WorldWideScience

Sample records for longitudinal clonal hiv

  1. An Evaluation of Phylogenetic Methods for Reconstructing Transmitted HIV Variants using Longitudinal Clonal HIV Sequence Data

    Science.gov (United States)

    McCloskey, Rosemary M.; Liang, Richard H.; Harrigan, P. Richard; Brumme, Zabrina L.

    2014-01-01

    ABSTRACT A population of human immunodeficiency virus (HIV) within a host often descends from a single transmitted/founder virus. The high mutation rate of HIV, coupled with long delays between infection and diagnosis, make isolating and characterizing this strain a challenge. In theory, ancestral reconstruction could be used to recover this strain from sequences sampled in chronic infection; however, the accuracy of phylogenetic techniques in this context is unknown. To evaluate the accuracy of these methods, we applied ancestral reconstruction to a large panel of published longitudinal clonal and/or single-genome-amplification HIV sequence data sets with at least one intrapatient sequence set sampled within 6 months of infection or seroconversion (n = 19,486 sequences, median [interquartile range] = 49 [20 to 86] sequences/set). The consensus of the earliest sequences was used as the best possible estimate of the transmitted/founder. These sequences were compared to ancestral reconstructions from sequences sampled at later time points using both phylogenetic and phylogeny-naive methods. Overall, phylogenetic methods conferred a 16% improvement in reproducing the consensus of early sequences, compared to phylogeny-naive methods. This relative advantage increased with intrapatient sequence diversity (P reconstructing ancestral indel variation, especially within indel-rich regions of the HIV genome. Although further improvements are needed, our results indicate that phylogenetic methods for ancestral reconstruction significantly outperform phylogeny-naive alternatives, and we identify experimental conditions and study designs that can enhance accuracy of transmitted/founder virus reconstruction. IMPORTANCE When HIV is transmitted into a new host, most of the viruses fail to infect host cells. Consequently, an HIV infection tends to be descended from a single “founder” virus. A priority target for the vaccine research, these transmitted/founder viruses are

  2. HIV genetic information and clonal growth

    Science.gov (United States)

    Based on an analysis of blood cells from five HIV-infected individuals, NCI researchers have identified more than 2,400 HIV DNA insertion sites. Analysis of these sites showed that there is extensive clonal expansion (growth) of HIV infected cells.

  3. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality

    Science.gov (United States)

    Laskey, Sarah B.; Pohlmeyer, Christopher W.; Bruner, Katherine M.; Siliciano, Robert F.

    2016-01-01

    In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings. PMID:27494508

  4. Evaluating Clonal Expansion of HIV-Infected Cells: Optimization of PCR Strategies to Predict Clonality.

    Directory of Open Access Journals (Sweden)

    Sarah B Laskey

    2016-08-01

    Full Text Available In HIV-infected individuals receiving suppressive antiretroviral therapy, the virus persists indefinitely in a reservoir of latently infected cells. The proliferation of these cells may contribute to the stability of the reservoir and thus to the lifelong persistence of HIV-1 in infected individuals. Because the HIV-1 replication process is highly error-prone, the detection of identical viral genomes in distinct host cells provides evidence for the clonal expansion of infected cells. We evaluated alignments of unique, near-full-length HIV-1 sequences to determine the relationship between clonality in a short region and clonality in the full genome. Although it is common to amplify and sequence short, subgenomic regions of the viral genome for phylogenetic analysis, we show that sequence identity of these amplicons does not guarantee clonality across the full viral genome. We show that although longer amplicons capture more diversity, no subgenomic region can recapitulate the diversity of full viral genomes. Consequently, some identical subgenomic amplicons should be expected even from the analysis of completely unique viral genomes, and the presence of identical amplicons alone is not proof of clonally expanded HIV-1. We present a method for evaluating evidence of clonal expansion in the context of these findings.

  5. Clonal expansion of genome-intact HIV-1 in functionally polarized Th1 CD4+ T cells.

    Science.gov (United States)

    Lee, Guinevere Q; Orlova-Fink, Nina; Einkauf, Kevin; Chowdhury, Fatema Z; Sun, Xiaoming; Harrington, Sean; Kuo, Hsiao-Hsuan; Hua, Stephane; Chen, Hsiao-Rong; Ouyang, Zhengyu; Reddy, Kavidha; Dong, Krista; Ndung'u, Thumbi; Walker, Bruce D; Rosenberg, Eric S; Yu, Xu G; Lichterfeld, Mathias

    2017-06-30

    HIV-1 causes a chronic, incurable disease due to its persistence in CD4+ T cells that contain replication-competent provirus, but exhibit little or no active viral gene expression and effectively resist combination antiretroviral therapy (cART). These latently infected T cells represent an extremely small proportion of all circulating CD4+ T cells but possess a remarkable long-term stability and typically persist throughout life, for reasons that are not fully understood. Here we performed massive single-genome, near-full-length next-generation sequencing of HIV-1 DNA derived from unfractionated peripheral blood mononuclear cells, ex vivo-isolated CD4+ T cells, and subsets of functionally polarized memory CD4+ T cells. This approach identified multiple sets of independent, near-full-length proviral sequences from cART-treated individuals that were completely identical, consistent with clonal expansion of CD4+ T cells harboring intact HIV-1. Intact, near-full-genome HIV-1 DNA sequences that were derived from such clonally expanded CD4+ T cells constituted 62% of all analyzed genome-intact sequences in memory CD4 T cells, were preferentially observed in Th1-polarized cells, were longitudinally detected over a duration of up to 5 years, and were fully replication- and infection-competent. Together, these data suggest that clonal proliferation of Th1-polarized CD4+ T cells encoding for intact HIV-1 represents a driving force for stabilizing the pool of latently infected CD4+ T cells.

  6. Reliable reconstruction of HIV-1 whole genome haplotypes reveals clonal interference and genetic hitchhiking among immune escape variants

    Science.gov (United States)

    2014-01-01

    Background Following transmission, HIV-1 evolves into a diverse population, and next generation sequencing enables us to detect variants occurring at low frequencies. Studying viral evolution at the level of whole genomes was hitherto not possible because next generation sequencing delivers relatively short reads. Results We here provide a proof of principle that whole HIV-1 genomes can be reliably reconstructed from short reads, and use this to study the selection of immune escape mutations at the level of whole genome haplotypes. Using realistically simulated HIV-1 populations, we demonstrate that reconstruction of complete genome haplotypes is feasible with high fidelity. We do not reconstruct all genetically distinct genomes, but each reconstructed haplotype represents one or more of the quasispecies in the HIV-1 population. We then reconstruct 30 whole genome haplotypes from published short sequence reads sampled longitudinally from a single HIV-1 infected patient. We confirm the reliability of the reconstruction by validating our predicted haplotype genes with single genome amplification sequences, and by comparing haplotype frequencies with observed epitope escape frequencies. Conclusions Phylogenetic analysis shows that the HIV-1 population undergoes selection driven evolution, with successive replacement of the viral population by novel dominant strains. We demonstrate that immune escape mutants evolve in a dependent manner with various mutations hitchhiking along with others. As a consequence of this clonal interference, selection coefficients have to be estimated for complete haplotypes and not for individual immune escapes. PMID:24996694

  7. The Latent Reservoir for HIV-1: How Immunologic Memory and Clonal Expansion Contribute to HIV-1 Persistence

    Science.gov (United States)

    Murray, Alexandra J.; Kwon, Kyungyoon J.; Farber, Donna L.; Siliciano, Robert F.

    2016-01-01

    Combination antiretroviral therapy (ART) for HIV-1 infection reduces plasma virus levels to below the limit of detection of clinical assays. However, even with prolonged suppression of viral replication with ART, viremia rebounds rapidly after treatment interruption. Thus ART is not curative. The principal barrier to cure is a remarkably stable reservoir of latent HIV-1 in resting memory CD4+ T cells. Here we consider explanations for the remarkable stability of the latent reservoir. Stability does not appear to reflect replenishment from new infection events but rather normal physiologic processes that provide for immunologic memory. Of particular importance are proliferative processes that drive clonal expansion of infected cells. Recent evidence suggests that in some infected cells, proliferation is a consequence of proviral integration into host genes associated with cell growth. Efforts to cure HIV-1 infection by targeting the latent reservoir may need to consider the potential of latently infected cells to proliferate. PMID:27382129

  8. Longitudinal analysis of HIV risk behaviour patterns and their ...

    African Journals Online (AJOL)

    The goal of this study was to identify various HIV risk behaviours among tuberculosis (TB) patients in a longitudinal study design in South Africa. In 42 public primary healthcare facilities in three districts in three provinces, adult new TB and TB retreatment patients with hazardous or harmful alcohol use were interviewed ...

  9. B cell clonal lineage alterations upon recombinant HIV-1 envelope immunization of Rhesus macaques

    Science.gov (United States)

    Broadly neutralizing HIV-1 antibodies (bNAbs) isolated from infected subjects display protective potential in animal models. Their elicitation by immunization is thus highly desirable. The HIV-1 envelope glycoprotein (Env) is the sole viral target of bnAbs, but is also targeted by binding, non-neutr...

  10. Modeling viral coevolution: HIV multi-clonal persistence and competition dynamics

    Science.gov (United States)

    Bagnoli, F.; Liò, P.; Sguanci, L.

    2006-07-01

    The coexistence of different viral strains (quasispecies) within the same host are nowadays observed for a growing number of viruses, most notably HIV, Marburg and Ebola, but the conditions for the formation and survival of new strains have not yet been understood. We present a model of HIV quasispecies competition, which describes the conditions of viral quasispecies coexistence under different immune system conditions. Our model incorporates both T and B cells responses, and we show that the role of B cells is important and additive to that of T cells. Simulations of coinfection (simultaneous infection) and superinfection (delayed secondary infection) scenarios in the early stages (days) and in the late stages of the infection (years) are in agreement with emerging molecular biology findings. The immune response induces a competition among similar phenotypes, leading to differentiation (quasispeciation), escape dynamics and complex oscillations of viral strain abundance. We found that the quasispecies dynamics after superinfection or coinfection has time scales of several months and becomes even slower when the immune system response is weak. Our model represents a general framework to study the speed and distribution of HIV quasispecies during disease progression, vaccination and therapy.

  11. From tailor-made to ready-to-wear meningococcal B vaccines: longitudinal study of a clonal meningococcal B outbreak.

    Science.gov (United States)

    Caron, François; du Châtelet, Isabelle Parent; Leroy, Jean-Philippe; Ruckly, Corinne; Blanchard, Myriam; Bohic, Nicole; Massy, Nathalie; Morer, Isabelle; Floret, Daniel; Delbos, Valérie; Hong, Eva; Révillion, Martin; Berthelot, Gilles; Lemée, Ludovic; Deghmane, Ala-Eddine; Bénichou, Jacques; Lévy-Bruhl, Daniel; Taha, Muhamed-Kheir

    2011-06-01

    Outer-membrane-vesicle vaccines for meningococcal B outbreaks are complex and time consuming to develop. We studied the use of already available vaccine to control an outbreak caused by a genetically close strain. From 2006 to 2009, all individuals younger than 20 years living in the region of Normandy, France, in which an outbreak caused by a B:14:P1.7,16 strain occurred, were eligible to receive MenBvac, a Norwegian vaccine designed 20 years earlier against a strain sharing the same serosubtype (B:15:P1.7,16). The immunogenicity (in a randomly selected cohort of 400 children aged 1-5 years), safety, and epidemiological effect of the vaccination were assessed. 26,014 individuals were eligible to receive the vaccine. Shortage of vaccine production prompted start of the campaign in the highest incidence groups (1-5 years). 16,709 (64%) received a complete vaccination schedule of whom 13,589 (81%) received a 2+1 dose schedule (week 0, week 6, and month 8). At 6 weeks after the third dose, of 235 vaccinees for whom samples were available, 206 (88%) had a seroresponse, and 108 (56 %) of 193 had a seroresponse at 15 months. These results were similar to those described for tailor-made vaccines and their homologous strain. Only previously described adverse effects occurred. The incidence of B:14:P1.7,16 cases decreased significantly in the vaccine targeted population after the primary vaccination period (from 31·6 per 100,000 to 5·9 per 100,000; p=0·001). The ready-to-wear approach is reliable if epidemic and vaccine strains are genetically close. Other meningococcal B clonal outbreaks might benefit from this strategy; and previously described outer-membrane-vesicle vaccines can be effective against various strains. French Ministry of Health. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. Longitudinal anthropometric assessment of infants born to HIV-1-infected mothers, Belo Horizonte, Southeastern Brazil

    OpenAIRE

    Fausto, Maria Arlene; Carneiro, Mariângela; Antunes, Carlos Maurício F; Colosimo, Enrico Antonio; Pinto, Jorge Andrade

    2011-01-01

    OBJECTIVE: To evaluate the growth parameters in infants who were born to HIV-1-infected mothers. METHODS: The study was a longitudinal evaluation of the z-scores for the weight-for-age (WAZ), weight-for-length (WLZ) and length-for-age (LAZ) data collected from a cohort. A total of 97 non-infected and 33 HIV-infected infants born to HIV-1-infected mothers in Belo Horizonte, Southeastern Brazil, between 1995 and 2003 was studied. The average follow-up period for the infected and non-infected ch...

  13. Long-Term Changes of Subcutaneous Fat Mass in HIV-Infected Children on Antiretroviral Therapy: A Retrospective Analysis of Longitudinal Data from Two Pediatric HIV-Cohorts

    NARCIS (Netherlands)

    Cohen, Sophie; Innes, Steve; Geelen, Sibyl P. M.; Wells, Jonathan C. K.; Smit, Colette; Wolfs, Tom F. W.; van Eck-Smit, Berthe L. F.; Kuijpers, Taco W.; Reiss, Peter; Scherpbier, Henriette J.; Pajkrt, Dasja; Bunders, Madeleine J.

    2015-01-01

    Longitudinal studies objectively evaluating changes in regional fat distribution of HIV-infected children assessed by whole body dual energy X-ray absorptiometry (DEXA) are scarce, whilst this long-term effect of HIV and antiretroviral therapy (cART) is an important issue in infected children in

  14. Long-Term Changes of Subcutaneous Fat Mass in HIV-Infected Children on Antiretroviral Therapy : A Retrospective Analysis of Longitudinal Data from Two Pediatric HIV-Cohorts

    NARCIS (Netherlands)

    Cohen, Sophie; Innes, Steve; Geelen, SPM; Wells, Jonathan C. K.; Smit, Colette; Wolfs, Tom F. W.; van Eck-Smit, Berthe L. F.; Kuijpers, Taco W.; Reiss, Peter; Scherpbier, Henriette J.; Pajkrt, Dasja; Bunders, Madeleine J.

    2015-01-01

    Objective Longitudinal studies objectively evaluating changes in regional fat distribution of HIV-infected children assessed by whole body dual energy X-ray absorptiometry (DEXA) are scarce, whilst this long-term effect of HIV and antiretroviral therapy (cART) is an important issue in infected

  15. Longitudinal Modeling of Depressive Trajectories Among HIV-Infected Men Using Cocaine.

    Science.gov (United States)

    Mukerji, Shibani; Haghighat, Roxanna; Misra, Vikas; Lorenz, David R; Holman, Alex; Dutta, Anupriya; Gabuzda, Dana

    2017-07-01

    Cocaine use is prevalent among HIV-infected individuals. While cross-sectional studies suggest that cocaine users may be at increased risk for depression, long-term effects of cocaine on depressive symptoms remain unclear. This is a longitudinal study of 341 HIV-infected and uninfected men (135 cocaine users and 206 controls) ages 30-60 enrolled in the Multicenter AIDS Cohort Study during 1996-2009. The median baseline age was 41; 73% were African-American. In mixed-effects models over a median of 4.8 years of observation, cocaine use was associated with higher depressive symptoms independent of age, education level, and smoking (n = 288; p = 0.02); HIV infection modified this association (p = 0.03). Latent class mixed models were used to empirically identify distinct depressive trajectories (n = 160). In adjusted models, cocaine use was associated with threefold increased odds of membership in the class with persistent high depressive symptoms (95% confidence interval (CI) 1.38-6.69) and eightfold increased odds (95% CI (2.73-25.83) when tested among HIV-infected subjects only. Cocaine use is a risk factor for chronic depressive symptoms, particularly among HIV-infected men, highlighting the importance of integrating mental health and substance use treatments to address barriers to well-being and successful HIV-care.

  16. Longitudinal dynamics of the HIV-specific B cell response during intermittent treatment of primary HIV infection.

    Directory of Open Access Journals (Sweden)

    Godelieve J de Bree

    Full Text Available Neutralizing antibodies develop in natural HIV-1 infection. Their development often takes several years and may rely on chronic virus exposure. At the same time recent studies show that treatment early in infection may provide opportunities for immune preservation. However, it is unknown how intermittent treatment in early infection affects development of the humoral immune response over time. We investigate the effect of cART in early HIV infection on the properties of the memory B cell compartment following 6 months of cART or in the absence of treatment. The patients included participated in the Primo-SHM trial where patients with an early HIV-1 infection were randomized to no treatment or treatment for 24 or 60 weeks.Primo-SHM trial patients selected for the present study were untreated (n = 23 or treated for 24 weeks (n = 24. Here we investigate memory B cell properties at viral set-point and at a late time point (respectively median 54 and 73 weeks before (re-initiation of treatment.At viral set-point, the memory B cell compartment in treated patients demonstrated significantly lower fractions of antigen-primed, activated, memory B cells (p = 0.006. In contrast to untreated patients, in treated patients the humoral HIV-specific response reached a set point over time. At a transcriptional level, sets of genes that showed enhanced expression in memory B cells at viral setpoint in untreated patients, conversely showed rapid increase of expression of the same genes in treated patients at the late time point.These data suggest that, although the memory B cell compartment is phenotypically preserved until viral setpoint after treatment interruption, the development of the HIV-specific antibody response may benefit from exposure to HIV. The effect of viral exposure on B cell properties is also reflected by longitudinal changes in transcriptional profile in memory B cells over time in early treated patients.

  17. Longitudinal spiritual coping with trauma in people with HIV: implications for health care.

    Science.gov (United States)

    Kremer, Heidemarie; Ironson, Gail

    2014-03-01

    This 10-year study (N=177) examines how people with HIV use spirituality to cope with life's trauma on top of HIV-related stress (e.g., facing death, stigma, poverty, limited healthcare) usual events. Spirituality, defined as a connection to a higher presence, is independent from religion (institutionalized spirituality). As a dynamic adaptive process, coping requires longitudinal studying. Qualitative content-analysis of interviews/essays yielded a coding of specific aspects and a longitudinal rating of overall spiritual coping. Most participants were rated as spiritual, using spiritual practices, about half experienced comfort, empowerment, growth/transformation, gratitude, less than one-third meaning, community, and positive reframing. Up to one-fifth perceived spiritual conflict, struggle, or anger, triggering post-traumatic stress, which sometimes converted into positive growth/transformation later. Over time, 65% used spiritual coping positively, 7% negatively, and 28% had no significant use. Spirituality was mainly beneficial for women, heterosexuals, and African Americans (pspirituality is a major source of positive and occasionally negative coping (e.g., viewing HIV as sin). We discuss how clinicians can recognize and prevent when spirituality is creating distress and barriers to HIV treatment, adding a literature review on ways of effective spiritual assessment. Spirituality may be a beneficial component of coping with trauma, considering socio-cultural contexts.

  18. A Livelihood Intervention to Reduce the Stigma of HIV in Rural Kenya: Longitudinal Qualitative Study.

    Science.gov (United States)

    Tsai, Alexander C; Hatcher, Abigail M; Bukusi, Elizabeth A; Weke, Elly; Lemus Hufstedler, Lee; Dworkin, Shari L; Kodish, Stephen; Cohen, Craig R; Weiser, Sheri D

    2017-01-01

    The scale-up of effective treatment has partially reduced the stigma attached to HIV, but HIV still remains highly stigmatized throughout sub-Saharan Africa. Most studies of anti-HIV stigma interventions have employed psycho-educational strategies such as information provision, counseling, and testimonials, but these have had varying degrees of success. Theory suggests that livelihood interventions could potentially reduce stigma by weakening the instrumental and symbolic associations between HIV and premature morbidity, economic incapacity, and death, but this hypothesis has not been directly examined. We conducted a longitudinal qualitative study among 54 persons with HIV participating in a 12-month randomized controlled trial of a livelihood intervention in rural Kenya. Our study design permitted assessment of changes over time in the perspectives of treatment-arm participants (N = 45), as well as an understanding of the experiences of control arm participants (N = 9, interviewed only at follow-up). Initially, participants felt ashamed of their seropositivity and were socially isolated (internalized stigma). They also described how others in the community discriminated against them, labeled them as being "already dead," and deemed them useless and unworthy of social investment (perceived and enacted stigma). At follow-up, participants in the treatment arm described less stigma and voiced positive changes in confidence and self-esteem. Concurrently, they observed that other community members perceived them as active, economically productive, and contributing citizens. None of these changes were noted by participants in the control arm, who described ongoing and continued stigma. In summary, our findings suggest a theory of stigma reduction: livelihood interventions may reduce internalized stigma among persons with HIV and also, by targeting core drivers of negative attitudes toward persons with HIV, positively change attitudes toward persons with HIV held by

  19. Longitudinal relationships between antiretroviral treatment adherence and discrimination due to HIV-serostatus, race, and sexual orientation among African-American men with HIV.

    Science.gov (United States)

    Bogart, Laura M; Wagner, Glenn J; Galvan, Frank H; Klein, David J

    2010-10-01

    African-Americans show worse HIV disease outcomes compared to Whites. Health disparities may be aggravated by discrimination, which is associated with worse health and maladaptive health behaviors. We examined longitudinal effects of discrimination on antiretroviral treatment adherence among 152 HIV-positive Black men who have sex with men. We measured adherence and discrimination due to HIV-serostatus, race/ethnicity, and sexual orientation at baseline and monthly for 6 months. Hierarchical repeated-measures models tested longitudinal effects of each discrimination type on adherence. Over 6 months, participants took 60% of prescribed medications on average; substantial percentages experienced discrimination (HIV-serostatus, 38%; race/ethnicity, 40%; and sexual orientation, 33%). Greater discrimination due to all three characteristics was significantly bivariately associated with lower adherence (all p's discrimination was significant (p < 0.05). Efforts to improve HIV treatment adherence should consider the context of multiple stigmas, especially racism.

  20. Dataset of longitudinal analysis of tear cytokine levels, CD4, CD8 counts and HIV viral load in dry eye patients with HIV infection

    Directory of Open Access Journals (Sweden)

    Praveen Kumar Balne

    2017-04-01

    Full Text Available The data presented in this article shows the longitudinal analysis of tear fluid cytokine profiles, blood CD4 and CD8 counts and HIV viral load in 34 dry eye patients with HIV infection during the HAART therapy. Clinical samples were collected from HIV patients with dry eye disease at the time of presentation to the clinic (visit 1, three months (visit 2 and 6 months (visit 3 after the presentation. At each time point tear samples were evaluated for 41 cytokines using Luminex bead based multiplex assay and blood samples were tested for HIV viral load and CD4 and CD8 counts.

  1. The Network for Analysing Longitudinal Population-based HIV/AIDS data on Africa (ALPHA): Data on mortality, by HIV status and stage on the HIV care continuum, among the general population in seven longitudinal studies between 1989 and 2014.

    Science.gov (United States)

    Slaymaker, Emma; McLean, Estelle; Wringe, Alison; Calvert, Clara; Marston, Milly; Reniers, Georges; Kabudula, Chodziwadziwa Whiteson; Crampin, Amelia; Price, Alison; Michael, Denna; Urassa, Mark; Kwaro, Daniel; Sewe, Maquins; Eaton, Jeffrey W; Rhead, Rebecca; Nakiyingi-Miiro, Jessica; Lutalo, Tom; Nabukalu, Dorean; Herbst, Kobus; Hosegood, Victoria; Zaba, Basia

    2017-11-06

    Timely progression of people living with HIV (PLHIV) from the point of infection through the pathway from diagnosis to treatment is important in ensuring effective care and treatment of HIV and preventing HIV-related deaths and onwards transmission of infection.  Reliable, population-based estimates of new infections are difficult to obtain for the generalised epidemics in sub-Saharan Africa.  Mortality data indicate disease burden and, if disaggregated along the continuum from diagnosis to treatment, can also reflect the coverage and quality of different HIV services.  Neither routine statistics nor observational clinical studies can estimate mortality prior to linkage to care nor following disengagement from care.  For this, population-based data are required. The Network for Analysing Longitudinal Population-based HIV/AIDS data on Africa brings together studies in Kenya, Malawi, South Africa, Tanzania, Uganda, and Zimbabwe.  Eight studies have the necessary data to estimate mortality by HIV status, and seven can estimate mortality at different stages of the HIV care continuum.  This data note describes a harmonised dataset containing anonymised individual-level information on survival by HIV status for adults aged 15 and above. Among PLHIV, the dataset provides information on survival during different periods: prior to diagnosis of infection; following diagnosis but before linkage to care; in pre-antiretroviral treatment (ART) care; in the first six months after ART initiation; among people continuously on ART for 6+ months; and among people who have ever interrupted ART.

  2. From HIV infection to therapeutic response: a population-based longitudinal HIV cascade-of-care study in KwaZulu-Natal, South Africa.

    Science.gov (United States)

    Haber, Noah; Tanser, Frank; Bor, Jacob; Naidu, Kevindra; Mutevedzi, Tinofa; Herbst, Kobus; Porter, Kholoud; Pillay, Deenan; Bärnighausen, Till

    2017-05-01

    Standard approaches to estimation of losses in the HIV cascade of care are typically cross-sectional and do not include the population stages before linkage to clinical care. We used indiviual-level longitudinal cascade data, transition by transition, including population stages, both to identify the health-system losses in the cascade and to show the differences in inference between standard methods and the longitudinal approach. We used non-parametric survival analysis to estimate a longitudinal HIV care cascade for a large population of people with HIV residing in rural KwaZulu-Natal, South Africa. We linked data from a longitudinal population health surveillance (which is maintained by the Africa Health Research Institute) with patient records from the local public-sector HIV treatment programme (contained in an electronic clinical HIV treatment and care database, ARTemis). We followed up all people who had been newly detected as having HIV between Jan 1, 2006, and Dec 31, 2011, across six cascade stages: three population stages (first positive HIV test, HIV status knowledge, and linkage to care) and three clinical stages (eligibility for antiretroviral therapy [ART], initiation of ART, and therapeutic response). We compared our estimates to cross-sectional cascades in the same population. We estimated the cumulative incidence of reaching a particular cascade stage at a specific time with Kaplan-Meier survival analysis. Our population consisted of 5205 individuals with HIV who were followed up for 24 031 person-years. We recorded 598 deaths. 4539 individuals gained knowledge of their positive HIV status, 2818 were linked to care, 2151 became eligible for ART, 1839 began ART, and 1456 had successful responses to therapy. We used Kaplan-Meier survival analysis to adjust for censorship due to the end of data collection, and found that 8 years after testing positive in the population health surveillance, 16% had died. Among living patients, 82% knew their HIV

  3. Food insecurity is longitudinally associated with depressive symptoms among homeless and marginally-housed individuals living with HIV

    Science.gov (United States)

    Palar, Kartika; Kushel, Margot; Frongillo, Edward A.; Riley, Elise D.; Grede, Nils; Bangsberg, David; Weiser, Sheri D.

    2014-01-01

    Introduction Depression and food insecurity are prevalent among people with HIV (PLHIV) and contribute to poor HIV outcomes. Longitudinal data can help clarify the effect of food insecurity on depression among PLHIV in the United States. Methods We assessed the longitudinal association of food insecurity with symptoms of depression using validated measures among participants living with HIV from the Research on Access to Care in the Homeless cohort in San Francisco. Results We followed 346 participants for a median of 28 months. Over half of participants (55.0%) were food insecure and 35.8% had symptoms of depression. In adjusted models, severe food insecurity in the previous period was associated with increased depressive symptom severity (b=1.22; pinsecurity was longitudinally associated with symptoms of depression. Efforts to increase access to and participation in food security safety net programs for PLHIV could improve depression. PMID:25351185

  4. Neonatal erythropoiesis and subsequent anemia in HIV-positive and HIV-negative Zimbabwean babies during the first year of life: a longitudinal study

    Directory of Open Access Journals (Sweden)

    Malaba Lucie C

    2006-01-01

    Full Text Available Abstract Background Anemia is common in HIV infection and independently associated with disease progression and mortality. The pathophysiology of HIV-related anemia is not well understood especially in infancy. Methods We conducted a longitudinal cohort study nested within the Zimbabwe Vitamin A for Mothers and Babies Project. We measured hemoglobin, erythropoietin (EPO, serum transferrin receptor (TfR and serum ferritin at 6 weeks, 3 and 6 months of age and hemoglobin at 9 and 12 months in 3 groups of randomly selected infants: 136 born to HIV-negative mothers, and 99 born to HIV-positive mothers and who were infected themselves by 6 weeks of age, and 324 born to HIV-positive mothers but who did not become infected in the 6 months following birth. Results At one year of age, HIV-positive infants were 5.26 (adjusted odds ratio, P Conclusion HIV strongly increases anemia risk and confounds interpretation of hematologic indicators in infants. Among HIV-infected infants, the EPO response to anemia is attenuated near the time of infection in the first weeks of life, but normalizes by 6 months.

  5. Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort.

    Directory of Open Access Journals (Sweden)

    Elise Landais

    2016-01-01

    Full Text Available Broadly neutralizing antibodies (bnAbs are thought to be a critical component of a protective HIV vaccine. However, designing vaccines immunogens able to elicit bnAbs has proven unsuccessful to date. Understanding the correlates and immunological mechanisms leading to the development of bnAb responses during natural HIV infection is thus critical to the design of a protective vaccine. The IAVI Protocol C program investigates a large longitudinal cohort of primary HIV-1 infection in Eastern and South Africa. Development of neutralization was evaluated in 439 donors using a 6 cross-clade pseudo-virus panel predictive of neutralization breadth on larger panels. About 15% of individuals developed bnAb responses, essentially between year 2 and year 4 of infection. Statistical analyses revealed no influence of gender, age or geographical origin on the development of neutralization breadth. However, cross-clade neutralization strongly correlated with high viral load as well as with low CD4 T cell counts, subtype-C infection and HLA-A*03(- genotype. A correlation with high overall plasma IgG levels and anti-Env IgG binding titers was also found. The latter appeared not associated with higher affinity, suggesting a greater diversity of the anti-Env responses in broad neutralizers. Broadly neutralizing activity targeting glycan-dependent epitopes, largely the N332-glycan epitope region, was detected in nearly half of the broad neutralizers while CD4bs and gp41-MPER bnAb responses were only detected in very few individuals. Together the findings suggest that both viral and host factors are critical for the development of bnAbs and that the HIV Env N332-glycan supersite may be a favorable target for vaccine design.

  6. HIV Futures 8: Protocol for a Repeated Cross-sectional and Longitudinal Survey of People Living with HIV in Australia

    OpenAIRE

    Power, Jennifer; Brown, Graham; Lyons, Anthony; Thorpe, Rachel; Dowsett, Gary W.; Lucke, Jayne

    2017-01-01

    Introduction More than 27,000 Australians currently live with HIV. Most of these people have access to quality clinical care and antiretroviral treatment (ART) and can expect good general health. However, HIV-related stigma is a problem and many people living with HIV experience poorer than average mental health. Issues of aging are also of increasing concern. This paper describes the methods and sample for the HIV Futures 8 study, a national survey of people living with HIV in Australia that...

  7. Violence, trauma and living with HIV: Longitudinal predictors of initiating crystal methamphetamine injection among sex workers.

    Science.gov (United States)

    Argento, Elena; Strathdee, Steffanie A; Goldenberg, Shira; Braschel, Melissa; Montaner, Julio; Shannon, Kate

    2017-06-01

    Despite rapid increases in crystal methamphetamine (CM) use worldwide and established gendered patterns of use, empirical research on CM injection initiation among sex workers is limited. Given the wide range of harms associated with CM, alongside stimulant effects including sexual dis-inhibition and prolonged awake-ness, this study aimed to longitudinally investigate socio-structural predictors of initiating CM injection among sex workers in Vancouver, Canada. Data (2010-2014) were drawn from a community-based cohort of women sex workers: AESHA (An Evaluation of Sex Workers Health Access). Participants completed bi-annual interviewer-administered questionnaires and HIV/STI testing. Kaplan Meier methods and Cox proportional hazards regression were used to model predictors of CM injection initiation among CM injection-naïve participants. Of 455 participants eligible at baseline, 14.3% (n=65) injected CM for the first time over follow-up, with an incidence density of 6.79 per 100 person-years (95% Confidence Interval [CI] 5.30-8.69). In multivariable analysis, injection heroin use (Adjusted Hazard Ratio [AHR] 6.11; 95%CI 3.24-11.52), having an intimate partner who injects drugs (AHR 2.93; 95%CI 1.57-5.46), workplace violence (AHR 2.85; 95%CI 1.74-4.67), HIV seropositivity (AHR 2.69; 95%CI 1.45-5.00), and childhood abuse (AHR 1.86; 95%CI 0.99-3.49) were independently associated with initiating CM injection. Findings underscore the gendered and social risk environment of CM injection initiation among sex workers. The strong influences of historical/workplace violence, coupled with heroin injection (known to be self-medicating for post-traumatic stress) as a primary risk pathway, emphasize the urgency of increasing access to integrated, trauma-informed addiction treatment and HIV care for marginalized women. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Economic Recession and Emergence of an HIV-1 Outbreak among Drug Injectors in Athens Metropolitan Area: A Longitudinal Study

    Science.gov (United States)

    Paraskevis, Dimitrios; Nikolopoulos, Georgios; Fotiou, Anastasios; Tsiara, Chrissa; Paraskeva, Dimitra; Sypsa, Vana; Lazanas, Marios; Gargalianos, Panagiotis; Psichogiou, Mina; Skoutelis, Athanasios; Wiessing, Lucas; Friedman, Samuel R.; Jarlais, Don C. d. e. s.; Terzidou, Manina; Kremastinou, Jenny; Malliori, Meni; Hatzakis, Angelos

    2013-01-01

    Background During 2011, a dramatic increase (1600%) of reported HIV-1 infections among injecting drug users (IDUs) was noted in Athens, Greece. We herein assess the potential causal pathways associated with this outbreak. Methods Our study employed high resolution HIV-1 phylogenetic and phylogeographic analyses. We examined also longitudinal data of ecological variables such as the annual growth of gross domestic product (GDP) of Greece in association with HIV-1 and HCV sentinel prevalence in IDUs, unemployment and homelessness rates and HIV transmission networks in Athens IDUs before and during economic recession (2008–2012). Results IDU isolates sampled in 2011 and 2012 suggested transmission networks in 94.6% and 92.7% of the cases in striking contrast with the sporadic networking (5%) during 1998–2009. The geographic origin of most HIV-1 isolates was consistent with the recently documented migratory waves in Greece. The decline in GDP was inversely correlated with annual prevalence rates of HIV and HCV and with unemployment and homelessness rates in IDUs (all pperiod. Conclusions Scaling-up harm reduction services and addressing social and structural factors related to the current economic crisis should be urgently considered in environments where HIV-1 outbreaks may occur. PMID:24265730

  9. Impact of Perinatally Acquired HIV Disease Upon Longitudinal Changes in Memory and Executive Functioning.

    Science.gov (United States)

    Malee, Kathleen M; Chernoff, Miriam C; Sirois, Patricia A; Williams, Paige L; Garvie, Patricia A; Kammerer, Betsy L; Harris, Lynnette L; Nozyce, Molly L; Yildirim, Cenk; Nichols, Sharon L

    2017-08-01

    Little is known regarding effects of perinatally acquired HIV infection (PHIV) on longitudinal change in memory and executive functioning (EF) during adolescence despite the importance of these skills for independence in adulthood. PHIV (n = 144) and perinatally HIV-exposed uninfected youth (PHEU, n = 79), ages 12-17, completed standardized tests of memory and EF at baseline and 2 years later. Changes from baseline for each memory and EF outcome were compared between PHEU and PHIV youth with (PHIV/C, n = 39) and without (PHIV/non-C, n = 105) history of CDC class C (AIDS-defining) diagnoses. Among PHIV youth, associations of baseline and past disease severity with memory and EF performance at follow-up were evaluated using adjusted linear regression models. Participants were primarily black (79%); 16% were Hispanic; 55% were female. Mean memory and EF scores at follow-up generally fell in the low-average to average range. Pairwise comparison of adjusted mean change from baseline to follow-up revealed significantly greater change for PHIV/non-C compared with PHEU youth in only one verbal recognition task, with a difference in mean changes for PHIV/non-C versus PHEU of -0.99 (95% CI: -1.80 to -0.19; P = 0.02). Among youth with PHIV, better immunologic status at baseline was positively associated with follow-up measures of verbal recall and recognition and cognitive inhibition/flexibility. Past AIDS-defining diagnoses and higher peak viral load were associated with lower performance across multiple EF tasks at follow-up. Youth with PHIV demonstrated stable memory and EF during a 2-year period of adolescence, allowing cautious optimism regarding long-term outcomes.

  10. Chest radiographic abnormalities in HIV-infected African children: a longitudinal study.

    Science.gov (United States)

    Pitcher, Richard D; Lombard, Carl J; Cotton, Mark F; Beningfield, Stephen J; Workman, Lesley; Zar, Heather J

    2015-09-01

    There is limited knowledge of chest radiographic abnormalities over time in HIV-infected children in resource-limited settings. To investigate the natural history of chest radiographic abnormalities in HIV-infected African children, and the impact of antiretroviral therapy (ART). Prospective longitudinal study of the association of chest radiographic findings with clinical and immunological parameters. Chest radiographs were performed at enrolment, 6-monthly, when initiating ART and if indicated clinically. Radiographic abnormalities were classified as normal, mild or moderate severity and considered persistent if present for 6 consecutive months or longer. An ordinal multiple logistic regression model assessed the association of enrolment and time-dependent variables with temporal radiographic findings. 258 children (median (IQR) age: 28 (13-51) months; median CD4+%: 21 (15-24)) were followed for a median of 24 (18-42) months. 70 (27%) were on ART at enrolment; 130 (50%) (median age: 33 (18-56) months) commenced ART during the study. 154 (60%) had persistent severe radiographic abnormalities, with median duration 18 (6-24) months. Among children on ART, 69% of radiographic changes across all 6-month transition periods were improvements, compared with 45% in those not on ART. Radiographic severity was associated with previous radiographic severity (OR=120.80; 95% CI 68.71 to 212.38), lack of ART (OR=1.72; 95% CI 1.29 to 2.27), enrolment age ART was beneficial, reducing the risk of radiographic deterioration or increasing the likelihood of radiological improvement. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  11. HIV incidence in rural South Africa: comparison of estimates from longitudinal surveillance and cross-sectional cBED assay testing.

    Directory of Open Access Journals (Sweden)

    Till Bärnighausen

    Full Text Available The BED IgG-Capture Enzyme Immunoassay (cBED assay, a test of recent HIV infection, has been used to estimate HIV incidence in cross-sectional HIV surveys. However, there has been concern that the assay overestimates HIV incidence to an unknown extent because it falsely classifies some individuals with non-recent HIV infections as recently infected. We used data from a longitudinal HIV surveillance in rural South Africa to measure the fraction of people with non-recent HIV infection who are falsely classified as recently HIV-infected by the cBED assay (the long-term false-positive ratio (FPR and compared cBED assay-based HIV incidence estimates to longitudinally measured HIV incidence.We measured the long-term FPR in individuals with two positive HIV tests (in the HIV surveillance, 2003-2006 more than 306 days apart (sample size n = 1,065. We implemented four different formulae to calculate HIV incidence using cBED assay testing (n = 11,755 and obtained confidence intervals (CIs by directly calculating the central 95(th percentile of incidence values. We observed 4,869 individuals over 7,685 person-years for longitudinal HIV incidence estimation. The long-term FPR was 0.0169 (95% CI 0.0100-0.0266. Using this FPR, the cross-sectional cBED-based HIV incidence estimates (per 100 people per year varied between 3.03 (95% CI 2.44-3.63 and 3.19 (95% CI 2.57-3.82, depending on the incidence formula. Using a long-term FPR of 0.0560 based on previous studies, HIV incidence estimates varied between 0.65 (95% CI 0.00-1.32 and 0.71 (95% CI 0.00-1.43. The longitudinally measured HIV incidence was 3.09 per 100 people per year (95% CI 2.69-3.52, after adjustment to the sex-age distribution of the sample used in cBED assay-based estimation.In a rural community in South Africa with high HIV prevalence, the long-term FPR of the cBED assay is substantially lower than previous estimates. The cBED assay performs well in HIV incidence estimation if the locally

  12. Insulin resistance change and antiretroviral therapy exposure in HIV-infected and uninfected Rwandan women: a longitudinal analysis.

    Science.gov (United States)

    Mutimura, Eugene; Hoover, Donald R; Shi, Qiuhu; Dusingize, Jean Claude; Sinayobye, Jean D'Amour; Cohen, Mardge; Anastos, Kathryn

    2015-01-01

    We longitudinally assessed predictors of insulin resistance (IR) change among HIV-uninfected and HIV-infected (ART-initiators and ART-non-initiators) Rwandan women. HIV-infected (HIV+) and uninfected (HIV-) women provided demographic and clinical measures: age, body mass index (BMI) in Kg/(height in meters)2, Fat-Mass (FMI) and Fat-Free-Mass (FFMI) index, fasting serum glucose and insulin. Homeostasis Model Assessment (HOMA) was calculated to estimate IR change over time in log10 transformed HOMA measured at study enrollment or prior to ART initiation in 3 groups: HIV- (n = 194), HIV+ ART-non-initiators (n=95) and HIV+ ART-initiators (n=371). ANCOVA linear regression models of change in log10-HOMA were fit with all models included the first log10 HOMA as a predictor. Mean±SD log10-HOMA was -0.18±0.39 at the 1st and -0.21±0.41 at the 2nd measure, with mean change of 0.03±0.44. In the final model (all women) BMI at 1st HOMA measure (0.014; 95% CI=0.006-0.021 per kg/m2; pchange in BMI from 1st to 2nd measure (0.024; 95% CI=0.013-0.035 per kg/m2; pchange. When restricted to subjects with FMI measures, FMI at 1st HOMA measure (0.020; 95% CI=0.010-0.030 per kg/m2; pchange in FMI from 1st to 2nd measure (0.032; 95% CI=0.020-0.043 per kg/m2; pchange in HOMA. While ART use did not predict change in log10-HOMA, untreated HIV+ women had a significant decline in IR over time. Use or duration of AZT, d4T and EFV was not associated with HOMA change in HIV+ women. Baseline BMI and change in BMI, and in particular fat mass and change in fat mass predicted insulin resistance change over ~3 years in HIV-infected and uninfected Rwandan women. Exposure to specific ART (d4T, AZT, EFV) did not predict insulin resistance change in ART-treated HIV-infected Rwandan women.

