,3/45,9, easy-graft CRYSTAL 23,8/56,6 Ncm, significance-level of differences throughout p < 0,05. Within the limits of this study the results suggest self-hardening solid-block-like bone-graft-materials to achieve significantly better DTV/ITV than loose granulate biomaterials for its suspected improvement of vascularization and mineralization of the subantral scaffold by full immobilization of the augmentation site towards pressure changes in the human sinus at normal breathing. PMID:25073446

Plastome Sequencing of Ten Nonmodel Crop Species Uncovers a Large Insertion of Mitochondrial DNA in Cashew.

PubMed

Rabah, Samar O; Lee, Chaehee; Hajrah, Nahid H; Makki, Rania M; Alharby, Hesham F; Alhebshi, Alawiah M; Sabir, Jamal S M; Jansen, Robert K; Ruhlman, Tracey A

2017-11-01

In plant evolution, intracellular gene transfer (IGT) is a prevalent, ongoing process. While nuclear and mitochondrial genomes are known to integrate foreign DNA via IGT and horizontal gene transfer (HGT), plastid genomes (plastomes) have resisted foreign DNA incorporation and only recently has IGT been uncovered in the plastomes of a few land plants. In this study, we completed plastome sequences for l0 crop species and describe a number of structural features including variation in gene and intron content, inversions, and expansion and contraction of the inverted repeat (IR). We identified a putative in cinnamon ( J. Presl) and other sequenced Lauraceae and an apparent functional transfer of to the nucleus of quinoa ( Willd.). In the orchard tree cashew ( L.), we report the insertion of an ∼6.7-kb fragment of mitochondrial DNA into the plastome IR. BLASTn analyses returned high identity hits to mitogenome sequences including an intact open reading frame. Using three plastome markers for five species of , we generated a phylogeny to investigate the distribution and timing of the insertion. Four species share the insertion, suggesting that this event occurred <20 million yr ago in a single clade in the genus. Our study extends the observation of mitochondrial to plastome IGT to include long-lived tree species. While previous studies have suggested possible mechanisms facilitating IGT to the plastome, more examples of this phenomenon, along with more complete mitogenome sequences, will be required before a common, or variable, mechanism can be elucidated. Copyright © 2017 Crop Science Society of America.

Partially covered self-expandable metal stents versus polyethylene stents for malignant biliary obstruction: A cost-effectiveness analysis

PubMed Central

Barkun, Alan N; Adam, Viviane; Martel, Myriam; AlNaamani, Khalid; Moses, Peter L

2015-01-01

BACKGROUND/OBJECTIVE: Partially covered self-expandable metal stents (SEMS) and polyethylene stents (PES) are both commonly used in the palliation of malignant biliary obstruction. Although SEMS are significantly more expensive, they are more efficacious than PES. Accordingly, a cost-effectiveness analysis was performed. METHODS: A cost-effectiveness analysis compared the approach of initial placement of PES versus SEMS for the study population. Patients with malignant biliary obstruction underwent an endoscopic retrograde cholangiopancreatography to insert the initial stent. If the insertion failed, a percutaneous transhepatic cholangiogram was performed. If stent occlusion occurred, a PES was inserted at repeat endoscopic retrograde cholangiopancreatography, either in an outpatient setting or after admission to hospital if cholangitis was present. A third-party payer perspective was adopted. Effectiveness was expressed as the likelihood of no occlusion over the one-year adopted time horizon. Probabilities were based on a contemporary randomized clinical trial, and costs were issued from national references. Deterministic and probabilistic sensitivity analyses were performed. RESULTS: A PES-first strategy was both more expensive and less efficacious than an SEMS-first approach. The mean per-patient costs were US$6,701 for initial SEMS and US$20,671 for initial PES, which were associated with effectiveness probabilities of 65.6% and 13.9%, respectively. Sensitivity analyses confirmed the robustness of these results. CONCLUSION: At the time of initial endoscopic drainage for patients with malignant biliary obstruction undergoing palliative stenting, an initial SEMS insertion approach was both more effective and less costly than a PES-first strategy. PMID:26125107

Improving Nurses' Peripheral Intravenous Catheter Insertion Knowledge, Confidence, and Skills Using a Simulation-Based Blended Learning Program: A Randomized Trial.