  13. Puberty in perinatal HIV-1 infection: a multicentre longitudinal study of 212 children.

    Science.gov (United States)

    de Martino, M; Tovo, P A; Galli, L; Gabiano, C; Chiarelli, F; Zappa, M; Gattinara, G C; Bassetti, D; Giacomet, V; Chiappini, E; Duse, M; Garetto, S; Caselli, D

    2001-08-17

    To define age at entry into Tanner stages in children with perinatal HIV-1 infection. Multicentre longitudinal study including 212 perinatally HIV-1-infected children (107 girls and 105 boys) followed-up during puberty (from 8 and 9 years onwards in girls and boys, respectively). Healthy children (843 girls and 821 boys) provided reference percentiles. P2 or B2 stages in girls and P2 or G2 stages in boys defined onset of puberty. The cumulative probability [95% confidence limit (CI)] of entry into each stage at different ages was estimated by the Kaplan-Meier product-limit method; differences were evaluated by log rank test. Relationships were tested using the Spearman's rank correlation coefficient. Ages of girls [years (95%CI)] at P2 [12.9 (12.6-13.2)], P3 [13.4 (13.0-13.8)], P4 [14.6 (14.0-15.2)], B2 [12.7 (12.2-13.2)], B3 [13.3 (12.8-14.0)] and B4 [14.6 (14.0-15.2)] stages were > 97th percentile (> or = 21 month delay) of controls. Ages of boys [years (95%CI)] at P2 [12.6 (12.1-13.1)], P3 [13.9 (13.4-14.4)], P4 [14.9 (14.2-15.6)], G2 [12.1 (11.5-12.7)], G3 [13.6 (13.1-14.1)] and G4 [14.9 (14.1-15.7)] stages were at the 75-97th percentiles (< or = 15 month delay). Age at onset of puberty was not related to clinical and immunological condition, antiretroviral treatment, weigh for height and age at onset of severe disease or immune suppression. Perinatal HIV-1 infection interferes with sexual maturation. The mechanisms by which this occurs should be elucidated and intervention strategies designed. Intervention could save much psychological distress, since associated linear growth failure can exacerbate adolescents' feelings of being different and unwell.

  14. Long-Term Changes of Subcutaneous Fat Mass in HIV-Infected Children on Antiretroviral Therapy: A Retrospective Analysis of Longitudinal Data from Two Pediatric HIV-Cohorts.

    Science.gov (United States)

    Cohen, Sophie; Innes, Steve; Geelen, Sibyl P M; Wells, Jonathan C K; Smit, Colette; Wolfs, Tom F W; van Eck-Smit, Berthe L F; Kuijpers, Taco W; Reiss, Peter; Scherpbier, Henriette J; Pajkrt, Dasja; Bunders, Madeleine J

    2015-01-01

    Longitudinal studies objectively evaluating changes in regional fat distribution of HIV-infected children assessed by whole body dual energy X-ray absorptiometry (DEXA) are scarce, whilst this long-term effect of HIV and antiretroviral therapy (cART) is an important issue in infected children in need for lifelong treatment. We assessed regional fat distribution over time, measured with sequential DEXA-scans in HIV-infected children on cART in cohorts from South Africa (SA) and the Netherlands (NL), and in healthy controls (SA). Limb and trunk fat Z-scores were calculated with the lambda-mu-sigma (LMS) method. Multivariable linear regression models with mixed effects were used to investigate the effect of cART compounds on body fat distribution over time. In total, 218 children underwent 445 DEXA assessments with a median follow-up of 3.5 years. Fat mass in all limbs was decreased in HIV-infected children compared to controls (arm fat Z-score: coefficient -0.4813; P = 0.006, leg fat Z-score: coefficient -0.4345; P = 0.013). In the HIV-infected group, stavudine treatment was associated with lower subcutaneous fat mass (arm fat Z-score: coefficient -0.5838; P = 0.001), with an additional cumulative exposure effect (arm fat Z-score: coefficient -0.0867; P = 0.003). Our study shows that subcutaneous fat loss is still prevalent in HIV-infected children on cART, and is strongly associated with cumulative stavudine exposure. These results underline the need for early detection of subcutaneous fat loss and alternative treatment options for HIV-infected children globally.

  15. Populations in clonal plants

    Directory of Open Access Journals (Sweden)

    Jussi Tammisola

    1986-12-01

    Full Text Available Population phenomena in higher plants are reviewed critically, particularly in relation to clonality. An array of concepts used in the field are discussed. In contrast to animals, higher plants are modular in structure. Plant populations show hierarchy at two levels: ramets and genets. In addition, their demography is far more complicated, since even the direction of development of a ramet may change by rejuvenation. Therefore, formulae concerning animal populations often require modification for plants. Furthermore, at the zygotic stage, higher plants are generally less mobile than animals. Accordingly, their population processes tend to be more local. Most populations of plants have a genetic structure: alleles and genotypes are spatially aggregated. Due to the short-ranged foraging behaviour of pollinators, genetically non-random pollination prevails. A generalized formula for parent-offspring dispersal variance is derived. It is used to analyze the effect of clonality on genetic patchiness in populations. In self-compatible species, an increase in clonality will tend to increase the degree of patchiness, while in self-incompatible species a decrease may result. Examples of population structure studies in different species are presented. A considerable degree of genetic variation appears to be found also in the populations of species with a strong allocation of resources to clonal growth or apomictic seed production. Some consequences of clonality are considered from the point of view of genetic conservation and plant breeding.

  16. Linkage to HIV care, postpartum depression, and HIV-related stigma in newly diagnosed pregnant women living with HIV in Kenya: a longitudinal observational study

    OpenAIRE

    Turan, Bulent; Stringer, Kristi L; Onono, Maricianah; Bukusi, Elizabeth A; Weiser, Sheri D; Cohen, Craig R; Turan, Janet M

    2014-01-01

    Background While studies have suggested that depression and HIV-related stigma may impede access to care, a growing body of literature also suggests that access to HIV care itself may help to decrease internalized HIV-related stigma and symptoms of depression in the general population of persons living with HIV. However, this has not been investigated in postpartum women living with HIV. Furthermore, linkage to care itself may have additional impacts on postpartum depression beyond the effect...

  17. MLST-Based Population Genetic Analysis in a Global Context Reveals Clonality amongst Cryptococcus neoformans var. grubii VNI Isolates from HIV Patients in Southeastern Brazil

    NARCIS (Netherlands)

    Ferreira-Paim, Kennio; Andrade-Silva, Leonardo; Fonseca, Fernanda; Ferreira, Thatiana; Mora, Delio; Andrade-Silva, Juliana; Khan, Aziza; Dao, Aiken; C. Reis, Eduardo; Almeida, Margarete; Maltos, André; Rodrigues Jr, Virmondes; Trilles, Luciana; Rickerts, Volker; Chindamporn, Ariya; Sykes, Jane; Cogliati, Massimo; Nielsen, Kirsten; Boekhout, Teun; L. Silva-Vergara, Mario

    2017-01-01

    Cryptococcosis is an important fungal infection in immunocompromised individuals, especially those infected with HIV. In Brazil, despite the free availability of antiretroviral therapy (ART) in the public health system, the mortality rate due to Cryptococcus neoformans meningitis is still high. To

  18. Using digital communication technology fails to improve longitudinal evaluation of an HIV prevention program aimed at Indian truck drivers and cleaners.

    Science.gov (United States)

    Schneider, John A; Kondareddy, Divya; Gandham, Sabitha; Dude, Annie M

    2012-07-01

    HIV prevention programs for truck drivers and cleaners (TDC) in India are limited. Longitudinal follow-up presents an obstacle to program effectiveness evaluation. We asked 3,028 TDC in a truck-driver HIV prevention program in Hyderabad to leave a cellular telephone number; we contacted participants 6 months after the intervention to assess sexual risk behavior change. Married, older, and better educated participants were more likely to leave phone numbers. Only 6.5% of TDC were reachable after 6 months. Longitudinal follow-up of this mobile sub-population remains a challenge, and more effective methods for evaluating HIV prevention programs are needed.

  19. Sexual behaviour of heterosexual men and women receiving antiretroviral pre-exposure prophylaxis for HIV prevention: a longitudinal analysis.

    Science.gov (United States)

    Mugwanya, Kenneth K; Donnell, Deborah; Celum, Connie; Thomas, Katherine K; Ndase, Patrick; Mugo, Nelly; Katabira, Elly; Ngure, Kenneth; Baeten, Jared M

    2013-12-01

    Scarce data are available to assess sexual behaviour of individuals using antiretroviral pre-exposure prophylaxis for HIV prevention. Increased sexual risk taking by individuals using effective HIV prevention strategies, like pre-exposure prophylaxis, could offset the benefits of HIV prevention. We studied whether the use of pre-exposure prophylaxis in HIV-uninfected men and women in HIV-serodiscordant couples was associated with increased sexual risk behaviour. We undertook a longitudinal analysis of data from the Partners PrEP Study, a double-blind, randomised, placebo-controlled trial of daily oral pre-exposure prophylaxis among HIV-uninfected partners of heterosexual HIV-serodiscordant couples (n=3163, ≥18 years of age). Efficacy for HIV prevention was publicly reported in July 2011, and participants continued monthly follow-up thereafter. We used regression analyses to compare the frequency of sex-unprotected by a condom-during the 12 months after compared with the 12 months before July 2011, to assess whether knowledge of pre-exposure prophylaxis efficacy for HIV prevention caused increased sexual risk behaviour. We analysed 56 132 person-months from 3024 HIV-uninfected individuals (64% male). The average frequency of unprotected sex with the HIV-infected study partner was 59 per 100 person-months before unmasking versus 53 after unmasking; we recorded no immediate change (p=0·66) or change over time (p=0·25) after July, 2011. We identified a significant increase in unprotected sex with outside partners after July, 2011, but the effect was small (average of 6·8 unprotected sex acts per year vs 6·2 acts in a predicted counterfactual scenario had patients remained masked, p=0·04). Compared with before July, 2011, we noted no significant increase in incident sexually transmitted infections or pregnancy after July, 2011. Pre-exposure prophylaxis, provided as part of a comprehensive prevention package, might not result in substantial changes in risk

  20. HIV-2 integrase polymorphisms and longitudinal genotypic analysis of HIV-2 infected patients failing a raltegravir-containing regimen.

    Science.gov (United States)

    Cavaco-Silva, Joana; Abecasis, Ana; Miranda, Ana Cláudia; Poças, José; Narciso, Jorge; Águas, Maria João; Maltez, Fernando; Almeida, Isabel; Germano, Isabel; Diniz, António; Gonçalves, Maria de Fátima; Gomes, Perpétua; Cunha, Celso; Camacho, Ricardo Jorge

    2014-01-01

    To characterize the HIV-2 integrase gene polymorphisms and the pathways to resistance of HIV-2 patients failing a raltegravir-containing regimen, we studied 63 integrase strand transfer inhibitors (INSTI)-naïve patients, and 10 heavily pretreated patients exhibiting virological failure while receiving a salvage raltegravir-containing regimen. All patients were infected by HIV-2 group A. 61.4% of the integrase residues were conserved, including the catalytic motif residues. No INSTI-major resistance mutations were detected in the virus population from naïve patients, but two amino acids that are secondary resistance mutations to INSTIs in HIV-1 were observed. The 10 raltegravir-experienced patients exhibited resistance mutations via three main genetic pathways: N155H, Q148R, and eventually E92Q - T97A. The 155 pathway was preferentially used (7/10 patients). Other mutations associated to raltegravir resistance in HIV-1 were also observed in our HIV-2 population (V151I and D232N), along with several novel mutations previously unreported. Data retrieved from this study should help build a more robust HIV-2-specific algorithm for the genotypic interpretation of raltegravir resistance, and contribute to improve the clinical monitoring of HIV-2-infected patients.

  1. Economic recession and emergence of an HIV-1 outbreak among drug injectors in Athens metropolitan area: a longitudinal study.

    Directory of Open Access Journals (Sweden)

    Dimitrios Paraskevis

    Full Text Available BACKGROUND: During 2011, a dramatic increase (1600% of reported HIV-1 infections among injecting drug users (IDUs was noted in Athens, Greece. We herein assess the potential causal pathways associated with this outbreak. METHODS: Our study employed high resolution HIV-1 phylogenetic and phylogeographic analyses. We examined also longitudinal data of ecological variables such as the annual growth of gross domestic product (GDP of Greece in association with HIV-1 and HCV sentinel prevalence in IDUs, unemployment and homelessness rates and HIV transmission networks in Athens IDUs before and during economic recession (2008-2012. RESULTS: IDU isolates sampled in 2011 and 2012 suggested transmission networks in 94.6% and 92.7% of the cases in striking contrast with the sporadic networking (5% during 1998-2009. The geographic origin of most HIV-1 isolates was consistent with the recently documented migratory waves in Greece. The decline in GDP was inversely correlated with annual prevalence rates of HIV and HCV and with unemployment and homelessness rates in IDUs (all p<0.001. The slope of anti-HCV prevalence in the sentinel populations of IDUs and in "new" drug injectors was found 120 and 1.9-fold (p = 0.007, p = 0.08 respectively higher in 2008-2012 (economic recession compared with 2002-2006. The median (25th, 75th size of transmission networks were 34 (12, 58 and 2 (2, 2 (p = 0.057 in 2008-2012 and 1998-2007, respectively. The coverage of harm reduction services was low throughout the study period. CONCLUSIONS: Scaling-up harm reduction services and addressing social and structural factors related to the current economic crisis should be urgently considered in environments where HIV-1 outbreaks may occur.

  2. Longitudinal anthropometric assessment of infants born to HIV-1-infected mothers, Belo Horizonte, Southeastern Brazil Evaluación antropométrica longitudinal de lactantes nacidos de madres infectadas por VIH-1 Avaliação antropométrica longitudinal de lactentes nascidos de mães infectadas pelo HIV-1

    OpenAIRE

    Maria Arlene Fausto; Mariângela Carneiro; Carlos Maurício F Antunes; Enrico Antonio Colosimo; Jorge Andrade Pinto

    2011-01-01

    OBJECTIVE: To evaluate the growth parameters in infants who were born to HIV-1-infected mothers. METHODS: The study was a longitudinal evaluation of the z-scores for the weight-for-age (WAZ), weight-for-length (WLZ) and length-for-age (LAZ) data collected from a cohort. A total of 97 non-infected and 33 HIV-infected infants born to HIV-1-infected mothers in Belo Horizonte, Southeastern Brazil, between 1995 and 2003 was studied. The average follow-up period for the infected and non-infected ch...

  3. Linkage to HIV care, postpartum depression, and HIV-related stigma in newly diagnosed pregnant women living with HIV in Kenya: a longitudinal observational study.

    Science.gov (United States)

    Turan, Bulent; Stringer, Kristi L; Onono, Maricianah; Bukusi, Elizabeth A; Weiser, Sheri D; Cohen, Craig R; Turan, Janet M

    2014-12-03

    While studies have suggested that depression and HIV-related stigma may impede access to care, a growing body of literature also suggests that access to HIV care itself may help to decrease internalized HIV-related stigma and symptoms of depression in the general population of persons living with HIV. However, this has not been investigated in postpartum women living with HIV. Furthermore, linkage to care itself may have additional impacts on postpartum depression beyond the effects of antiretroviral therapy. We examined associations between linkage to HIV care, postpartum depression, and internalized stigma in a population with a high risk of depression: newly diagnosed HIV-positive pregnant women. In this prospective observational study, data were obtained from 135 HIV-positive women from eight antenatal clinics in the rural Nyanza Province of Kenya at their first antenatal visit (prior to testing HIV-positive for the first time) and subsequently at 6 weeks after giving birth. At 6 weeks postpartum, women who had not linked to HIV care after testing positive at their first antenatal visit had higher levels of depression and internalized stigma, compared to women who had linked to care. Internalized stigma mediated the effect of linkage to care on depression. Furthermore, participants who had both linked to HIV care and initiated antiretroviral therapy reported the lowest levels of depressive symptoms. These results provide further support for current efforts to ensure that women who are newly diagnosed with HIV during pregnancy become linked to HIV care as early as possible, with important benefits for both physical and mental health.

  4. HIV-1 transmission within marriage in rural Uganda: a longitudinal study.

    Directory of Open Access Journals (Sweden)

    Samuel Biraro

    Full Text Available BACKGROUND: Early initiation of antiretroviral therapy reduces risk of transmission to the uninfected partner in HIV discordant couples, but there are relatively little observational data on HIV transmission within couples from non-trial settings. The aims of this paper are to estimate HIV incidence among HIV discordant couples using longstanding observational data from a rural Ugandan population and to identify factors associated with HIV transmission within couples, including the role of HSV-2 infection. METHODS: Using existing data collected at population-wide annual serological and behavioural surveys in a rural district in southwest Uganda between 1989 and 2007, HIV discordant partners were identified. Stored serum samples were tested for HSV-2 serostatus using the Kalon ELISA test. HIV seroconversion rates and factors association with HIV seroconversion were analysed using Poisson regression. RESULTS: HIV status of both partners was known in 2465 couples and of these 259 (10.5% were HIV serodiscordant. At enrollment, HSV-2 prevalence was 87.3% in HIV positive partners and 71.5% in HIV negative partners. Of the 259 discordant couples, 62 converted to HIV (seroconversion rate 7.11/100 PYAR, 95%CI; 5.54, 9.11 with the rate decreasing from 10.89 in 1990-1994 to 4.32 in 2005-2007. Factors independently associated with HIV seroconversion were female sex, non-Muslim religion, greater age difference (man older than woman by more than 15 years, higher viral load in the positive partner and earlier calendar period. HSV-2 was not independently associated with HIV acquisition (HR 1.62, 95%CI; 0.57, 4.55 or transmission (HR 0.61, 95%CI; 0.24, 1.57. No transmissions occurred in the 29 couples where the index partner was on ART during follow up (872 person-years on ART. DISCUSSION: HIV negative partners in serodiscordant couples have a high incidence of HIV if the index partner is not on antiretroviral therapy and should be provided with interventions

  5. Observed versus predicted cardiovascular events and all-cause death in HIV infection: a longitudinal cohort study.

    Science.gov (United States)

    De Socio, Giuseppe Vittorio; Pucci, Giacomo; Baldelli, Franco; Schillaci, Giuseppe

    2017-06-12

    The aim of the study was to assess the applicability of an algorithm predicting 10-year cardiovascular disease (CVD) generated in the setting of the Framingham Heart Study to a real-life, contemporary Italian cohort of HIV-positive subjects. The study was an observational longitudinal cohort study. The probability for 10-year CVD events according to the Framingham algorithm was assessed in 369 consecutive HIV-positive participants free from overt CVD enrolled in 2004, who were followed for a median of 10.0 years (interquartile range, 9.1-10.1). Cardiovascular events included myocardial infarction, hospitalized heart failure, revascularized angina, sudden cardiac death, stroke, peripheral arterial disease. Over 3097 person-years of observation, we observed a total of 34 CVD events, whereas Framingham algorithm predicted the occurrence of 34.3 CVD events. CVD event rate was 11.0/1000 person-years of follow-up. In a receiver operating characteristics curve analysis, Framingham risk equation showed an excellent predictive value for incident CVD events (c-statistics, 0.83; 95% confidence interval, 0.76-0.90). In a multivariable Cox analysis, age, smoking and diabetes were independent predictors of CVD events. All-cause death rate was 20.0/1000 person-years of follow-up (n = 62 deaths). Causes of death included liver diseases (18), malignancies (14), AIDS-related (11); cardiovascular (9) and others (10). In a Cox analysis, age, AIDS diagnosis and chronic hepatitis were independent predictors of death. Observed CVD events in HIV-infected patients were well predicted by Framingham algorithm. Established major CVD risk factors are the strongest determinants of CVD morbidity in an Italian contemporary cohort of HIV-positive subjects. Interventions to modify traditional risk factors are urgently needed in HIV people.

  6. ClonEvol: clonal ordering and visualization in cancer sequencing.

    Science.gov (United States)

    Dang, H X; White, B S; Foltz, S M; Miller, C A; Luo, J; Fields, R C; Maher, C A

    2017-12-01

    throughout metastatic progression observed in the tumors of a published breast cancer patient. ClonEvol has broad applicability for longitudinal monitoring of clonal populations in tumor biopsies, or noninvasively, to guide precision medicine. ClonEvol is written in R and is available at https://github.com/ChrisMaherLab/ClonEvol. © The Author 2017. Published by Oxford University Press on behalf of the European Society for Medical Oncology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  7. Shift in HIV/AIDS Epidemic in Southeastern China: A Longitudinal Study from 1987 to 2015.

    Science.gov (United States)

    Yan, Yansheng; Wu, Shouli; Chen, Liang; Yan, Pingping; Qiu, Yuefeng; Xie, Meirong; Wang, Zhenghua; Lin, Xun

    2016-08-06

    The aim of this study was to investigate the shift in the epidemiological features of HIV/AIDS during the last three decades in Fujian Province, southeastern China, so as to provide evidence for the development of novel HIV/AIDS control strategies. Data pertaining to the conventional surveillance, sentinel surveillance and epidemiological survey in Fujian Province during the period from 1987 to 2015 were collected. The epidemiological trends were described, and the subtypes of HIV strain were genotyped. In addition, the response to antiretroviral therapy was evaluated, and HIV genotypic resistance was assayed. There was an increasing trend observed in the reported cases of HIV/AIDS in Fujian Province. From 1987 to the end of 2015, a total of 8651 HIV/AIDS cases were reported across the province, with totally 1557 deaths found. Among the total cases, the ratio of male/female cases was 3.7:1, which appeared to be an increasing trend; 77.1% cases were detected in young and middle-aged populations aged 19 to 50 years, however, the new HIV infections recently tended to occur in young people aged 15 to 18 years and in populations aged 50 years and older. Among all infected individuals, 49.3% were married, however, the percentage of unmarried cases increased from 6.67% before 1994 to 40.1% in 2015; 64.8% had junior high school education or lower, however, the proportion of HIV/AIDS cases with junior college education or above gradually increased from 6.5% in 2009 to 21.4% in 2015. The reported HIV/AIDS cases were predominantly found in coastal regions; however, a rapidly increasing trend was seen in the number of HIV/AIDS cases in inland regions, and the geographical variation of the cases gradually reduced. There were multiple routes of HIV transmission found in Fujian Province, and 94.2% infections were sexually transmitted, with a large increase in the percentage of male homosexual transmission. A variety of HIV-1 subtypes were genotyped in the province during the

  8. Longitudinal analysis of HIV risk behaviour patterns and their predictors among public primary care patients with tuberculosis in South Africa.

    Science.gov (United States)

    Peltzer, Karl

    2018-12-01

    The goal of this study was to identify various HIV risk behaviours among tuberculosis (TB) patients in a longitudinal study design in South Africa. In 42 public primary healthcare facilities in three districts in three provinces, adult new TB and TB retreatment patients with hazardous or harmful alcohol use were interviewed within 1 month of initiation of anti-TB treatment and were followed up at 6 months. The total sample with a complete 6-month follow-up assessment was 853. At the follow-up assessment, several HIV risk behaviours significantly reduced from baseline to follow-up. In multivariate Generalized Estimating Equations logistic regression analyses, high poverty (odds ratio (OR): 2.68, 95% confidence interval (CI): 1.56-4.62), Posttraumatic Stress Disorder (PTSD) symptoms (OR = 1.55, 95% CI = 1.03-2.36), and sexual partner on antiretroviral therapy (ART) (OR = 1.84, 95% CI = 1.09-3.10) were associated with a higher odds, and excellent/very good perceived health status (OR: 0.61, 95% CI: 0.37-0.98), severe psychological stress (OR = 0.51, 95% CI = 0.34-0.77), and HIV non-disclosure to most recent sexual partner (OR = 0.40, 95% CI = 0.25-0.65) were associated with a lower odds of inconsistent condom use. Being HIV positive (OR = 4.18, 95% CI = 2.68-6.53) and excellent/very subjective health status (OR = 2.98, 95% CI = 1.73-5.13) were associated with a higher odds, and having PTSD symptoms (OR = 0.60, 95% CI = 0.36-0.99), being on ART (OR = 0.48, 95% CI = 0.25-0.95), having a sexual partner on ART (OR = 0.41, 95% CI = 0.18-0.96), and HIV status non-disclosure (OR = 0.25, 95% CI = 0.15-0.41) were associated with a lower odds of having sex with an HIV-positive or HIV status unknown person. High poverty index (OR = 1.97, 95% CI = 1.19-3.25) and having a sexual partner on ART (OR = 4.37, 95% CI = 1.82-10.48) were associated with a higher odds, and having a partner with

  9. Rural habitat as risk factor for hepatitis E virus seroconversion in HIV-infected patients: A prospective longitudinal study.

    Science.gov (United States)

    Rivero-Juarez, A; Cuenca-Lopez, F; Martinez-Peinado, A; Camacho, A; Real, L M; Frias, M; Gordon, A; Cantisán, S; Torre-Cisneros, J; Pineda, J A; Rivero, A

    2017-11-01

    Our objective was to determine the incidence and clinical manifestations of acute hepatitis E virus (HEV) in HIV-infected patients. A prospective longitudinal study including HIV-infected HEV-seronegative patients was conducted; HEV seroconversion (to IgG and/or IgM) was the main outcome variable. All patients were tested for HEV antibodies every 3-6 months. For patients who developed HEV seroconversion, a data collection protocol was followed to identify associated clinical manifestations and analytical alterations. A total of 627 patients (89.9%) were followed during a median of 11.96 months (IQR: 8.52-14.52 months) and formed the study population. Forty-one patients developed detectable anti-HEV antibodies (7.2 cases per 100 patients/year). Our study found a high incidence of HEV in HIV-infected patients in southern Spain strongly associated with a rural habitat. © 2017 Blackwell Verlag GmbH.

  10. Functional, non-clonal IgMa-restricted B cell receptor interactions with the HIV-1 envelope gp41 membrane proximal external region.

    Directory of Open Access Journals (Sweden)

    Laurent Verkoczy

    Full Text Available The membrane proximal external region (MPER of HIV-1 gp41 has several features that make it an attractive antibody-based vaccine target, but eliciting an effective gp41 MPER-specific protective antibody response remains elusive. One fundamental issue is whether the failure to make gp41 MPER-specific broadly neutralizing antibodies like 2F5 and 4E10 is due to structural constraints with the gp41 MPER, or alternatively, if gp41 MPER epitope-specific B cells are lost to immunological tolerance. An equally important question is how B cells interact with, and respond to, the gp41 MPER epitope, including whether they engage this epitope in a non-canonical manner i.e., by non-paratopic recognition via B cell receptors (BCR. To begin understanding how B cells engage the gp41 MPER, we characterized B cell-gp41 MPER interactions in BALB/c and C57BL/6 mice. Surprisingly, we found that a significant (approximately 7% fraction of splenic B cells from BALB/c, but not C57BL/6 mice, bound the gp41 MPER via their BCRs. This strain-specific binding was concentrated in IgM(hi subsets, including marginal zone and peritoneal B1 B cells, and correlated with enriched fractions (approximately 15% of gp41 MPER-specific IgM secreted by in vitro-activated splenic B cells. Analysis of Igh(a (BALB/c and Igh(b (C57BL/6 congenic mice demonstrated that gp41 MPER binding was controlled by determinants of the Igh(a locus. Mapping of MPER gp41 interactions with IgM(a identified MPER residues distinct from those to which mAb 2F5 binds and demonstrated the requirement of Fc C(H regions. Importantly, gp41 MPER ligation produced detectable BCR-proximal signaling events, suggesting that interactions between gp41 MPER and IgM(a determinants may elicit partial B cell activation. These data suggest that low avidity, non-paratopic interactions between the gp41 MPER and membrane Ig on naïve B cells may interfere with or divert bnAb responses.

  11. Becoming "Undetectable": Longitudinal Narratives of Gay Men's Sex Lives After a Recent HIV Diagnosis.

    Science.gov (United States)

    Grace, Daniel; Chown, Sarah A; Kwag, Michael; Steinberg, Malcolm; Lim, Elgin; Gilbert, Mark

    2015-08-01

    We explore gay men's sex life narratives following their diagnosis with an acute or recent HIV infection. All participants received an acute (n = 13) or recent (n = 12) HIV diagnosis and completed a series of self-administered questionnaires and in-depth qualitative interviews over a one-year period or longer. Over the course of four qualitative interviews, participants frequently spoke of the role of medications (e.g., decisions to start treatment) and changing viral loads (e.g., discourses of becoming "undetectable") in relation to their sex lives since being diagnosed with HIV. Many men talked about milestones relating to initiating medication and viral load as informing their shifting sexual behaviors and identities as HIV-positive--or "undetectable"--gay men. The narratives of our participants provide insight regarding complex negotiations and processes of decision-making over time related to sex, counseling needs, treatment initiation, viral load, and the significance of undetectability as an emergent identity.

  12. Exploratory Analysis of Time from HIV Diagnosis to ART Start, Factors and effect on survival: A longitudinal follow up study at seven teaching hospitals in Ethiopia.

    Science.gov (United States)

    Teklu, Alula M; Delele, Kesetebirhan; Abraha, Mulu; Belayhun, Bekele; Gudina, Esayas Kebede; Nega, Abiy

    2017-02-01

    The HIV care in Ethiopia has reached 79% coverage. The timeliness of the care provided at the different levels in the course of the disease starting from knowing HIV positive status to ART initiation is not well known. This study intends to explore the timing of the care seeking, the care provision and associated factors. This is a longitudinal follow-up study at seven university hospitals. Patients enrolled in HIV care from September 2005 to December 2013 and aged ≥14 years were studied. Different times in the cascade of HIV care were examined including the duration from date HIV diagnosed to enrollment in HIV care, duration from enrollment to eligibility for ART and time from eligibility to initiation of ART. Ordinal logistic regression was used to investigate their determinants while the effect of these periods on survival of patients was determined using cox-proportional hazards regression. 4159 clients were studied. Time to enrollment after HIV test decreased from 39 days in 2005 to 1 day after 2008. It took longer if baseline CD4 was higher, and eligibility for ART was assessed late. Young adults, lower baseline CD4, HIV diagnosisART initiation. Male gender, advanced disease stage and lower baseline CD4 were consistent risk factors for mortality. Time to enrollment and duration of ART eligibility assessment as well as ART initiation time after eligibility is improving. Further study is required to identify why mortality is slightly increasing after 2010.

  13. Emergency department use by released prisoners with HIV: an observational longitudinal study.

    Directory of Open Access Journals (Sweden)

    Jaimie P Meyer

    Full Text Available Many people living with HIV access healthcare systems through the emergency department (ED, and increased ED use may be indicative of disenfranchisement with primary HIV care, under-managed comorbid disease, or coincide with use of other healthcare resources. The goal of this study was to investigate ED use by HIV-infected prisoners transitioning to communities.We evaluated ED use by 151 HIV-infected released prisoners who were enrolled in a randomized controlled trial of directly administered versus self-administered antiretroviral therapy in Connecticut. Primary outcomes were quantity and type of ED visits and correlates of ED use were evaluated with multivariate models by Poisson regression.In the 12 months post-release, there were 227 unique ED contacts made by 85/151 (56% subjects. ED visits were primarily for acute febrile syndromes (32.6% or pain (20.3%, followed by substance use issues (19.4%, trauma (18%, mental illness (11%, and social access issues (4.4%. Compared to those not utilizing the ED, users were more likely to be white, older, and unmarried, with less trust in their physician and poorer perceived physical health but greater social support. In multivariate models, ED use was correlated with moderate to severe depression (IRR = 1.80, being temporarily housed (IRR = 0.54, and alcohol addiction severity (IRR = 0.21 but not any surrogates of HIV severity.EDs are frequent sources of care after prison-release with visits often reflective of social and psychiatric instability. Future interventions should attempt to fill resource gaps, engage released prisoners in continuous HIV care, and address these substantial needs.

  14. Copenhagen comorbidity in HIV infection (COCOMO study: a study protocol for a longitudinal, non-interventional assessment of non-AIDS comorbidity in HIV infection in Denmark

    Directory of Open Access Journals (Sweden)

    Andreas Ronit

    2016-11-01

    Full Text Available Abstract Background Modern combination antiretroviral therapy (cART has improved survival for people living with HIV (PLWHIV. Non-AIDS comorbidities have replaced opportunistic infections as leading causes of mortality and morbidity, and are becoming a key health concern as this population continues to age. The aim of this study is to estimate the prevalence and incidence of non-AIDS comorbidity among PLWHIV in Denmark in the cART era and to determine risk factors contributing to the pathogenesis. The study primarily targets cardiovascular, respiratory, and hepatic non-AIDS comorbidity. Methods/design The Copenhagen comorbidity in HIV-infection (COCOMO study is an observational, longitudinal cohort study. The study was initiated in 2015 and recruitment is ongoing with the aim of including 1500 PLWHIV from the Copenhagen area. Follow-up examinations after 2 and 10 years are planned. Uninfected controls are derived from the Copenhagen General Population Study (CGPS, a cohort study including 100,000 uninfected participants from the same geographical region. Physiological and biological measures including blood pressure, ankle-brachial index, electrocardiogram, spirometry, exhaled nitric oxide, transient elastography of the liver, computed tomography (CT angiography of the heart, unenhanced CT of the chest and upper abdomen, and a number of routine biochemical analysis are uniformly collected in participants from the COCOMO study and the CGPS. Plasma, serum, buffy coat, peripheral blood mononuclear cells (PBMC, urine, and stool samples are collected in a biobank for future studies. Data will be updated through periodical linking to national databases. Discussion As life expectancy for PLWHIV improves, it is essential to study long-term impact of HIV and cART. We anticipate that findings from this cohort study will increase knowledge on non-AIDS comorbidity in PLWHIV and identify targets for future interventional trials. Recognizing the demographic

  15. Structural Barriers to Antiretroviral Therapy Among Sex Workers Living with HIV: Findings of a Longitudinal Study in Vancouver, Canada.

    Science.gov (United States)

    Goldenberg, Shira M; Montaner, Julio; Duff, Putu; Nguyen, Paul; Dobrer, Sabina; Guillemi, Silvia; Shannon, Kate

    2016-05-01

    In light of limited data on structural determinants of access and retention in antiretroviral therapy (ART) among sex workers, we examined structural correlates of ART use among sex workers living with HIV over time. Longitudinal data were drawn from a cohort of 646 female sex workers in Vancouver, Canada (2010-2012) and linked pharmacy records on ART dispensation. We used logistic regression with generalized estimating equations (GEE) to examine correlates of gaps in ART use (i.e., treatment interruptions or delayed ART initiation), among HIV seropositive participants (n = 74). Over a 2.5-year period, 37.8 % of participants experienced gaps in ART use (i.e., no ART dispensed in a 6-month period). In a multivariable GEE model, younger age, migration/mobility, incarceration, and non-injection drug use independently correlated with gaps in ART use. In spite of successes scaling-up ART in British Columbia, younger, mobile, or incarcerated sex workers face persistent gaps in access and retention irrespective of drug use. Community-based, tailored interventions to scale-up entry and retention in ART for sex workers should be further explored in this setting.

  16. Reckoning HIV/AIDS care: A longitudinal study of community home-based caregivers and clients in Swaziland.

    Science.gov (United States)

    Root, Robin; Van Wyngaard, Arnau; Whiteside, Alan

    2015-01-01

    The article is a descriptive case study of a community home-based care (CHBC) organisation in Swaziland that depicts the convergence of CHBC expansion with substantially improved health outcomes. Comprised of 993 care supporters who tend to 3 839 clients in 37 communities across southern Swaziland, Shiselweni Home-based Care (SHBC) is illustrative of many resource-limited communities throughout Africa that have mobilised, at varying degrees of formality, to address the individual and household suffering associated with HIV/AIDS. To better understand the potential significance of global and national health policy/programming reliance on community health workers (task shifting), we analysed longitudinal data on both care supporter and client cohorts from 2008 to 2013. Most CHBC studies report data from only one cohort. Foremost, our analysis demonstrated a dramatic decline (71.4%) among SHBC clients in overall mortality from 32.2% to 9.2% between 2008 and 2013. Although the study was not designed to establish statistical significance or causality between SHBC expansion and health impact, our findings detail a compelling convergence among CHBC, improved HIV health practices, and declines in client mortality. Our analysis indicated (1) the potential contributions of community health workers to individual and community wellbeing, (2) the challenges of task-shifting agendas, above all comprehensive support of community health workers/care supporters, and (3) the importance of data collection to monitor and strengthen the critical health services assigned to CHBC. Detailed study of CHBC operations and practices is helpful also for advancing government and donor HIV/AIDS strategies, especially with respect to health services decentralisation, in Swaziland and similarly profiled settings.

  17. Longitudinal Trends in the Prevalence of Detectable HIV Viremia: Population-Based Evidence From Rural KwaZulu-Natal, South Africa.

    Science.gov (United States)

    Vandormael, Alain; Bärnighausen, Till; Herbeck, Joshua; Tomita, Andrew; Phillips, Andrew; Pillay, Deenan; de Oliveira, Tulio; Tanser, Frank

    2018-04-03

    The prevalence of detectable viremia has previously been used to infer the potential for ongoing human immunodeficiency virus (HIV) transmission. To date, no study has evaluated the longitudinal change in the prevalence of detectable viremia within the HIV-positive community (PDV+) and the entire population (PDVP) using data from a sub-Saharan African setting. In 2011, 2013, and 2014, we obtained 6752 HIV-positive and 15415 HIV-negative test results from a population-based surveillance system in the KwaZulu-Natal province of South Africa. We quantified the PDV+ as the proportion of the 6752 HIV-positive results with a viral load >1550 copies/mL and the PDVP as the proportion of the 6752 HIV-positive and 15415 HIV-negative results with a viral load >1550 copies/mL. Between 2011 and 2014, the PDV+ decreased by 16.5 percentage points (pp) for women (from 71.8% to 55.3%) and 10.6 pp for men (from 77.8% to 67.2%). However, a steady rise in the overall HIV prevalence, from 26.7% to 32.4%, offset the declines in the PDV+ for both sexes. For women, the PDVP decreased by only 2.1 pp, from 21.3% to 19.2%, but for men, the PDVP actually increased by 1.6 pp, from 14.6% to 16.2%, over the survey period. The PDV+, which is currently being tracked under the UNAIDS 90-90-90 targets, may not be an accurate indicator of the potential for ongoing HIV transmission. There is a critical need for countries to monitor and report the prevalence of detectable viremia among all adults, irrespective of HIV status.

  18. Reckoning HIV/AIDS care: A longitudinal study of community home ...

    African Journals Online (AJOL)

    To better understand the potential significance of global and national health policy/programming reliance on community health workers (task shifting), we analysed longitudinal data on both care supporter and client cohorts from 2008 to 2013. Most CHBC studies report data from only one cohort. Foremost, our analysis ...

  19. Dorsal longitudinal foreskin cut is associated with reduced risk of HIV, syphilis and genital herpes in men: a cross-sectional study in Papua New Guinea.

    Science.gov (United States)

    Vallely, Andrew J; MacLaren, David; David, Matthew; Toliman, Pamela; Kelly-Hanku, Angela; Toto, Ben; Tommbe, Rachael; Kombati, Zure; Kaima, Petronia; Browne, Kelwyn; Manineng, Clement; Simeon, Lalen; Ryan, Claire; Wand, Handan; Hill, Peter; Law, Greg; Siba, Peter M; McBride, W John H; Kaldor, John M

    2017-04-03

    Various forms of penile foreskin cutting are practised in Papua New Guinea. In the context of an ecological association observed between HIV infection and the dorsal longitudinal foreskin cut, we undertook an investigation of this relationship at the individual level. We conducted a cross-sectional study among men attending voluntary confidential HIV counselling and testing clinics. Following informed consent, participants had a face-to-face interview and an examination to categorize foreskin status. HIV testing was conducted on site and relevant specimens collected for laboratory-based Herpes simplex type-2 (HSV-2), syphilis, Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG), and Trichomonas vaginalis (TV) testing. Overall, 1073 men were enrolled: 646 (60.2%) were uncut; 339 (31.6%) had a full dorsal longitudinal cut; 72 (6.7%) a partial dorsal longitudinal cut; and 14 (1.3%) were circumcised. Overall, the prevalence of HIV was 12.3%; HSV-2, 33.6%; active syphilis, 12.1%; CT, 13.4%; NG, 14.1%; and TV 7.6%. Compared with uncut men, men with a full dorsal longitudinal cut were significantly less likely to have HIV (adjusted odds ratio [adjOR] 0.25, 95%CI: 0.12, 0.51); HSV-2 (adjOR 0.60, 95%CI: 0.41, 0.87); or active syphilis (adjOR 0.55, 95%CI: 0.31, 0.96). This apparent protective effect was restricted to men cut prior to sexual debut. There was no difference between cut and uncut men for CT, NG or TV. In this large cross-sectional study, men with a dorsal longitudinal foreskin cut were significantly less likely to have HIV, HSV-2 and syphilis compared with uncut men, despite still having a complete (albeit morphologically altered) foreskin. The protective effect of the dorsal cut suggests that the mechanism by which male circumcision works is not simply due to the removal of the inner foreskin and its more easily accessible HIV target cells. Exposure of the penile glans and inner foreskin appear to be key mechanisms by which male circumcision confers

  20. Clonality evaluation in human tissues

    Directory of Open Access Journals (Sweden)

    Villamizar-Rivera, Nicolás

    2015-07-01

    Full Text Available Malignant proliferations are usually clonal. While most times the biological potential can be established through routine pathologic and clinical examinations, some cases are difficult to classify. Moreover, in some situations there are dominant clones whose analysis is important, such as in autoimmune diseases and immunodeficiency. This paper presents in an understandable way the main techniques for the study of clonality, namely: evaluation of gene rearrangements of antigen receptor, and evaluation of human antigen receptor gene.

  1. Longitudinal trends of HIV drug resistance in a large Canadian cohort, 1996-2016.

    Science.gov (United States)

    Rocheleau, G; Brumme, C J; Shoveller, J; Lima, V D; Harrigan, P R

    2018-02-01

    We aim to identify long-term trends in HIV drug resistance before and after combined antiretroviral therapy (cART) initiation. IAS-USA (2015) mutations were identified in 23 271 HIV protease-reverse transcriptase sequences from 6543 treatment naïve adults in British Columbia. Participants who started cART between 1996 and 2014 were followed until April 2016. Equality of proportions test was used to compare the percentage of participants with acquired drug resistance (ADR) or transmitted drug resistance (TDR) in 1996, to those in 2014. Kaplan-Meier was used to estimate time to ADR in four drug resistance categories. Multivariable regression odds ratios (OR) of ADR for select clinical variables were determined by 5-year eras of cART initiation. The proportion of individuals with ADR declined from 39% (51/132) to 3% (8/322) in 1996-2014 (p 16 years of therapy. After 5 years on therapy, participants initiating cART in 1996-2000 had 5.5-times more 3TC/FTC ADR, 5.3-times more other nRTI ADR, 4.7-times more NNRTI ADR, and 24-times more PI ADR than those starting in 2011-2014. The individuals with highest odds of developing ADR in 1996-2010 were adherent to regimens at levels between 60% and 80%, which shifted to 40% adherent in 2011-2014. HIV drug resistance transitioned from being primarily selected de-novo to being driven by TDR. Among those who started treatment in the past 5 years, ADR is rare and observed mostly in the lowest adherence strata. Copyright © 2017 European Society of Clinical Microbiology and Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

  2. Depressive symptoms, lifestyle structure, and ART adherence among HIV-infected individuals: a longitudinal mediation analysis.

    Science.gov (United States)

    Magidson, Jessica F; Blashill, Aaron J; Safren, Steven A; Wagner, Glenn J

    2015-01-01

    Despite the well-documented relationship between depression and antiretroviral therapy (ART) nonadherence, few studies have identified explanatory pathways through which depression affects adherence. The current study tested lifestyle structure-the degree of organization and routinization of daily activities-as a mediator of this relationship, given previous evidence of lifestyle structure being associated with both depression and ART nonadherence. HIV-infected individuals starting or re-starting ART in the California Collaborative Treatment Group 578 study (n = 199) were assessed over 48 weeks. Adherence was measured using electronic monitoring caps to determine dose timing and doses taken, and viral load was assessed. The mediating role of lifestyle structure was tested using generalized linear mixed-effects modeling and bootstrapping. Lifestyle significantly mediated the relationship between depression and both measures of ART adherence behavior. Interventions that minimize disruptions to lifestyle structure and link adherence to daily activities may be useful for individuals with depression and ART nonadherence.

  3. Extending the Minority Stress Model to Incorporate HIV-Positive Gay and Bisexual Men's Experiences: a Longitudinal Examination of Mental Health and Sexual Risk Behavior.

    Science.gov (United States)

    Rendina, H Jonathon; Gamarel, Kristi E; Pachankis, John E; Ventuneac, Ana; Grov, Christian; Parsons, Jeffrey T

    2017-04-01

    Minority stress theory represents the most plausible conceptual framework for explaining health disparities for gay and bisexual men (GBM). However, little focus has been given to including the unique stressors experienced by HIV-positive GBM. We explored the role of HIV-related stress within a minority stress model of mental health and condomless anal sex. Longitudinal data were collected on a diverse convenience sample of 138 highly sexually active, HIV-positive GBM in NYC regarding sexual minority (internalized homonegativity and gay-related rejection sensitivity) and HIV-related stressors (internalized HIV stigma and HIV-related rejection sensitivity), emotion dysregulation, mental health (symptoms of depression, anxiety, sexual compulsivity, and hypersexuality), and sexual behavior (condomless anal sex with all male partners and with serodiscordant male partners). Across both sexual minority and HIV-related stressors, internalized stigma was significantly associated with mental health and sexual behavior outcomes while rejection sensitivity was not. Moreover, path analyses revealed that emotion dysregulation mediated the influence of both forms of internalized stigma on symptoms of depression/anxiety and sexual compulsivity/hypersexuality as well as serodiscordant condomless anal sex. We identified two targets of behavioral interventions that may lead to improvements in mental health and reductions in sexual transmission risk behaviors-maladaptive cognitions underlying negative self-schemas and difficulties with emotion regulation. Techniques for cognitive restructuring and emotion regulation may be particularly useful in the development of interventions that are sensitive to the needs of this population while also highlighting the important role that structural interventions can have in preventing these disparities for future generations.

  4. Stability of infant and child feeding index over time and its association with nutritional status of HIV exposed infants in Sidama Zone, Southern Ethiopia: a longitudinal study.

    Science.gov (United States)

    Haile, Demewoz; Belachew, Tefera; Berhanu, Getenesh; Setegn, Tesfaye; Biadgilign, Sibhatu

    2014-12-01

    Even though many studies showed that infant and child feeding index has a statistically significant association with nutritional status, there is paucity of studies on stability of infant and child feeding index over time and its association with nutritional status of HIV exposed infants. This study aimed to investigate the stability of infant and child feeding index over time that is developed based on the current recommendations and its association with nutritional status of HIV exposed infants in Sidama Zone, Southern Ethiopia. A panel study design was conducted in health institutions in Sidama Zone from February to July, 2012. Three repeated measurements of data were collected from each HIV exposed infant aged 6-17 months over the 6 month follow-up period approximately per 2 month interval. The cross-sectional index was found stable overtime with the repeatability coefficient of 0.802 which differed significantly from zero (95% CI: 0.75-0.85). A longitudinal infant and child feeding index (L-ICFI) has a statistically significant association with length for age Z scores (LAZ) and weight for age Z scores (WAZ) at visit three (β=0.262, p=0.007; β=0.226, p=0.017), respectively. But the longitudinal index has no statistically significant association with WLZ score (p=0.552). There was no significant difference in change of LAZ and WAZ over time between L-ICFI tertiles for both female and male HIV exposed infants. The index is stable overtime at individual level even though one third of the index components were not stable. The L-CFI was associated with LAZ and WAZ but not with WLZ. However there was no significant difference in change of HAZ and WAZ over time between L-ICFI tertiles for both female and male HIV exposed infants. Copyright © 2014 Elsevier Ltd. All rights reserved.

  5. Longitudinal anthropometric assessment of infants born to HIV-1-infected mothers, Belo Horizonte, Southeastern Brazil Evaluación antropométrica longitudinal de lactantes nacidos de madres infectadas por VIH-1 Avaliação antropométrica longitudinal de lactentes nascidos de mães infectadas pelo HIV-1

    Directory of Open Access Journals (Sweden)

    Maria Arlene Fausto

    2011-08-01

    Full Text Available OBJECTIVE: To evaluate the growth parameters in infants who were born to HIV-1-infected mothers. METHODS: The study was a longitudinal evaluation of the z-scores for the weight-for-age (WAZ, weight-for-length (WLZ and length-for-age (LAZ data collected from a cohort. A total of 97 non-infected and 33 HIV-infected infants born to HIV-1-infected mothers in Belo Horizonte, Southeastern Brazil, between 1995 and 2003 was studied. The average follow-up period for the infected and non-infected children was 15.8 months (variation: 6.8 to 18.0 months and 14.3 months (variation: 6.3 to 18.6 months, respectively. A mixed-effects linear regression model was used and was fitted using a restricted maximum likelihood. RESULTS: There was an observed decrease over time in the WAZ, LAZ and WLZ among the infected infants. At six months of age, the mean differences in the WAZ, LAZ and WLZ between the HIV-infected and non-infected infants were 1.02, 0.59, and 0.63 standard deviations, respectively. At 12 months, the mean differences in the WAZ, LAZ and WLZ between the HIV-infected and non-infected infants were 1.15, 1.01, and 0.87 standard deviations, respectively. CONCLUSIONS: The precocious and increasing deterioration of the HIV-infected infants' anthropometric indicators demonstrates the importance of the early identification of HIV-infected infants who are at nutritional risk and the importance of the continuous assessment of nutritional interventions for these infants.OBJETIVO: Evaluar los parámetros de crecimiento en lactantes nacidos de madres infectadas con el VIH-1. MÉTODOS: Evaluación longitudinal de los z-escores peso-edad (PI, estatura-edad (EI, peso-estatura (PE fue realizada en una cohorte. Fueran estudiados 97 lactantes no infectados y 33 lactantes infectados nacidos de madres infectadas con el VIH-1 en Belo Horizonte, Sureste de Brasil, de 1995 a 2003. El tiempo medio de seguimiento para los lactantes infectados y no infectados fue de 15,8 meses

  6. Longitudinal trends of recent HIV-1 infections in Slovenia (1986-2012) determined using an incidence algorithm.

    Science.gov (United States)

    Lunar, Maja M; Matković, Ivana; Tomažič, Janez; Vovko, Tomaž D; Pečavar, Blaž; Poljak, Mario

    2015-09-01

    Resolving dilemma whether the rise in the number of HIV diagnoses represents an actual increase in HIV transmissions or is a result of improved HIV surveillance is crucial before implementing national HIV prevention strategies. Annual proportions of recent infections (RI) among newly diagnosed persons infected with HIV-1 in Slovenia during 27 years (1986-2012) were determined using an algorithm consisting of routine baseline CD4 and HIV viral load measurements and the Aware BED EIA HIV-1 Incidence Test (BED test). The study included the highest coverage of persons diagnosed with HIV during the entire duration of an HIV epidemic in a given country/region (71%). Out of 416 patients, 170 (40.9%) had a baseline CD4 cell count less than 200 cells/mm(3) and/or HIV-1 viral load less than 400 copies/ml and were characterized as having a long-standing infection (LSI). The remaining 246 patients were additionally tested using the BED test. Overall, 23% (97/416) of the patients were labeled RI. The characteristics significantly associated with RI were as follows: younger age, acute retroviral syndrome, CDC class A and other than C, no AIDS defining illnesses, HIV test performed in the past, a higher viral load, and a higher CD4 cell count. An interesting trend in the proportion of RI was observed, with a peak in 2005 (47% of RI) and the lowest point in 2008 (12%) in parallel with a rise in the numbers of new HIV diagnoses. This study could help promote the idea of introducing periodic HIV incidence monitoring using a simple and affordable algorithm. © 2015 Wiley Periodicals, Inc.

  7. Depression longitudinally mediates the association of appearance concerns to ART non-adherence in HIV-infected individuals with a history of injection drug use.

    Science.gov (United States)

    Blashill, Aaron J; Gordon, Janna R; Safren, Steven A

    2014-02-01

    Appearance concerns are common among HIV-infected individuals, and previous cross-sectional and longitudinal data indicate that these concerns are associated with antiretroviral therapy (ART) non-adherence. However, to date, no known prospective data have explored the mechanism behind this relationship. Thus, the aim of the current study was to test depression severity as a prospective mediator of the relationship between appearance concerns and ART non-adherence in HIV-infected individuals with a history of injection drug use (IDU). Participants were 89 HIV-infected individuals with a history of IDU who participated in a prospective, randomized controlled trial of cognitive behavioral therapy for depression and medication adherence. Clinician-administered measures of depression severity and appearance concerns, along with electronic monitoring of ART non-adherence were included. Data were analyzed using longitudinal linear mixed-level modeling, and mediation was tested via the Monte Carlo Method of Assessing Mediation. Appearance concerns were predictive of depression severity, γ = .31, SE = .076, 95 % CI [.16, .46], t = 4.1, p = .0001, and depression severity was predictive of ART non-adherence, γ = 3.3, SE = 1.3, 95 % CI [.8, 5.8], t = 2.6, p = .01. The effect of appearance concerns on ART non-adherence, however, was significantly mediated by depression severity, γ = 1.02, 95 % CI [.21, 2.1]. Appearance concerns are associated with depression severity, which in turn is associated with ART non-adherence. Integrative interventions addressing appearance concerns, depression and ART adherence are needed, as this is one potential pathway towards worse health outcomes in HIV-infected individuals.

  8. Transgenerational plasticity in clonal plants

    Czech Academy of Sciences Publication Activity Database

    Latzel, Vít; Klimešová, Jitka

    2010-01-01

    Roč. 24, č. 6 (2010), s. 1537-1543 ISSN 0269-7653 R&D Projects: GA ČR GD206/08/H044; GA ČR GA526/09/0963; GA ČR GPP505/10/P173 Institutional research plan: CEZ:AV0Z60050516 Keywords : maternal effect * evolution * clonal plants Subject RIV: EF - Botanics Impact factor: 2.398, year: 2010

  9. The effects of caregiver and household HIV on child development: a community-based longitudinal study of young children.

    Science.gov (United States)

    Sherr, L; Skeen, S; Hensels, I S; Tomlinson, M; Macedo, A

    2016-11-01

    Many studies that document child outcomes in the context of parental HIV - which has been established as a risk factor for child development - focus on older children/adolescents. Studies also concentrate on the status of the primary caregiver, not other household members who might be infected. This study examined the effects of caregiver and household HIV on child development (4-13 years) in South Africa and Malawi (2011-2014). Data were gathered from 989 children and their primary caregivers at baseline and repeated at 12-15 months follow-up (86.5% follow-up rate). Only caregivers of a single child and caregiver/child dyads without missing data were included, providing a sample of 808 dyads for analysis. Children were divided into three groups according to caregiver-reported HIV burden: having an HIV-positive primary caregiver (19.8%), having HIV in the household (14.2%) or no HIV (66%). The HIV burden was positively associated with an array of negative child outcomes, often mediated by caregiver depression levels. Family HIV burden at baseline affected child behavioural problems at follow-up indirectly through carer depression (B = 0.02; CI = 0.003, 0.06). Internalizing (B = 0.02; CI = 0.002, 0.05) and externalizing problems at follow-up (B = 0.01; CI = 0.0002, 0.03) were also indirectly affected by family HIV burden through caregiver depression. The data suggest that family HIV can affect child development, emphasizing the important role of depression in the pathway to such an effect. Community-based interventions directed at alleviating parental depression in the presence of HIV may help to interrupt the cycle of family HIV and adverse child outcomes. © 2016 The Authors. Child: Care, Health and Development Published by John Wiley & Sons Ltd.

  10. Sexual behaviors of US women at risk of HIV acquisition: A longitudinal analysis of findings from HPTN 064

    OpenAIRE

    Justman, J.; Befus, M.; Hughes, J.; Wang, J.; Golin, C. E.; Adimora, A.A.; Kuo, I.; Haley, D. F.; del Rio, C.; El-Sadr, W. M.; Rompalo, A.; Mannheimer, S.; Soto-Torres, L.; Hodder, S.

    2015-01-01

    We describe the sexual behaviors of women at elevated risk of HIV acquisition who reside in areas of high HIV prevalence and poverty in the US. Participants in HPTN 064, a prospective HIV incidence study, provided information about participants’ sexual behaviors and male sexual partners in the past 6 months at baseline, 6- and 12-months. Independent predictors of consistent or increased temporal patterns for three high-risk sexual behaviors were assessed separately: exchange sex, unprotected ...

  11. Maternal post-traumatic stress disorder, depression and alcohol dependence and child behaviour outcomes in mother-child dyads infected with HIV: a longitudinal study.

    Science.gov (United States)

    Nöthling, Jani; Martin, Cherie L; Laughton, Barbara; Cotton, Mark F; Seedat, Soraya

    2013-12-10

    HIV and psychiatric disorders are prevalent and often concurrent. Childbearing women are at an increased risk for both HIV and psychiatric disorders, specifically depression and post-traumatic stress disorder (PTSD). Poor mental health in the peripartum period has adverse effects on infant development and behaviour. Few studies have investigated the relationship between maternal PTSD and child behaviour outcomes in an HIV vertically infected sample. The aim of this study was to investigate whether maternal postpartum trauma exposure and PTSD were risk factors for child behaviour problems. In addition, maternal depression, alcohol abuse and functional disability were explored as cofactors. The study was conducted in Cape Town, South Africa. 70 mother-child dyads infected with HIV were selected from a group of participants recruited from community health centres. The study followed a longitudinal design. Five measures were used to assess maternal trauma exposure, PTSD, depression, alcohol abuse and functional disability at 12 months postpartum: Life Events Checklist (LEC), Harvard Trauma Scale (HTS), Alcohol Use Disorders Identification Test (AUDIT), Center for Epidemiological Studies Depression (CESD) Scale and the Sheehan Disability Scale (SDS). Child behaviour was assessed at 42 months with the Child Behaviour Checklist (CBCL). The rate of maternal disorder was high with 50% scoring above the cut-off for depression, 22.9% for PTSD and 7% for alcohol abuse. Half of the children scored within the clinical range for problematic behaviour. Children of mothers with depression were significantly more likely to display total behaviour problems than children of mothers without depression. Maternal PTSD had the greatest explanatory power for child behaviour problems, although it did not significantly predict child outcomes. This study highlights the importance of identifying and managing maternal PTSD and depression in mothers of children infected with HIV. The

  12. Social Network Characteristics Moderate the Association Between Stigmatizing Attributions About HIV and Non-adherence Among Black Americans Living with HIV: a Longitudinal Assessment.

    Science.gov (United States)

    Bogart, Laura M; Wagner, Glenn J; Green, Harold D; Mutchler, Matt G; Klein, David J; McDavitt, Bryce

    2015-12-01

    Stigma may contribute to HIV-related disparities among HIV-positive Black Americans. We examined whether social network characteristics moderate stigma's effects. At baseline and 6 months post-baseline, 147 HIV-positive Black Americans on antiretroviral treatment completed egocentric social network assessments, from which we derived a structural social support capacity measure (i.e., ability to leverage support from the network, represented by the average interaction frequency between the participant and each alter). Stigma was operationalized with an indicator of whether any social network member had expressed stigmatizing attributions of blame or responsibility about HIV. Daily medication adherence was monitored electronically. In a multivariate regression, baseline stigma was significantly related to decreased adherence over time. The association between stigma and non-adherence was attenuated among participants who increased the frequency of their interactions with alters over time. Well-connected social networks have the potential to buffer the effects of stigma.

  13. The impact of HAART on the respiratory complications of HIV infection: longitudinal trends in the MACS and WIHS cohorts.

    Directory of Open Access Journals (Sweden)

    Matthew R Gingo

    Full Text Available To review the incidence of respiratory conditions and their effect on mortality in HIV-infected and uninfected individuals prior to and during the era of highly active antiretroviral therapy (HAART.Two large observational cohorts of HIV-infected and HIV-uninfected men (Multicenter AIDS Cohort Study [MACS] and women (Women's Interagency HIV Study [WIHS], followed since 1984 and 1994, respectively.Adjusted odds or hazards ratios for incident respiratory infections or non-infectious respiratory diagnoses, respectively, in HIV-infected compared to HIV-uninfected individuals in both the pre-HAART (MACS only and HAART eras; and adjusted Cox proportional hazard ratios for mortality in HIV-infected persons with lung disease during the HAART era.Compared to HIV-uninfected participants, HIV-infected individuals had more incident respiratory infections both pre-HAART (MACS, odds ratio [adjusted-OR], 2.4; 95% confidence interval [CI], 2.2-2.7; p<0.001 and after HAART availability (MACS, adjusted-OR, 1.5; 95%CI 1.3-1.7; p<0.001; WIHS adjusted-OR, 2.2; 95%CI 1.8-2.7; p<0.001. Chronic obstructive pulmonary disease was more common in MACS HIV-infected vs. HIV-uninfected participants pre-HAART (hazard ratio [adjusted-HR] 2.9; 95%CI, 1.02-8.4; p = 0.046. After HAART availability, non-infectious lung diseases were not significantly more common in HIV-infected participants in either MACS or WIHS participants. HIV-infected participants in the HAART era with respiratory infections had an increased risk of death compared to those without infections (MACS adjusted-HR, 1.5; 95%CI, 1.3-1.7; p<0.001; WIHS adjusted-HR, 1.9; 95%CI, 1.5-2.4; p<0.001.HIV infection remained a significant risk for infectious respiratory diseases after the introduction of HAART, and infectious respiratory diseases were associated with an increased risk of mortality.

  14. Clonal hematopoiesis in acquired aplastic anemia

    OpenAIRE

    Ogawa, Seishi

    2016-01-01

    Clonal hematopoiesis (CH) in aplastic anemia (AA) has been closely linked to the evolution of late clonal disorders, including paroxysmal nocturnal hemoglobinuria and myelodysplastic syndromes (MDS)/acute myeloid leukemia (AML), which are common complications after successful immunosuppressive therapy (IST). With the advent of high-throughput sequencing of recent years, the molecular aspect of CH in AA has been clarified by comprehensive detection of somatic mutations that drive clonal evolut...

  15. Clonal sets of a binary relation

    Science.gov (United States)

    Zedam, Lemnaouar; Pérez-Fernández, Raúl; Bouremel, Hassane; De Baets, Bernard

    2018-05-01

    In a recent paper, we have introduced the notion of clone relation of a given binary relation. Intuitively, two elements are said to be "clones" if they are related in the same way w.r.t. every other element. In this paper, we generalize this notion from pairs of elements to sets of elements of any cardinality, resulting in the introduction of clonal sets. We investigate the most important properties of clonal sets, paying particular attention to the introduction of the clonal closure operator, to the analysis of the (lattice) structure of the set of clonal sets and to a distance metric expressing how close two elements are to being clones.

  16. Longitudinal Trends in Sexual Behaviors with Advancing Age and Menopause Among Women With and Without HIV-1 Infection

    Science.gov (United States)

    Weedon, Jeremy; Golub, Elizabeth T.; Karpiak, Stephen E.; Gandhi, Monica; Cohen, Mardge H.; Levine, Alexandra M.; Minkoff, Howard L.; Adedimeji, Adebola A.; Goparaju, Lakshmi; Holman, Susan; Wilson, Tracey E.

    2014-01-01

    We assessed changes in self-reported sexual activity (SA) over 13 years among HIV-infected and uninfected women. The impact of aging and menopause on SA and unprotected anal or vaginal intercourse (UAVI) was examined among women in the Women’s Interagency HIV Study (WIHS), stratifying by HIV status and detectable viral load among HIV-infected women. Generalized mixed linear models were fitted for each outcome, adjusted for relevant covariates. HIV-uninfected women evidenced higher levels of SA and UAVI than HIV-infected. The odds of SA declined by 62–64 % per decade of age. The odds of SA in a 6-month interval for women aged 40–57 declined by 18–22 % post-menopause (controlling for age). Among HIV+/detectable women only, the odds of any UAVI decreased by 17 % per decade of age; the odds of UAVI were unchanged pre-menopause, and then decreased by 28 % post-menopause. Elucidating the factors accounting for ongoing unprotected sex among older women should inform interventions. PMID:25245474

  17. HIV Risk Characteristics Associated with Violence Against Women: A Longitudinal Study Among Women in the United States.

    Science.gov (United States)

    Montgomery, Brooke E E; Frew, Paula M; Hughes, James P; Wang, Jing; Adimora, Adaora A; Haley, Danielle F; Kuo, Irene; Jennings, Larissa; El-Bassel, Nabila; Hodder, Sally L

    2018-06-15

    Using data from HIV Prevention Trials Network 064, a multisite, observational cohort study conducted to estimate HIV incidence rates among women living in areas of high poverty and HIV prevalence in the United States, we examined the use of HIV risk characteristics to predict emotional abuse, physical violence, and forced sex. Participants included 2099 women, 18-44 years of age, who reported unprotected vaginal or anal sex with a male partner and an additional personal or perceived male partner HIV risk characteristic in the past 6 months. Adjusting for time-varying covariates, generalized estimating equations were used to assess the ability of HIV risk characteristics to predict violence 6 months later. Reported analyses were limited to the 1980 study participants who reported having a male sex partner at that assessment. Exchanging sex, perceived partner concurrency, and perceived partner incarceration were significantly predictive of emotional abuse 6 months later (adjusted odds ratio [AOR]: 1.60; 1.59; 1.34, respectively). Prior sexually transmitted infection diagnosis, exchanging sex, and binge drinking were significantly predictive of physical violence 6 months later (AOR: 1.62; 1.71; 1.47, respectively). None of the variables measured was significantly predictive of forced sex. Strategies that address reducing violence against women should be studied further in the context of HIV prevention programs.

  18. A Proposed Approach for Joint Modeling of the Longitudinal and Time-To-Event Data in Heterogeneous Populations: An Application to HIV/AIDS's Disease.

    Science.gov (United States)

    Roustaei, Narges; Ayatollahi, Seyyed Mohammad Taghi; Zare, Najaf

    2018-01-01

    In recent years, the joint models have been widely used for modeling the longitudinal and time-to-event data simultaneously. In this study, we proposed an approach (PA) to study the longitudinal and survival outcomes simultaneously in heterogeneous populations. PA relaxes the assumption of conditional independence (CI). We also compared PA with joint latent class model (JLCM) and separate approach (SA) for various sample sizes (150, 300, and 600) and different association parameters (0, 0.2, and 0.5). The average bias of parameters estimation (AB-PE), average SE of parameters estimation (ASE-PE), and coverage probability of the 95% confidence interval (CP) among the three approaches were compared. In most cases, when the sample sizes increased, AB-PE and ASE-PE decreased for the three approaches, and CP got closer to the nominal level of 0.95. When there was a considerable association, PA in comparison with SA and JLCM performed better in the sense that PA had the smallest AB-PE and ASE-PE for the longitudinal submodel among the three approaches for the small and moderate sample sizes. Moreover, JLCM was desirable for the none-association and the large sample size. Finally, the evaluated approaches were applied on a real HIV/AIDS dataset for validation, and the results were compared.

  19. A Proposed Approach for Joint Modeling of the Longitudinal and Time-To-Event Data in Heterogeneous Populations: An Application to HIV/AIDS’s Disease

    Directory of Open Access Journals (Sweden)

    Narges Roustaei

    2018-01-01

    Full Text Available In recent years, the joint models have been widely used for modeling the longitudinal and time-to-event data simultaneously. In this study, we proposed an approach (PA to study the longitudinal and survival outcomes simultaneously in heterogeneous populations. PA relaxes the assumption of conditional independence (CI. We also compared PA with joint latent class model (JLCM and separate approach (SA for various sample sizes (150, 300, and 600 and different association parameters (0, 0.2, and 0.5. The average bias of parameters estimation (AB-PE, average SE of parameters estimation (ASE-PE, and coverage probability of the 95% confidence interval (CP among the three approaches were compared. In most cases, when the sample sizes increased, AB-PE and ASE-PE decreased for the three approaches, and CP got closer to the nominal level of 0.95. When there was a considerable association, PA in comparison with SA and JLCM performed better in the sense that PA had the smallest AB-PE and ASE-PE for the longitudinal submodel among the three approaches for the small and moderate sample sizes. Moreover, JLCM was desirable for the none-association and the large sample size. Finally, the evaluated approaches were applied on a real HIV/AIDS dataset for validation, and the results were compared.

  20. HIV-related symptoms and management in HIV and antiretroviral therapy patients in KwaZulu-Natal, South Africa: A longitudinal study

    Science.gov (United States)

    Peltzer, Karl

    2014-01-01

    Aim The study aimed to determine the prevalence, predictors, and self-reported management of HIV- or ARV-related symptoms among HIV patients prior to antiretroviral therapy (ART) and over three time points while receiving ART in KwaZulu-Natal, South Africa. Method A total of 735 consecutive patients (29.8% male and 70.2% female) who attended three HIV clinics completed assessments prior to ARV initiation, 519 after 6 months, 557 after 12 months, and 499 after 20 months on ART. Results The HIV patients reported an average of 7.5 symptoms (prior to ART), 1.2 symptoms after 6 months on ART, 0.3 symptoms after 12 months on ART, and 0.2 symptoms after 20 months on ART on the day of the interview, with a higher symptom frequency amongst patients who were not employed, had lower CD4 cell counts, experienced internalised stigma, and used alcohol. The most common symptoms or conditions identified by the self-report included tuberculosis, diarrhoea, headaches, rash, nausea and vomiting, pain, neuropathy, lack of appetite, cough, and chills. Overall, the participants reported medications as the most frequently occurring management strategy, with the second being spiritual, and the third being complementary or traditional treatments. The use of all other management strategies decreased over the four different assessment periods from prior to ART to 20 months on ART. Conclusion This study found a high symptom burden among HIV patients, which significantly decreased with progression on antiretroviral treatment. Several symptoms that persisted over time and several sociodemographic factors were identified that can guide symptom management. The utilisation of different symptom management strategies (medical, spiritual, complementary, and traditional) should be taken into consideration in HIV treatment. PMID:24405285

  1. Burden of Respiratory Syncytial Virus Infection in South African Human Immunodeficiency Virus (HIV)-Infected and HIV-Uninfected Pregnant and Postpartum Women: A Longitudinal Cohort Study.

    Science.gov (United States)

    Madhi, Shabir A; Cutland, Clare L; Downs, Sarah; Jones, Stephanie; van Niekerk, Nadia; Simoes, Eric A F; Nunes, Marta C

    2018-05-17

    Limited data exist on the burden of respiratory syncytial virus (RSV) illness among pregnant women, to determine their potential benefit from RSV vaccination. We evaluated the incidence of RSV illness from midpregnancy until 24 weeks postpartum in human immunodeficiency virus (HIV)-uninfected and HIV-infected women and their infants. Mother-infant dyads were enrolled in maternal influenza vaccine efficacy trials. These included 1060 and 1056 HIV-uninfected pregnant women in 2011 and 2012, respectively, 194 HIV-infected pregnant women in 2011, and their infants. Upper respiratory tract samples obtained at illness visits were tested for RSV. The incidence (per 1000 person-months) of RSV illness (n = 43 overall) among HIV-uninfected women was lower in 2011 (1.2; 95% confidence interval [CI], .6-2.2) than in 2012 (4.0; 95% CI, 2.8-5.6). The incidence of RSV illness (n = 5) in HIV-infected women was 3.4 (95% CI, 1.4-8.1). Maternal RSV infection was associated with respiratory symptoms including cough (72.1%), rhinorrhea (39.5%), sore throat (37.2%), and headache (42%), but fever was absent. RSV infection during pregnancy was not associated with adverse pregnancy outcomes. Postpartum, RSV infection in mothers (n = 27) was associated with concurrent infection among 51.9% of their infants and, conversely, 29.8% of mothers investigated within 7 days of their infants having an RSV illness also tested positive for RSV. RSV infection is associated with respiratory illness during pregnancy and postpartum. Vaccination of pregnant women against RSV could benefit the mother, albeit primarily against nonfebrile illness, and her infant. NCT01306669 and NCT01306682.

  2. Sexual Behaviors of US Women at Risk of HIV Acquisition: A Longitudinal Analysis of Findings from HPTN 064.

    Science.gov (United States)

    Justman, J; Befus, M; Hughes, J; Wang, J; Golin, C E; Adimora, A A; Kuo, I; Haley, D F; Del Rio, C; El-Sadr, W M; Rompalo, A; Mannheimer, S; Soto-Torres, L; Hodder, S

    2015-07-01

    We describe the sexual behaviors of women at elevated risk of HIV acquisition who reside in areas of high HIV prevalence and poverty in the US. Participants in HPTN 064, a prospective HIV incidence study, provided information about individual sexual behaviors and male sexual partners in the past 6 months at baseline, 6- and 12-months. Independent predictors of consistent or increased temporal patterns for three high-risk sexual behaviors were assessed separately: exchange sex, unprotected anal intercourse (UAI) and concurrent partnerships. The baseline prevalence of each behavior was >30 % among the 2,099 participants, 88 % reported partner(s) with >1 HIV risk characteristic and both individual and partner risk characteristics decreased over time. Less than high school education and food insecurity predicted consistent/increased engagement in exchange sex and UAI, and partner's concurrency predicted participant concurrency. Our results demonstrate how interpersonal and social factors may influence sustained high-risk behavior by individuals and suggest that further study of the economic issues related to HIV risk could inform future prevention interventions.

  3. Hodgkin lymphoma, HIV, and Epstein-Barr virus in Malawi: Longitudinal results from the Kamuzu Central Hospital Lymphoma study.

    Science.gov (United States)

    Westmoreland, Katherine D; Stanley, Christopher C; Montgomery, Nathan D; Kaimila, Bongani; Kasonkanji, Edwards; El-Mallawany, Nader Kim; Wasswa, Peter; Mtete, Idah; Butia, Mercy; Itimu, Salama; Chasela, Mary; Mtunda, Mary; Chikasema, Maria; Makwakwa, Victor; Kampani, Coxcilly; Dhungel, Bal M; Sanders, Marcia K; Krysiak, Robert; Tomoka, Tamiwe; Liomba, N George; Dittmer, Dirk P; Fedoriw, Yuri; Gopal, Satish

    2017-05-01

    Contemporary descriptions of classical Hodgkin lymphoma (cHL) are lacking from sub-Saharan Africa where human immunodeficiency virus (HIV) and Epstein-Barr virus (EBV) are prevalent. We describe a prospective cHL cohort in Malawi enrolled from 2013 to 2015. Patients received standardized treatment and evaluation, including HIV status and EBV testing of tumors and plasma. Among 31 patients with confirmed cHL, the median age was 19 years (range, 2-51 years) and 22 (71%) were male. Sixteen patients (52%) had stage III/IV, 25 (81%) B symptoms, and 16 (52%) performance status impairment. Twenty-three patients (74%) had symptoms >6 months, and 11 of 29 (38%) had received empiric antituberculosis treatment. Anemia was common with median hemoglobin 8.2 g/dL (range, 3.1-17.1 g/dL), which improved during treatment. No children and 5 of 15 adults (33%) were HIV+. All HIV+ patients were on antiretroviral therapy for a median 15 months (range, 2-137 months), with median CD4 count 138 cells/μL (range, 23-329 cells/μL) and four (80%) having undetectable HIV. EBV was present in 18 of 24 (75%) tumor specimens, including 14 of 20 (70%) HIV- and 4 of 4 (100%) HIV+. Baseline plasma EBV DNA was detected in 25 of 28 (89%) patients, with median viral load 4.7 (range, 2.0-6.7) log 10 copies/mL, and subsequently declined in most patients. At 12 months, overall survival was 75% (95% confidence interval [CI], 55%-88%) and progression-free survival 65% (95% CI, 42%-81%). Baseline plasma EBV DNA and persistent viremia during treatment were associated with poorer outcomes. cHL in Malawi is characterized by delayed diagnosis and advanced disease. Most cases were EBV associated and one-third of adults were HIV+. Despite resource limitations, 12-month outcomes were good. © 2016 Wiley Periodicals, Inc.

  4. Characteristics of participants in an HIV prevention intervention for youth in Rwanda: results from a longitudinal study

    Directory of Open Access Journals (Sweden)

    Hanne Celis

    2014-08-01

    Full Text Available Introduction. This paper studies determinants of participation in a peer-led school-based HIV prevention intervention in Rwanda. Methods. A baseline survey among 1071 students (mean age 17 years assessed potential determinants of participation, while a follow-up six months in the intervention measured actual participation in the intervention. Statistical models were built using multivariate linear and multinomial regression analysis predicting overall participation, par- ticipation in group discussions and individual counseling. Results. Those who recently had sex, had been tested for HIV, feel more susceptible to HIV, have a higher sexual self-concept, a more positive future perspective (only for non-sexually active, and boys, were more likely to participate in group activities. Also students from the same class as the peer educator and boarding school students were more likely to participate in group activities. Older students and those with low external health locus of control participated more in individual counseling. Discussion. Participation could be increased by investing in general well-being of young people, organizing girls-only activities, and diversifying activities. Key words: selection bias, HIV prevention, participation rate, young people, Rwanda

  5. The role of perceived social support in loneliness and self-esteem among children affected by HIV/AIDS: a longitudinal multilevel analysis in rural China.

    Science.gov (United States)

    Qiao, Shan; Li, Xiaoming; Zhao, Guoxiang; Zhao, Junfeng; Stanton, Bonita

    2014-07-01

    To delineate the trajectories of loneliness and self-esteem over time among children affected by parental HIV and AIDS, and to examine how their perceived social support (PSS) influenced initial scores and change rates of these two psychological outcomes. We collected longitudinal data from children affected by parental HIV/AIDS in rural central China. Children 6-18 years of age at baseline were eligible to participate in the study and were assessed annually for 3 years. Multilevel regression models for change were used to assess the effect of baseline PSS on the trajectories of loneliness and self-esteem over time. We employed maximum likelihood estimates to fit multilevel models and specified the between-individual covariance matrix as 'unstructured' to allow correlation among the different sources of variance. Statistics including -2 Log Likelihood, Akaike Information Criterion and Bayesian Information Criterion were used in evaluating the model fit. The results of multilevel analyses indicated that loneliness scores significantly declined over time. Controlling for demographic characteristics, children with higher PSS reported significantly lower baseline loneliness score and experienced a slower rate of decline in loneliness over time. Children with higher PSS were more likely to report higher self-esteem scores at baseline. However, the self-esteem scores remained stable over time controlling for baseline PSS and all the other variables. The positive effect of PSS on psychological adjustment may imply a promising approach for future intervention among children affected by HIV/AIDS, in which efforts to promote psychosocial well being could focus on children and families with lower social support. We also call for a greater understanding of children's psychological adjustment process in various contexts of social support and appropriate adaptations of evidence-based interventions to meet their diverse needs.

  6. The Importance of the Family: A Longitudinal Study of the Predictors of Depression in HIV Patients in South Africa.

    Science.gov (United States)

    Wouters, Edwin; Masquillier, Caroline; le Roux Booysen, Frederik

    2016-08-01

    As a chronic illness, HIV/AIDS requires life-long treatment adherence and retention-and thus sufficient attention to the psychosocial dimensions of chronic disease care in order to produce favourable antiretroviral treatment (ART) outcomes in a sustainable manner. Given the high prevalence of depression in chronic HIV patients, there is a clear need for further research into the determinants of depression in this population. In order to comprehensively study the predictors of depressive symptoms in HIV patients on ART, the socio-ecological theory postulates to not only incorporate the dominant individual-level and the more recent community-level approaches, but also incorporate the intermediate, but crucial family-level approach. The present study aims to extend the current literature by simultaneously investigating the impact of a wide range individual-level, family-level and community-level determinants of depression in a sample of 435 patients enrolled in the Free State Province of South Africa public-sector ART program. Structural equation modeling is used to explore the relationships between both latent and manifest variables at two time points. Besides a number of individual-level correlates-namely education, internalized and external stigma, and avoidant and seeking social support coping styles-of depressive symptoms in HIV patients on ART, the study also revealed the important role of family functioning in predicting depression. While family attachment emerged as the only factor to continuously and negatively impact depression at both time points, the second dimension of family functioning, changeability, was the only factor to produce a negative cross-lagged effect on depression. The immediate and long-term impact of family functioning on depression draws attention to the role of family dynamics in the mental health of people living with HIV/AIDS. In addition to individual-level and community-based factors, future research activities should also

  7. HIV/HTLV-1 co-infection

    African Journals Online (AJOL)

    result of a lymphoproliferative disorder. In the context of HIV co-infection, lympho- cytosis has been described during early sero- conversion associated with CMV, as well as in HIV/HTLV-1 co-infection where CD4+ lymphocytosis can be caused by both a reactive or clonal expansion. Consequently, patients with untreated ...

  8. Clonal growth and plant species abundance.

    Science.gov (United States)

    Herben, Tomáš; Nováková, Zuzana; Klimešová, Jitka

    2014-08-01

    Both regional and local plant abundances are driven by species' dispersal capacities and their abilities to exploit new habitats and persist there. These processes are affected by clonal growth, which is difficult to evaluate and compare across large numbers of species. This study assessed the influence of clonal reproduction on local and regional abundances of a large set of species and compared the predictive power of morphologically defined traits of clonal growth with data on actual clonal growth from a botanical garden. The role of clonal growth was compared with the effects of seed reproduction, habitat requirements and growth, proxied both by LHS (leaf-height-seed) traits and by actual performance in the botanical garden. Morphological parameters of clonal growth, actual clonal reproduction in the garden and LHS traits (leaf-specific area - height - seed mass) were used as predictors of species abundance, both regional (number of species records in the Czech Republic) and local (mean species cover in vegetation records) for 836 perennial herbaceous species. Species differences in habitat requirements were accounted for by classifying the dataset by habitat type and also by using Ellenberg indicator values as covariates. After habitat differences were accounted for, clonal growth parameters explained an important part of variation in species abundance, both at regional and at local levels. At both levels, both greater vegetative growth in cultivation and greater lateral expansion trait values were correlated with higher abundance. Seed reproduction had weaker effects, being positive at the regional level and negative at the local level. Morphologically defined traits are predictive of species abundance, and it is concluded that simultaneous investigation of several such traits can help develop hypotheses on specific processes (e.g. avoidance of self-competition, support of offspring) potentially underlying clonal growth effects on abundance. Garden

  9. Longitudinal associations between case management and supportive services use among black and Latina HIV-positive women in New York City.

    Science.gov (United States)

    Halkitis, Perry N; Kupprat, Sandra A; Mukherjee, Preetika Pandey

    2010-01-01

    The literature analyzing the relationship between case management and supportive service use longitudinally among African American and Latina HIV-positive women is limited. This retrospective analysis of participant case management, supportive service, and medical charts sought to examine both descriptive and relational data on use of case management and supportive services over a 2-year period from 2002 to 2005 and to analyze moderating person- level or institution-level factors. The analyzed case management, supportive service, and medical charts revealed that participants interacted with their case manager four times and received 3.6 supportive services per month. Transportation, primary healthcare/medical specialists, and support groups were the services most used, with rates ranging from 70% to 80%. Using hierarchical linear modeling (HLM), the unconditional growth models showed that case management and supportive service use patterns remained constant over the 24-month period. Additionally, the multivariate unconditional model suggests a significant positive relationship between case management and supportive services. No moderation was indicated in the association between case management and supportive service use by person-level (e.g., mental illness, substance use) and institution-level (i.e., service delivery model) factors. Participants use supportive and case management services in a similar manner based on individual need. This synergistic relationship suggests that increases in either may result in retaining women in care. Implications for service delivery point to the need for skills building training for case managers, outreach workers, or system navigators to assist with short-term goals of establishing rapport and maintaining the client relationship, as this may lead to HIV-positive women accessing services. Additionally, outreach and engagement strategies need to be developed for those who typically underuse these services.

  10. A Longitudinal Test of the Parent–Adolescent Family Functioning Discrepancy Hypothesis: A Trend toward Increased HIV Risk Behaviors among Immigrant Hispanic Adolescents

    Science.gov (United States)

    Cordova, David; Schwartz, Seth J.; Unger, Jennifer B.; Baezconde-Garbanati, Lourdes; Villamar, Juan A.; Soto, Daniel W.; Des Rosiers, Sabrina E.; Lee, Tae Kyoung; Meca, Alan; Cano, Miguel Ángel; Lorenzo-Blanco, Elma I.; Oshri, Assaf; Salas-Wright, Christopher P.; Piña-Watson, Brandy M.; Romero, Andrea J.