PubMed

Keleekai, Nowai L; Schuster, Catherine A; Murray, Connie L; King, Mary Anne; Stahl, Brian R; Labrozzi, Laura J; Gallucci, Susan; LeClair, Matthew W; Glover, Kevin R

2016-12-01

Peripheral intravenous catheter (PIVC) insertion is one of the most common invasive procedures performed in a hospital, but most nurses receive little formal training in this area. Blended PIVC insertion training programs that incorporate deliberate simulated practice have the potential to improve clinical practice and patient care. The study was a randomized, wait-list control group with crossover using nurses on three medical/surgical units. Baseline PIVC knowledge, confidence, and skills assessments were completed for both groups. The intervention group then received a 2-hour PIVC online course, followed by an 8-hour live training course using a synergistic mix of three simulation tools. Both groups were then reassessed. After crossover, the wait-list group received the same intervention and both groups were reassessed. At baseline, both groups were similar for knowledge, confidence, and skills. Compared with the wait-list group, the intervention group had significantly higher scores for knowledge, confidence, and skills upon completing the training program. After crossover, the wait-list group had similarly higher scores for knowledge, confidence, and skills than the intervention group. Between the immediate preintervention and postintervention periods, the intervention group improved scores for knowledge by 31%, skills by 24%, and decreased confidence by 0.5%, whereas the wait-list group improved scores for knowledge by 28%, confidence by 16%, and skills by 15%. Results demonstrate significant improvements in nurses' knowledge, confidence, and skills with the use of a simulation-based blended learning program for PIVC insertion. Transferability of these findings from a simulated environment into clinical practice should be further explored.

A Genetic Screen for Pathogenicity Genes in the Hemibiotrophic Fungus Colletotrichum higginsianum Identifies the Plasma Membrane Proton Pump Pma2 Required for Host Penetration

PubMed Central

Dahl, Marlis; Müller, Susanne; Voll, Lars M.; Koch, Christian

2015-01-01

We used insertional mutagenesis by Agrobacterium tumefaciens mediated transformation (ATMT) to isolate pathogenicity mutants of Colletotrichum higginsianum. From a collection of 7200 insertion mutants we isolated 75 mutants with reduced symptoms. 19 of these were affected in host penetration, while 17 were affected in later stages of infection, like switching to necrotrophic growth. For 16 mutants the location of T-DNA insertions could be identified by PCR. A potential plasma membrane H+-ATPase Pma2 was targeted in five independent insertion mutants. We genetically inactivated the Ku80 component of the non-homologous end-joining pathway in C. higginsianum to establish an efficient gene knockout protocol. Chpma2 deletion mutants generated by homologous recombination in the ΔChku80 background form fully melanized appressoria but entirely fail to penetrate the host tissue and are non-pathogenic. The ChPMA2 gene is induced upon appressoria formation and infection of A. thaliana. Pma2 activity is not important for vegetative growth of saprophytically growing mycelium, since the mutant shows no growth penalty under these conditions. Colletotrichum higginsianum codes for a closely related gene (ChPMA1), which is highly expressed under most growth conditions. ChPMA1 is more similar to the homologous yeast genes for plasma membrane pumps. We propose that expression of a specific proton pump early during infection may be common to many appressoria forming fungal pathogens as we found ChPMA2 orthologs in several plant pathogenic fungi. PMID:25992547

Three-dimensional analysis of elbow soft tissue footprints and anatomy.