    2016-01-01

    Parent-adolescent discrepancies in family functioning play an important role in HIV risk behaviors among adolescents, yet longitudinal research with recent immigrant Hispanic families remains limited. This study tested the effects of trajectories of parent–adolescent family functioning discrepancies on HIV risk behaviors among recent-immigrant Hispanic adolescents. Additionally, we examined whether and to what extent trajectories of parent-adolescent family functioning discrepancies vary as a function of gender. We assessed family functioning of 302 Hispanic adolescents (47% female) and their parent (70% female) at six time points over a three-year period and computed latent discrepancy scores between parent and adolescent reports at each timepoint. Additionally, adolescents completed measures of sexual risk behaviors and alcohol use. We conducted a confirmatory factor analysis to determine the feasibility of collapsing parent and adolescent reported family functioning indicators onto a single latent discrepancy variable, tested model invariance over time, and conducted growth mixture modeling (GMM). GMM yielded a three-class solution for discrepancies: High-Increasing, High-Stable, and Low-Stable. Relative to the Low-Stable class, parent–adolescent dyads in the High-Increasing and High-Stable classes were at greater risk for adolescents reporting sexual debut at time 6. Additionally, the High-Stable class was at greater risk, relative to the Low-Stable class, in terms of adolescent lifetime alcohol use at 30 months post-baseline. Multiple group GMM indicated that trajectories of parent-adolescent family functioning trajectories did not vary by gender. Implications for future research and practice are discussed. PMID:27216199

  11. Orphanhood and Self-Esteem: An 18-Year Longitudinal Study From an HIV-Affected Area in Tanzania.

    Science.gov (United States)

    De Weerdt, Joachim; Beegle, Kathleen; Dercon, Stefan

    2017-11-01

    The HIV epidemic exacerbated the prevalence of prime-aged adult death in many parts of sub-Saharan Africa, resulting in increased rates of orphanhood. Little is known about whether this will coincide with adverse psychosocial well-being in adulthood for those who were orphaned at childhood. We studied a cohort of 1108 children from Kagera, a region of Tanzania that was heavily affected by HIV early in the epidemic. During the baseline data collection in 1991-1994, these children were aged 0-16 years and had both parents alive. We followed them roughly 16-19 years later in 2010, by which time 531 children (36%) had lost either one or both parents before their 19th birthday. We compared the 2010 10-item Rosenberg Self-Esteem Scale (RSES) score between children who lost a parent before the age of 19 and those who did not. We used the baseline data to control for preorphanhood confounders. This is important because we find that children who will lose their fathers in the future before age 19 came from somewhat lower socioeconomic backgrounds. We found no correlation between maternal death and self-esteem measured through RSES. Paternal death was strongly correlated with lower levels of self-esteem (0.2 SDs lower RSES 95% confidence interval: 0.059 to 0.348), and the correlation was stronger when the death occurred during the child's teenage years. These effects are a net of socioeconomic differences that existed before the orphanhood event. Our study supports the further development and piloting of programs that address psychosocial problems of orphans.

  12. Longitudinal Analysis of Adherence to First-Line Antiretroviral Therapy: Evidence of Treatment Sustainability from an Indian HIV Cohort.

    Science.gov (United States)

    Shet, Anita; Kumarasamy, N; Poongulali, Selvamuthu; Shastri, Suresh; Kumar, Dodderi Sunil; Rewari, Bharath B; Arumugam, Karthika; Antony, Jimmy; De Costa, Ayesha; D'Souza, George

    2016-01-01

    Given the chronic nature of HIV infection and the need for life-long antiretroviral therapy (ART), maintaining long-term optimal adherence is an important strategy for maximizing treatment success. In order to understand better the dynamic nature of adherence behaviors in India where complex cultural and logistic features prevail, we assessed the patterns, trajectories and time-dependent predictors of adherence levels in relation to virological failure among individuals initiating first-line ART in India. Between July 2010 and August 2013, eligible ART-naïve HIV-infected individuals newly initiating first-line ART within the national program at three sites in southern India were enrolled and monitored for two years. ART included zidovudine/stavudine/tenofovir plus lamivudine plus nevirapine/efavirenz. Patients were assessed using clinical, laboratory and adherence parameters. Every three months, medication adherence was measured using pill count, and a structured questionnaire on adherence barriers was administered. Optimal adherence was defined as mean adherence ≥95%. Statistical analysis was performed using a bivariate and a multivariate model of all identified covariates. Adherence trends and determinants were modeled as rate ratios using generalized estimating equation analysis in a Poisson distribution. A total of 599 eligible ART-naïve patients participated in the study, and contributed a total of 921 person-years of observation time. Women constituted 43% and mean CD4 count prior to initiating ART was 192 cells/mm3. Overall mean adherence among all patients was 95.4%. The proportion of patients optimally adherent was 75.6%. Predictors of optimal adherence included older age (≥40 years), high school-level education and beyond, lower drug toxicity-related ART interruption, full disclosure, sense of satisfaction with one's own health and patient's perception of having good access to health-care services. Adherence was inversely proportional to virological

  13. Impact of a longitudinal community HIV intervention targeting injecting drug users' stage of change for condom and bleach use.

    Science.gov (United States)

    Jamner, M S; Wolitski, R J; Corby, N H

    1997-01-01

    To evaluate the impact of the Long Beach AIDS Community Demonstration Project, a community-based HIV-prevention intervention incorporating principles from the Transtheoretical model in its design and evaluation. Repeated cross-sectional sampling with matched intervention and comparison communities. Neighborhoods in Long Beach, California, having a high prevalence of drug abuse and prostitution. 3081 injecting drug users who were sexually active and/or shared injection equipment. Trained peer volunteers distributed fliers featuring role model stories targeted to the population's stage of change. Fliers were packaged with bleaching kits and/or condoms. Primary outcome measures were exposure to the intervention, condom carrying, and stage of change for disinfecting injection equipment with bleach and for using condoms with main and other partners. Toward the end of the study, 77% of injection drug users in the intervention area reported being exposed to the intervention. In the intervention area, rates of condom carrying increased from 10 to 27% (p project exposure had higher stage-of-change scores for using condoms with a main partner (p Project intervention for reaching injecting drug users in the community and for motivating the adoption of risk-reducing practices.

  14. Differential evolution of a CXCR4-using HIV-1 strain in CCR5wt/wt and CCR5∆32/∆32 hosts revealed by longitudinal deep sequencing and phylogenetic reconstruction.

    Science.gov (United States)

    Le, Anh Q; Taylor, Jeremy; Dong, Winnie; McCloskey, Rosemary; Woods, Conan; Danroth, Ryan; Hayashi, Kanna; Milloy, M-J; Poon, Art F Y; Brumme, Zabrina L

    2015-12-03

    Rare individuals homozygous for a naturally-occurring 32 base pair deletion in the CCR5 gene (CCR5∆32/∆32) are resistant to infection by CCR5-using ("R5") HIV-1 strains but remain susceptible to less common CXCR4-using ("X4") strains. The evolutionary dynamics of X4 infections however, remain incompletely understood. We identified two individuals, one CCR5wt/wt and one CCR5∆32/∆32, within the Vancouver Injection Drug Users Study who were infected with a genetically similar X4 HIV-1 strain. While early-stage plasma viral loads were comparable in the two individuals (~4.5-5 log10 HIV-1 RNA copies/ml), CD4 counts in the CCR5wt/wt individual reached a nadir of 250 cells/mm(3) in the CCR5∆32/∆32 individual. Ancestral phylogenetic reconstructions using longitudinal envelope-V3 deep sequences suggested that both individuals were infected by a single transmitted/founder (T/F) X4 virus that differed at only one V3 site (codon 24). While substantial within-host HIV-1 V3 diversification was observed in plasma and PBMC in both individuals, the CCR5wt/wt individual's HIV-1 population gradually reverted from 100% X4 to ~60% R5 over ~4 years whereas the CCR5∆32/∆32 individual's remained consistently X4. Our observations illuminate early dynamics of X4 HIV-1 infections and underscore the influence of CCR5 genotype on HIV-1 V3 evolution.

  15. Rhizome elongation and seagrass clonal growth

    NARCIS (Netherlands)

    Marbà, N.; Duarte, C.M.

    1998-01-01

    A compilation of published and original data on rhizome morphometry, horizontal and vertical elongation rates and branching patterns for 27 seagrass species developing in 192 seagrass stands allowed an examination of the variability of seagrass rhizome and clonal growth programmes across and within

  16. Distribution of clonal growth forms in wetlands

    Czech Academy of Sciences Publication Activity Database

    Sosnová, Monika; van Diggelen, R.; Klimešová, Jitka

    2010-01-01

    Roč. 92, č. 1 (2010), s. 33-39 ISSN 0304-3770 R&D Projects: GA ČR GD206/08/H044 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal growth organ * the Netherlands * wetland plant community Subject RIV: EF - Botanics Impact factor: 2.087, year: 2010

  17. Quality improvement in Vignoles through clonal selection

    Science.gov (United States)

    Our goal is to select an improved, loose-clustered clone of Vignoles that will contribute to an integrated approach to disease control. Clonal selection has historically proven useful in reducing cluster compactness through a variety of mechanisms, including decreased berry size, lengthening of the ...

  18. Clonal growth and plant species abundance

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš; Nováková, Z.; Klimešová, Jitka

    2014-01-01

    Roč. 114, č. 2 (2014), s. 377-388 ISSN 0305-7364 R&D Projects: GA ČR GA526/09/0963 Institutional support: RVO:67985939 Keywords : clonal plants * frequency * plant communities of Central Europe Subject RIV: EF - Botanics Impact factor: 3.654, year: 2014

  19. Clonality analysis of lymphoid proliferations using the BIOMED-2 clonality assays: a single institution experience

    Science.gov (United States)

    Kokovic, Ira; Novakovic, Barbara Jezersek; Cerkovnik, Petra; Novakovic, Srdjan

    2014-01-01

    Background Clonality determination in patients with lymphoproliferative disorders can improve the final diagnosis. The aim of our study was to evaluate the applicative value of standardized BIOMED-2 gene clonality assay protocols for the analysis of clonality of lymphocytes in a group of different lymphoid proliferations. Materials and methods. With this purpose, 121 specimens from 91 patients with suspected lymphoproliferations submitted for routine diagnostics from January to December 2011 were retrospectively analyzed. According to the final diagnosis, our series comprised 32 cases of B-cell lymphomas, 38 cases of non-Hodgkin’s T-cell lymphomas and 51 cases of reactive lymphoid proliferations. Clonality testing was performed using the BIOMED-2 clonality assays. Results The determined sensitivity of the TCR assay was 91.9%, while the sensitivity of the IGH assay was 74.2%. The determined specificity of the IGH assay was 73.3% in the group of lymphomas and 87.2% in the group of reactive lesions. The determined specificity of the TCR assay was 62.5% in the group of lymphomas and 54.3% in the group of reactive lesions. Conclusions In the present study, we confirmed the utility of standardized BIOMED-2 clonality assays for the detection of clonality in a routine diagnostical setting of non-Hodgkin’s lymphomas. Reactions for the detection of the complete IGH rearrangements and reactions for the detection of the TCR rearrangements are a good choice for clonality testing of a wide range of lymphoid proliferations and specimen types while the reactions for the detection of incomplete IGH rearrangements have not shown any additional diagnostic value. PMID:24991205

  20. Frequency and determinants of consistent STI/HIV testing among men who have sex with men testing at STI outpatient clinics in the Netherlands: a longitudinal study.

    Science.gov (United States)

    Visser, Maartje; Heijne, Janneke C M; Hogewoning, Arjan A; van Aar, Fleur

    2017-09-01

    Men who have sex with men (MSM) are at highest risk for STIs and HIV infections in the Netherlands. However, official guidelines on STI testing among MSM are lacking. They are advised to test for STIs at least every six months, but their testing behaviour is not well known. This study aimed to get insight into the proportion and determinants of consistent 6-monthly STI testing among MSM testing at STI outpatient clinics in the Netherlands. This study included longitudinal surveillance data of STI consultations among MSM from all 26 STI outpatient clinics in the Netherlands between 1 June 2014 and 31 December 2015. Multinomial logistic regression analysis was used to identify determinants of consistent 6-monthly testing compared with single testing and inconsistent testing. Determinants of time between consultations among men with multiple consultations were analysed using a Cox Prentice-Williams-Peterson gap-time model. A total of 34 605 STI consultations of 18 634 MSM were included. 8966 (48.1%) men had more than one consultation, and 3516 (18.9%) men tested consistently 6-monthly. Indicators of high sexual risk behaviour, including having a history of STI, being HIV positive and having more than 10 sex partners, were positively associated with both being a consistent tester and returning to the STI clinic sooner. Men who were notified by a partner or who reported STI symptoms were also more likely to return to the STI clinic sooner, but were less likely to be consistent testers, identifying a group of event-driven testers. The proportion of consistent 6-monthly testers among MSM visiting Dutch STI outpatient clinics was low. Testing behaviour was associated with sexual risk behaviour, but exact motives to test consistently remain unclear. Evidence-based testing guidelines are needed to achieve optimal reductions in STI transmission in the future. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence

  1. Clonal hematopoiesis in acquired aplastic anemia.

    Science.gov (United States)

    Ogawa, Seishi

    2016-07-21

    Clonal hematopoiesis (CH) in aplastic anemia (AA) has been closely linked to the evolution of late clonal disorders, including paroxysmal nocturnal hemoglobinuria and myelodysplastic syndromes (MDS)/acute myeloid leukemia (AML), which are common complications after successful immunosuppressive therapy (IST). With the advent of high-throughput sequencing of recent years, the molecular aspect of CH in AA has been clarified by comprehensive detection of somatic mutations that drive clonal evolution. Genetic abnormalities are found in ∼50% of patients with AA and, except for PIGA mutations and copy-neutral loss-of-heterozygosity, or uniparental disomy (UPD) in 6p (6pUPD), are most frequently represented by mutations involving genes commonly mutated in myeloid malignancies, including DNMT3A, ASXL1, and BCOR/BCORL1 Mutations exhibit distinct chronological profiles and clinical impacts. BCOR/BCORL1 and PIGA mutations tend to disappear or show stable clone size and predict a better response to IST and a significantly better clinical outcome compared with mutations in DNMT3A, ASXL1, and other genes, which are likely to increase their clone size, are associated with a faster progression to MDS/AML, and predict an unfavorable survival. High frequency of 6pUPD and overrepresentation of PIGA and BCOR/BCORL1 mutations are unique to AA, suggesting the role of autoimmunity in clonal selection. By contrast, DNMT3A and ASXL1 mutations, also commonly seen in CH in the general population, indicate a close link to CH in the aged bone marrow, in terms of the mechanism for selection. Detection and close monitoring of somatic mutations/evolution may help with prediction and diagnosis of clonal evolution of MDS/AML and better management of patients with AA. © 2016 by The American Society of Hematology.

  2. Drug hypersensitivity in clonal mast cell disorders

    DEFF Research Database (Denmark)

    Bonadonna, P; Pagani, M; Aberer, W

    2015-01-01

    and severity of immediate hypersensitivity reactions. Mastocytosis in adults is associated with a history of anaphylaxis in 22-49%. Fatal anaphylaxis has been described particularly following hymenoptera stings, but also occasionally after the intake of drugs such as nonsteroidal anti-inflammatory drugs......, opioids and drugs in the perioperative setting. However, data on the frequency of drug hypersensitivity in mastocytosis and vice versa are scarce and evidence for an association appears to be limited. Nevertheless, clonal MC disorders should be ruled out in cases of severe anaphylaxis: basal serum...... tryptase determination, physical examination for cutaneous mastocytosis lesions, and clinical characteristics of anaphylactic reaction might be useful for differential diagnosis. In this position paper, the ENDA group performed a literature search on immediate drug hypersensitivity reactions in clonal MC...

  3. Big Bang Tumor Growth and Clonal Evolution.

    Science.gov (United States)

    Sun, Ruping; Hu, Zheng; Curtis, Christina

    2018-05-01

    The advent and application of next-generation sequencing (NGS) technologies to tumor genomes has reinvigorated efforts to understand clonal evolution. Although tumor progression has traditionally been viewed as a gradual stepwise process, recent studies suggest that evolutionary rates in tumors can be variable with periods of punctuated mutational bursts and relative stasis. For example, Big Bang dynamics have been reported, wherein after transformation, growth occurs in the absence of stringent selection, consistent with effectively neutral evolution. Although first noted in colorectal tumors, effective neutrality may be relatively common. Additionally, punctuated evolution resulting from mutational bursts and cataclysmic genomic alterations have been described. In this review, we contrast these findings with the conventional gradualist view of clonal evolution and describe potential clinical and therapeutic implications of different evolutionary modes and tempos. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

  4. Metabolic heterogeneity in clonal microbial populations.

    Science.gov (United States)

    Takhaveev, Vakil; Heinemann, Matthias

    2018-02-21

    In the past decades, numerous instances of phenotypic diversity were observed in clonal microbial populations, particularly, on the gene expression level. Much less is, however, known about phenotypic differences that occur on the level of metabolism. This is likely explained by the fact that experimental tools probing metabolism of single cells are still at an early stage of development. Here, we review recent exciting discoveries that point out different causes for metabolic heterogeneity within clonal microbial populations. These causes range from ecological factors and cell-inherent dynamics in constant environments to molecular noise in gene expression that propagates into metabolism. Furthermore, we provide an overview of current methods to quantify the levels of metabolites and biomass components in single cells. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

  5. Recent advances in understanding clonal haematopoiesis in aplastic anaemia.

    Science.gov (United States)

    Stanley, Natasha; Olson, Timothy S; Babushok, Daria V

    2017-05-01

    Acquired aplastic anaemia (AA) is an immune-mediated bone marrow failure disorder inextricably linked to clonal haematopoiesis. The majority of AA patients have somatic mutations and/or structural chromosomal abnormalities detected as early as at diagnosis. In contrast to other conditions linked to clonal haematopoiesis, the clonal signature of AA reflects its immune pathophysiology. The most common alterations are clonal expansions of cells lacking glycophosphotidylinositol-anchored proteins, loss of human leucocyte antigen alleles, and mutations in BCOR/BCORL1, ASXL1 and DNMT3A. Here, we present the current knowledge of clonal haematopoiesis in AA as it relates to aging, inherited bone marrow failure, and the grey-zone overlap of AA and myelodysplastic syndrome (MDS). We conclude by discussing the significance of clonal haematopoiesis both for improved diagnosis of AA, as well as for a more precise, personalized approach to prognostication of outcomes and therapy choices. © 2017 John Wiley & Sons Ltd.

  6. Traumatic stress and the mediating role of alcohol use on HIV-related sexual risk behavior: results from a longitudinal cohort of South African women who attend alcohol-serving venues.

    Science.gov (United States)

    Abler, Laurie; Sikkema, Kathleen J; Watt, Melissa H; Pitpitan, Eileen V; Kalichman, Seth C; Skinner, Donald; Pieterse, Desiree

    2015-03-01

    In South Africa, alcohol contributes to the HIV epidemic, in part, by influencing sexual behaviors. For some, high levels of alcohol consumption may be driven by previous traumatic experiences that result in traumatic stress. The purpose of this study was to quantify the longitudinal association between traumatic stress and unprotected sex among women who attend drinking venues and to assess whether this association was explained by mediation through alcohol use. Data were collected in 4 waves over a year from a prospective cohort of 560 women who regularly attended alcohol-serving venues in a Cape Town township. Longitudinal mixed models examined (1) the relationship between traumatic stress and counts of unprotected sex and (2) whether alcohol use mediated the association between traumatic stress and unprotected sex. Most women reported elevated traumatic stress (80%) and hazardous alcohol use (88%) at least once during the study period. In models adjusted for covariates, traumatic stress was associated with unprotected sex (b = 0.28, SE = 0.06, t = 4.82, P traumatic stress was associated with alcohol use (b = 0.27, SE = 0.02, t = 14.25, P traumatic stress on unprotected sex. These results highlight the need to address traumatic stress among female venue patrons as an important precursor of HIV risk due to alcohol use.

  7. The evolutionary ecology of clonally propagated domesticated plants.

    Science.gov (United States)

    McKey, Doyle; Elias, Marianne; Pujol, Benoît; Duputié, Anne

    2010-04-01

    While seed-propagated crops have contributed many evolutionary insights, evolutionary biologists have often neglected clonally propagated crops. We argue that widespread notions about their evolution under domestication are oversimplified, and that they offer rich material for evolutionary studies. The diversity of their wild ancestors, the diverse ecologies of the crop populations themselves, and the intricate mix of selection pressures, acting not only on the parts harvested but also on the parts used by humans to make clonal propagules, result in complex and diverse evolutionary trajectories under domestication. We examine why farmers propagate some plants clonally, and discuss the evolutionary dynamics of sexual reproduction in clonal crops. We explore how their mixed clonal/sexual reproductive systems function, based on the sole example studied in detail, cassava (Manihot esculenta). Biotechnology is now expanding the number of clonal crops, continuing the 10 000-yr-old trend to increase crop yields by propagating elite genotypes. In an era of rapid global change, it is more important than ever to understand how the adaptive potential of clonal crops can be maintained. A key component of strategies for preserving this adaptive potential is the maintenance of mixed clonal/sexual systems, which can be achieved by encouraging and valuing farmer knowledge about the sexual reproductive biology of their clonal crops.

  8. "I Do Not Take My Medicine while Hiding" - A Longitudinal Qualitative Assessment of HIV Discordant Couples' Beliefs in Discordance and ART as Prevention in Uganda.

    Directory of Open Access Journals (Sweden)

    Rachel King

    Full Text Available HIV negative members of serostatus discordant couples are at high risk for HIV acquisition, but few interventions are in place to target them in sub-Saharan Africa.In this study, we interviewed 28 couples, 3 times over a period of one year to understand their perceptions and attitudes around discordance, their relationship dynamics, their HIV risk behaviour, their beliefs and attitudes about antiretroviral therapy (ART and their views of the community perceptions of discordance and treatment for HIV.Findings revealed that at baseline there were multiple complex explanations and interpretations about discordance among discordant couples and their surrounding community. Shifts in beliefs and attitudes about discordance, HIV risk reduction and ART over time were enabled through re-testing negative members of discordant couples and repeat counselling but some beliefs remain solidly embedded in cultural imperatives of the importance of childbearing as well as culturally determined and enforced gender roles.Interventions that aim to target discordant couples must embrace the complex and dynamic understandings of HIV diagnosis and treatment in context of fluid relationships, and changing beliefs about HIV risk and treatment.

  9. Extensive clonal spread and extreme longevity in saw palmetto, a foundation clonal plant.

    Science.gov (United States)

    Takahashi, Mizuki K; Horner, Liana M; Kubota, Toshiro; Keller, Nathan A; Abrahamson, Warren G

    2011-09-01

    The lack of effective tools has hampered out ability to assess the size, growth and ages of clonal plants. With Serenoa repens (saw palmetto) as a model, we introduce a novel analytical framework that integrates DNA fingerprinting and mathematical modelling to simulate growth and estimate ages of clonal plants. We also demonstrate the application of such life-history information of clonal plants to provide insight into management plans. Serenoa is an ecologically important foundation species in many Southeastern United States ecosystems; yet, many land managers consider Serenoa a troublesome invasive plant. Accordingly, management plans have been developed to reduce or eliminate Serenoa with little understanding of its life history. Using Amplified Fragment Length Polymorphisms, we genotyped 263 Serenoa and 134 Sabal etonia (a sympatric non-clonal palmetto) samples collected from a 20 × 20 m study plot in Florida scrub. Sabal samples were used to assign small field-unidentifiable palmettos to Serenoa or Sabal and also as a negative control for clone detection. We then mathematically modelled clonal networks to estimate genet ages. Our results suggest that Serenoa predominantly propagate via vegetative sprouts and 10,000-year-old genets may be common, while showing no evidence of clone formation by Sabal. The results of this and our previous studies suggest that: (i) Serenoa has been part of scrub associations for thousands of years, (ii) Serenoa invasion are unlikely and (ii) once Serenoa is eliminated from local communities, its restoration will be difficult. Reevaluation of the current management tools and plans is an urgent task. © 2011 Blackwell Publishing Ltd.

  10. A longitudinal examination of factors associated with social support satisfaction among HIV-positive young Black men who have sex with men.

    Science.gov (United States)

    McCullagh, Charlotte; Quinn, Katherine; Voisin, Dexter R; Schneider, John

    2017-12-01

    This study examined the long-term predictors of social support satisfaction among HIV-positive young Black men who have sex with men (YBMSM). Data were collected across three waves between October 2012 and November 2014 as part of the baseline assessment from Project nGage, a preliminary efficacy randomized control study examining the role of social support in improving HIV care among YBMSM. The sample included 92 YBMSM aged 18-29. Major results controlling for age, education and intervention effects indicated that psychological health, social network size, and education at baseline predicted differences in social support satisfaction at Wave 3, with no significant effects based on length of HIV diagnosis. Therefore, interventions that are intended to promote the quality of life for YBMSM and their engagement and retention in HIV care must focus on their psychological health concerns and network size.

  11. Effect of clonal integration on nitrogen cycling in rhizosphere of rhizomatous clonal plant, Phyllostachys bissetii, under heterogeneous light.

    Science.gov (United States)

    Li, Yang; Chen, Jing-Song; Xue, Ge; Peng, Yuanying; Song, Hui-Xing

    2018-07-01

    Clonal integration plays an important role in clonal plant adapting to heterogeneous habitats. It was postulated that clonal integration could exhibit positive effects on nitrogen cycling in the rhizosphere of clonal plant subjected to heterogeneous light conditions. An in-situ experiment was conducted using clonal fragments of Phyllostachys bissetii with two successive ramets. Shading treatments were applied to offspring or mother ramets, respectively, whereas counterparts were treated to full sunlight. Rhizomes between two successive ramets were either severed or connected. Extracellular enzyme activities and nitrogen turnover were measured, as well as soil properties. Abundance of functional genes (archaeal or bacterial amoA, nifH) in the rhizosphere of shaded, offspring or mother ramets were determined using quantitative polymerase chain reaction. Carbon or nitrogen availabilities were significantly influenced by clonal integration in the rhizosphere of shaded ramets. Clonal integration significantly increased extracellular enzyme activities and abundance of functional genes in the rhizosphere of shaded ramets. When rhizomes were connected, higher nitrogen turnover (nitrogen mineralization or nitrification rates) was exhibited in the rhizosphere of shaded offspring ramets. However, nitrogen turnover was significantly decreased by clonal integration in the rhizosphere of shaded mother ramets. Path analysis indicated that nitrogen turnover in the rhizosphere of shaded, offspring or mother ramets were primarily driven by the response of soil microorganisms to dissolved organic carbon or nitrogen. This unique in-situ experiment provided insights into the mechanism of nutrient recycling mediated by clonal integration. It was suggested that effects of clonal integration on the rhizosphere microbial processes were dependent on direction of photosynthates transport in clonal plant subjected to heterogeneous light conditions. Copyright © 2018 Elsevier B.V. All rights

  12. On the ecological genetics of the clonal perennial Agrostis stolonifera

    NARCIS (Netherlands)

    Kik, Christoffel

    1987-01-01

    There have to date been few studies specifically addressed to the evolution of clonal organisms. The present study attempts to fill this gap and aims to analyse the distribution pattern of a clonal plant species, using the wide-spread grass Agrostis stolonifera L.(Creeping Bent) as a model species.

  13. Introduction to special issue on the ecology of clonal plants

    Czech Academy of Sciences Publication Activity Database

    Gross, K. L.; Herben, T.; Klimešová, Jitka

    2017-01-01

    Roč. 52, 3-4 (2017), s. 265-267 ISSN 1211-9520 Institutional support: RVO:67985939 Keywords : Introduction to special issue * clonal plants * clonal meeting Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 1.017, year: 2016

  14. Stomatal characteristics of Eucalyptus grandis clonal hybrids in ...

    African Journals Online (AJOL)

    This study describes the stomatal response occurring during water stress and subsequent recovery of three Eucalyptus grandis clonal hybrids. The aim was to investigate the degree to which stomatal conductance (gs) and stomatal density differ between the clonal hybrids across seasons and in response to water stress.

  15. Insights in Anaphylaxis and Clonal Mast Cell Disorders

    Directory of Open Access Journals (Sweden)

    David González-de-Olano

    2017-07-01

    Full Text Available The prevalence of anaphylaxis among patients with clonal mast cell disorders (MCD is clearly higher comparing to the general population. Due to a lower frequency of symptoms outside of acute episodes, clonal MCD in the absence of skin lesions might sometimes be difficult to identify which may lead to underdiagnosis, and anaphylaxis is commonly the presenting symptom in these patients. Although the release of mast cell (MC mediators upon MC activation might present with a wide variety of symptoms, particular clinical features typically characterize MC mediator release episodes in patients with clonal MCD without skin involvement. Final diagnosis requires a bone marrow study, and it is recommended that this should be done in reference centers. In this article, we address the main triggers for anaphylaxis, risk factors, clinical presentation, diagnosis, and management of patients with MC activation syndromes (MCASs, with special emphasis on clonal MCAS [systemic mastocytosis and mono(clonal MC activations syndromes].

  16. Divergent clonal selection dominates medulloblastoma at recurrence

    Science.gov (United States)

    Morrissy, A. Sorana; Garzia, Livia; Shih, David J. H.; Zuyderduyn, Scott; Huang, Xi; Skowron, Patryk; Remke, Marc; Cavalli, Florence M. G.; Ramaswamy, Vijay; Lindsay, Patricia E.; Jelveh, Salomeh; Donovan, Laura K.; Wang, Xin; Luu, Betty; Zayne, Kory; Li, Yisu; Mayoh, Chelsea; Thiessen, Nina; Mercier, Eloi; Mungall, Karen L.; Ma, Yusanne; Tse, Kane; Zeng, Thomas; Shumansky, Karey; Roth, Andrew J. L.; Shah, Sohrab; Farooq, Hamza; Kijima, Noriyuki; Holgado, Borja L.; Lee, John J. Y.; Matan-Lithwick, Stuart; Liu, Jessica; Mack, Stephen C.; Manno, Alex; Michealraj, K. A.; Nor, Carolina; Peacock, John; Qin, Lei; Reimand, Juri; Rolider, Adi; Thompson, Yuan Y.; Wu, Xiaochong; Pugh, Trevor; Ally, Adrian; Bilenky, Mikhail; Butterfield, Yaron S. N.; Carlsen, Rebecca; Cheng, Young; Chuah, Eric; Corbett, Richard D.; Dhalla, Noreen; He, An; Lee, Darlene; Li, Haiyan I.; Long, William; Mayo, Michael; Plettner, Patrick; Qian, Jenny Q.; Schein, Jacqueline E.; Tam, Angela; Wong, Tina; Birol, Inanc; Zhao, Yongjun; Faria, Claudia C.; Pimentel, José; Nunes, Sofia; Shalaby, Tarek; Grotzer, Michael; Pollack, Ian F.; Hamilton, Ronald L.; Li, Xiao-Nan; Bendel, Anne E.; Fults, Daniel W.; Walter, Andrew W.; Kumabe, Toshihiro; Tominaga, Teiji; Collins, V. Peter; Cho, Yoon-Jae; Hoffman, Caitlin; Lyden, David; Wisoff, Jeffrey H.; Garvin, James H.; Stearns, Duncan S.; Massimi, Luca; Schüller, Ulrich; Sterba, Jaroslav; Zitterbart, Karel; Puget, Stephanie; Ayrault, Olivier; Dunn, Sandra E.; Tirapelli, Daniela P. C.; Carlotti, Carlos G.; Wheeler, Helen; Hallahan, Andrew R.; Ingram, Wendy; MacDonald, Tobey J.; Olson, Jeffrey J.; Van Meir, Erwin G.; Lee, Ji-Yeoun; Wang, Kyu-Chang; Kim, Seung-Ki; Cho, Byung-Kyu; Pietsch, Torsten; Fleischhack, Gudrun; Tippelt, Stephan; Ra, Young Shin; Bailey, Simon; Lindsey, Janet C.; Clifford, Steven C.; Eberhart, Charles G.; Cooper, Michael K.; Packer, Roger J.; Massimino, Maura; Garre, Maria Luisa; Bartels, Ute; Tabori, Uri; Hawkins, Cynthia E.; Dirks, Peter; Bouffet, Eric; Rutka, James T.; Wechsler-Reya, Robert J.; Weiss, William A.; Collier, Lara S.; Dupuy, Adam J.; Korshunov, Andrey; Jones, David T. W.; Kool, Marcel; Northcott, Paul A.; Pfister, Stefan M.; Largaespada, David A.; Mungall, Andrew J.; Moore, Richard A.; Jabado, Nada; Bader, Gary D.; Jones, Steven J. M.; Malkin, David; Marra, Marco A.; Taylor, Michael D.

    2016-01-01

    The development of targeted anti-cancer therapies through the study of cancer genomes is intended to increase survival rates and decrease treatment-related toxicity. We treated a transposon–driven, functional genomic mouse model of medulloblastoma with ‘humanized’ in vivo therapy (microneurosurgical tumour resection followed by multi-fractionated, image-guided radiotherapy). Genetic events in recurrent murine medulloblastoma exhibit a very poor overlap with those in matched murine diagnostic samples (sequencing of 33 pairs of human diagnostic and post-therapy medulloblastomas demonstrated substantial genetic divergence of the dominant clone after therapy (recurrence). In both mice and humans, the dominant clone at recurrence arose through clonal selection of a pre-existing minor clone present at diagnosis. Targeted therapy is unlikely to be effective in the absence of the target, therefore our results offer a simple, proximal, and remediable explanation for the failure of prior clinical trials of targeted therapy. PMID:26760213

  17. HIV integration sites and implications for maintenance of the reservoir.

    Science.gov (United States)

    Symons, Jori; Cameron, Paul U; Lewin, Sharon R

    2018-03-01

    To provide an overview of recent research of how HIV integration relates to productive and latent infection and implications for cure strategies. How and where HIV integrates provides new insights into how HIV persists on antiretroviral therapy (ART). Clonal expansion of infected cells with the same integration site demonstrates that T-cell proliferation is an important factor in HIV persistence, however, the driver of proliferation remains unclear. Clones with identical integration sites harbouring defective provirus can accumulate in HIV-infected individuals on ART and defective proviruses can express RNA and produce protein. HIV integration sites differ in clonally expanded and nonexpanded cells and in latently and productively infected cells and this influences basal and inducible transcription. There is a growing number of cellular proteins that can alter the pattern of integration to favour latency. Understanding these pathways may identify new interventions to eliminate latently infected cells. Using advances in analysing HIV integration sites, T-cell proliferation of latently infected cells is thought to play a major role in HIV persistence. Clonal expansion has been demonstrated with both defective and intact viruses. Production of viral RNA and protein from defective viruses may play a role in driving chronic immune activation. The site of integration may determine the likelihood of proliferation and the degree of basal and induced transcription. Finally, host factors and gene expression at the time of infection may determine the integration site. Together these new insights may lead to novel approaches to elimination of latently infected cells.

  18. Impact of exposure to intimate partner violence on CD4+ and CD8+ T cell decay in HIV infected women: longitudinal study.

    Directory of Open Access Journals (Sweden)

    Rachel Jewkes

    Full Text Available Intimate partner violence (IPV is a risk factor for HIV acquisition in many settings, but little is known about its impact on cellular immunity especially in HIV infected women, and if any impact differs according to the form of IPV. We tested hypotheses that exposure to IPV, non-partner rape, hunger, pregnancy, depression and substance abuse predicted change in CD4+ and CD8+ T-cell count in a dataset of 103 HIV infected young women aged 15-26 enrolled in a cluster randomised controlled trial. Multiple regression models were fitted to measure rate of change in CD4 and CD8 and including terms for age, person years of CD4+/CD8+ T-cell observation, HIV positivity at baseline, and stratum. Exposure variables included drug use, emotional, physical or sexual IPV exposure, non-partner rape, pregnancy and food insecurity. Mean CD4+ T cell count at baseline (or first HIV+ test was 567.6 (range 1121-114. Participants were followed for an average of 1.3 years. The magnitude of change in CD4 T-cells was significantly associated with having ever experienced emotional abuse from a current partner at baseline or first HIV+ test (Coeff -132.9 95% CI -196.4, -69.4 p<0.0001 and drug use (Coeff -129.9 95% CI -238.7, -21.2 p=0.02. It was not associated with other measures. The change in CD8 T-cells was associated with having ever experienced emotional abuse at baseline or prior to the first HIV+ test (Coeff -178.4 95%CI -330.2, -26.5 p=0.02. In young ART-naive HIV positive women gender-based violence exposure in the form of emotional abuse is associated with a faster rate of decline in markers of cellular immunity. This highlights the importance of attending to emotional abuse when studying the physiological impact of IPV experience and the mechanisms of its impact on women's health.

  19. Effects of Clonal Reproduction on Evolutionary Lag and Evolutionary Rescue.

    Science.gov (United States)

    Orive, Maria E; Barfield, Michael; Fernandez, Carlos; Holt, Robert D

    2017-10-01

    Evolutionary lag-the difference between mean and optimal phenotype in the current environment-is of keen interest in light of rapid environmental change. Many ecologically important organisms have life histories that include stage structure and both sexual and clonal reproduction, yet how stage structure and clonality interplay to govern a population's rate of evolution and evolutionary lag is unknown. Effects of clonal reproduction on mean phenotype partition into two portions: one that is phenotype dependent, and another that is genotype dependent. This partitioning is governed by the association between the nonadditive genetic plus random environmental component of phenotype of clonal offspring and their parents. While clonality slows phenotypic evolution toward an optimum, it can dramatically increase population survival after a sudden step change in optimal phenotype. Increased adult survival slows phenotypic evolution but facilitates population survival after a step change; this positive effect can, however, be lost given survival-fecundity trade-offs. Simulations indicate that the benefits of increased clonality under environmental change greatly depend on the nature of that change: increasing population persistence under a step change while decreasing population persistence under a continuous linear change requiring de novo variation. The impact of clonality on the probability of persistence for species in a changing world is thus inexorably linked to the temporal texture of the change they experience.

  20. Effect of deworming on disease progression markers in HIV-1-infected pregnant women on antiretroviral therapy: a longitudinal observational study from Rwanda.

    Science.gov (United States)

    Ivan, Emil; Crowther, Nigel J; Mutimura, Eugene; Rucogoza, Aniceth; Janssen, Saskia; Njunwa, Kato K; Grobusch, Martin P

    2015-01-01

    Deworming human immunodeficiency virus (HIV)-infected individuals on antiretroviral therapy (ART) may be beneficial, particularly during pregnancy. We determined the efficacy of targeted and nontargeted antihelminth therapy and its effects on Plasmodium falciparum infection status, hemoglobin levels, CD4 counts, and viral load in pregnant, HIV-positive women receiving ART. Nine hundred eighty HIV-infected pregnant women receiving ART were examined at 2 visits during pregnancy and 2 postpartum visits within 12 weeks. Women were given antimalarials when malaria-positive whereas albendazole was given in a targeted (n = 467; treatment when helminth stool screening was positive) or nontargeted (n = 513; treatment at all time points, with stool screening) fashion. No significant differences were noted between targeted and nontargeted albendazole treatments for the variables measured at each study visit except for CD4 counts, which were lower (P pregnant HIV-infected women with helminth coinfections receiving ART. © The Author 2014. Published by Oxford University Press on behalf of the Infectious Diseases Society of America. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. NSAIDs modulate clonal evolution in Barrett's esophagus.

    Directory of Open Access Journals (Sweden)

    Rumen L Kostadinov

    2013-06-01

    Full Text Available Cancer is considered an outcome of decades-long clonal evolution fueled by acquisition of somatic genomic abnormalities (SGAs. Non-steroidal anti-inflammatory drugs (NSAIDs have been shown to reduce cancer risk, including risk of progression from Barrett's esophagus (BE to esophageal adenocarcinoma (EA. However, the cancer chemopreventive mechanisms of NSAIDs are not fully understood. We hypothesized that NSAIDs modulate clonal evolution by reducing SGA acquisition rate. We evaluated thirteen individuals with BE. Eleven had not used NSAIDs for 6.2±3.5 (mean±standard deviation years and then began using NSAIDs for 5.6±2.7 years, whereas two had used NSAIDs for 3.3±1.4 years and then discontinued use for 7.9±0.7 years. 161 BE biopsies, collected at 5-8 time points over 6.4-19 years, were analyzed using 1Million-SNP arrays to detect SGAs. Even in the earliest biopsies there were many SGAs (284±246 in 10/13 and 1442±560 in 3/13 individuals and in most individuals the number of SGAs changed little over time, with both increases and decreases in SGAs detected. The estimated SGA rate was 7.8 per genome per year (95% support interval [SI], 7.1-8.6 off-NSAIDs and 0.6 (95% SI 0.3-1.5 on-NSAIDs. Twelve individuals did not progress to EA. In ten we detected 279±86 SGAs affecting 53±30 Mb of the genome per biopsy per time point and in two we detected 1,463±375 SGAs affecting 180±100 Mb. In one individual who progressed to EA we detected a clone having 2,291±78 SGAs affecting 588±18 Mb of the genome at three time points in the last three of 11.4 years of follow-up. NSAIDs were associated with reduced rate of acquisition of SGAs in eleven of thirteen individuals. Barrett's cells maintained relative equilibrium level of SGAs over time with occasional punctuations by expansion of clones having massive amount of SGAs.

  2. Involvement of histone methyltransferase GLP in HIV-1 latency through catalysis of H3K9 dimethylation

    International Nuclear Information System (INIS)

    Ding, Donglin; Qu, Xiying; Li, Lin; Zhou, Xin; Liu, Sijie; Lin, Shiguan; Wang, Pengfei; Liu, Shaohui; Kong, Chuijin; Wang, Xiaohui; Liu, Lin; Zhu, Huanzhang

    2013-01-01

    Understanding the mechanism of HIV-1 latency is crucial to eradication of the viral reservoir in HIV-1-infected individuals. However, the role of histone methyltransferase (HMT) G9a-like protein (GLP) in HIV-1 latency is still unclear. In the present work, we established four clonal cell lines containing HIV-1 vector. We found that the integration sites of most clonal cell lines favored active gene regions. However, we also observed hypomethylation of CpG of HIV 5′LTR in all four clonal cell lines. Additionally, 5′-deoxy-5′-methylthioadenosine (MTA), a broad-spectrum histone methyltransferase inhibitor, was used to examine the role of histone methylation in HIV-1 latency. MTA was found to decrease the level of H3K9 dimethylation, causing reactivation of latent HIV-1 in C11 cells. GLP knockdown by small interfering RNA clearly induced HIV-1 LTR expression. Results suggest that GLP may play a significant role in the maintenance of HIV-1 latency by catalyzing dimethylation of H3K9. - Highlights: ► We have established an in vitro model of HIV-1 latency. ► The integration sites of most clonal cell lines favor in active gene regions. ► Hypomethylation occurs in CpG islands of HIV 5′LTR in all four clonal cell lines. ► MTA can reactivate latent HIV-1 by decreasing the level of H3K9 me2 in C11 cells. ► HMT GLP may play a significant role in the maintenance of HIV-1 latency

  3. PCR-based clonality assessment in patients with lymphocytic ...

    Indian Academy of Sciences (India)

    study was to assess the clinical benefits of clonality testing with previously evaluated .... with the samples, negative controls containing no DNA were ..... 2003 Standardization and quality con- ... In Molecular cloning, a laboratory manual (ed.

  4. Adjusting to global change through clonal growth and epigenetic variation

    Directory of Open Access Journals (Sweden)

    Richard S Dodd

    2016-07-01

    Full Text Available The earth is experiencing major changes in global and regional climates and changes are predicted to accelerate in the future. Many species will be under considerable pressure to evolve, to migrate, or be faced with extinction. Clonal plants would appear to be at a particular disadvantage due to their limited mobility and limited capacity for adaptation. However, they have outlived previous environmental shifts and clonal species have persisted for millenia. Clonal spread offers unique ecological advantages, such as resource sharing, risk sharing, and economies of scale among ramets within genotypes. We suggest that ecological attributes of clonal plants, in tandem with variation in gene regulation through epigenetic mechanisms that facilitate and optimize phenotype variation in response to environmental change may permit them to be well suited to projected conditions.

  5. Early ART Results in Greater Immune Reconstitution Benefits in HIV-Infected Infants: Working with Data Missingness in a Longitudinal Dataset.

    Directory of Open Access Journals (Sweden)

    Livio Azzoni

    Full Text Available Early initiation of anti-retroviral treatment (ART decreases mortality as compared to deferred treatment, but whether it preserves immune cells from early loss or promotes their recovery remains undefined. Determination of complex immunological endpoints in infants is often marred by missing data due to missed visits and/or inadequate sampling. Specialized methods are required to address missingness and facilitate data analysis.We characterized the changes in cellular and humoral immune parameters over the first year of life in 66 HIV-infected infants (0-1 year of age enrolled in the CHER study starting therapy within 12 weeks of birth (n = 42 or upon disease progression (n = 24. A convenience cohort of 23 uninfected infants aged 0-6 months born to mothers with HIV-1 infection was used as controls. Flow cytometry and ELISA were used to evaluate changes in natural killer (NK cells, plasmacytoid dendritic cells (pDC, and CD4+ or CD8+ T-cell frequencies. Data missingness was assessed using Little's test. Complete datasets for analysis were created using Multiple Imputation (MI or Bayesian modeling and multivariate analysis was conducted on the imputed datasets.HIV-1-infected infants had greater frequency of CD4+ T cells with naïve phenotype, as well as higher serum IL-7 levels than HIV exposed/uninfected infants. The elevated data missingness was completely at random, allowing the use of both MI and Bayesian modeling. Both methods indicate that early ART initiation results in higher CD4+ T cell frequency, lower expression of CD95 in CD8+ T cell, and preservation of naïve T cell subsets. In contrast, innate immune effectors appeared to be similar independently of the timing of ART initiation.Early ART initiation in infants with perinatal HIV infection reduces immune activation and preserves an early expansion of naïve T-cells with undiminished innate cell numbers, giving greater immune reconstitution than achieved with deferred ART. Both

  6. Predictors of change in CD4 lymphocyte count and weight among HIV infected patients on anti-retroviral treatment in Ethiopia: a retrospective longitudinal study.

    Directory of Open Access Journals (Sweden)

    Ayalu A Reda

    Full Text Available Antiretroviral treatment (ART has been introduced in Ethiopia a decade ago and continues to be scaled up. However, there is dearth of literature on the impact of ART on changes in CD4 lymphocyte count and weight among patients on treatment.To determine the predictors of change in CD4 lymphocyte count and weight among HIV/AIDS infected patients taking antiretroviral treatment in eastern Ethiopia.A retrospective cohort study was conducted among HIV/AIDS patients taking ART from 2005 to 2010. A sample of 1540 HIV infected adult patients who started antiretroviral therapy in hospitals located in eastern Ethiopia were included in the study. The primary outcomes of interest were changes in CD4 count and weight. Descriptive statistics and multivariable regression analyses were performed to examine the outcomes among the cohort.Both the median CD4 lymphocyte counts and weight showed improvements in the follow up periods. The multivariate analysis shows that the duration of ART was an important predictor of improvements in CD4 lymphocyte count (beta 7.91; 95% CI 7.48-8.34; p 0.000 and weight (beta 0.15; 95% CI 0.13-0.18; p 0.000. Advanced WHO clinical stage, lower baseline CD4 cell count, and baseline hemoglobin levels were factors associated with decline in weight. Actively working patients had higher CD4 lymphocyte count and weight compared to those that were ambulatory (p<0.05.We detected a substantial increment in weight and CD4 lymphocyte count among the patients who were taking ART in eastern Ethiopia. Patients who are of older age, with low initial CD4 lymphocyte count, late stage of the WHO clinical stages and lower hemoglobin level may need special attention. The reasons for the improved findings on CD4 count and weight throughout the five years of follow up merit further investigation.

  7. Impact of Alcohol and Coffee Intake on the Risk of Advanced Liver Fibrosis: A Longitudinal Analysis in HIV-HCV Coinfected Patients (ANRS HEPAVIH CO-13 Cohort

    Directory of Open Access Journals (Sweden)

    Issifou Yaya

    2018-05-01

    Full Text Available Background: Coffee intake has been shown to modulate both the effect of ethanol on serum GGT activities in some alcohol consumers and the risk of alcoholic cirrhosis in some patients with chronic diseases. This study aimed to analyze the impact of coffee intake and alcohol consumption on advanced liver fibrosis (ALF in HIV-HCV co-infected patients. Methods: ANRS CO13-HEPAVIH is a French, nationwide, multicenter cohort of HIV-HCV-co-infected patients. Sociodemographic, behavioral, and clinical data including alcohol and coffee consumption were prospectively collected using annual self-administered questionnaires during five years of follow-up. Mixed logistic regression models were performed, relating coffee intake and alcohol consumption to ALF. Results: 1019 patients were included. At the last available visit, 5.8% reported high-risk alcohol consumption, 27.4% reported high coffee intake and 14.5% had ALF. Compared with patients with low coffee intake and high-risk alcohol consumption, patients with low coffee intake and low-risk alcohol consumption had a lower risk of ALF (aOR (95% CI 0.24 (0.12–0.50. In addition, patients with high coffee intake had a lower risk of ALF than the reference group (0.14 (0.03–0.64 in high-risk alcohol drinkers and 0.11 (0.05–0.25 in low-risk alcohol drinkers. Conclusions: High coffee intake was associated with a low risk of liver fibrosis even in HIV-HCV co-infected patients with high-risk alcohol consumption.

  8. An Invasive Clonal Plant Benefits from Clonal Integration More than a Co-Occurring Native Plant in Nutrient-Patchy and Competitive Environments

    Science.gov (United States)

    You, Wenhua; Fan, Shufeng; Yu, Dan; Xie, Dong; Liu, Chunhua

    2014-01-01

    Many notorious invasive plants are clonal, however, little is known about the different roles of clonal integration effects between invasive and native plants. Here, we hypothesize that clonal integration affect growth, photosynthetic performance, biomass allocation and thus competitive ability of invasive and native clonal plants, and invasive clonal plants benefit from clonal integration more than co-occurring native plants in heterogeneous habitats. To test these hypotheses, two stoloniferous clonal plants, Alternanthera philoxeroides (invasive), Jussiaea repens (native) were studied in China. The apical parts of both species were grown either with or without neighboring vegetation and the basal parts without competitors were in nutrient- rich or -poor habitats, with stolon connections were either severed or kept intact. Competition significantly reduced growth and photosynthetic performance of the apical ramets in both species, but not the biomass of neighboring vegetation. Without competition, clonal integration greatly improved the growth and photosynthetic performance of both species, especially when the basal parts were in nutrient-rich habitats. When grown with neighboring vegetation, growth of J. repens and photosynthetic performance of both species were significantly enhanced by clonal integration with the basal parts in both nutrient-rich and -poor habitats, while growth and relative neighbor effect (RNE) of A. philoxeroides were greatly improved by clonal integration only when the basal parts were in nutrient-rich habitats. Moreover, clonal integration increased A. philoxeroides's biomass allocation to roots without competition, but decreased it with competition, especially when the basal ramets were in nutrient-rich sections. Effects of clonal integration on biomass allocation of J. repens was similar to that of A. philoxeroides but with less significance. These results supported our hypothesis that invasive clonal plants A. philoxeroides benefits

  9. Propagule pressure, habitat conditions and clonal integration influence the establishment and growth of an invasive clonal plant, Alternanthera philoxeroides

    Directory of Open Access Journals (Sweden)

    Wen-Hua eYou

    2016-05-01

    Full Text Available Many notorious invasive plants are clonal, spreading mainly by vegetative propagules. Propagule pressure (the number of propagules may affect the establishment, growth and thus invasion success of these clonal plants, and such effects may also depend on habitat conditions. To understand how propagule pressure, habitat conditions and clonal integration affect the establishment and growth of the invasive clonal plants, an 8-week greenhouse with an invasive clonal plant, Alternanthera philoxeroides was conducted. High (five fragments or low (one fragment propagule pressure was established either in bare soil (open habitat or dense native vegetation of Jussiaea repens (vegetative habitat, with the stolon connections either severed from or connected to the relatively older ramets. High propagule pressure greatly increased the establishment and growth of A. philoxeroides, especially when it grew in vegetative habitats. Surprisingly, high propagule pressure significantly reduced the growth of individual plants of A. philoxeroides in open habitats, whereas it did not affect the individual growth in vegetative habitats. A shift in the intraspecific interaction on A. philoxeroides from competition in open habitats to facilitation in vegetative habitats may be the main reason. Moreover, clonal integration significantly improved the growth of A. philoxeroides only in open habitats, especially with low propagule pressure, whereas it had no effects on the growth and competitive ability of A. philoxeroides in vegetative habitats, suggesting that clonal integration may be of most important for A. philoxeroides to explore new open space and spread. These findings suggest that propagule pressure may be crucial for the invasion success of A. philoxeroides, and such an effect also depends on habitat conditions.

  10. Use of X-Chromosome Inactivation Pattern to Analyze the Clonality of 14 Female Cases of Kaposi Sarcoma.

    Science.gov (United States)

    Yuan, Ding; XiuJuan, Wu; Yan, Zhang; JunQin, Liang; Fang, Xiang; Shirong, Yu; Xiaojing, Kang; Yanyan, Feng; Weidong, Wu; Dong, Luo; Qingli, Lu; DeZhi, Zhang; XiongMing, Pu

    2015-06-16

    Kaposi sarcoma (KS) has features of both neoplastic growth and hyperplastic proliferation. It is the most common tumor seen in patients with HIV infection. Whether KS is a real tumor or a benign hyperplastic disease is not known. Tissues from KS and cutaneous hemangioma lesion DNA were extracted, and then digested with methylation-sensitive restriction endonuclease HpaII. Human androgen receptor gene (HUMARA) was amplified with PCR method and the product was separated on 10% denaturing polyacrylamide gels and stained with ethylene dibromide (EB) to show the polymorphism of HUMARA. Phosphoglycerate kinase (PGK) was amplified and the product was digested by BStXI, agarose gel and EB stained to show the polymorphism of PGK. Finally, we analyzed the clonality of KS. In the 14 patients with KS, heterozygosity of the HUMARA gene was observed in 12 (85.7%) cases. Loss of heterozygosity of HUMARA gene on X-chromosome (without HpaII digestion there were 2 bands, after HpaII digestion there were just 1 of the bands), representing monoclonal origin, was present in 11 cases of Kaposi sarcoma. Heterozygosity of the PGK gene was observed in 5 (35.7%) cases, which all represent monoclonal origin. There was no significant difference according to country, stage, or HIV and HHV-8 (P>0.05). The current findings suggest that Kaposi sarcoma is a clonal neoplasm, not a reactive proliferation.

  11. Performance of HIV Prevention of Mother-To-Child Transmission Programs in Sub-Saharan Africa: Longitudinal Assessment of 64 Nevirapine-Based Programs Implemented in 25 Countries, 2000-2011.

    Directory of Open Access Journals (Sweden)

    Joël Ladner

    Full Text Available To evaluate the performance and to identify predictive factors of performance in prevention of mother-to-child HIV transmission programs (PMTCT in sub-Saharan African countries.From 2000 to 2011, PMTCT programs included in the Viramune Donation Programme (VDP were prospectively followed. Each institution included in the VDP provided data on program implementation, type of management institution, number of PMTCT sites, key programs outputs (HIV counseling and testing, NVP regimens received by mothers and newborns. Nevirapine Coverage Ratio (NCR, defined as the number of women who should have received nevirapine (observed HIV prevalence x number of women in antenatal care, was used to measure performance. Included programs were followed every six months through progress reports.A total of 64 programs in 25 sub-Saharan African countries were included. The mean program follow-up was 48.0 months (SD = 24.5; 20,084,490 women attended in antenatal clinics were included. The overall mean NCR was 0.52 (SD = 0.25, with an increase from 0.37 to 0.57 between the first and last progress reports (p<.0001; NCR increased by 3.26% per year-program. Between the first and the last report, the number of women counseled and tested increased from 64.3% to 86.0% (p<.0001, the number of women post-counseled from 87.5% to 91.3% (p = 0.08. After mixed linear regression analysis, type of responsible institution, number of women attended in ANC, and program initiation in 2005-2006 were significant predictive factors associated with the NCR. The effect of the time period increased from earlier to later periods.A longitudinal assessment of large PMTCT programs shows that scaling-up of programs was increased in sub-Saharan African countries. The PMTCT coverage increased throughout the study period, especially after 2006. Performance may be better for programs with a small or medium number of women attended in ANC. Identification of factors that predict PMTCT program

  12. Clonal selection versus clonal cooperation: the integrated perception of immune objects [version 1; referees: 2 approved

    Directory of Open Access Journals (Sweden)

    Serge Nataf

    2016-09-01

    Full Text Available Analogies between the immune and nervous systems were first envisioned by the immunologist Niels Jerne who introduced the concepts of antigen "recognition" and immune "memory". However, since then, it appears that only the cognitive immunology paradigm proposed by Irun Cohen, attempted to further theorize the immune system functions through the prism of neurosciences. The present paper is aimed at revisiting this analogy-based reasoning. In particular, a parallel is drawn between the brain pathways of visual perception and the processes allowing the global perception of an "immune object". Thus, in the visual system, distinct features of a visual object (shape, color, motion are perceived separately by distinct neuronal populations during a primary perception task. The output signals generated during this first step instruct then an integrated perception task performed by other neuronal networks. Such a higher order perception step is by essence a cooperative task that is mandatory for the global perception of visual objects. Based on a re-interpretation of recent experimental data, it is suggested that similar general principles drive the integrated perception of immune objects in secondary lymphoid organs (SLOs. In this scheme, the four main categories of signals characterizing an immune object (antigenic, contextual, temporal and localization signals are first perceived separately by distinct networks of immunocompetent cells.  Then, in a multitude of SLO niches, the output signals generated during this primary perception step are integrated by TH-cells at the single cell level. This process eventually generates a multitude of T-cell and B-cell clones that perform, at the scale of SLOs, an integrated perception of immune objects. Overall, this new framework proposes that integrated immune perception and, consequently, integrated immune responses, rely essentially on clonal cooperation rather than clonal selection.

  13. Processing-Dependent and Clonal Contamination Patterns of Listeria monocytogenes in the Cured Ham Food Chain Revealed by Genetic Analysis.

    Science.gov (United States)

    Morganti, Marina; Scaltriti, Erika; Cozzolino, Paolo; Bolzoni, Luca; Casadei, Gabriele; Pierantoni, Marco; Foni, Emanuela; Pongolini, Stefano

    2016-02-01

    The quantitative and qualitative patterns of environmental contamination by Listeria monocytogenes were investigated in the production chain of dry-cured Parma ham. Standard arrays of surfaces were sampled in processing facilities during a single visit per plant in the three compartments of the food chain, i.e., ham production (19 plants) and postproduction, which was divided into deboning (43 plants) and slicing (25 plants) steps. The numbers of sampled surfaces were 384 in ham production, with 25 positive for L. monocytogenes, and 1,084 in postproduction, with 83 positives. Statistical analysis of the prevalence of contaminated surfaces showed that in ham production, contamination was higher at the beginning of processing and declined significantly toward the end, while in postproduction, prevalence rose toward the end of processing. Prevalence was higher in the deboning facilities than in slicing facilities and was dependent on the type of surface (floor/drainage > clothing > equipment). The qualitative pattern of contamination was investigated through an analysis of the survey isolates and a set of isolates derived from routine monitoring, including longitudinal isolations. Pulsed-field gel electrophoresis (PFGE) and whole-genome single-nucleotide polymorphism (SNP) analysis revealed a remarkable clonality of L. monocytogenes within plants, with the detection of 16 plant-specific clones out of 17 establishments with multiple isolates. Repeated detections of clonal isolates >6 months apart were also observed. Six was the maximum number of between-isolate differences in core SNPs observed within these clones. Based on the same six-SNP threshold, three clusters of clonal isolates, shared by six establishments, were also identified. The spread of L. monocytogenes within and between plants, as indicated by its clonal behavior, is a matter of concern for the hygienic management of establishments. Copyright © 2016, American Society for Microbiology. All Rights

  14. Clonal analysis of stem cells in differentiation and disease.

    Science.gov (United States)

    Colom, Bartomeu; Jones, Philip H

    2016-12-01

    Tracking the fate of individual cells and their progeny by clonal analysis has redefined the concept of stem cells and their role in health and disease. The maintenance of cell turnover in adult tissues is achieved by the collective action of populations of stem cells with an equal likelihood of self-renewal or differentiation. Following injury stem cells exhibit striking plasticity, switching from homeostatic behavior in order to repair damaged tissues. The effects of disease states on stem cells are also being uncovered, with new insights into how somatic mutations trigger clonal expansion in early neoplasia. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  15. Clonal Evolution of Glioblastoma under Therapy

    Science.gov (United States)

    Wang, Jiguang; Cazzato, Emanuela; Ladewig, Erik; Frattini, Veronique; Rosenbloom, Daniel I. S.; Zairis, Sakellarios; Abate, Francesco; Liu, Zhaoqi; Elliott, Oliver; Shin, Yong-Jae; Lee, Jin-Ku; Lee, In-Hee; Park, Woong-Yang; Eoli, Marica; Blumberg, Andrew J.; Lasorella, Anna; Nam, Do-Hyun; Finocchiaro, Gaetano; Iavarone, Antonio; Rabadan, Raul

    2017-01-01

    Glioblastoma (GBM) constitutes the most common and aggressive primary brain tumor. To better understand how GBM evolves we analyzed longitudinal genomic and transcriptomic data of 114 patients. The analysis reveals a highly branched evolutionary pattern in which 63% of patients experience expression-based subtype changes. The branching pattern together with estimates of evolutionary rates suggest that the relapse associated clone typically preexisted years before diagnosis. 15% of tumors present hypermutations at relapse in highly expressed genes with a clear mutational signature. We find that 11% of recurrent tumors harbor mutations in LTBP4, a protein binding to TGF-β. Silencing LTBP4 in GBM cells leads to TGF-β activity suppression and decreased proliferation. In IDH1-wild-type recurrent GBM, high LTBP4 expression is associated with worse prognosis, highlighting the TGF-β pathway as a potential therapeutic target in GBM. PMID:27270107

  16. Effect of environmental stress on clonal structure of Eucypris virens (Crustacea, Ostracoda)

    OpenAIRE

    Martins M. J. F.; Vandekerkhove J.; Adolfsson S.; Rossetti G.; Namiotko T.; Jokela J.

    2010-01-01

    Environmental stress imposes strong natural selection on clonal populations, promoting evolutionary change in clonal structure. Environmental stress may also lead to reduction in population size, which together with clonal selection may reduce genotypic diversity of the local populations. We examined how clonal structure in wild-collected samples of two parthenogenetic populations of the freshwater ostracod Eucypris virens responded to hypersalinity and starvation, and the combination of the ...

  17. Aging in a long-lived clonal tree.

    Directory of Open Access Journals (Sweden)

    Dilara Ally

    2010-08-01

    Full Text Available From bacteria to multicellular animals, most organisms exhibit declines in survivorship or reproductive performance with increasing age ("senescence". Evidence for senescence in clonal plants, however, is scant. During asexual growth, we expect that somatic mutations, which negatively impact sexual fitness, should accumulate and contribute to senescence, especially among long-lived clonal plants. We tested whether older clones of Populus tremuloides (trembling aspen from natural stands in British Columbia exhibited significantly reduced reproductive performance. Coupling molecular-based estimates of clone age with male fertility data, we observed a significant decline in the average number of viable pollen grains per catkin per ramet with increasing clone age in trembling aspen. We found that mutations reduced relative male fertility in clonal aspen populations by about 5.8 x 10(-5 to 1.6 x 10(-3 per year, leading to an 8% reduction in the number of viable pollen grains, on average, among the clones studied. The probability that an aspen lineage ultimately goes extinct rises as its male sexual fitness declines, suggesting that even long-lived clonal organisms are vulnerable to senescence.

  18. THE EXTENT OF CLONAL STRUCTURE IN DIFFERENT LYMPHOID ORGANS

    NARCIS (Netherlands)

    HERMANS, MHA; WUBBENA, A; KROESE, FGM; HUNT, SV; COWAN, R; OPSTELTEN, D

    1992-01-01

    To gain insight into the clonal organization of lymphoid organs, we studied the distribution in situ of donor-derived cells in near-physiological chimeras. We introduced RT7b fetal liver cells into nonirradiated congenic RT7a neonatal rats. The chimerism 6-20 wk after injection ranged from 0.3 to

  19. Productivity gains by fertilisation in Eucalyptus urophylla clonal ...

    African Journals Online (AJOL)

    Productivity gains by fertilisation in Eucalyptus urophylla clonal plantations across gradients in site and stand conditions. ... The control plot may typically be a permanent plot of an inventory network, providing representative information for a company's decisionmaking. The paired twin-plot receives intensive management ...

  20. Negative plant soil feedback explaining ring formation in clonal plants

    NARCIS (Netherlands)

    Carteni, F.; Marasco, A.; Bonanomi, G.; Mazzoleni, S.; Rietkerk, M.G.; Giannino, F.

    2012-01-01

    Ring shaped patches of clonal plants have been reported in different environments, but the mechanisms underlying such pattern formation are still poorly explained. Water depletion in the inner tussocks zone has been proposed as a possible cause, although ring patterns have been also observed in

  1. Clonal differences in log end splitting in Eucalyptus grandis in ...

    African Journals Online (AJOL)

    This paper discusses the juvenile–mature correlation of log end splitting among Eucalyptus grandis clones from two trials and how differences in splitting relate to differences in wood density, pith-to-bark gradient and growth rate. Two approximately 20-year-old Eucalyptus grandis clonal trials at Bergvliet plantation were ...

  2. Molecular marker analysis to differentiate a clonal selection of ...

    African Journals Online (AJOL)

    Lalit Kumar

    2013-04-03

    Apr 3, 2013 ... Microsatellite and amplified fragment length polymorphism (AFLP) markers were used to differentiate. Manjari Naveen, a clonal selection of Centennial Seedless variety of grape. Twenty one (21) microsatellite primers could not detect variation between parent variety and its clone. AFLP analysis.

  3. Assessment of various strategies for the preservation of clonal ...

    African Journals Online (AJOL)

    Clonal conformity of ramets resulting from the re-cloning of somaplants depended, on one hand, on the floral status of the mother plant at the time of sampling and, on the other hand, on its origin. Re-cloning of abnormal regenerants led, in all cases, to 100 % abnormal offspring. The age of the ramet used as mother palm at ...

  4. EuroClonality/BIOMED-2 guidelines for interpretation and reporting of Ig/TCR clonality testing in suspected lymphoproliferations

    NARCIS (Netherlands)

    Langerak, A. W.; Groenen, P. J. T. A.; Brüggemann, M.; Beldjord, K.; Bellan, C.; Bonello, L.; Boone, E.; Carter, G. I.; Catherwood, M.; Davi, F.; Delfau-Larue, M.-H.; Diss, T.; Evans, P. A. S.; Gameiro, P.; Garcia Sanz, R.; Gonzalez, D.; Grand, D.; Håkansson, A.; Hummel, M.; Liu, H.; Lombardia, L.; Macintyre, E. A.; Milner, B. J.; Montes-Moreno, S.; Schuuring, E.; Spaargaren, M.; Hodges, E.; van Dongen, J. J. M.

    2012-01-01

    PCR-based immunoglobulin (Ig)/T-cell receptor (TCR) clonality testing in suspected lymphoproliferations has largely been standardized and has consequently become technically feasible in a routine diagnostic setting. Standardization of the pre-analytical and post-analytical phases is now essential to

  5. Functional specialization of ramets in a clonal plant network functional specialization of ramets in a clonal plant network

    NARCIS (Netherlands)

    Ikegami, M.

    2004-01-01

    Functional specialization of ramets and co-operation between interconnected ramets in heterogeneous environments are studied in this thesis. Since clonal plants can spread horizontally by vegetative growth, a genet has the potential to grow across a heterogeneous environment. Therefore, ramets can

  6. HIV Testing

    Science.gov (United States)

    ... Abroad Treatment Basic Statistics Get Tested Find an HIV testing site near you. Enter ZIP code or city Follow HIV/AIDS CDC HIV CDC HIV/AIDS See RSS | ... All Collapse All Should I get tested for HIV? CDC recommends that everyone between the ages of ...

  7. Comparative drug susceptibility study of five clonal strains of Trichomonas vaginalis in vitro

    Institute of Scientific and Technical Information of China (English)

    Hemantkumar Somabhai Chaudhari; Prati Pal Singh

    2011-01-01

    Objective: To produce comparative data on a group of Trichomonas vaginalis clonal strains with varied drug responses using identical methods and materials. Methods: Five clonal strains of Trichomonas vaginalis were isolated from reference strain using agar plate technique. The variability of growth kinetic and susceptibility of clonal strain to metronidazole, tinidazole, satranidazole and nitazoxanide were observed in 96 well microtitre plate. Results: Among these clonal strains there was a good correlation between rates of growth with the relative susceptibility of the strains to drugs in vitro. Regarding metronidazole, tinidazole and satranidazole susceptibility, different degrees of susceptibility were determined. However, no difference in nitazoxanide susceptibility was found between the clonal strain tested and a reference strain.Conclusions: This is the first description of biological variability in clonal stock of Trichomonas vaginalis. Different degrees of drug susceptibility were determined among clonal strains tested. Further studies will be necessary to ascertain the importance of this variability in clinical infection.

  8. Clonal forestry, heterosis and advanced-generation breeding

    Energy Technology Data Exchange (ETDEWEB)

    Tuskan, G.A.

    1997-08-01

    This report discusses the clonal planting stock offers many advantages to the forest products industry. Advanced-generation breeding strategies should be designed to maximize within-family variance and at the same time allow the capture of heterosis. Certainly there may be a conflict in the choice of breeding strategy based on the trait of interest. It may be that the majority of the traits express heterosis due to overdominance. Alternatively, disease resistance is expressed as the lack of a specific metabolite or infection court then the homozygous recessive genotype may be the most desirable. Nonetheless, as the forest products industry begins to utilize the economic advantages of clonal forestry, breeding strategies will have to be optimized for these commercial plant materials. Here, molecular markers can be used to characterize the nature of heterosis and therefore define the appropriate breeding strategy.

  9. Clonal multiplication of guava through softwood cuttings under mist conditions

    International Nuclear Information System (INIS)

    Kareem, A.; Jaskkani, M.J.; Fatima, B.; Sadia, B.

    2012-01-01

    Guava (psidium guajava l.) is a luscious and important tropical fruit crop. the objective of the study was to develop vegetative propagation system to avoid clonal degradation in guava fruit plants. softwood cuttings from five year old gola accession were prepared from the shoot tops of current season growth, measuring 12 cm in length and carrying 2 to 4 nodes. iba and naa (0, 2000, 4000, 6000, 8000 ppm) were selected to treat cuttings for root induction. cuttings were planted under mist conditions by maintaining temperature at 25 degree c and 85% relative humidity for 25 days. maximum survival percentage (92.17%) of plants at transplanting was noted with 4000 ppm concentration followed by 2000 ppm (85.50%). In general iba 4000 ppm concentration performed better as compared to naa for all parameters studied. This study revealed the potential of clonal propagation of guava through softwood cuttings treated with auxins. (author)

  10. Dynamics of Tumor Heterogeneity Derived from Clonal Karyotypic Evolution

    Directory of Open Access Journals (Sweden)

    Ashley M. Laughney

    2015-08-01

    Full Text Available Numerical chromosomal instability is a ubiquitous feature of human neoplasms. Due to experimental limitations, fundamental characteristics of karyotypic changes in cancer are poorly understood. Using an experimentally inspired stochastic model, based on the potency and chromosomal distribution of oncogenes and tumor suppressor genes, we show that cancer cells have evolved to exist within a narrow range of chromosome missegregation rates that optimizes phenotypic heterogeneity and clonal survival. Departure from this range reduces clonal fitness and limits subclonal diversity. Mapping of the aneuploid fitness landscape reveals a highly favorable, commonly observed, near-triploid state onto which evolving diploid- and tetraploid-derived populations spontaneously converge, albeit at a much lower fitness cost for the latter. Finally, by analyzing 1,368 chromosomal translocation events in five human cancers, we find that karyotypic evolution also shapes chromosomal translocation patterns by selecting for more oncogenic derivative chromosomes. Thus, chromosomal instability can generate the heterogeneity required for Darwinian tumor evolution.

  11. Clonal and bud bank traits: patterns across temperate plant communities

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Herben, Tomáš

    2015-01-01

    Roč. 26, č. 2 (2015), s. 243-253 ISSN 1100-9233 R&D Projects: GA ČR GB14-36079G; GA ČR GA13-17118S; GA ČR GAP505/12/1007 Institutional support: RVO:67985939 Keywords : clonal and bud bank traits * vegetation * central Europe Subject RIV: EH - Ecology, Behaviour Impact factor: 3.151, year: 2015

  12. Nutrient leaching under zero tension in a subtropical clonal eucalypt ...

    African Journals Online (AJOL)

    Little is known about the effects of residue burning or retention on nutrient leaching during the inter-rotation of clonal Eucalyptus grown on the sandy soils of subtropical Zululand, South Africa. A study compared zero-tension nutrient leaching through the top metre of soil at depths of 0.15, 0.5 and 1.0 m in an undisturbed crop ...

  13. Clonal status and clinicopathological observation of cervical minimal deviation adenocarcinoma

    Directory of Open Access Journals (Sweden)

    Lan Miao

    2010-04-01

    Full Text Available Abstract Background Minimal deviation adenocarcinoma (MDA of the uterine cervix is defined as an extremely well differentiated variant of cervical adenocarcinoma, with well-formed glands that resemble benign glands but show distinct nuclear anaplasia or evidence of stromal invasion. Thus, MDA is difficult to differentiate from other cervical hyperplastic lesions. Monoclonality is a major characteristic of most tumors, whereas normal tissue and reactive hyperplasia are polyclonal. Methods The clinicopathological features and clonality of MDA were investigated using laser microdissection and a clonality assay based on the polymorphism of androgen receptor (AR and X-chromosomal inactivation mosaicism in female somatic tissues. Results The results demonstrated that the glands were positive for CEA, Ki-67, and p53 and negative for estrogen receptor (ER, progesterone receptor (PR, and high-risk human papilloma virus (HPV DNA. The index of proliferation for Ki-67 was more than 50%. However, the stromal cells were positive for ER, PR, vimentin, and SM-actin. The clonal assay showed that MDA was monoclonal. Thus, our findings indicate that MDA is a true neoplasm but is not associated with high-risk HPV. Conclusions Diagnosis of MDA depends mainly on its clinical manifestations, the pathological feature that MDA glands are located deeper than the lower level of normal endocervical glands, and immunostaining.

  14. Multiplexing clonality: combining RGB marking and genetic barcoding

    Science.gov (United States)

    Cornils, Kerstin; Thielecke, Lars; Hüser, Svenja; Forgber, Michael; Thomaschewski, Michael; Kleist, Nadja; Hussein, Kais; Riecken, Kristoffer; Volz, Tassilo; Gerdes, Sebastian; Glauche, Ingmar; Dahl, Andreas; Dandri, Maura; Roeder, Ingo; Fehse, Boris

    2014-01-01

    RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies. PMID:24476916

  15. Likelihood-Based Inference of B Cell Clonal Families.

    Directory of Open Access Journals (Sweden)

    Duncan K Ralph

    2016-10-01

    Full Text Available The human immune system depends on a highly diverse collection of antibody-making B cells. B cell receptor sequence diversity is generated by a random recombination process called "rearrangement" forming progenitor B cells, then a Darwinian process of lineage diversification and selection called "affinity maturation." The resulting receptors can be sequenced in high throughput for research and diagnostics. Such a collection of sequences contains a mixture of various lineages, each of which may be quite numerous, or may consist of only a single member. As a step to understanding the process and result of this diversification, one may wish to reconstruct lineage membership, i.e. to cluster sampled sequences according to which came from the same rearrangement events. We call this clustering problem "clonal family inference." In this paper we describe and validate a likelihood-based framework for clonal family inference based on a multi-hidden Markov Model (multi-HMM framework for B cell receptor sequences. We describe an agglomerative algorithm to find a maximum likelihood clustering, two approximate algorithms with various trade-offs of speed versus accuracy, and a third, fast algorithm for finding specific lineages. We show that under simulation these algorithms greatly improve upon existing clonal family inference methods, and that they also give significantly different clusters than previous methods when applied to two real data sets.

  16. A computational clonal analysis of the developing mouse limb bud.

    Directory of Open Access Journals (Sweden)

    Luciano Marcon

    Full Text Available A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study tissue movement during morphogenesis. Such experiments allow cell populations to be labeled at an early stage of development and to follow their spatial evolution over time. However, disentangling the cumulative effects of the multiple events responsible for the expansion of the labeled cell population is not always straightforward. To overcome this problem, we develop a novel computational method that combines accurate quantification of 2D limb bud morphologies and growth modeling to analyze mouse clonal data of early limb development. Firstly, we explore various tissue movements that match experimental limb bud shape changes. Secondly, by comparing computational clones with newly generated mouse clonal data we are able to choose and characterize the tissue movement map that better matches experimental data. Our computational analysis produces for the first time a two dimensional model of limb growth based on experimental data that can be used to better characterize limb tissue movement in space and time. The model shows that the distribution and shapes of clones can be described as a combination of anisotropic growth with isotropic cell mixing, without the need for lineage compartmentalization along the AP and PD axis. Lastly, we show that this comprehensive description can be used to reassess spatio-temporal gene regulations taking tissue movement into account and to investigate PD patterning hypothesis.

  17. Circulating mutational portrait of cancer: manifestation of aggressive clonal events in both early and late stages

    Directory of Open Access Journals (Sweden)

    Meng Yang

    2017-05-01

    Full Text Available Abstract Background Solid tumors residing in tissues and organs leave footprints in circulation through circulating tumor cells (CTCs and circulating tumor DNAs (ctDNA. Characterization of the ctDNA portraits and comparison with tumor DNA mutational portraits may reveal clinically actionable information on solid tumors that is traditionally achieved through more invasive approaches. Methods We isolated ctDNAs from plasma of patients of 103 lung cancer and 74 other solid tumors of different tissue origins. Deep sequencing using the Guardant360 test was performed to identify mutations in 73 clinically actionable genes, and the results were associated with clinical characteristics of the patient. The mutation profiles of 37 lung cancer cases with paired ctDNA and tumor genomic DNA sequencing were used to evaluate clonal representation of tumor in circulation. Five lung cancer cases with longitudinal ctDNA sampling were monitored for cancer progression or response to treatments. Results Mutations in TP53, EGFR, and KRAS genes are most prevalent in our cohort. Mutation rates of ctDNA are similar in early (I and II and late stage (III and IV cancers. Mutation in DNA repair genes BRCA1, BRCA2, and ATM are found in 18.1% (32/177 of cases. Patients with higher mutation rates had significantly higher mortality rates. Lung cancer of never smokers exhibited significantly higher ctDNA mutation rates as well as higher EGFR and ERBB2 mutations than ever smokers. Comparative analysis of ctDNA and tumor DNA mutation data from the same patients showed that key driver mutations could be detected in plasma even when they were present at a minor clonal population in the tumor. Mutations of key genes found in the tumor tissue could remain in circulation even after frontline radiotherapy and chemotherapy suggesting these mutations represented resistance mechanisms. Longitudinal sampling of five lung cancer cases showed distinct changes in ctDNA mutation portraits that

  18. Creating a National HIV Curriculum.

    Science.gov (United States)

    Spach, David H; Wood, Brian R; Karpenko, Andrew; Unruh, Kenton T; Kinney, Rebecca G; Roscoe, Clay; Nelson, John

    2016-01-01

    In recent years, the HIV care provider workforce has not kept pace with an expanding HIV epidemic. To effectively address this HIV workforce shortage, a multipronged approach is needed that includes high-quality, easily accessible, up-to-date HIV education for trainees and practicing providers. Toward this objective, the University of Washington, in collaboration with the AIDS Education and Training Center National Coordinating Resource Center, is developing a modular, dynamic curriculum that addresses the entire spectrum of the HIV care continuum. Herein, we outline the general principles, content, organization, and features of this federally funded National HIV Curriculum, which allows for longitudinal, active, self-directed learning, as well as real-time evaluation, tracking, and feedback at the individual and group level. The online curriculum, which is in development, will provide a free, comprehensive, interactive HIV training and resource tool that can support national efforts to expand and strengthen the United States HIV clinical care workforce. Copyright © 2016 Association of Nurses in AIDS Care. Published by Elsevier Inc. All rights reserved.

  19. Invasive clonal plant species have a greater root-foraging plasticity than non-invasive ones.

    Science.gov (United States)

    Keser, Lidewij H; Dawson, Wayne; Song, Yao-Bin; Yu, Fei-Hai; Fischer, Markus; Dong, Ming; van Kleunen, Mark

    2014-03-01

    Clonality is frequently positively correlated with plant invasiveness, but which aspects of clonality make some clonal species more invasive than others is not known. Due to their spreading growth form, clonal plants are likely to experience spatial heterogeneity in nutrient availability. Plasticity in allocation of biomass to clonal growth organs and roots may allow these plants to forage for high-nutrient patches. We investigated whether this foraging response is stronger in species that have become invasive than in species that have not. We used six confamilial pairs of native European clonal plant species differing in invasion success in the USA. We grew all species in large pots under homogeneous or heterogeneous nutrient conditions in a greenhouse, and compared their nutrient-foraging response and performance. Neither invasive nor non-invasive species showed significant foraging responses to heterogeneity in clonal growth organ biomass or in aboveground biomass of clonal offspring. Invasive species had, however, a greater positive foraging response in terms of root and belowground biomass than non-invasive species. Invasive species also produced more total biomass. Our results suggest that the ability for strong root foraging is among the characteristics promoting invasiveness in clonal plants.

  20. Somatic Mutations and Clonal Hematopoiesis in Aplastic Anemia.

    Science.gov (United States)

    Yoshizato, Tetsuichi; Dumitriu, Bogdan; Hosokawa, Kohei; Makishima, Hideki; Yoshida, Kenichi; Townsley, Danielle; Sato-Otsubo, Aiko; Sato, Yusuke; Liu, Delong; Suzuki, Hiromichi; Wu, Colin O; Shiraishi, Yuichi; Clemente, Michael J; Kataoka, Keisuke; Shiozawa, Yusuke; Okuno, Yusuke; Chiba, Kenichi; Tanaka, Hiroko; Nagata, Yasunobu; Katagiri, Takamasa; Kon, Ayana; Sanada, Masashi; Scheinberg, Phillip; Miyano, Satoru; Maciejewski, Jaroslaw P; Nakao, Shinji; Young, Neal S; Ogawa, Seishi

    2015-07-02

    In patients with acquired aplastic anemia, destruction of hematopoietic cells by the immune system leads to pancytopenia. Patients have a response to immunosuppressive therapy, but myelodysplastic syndromes and acute myeloid leukemia develop in about 15% of the patients, usually many months to years after the diagnosis of aplastic anemia. We performed next-generation sequencing and array-based karyotyping using 668 blood samples obtained from 439 patients with aplastic anemia. We analyzed serial samples obtained from 82 patients. Somatic mutations in myeloid cancer candidate genes were present in one third of the patients, in a limited number of genes and at low initial variant allele frequency. Clonal hematopoiesis was detected in 47% of the patients, most frequently as acquired mutations. The prevalence of the mutations increased with age, and mutations had an age-related signature. DNMT3A-mutated and ASXL1-mutated clones tended to increase in size over time; the size of BCOR- and BCORL1-mutated and PIGA-mutated clones decreased or remained stable. Mutations in PIGA and BCOR and BCORL1 correlated with a better response to immunosuppressive therapy and longer and a higher rate of overall and progression-free survival; mutations in a subgroup of genes that included DNMT3A and ASXL1 were associated with worse outcomes. However, clonal dynamics were highly variable and might not necessarily have predicted the response to therapy and long-term survival among individual patients. Clonal hematopoiesis was prevalent in aplastic anemia. Some mutations were related to clinical outcomes. A highly biased set of mutations is evidence of Darwinian selection in the failed bone marrow environment. The pattern of somatic clones in individual patients over time was variable and frequently unpredictable. (Funded by Grant-in-Aid for Scientific Research and others.).