PubMed

Capo, John T; Collins, Christopher; Beutel, Bryan G; Danna, Natalie R; Manigrasso, Michaele; Uko, Linda A; Chen, Linda Y

2014-11-01

Tendinous and ligamentous injuries commonly occur in the elbow. This study characterized the location, surface areas, and origin and insertional footprints of major elbow capsuloligamentous and tendinous structures in relation to bony landmarks with the use of a precision 3-dimensional modeling system. Nine unpaired cadaveric elbow specimens were dissected and mounted on a custom jig. Mapping of the medial collateral ligament (MCL), lateral ulnar collateral ligament (LUCL), triceps, biceps, brachialis, and capsular reflections was then performed with 3-dimensional digitizing technology. The location, surface areas, and footprints of the soft tissues were calculated. The MCL had a mean origin (humeral) footprint of 216 mm(2), insertional footprint of 154 mm(2), and surface area of 421 mm(2). The LUCL had a mean origin footprint of 136 mm(2), an insertional footprint of 142 mm(2), and a surface area of 532 mm(2). Of the tendons, the triceps maintained the largest insertional footprint, followed by the brachialis and the biceps (P < .001-.03). The MCL, LUCL, and biceps footprint locations were consistent, with little variability. The surface areas of the anterior (1251 mm(2)) and posterior (1147 mm(2)) capsular reflections were similar (P = .82), and the anterior capsule extended farther proximally. Restoring the normal anatomy of key elbow capsuloligamentous and tendinous structures is crucial for effective reconstruction after bony or soft tissue trauma. This study provides the upper extremity surgeon with information that may aid in restoring elbow biomechanics and preserving range of motion in these patients. Copyright © 2014 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Acceptability of the vaginal contraceptive ring among adolescent women.

PubMed

Terrell, Lekeisha R; Tanner, Amanda E; Hensel, Devon J; Blythe, Margaret J; Fortenberry, J Dennis

2011-08-01

Although underutilized, the vaginal contraceptive ring has several advantages over other contraceptive methods that could benefit adolescents. We examined factors that may influence willingness to try the vaginal ring including: sexual and contraceptive history, genital comfort, and vaginal ring characteristics. Cross sectional Midwestern adolescent health clinics Adolescent women (N = 200; 14-18 years; 89% African-American) INTERVENTIONS/MAIN OUTCOME MEASURES: All participants received education about the vaginal ring and viewed pictures demonstrating insertion; they then completed a visual/audio computer-assisted self interview. The primary outcome variable, willingness to try the vaginal ring, was a single Likert-scale item. Over half the participants reported knowledge of the vaginal ring with healthcare providers identified as the most important source of contraceptive information. Comfort with one's genitals, insertion and removal, using alternative methods of insertion, and knowing positive method characteristics were significantly associated with willingness to try the vaginal ring. A decreased willingness to try the vaginal ring was related to concerns of the ring getting lost inside or falling out of the vagina. Willingness to try the ring was associated with positive feelings about genitals (e.g., comfort with appearance, hygiene, function). Thus, to increase willingness to try the vaginal ring among adolescents, providers should make it common practice to discuss basic female reproductive anatomy, raise awareness about female genital health and address concerns about their genitals. Providers can offer alternative insertion techniques (e.g., gloves) to make use more accessible. These strategies may increase vaginal ring use among adolescents. 2011 North American Society for Pediatric and Adolescent Gynecology. Published by Elsevier Inc. All rights reserved.

Primary implant stability in augmented sinuslift-sites after completed bone regeneration: a randomized controlled clinical study comparing four subantrally inserted biomaterials.

PubMed

Troedhan, Angelo; Schlichting, Izabela; Kurrek, Andreas; Wainwright, Marcel

2014-07-30

Implant-Insertion-Torque-Value (ITV) proved to be a significant clinical parameter to predict long term implant success-rates and to decide upon immediate loading. The study evaluated ITVs, when four different and commonly used biomaterials were used in sinuslift-procedures compared to natural subantral bone in two-stage-implant-procedures. The tHUCSL-INTRALIFT-method was chosen for sinuslifting in 155 sinuslift-sites for its minimal invasive transcrestal approach and scalable augmentation volume. Four different biomaterials were inserted randomly (easy-graft CRYSTAL n = 38, easy-graft CLASSIC n = 41, NanoBone n = 42, BioOss n = 34), 2 ccm in each case. After a mean healing period of 8,92 months uniform tapered screw Q2-implants were inserted and Drill-Torque-Values (DTV) and ITV were recorded and compared to a group of 36 subantral sites without need of sinuslifting. DTV/ITV were processed for statistics by ANOVA-tests. Mean DTV/ITV obtained in Ncm were: Control Group 10,2/22,2, Bio-Oss 12,7/26,2, NanoBone 17,5/33,3, easy-graft CLASSIC 20,3/45,9, easy-graft CRYSTAL 23,8/56,6 Ncm, significance-level of differences throughout p < 0,05. Within the limits of this study the results suggest self-hardening solid-block-like bone-graft-materials to achieve significantly better DTV/ITV than loose granulate biomaterials for its suspected improvement of vascularization and mineralization of the subantral scaffold by full immobilization of the augmentation site towards pressure changes in the human sinus at normal breathing.