  1. Clonal architectures and driver mutations in metastatic melanomas.

    Directory of Open Access Journals (Sweden)

    Li Ding

    Full Text Available To reveal the clonal architecture of melanoma and associated driver mutations, whole genome sequencing (WGS and targeted extension sequencing were used to characterize 124 melanoma cases. Significantly mutated gene analysis using 13 WGS cases and 15 additional paired extension cases identified known melanoma genes such as BRAF, NRAS, and CDKN2A, as well as a novel gene EPHA3, previously implicated in other cancer types. Extension studies using tumors from another 96 patients discovered a large number of truncation mutations in tumor suppressors (TP53 and RB1, protein phosphatases (e.g., PTEN, PTPRB, PTPRD, and PTPRT, as well as chromatin remodeling genes (e.g., ASXL3, MLL2, and ARID2. Deep sequencing of mutations revealed subclones in the majority of metastatic tumors from 13 WGS cases. Validated mutations from 12 out of 13 WGS patients exhibited a predominant UV signature characterized by a high frequency of C->T transitions occurring at the 3' base of dipyrimidine sequences while one patient (MEL9 with a hypermutator phenotype lacked this signature. Strikingly, a subclonal mutation signature analysis revealed that the founding clone in MEL9 exhibited UV signature but the secondary clone did not, suggesting different mutational mechanisms for two clonal populations from the same tumor. Further analysis of four metastases from different geographic locations in 2 melanoma cases revealed phylogenetic relationships and highlighted the genetic alterations responsible for differential drug resistance among metastatic tumors. Our study suggests that clonal evaluation is crucial for understanding tumor etiology and drug resistance in melanoma.

  2. Clonal origins of ETV6-RUNX1+ acute lymphoblastic leukemia

    DEFF Research Database (Denmark)

    Alpar, D.; Wren, D.; Ermini, Luca

    2015-01-01

    Studies on twins with concordant acute lymphoblastic leukemia (ALL) have revealed that ETV6-RUNX1 gene fusion is a common, prenatal genetic event with other driver aberrations occurring subclonally and probably postnatally. The fetal cell type that is transformed by ETV6-RUNX1 is not identified...... by such studies or by the analysis of early B-cell lineage phenotype of derived progeny. Ongoing, clonal immunoglobulin (IG) and cross-lineage T-cell receptor (TCR) gene rearrangements are features of B-cell precursor leukemia and commence at the pro-B-cell stage of normal B-cell lineage development. We reasoned...

  3. Women and HIV

    Science.gov (United States)

    ... Consumer Information by Audience For Women Women and HIV: Get the Facts on HIV Testing, Prevention, and Treatment Share Tweet Linkedin Pin ... How can you lower your chance of HIV? HIV Quick Facts What is HIV? HIV is the ...

  4. HIV prevention fatigue and HIV treatment optimism among young men who have sex with men

    Science.gov (United States)

    Macapagal, Kathryn; Birkett, Michelle; Janulis, Patrick; Garofalo, Robert; Mustanski, Brian

    2017-01-01

    HIV prevention fatigue (the sense that prevention messages are tiresome) and being overly optimistic about HIV treatments are hypothesized to increase HIV risk behavior. Little research has examined these constructs and their correlates among young men who have sex with men (YMSM), who are at high risk for HIV. YMSM (N = 352; M age = 20; 50% Black) completed measures of prevention fatigue, treatment optimism, HIV risk behaviors, and HIV-related knowledge and attitudes during a longitudinal study. Overall, YMSM reported low levels of HIV prevention fatigue and treatment optimism. Path analysis (n = 307) indicated that greater prevention fatigue and treatment optimism predicted higher rates of condomless sex, but condomless sex did not predict later increases in prevention fatigue or treatment optimism. Results are inconsistent with the hypothesis of high prevention fatigue and treatment optimism among YMSM and point to potential causal relationships among these variables and condomless sex. PMID:28825861

  5. A longitudinal cohort study of HIV 'treatment as prevention' in gay, bisexual and other men who have sex with men: the Treatment with Antiretrovirals and their Impact on Positive And Negative men (TAIPAN) study protocol.

    Science.gov (United States)

    Callander, D; Stoové, M; Carr, A; Hoy, J F; Petoumenos, K; Hellard, M; Elliot, J; Templeton, D J; Liaw, S; Wilson, D P; Grulich, A; Cooper, D A; Pedrana, A; Donovan, B; McMahon, J; Prestage, G; Holt, M; Fairley, C K; McKellar-Stewart, N; Ruth, S; Asselin, J; Keen, P; Cooper, C; Allan, B; Kaldor, J M; Guy, R

    2016-12-12

    Australia has increased coverage of antiretroviral treatment (ART) over the past decade, reaching 73% uptake in 2014. While ART reduces AIDS-related deaths, accumulating evidence suggests that it could also bolster prevention efforts by reducing the risk of HIV transmission ('treatment as prevention'). While promising, evidence of community-level impact of treatment as prevention on reducing HIV incidence among gay and bisexual men is limited. We describe a study protocol that aims to determine if scale up of testing and treatment for HIV leads to a reduction in community viraemia and, in turn, if this reduction is temporally associated with a reduction in HIV incidence among gay and bisexual men in Australia's two most populous states. Over the period 2009 to 2017, we will establish two cohorts making use of clinical and laboratory data electronically extracted retrospectively and prospectively from 73 health services and laboratories in the states of New South Wales and Victoria. The 'positive cohort' will consist of approximately 13,000 gay and bisexual men (>90% of all people living with HIV). The 'negative cohort' will consist of at least 40,000 HIV-negative gay and bisexual men (approximately half of the total population). Within the negative cohort we will use standard repeat-testing methods to calculate annual HIV incidence. Community prevalence of viraemia will be defined as the proportion of men with a viral load ≥200RNA copies/mm 3 , which will combine viral load data from the positive cohort and viraemia estimates among those with an undiagnosed HIV infection. Using regression analyses and adjusting for behavioural and demographic factors associated with infection, we will assess the temporal association between the community prevalence of viraemia and the incidence of HIV infection. Further analyses will make use of these cohorts to assess incidence and predictors of treatment initiation, repeat HIV testing, and viral suppression. This study will

  6. Age-related cancer mutations associated with clonal hematopoietic expansion

    Science.gov (United States)

    Xie, Mingchao; Lu, Charles; Wang, Jiayin; McLellan, Michael D.; Johnson, Kimberly J.; Wendl, Michael C.; McMichael, Joshua F.; Schmidt, Heather K.; Yellapantula, Venkata; Miller, Christopher A.; Ozenberger, Bradley A.; Welch, John S.; Link, Daniel C.; Walter, Matthew J.; Mardis, Elaine R.; Dipersio, John F.; Chen, Feng; Wilson, Richard K.; Ley, Timothy J.; Ding, Li

    2015-01-01

    Several genetic alterations characteristic of leukemia and lymphoma have been detected in the blood of individuals without apparent hematological malignancies. We analyzed blood-derived sequence data from 2,728 individuals within The Cancer Genome Atlas, and discovered 77 blood-specific mutations in cancer-associated genes, the majority being associated with advanced age. Remarkably, 83% of these mutations were from 19 leukemia/lymphoma-associated genes, and nine were recurrently mutated (DNMT3A, TET2, JAK2, ASXL1, TP53, GNAS, PPM1D, BCORL1 and SF3B1). We identified 14 additional mutations in a very small fraction of blood cells, possibly representing the earliest stages of clonal expansion in hematopoietic stem cells. Comparison of these findings to mutations in hematological malignancies identified several recurrently mutated genes that may be disease initiators. Our analyses show that the blood cells of more than 2% of individuals (5–6% of people older than 70 years) contain mutations that may represent premalignant, initiating events that cause clonal hematopoietic expansion. PMID:25326804

  7. Escherichia coli ST131, an Intriguing Clonal Group

    Science.gov (United States)

    Bertrand, Xavier; Madec, Jean-Yves

    2014-01-01

    SUMMARY In 2008, a previously unknown Escherichia coli clonal group, sequence type 131 (ST131), was identified on three continents. Today, ST131 is the predominant E. coli lineage among extraintestinal pathogenic E. coli (ExPEC) isolates worldwide. Retrospective studies have suggested that it may originally have risen to prominence as early as 2003. Unlike other classical group B2 ExPEC isolates, ST131 isolates are commonly reported to produce extended-spectrum β-lactamases, such as CTX-M-15, and almost all are resistant to fluoroquinolones. Moreover, ST131 E. coli isolates are considered to be truly pathogenic, due to the spectrum of infections they cause in both community and hospital settings and the large number of virulence-associated genes they contain. ST131 isolates therefore seem to contradict the widely held view that high levels of antimicrobial resistance are necessarily associated with a fitness cost leading to a decrease in pathogenesis. Six years after the first description of E. coli ST131, this review outlines the principal traits of ST131 clonal group isolates, based on the growing body of published data, and highlights what is currently known and what we need to find out to provide public health authorities with better information to help combat ST131. PMID:24982321

  8. Clonal variation in proliferation rate of cultures of GPK cells.

    Science.gov (United States)

    Riley, P A; Hola, M

    1981-09-01

    Pedigrees of twenty-six clones of a line of keratocytes derived from guinea-pig ear epidermis (GPK cells) were analysed from time-lapse film. The mean interdivision time (IDT) for the culture was 1143 +/- 215 (SD) min. The mean generation rates (mean reciprocal interdivision times) of clones varied over a range of 3.93--10.2 x 10(-4)/min and the standard deviation of the clonal mean generation rates was 16.8% of the average value. Transient intraclonal variations in IDT due to mitoses in a plane perpendicular to the substratum were observed. The data were also analysed on the basis of cell location in sixteen equal zones (quadrats) of the filmed area. The mean generation rate of quadrats was 8.73 x 10(-4)/min (SD = 4.9%). The spatial distribution showed some clustering of cells. The mean local density of the clones (2.25 +/- 0.62 cells/10(-4) cm2) was significantly higher than the quadrat density (1.76 +/- 0.8 cells/10(-4) cm2). There was no significant correlation between clonal density and mean generation rates, whereas for quadrats a significant negative correlation was found (P = 2.7%). The results support the proposition that cell lineage is the major determinant of the proliferation rate of subconfluent cultures.

  9. Competition, salinity, and clonal growth in native and introduced irises.

    Science.gov (United States)

    Mopper, Susan; Wiens, Karen C; Goranova, Greta A

    2016-09-01

    Iris pseudacorus spread rapidly into North America after introduction from Europe in the 1800s and now co-occurs with native I. hexagona in freshwater Louisiana wetlands. Native irises support and interact with multiple trophic levels, whereas I. pseudacorus is classified an invasive pest because it grows aggressively, reduces biodiversity, and displaces native vegetation. Salinity levels are increasing in coastal wetlands worldwide. We examined how salt-stress affects competitive interactions between these conspecifics. We established a three-way full-factorial common-garden experiment that included species (I. pseudacorus, I. hexagona), competition (no competition, intraspecific competition, and interspecific competition), and salinity (0, 4, 8 parts per thousand NaCl), with six replicates per treatment. After 18 mo, Iris pseudacorus produced much more biomass than the native species did (F1, 92 = 71.5, P Interspecific competition did not affect the introduced iris, but biomass of the native was strongly reduced (competition × species interaction: F2, 95 = 76.7, P = 0.002). Salinity significantly reduced biomass of both species (F2, 92 = 21.8, P competitive advantage over the native, regardless of environmental salinity levels. Based on patterns in clonal reproduction, the introduced iris could potentially threaten native iris populations. We are currently investigating seed production and mortality during competition and stress because both clonal and sexual reproduction must be considered when predicting long-term population dynamics. © 2016 Botanical Society of America.

  10. Clonal expansion of renal cell carcinoma-infiltrating T lymphocytes

    DEFF Research Database (Denmark)

    Sittig, Simone; Køllgaard, Tania; Grønbæk, Kirsten

    2013-01-01

    T lymphocytes can mediate the destruction of cancer cells by virtue of their ability to recognize tumor-derived antigenic peptides that are presented on the cell surface in complex with HLA molecules and expand. Thus, the presence of clonally expanded T cells within neoplastic lesions is an indic......T lymphocytes can mediate the destruction of cancer cells by virtue of their ability to recognize tumor-derived antigenic peptides that are presented on the cell surface in complex with HLA molecules and expand. Thus, the presence of clonally expanded T cells within neoplastic lesions...... is an indication of ongoing HLA-restricted T cell-mediated immune responses. Multiple tumors, including renal cell carcinomas (RCCs), are often infiltrated by significant amounts of T cells, the so-called tumor-infiltrating lymphocytes (TILs). In the present study, we analyzed RCC lesions (n = 13) for the presence...... of expanded T-cell clonotypes using T-cell receptor clonotype mapping. Surprisingly, we found that RCCs comprise relatively low numbers of distinct expanded T-cell clonotypes as compared with melanoma lesions. The numbers of different T-cell clonotypes detected among RCC-infiltrating lymphocytes were...

  11. Internato Longitudinal

    Directory of Open Access Journals (Sweden)

    Marcelo Marcos Piva Demarzo

    Full Text Available O internato médico tem gerado recorrente debate frente às transformações curriculares em andamento no País. A despeito das discussões, um modelo de internato consonante com essas mudanças ainda não foi consistentemente delineado. Neste ensaio, trazemos uma proposta de matriz estruturante para o internato médico. Propomos que o internato médico seja realizado durante os seis anos do curso, de forma longitudinal, tendo como eixo estruturante a clínica da Atenção Básica (AB. Esse modelo de "internato longitudinal" prevê a introdução progressiva na prática clínica, iniciando-se pela AB nos dois primeiros anos, acrescentando-se progressivamente os ambulatórios de especialidades, os estágios hospitalares e demais atividades práticas, alcançando-se, dessa forma, o rol de diversidade e complexidade previsto para o egresso da escola médica.

  12. Clonal Spread in Second Growth Stands of Coast Redwood, Sequoia sempervirens

    Science.gov (United States)

    Vladimir Douhovnikoff; Richard S. Dodd

    2007-01-01

    Coast redwood (Sequoia sempervirens) is one of the rare conifers to reproduce successfully through clonal spread. The importance of this mode of reproduction in stand development is largely unknown. Understanding the importance of clonal spread and the spatial structure of clones is crucial for stand management strategies that would aim to maximize...

  13. Virulence, sporulation, and elicitin production in three clonal lineages of Phytophthora ramorum

    Science.gov (United States)

    Phytophthora ramorum populations are clonal and consist of three lineages. Recent studies have shown that the clonal lineages may have varying degrees of aggressiveness on some host species, such as Quercus rubra. In this study, we examined virulence, sporulation and elicitin production of five P. ...

  14. Clonal relation in a case of CLL, ALCL, and Hodgkin composite lymphoma

    NARCIS (Netherlands)

    van den Berg, Anke; Maggio, Ewerton; Rust, R; Kooistra, K; Diepstra, A; Poppema, S

    2002-01-01

    Large cell lymphomas and Hodgkin disease may develop during the course of chronic lymphocytic leukemia (CLL). In some cases the transformed cells are Epstein-Barr virus (EBV)-positive and not clonally related to the CLL cells. In other cases the transformed cells have the same clonal rearrangements

  15. Growth and stem form quality of clonal Pinus taeda following fertilization in the Virginia Piedmont

    Science.gov (United States)

    Jeremy P. Stovall; Colleen A. Carlson; John R. Seiler; Thomas R. Fox

    2013-01-01

    Clonal forestry offers the opportunity to increase yields, enhance uniformity, and improve wood characteristics. Intensive silvicultural practices, including fertilization, will be required to capture the full growth potential of clonal plantations. However, variation in nutrient use efficiency that exists among clones could affect growth responses. Our research...

  16. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

    DEFF Research Database (Denmark)

    McGranahan, Nicholas; Furness, Andrew J S; Rosenthal, Rachel

    2016-01-01

    demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8(+)tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non-small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4...

  17. Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

    Science.gov (United States)

    To gain a detailed understanding of how plant microbes evolve and adapt to hosts, pesticides, and other factors, knowledge of the population dynamics and evolutionary history of populations is crucial. Plant pathogen populations are often clonal or partially clonal which requires different analytica...

  18. Clonal Growth Forms in Eastern Ladakh, Western Himalayas: Classification and Habitat Preferences

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Doležal, Jiří; Dvorský, Miroslav; de Bello, Francesco; Klimeš, Leoš

    2011-01-01

    Roč. 46, 2-3 (2011), 191-217 ISSN 1211-9520 R&D Projects: GA AV ČR IAA600050802 Institutional research plan: CEZ:AV0Z60050516 Keywords : Clonal growth form * Clonal space occupancy strategies * Habitat types Subject RIV: EF - Botanics Impact factor: 1.500, year: 2011

  19. Increasing rates of obesity among HIV-infected persons during the HIV epidemic.

    Directory of Open Access Journals (Sweden)

    Nancy Crum-Cianflone

    2010-04-01

    Full Text Available The prevalence and factors associated with overweight/obesity among human immunodeficiency virus (HIV-infected persons are unknown.We evaluated prospective data from a U.S. Military HIV Natural History Study (1985-2004 consisting of early diagnosed patients. Statistics included multivariate linear regression and longitudinal linear mixed effects models.Of 1682 patients, 2% were underweight, 37% were overweight, and 9% were obese at HIV diagnosis. Multivariate predictors of a higher body mass index (BMI at diagnosis included more recent year of HIV diagnosis, older age, African American race, and earlier HIV stage (all p<0.05. The majority of patients (62% gained weight during HIV infection. Multivariate factors associated with a greater increase in BMI during HIV infection included more recent year of diagnosis, lower BMI at diagnosis, higher CD4 count, lower HIV RNA level, lack of AIDS diagnosis, and longer HIV duration (all p<0.05. Nucleoside agents were associated with less weight gain; other drug classes had no significant impact on weight change in the HAART era.HIV-infected patients are increasingly overweight/obese at diagnosis and during HIV infection. Weight gain appears to reflect improved health status and mirror trends in the general population. Weight management programs may be important components of HIV care.

  20. Analysis of allelic expression patterns in clonal somatic cells by single-cell RNA-seq.

    Science.gov (United States)

    Reinius, Björn; Mold, Jeff E; Ramsköld, Daniel; Deng, Qiaolin; Johnsson, Per; Michaëlsson, Jakob; Frisén, Jonas; Sandberg, Rickard

    2016-11-01

    Cellular heterogeneity can emerge from the expression of only one parental allele. However, it has remained controversial whether, or to what degree, random monoallelic expression of autosomal genes (aRME) is mitotically inherited (clonal) or stochastic (dynamic) in somatic cells, particularly in vivo. Here we used allele-sensitive single-cell RNA-seq on clonal primary mouse fibroblasts and freshly isolated human CD8 + T cells to dissect clonal and dynamic monoallelic expression patterns. Dynamic aRME affected a considerable portion of the cells' transcriptomes, with levels dependent on the cells' transcriptional activity. Notably, clonal aRME was detected, but it was surprisingly scarce (aRME occurs transiently within individual cells, and patterns of aRME are thus primarily scattered throughout somatic cell populations rather than, as previously hypothesized, confined to patches of clonally related cells.

  1. Uncovering the Number and Clonal Dynamics of Mesp1 Progenitors during Heart Morphogenesis

    Directory of Open Access Journals (Sweden)

    Samira Chabab

    2016-01-01

    Full Text Available The heart arises from distinct sources of cardiac progenitors that independently express Mesp1 during gastrulation. The precise number of Mesp1 progenitors that are specified during the early stage of gastrulation, and their clonal behavior during heart morphogenesis, is currently unknown. Here, we used clonal and mosaic tracing of Mesp1-expressing cells combined with quantitative biophysical analysis of the clonal data to define the number of cardiac progenitors and their mode of growth during heart development. Our data indicate that the myocardial layer of the heart derive from ∼250 Mesp1-expressing cardiac progenitors born during gastrulation. Despite arising at different time points and contributing to different heart regions, the temporally distinct cardiac progenitors present very similar clonal dynamics. These results provide insights into the number of cardiac progenitors and their mode of growth and open up avenues to decipher the clonal dynamics of progenitors in other organs and tissues.

  2. Clonal neoantigens elicit T cell immunoreactivity and sensitivity to immune checkpoint blockade

    Science.gov (United States)

    McGranahan, Nicholas; Furness, Andrew J. S.; Rosenthal, Rachel; Ramskov, Sofie; Lyngaa, Rikke; Saini, Sunil Kumar; Jamal-Hanjani, Mariam; Wilson, Gareth A.; Birkbak, Nicolai J.; Hiley, Crispin T.; Watkins, Thomas B. K.; Shafi, Seema; Murugaesu, Nirupa; Mitter, Richard; Akarca, Ayse U.; Linares, Joseph; Marafioti, Teresa; Henry, Jake Y.; Van Allen, Eliezer M.; Miao, Diana; Schilling, Bastian; Schadendorf, Dirk; Garraway, Levi A.; Makarov, Vladimir; Rizvi, Naiyer A.; Snyder, Alexandra; Hellmann, Matthew D.; Merghoub, Taha; Wolchok, Jedd D.; Shukla, Sachet A.; Wu, Catherine J.; Peggs, Karl S.; Chan, Timothy A.; Hadrup, Sine R.; Quezada, Sergio A.; Swanton, Charles

    2016-01-01

    As tumors grow, they acquire mutations, some of which create neoantigens that influence the response of patients to immune checkpoint inhibitors. We explored the impact of neoantigen intratumor heterogeneity (ITH) on antitumor immunity. Through integrated analysis of ITH and neoantigen burden, we demonstrate a relationship between clonal neoantigen burden and overall survival in primary lung adenocarcinomas. CD8+ tumor-infiltrating lymphocytes reactive to clonal neoantigens were identified in early-stage non–small cell lung cancer and expressed high levels of PD-1. Sensitivity to PD-1 and CTLA-4 blockade in patients with advanced NSCLC and melanoma was enhanced in tumors enriched for clonal neoantigens. T cells recognizing clonal neoantigens were detectable in patients with durable clinical benefit. Cytotoxic chemotherapy–induced subclonal neoantigens, contributing to an increased mutational load, were enriched in certain poor responders. These data suggest that neoantigen heterogeneity may influence immune surveillance and support therapeutic developments targeting clonal neoantigens. PMID:26940869

  3. Determinants of the risk of dying of HIV/AIDS in a rural South African community over the period of the decentralised roll-out of antiretroviral therapy: a longitudinal study

    Directory of Open Access Journals (Sweden)

    Paul Mee

    2014-11-01

    Full Text Available Background: Antiretroviral treatment (ART has significantly reduced HIV mortality in South Africa. The benefits have not been experienced by all groups. Here we investigate the factors associated with these inequities. Design: This study was located in a rural South African setting and used data collected from 2007 to 2010, the period when decentralised ART became available. Approximately one-third of the population were of Mozambican origin. There was a pattern of repeated circular migration between urban areas and this community. Survival analysis models were developed to identify demographic, socioeconomic, and spatial risk factors for HIV mortality. Results: Among the study population of 105,149 individuals, there were 2,890 deaths. The HIV/TB mortality rate decreased by 27% between 2007–2008 and 2009–2010. For other causes of death, the reduction was 10%. Bivariate analysis found that the HIV/TB mortality risk was lower for: those living within 5 km of the Bhubezi Community Health Centre; women; young adults; in-migrants with a longer period of residence; permanent residents; and members of households owning motorised transport, holding higher socioeconomic positions, and with higher levels of education. Multivariate modelling showed, in addition, that those with South Africa as their country of origin had an increased risk of HIV/TB mortality compared to those with Mozambican origins. For males, those of South African origin, and recent in-migrants, the risk of death associated with HIV/TB was significantly greater than that due to other causes. Conclusions: In this community, a combination of factors was associated with an increased risk of dying of HIV/TB over the period of the roll-out of ART. There is evidence for the presence of barriers to successful treatment for particular sub-groups in the population, which must be addressed if the recent improvements in population-level mortality are to be maintained.

  4. Determinants of the risk of dying of HIV/AIDS in a rural South African community over the period of the decentralised roll-out of antiretroviral therapy: a longitudinal study

    Science.gov (United States)

    Mee, Paul; Collinson, Mark A.; Madhavan, Sangeetha; Kabudula, Chodziwadziwa; Gómez-Olivé, Francesc Xavier; Kahn, Kathleen; Tollman, Stephen M.; Hargreaves, James; Byass, Peter

    2014-01-01

    Background Antiretroviral treatment (ART) has significantly reduced HIV mortality in South Africa. The benefits have not been experienced by all groups. Here we investigate the factors associated with these inequities. Design This study was located in a rural South African setting and used data collected from 2007 to 2010, the period when decentralised ART became available. Approximately one-third of the population were of Mozambican origin. There was a pattern of repeated circular migration between urban areas and this community. Survival analysis models were developed to identify demographic, socioeconomic, and spatial risk factors for HIV mortality. Results Among the study population of 105,149 individuals, there were 2,890 deaths. The HIV/TB mortality rate decreased by 27% between 2007–2008 and 2009–2010. For other causes of death, the reduction was 10%. Bivariate analysis found that the HIV/TB mortality risk was lower for: those living within 5 km of the Bhubezi Community Health Centre; women; young adults; in-migrants with a longer period of residence; permanent residents; and members of households owning motorised transport, holding higher socioeconomic positions, and with higher levels of education. Multivariate modelling showed, in addition, that those with South Africa as their country of origin had an increased risk of HIV/TB mortality compared to those with Mozambican origins. For males, those of South African origin, and recent in-migrants, the risk of death associated with HIV/TB was significantly greater than that due to other causes. Conclusions In this community, a combination of factors was associated with an increased risk of dying of HIV/TB over the period of the roll-out of ART. There is evidence for the presence of barriers to successful treatment for particular sub-groups in the population, which must be addressed if the recent improvements in population-level mortality are to be maintained. PMID:25416322

  5. Demographic consequences of greater clonal than sexual reproduction in Dicentra canadensis.

    Science.gov (United States)

    Lin, Chia-Hua; Miriti, Maria N; Goodell, Karen

    2016-06-01

    Clonality is a widespread life history trait in flowering plants that may be essential for population persistence, especially in environments where sexual reproduction is unpredictable. Frequent clonal reproduction, however, could hinder sexual reproduction by spatially aggregating ramets that compete with seedlings and reduce inter-genet pollination. Nevertheless, the role of clonality in relation to variable sexual reproduction in population dynamics is often overlooked. We combined population matrix models and pollination experiments to compare the demographic contributions of clonal and sexual reproduction in three Dicentra canadensis populations, one in a well-forested landscape and two in isolated forest remnants. We constructed stage-based transition matrices from 3 years of census data to evaluate annual population growth rates, λ. We used loop analysis to evaluate the relative contribution of different reproductive pathways to λ. Despite strong temporal and spatial variation in seed set, populations generally showed stable growth rates. Although we detected some pollen limitation of seed set, manipulative pollination treatments did not affect population growth rates. Clonal reproduction contributed significantly more than sexual reproduction to population growth in the forest remnants. Only at the well-forested site did sexual reproduction contribute as much as clonal reproduction to population growth. Flowering plants were more likely to transition to a smaller size class with reduced reproductive potential in the following year than similarly sized nonflowering plants, suggesting energy trade-offs between sexual and clonal reproduction at the individual level. Seed production had negligible effects on growth and tuber production of individual plants. Our results demonstrate that clonal reproduction is vital for population persistence in a system where sexual reproduction is unpredictable. The bias toward clonality may be driven by low fitness returns

  6. Endothelial progenitor cells display clonal restriction in multiple myeloma

    International Nuclear Information System (INIS)

    Braunstein, Marc; Özçelik, Tayfun; Bağişlar, Sevgi; Vakil, Varsha; Smith, Eric LP; Dai, Kezhi; Akyerli, Cemaliye B; Batuman, Olcay A

    2006-01-01

    In multiple myeloma (MM), increased neoangiogenesis contributes to tumor growth and disease progression. Increased levels of endothelial progenitor cells (EPCs) contribute to neoangiogenesis in MM, and, importantly, covary with disease activity and response to treatment. In order to understand the mechanisms responsible for increased EPC levels and neoangiogenic function in MM, we investigated whether these cells were clonal by determining X-chromosome inactivation (XCI) patterns in female patients by a human androgen receptor assay (HUMARA). In addition, EPCs and bone marrow cells were studied for the presence of clonotypic immunoglobulin heavy-chain (IGH) gene rearrangement, which indicates clonality in B cells; thus, its presence in EPCs would indicate a close genetic link between tumor cells in MM and endothelial cells that provide tumor neovascularization. A total of twenty-three consecutive patients who had not received chemotherapy were studied. Screening in 18 patients found that 11 displayed allelic AR in peripheral blood mononuclear cells, and these patients were further studied for XCI patterns in EPCs and hair root cells by HUMARA. In 2 patients whose EPCs were clonal by HUMARA, and in an additional 5 new patients, EPCs were studied for IGH gene rearrangement using PCR with family-specific primers for IGH variable genes (V H ). In 11 patients, analysis of EPCs by HUMARA revealed significant skewing (≥ 77% expression of a single allele) in 64% (n = 7). In 4 of these patients, XCI skewing was extreme (≥ 90% expression of a single allele). In contrast, XCI in hair root cells was random. Furthermore, PCR amplification with V H primers resulted in amplification of the same product in EPCs and bone marrow cells in 71% (n = 5) of 7 patients, while no IGH rearrangement was found in EPCs from healthy controls. In addition, in patients with XCI skewing in EPCs, advanced age was associated with poorer clinical status, unlike patients whose EPCs had random XCI

  7. Aging, Clonality and Rejuvenation of Hematopoietic Stem Cells

    Science.gov (United States)

    Akunuru, Shailaja; Geiger, Hartmut

    2016-01-01

    Aging is associated with reduced organ function and increased disease incidence. Hematopoietic stem cell (HSC) aging driven by both cell intrinsic and extrinsic factors is linked to impaired HSC self-renewal and regeneration, aging-associated immune remodeling, and increased leukemia incidence. Compromised DNA damage responses and increased production of reactive oxygen species have been previously causatively attributed to HSC aging. However, recent paradigm-shifting concepts such as global epigenetic and cytoskeletal polarity shifts, cellular senescence, as well as clonal selection of HSCs upon aging provide new insights into HSC aging mechanisms. Rejuvenating agents that can reprogram the epigenetic status of aged HSCs or senolytic drugs that selectively deplete senescent cells provide promising translational avenues for attenuating hematopoietic aging and potentially, alleviating aging-associated immune remodeling and myeloid malignancies. PMID:27380967

  8. Atherosclerosis and clonal hematopoyesis: A new risk factor.

    Science.gov (United States)

    Páramo Fernández, José A

    Recent research has revealed that clonal hematopoyesis of indeterminate potential (CHIP) characterized by the acquisition of somatic mutations in hematopoietic stem cells, is not only a common age-related disorder and a premalignant condition, but it is also associated with the development of atherosclerotic vascular diseases. Mutations in DNMT3A, TET2 and ASXL1 were each individually associated with coronary heart disease, stroke and coronary calcification. Therefore, CHIP emerges as a new risk factor for atherosclerotic vascular pathologies and its detection may be relevant as a new therapeutic target in order to modify the natural course of the disease. Copyright © 2018 Sociedad Española de Arteriosclerosis. Publicado por Elsevier España, S.L.U. All rights reserved.

  9. Clonal proliferation of cultured nonmalignant and malignant human breast epithelia

    International Nuclear Information System (INIS)

    Smith, H.S.; Lan, S.; Ceriani, R.; Hackett, A.J.; Stampfer, M.R.

    1981-01-01

    We have developed a method for clonal growth of human mammary epithelial cells of both nonmalignant and malignant origin. Plating efficiencies of 1 to 50% were obtained by seeding second-passage mammary epithelial cells on fibroblast feeder layers in an enriched medium composed of various hormones and growth factors, as well as conditioned media from three specific human cell lines. Single mammary epithelial cells seeded sparsely onto the fibroblasts underwent at least eight population doublings to form large, readily visible colonies. Optimal colony formation required both feeder cells and the enriched medium. Epithelial colonies containing at least 16 cells were visible 5 days postseeding, and these colonies continued to grow progressively. Plating efficiency and colony size were similar on ultraviolet-irradiated or nonirradiated fibroblasts. The number of colonies formed was proportional to the number of epithelial cells plated. The colonies were identified as epithelial by the presence of human mammary epithelial antigens

  10. Comparing nonparametric Bayesian tree priors for clonal reconstruction of tumors.

    Science.gov (United States)

    Deshwar, Amit G; Vembu, Shankar; Morris, Quaid

    2015-01-01

    Statistical machine learning methods, especially nonparametric Bayesian methods, have become increasingly popular to infer clonal population structure of tumors. Here we describe the treeCRP, an extension of the Chinese restaurant process (CRP), a popular construction used in nonparametric mixture models, to infer the phylogeny and genotype of major subclonal lineages represented in the population of cancer cells. We also propose new split-merge updates tailored to the subclonal reconstruction problem that improve the mixing time of Markov chains. In comparisons with the tree-structured stick breaking prior used in PhyloSub, we demonstrate superior mixing and running time using the treeCRP with our new split-merge procedures. We also show that given the same number of samples, TSSB and treeCRP have similar ability to recover the subclonal structure of a tumor…

  11. Transcriptomic variation in a coral reveals pathways of clonal organisation

    DEFF Research Database (Denmark)

    K Bay, Line; Nielsen, Henrik Bjørn; Jarmer, Hanne Østergaard

    2009-01-01

    A microarray study was undertaken to examine the potential for clonal gene expression variation in a branching reef building coral, Acropora millepora. The role of small-scale gradients in light and water flow was examined by comparing gene expression levels between branch elevation (tip and base......) and position (centre and edge) of replicate coral colonies (n=3). Analyses of variance revealed that almost 60% of variation in gene expression was present between colonies and 34 genes were considered differentially expressed between colonies (minimum P=6.5 x 10(-4)). These genes are associated with energy...... of corymbose-like branching coral colonies such as A. millepora. Four genes were differentially expressed between the tip and base of branches (P=3.239 x 10(-4)) and were associated with lysosome lipase activity and fluorescence, suggesting that branch tips may encounter higher pathogen loads or levels...

  12. Evaluation of the Positive Prevention HIV/STD Curriculum

    Science.gov (United States)

    LaChausse, Robert G.

    2006-01-01

    This study evaluated the effectiveness of Positive Prevention, a theory-based, HIV/STD prevention education curriculum for high school youth. Three hundred fifty-three students participated in a longitudinal experimental design to determine the impact of the curriculum on HIV/AIDS knowledge, self-efficacy to abstain from sex, self-efficacy of…

  13. Predictors of incident tuberculosis in HIV-exposed children in ...

    African Journals Online (AJOL)

    Objective: To examine the predictors of tuberculosis infection in HIV-exposed children. Design: A longitudinal cohort study nested within a randomised controlled trial. Setting: Antenatal clinics in Dar-es-Salaam, Tanzania. Subjects: Children born to 875 HIV-infected women in Tanzania. Results: A total of 82 children ...

  14. a study of nevirapine toxicity in hiv infected pregnant women

    African Journals Online (AJOL)

    Esem

    HIV infected women commenced on nevirapine-based regimen in the current pregnancy with CD4 counts up to. 3. 350 cells/mm at the University Teaching Hospital,. Lusaka, Zambia. Design: Longitudinal observational study with 2 arms. Group 1 (low CD4 count arm): HIV infected pregnant. 3 women with CD4 counts less ...

  15. HIV Stigma and Unhealthy Alcohol Use Among People Living with HIV in Russia.

    Science.gov (United States)

    Lunze, Karsten; Lioznov, Dmitry; Cheng, Debbie M; Nikitin, Ruslan V; Coleman, Sharon M; Bridden, Carly; Blokhina, Elena; Krupitsky, Evgeny; Samet, Jeffrey H

    2017-09-01

    Unhealthy alcohol use, highly prevalent in the Russian Federation (Russia), is associated with HIV risk behaviors among people living with HIV (PLWH). HIV stigma contributes to the HIV risk environment in Russia. To examine HIV stigma among Russian PLWH and to explore its association with unhealthy alcohol use, we conducted a longitudinal analysis of 700 PLWH in St. Petersburg, Russia. We assessed the association between alcohol dependence and HIV stigma measured at baseline and 12 months follow-up. Participants with alcohol dependence (n = 446) reported significantly higher HIV stigma scores over time than those without dependence (n = 254) (adjusted mean difference 0.60, 95% CI 0.03-1.17; p = 0.04). In secondary analyses, we examined recent risky alcohol use and did not detect an association with HIV stigma. Alcohol dependence is associated with high HIV stigma among Russian PLWH but the nature of the association is conjectural. HIV prevention efforts in Russia that address alcohol use disorders hold potential to mitigate HIV-related stigma and its possible adverse effects among PLWH.

  16. Clonal diversity and estimation of relative clone age: application to agrobiodiversity of yam (Dioscorea rotundata).

    Science.gov (United States)

    Scarcelli, Nora; Couderc, Marie; Baco, Mohamed N; Egah, Janvier; Vigouroux, Yves

    2013-11-13

    Clonal propagation is a particular reproductive system found in both the plant and animal kingdoms, from human parasites to clonally propagated crops. Clonal diversity provides information about plant and animal evolutionary history, i.e. how clones spread, or the age of a particular clone. In plants, this could provide valuable information about agrobiodiversity dynamics and more broadly about the evolutionary history of a particular crop. We studied the evolutionary history of yam, Dioscorea rotundata. In Africa, Yam is cultivated by tuber clonal propagation. We used 12 microsatellite markers to identify intra-clonal diversity in yam varieties. We then used this diversity to assess the relative ages of clones. Using simulations, we assessed how Approximate Bayesian Computation could use clonal diversity to estimate the age of a clone depending on the size of the sample, the number of independent samples and the number of markers. We then applied this approach to our particular dataset and showed that the relative ages of varieties could be estimated, and that each variety could be ranked by age. We give a first estimation of clone age in an approximate Bayesian framework. However the precise estimation of clone age depends on the precision of the mutation rate. We provide useful information on agrobiodiversity dynamics and suggest recurrent creation of varietal diversity in a clonally propagated crop.

  17. Clonal integration facilitates spread of Paspalum paspaloides from terrestrial to cadmium-contaminated aquatic habitats.

    Science.gov (United States)

    Luo, F-L; Xing, Y-P; Wei, G-W; Li, C-Y; Yu, F-H

    2017-11-01

    Cadmium (Cd) is a hazardous environmental pollutant with high toxicity to plants, which has been detected in many wetlands. Clonal integration (resource translocation) between connected ramets of clonal plants can increase their tolerance to stress. We hypothesised that clonal integration facilitates spread of amphibious clonal plants from terrestrial to Cd-contaminated aquatic habitats. The spread of an amphibious grass Paspalum paspaloides was simulated by growing basal older ramets in uncontaminated soil connected (allowing integration) or not connected (preventing integration) to apical younger ramets of the same fragments in Cd-contaminated water. Cd contamination of apical ramets of P. paspaloides markedly decreased growth and photosynthetic capacity of the apical ramets without connection to the basal ramets, but did not decrease these properties with connection. Cd contamination did not affect growth of the basal ramets without connection to the apical ramets, but Cd contamination of 4 and 12 mg·l -1 significantly increased growth with connection. Consequently, clonal integration increased growth of the apical ramets, basal ramets and whole clones when the apical ramets were grown in Cd-contaminated water of 4 and 12 mg·l -1 . Cd was detected in the basal ramets with connection to the apical ramets, suggesting Cd could be translocated due to clonal integration. Clonal integration, most likely through translocation of photosynthates, can support P. paspaloides to spread from terrestrial to Cd-contaminated aquatic habitats. Amphibious clonal plants with a high ability for clonal integration are particularly useful for re-vegetation of degraded aquatic habitats caused by Cd contamination. © 2017 German Society for Plant Sciences and The Royal Botanical Society of the Netherlands.

  18. Clonal growth strategy, diversity and structure: A spatiotemporal response to sedimentation in tropical Cyperus papyrus swamps.

    Science.gov (United States)

    Geremew, Addisie; Stiers, Iris; Sierens, Tim; Kefalew, Alemayehu; Triest, Ludwig

    2018-01-01

    Land degradation and soil erosion in the upper catchments of tropical lakes fringed by papyrus vegetation can result in a sediment load gradient from land to lakeward. Understanding the dynamics of clonal modules (ramets and genets) and growth strategies of plants on such a gradient in both space and time is critical for exploring a species adaptation and processes regulating population structure and differentiation. We assessed the spatial and temporal dynamics in clonal growth, diversity, and structure of an emergent macrophyte, Cyperus papyrus (papyrus), in response to two contrasting sedimentation regimes by combining morphological traits and genotype data using 20 microsatellite markers. A total of 636 ramets from six permanent plots (18 x 30 m) in three Ethiopian papyrus swamps, each with discrete sedimentation regimes (high vs. low) were sampled for two years. We found that ramets under the high sedimentation regime (HSR) were significantly clumped and denser than the sparse and spreading ramets under the low sedimentation regime (LSR). The HSR resulted in significantly different ramets with short culm height and girth diameter as compared to the LSR. These results indicated that C. papyrus ameliorates the effect of sedimentation by shifting clonal growth strategy from guerrilla (in LSR) to phalanx (in HSR). Clonal richness, size, dominance, and clonal subrange differed significantly between sediment regimes and studied time periods. Each swamp under HSR revealed a significantly high clonal richness (R = 0.80) as compared to the LSR (R = 0.48). Such discrepancy in clonal richness reflected the occurrence of initial and repeated seedling recruitment strategies as a response to different sedimentation regimes. Overall, our spatial and short-term temporal observations highlighted that HSR enhances clonal richness and decreases clonal subrange owing to repeated seedling recruitment and genets turnover.

  19. Prediction for the occurrence of clonal chromosome aberrations in human blood lymphocytes

    International Nuclear Information System (INIS)

    Nakano, M.; Kadama, Y.; Ohtaki, K.; Itoh, M.; Awa, A.; Cologne, J.; Nakamura, N.

    2003-01-01

    Full text: Identical chromosome aberrations among multiple blood lymphocytes in a blood sample (clonal aberrations) are encountered occasionally during cytogenetic examination of radiation-exposed people. Clonal aberrations are found primarily among high-dose exposed people but no systematic surveys were ever conducted. Therefore, the underlying mechanism is unknown. Here we conducted a large-scale screening for detecting clonal aberrations using FISH followed by Q-banding. Examinations of 500 cells from each of 513 A-bomb survivors led us to detect 96 clones. The clonal cell fraction (Cf) varied from 0.6% to 20% among the 500 cells. As the number of clonal event was inversely proportional to Cf, we hypothesized that the progenitor cells vary extensively in the number of offspring that they can produce and relative number of progenitor cells decreases as the increase of treatment, while other genes such as DNA repair proteinsnumber of progenitor cells capable to form clones (Cf >=0.6%) to be 2 (1 to 3) in non-exposed individuals. The number increased to up to 7 among the high-dose exposed survivors. Further, our preliminary results for the origins of 10 clones indicated that both hematopoietic stem cells (HSCs) and mature T cells contributed to the clone formation roughly equally. Thus, the estimated number of 2 in non-exposed individuals is shared as one HSC and one mature T cells. The model could neatly explain the frequency of clones in two reports. Our model predicts that clonal aberrations are rarely found but clonal expansion of T lymphocytes occurs commonly. In fact, clonal expansions of non-aberrant cells are reported using TCR gene rearrangement patterns as a marker. We now understand the rough structure of lymphocyte pool in humans and can predict the probability of detecting a clone if the individual frequency of non-clonal translocations and the number of cells scored are given

  20. Impact of alemtuzumab on HIV persistence in an HIV-infected individual on antiretroviral therapy with Sezary syndrome.

    Science.gov (United States)

    Rasmussen, Thomas A; McMahon, James; Chang, J Judy; Symons, Jori; Roche, Michael; Dantanarayana, Ashanti; Okoye, Afam; Hiener, Bonnie; Palmer, Sarah; Lee, Wen Shi; Kent, Stephen J; Van Der Weyden, Carrie; Prince, H Miles; Cameron, Paul U; Lewin, Sharon R

    2017-08-24

    To study the effects of alemtuzumab on HIV persistence in an HIV-infected individual on antiretroviral therapy (ART) with Sezary syndrome, a rare malignancy of CD4 T cells. Case report. Blood was collected 30 and 18 months prior to presentation with Sezary syndrome, at the time of presentation and during alemtuzumab. T-cell subsets in malignant (CD7-CD26-TCR-VBeta2+) and nonmalignant cells were quantified by flow cytometry. HIV-DNA in total CD4 T cells, in sorted malignant and nonmalignant CD4 T cells, was quantified by PCR and clonal expansion of HIV-DNA assessed by full-length next-generation sequencing. HIV-hepatitis B virus coinfection was diagnosed and antiretroviral therapy initiated 4 years prior to presentation with Sezary syndrome and primary cutaneous anaplastic large cell lymphoma. The patient received alemtuzumab 10 mg three times per week for 4 weeks but died 6 weeks post alemtuzumab. HIV-DNA was detected in nonmalignant but not in malignant CD4 T cells, consistent with expansion of a noninfected CD4 T-cell clone. Full-length HIV-DNA sequencing demonstrated multiple defective viruses but no identical or expanded sequences. Alemtuzumab extensively depleted T cells, including more than 1 log reduction in total T cells and more than 3 log reduction in CD4 T cells. Finally, alemtuzumab decreased HIV-DNA in CD4 T cells by 57% but HIV-DNA remained detectable at low levels even after depletion of nearly all CD4 T cells. Alemtuzumab extensively depleted multiple T-cell subsets and decreased the frequency of but did not eliminate HIV-infected CD4 T cells. Studying the effects on HIV persistence following immune recovery in HIV-infected individuals who require alemtuzumab for malignancy or in animal studies may provide further insights into novel cure strategies.

  1. Diverse cellular architecture of atherosclerotic plaque derives from clonal expansion of a few medial SMCs

    DEFF Research Database (Denmark)

    Jacobsen, Kevin; Lund, Marie Bek; Shim, Jeong

    2017-01-01

    Fibrous cap smooth muscle cells (SMCs) protect atherosclerotic lesions from rupturing and causing thrombosis, while other plaque SMCs may have detrimental roles in plaque development. To gain insight into recruitment of different plaque SMCs, we mapped their clonal architecture in aggregation...... in the cap and heterogeneous ACTA2– SMCs in the plaque interior, including chondrocyte-like cells and cells with intracellular lipid and crystalline material. Fibrous cap SMCs were invariably arranged in endothelium-aligned clonal sheets, confirming results in the aggregation chimeras. Analysis of the clonal...

  2. HIV Prevention

    Centers for Disease Control (CDC) Podcasts

    2012-02-01

    Dr. Kevin Fenton, Director of CDC’s National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, talks about steps people can take to protect their health from HIV.  Created: 2/1/2012 by National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (NCHHSTP).   Date Released: 2/1/2012.

  3. Directional growth of a clonal bromeliad species in response to spatial habitat heterogeneity

    NARCIS (Netherlands)

    Sampaio, M.C.; Araujo, T.F.; Scarano, F.R.; Stuefer, J.F.

    2004-01-01

    Habitat selection by directional growth of plants has previously been investigated but field evidence for this phenomenon is extremely scarce. In this study we demonstrate directional clonal growth in Aechmea nudicaulis, a monocarpic, perennial bromeliad native to spatially heterogeneous sandy

  4. Screening of clonal chromosome aberrations present in A-bomb survivors by FISH method

    International Nuclear Information System (INIS)

    Nakano, Mimako; Kodama, Yoshiaki; Ito, Masahiro; Otaki, Kazuo; Nakamura, Nori

    1997-01-01

    Significance of FISH method for detection of clonal chromosome aberration was reviewed. A clonal chromosome aberration is derived from one abnormal cell clone and gives the influence on the frequency of the aberration. As well, the size and frequency of the aberration give an important information concerning lymphocyte kinetics. FISH method is meaningful for detection of the clonal aberration. Fifteen kinds of clonal aberrations were detected in A-bomb survivors, of which 10 were specifically detected by the method, indicating that its detection rate was 2-3 time as high as the ordinary method. The results were those on the DNA probe on no.1, no.2 and no.3 chromosomes, which consisting of about 23% of the genome. (K.H.)

  5. Implementation of Microfluidic Chip Electrophoresis for the Detection of B-cell Clonality

    Directory of Open Access Journals (Sweden)

    Vazan M

    2016-04-01

    Full Text Available Introduction: A clonal population of B-cells is defined as those cells arising from the mitotic division of a single somatic cell with the same rearrangement of immunoglobulin genes. This gives rise to DNA markers for each individual lymphoid cell and its progenies and enables us to study clonality in different B-cell malignancies using multiplex polymerase chain reaction - PCR. The BIOMED-2 protocol has been implemented for clonality detection in lymphoproliferative diseases and exploits multiplex PCR reaction, subsequently analyzed by heteroduplex analysis (HDA using polyacrylamide gel electrophoresis (PAGE. With the advent of miniaturization and automation of molecular biology methods, lab-on-chip technologies were developed and replace partially the conventional approaches. We tested device for microfluidic chip, which is used for B-cells clonality analysis, using a PCR reaction for three subregions called frameworks (FR of the immunoglobulin heavy locus (IGH gene.

  6. Clonal diversity analysis using SNP microarray: a new prognostic tool for chronic lymphocytic leukemia.

    Science.gov (United States)

    Zhang, Linsheng; Znoyko, Iya; Costa, Luciano J; Conlin, Laura K; Daber, Robert D; Self, Sally E; Wolff, Daynna J

    2011-12-01

    Chronic lymphocytic leukemia (CLL) is a clinically heterogeneous disease. The methods currently used for monitoring CLL and determining conditions for treatment are limited in their ability to predict disease progression, patient survival, and response to therapy. Although clonal diversity and the acquisition of new chromosomal abnormalities during the disease course (clonal evolution) have been associated with disease progression, their prognostic potential has been underappreciated because cytogenetic and fluorescence in situ hybridization (FISH) studies have a restricted ability to detect genomic abnormalities and clonal evolution. We hypothesized that whole genome analysis using high resolution single nucleotide polymorphism (SNP) microarrays would be useful to detect diversity and infer clonal evolution to offer prognostic information. In this study, we used the Infinium Omni1 BeadChip (Illumina, San Diego, CA) array for the analysis of genetic variation and percent mosaicism in 25 non-selected CLL patients to explore the prognostic value of the assessment of clonal diversity in patients with CLL. We calculated the percentage of mosaicism for each abnormality by applying a mathematical algorithm to the genotype frequency data and by manual determination using the Simulated DNA Copy Number (SiDCoN) tool, which was developed from a computer model of mosaicism. At least one genetic abnormality was identified in each case, and the SNP data was 98% concordant with FISH results. Clonal diversity, defined as the presence of two or more genetic abnormalities with differing percentages of mosaicism, was observed in 12 patients (48%), and the diversity correlated with the disease stage. Clonal diversity was present in most cases of advanced disease (Rai stages III and IV) or those with previous treatment, whereas 9 of 13 patients without detected clonal diversity were asymptomatic or clinically stable. In conclusion, SNP microarray studies with simultaneous evaluation

  7. Immune defence against HIV-1 infection in HIV-1-exposed seronegative persons.

    Science.gov (United States)

    Schmechel, S C; Russell, N; Hladik, F; Lang, J; Wilson, A; Ha, R; Desbien, A; McElrath, M J

    2001-11-01

    Rare individuals who are repeatedly exposed to HIV-1 through unprotected sexual contact fail to acquire HIV-1 infection. These persons represent a unique study population to evaluate mechanisms by which HIV-1 replication is either prevented or controlled. We followed longitudinally a group of healthy HIV-1 seronegative persons each reporting repeated high-risk sexual activities with their HIV-1-infected partner at enrollment. The volunteers were primarily (90%) male homosexuals, maintaining high risk activities with their known infected partner (45%) or multiple other partners (61%). We evaluated the quantity and specificity of HIV-1-specific T cells in 31 exposed seronegatives (ES) using a IFN-gamma ELISPOT assay to enumerate T cells recognizing epitopes within HIV-1 Env, Gag, Pol and Nef. PBMC from only three of the 31 volunteers demonstrated ex vivo HIV-1-specific IFN-gamma secretion, in contrast to nearly 30% exhibiting cytolytic responses in previous studies. These findings suggest that if T cell responses in ES are induced by HIV-1 exposure, the frequency is at low levels in most of them, and below the level of detection using the ELISPOT assay. Alternative approaches to improve the sensitivity of detection may include use of dendritic cells as antigen-presenting cells in the ex vivo assay and more careful definition of the risk behavior and extent of HIV-1 exposure in conjunction with the evaluation of T cell responses.

  8. Clonal diversity and fine-scale genetic structure in a high andean treeline population

    Czech Academy of Sciences Publication Activity Database

    Peng, Y.; Macek, P.; Macková, Jana; Romoleroux, K.; Hensen, I.

    2015-01-01

    Roč. 47, č. 1 (2015), s. 59-65 ISSN 0006-3606 Grant - others:GA AV ČR(CZ) IAA601110702; GA MŠk(CZ) LM2010009 Program:IA Institutional support: RVO:60077344 Keywords : AFLP * clonal diversity * clonal propagation * fine-scale genetic structure * Polylepis reticulata * treeline Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 1.944, year: 2015

  9. Clonal Evaluation of Prostate Cancer by ERG/SPINK1 Status to Improve Prognosis Prediction

    Science.gov (United States)

    2017-12-01

    19 NIH Exploiting drivers of androgen receptor signaling negative prostate cancer for precision medicine Goal(s): Identify novel potential drivers...AWARD NUMBER: W81XWH-14-1-0466 TITLE: Clonal evaluation of prostate cancer by ERG/SPINK1 status to improve prognosis prediction PRINCIPAL...Sept 2017 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Clonal Evaluation of Prostate Cancer by ERG/SPINK1 Status to Improve Prognosis Prediction 5b

  10. Mutational Profiling Can Establish Clonal or Independent Origin in Synchronous Bilateral Breast and Other Tumors.

    Directory of Open Access Journals (Sweden)

    Lei Bao

    Full Text Available Synchronous tumors can be independent primary tumors or a primary-metastatic (clonal pair, which may have clinical implications. Mutational profiling of tumor DNA is increasingly common in the clinic. We investigated whether mutational profiling can distinguish independent from clonal tumors in breast and other cancers, using a carefully defined test based on the Clonal Likelihood Score (CLS = 100 x # shared high confidence (HC mutations/ # total HC mutations.Statistical properties of a formal test using the CLS were investigated. A high CLS is evidence in favor of clonality; the test is implemented as a one-sided binomial test of proportions. Test parameters were empirically determined using 16,422 independent breast tumor pairs and 15 primary-metastatic tumor pairs from 10 cancer types using The Cancer Genome Atlas.We validated performance of the test with its established parameters, using five published data sets comprising 15,758 known independent tumor pairs (maximum CLS = 4.1%, minimum p-value = 0.48 and 283 known tumor clonal pairs (minimum CLS 13%, maximum p-value 0.99, supporting independence. A plausible molecular mechanism for the shift from hormone receptor positive to triple negative was identified in the clonal pair.We have developed the statistical properties of a carefully defined Clonal Likelihood Score test from mutational profiling of tumor DNA. Under identified conditions, the test appears to reliably distinguish between synchronous tumors of clonal and of independent origin in several cancer types. This approach may have scientific and clinical utility.

  11. Detectable clonal mosaicism and its relationship to aging and cancer

    Science.gov (United States)

    Jacobs, Kevin B; Yeager, Meredith; Zhou, Weiyin; Wacholder, Sholom; Wang, Zhaoming; Rodriguez-Santiago, Benjamin; Hutchinson, Amy; Deng, Xiang; Liu, Chenwei; Horner, Marie-Josephe; Cullen, Michael; Epstein, Caroline G; Burdett, Laurie; Dean, Michael C; Chatterjee, Nilanjan; Sampson, Joshua; Chung, Charles C; Kovaks, Joseph; Gapstur, Susan M; Stevens, Victoria L; Teras, Lauren T; Gaudet, Mia M; Albanes, Demetrius; Weinstein, Stephanie J; Virtamo, Jarmo; Taylor, Philip R; Freedman, Neal D; Abnet, Christian C; Goldstein, Alisa M; Hu, Nan; Yu, Kai; Yuan, Jian-Min; Liao, Linda; Ding, Ti; Qiao, You-Lin; Gao, Yu-Tang; Koh, Woon-Puay; Xiang, Yong-Bing; Tang, Ze-Zhong; Fan, Jin-Hu; Aldrich, Melinda C; Amos, Christopher; Blot, William J; Bock, Cathryn H; Gillanders, Elizabeth M; Harris, Curtis C; Haiman, Christopher A; Henderson, Brian E; Kolonel, Laurence N; Le Marchand, Loic; McNeill, Lorna H; Rybicki, Benjamin A; Schwartz, Ann G; Signorello, Lisa B; Spitz, Margaret R; Wiencke, John K; Wrensch, Margaret; Wu, Xifeng; Zanetti, Krista A; Ziegler, Regina G; Figueroa, Jonine D; Garcia-Closas, Montserrat; Malats, Nuria; Marenne, Gaelle; Prokunina-Olsson, Ludmila; Baris, Dalsu; Schwenn, Molly; Johnson, Alison; Landi, Maria Teresa; Goldin, Lynn; Consonni, Dario; Bertazzi, Pier Alberto; Rotunno, Melissa; Rajaraman, Preetha; Andersson, Ulrika; Freeman, Laura E Beane; Berg, Christine D; Buring, Julie E; Butler, Mary A; Carreon, Tania; Feychting, Maria; Ahlbom, Anders; Gaziano, J Michael; Giles, Graham G; Hallmans, Goran; Hankinson, Susan E; Hartge, Patricia; Henriksson, Roger; Inskip, Peter D; Johansen, Christoffer; Landgren, Annelie; McKean-Cowdin, Roberta; Michaud, Dominique S; Melin, Beatrice S; Peters, Ulrike; Ruder, Avima M; Sesso, Howard D; Severi, Gianluca; Shu, Xiao-Ou; Visvanathan, Kala; White, Emily; Wolk, Alicja; Zeleniuch-Jacquotte, Anne; Zheng, Wei; Silverman, Debra T; Kogevinas, Manolis; Gonzalez, Juan R; Villa, Olaya; Li, Donghui; Duell, Eric J; Risch, Harvey A; Olson, Sara H; Kooperberg, Charles; Wolpin, Brian M; Jiao, Li; Hassan, Manal; Wheeler, William; Arslan, Alan A; Bas Bueno-de-Mesquita, H; Fuchs, Charles S; Gallinger, Steven; Gross, Myron D; Holly, Elizabeth A; Klein, Alison P; LaCroix, Andrea; Mandelson, Margaret T; Petersen, Gloria; Boutron-Ruault, Marie-Christine; Bracci, Paige M; Canzian, Federico; Chang, Kenneth; Cotterchio, Michelle; Giovannucci, Edward L; Goggins, Michael; Bolton, Judith A Hoffman; Jenab, Mazda; Khaw, Kay-Tee; Krogh, Vittorio; Kurtz, Robert C; McWilliams, Robert R; Mendelsohn, Julie B; Rabe, Kari G; Riboli, Elio; Tjønneland, Anne; Tobias, Geoffrey S; Trichopoulos, Dimitrios; Elena, Joanne W; Yu, Herbert; Amundadottir, Laufey; Stolzenberg-Solomon, Rachael Z; Kraft, Peter; Schumacher, Fredrick; Stram, Daniel; Savage, Sharon A; Mirabello, Lisa; Andrulis, Irene L; Wunder, Jay S; García, Ana Patiño; Sierrasesúmaga, Luis; Barkauskas, Donald A; Gorlick, Richard G; Purdue, Mark; Chow, Wong-Ho; Moore, Lee E; Schwartz, Kendra L; Davis, Faith G; Hsing, Ann W; Berndt, Sonja I; Black, Amanda; Wentzensen, Nicolas; Brinton, Louise A; Lissowska, Jolanta; Peplonska, Beata; McGlynn, Katherine A; Cook, Michael B; Graubard, Barry I; Kratz, Christian P; Greene, Mark H; Erickson, Ralph L; Hunter, David J; Thomas, Gilles; Hoover, Robert N; Real, Francisco X; Fraumeni, Joseph F; Caporaso, Neil E; Tucker, Margaret; Rothman, Nathaniel; Pérez-Jurado, Luis A; Chanock, Stephen J

    2012-01-01

    In an analysis of 31,717 cancer cases and 26,136 cancer-free controls drawn from 13 genome-wide association studies (GWAS), we observed large chromosomal abnormalities in a subset of clones from DNA obtained from blood or buccal samples. Mosaic chromosomal abnormalities, either aneuploidy or copy-neutral loss of heterozygosity, of size >2 Mb were observed in autosomes of 517 individuals (0.89%) with abnormal cell proportions between 7% and 95%. In cancer-free individuals, the frequency increased with age; 0.23% under 50 and 1.91% between 75 and 79 (p=4.8×10−8). Mosaic abnormalities were more frequent in individuals with solid-tumors (0.97% versus 0.74% in cancer-free individuals, OR=1.25, p=0.016), with a stronger association for cases who had DNA collected prior to diagnosis or treatment (OR=1.45, p=0.0005). Detectable clonal mosaicism was common in individuals for whom DNA was collected at least one year prior to diagnosis of leukemia compared to cancer-free individuals (OR=35.4, p=3.8×10−11). These findings underscore the importance of the role and time-dependent nature of somatic events in the etiology of cancer and other late-onset diseases. PMID:22561519

  12. Clonal cell populations unresponsive to radiosensitization induced by telomerase inhibition

    International Nuclear Information System (INIS)

    Ju, Yeun-Jin; Shin, Hyun-Jin; Park, Jeong-Eun; Juhn, Kyoung-Mi; Woo, Seon Rang; Kim, Hee-Young; Han, Young-Hoon; Hwang, Sang-Gu; Hong, Sung-Hee; Kang, Chang-Mo; Yoo, Young-Do; Park, Won-Bong; Cho, Myung-Haing; Park, Gil Hong; Lee, Kee-Ho

    2010-01-01

    Research highlights: → In our present manuscript, we have clearly showed an interesting but problematic obstacle of a radiosensitization strategy based on telomerase inhibition by showing that: Clonal population unresponsive to this radiosensitization occasionally arise. → The telomere length of unsensitized clones was reduced, as was that of most sensitized clones. → The unsensitized clones did not show chromosome end fusion which was noted in all sensitized clones. → P53 status is not associated with the occurrence of unsensitized clone. → Telomere end capping in unsensitized clone is operative even under telomerase deficiency. -- Abstract: A combination of a radiotherapeutic regimen with telomerase inhibition is valuable when tumor cells are to be sensitized to radiation. Here, we describe cell clones unresponsive to radiosensitization after telomere shortening. After extensive division of individual transformed clones of mTERC -/- cells, about 22% of clones were unresponsive to radiosensitization even though telomerase action was inhibited. The telomere lengths of unsensitized mTERC -/- clones were reduced, as were those of most sensitized clones. However, the unsensitized clones did not exhibit chromosomal end-to-end fusion to the extent noted in all sensitized clones. Thus, a defense mechanism preventing telomere erosion is operative even when telomeres become shorter under conditions of telomerase deficiency, and results in unresponsiveness to the radiosensitization generally mediated by telomere shortening.

  13. Clonal dominance among T-lymphocyte infiltrates in arthritis

    International Nuclear Information System (INIS)

    Stamenkovic, I.; Stegagno, M.; Wright, K.A.; Krane, S.M.; Amento, E.P.; Colvin, R.B.; Duquesnoy, R.J.; Kurnick, J.T.

    1988-01-01

    Synovial membranes in patients with rheumatoid arthritis as well as other types of chronic destructive inflammatory arthritis contain infiltrates of activated T lymphocytes that probably contribute to the pathogenesis of the disease. In an effort to elucidate the nature of these infiltrates, interleukin 2 (IL-2)-responsive T lymphocytes were grown out of synovial fragments from 14 patients undergoing surgery for advanced destructive inflammatory joint disease. Eleven of the samples examined were from patients with classical rheumatoid arthritis, while three others were obtained from individuals with clinical osteoarthritis. Southern blot analysis of T-cell receptor (TCR) β-chain genes in 13 of 14 cultures showed distinct rearrangements, indicating that each culture was characterized by the predominance of a limited number of clones. T-cell populations from peripheral blood stimulated with a variety of activators and expanded with IL-2 did not demonstrate evidence of similar clonality in long-term culture. These results suggest that a limited number of activated T-cell clones predominate at the site of tissue injury in rheumatoid synovial membranes as well as in other types of destructive inflammatory joint disease. Further characterization of these T-cell clones may aid our understanding of the pathogenesis of these rheumatic disorders

  14. Clonal dominance and transplantation dynamics in hematopoietic stem cell compartments.

    Directory of Open Access Journals (Sweden)

    Peter Ashcroft

    2017-10-01

    Full Text Available Hematopoietic stem cells in mammals are known to reside mostly in the bone marrow, but also transitively passage in small numbers in the blood. Experimental findings have suggested that they exist in a dynamic equilibrium, continuously migrating between these two compartments. Here we construct an individual-based mathematical model of this process, which is parametrised using existing empirical findings from mice. This approach allows us to quantify the amount of migration between the bone marrow niches and the peripheral blood. We use this model to investigate clonal hematopoiesis, which is a significant risk factor for hematologic cancers. We also analyse the engraftment of donor stem cells into non-conditioned and conditioned hosts, quantifying the impact of different treatment scenarios. The simplicity of the model permits a thorough mathematical analysis, providing deeper insights into the dynamics of both the model and of the real-world system. We predict the time taken for mutant clones to expand within a host, as well as chimerism levels that can be expected following transplantation therapy, and the probability that a preconditioned host is reconstituted by donor cells.

  15. High-throughput monitoring of integration site clonality in preclinical and clinical gene therapy studies

    Directory of Open Access Journals (Sweden)

    Frank A Giordano

    Full Text Available Gene transfer to hematopoietic stem cells with integrating vectors not only allows sustained correction of monogenic diseases but also tracking of individual clones in vivo. Quantitative real-time PCR (qPCR has been shown to be an accurate method to quantify individual stem cell clones, yet due to frequently limited amounts of target material (especially in clinical studies, it is not useful for large-scale analyses. To explore whether vector integration site (IS recovery techniques may be suitable to describe clonal contributions if combined with next-generation sequencing techniques, we designed artificial ISs of different sizes which were mixed to simulate defined clonal situations in clinical settings. We subjected all mixes to either linear amplification–mediated PCR (LAM-PCR or nonrestrictive LAM-PCR (nrLAM-PCR, both combined with 454 sequencing. We showed that nrLAM-PCR/454-detected clonality allows estimating qPCR-detected clonality in vitro. We then followed the kinetics of two clones detected in a patient enrolled in a clinical gene therapy trial using both, nrLAM-PCR/454 and qPCR and also saw nrLAM-PCR/454 to correlate to qPCR-measured clonal contributions. The method presented here displays a feasible high-throughput strategy to monitor clonality in clinical gene therapy trials is at hand.

  16. Plant Clonal Integration Mediates the Horizontal Redistribution of Soil Resources, Benefiting Neighboring Plants.

    Science.gov (United States)

    Ye, Xue-Hua; Zhang, Ya-Lin; Liu, Zhi-Lan; Gao, Shu-Qin; Song, Yao-Bin; Liu, Feng-Hong; Dong, Ming

    2016-01-01

    Resources such as water taken up by plants can be released into soils through hydraulic redistribution and can also be translocated by clonal integration within a plant clonal network. We hypothesized that the resources from one (donor) microsite could be translocated within a clonal network, released into different (recipient) microsites and subsequently used by neighbor plants in the recipient microsite. To test these hypotheses, we conducted two experiments in which connected and disconnected ramet pairs of Potentilla anserina were grown under both homogeneous and heterogeneous water regimes, with seedlings of Artemisia ordosica as neighbors. The isotopes [(15)N] and deuterium were used to trace the translocation of nitrogen and water, respectively, within the clonal network. The water and nitrogen taken up by P. anserina ramets in the donor microsite were translocated into the connected ramets in the recipient microsites. Most notably, portions of the translocated water and nitrogen were released into the recipient microsite and were used by the neighboring A. ordosica, which increased growth of the neighboring A. ordosica significantly. Therefore, our hypotheses were supported, and plant clonal integration mediated the horizontal hydraulic redistribution of resources, thus benefiting neighboring plants. Such a plant clonal integration-mediated resource redistribution in horizontal space may have substantial effects on the interspecific relations and composition of the community and consequently on ecosystem processes.

  17. Plant clonal integration mediates the horizontal redistribution of soil resources, benefiting neighbouring plants

    Directory of Open Access Journals (Sweden)

    Xuehua eYe

    2016-02-01

    Full Text Available Resources such as water taken up by plants can be released into soils through hydraulic redistribution and can also be translocated by clonal integration within a plant clonal network. We hypothesized that the resources from one (donor microsite could be translocated within a clonal network, released into different (recipient microsites and subsequently used by neighbour plants in the recipient microsite. To test these hypotheses, we conducted two experiments in which connected and disconnected ramet pairs of Potentilla anserina were grown under both homogeneous and heterogeneous water regimes, with seedlings of Artemisia ordosica as neighbours. The isotopes [15N] and deuterium were used to trace the translocation of nitrogen and water, respectively, within the clonal network. The water and nitrogen taken up by P. anserina ramets in the donor microsite were translocated into the connected ramets in the recipient microsites. Most notably, portions of the translocated water and nitrogen were released into the recipient microsite and were used by the neighbouring A. ordosica, which increased growth of the neighbouring A. ordosica significantly. Therefore, our hypotheses were supported, and plant clonal integration mediated the horizontal hydraulic redistribution of resources, thus benefiting neighbouring plants. Such a plant clonal integration-mediated resource redistribution in horizontal space may have substantial effects on the interspecific relations and composition of the community and consequently on ecosystem processes.

  18. Applied longitudinal analysis

    CERN Document Server

    Fitzmaurice, Garrett M; Ware, James H

    2012-01-01

    Praise for the First Edition "". . . [this book] should be on the shelf of everyone interested in . . . longitudinal data analysis.""-Journal of the American Statistical Association   Features newly developed topics and applications of the analysis of longitudinal data Applied Longitudinal Analysis, Second Edition presents modern methods for analyzing data from longitudinal studies and now features the latest state-of-the-art techniques. The book emphasizes practical, rather than theoretical, aspects of methods for the analysis of diverse types of lo

  19. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

    OpenAIRE

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

    2016-01-01

    ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST...

  20. HIV/AIDS Coinfection

    Science.gov (United States)

    ... Coinfection Hepatitis C Coinfection HIV/AIDS Coinfection HIV/AIDS Coinfection Approximately 10% of the HIV-infected population ... Control and Prevention website to learn about HIV/AIDS and Viral Hepatitis guidelines and resources. Home About ...

  1. HIV/AIDS

    Science.gov (United States)

    HIV stands for human immunodeficiency virus. It harms your immune system by destroying the white blood cells ... It is the final stage of infection with HIV. Not everyone with HIV develops AIDS. HIV most ...

  2. HIV and Immunizations

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content HIV Treatment Home Understanding HIV/AIDS Fact Sheets HIV ... 4 p.m. ET) Send us an email HIV and Immunizations Last Reviewed: February 6, 2018 Key ...

  3. HIV Medication Adherence

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content HIV Treatment Home Understanding HIV/AIDS Fact Sheets HIV ... 4 p.m. ET) Send us an email HIV Medication Adherence Last Reviewed: January 17, 2018 Key ...

  4. HIV and AIDS

    Science.gov (United States)

    ... Staying Safe Videos for Educators Search English Español HIV and AIDS KidsHealth / For Kids / HIV and AIDS ... actually the virus that causes the disease AIDS. HIV Hurts the Immune System People who are HIV ...

  5. HIV Treatment: The Basics

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content HIV Treatment Home Understanding HIV/AIDS Fact Sheets HIV ... 4 p.m. ET) Send us an email HIV Treatment: The Basics Last Reviewed: March 22, 2018 ...

  6. HIV and Pregnancy

    Science.gov (United States)

    ... Management Education & Events Advocacy For Patients About ACOG HIV and Pregnancy Home For Patients Search FAQs HIV ... HIV and Pregnancy FAQ113, July 2017 PDF Format HIV and Pregnancy Pregnancy What is human immunodeficiency virus ( ...

  7. HIV and Cardiovascular Disease

    Science.gov (United States)

    ... Select a Language: Fact Sheet 652 HIV and Cardiovascular Disease HIV AND CARDIOVASCULAR DISEASE WHY SHOULD PEOPLE WITH HIV CARE ABOUT CVD? ... OF CVD? WHAT ABOUT CHANGING MEDICATIONS? HIV AND CARDIOVASCULAR DISEASE Cardiovascular disease (CVD) includes a group of problems ...

  8. A Prospective Longitudinal Study on Implant Prosthetic Rehabilitation in Controlled HIV-Positive Patients with 1-Year Follow-Up: The Role of CD4+ Level, Smoking Habits, and Oral Hygiene.

    Science.gov (United States)

    Gherlone, Enrico F; Capparé, Paolo; Tecco, Simona; Polizzi, Elisabetta; Pantaleo, Giuseppe; Gastaldi, Giorgio; Grusovin, Maria Gabriella

    2016-10-01

    A recent study showed that implant-prosthetic rehabilitation in well-controlled HIV patients gave slightly worse results than in an healthy population, and failures were all linked to infection. The aim of this study was to examine the associations between the success of implant-prosthetic treatment and systemic CD4+ level, smoking habits, and oral hygiene. This mono-centric study included HIV patients with a stable disease and good oral hygiene requiring implant rehabilitation. Each patient received at least one dental implant. Prosthesis were delivered after 90 days in the upper jaw and 60 days in the lower jaw. Primary outcome measures were prosthetic failures, implant failures, peri-implant marginal bone level changes, and biological complications (peri-implantitis, pus, pain, paresthesia). The possible association with CD4 count, smoking habits, and oral hygiene was analyzed. Sixty-eight patients received 194 implants, and 66 patients (190 implants) were followed for 1 year. No significant associations were found between CD4+ count, oral hygiene-associated variables, and any of the outcome measures. If compared with nonsmoking/light smoking patients, patients who smoked >10 cigarettes/day suffered a statistically significant greater number of implant failures (p ≤ .005), presented a comparatively higher number of peri-implantitis (p 10 cigarettes/day) demonstrated an increased risk of early implant failure, peri-implantitis, episodes of pus, and self-reported pain. © 2015 Wiley Periodicals, Inc.

  9. HIV/AIDS - Multiple Languages

    Science.gov (United States)

    ... HIV - Newly diagnosed with HIV, part 5 - English MP3 Children and HIV - Newly diagnosed with HIV, part 5 - 简体中文 (Chinese, Simplified (Mandarin dialect)) MP3 Children and HIV - Newly diagnosed with HIV, part ...

  10. Basic HIV/AIDS Statistics

    Science.gov (United States)

    ... HIV Syndicated Content Website Feedback HIV/AIDS Basic Statistics Recommend on Facebook Tweet Share Compartir HIV and ... HIV. Interested in learning more about CDC's HIV statistics? Terms, Definitions, and Calculations Used in CDC HIV ...

  11. Living with HIV

    Science.gov (United States)

    ... Abroad Treatment Basic Statistics Get Tested Find an HIV testing site near you. Enter ZIP code or city Follow HIV/AIDS CDC HIV CDC HIV/AIDS See RSS | ... Syndicated Content Website Feedback HIV/AIDS Living With HIV Language: English (US) Español (Spanish) Recommend on Facebook ...

  12. HIV Risk and Prevention

    Science.gov (United States)

    ... Prevention VIH En Español Get Tested Find an HIV testing site near you. Enter ZIP code or city Follow HIV/AIDS CDC HIV CDC HIV/AIDS See RSS | ... Email Updates on HIV Syndicated Content Website Feedback HIV Risk and Prevention Recommend on Facebook Tweet Share ...

  13. [Lymphocytic Clonal Expansion in Adult Patients with Epstein-Barr Virus-Associated Lymphoproliferative Disease].

    Science.gov (United States)

    Zhong, Feng-Luan; Zhang, Hong-Yu; Zhang, Qian; Feng, Jia; Zhang, Wen-Li; Xu, Lei; Xu, Hai-Chan; Wen, Juan-Juan; Meng, Qing-Xiang

    2017-12-01

    To explore the lymphocytic clonal expansion in adult patients with Epstein-Barr virus-associated lymphoproliferative diseases (EBV+LPD), and to investigate the experimental methods for EBV+LPD cells so as to provide a more objective measure for the diagnosis, classification and prognosis in the early stage of this disease. Peripheral blood samples from 5 patients with EBV+LPD, 4 patients with adult infectious mononucleosis(IM) as negative control and 3 patients with acute NK-cell leukemia(ANKL) as positive control were collected. Prior to immunochemotherapy, viral loads and clonality were analysed by flow cytometry (FCM), T cell receptor gene rearrangement (TCR) was detected by real-time polymerase chain reaction (RT-PCR), and diversity of EB virus terminal repeat (EBV-TR) was detected by Southern blot. FCM showed only 1 case with clonal TCRVβ in 5 patients with EBV+LPD, TCR clonal expansion could be detected both in patients with IM(4 of 4) and 4 patients with EBV+LPD(4 of 5), Out of patients with EBV+LPD, 1 patient displayed a monoclonal band and 2 patients showed oligoclonal bands when detecting EBV-TR by southen blot. Detecting the diversity of EBV-TR by Southern blot may be the most objective way to reflex clonal transformation of EBV+LPD, which is of great benefit to the diagnosis, classification and prognosis in the early stage of this disease.

  14. Emergence of clonal hematopoiesis in the majority of patients with acquired aplastic anemia.

    Science.gov (United States)

    Babushok, Daria V; Perdigones, Nieves; Perin, Juan C; Olson, Timothy S; Ye, Wenda; Roth, Jacquelyn J; Lind, Curt; Cattier, Carine; Li, Yimei; Hartung, Helge; Paessler, Michele E; Frank, Dale M; Xie, Hongbo M; Cross, Shanna; Cockroft, Joshua D; Podsakoff, Gregory M; Monos, Dimitrios; Biegel, Jaclyn A; Mason, Philip J; Bessler, Monica

    2015-04-01

    Acquired aplastic anemia (aAA) is a nonmalignant disease caused by autoimmune destruction of early hematopoietic cells. Clonal hematopoiesis is a late complication, seen in 20-25% of older patients. We hypothesized that clonal hematopoiesis in aAA is a more general phenomenon, which can arise early in disease, even in younger patients. To evaluate clonal hematopoiesis in aAA, we used comparative whole exome sequencing of paired bone marrow and skin samples in 22 patients. We found somatic mutations in 16 patients (72.7%) with a median disease duration of 1 year; of these, 12 (66.7%) were patients with pediatric-onset aAA. Fifty-eight mutations in 51 unique genes were found primarily in pathways of immunity and transcriptional regulation. Most frequently mutated was PIGA, with seven mutations. Only two mutations were in genes recurrently mutated in myelodysplastic syndrome. Two patients had oligoclonal loss of the HLA alleles, linking immune escape to clone emergence. Two patients had activating mutations in key signaling pathways (STAT5B (p.N642H) and CAMK2G (p.T306M)). Our results suggest that clonal hematopoiesis in aAA is common, with two mechanisms emerging-immune escape and increased proliferation. Our findings expand conceptual understanding of this nonneoplastic blood disorder. Future prospective studies of clonal hematopoiesis in aAA will be critical for understanding outcomes and for designing personalized treatment strategies. Copyright © 2015 Elsevier Inc. All rights reserved.

  15. HIV-1-Specific IgA Monoclonal Antibodies from an HIV-1 Vaccinee Mediate Galactosylceramide Blocking and Phagocytosis

    Science.gov (United States)

    2018-01-01

    ABSTRACT Vaccine-elicited humoral immune responses comprise an array of antibody forms and specificities, with only a fraction contributing to protective host immunity. Elucidation of antibody effector functions responsible for protective immunity against human immunodeficiency virus type 1 (HIV-1) acquisition is a major goal for the HIV-1 vaccine field. Immunoglobulin A (IgA) is an important part of the host defense against pathogens; however, little is known about the role of vaccine-elicited IgA and its capacity to mediate antiviral functions. To identify the antiviral functions of HIV-1-specific IgA elicited by vaccination, we cloned HIV-1 envelope-specific IgA monoclonal antibodies (MAbs) by memory B cell cultures from peripheral blood mononuclear cells from an RV144 vaccinee and produced two IgA clonal cell lines (HG129 and HG130) producing native, nonrecombinant IgA MAbs. The HG129 and HG130 MAbs mediated phagocytosis by monocytes, and HG129 blocked HIV-1 Env glycoprotein binding to galactosylceramide, an alternative HIV-1 receptor. These findings elucidate potential antiviral functions of vaccine-elicited HIV-1 envelope-specific IgA that may act to block HIV-1 acquisition at the portal of entry by preventing HIV-1 binding to galactosylceramide and mediating antibody Fc receptor-mediated virion phagocytosis. Furthermore, these findings highlight the complex and diverse interactions of vaccine-elicited IgA with pathogens that depend on IgA fine specificity and form (e.g., multimeric or monomeric) in the systemic circulation and mucosal compartments. IMPORTANCE Host-pathogen interactions in vivo involve numerous immune mechanisms that can lead to pathogen clearance. Understanding the nature of antiviral immune mechanisms can inform the design of efficacious HIV-1 vaccine strategies. Evidence suggests that both neutralizing and nonneutralizing antibodies can mediate some protection against HIV in animal models. Although numerous studies have characterized the

  16. Variation of functional clonal traits along elevation in two fern species

    International Nuclear Information System (INIS)

    Song, Y.B.; Chen, L.Y.; Xiong, W.

    2015-01-01

    Phenotypical plasticity is generally considered among adaptive strategies by which plants can cope with environmental variation in space and time. Although much is known about plasticity in seed plants in terms of functional clonal traits while little is known about ferns. Variation of functional clonal traits of two ferns Dicranopteris dichotoma and Diplopterygium glaucum among plots differing in elevation in a subtropical evergreen broad-leaved forest in southern China was investigated. Along with elevation increasing the two fern species showed similar variation pattern of functional clonal traits: stable spacer length, increasing specific spacer length and decreasing spacer weight per ramet and specific spacer weight. The two ferns species had similar variation pattern of ramet performance traits but different variation pattern of ramet population properties. These results suggest an evolutionary trade-off between functions of foraging for and storing of resources in the two ferns, with a functional preference for the foraging in response to environmental change. (author)

  17. A comparison of two measures of HIV diversity in multi-assay algorithms for HIV incidence estimation.

    Directory of Open Access Journals (Sweden)

    Matthew M Cousins

    Full Text Available Multi-assay algorithms (MAAs can be used to estimate HIV incidence in cross-sectional surveys. We compared the performance of two MAAs that use HIV diversity as one of four biomarkers for analysis of HIV incidence.Both MAAs included two serologic assays (LAg-Avidity assay and BioRad-Avidity assay, HIV viral load, and an HIV diversity assay. HIV diversity was quantified using either a high resolution melting (HRM diversity assay that does not require HIV sequencing (HRM score for a 239 base pair env region or sequence ambiguity (the percentage of ambiguous bases in a 1,302 base pair pol region. Samples were classified as MAA positive (likely from individuals with recent HIV infection if they met the criteria for all of the assays in the MAA. The following performance characteristics were assessed: (1 the proportion of samples classified as MAA positive as a function of duration of infection, (2 the mean window period, (3 the shadow (the time period before sample collection that is being assessed by the MAA, and (4 the accuracy of cross-sectional incidence estimates for three cohort studies.The proportion of samples classified as MAA positive as a function of duration of infection was nearly identical for the two MAAs. The mean window period was 141 days for the HRM-based MAA and 131 days for the sequence ambiguity-based MAA. The shadows for both MAAs were <1 year. Both MAAs provided cross-sectional HIV incidence estimates that were very similar to longitudinal incidence estimates based on HIV seroconversion.MAAs that include the LAg-Avidity assay, the BioRad-Avidity assay, HIV viral load, and HIV diversity can provide accurate HIV incidence estimates. Sequence ambiguity measures obtained using a commercially-available HIV genotyping system can be used as an alternative to HRM scores in MAAs for cross-sectional HIV incidence estimation.

  18. A Comparison of Two Measures of HIV Diversity in Multi-Assay Algorithms for HIV Incidence Estimation

    Science.gov (United States)

    Cousins, Matthew M.; Konikoff, Jacob; Sabin, Devin; Khaki, Leila; Longosz, Andrew F.; Laeyendecker, Oliver; Celum, Connie; Buchbinder, Susan P.; Seage, George R.; Kirk, Gregory D.; Moore, Richard D.; Mehta, Shruti H.; Margolick, Joseph B.; Brown, Joelle; Mayer, Kenneth H.; Kobin, Beryl A.; Wheeler, Darrell; Justman, Jessica E.; Hodder, Sally L.; Quinn, Thomas C.; Brookmeyer, Ron; Eshleman, Susan H.