Common agents used to unblock blood clots within tympanostomy tubes: an ex vivo study and review of literature.

PubMed

Burke, Emily L; Walvekar, Rohan R; Lin, James; Hagan, Joseph; Kluka, Evelyn A

2009-12-01

To determine the efficacy of common solutions used to dissolve blood clots blocking tympanostomy tubes (TTs) of differing lengths and diameters. An ex vivo experimental study. Ear models were built by the study investigator. Tympanostomy tubes were inserted into the models and blocked with blood clots. Test solutions were applied to the blood clots, and time for clearance was recorded via microscopic visual confirmation. Richards T-tube had higher odds of unclogging than collar button tubes (odds ratio: 2.37, 95% confidence intervals 1.02-5.54, p=0.042). Vinegar and 3% hydrogen peroxide were most effective for Richards T-tubes and collar button tubes, respectively. Common solutions (vinegar and hydrogen peroxide) were more effective than antibiotic drops in clearing blood clot blocking TTs.

Ventriculostomy for acute hydrocephalus in critically ill patients on the ICU--outcome analysis of two different procedures.

PubMed

Schödel, Petra; Proescholdt, Martin; Brawanski, Alexander; Bele, Sylvia; Schebesch, Karl-Michael

2012-04-01

Burr-hole trephine and insertion of an external ventricular drainage (EVD) is a common procedure in neurosurgical practice. In critically ill patients, the transport to the operating room, OR represents a major risk. Thus, the burr-hole trephine and implantation of an EVD is frequently performed on the Intensive Care Unit (ICU). Since 2004, we have applied two different procedures: the conventional method with a mechanical compressed air or an electric drill, and an alternative method with a manual twist drill, including fixation of the EVD in a skull screw (Bolt Kit, Raumedic AG, Germany). This study was designed to evaluate the outcome of both surgical procedures. In this retrospective analysis we included 166 consecutive patients with acute hydrocephalus due to intracranial hemorrhage that had been operated at our neurosurgical ICU in a six years interval. We reviewed the charts for gender and age, kind of surgical procedure, cerebrospinal fluid (CSF)-infections, duration of drainage, attempts of insertions, wound infections, misplacement rate, post-surgical hemorrhages, revisions, comorbidities and shunt-dependency. In 122 patients we applied the Bolt Kit System, in 44 patients the conventional method was performed. We found a significantly lower rate of CSF-infections and significantly fewer attempts of insertions in the Bolt Kit group (p = 0.002 and p = 0.001, respectively). The rate of wound infections, misplacement, revisions, shunt-dependency and the post-surgical hemorrhages did not differ significantly. Our data indicate that the manual drill and the skull screw are safe and feasible tools in the treatment of acute hydrocephalus. Presumably, the direct skin contact is causative for the higher rate of CSF-infections when the conventional method is performed. The skull screw guides the EVD into the ventricle without skin contact. The lower number of insertions needed may be due to the fact that the skull screw allows just one trajectory for the insertion of the EVD.

Structure and expression of the attacin genes in Hyalophora cecropia.

PubMed

Sun, S C; Lindström, I; Lee, J Y; Faye, I

1991-02-26

To study the regulation of the immune genes in insects, we have cloned and sequenced the attacin gene locus of the giant silk moth Hyalophora cecropia. The locus contains one acidic and one basic attacin gene as well as two pseudogenes, which are remnants of basic attacin genes. A small insertion element was found within the locus. The two functional attacin genes are transcribed in opposite directions and have two introns inserted at homologous positions. A common sequence, GGGGATTCCT, is found at nucleotide position -48 in the acidic gene and at nucleotide position -58 in the basic gene. Interestingly, this decanucleotide is similar to the consensus of the NF-k B-binding site. Expression studies revealed that both attacins are strongly induced by phorbol 12-myristate 13-acetate, lipopolysaccharide and bacteria. However, only the acidic attacin gene showed a clear response to injury.

Intraoperative laser speckle contrast imaging improves the stability of rodent middle cerebral artery occlusion model

NASA Astrophysics Data System (ADS)

Yuan, Lu; Li, Yao; Li, Hangdao; Lu, Hongyang; Tong, Shanbao

2015-09-01

Rodent middle cerebral artery occlusion (MCAO) model is commonly used in stroke research. Creating a stable infarct volume has always been challenging for technicians due to the variances of animal anatomy and surgical operations. The depth of filament suture advancement strongly influences the infarct volume as well. We investigated the cerebral blood flow (CBF) changes in the affected cortex using laser speckle contrast imaging when advancing suture during MCAO surgery. The relative CBF drop area (CBF50, i.e., the percentage area with CBF less than 50% of the baseline) showed an increase from 20.9% to 69.1% when the insertion depth increased from 1.6 to 1.8 cm. Using the real-time CBF50 marker to guide suture insertion during the surgery, our animal experiments showed that intraoperative CBF-guided surgery could significantly improve the stability of MCAO with a more consistent infarct volume and less mortality.

Semiextended approach for intramedullary nailing via a patellar eversion technique for tibial-shaft fractures: Evaluation of the patellofemoral joint.

PubMed

Yasuda, Tomohiro; Obara, Shu; Hayashi, Junji; Arai, Masayuki; Sato, Kaoru

2017-06-01

Intramedullary nail fixation is a common treatment for tibial-shaft fractures, and it offers a better functional prognosis than other conservative treatments. Currently, the primary approach employed during intramedullary nail insertion is the semiextended position is the suprapatellar approach, which involves a vertical incision of the quadriceps tendon Damage to the patellofemoral joint cartilage has been highlighted as a drawback associated with this approach. To avoid this issue, we perform surgery using the patellar eversion technique and a soft sleeve. This method allows the articular surface to be monitored during intramedullary nail insertion. We arthroscopically assessed the effect of this technique on patellofemoral joint cartilage. The patellar eversion technique allows a direct view and protection of the patellofemoral joint without affecting the patella. Thus, damage to the patellofemoral joint cartilage can be avoided. Copyright © 2017 Elsevier Ltd. All rights reserved.

Functional nicotinic acetylcholine receptor reconstitution in Au(111)-supported thiolipid monolayers

NASA Astrophysics Data System (ADS)

Pissinis, Diego E.; Diaz, Carolina; Maza, Eliana; Bonini, Ida C.; Barrantes, Francisco J.; Salvarezza, Roberto C.; Schilardi, Patricia L.

2015-09-01

The insertion and function of the muscle-type nicotinic acetylcholine receptor (nAChR) in Au(111)-supported thiolipid self-assembled monolayers have been studied by atomic force microscopy (AFM), surface plasmon resonance (SPR), and electrochemical techniques. It was possible for the first time to resolve the supramolecular arrangement of the protein spontaneously inserted in a thiolipid monolayer in an aqueous solution. Geometric supramolecular arrays of nAChRs were observed, most commonly in a triangular form compatible with three nAChR dimers of ~20 nm each. Addition of the full agonist carbamoylcholine activated and opened the nAChR ion channel, as revealed by the increase in capacitance relative to that of the nAChR-thiolipid system under basal conditions. Thus, the self-assembled system appears to be a viable biomimetic model to measure ionic conductance mediated by ion-gated ion channels under different experimental conditions, with potential applications in biotechnology and pharmacology.

Cardiovascular results from a rhesus monkey flown aboard the Cosmos 1514 spaceflight

NASA Technical Reports Server (NTRS)

Sandler, H.; Hines, J.; Benjamin, B. A.; Halpryn, B. M.; Krotov, V. P.

1987-01-01

The results of the Cosmos 1514 cardiovascular experiment, in which the blood flow to the head and the carotid pressure of a rhesus monkey were measured during the 5-d spaceflight, are reported. A single cylindrical probe containing both pressure and flow transducers was chronically implanted as a cuff around the left common carotid artery; measurements were obtained for 4 min every 2 h and compared to identical recordings obtained during a preflight control period and during 12 h on a launch pad. Immediately on its insertion into orbit, mean arterial pressure increased by 10 percent and has maintained a 16-27 percent increase over the first few hours of flight before returning to baseline level. Blood flow showed reciprocal changes to pressure on orbital insertion. Cardiovascular system changes persisted into the second day of flight, with the signs of adaptation appearing on days 3-5.

Evaluation of the effect of custom burr holes on a surgeon's sense of screw fixation in revision porous metal cups.

PubMed

Nyland, Mark A; Lanting, Brent A; Nikolov, Hristo N; Somerville, Lyndsay E; Teeter, Matthew G; Howard, James L

2016-12-01

It is common practice to burr custom holes in revision porous metal cups for screw insertion. The objective of this study was to determine how different hole types affect a surgeon's sense of screw fixation. Porous revision cups were prepared with pre-drilled and custom burred holes. Cups were held in place adjacent to synthetic bone material of varying density. Surgeons inserted screws through the different holes and materials. Surgeon subjective rating, compression, and torque was recorded. The torque achieved was greater ( p  = 0.002) for screws through custom holes than pre-fabricated holes in low and medium density material, with no difference for high density. Peak compression was greater ( p  = 0.026) through the pre-fabricated holes only in high density material. Use of burred holes affects the torque generated, and may decrease the amount of cup-acetabulum compression achieved.

DebriSat Laboratory Analyses

DTIC Science & Technology

2015-01-05

droplets. Fluorine from Teflon wire insulation was also common in the SEM stub and witness plates deposits. Nano droplets of metallic materials...and Debris-LV debris. Aluminum was from the Al honeycomb, nadir and zenith panels, structural core and COPV liner. Aluminum oxide particles were...three pieces: Outer Nylon shell (sabot) with 2 part hollow aluminum insert. • ~600 grams, 8.6 cm diameter X 10.3 cm long – size of a soup can

An MMI-based demultiplexer with reduced cross-talk

NASA Astrophysics Data System (ADS)

Xiao, Yueyu; He, Sailing

2005-03-01

The crosstalk of a multimode interference (MMI)-based demultiplexer is reduced by connecting appropriately designed cascaded MMI filters of high-order. Numerical results show that the designed demultiplexer greatly improves the bandwidth of 20 dB cross-talk loss and has an excellent performance in terms of the insertion loss and chromatic dispersion. Formed with commonly used MMI couplers, the present structure is much easier to implement than other structures.

Primary Care Management of Plantar Fasciitis.

PubMed

Melvin, Thomas J; Tankersley, Zach J; Qazi, Zain N; Jasko, John J; Odono, Russell; Shuler, Franklin D

2015-01-01

Plantar fasciitis (PF) is present in 10% of the population and is the most common cause of plantar heel pain. PF is painful, can alter daily activities and presents as a sharp pain localized to the plantar foot and medial heel. The underlying etiology involves microtrauma to the plantar fascia, specifically at its insertion point on the calcaneus. Successful management of plantar fasciitis is typically achieved with the conservative therapy approaches discussed.

Endourethral MRI Guidance for Prostatic RF Ablation

DTIC Science & Technology

2005-06-01

head (3 cm wide) attached to a 24-cm plastic handle,. Copper tape and then covered with a coat of protective plastic. In addition, bazooka baluns made...in the perineum , advanced posterior surface. This arrangement was used to mimic the into the prostatic urethra, and fixated in the prostate by...are inserted through the perineum placed in the left lateral decubitus position to maximize and into the prostate gland, commonly under ultrasound