    2014-01-01

    Background Multi-assay algorithms (MAAs) can be used to estimate HIV incidence in cross-sectional surveys. We compared the performance of two MAAs that use HIV diversity as one of four biomarkers for analysis of HIV incidence. Methods Both MAAs included two serologic assays (LAg-Avidity assay and BioRad-Avidity assay), HIV viral load, and an HIV diversity assay. HIV diversity was quantified using either a high resolution melting (HRM) diversity assay that does not require HIV sequencing (HRM score for a 239 base pair env region) or sequence ambiguity (the percentage of ambiguous bases in a 1,302 base pair pol region). Samples were classified as MAA positive (likely from individuals with recent HIV infection) if they met the criteria for all of the assays in the MAA. The following performance characteristics were assessed: (1) the proportion of samples classified as MAA positive as a function of duration of infection, (2) the mean window period, (3) the shadow (the time period before sample collection that is being assessed by the MAA), and (4) the accuracy of cross-sectional incidence estimates for three cohort studies. Results The proportion of samples classified as MAA positive as a function of duration of infection was nearly identical for the two MAAs. The mean window period was 141 days for the HRM-based MAA and 131 days for the sequence ambiguity-based MAA. The shadows for both MAAs were cross-sectional HIV incidence estimates that were very similar to longitudinal incidence estimates based on HIV seroconversion. Conclusions MAAs that include the LAg-Avidity assay, the BioRad-Avidity assay, HIV viral load, and HIV diversity can provide accurate HIV incidence estimates. Sequence ambiguity measures obtained using a commercially-available HIV genotyping system can be used as an alternative to HRM scores in MAAs for cross-sectional HIV incidence estimation. PMID:24968135

  19. Usefullness of IGH/TCR PCR studies in lymphoproliferative disorders with inconclusive clonality by flow cytometry.

    Science.gov (United States)

    Ribera, Jordi; Zamora, Lurdes; Juncà, Jordi; Rodríguez, Inés; Marcé, Silvia; Cabezón, Marta; Millá, Fuensanta

    2013-07-25

    In up to 5-15% of studies of lymphoproliferative disorders (LPD) flow cytometry (FCM) or immunomorphologic methods cannot discriminate malignant from reactive processes. The aim of this work was to determine the usefulness of PCR for solving these diagnostic uncertainties. We analyzed IGH and TCRγ genes by PCR in 106 samples with inconclusive FCM results. A clonal result was registered in 36/106 studies, with a LPD being confirmed in 27 (75%) of these cases. Specifically, 9/9 IGH clonal and 16/25 TCRγ clonal results were finally diagnosed with LPD. Additionally, 2 clonal TCRγ samples with suspicion of undefined LPD were finally diagnosed with T LPD. Although polyclonal results were obtained in 47 of the cases studied (38 IGH and 9 TCRγ), hematologic neoplasms were diagnosed in 4/38 IGH polyclonal and in 1/9 TCRγ polyclonal studies. There were also 14 PCR polyclonal results (4 IGH, 10 TCRγ), albeit non-conclusive. Of these, 2/4 were eventually diagnosed with B-cell lymphoma and 3/10 with T-cell LPD. In 8 IGH samples the results of PCR techniques were non-informative but in 3/8 cases a B lymphoma was finally confirmed. We concluded that PCR is a useful technique to identify LPD when FCM is inconclusive. A PCR clonal B result is indicative of malignancy but IGH polyclonal and non-conclusive results do not exclude lymphoid neoplasms. Interpretation of T-cell clonality should be based on all the available clinical and analytical data. © 2013 Clinical Cytometry Society. Copyright © 2013 Clinical Cytometry Society.

  20. Clonal relatedness between lobular carcinoma in situ and synchronous malignant lesions

    Science.gov (United States)

    2012-01-01

    Introduction Lobular carcinoma in situ (LCIS) has been accepted as a marker of risk for the development of invasive breast cancer, yet modern models of breast carcinogenesis include LCIS as a precursor of low-grade carcinomas. We provide evidence favoring a clonal origin for LCIS and synchronous estrogen receptor-positive malignant lesions of the ductal and lobular phenotype. Methods Patients with prior LCIS undergoing mastectomy were identified preoperatively from 2003 to 2008. Specimens were widely sampled, and frozen blocks were screened for LCIS and co-existing malignant lesions, and were subject to microdissection. Samples from 65 patients were hybridized to the Affymetrix SNP 6.0 array platform. Cases with both an LCIS sample and an associated ductal carcinoma in situ (DCIS) or invasive tumor sample were evaluated for patterns of somatic copy number changes to assess evidence of clonal relatedness. Results LCIS was identified in 44 of the cases, and among these a DCIS and/or invasive lesion was also identified in 21 cases. A total of 17 tumor pairs had adequate DNA/array data for analysis, including nine pairs of LCIS/invasive lobular cancer, four pairs of LCIS/DCIS, and four pairs of LCIS/invasive ductal cancer. Overall, seven pairs (41%) were judged to be clonally related; in five (29%) evidence suggested clonality but was equivocal, and five (29%) were considered independent. Clonal pairs were observed with all matched lesion types and low and high histological grades. We also show anecdotal evidence of clonality between a patient-matched triplet of LCIS, DCIS, and invasive ductal cancer. Conclusion Our results support the role of LCIS as a precursor in the development of both high-grade and low-grade ductal and lobular cancers. PMID:22776144

  1. Intravaginal practices, bacterial vaginosis, and HIV infection in women: individual participant data meta-analysis

    NARCIS (Netherlands)

    Low, Nicola; Chersich, Matthew F.; Schmidlin, Kurt; Egger, Matthias; Francis, Suzanna C.; van de Wijgert, Janneke H. H. M.; Hayes, Richard J.; Baeten, Jared M.; Brown, Joelle; Delany-Moretlwe, Sinead; Kaul, Rupert; McGrath, Nuala; Morrison, Charles; Myer, Landon; Temmerman, Marleen; van der Straten, Ariane; Watson-Jones, Deborah; Zwahlen, Marcel; Hilber, Adriane Martin

    2011-01-01

    Identifying modifiable factors that increase women's vulnerability to HIV is a critical step in developing effective female-initiated prevention interventions. The primary objective of this study was to pool individual participant data from prospective longitudinal studies to investigate the

  2. Intravaginal Practices, Bacterial Vaginosis, and HIV Infection in Women: Individual Participant Data Meta-analysis

    NARCIS (Netherlands)

    Low, N.; Chersich, M.F.; Schmidlin, K.; Egger, M.; Francis, S.C.; van de Wijgert, J.H.H.M.; Hayes, R.J.; Baeten, J.M.; Brown, J.; Delany-Moretlwe, S.; Kaul, R.; McGrath, N.; Morrison, C.; Myer, L.; Temmerman, M.; van Straten, A.; Watson-Jones, D.; Zwahlen, M.; Hilber, A.M.

    2011-01-01

    Background: Identifying modifiable factors that increase women's vulnerability to HIV is a critical step in developing effective female-initiated prevention interventions. The primary objective of this study was to pool individual participant data from prospective longitudinal studies to investigate

  3. PPARγ ligand production is tightly linked to clonal expansion during initiation of adipocyte differentiation

    DEFF Research Database (Denmark)

    Hallenborg, Philip; Petersen, Rasmus Koefoed; Feddersen, Søren

    2014-01-01

    of differentiation. Concomitant with agonist production, murine fibroblasts undergo two rounds of mitosis referred to as mitotic clonal expansion. Here we show that mouse embryonic fibroblasts deficient in either of two cell cycle inhibitors, the transcription factor p53 or its target gene encoding the cyclin...... cycle inhibitory compounds decreased PPAR ligand production in differentiating 3T3-L1 preadipocytes. Furthermore, these inhibitors abolished the release of arachidonic acid induced by the hormonal cocktail initiating adipogenesis. Collectively, our results suggest that murine fibroblasts require clonal...... expansion for PPAR ligand production at the onset of adipocyte differentiation....

  4. Diverse cellular architecture of atherosclerotic plaque derives from clonal expansion of a few medial SMCs

    DEFF Research Database (Denmark)

    Jacobsen, Kevin; Lund, Marie Bek; Shim, Jeong

    2017-01-01

    chimeras of eGFP+Apoe-/- and Apoe-/- mouse embryos and in mice with a mosaic expression of fluorescent proteins in medial SMCs that were rendered atherosclerotic by PCSK9-induced hypercholesterolemia. Fibrous caps in aggregation chimeras were found constructed from large, endothelial-aligned layers...... in the cap and heterogeneous ACTA2- SMCs in the plaque interior, including chondrocyte-like cells and cells with intracellular lipid and crystalline material. Fibrous cap SMCs were invariably arranged in endothelium-aligned clonal sheets, confirming results in the aggregation chimeras. Analysis of the clonal...

  5. HIV prevention intervention to reduce HIV-related stigma: evidence from China.

    Science.gov (United States)

    Li, Li; Liang, Li-Jung; Lin, Chunqing; Wu, Zunyou; Rotheram-Borus, Mary Jane

    2010-01-02

    The National Institute of Mental Health Collaborative HIV/Sexually Transmitted Disease Prevention Trial provided a unique opportunity to test whether, with the community-based diffusion of HIV/sexually transmitted disease prevention information and an elevated understanding of HIV, the level of stigmatizing attitudes toward people living with HIV/AIDS in the community would be reduced. A total of 4510 market workers in Fuzhou, China, participated in the study, and longitudinal analyses included study samples of 3785 participants in the 12-month follow-up and 3716 participants in the 24-month follow-up. We graphically examined the change in HIV-related stigma indicators over time between control and intervention groups using boxplot and kernel density estimation. A logistic regression analysis with proportional odds model was further used to examine the intervention effect on HIV-related stigmatizing attitudes. Compared with no change over time for the control group, the intervention successfully reduced the level of HIV-related stigmatizing attitudes among the target population at the 12-month follow-up, and the effect increased by two-fold (with respect to odds ratios) at the 24-month follow-up. The intervention demonstrated positive attitude changes associated with HIV-related stigma. Our results show the importance of social norms, rather than simply individual behaviors, in developing and implementing stigma reduction campaigns.

  6. A comparison of 454 sequencing and clonal sequencing for the characterization of hepatitis C virus NS3 variants

    NARCIS (Netherlands)

    Ho, Cynthia K. Y.; Welkers, Matthijs R. A.; Thomas, Xiomara V.; Sullivan, James C.; Kieffer, Tara L.; Reesink, Henk W.; Rebers, Sjoerd P. H.; de Jong, Menno D.; Schinkel, Janke; Molenkamp, Richard

    2015-01-01

    We compared 454 amplicon sequencing with clonal sequencing for the characterization of intra-host hepatitis C virus (HCV) NS3 variants. Clonal and 454 sequences were obtained from 12 patients enrolled in a clinical phase I study for telaprevir, an NS3-4a protease inhibitor. Thirty-nine datasets were

  7. Clinical significance of T-cell clonality in mycosis fungoides and other cutaneous T-cell lymphomas

    NARCIS (Netherlands)

    Muche, Joachim Marcus

    2010-01-01

    The purpose of this thesis was to obtain more insight into T-cell clonality in blood of mycosis fungoides (MF) patients. Investigation of the frequency of blood T-cell clonality clearly indicated early dissemination of neoplastic T-cells into skin and blood as a sign of physiological recirculation.

  8. Synergy against drug-resistant HIV-1 with the microbicide antiretrovirals, dapivirine and tenofovir, in combination.

    Science.gov (United States)

    Schader, Susan M; Colby-Germinario, Susan P; Schachter, Jordana R; Xu, Hongtao; Wainberg, Mark A

    2011-08-24

    To evaluate the candidate antiretroviral microbicide compounds, dapivirine (DAP) and tenofovir (TFV), alone and in combination against the transmission of wild-type and nonnucleoside reverse transcriptase inhibitor (NNRTI)-resistant HIV-1 from different subtypes. We determined single-drug efficacy of the RTIs, DAP and TFV, against subtype B and non-B wild-type and NNRTI-resistant HIV-1 in vitro. To assess breadth of activity, compounds were tested alone and in combination against wild-type and NNRTI-resistant subtype C primary HIV-1 isolates and complimentary clonal HIV-1 from subtypes B, C and CRF02_AG to control for viral variation. Early infection was quantified by counting light units emitted from TZM-bl cells less than 48-h postinfection. Combination ratios were based on drug inhibitory concentrations (IC(50)s) and combined effects were determined by calculating combination indices. Both candidate microbicide antiretrovirals demonstrated potent anti-NNRTI-resistant HIV-1 activity in vitro, albeit the combination protected better than the single-drug treatments. Of particular interest, the DAP with TFV combination exhibited synergy (50% combination index, CI(50) = 0.567) against subtype C NNRTI-resistant HIV-1, whereas additivity (CI(50) = 0.987) was observed against the wild-type counterpart from the same patient. The effect was not compounded by the presence of subdominant viral fractions, as experiments using complimentary clonal subtype C wild-type (CI(50) = 0.968) and NNRTI-resistant (CI(50) = 0.672) HIV-1, in lieu of the patient quasispecies, gave similar results. This study supports the notion that antiretroviral drug combinations may retain antiviral activity against some drug-resistant HIV-1 despite subtype classification and quasispecies diversity.

  9. Restoration of longitudinal images.

    Science.gov (United States)

    Hu, Y; Frieden, B R

    1988-01-15

    In this paper, a method of restoring longitudinal images is developed. By using the transfer function for longitudinal objects, and inverse filtering, a longitudinal image may be restored. The Fourier theory and sampling theorems for transverse images cannot be used directly in the longitudinal case. A modification and reasonable approximation are introduced. We have numerically established a necessary relationship between just-resolved longitudinal separation (after inverse filtering), noise level, and the taking conditions of object distance and lens diameter. An empirical formula is also found to well-fit the computed results. This formula may be of use for designing optical systems which are to image longitudinal details, such as in robotics or microscopy.

  10. CD4 cell count and the risk of AIDS or death in HIV-Infected adults on combination antiretroviral therapy with a suppressed viral load: a longitudinal cohort study from COHERE.

    Directory of Open Access Journals (Sweden)

    Jim Young

    Full Text Available Most adults infected with HIV achieve viral suppression within a year of starting combination antiretroviral therapy (cART. It is important to understand the risk of AIDS events or death for patients with a suppressed viral load.Using data from the Collaboration of Observational HIV Epidemiological Research Europe (2010 merger, we assessed the risk of a new AIDS-defining event or death in successfully treated patients. We accumulated episodes of viral suppression for each patient while on cART, each episode beginning with the second of two consecutive plasma viral load measurements 500 copies/µl, the first of two consecutive measurements between 50-500 copies/µl, cART interruption or administrative censoring. We used stratified multivariate Cox models to estimate the association between time updated CD4 cell count and a new AIDS event or death or death alone. 75,336 patients contributed 104,265 suppression episodes and were suppressed while on cART for a median 2.7 years. The mortality rate was 4.8 per 1,000 years of viral suppression. A higher CD4 cell count was always associated with a reduced risk of a new AIDS event or death; with a hazard ratio per 100 cells/µl (95% CI of: 0.35 (0.30-0.40 for counts <200 cells/µl, 0.81 (0.71-0.92 for counts 200 to <350 cells/µl, 0.74 (0.66-0.83 for counts 350 to <500 cells/µl, and 0.96 (0.92-0.99 for counts ≥500 cells/µl. A higher CD4 cell count became even more beneficial over time for patients with CD4 cell counts <200 cells/µl.Despite the low mortality rate, the risk of a new AIDS event or death follows a CD4 cell count gradient in patients with viral suppression. A higher CD4 cell count was associated with the greatest benefit for patients with a CD4 cell count <200 cells/µl but still some slight benefit for those with a CD4 cell count ≥500 cells/µl.

  11. Altered structural brain changes and neurocognitive performance in pediatric HIV

    Directory of Open Access Journals (Sweden)

    Santosh K. Yadav

    2017-01-01

    Full Text Available Pediatric HIV patients often suffer with neurodevelopmental delay and subsequently cognitive impairment. While tissue injury in cortical and subcortical regions in the brain of adult HIV patients has been well reported there is sparse knowledge about these changes in perinatally HIV infected pediatric patients. We analyzed cortical thickness, subcortical volume, structural connectivity, and neurocognitive functions in pediatric HIV patients and compared with those of pediatric healthy controls. With informed consent, 34 perinatally infected pediatric HIV patients and 32 age and gender matched pediatric healthy controls underwent neurocognitive assessment and brain magnetic resonance imaging (MRI on a 3 T clinical scanner. Altered cortical thickness, subcortical volumes, and abnormal neuropsychological test scores were observed in pediatric HIV patients. The structural network connectivity analysis depicted lower connection strengths, lower clustering coefficients, and higher path length in pediatric HIV patients than healthy controls. The network betweenness and network hubs in cortico-limbic regions were distorted in pediatric HIV patients. The findings suggest that altered cortical and subcortical structures and regional brain connectivity in pediatric HIV patients may contribute to deficits in their neurocognitive functions. Further, longitudinal studies are required for better understanding of the effect of HIV pathogenesis on brain structural changes throughout the brain development process under standard ART treatment.

  12. Effectiveness of Psycho-Educational Intervention in HIV Patients? Treatment

    OpenAIRE

    Ribeiro, Clarisse; Sarmento e Castro, Rui; Dinis-Ribeiro, M?rio; Fernandes, Lia

    2015-01-01

    Adherence to Highly Active Antiretroviral Therapy (HAART) is the main prognostic factor associated with HIV disease progression and death. The aim was to evaluate the effectiveness of a psycho-educational program to promote adherence to HAART in HIV patients. A longitudinal study (n=102) over 9 months in an Infectious Diseases Hospital was carried out. Adherence to HAART was measured with standardized scales and values of viral load. Two groups were defined: adherents and non-adherents. In th...

  13. Augmented Cross-Sectional Prevalence Testing for Estimating HIV Incidence

    OpenAIRE

    Wang, R.; Lagakos, S. W.

    2010-01-01

    Estimation of an HIV incidence rate based on a cross-sectional sample of individuals evaluated with both a sensitive and less-sensitive diagnostic test offers important advantages to incidence estimation based on a longitudinal cohort study. However, the reliability of the cross-sectional approach has been called into question because of two major concerns. One is the difficulty in obtaining a reliable external approximation for the mean “window period” between detectability of HIV infection ...

  14. Impact of HIV and AIDS on household food and nutrition security in ...

    African Journals Online (AJOL)

    The impact of HIV/AIDS on household food and nutrition security in Suba district was studied in a quasi longitudinal study. Households with People Living with HIV/AIDS (Index- 25%) and three surrounding households (control- 75%) were considered for the study. Data were collected on demographic characteristics of the ...

  15. Clonally Expanding Thymocytes Having Lineage Capability in Gamma-Ray-Induced Mouse Atrophic Thymus

    International Nuclear Information System (INIS)

    Yamamoto, Takashi; Morita, Shin-ichi; Go, Rieka; Obata, Miki; Katsuragi, Yoshinori; Fujita, Yukari; Maeda, Yoshitaka; Yokoyama, Minesuke; Aoyagi, Yutaka; Ichikawa, Hitoshi; Mishima, Yukio; Kominami, Ryo

    2010-01-01

    Purpose: To characterize, in the setting of γ-ray-induced atrophic thymus, probable prelymphoma cells showing clonal growth and changes in signaling, including DNA damage checkpoint. Methods and Materials: A total of 111 and 45 mouse atrophic thymuses at 40 and 80 days, respectively, after γ-irradiation were analyzed with polymerase chain reaction for D-J rearrangements at the TCRβ locus, flow cytometry for cell cycle, and Western blotting for the activation of DNA damage checkpoints. Results: Limited D-J rearrangement patterns distinct from normal thymus were detected at high frequencies (43 of 111 for 40-day thymus and 21 of 45 for 80-day thymus). Those clonally expanded thymocytes mostly consisted of CD4 + CD8 + double-positive cells, indicating the retention of lineage capability. They exhibited pausing at a late G1 phase of cell cycle progression but did not show the activation of DNA damage checkpoints such as γH2AX, Chk1/2, or p53. Of interest is that 17 of the 52 thymuses showing normal D-J rearrangement patterns at 40 days after irradiation showed allelic loss at the Bcl11b tumor suppressor locus, also indicating clonal expansion. Conclusion: The thymocytes of clonal growth detected resemble human chronic myeloid leukemia in possessing self-renewal and lineage capability, and therefore they can be a candidate of the lymphoma-initiating cells.

  16. In vitro clonal propagation of the neem tree ( Azadirachta indica A ...

    African Journals Online (AJOL)

    In vitro clonal propagation of the neem tree (Azadirachta indica A. Juss.) M Shahin-uz-zaman, M Ashrafuzzaman, MS Haque, LN Luna. Abstract. A study was conducted with root and shoot tip explants of neem to develop an efficient protocol of regeneration. Shoot tips and root tips from 10 - 20 days old seedlings of neem ...

  17. [Chronologic analysis of clonal evolution in acquired aplastic anemia and sMDS].

    Science.gov (United States)

    Yoshizato, Tetsuichi

    2016-04-01

    Acquired aplastic anemia (AA) is a prototype of idiopathic bone marrow failure, which is caused by immune-mediated destruction of hematopoietic progenitors but is also characterized by frequent evolution to clonal myeloid disorders, such as myelodysplastic syndromes or acute myeloid leukemia. However, the chronological behavior of the clonality and its link to myelodysplastic syndrome or acute myeloid leukemia has not been fully explored. To define the clonality and its chronological behavior in AA, we performed targeted sequencing (N=439) in cases with AA. Somatic mutations were detected in 1/3 of our cases. Mutations were most frequently found in DNMT3A, followed by BCOR, PIGA and ASXL1. The prevalence of mutations increased with age. The clone sizes in DNMT3A and ASXL1 were prone to increase, whereas those of BCOR and PIGA were more likely to decrease or remain stable. Mutations in PIGA, BCOR and BCORL1 correlated with a better response to immunosuppressive therapy and more favorable survival. On the other hand, other mutations were associated with worse outcomes. The chronological dynamics of clonality showed marked variability and were not necessarily associated with prognosis.

  18. Epigenetic memory as a basis for intelligent behavior in clonal plants

    Czech Academy of Sciences Publication Activity Database

    Latzel, Vít; González, Alejandra Pilar Rendina; Rosenthal, J.

    2016-01-01

    Roč. 7, AUG 31 (2016), s. 1-7, č. článku 1354. ISSN 1664-462X R&D Projects: GA ČR(CZ) GA14-06802S Institutional support: RVO:67985939 Keywords : epigenetic variability * memory * clonal plant s Subject RIV: EF - Botanics Impact factor: 4.298, year: 2016

  19. Descriptions of new varieties recently distributed from the Citrus Clonal Protection Program

    Science.gov (United States)

    The Citrus Clonal Protection Program (CCPP) is operated through the Department of Plant Pathology and Microbiology at University of California (UC) Riverside and is funded in large part by The California Citrus Research Board (CRB). The CCPP processes citrus propagative material in two phases. First...

  20. Clonal genotype of Geomyces destructans among bats with White Nose Syndrome, New York, USA.

    Science.gov (United States)

    Rajkumar, Sunanda S; Li, Xiaojiang; Rudd, Robert J; Okoniewski, Joseph C; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

    2011-07-01

    The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008-2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

  1. Clonal Genotype of Geomyces destructans among Bats with White Nose Syndrome, New York, USA

    OpenAIRE

    Rajkumar, Sunanda S.; Li, Xiaojiang; Rudd, Robert J.; Okoniewski, Joseph C.; Xu, Jianping; Chaturvedi, Sudha; Chaturvedi, Vishnu

    2011-01-01

    The dispersal mechanism of Geomyces destructans, which causes geomycosis (white nose syndrome) in hibernating bats, remains unknown. Multiple gene genealogic analyses were conducted on 16 fungal isolates from diverse sites in New York State during 2008–2010. The results are consistent with the clonal dispersal of a single G. destructans genotype.

  2. Fatal septicemia linked to transmission of MRSA clonal complex 398 in hospital and nursing home, Denmark

    DEFF Research Database (Denmark)

    Nielsen, Rikke Thoft; Kemp, Michael; Holm, Anette

    2016-01-01

    We describe 2 fatal cases of methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 398 septicemia in persons who had no contact with livestock. Whole-genome sequencing of the isolated MRSA strains strongly suggest that both were of animal origin and that the patients had been infected...

  3. Diverse cellular architecture of atherosclerotic plaque derives from clonal expansion of a few medial SMCs.

    Science.gov (United States)

    Jacobsen, Kevin; Lund, Marie Bek; Shim, Jeong; Gunnersen, Stine; Füchtbauer, Ernst-Martin; Kjolby, Mads; Carramolino, Laura; Bentzon, Jacob Fog

    2017-10-05

    Fibrous cap smooth muscle cells (SMCs) protect atherosclerotic lesions from rupturing and causing thrombosis, while other plaque SMCs may have detrimental roles in plaque development. To gain insight into recruitment of different plaque SMCs, we mapped their clonal architecture in aggregation chimeras of eGFP+Apoe-/- and Apoe-/- mouse embryos and in mice with a mosaic expression of fluorescent proteins in medial SMCs that were rendered atherosclerotic by PCSK9-induced hypercholesterolemia. Fibrous caps in aggregation chimeras were found constructed from large, endothelial-aligned layers of either eGFP+ or nonfluorescent SMCs, indicating substantial clonal expansion of a few cells. Similarly, plaques in mice with SMC-restricted Confetti expression showed oligoclonal SMC populations with little intermixing between the progeny of different medial SMCs. Phenotypes comprised both ACTA2+ SMCs in the cap and heterogeneous ACTA2- SMCs in the plaque interior, including chondrocyte-like cells and cells with intracellular lipid and crystalline material. Fibrous cap SMCs were invariably arranged in endothelium-aligned clonal sheets, confirming results in the aggregation chimeras. Analysis of the clonal structure showed that a low number of local medial SMCs partake in atherosclerosis and that single medial SMCs can produce several different SMC phenotypes in plaque. The combined results show that few medial SMCs proliferate to form the entire phenotypically heterogeneous plaque SMC population in murine atherosclerosis.

  4. CLO-PLA: the database of clonal and bud bank traits of Central European flora

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; de Bello, F.

    2009-01-01

    Roč. 20, č. 3 (2009), s. 511-516 ISSN 1100-9233 R&D Projects: GA ČR(CZ) GA526/06/0723 Institutional research plan: CEZ:AV0Z60050516 Keywords : bud bank * clonal traits * database Subject RIV: EF - Botanics Impact factor: 2.376, year: 2009

  5. Clonal splitters and integrators in harsh environments of the Trans-Himalaya

    Czech Academy of Sciences Publication Activity Database

    Klimeš, Leoš

    2008-01-01

    Roč. 22, č. 3 (2008), s. 351-367 ISSN 0269-7653 R&D Projects: GA ČR GA206/03/1219 Institutional research plan: CEZ:AV0Z60050516 Keywords : Ladakh * altitude * clonal growth Subject RIV: EF - Botanics Impact factor: 3.448, year: 2008

  6. Analysis of the clonal repertoire of gene-corrected cells in gene therapy.

    Science.gov (United States)

    Paruzynski, Anna; Glimm, Hanno; Schmidt, Manfred; Kalle, Christof von

    2012-01-01

    Gene therapy-based clinical phase I/II studies using integrating retroviral vectors could successfully treat different monogenetic inherited diseases. However, with increased efficiency of this therapy, severe side effects occurred in various gene therapy trials. In all cases, integration of the vector close to or within a proto-oncogene contributed substantially to the development of the malignancies. Thus, the in-depth analysis of integration site patterns is of high importance to uncover potential clonal outgrowth and to assess the safety of gene transfer vectors and gene therapy protocols. The standard and nonrestrictive linear amplification-mediated PCR (nrLAM-PCR) in combination with high-throughput sequencing exhibits technologies that allow to comprehensively analyze the clonal repertoire of gene-corrected cells and to assess the safety of the used vector system at an early stage on the molecular level. It enables clarifying the biological consequences of the vector system on the fate of the transduced cell. Furthermore, the downstream performance of real-time PCR allows a quantitative estimation of the clonality of individual cells and their clonal progeny. Here, we present a guideline that should allow researchers to perform comprehensive integration site analysis in preclinical and clinical studies. Copyright © 2012 Elsevier Inc. All rights reserved.

  7. Production and carbon allocation in a clonal Eucalyptus plantation with water and nutrient manipulations

    Science.gov (United States)

    Jose Luiz Stape; Dan Binkley; Michael G. Ryan

    2008-01-01

    We examined resource limitations on growth and carbon allocation in a fast-growing, clonal plantation of Eucalyptus grandis urophylla in Brazil by characterizing responses to annual rainfall, and response to irrigation and fertililization for 2 years. Productivity measures included gross primary production (GPP), total belowground carbon allocation (...

  8. Integration Site and Clonal Expansion in Human Chronic Retroviral Infection and Gene Therapy

    Science.gov (United States)

    Niederer, Heather A.; Bangham, Charles R. M.

    2014-01-01

    Retroviral vectors have been successfully used therapeutically to restore expression of genes in a range of single-gene diseases, including several primary immunodeficiency disorders. Although clinical trials have shown remarkable results, there have also been a number of severe adverse events involving malignant outgrowth of a transformed clonal population. This clonal expansion is influenced by the integration site profile of the viral integrase, the transgene expressed, and the effect of the viral promoters on the neighbouring host genome. Infection with the pathogenic human retrovirus HTLV-1 also causes clonal expansion of cells containing an integrated HTLV-1 provirus. Although the majority of HTLV-1-infected people remain asymptomatic, up to 5% develop an aggressive T cell malignancy. In this review we discuss recent findings on the role of the genomic integration site in determining the clonality and the potential for malignant transformation of cells carrying integrated HTLV-1 or gene therapy vectors, and how these results have contributed to the understanding of HTLV-1 pathogenesis and to improvements in gene therapy vector safety. PMID:25365582

  9. Analyzing clonal fidelity of micropropagated Psidium guajava L. plants using simple sequence repeat markers

    Science.gov (United States)

    Micropropagation of Psidium guajava L. (guava) is a viable alternative to currently adopted techniques for large-scale plant propagation of commercial cultivars. Assessment of clonal fidelity in micropropagated plants is the first step towards ensuring genetic uniformity in mass production of planti...

  10. Searching for the relevance of clonal and bud bank traits across floras and communities

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; de Bello, Francesco; Herben, Tomáš

    2011-01-01

    Roč. 46, 2-3 (2011), 109-115 ISSN 1211-9520 R&D Projects: GA ČR GA526/09/0963; GA ČR GA526/07/0808 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal growth * bud bank * database Subject RIV: EF - Botanics Impact factor: 1.500, year: 2011

  11. Age and distribution of an evergreen clonal shrub in the Coweeta basin: Rhododendron maximum L

    Science.gov (United States)

    Katherine J. Elliott; James M. Vose

    2012-01-01

    Rhododendron maximum L. is an evergreen, clonal shrub that forms a dominant sub-canopy layer and is a key species in southern Appalachian forests. We investigated the age and distribution of R. maximum across the Coweeta Basin, a 1626 ha watershed in western North Carolina. We selected 16 perennial, second-order streams and used a Global Positioning System to establish...

  12. Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia

    NARCIS (Netherlands)

    Jethwa, Alexander; Hüllein, Jennifer; Stolz, Tatjana; Blume, Carolin; Sellner, Leopold; Jauch, Anna; Sill, Martin; Kater, Arnon P.; te Raa, G. Doreen; Geisler, Christian; van Oers, Marinus; Dietrich, Sascha; Dreger, Peter; Ho, Anthony D.; Paruzynski, Anna; Schmidt, Manfred; von Kalle, Christof; Glimm, Hanno; Zenz, Thorsten

    2013-01-01

    Recurrent gene mutations contribute to the pathogenesis of chronic lymphocytic leukaemia (CLL). We developed a next-generation sequencing (NGS) platform to determine the genetic profile, intratumoural heterogeneity, and clonal structure of two independent CLL cohorts. TP53, SF3B1, and NOTCH1 were

  13. Clonal vs leaf-height-seed (LHS) traits: which are filtered more strongly across habitats?

    Czech Academy of Sciences Publication Activity Database

    E.-Vojtkó, A.; Freitag, M.; Bricca, A.; Martello, F.; Compañ, J. M.; Küttim, M.; Kun, R.; de Bello, Francesco; Klimešová, Jitka; Götzenberger, Lars

    2017-01-01

    Roč. 52, 3-4 (2017), s. 269-281 ISSN 1211-9520 R&D Projects: GA ČR(CZ) GA16-15012S Institutional support: RVO:67985939 Keywords : environmental filtering * functional diversity * clonal traits Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 1.017, year: 2016

  14. Reverse Transcriptase Mechanism of Somatic Hypermutation: 60 Years of Clonal Selection Theory

    Directory of Open Access Journals (Sweden)

    Edward J. Steele

    2017-11-01

    Full Text Available The evidence for the reverse transcriptase mechanism of somatic hypermutation is substantial and multifactorial. In this 60th anniversary year of the publication of Sir MacFarlane Burnet’s Clonal Selection Theory, the evidence is briefly reviewed and updated.

  15. Rapid clonal analysis of recurrent tuberculosis by direct MIRU-VNTR typing on stored isolates

    Directory of Open Access Journals (Sweden)

    de Viedma Darío

    2007-07-01

    Full Text Available Abstract Background The application of molecular tools to the analysis of tuberculosis has revealed examples of clonal complexity, such as exogenous reinfection, coinfection, microevolution or compartmentalization. The detection of clonal heterogeneity by standard genotyping approaches is laborious and often requires expertise. This restricts the rapid availability of Mycobacterium tuberculosis (MTB genotypes for clinical or therapeutic decision-making. A new PCR-based technique, MIRU-VNTR, has made it possible to genotype MTB in a time frame close to real-time fingerprinting. Our purpose was to evaluate the capacity of this technique to provide clinicians with a rapid discrimination between reactivation and exogenous reinfection and whether MIRU-VNTR makes it possible to obtain data directly from stored MTB isolates from recurrent episodes. Results We detected differences, between the MIRUtypes of recurrent isolates in 38.5% (5/13 of the cases studied. These included cases of i exogenous reinfection, often with more resistant strains, ii likely examples of microevolution, leading to the appearance of new clonal variants and iii a combination of microevolution, coinfection and competition. Conclusion MIRU-VNTR rapidly obtained clinically useful genotyping data in a challenging situation, directly from stored MTB isolates without subculturing them or purifying their DNA. Our results also mean that MIRU-VNTR could be applied for easy, rapid and affordable massive screening of collections of stored MTB isolates, which could establish the real dimension of clonal heterogeneity in MTB infection.

  16. Clonality and Micro-Diversity of a Nationwide Spreading Genotype of Mycobacterium tuberculosis in Japan

    Science.gov (United States)

    Wada, Takayuki; Iwamoto, Tomotada; Tamaru, Aki; Seto, Junji; Ahiko, Tadayuki; Yamamoto, Kaori; Hase, Atushi; Maeda, Shinji; Yamamoto, Taro

    2015-01-01

    Mycobacterium tuberculosis transmission routes can be estimated from genotypic analysis of clinical isolates from patients. In Japan, still a middle-incidence country of TB, a unique genotype strain designated as ‘M-strain’ has been isolated nationwide recently. To ascertain the history of the wide spread of the strain, 10 clinical isolates from different areas were subjected to genome-wide analysis based on deep sequencers. Results show that all isolates possessed common mutations to those of referential strains. The greatest number of accumulated single nucleotide variants (SNVs) from the oldest coalescence was 13 nucleotides, indicating high clonality of these isolates. When an SNV common to the isolates was used as a surrogate marker of the clone, authentic clonal isolates with variation in a reliable subset of variable number of tandem repeat (VNTR) genotyping method can be selected successfully from clinical isolates populations of M. tuberculosis. When the authentic clones can also be assigned to sub-clonal groups by SNVs derived from the genomic comparison, they are classifiable into three sub-clonal groups with a bias of geographical origins. Feedback from genomic analysis of clinical isolates of M. tuberculosis to genotypic markers will be an efficient strategy for the big data in various settings for public health actions against TB. PMID:25734518

  17. Clonal diversity of Staphylococcus aureus originating from the small ruminants goats and sheep

    DEFF Research Database (Denmark)

    Concepción Porrero, M.; Hasman, Henrik; Vela, Ana I.

    2012-01-01

    Staphylococcus aureus is an important pathogen in humans and many animal species. The prevalence of different clonal types in animal species remains largely unknown. We analyzed 267 S. aureus from intramammary infections in goats (47) and sheep (220) by spa typing, multi-locus sequence typing (ML...

  18. Targeted resequencing for analysis of clonal composition of recurrent gene mutations in chronic lymphocytic leukaemia

    DEFF Research Database (Denmark)

    Jethwa, Alexander; Hüllein, Jennifer; Stolz, Tatjana

    2013-01-01

    Recurrent gene mutations contribute to the pathogenesis of chronic lymphocytic leukaemia (CLL). We developed a next-generation sequencing (NGS) platform to determine the genetic profile, intratumoural heterogeneity, and clonal structure of two independent CLL cohorts. TP53, SF3B1, and NOTCH1 were...

  19. Implications of self/non-self discrimination for spatial patterning of clonal plants

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš; Novoplansky, A.

    2008-01-01

    Roč. 22, č. 3 (2008), s. 337-350 ISSN 0269-7653 R&D Projects: GA ČR GA206/06/0098 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal plants * clustering * competition * facilitation Subject RIV: EF - Botanics Impact factor: 3.448, year: 2008

  20. Physiological integration affects growth form and competitive ability in clonal plants

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš

    2004-01-01

    Roč. 18, - (2004), s. 493-520 ISSN 0269-7653 R&D Projects: GA ČR(CZ) GA206/02/0953 Institutional research plan: CEZ:AV0Z6005908 Keywords : competitive ability * Physiological integration * clonal plants Subject RIV: EF - Botanics Impact factor: 3.215, year: 2004

  1. Clonal diversity and genetic differentiation of Maianthemum bifolium among forest fragments of different age

    NARCIS (Netherlands)

    Arens, P.F.P.; Grashof-Bokdam, C.J.; Sluis, van der T.; Smulders, M.J.M.

    2005-01-01

    Maianthemum bifolium Schmidt (May Lily) is a woodland species with low colonisation ability and high demands for seedling establishment conditions. To study the colonisation process, we analysed the clonal organisation and population structure of Maianthemum bifolium populations in a number of

  2. OCCURRENCE OF ANTIBIOTIC-RESISTANT UROPATHOGENIC ESCHERICHIA COLI CLONAL GROUP A IN WASTEWATER EFFLUENTS

    Science.gov (United States)

    Isolates of Escherichia coli belonging to clonal group A (CGA), a recently described disseminated cause of drug-resistant urinary tract infections in humans, were present in four of seven sewage effluents collected from geographically dispersed areas of the United States. ...

  3. Reproduction by seed and clonality in plants: correlated syndromes or independent strategies?

    Czech Academy of Sciences Publication Activity Database

    Herben, Tomáš; Tackenberg, O.; Klimešová, Jitka

    2016-01-01

    Roč. 104, č. 6 (2016), s. 1696-1706 ISSN 0022-0477 R&D Projects: GA ČR(CZ) GA16-19245S; GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : bud bank traits * clonal traits * CLOPLA database * dispersal * phylogenetic regressions Subject RIV: EF - Botanics Impact factor: 5.813, year: 2016

  4. Clonal growth forms in Arctic plants and their habitat preferences: a study from Petuniabukta, Spitsbergen

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Doležal, Jiří; Prach, Karel; Košnar, J.

    2012-01-01

    Roč. 33, č. 4 (2012), 421-442 ISSN 0138-0338 R&D Projects: GA MŠk LA341; GA AV ČR IAA600050802 Institutional research plan: CEZ:AV0Z60050516 Institutional support: RVO:67985939 Keywords : clonality * plants * Arctic Subject RIV: EH - Ecology, Behaviour Impact factor: 0.745, year: 2012

  5. Prevalence, serotype, virulence characteristics, clonality and antibiotic susceptibility of pathogenic Yersinia enterocolitica from swine feces

    Science.gov (United States)

    Introduction: Swine are the only known animal reservoir of Yersinia enterocolitica (YE), a human pathogen. Since YE is a fecal organism of swine, the primary goal of this study was to evaluate the prevalence, serotype, virulence plasmid (pYV)-associated characteristics, clonality, and antibiotic su...

  6. Get Tested for HIV

    Science.gov (United States)

    ... AIDS: What is HIV/AIDS? Women and HIV/AIDS Next section ... Tested? Why do I need to get tested for HIV? The only way to know if you have HIV is to get tested. Many people with HIV don’t have any symptoms. In the United States, about 1 in 7 ...

  7. Transmission of clonal chromosomal abnormalities in human hematopoietic stem and progenitor cells surviving radiation exposure

    Energy Technology Data Exchange (ETDEWEB)

    Kraft, Daniela, E-mail: d.kraft@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Institute for Transfusion Medicine und Immunohematology, DRK-Blutspendedienst Baden-Wuerttemberg—Hessen, Johann Wolfgang Goethe-University Hospital, Sandhofstrasse 1, 60528 Frankfurt (Germany); Ritter, Sylvia, E-mail: s.ritter@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Durante, Marco, E-mail: m.durante@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Institute for Condensed Matter Physics, Physics Department, Technical University Darmstadt, Hochschulstraße 6-8, 64289 Darmstadt (Germany); Seifried, Erhard, E-mail: e.seifried@blutspende.de [Institute for Transfusion Medicine und Immunohematology, DRK-Blutspendedienst Baden-Wuerttemberg—Hessen, Johann Wolfgang Goethe-University Hospital, Sandhofstrasse 1, 60528 Frankfurt (Germany); Fournier, Claudia, E-mail: c.fournier@gsi.de [GSI Helmholtz Center for Heavy Ion Research, Department of Biophysics, Planckstr. 1, 64291 Darmstadt (Germany); Tonn, Torsten, E-mail: t.tonn@blutspende.de [Institute for Transfusion Medicine und Immunohematology, DRK-Blutspendedienst Baden-Wuerttemberg—Hessen, Johann Wolfgang Goethe-University Hospital, Sandhofstrasse 1, 60528 Frankfurt (Germany); Technische Universität Dresden, Med. Fakultät Carl Gustav Carus, Institute for Transfusion Medicine Dresden, German Red Cross Blood Donation Service North-East, Blasewitzer Straße 68/70, 01307 Dresden (Germany)

    2015-07-15

    Highlights: • Radiation induced formation and transmission of chromosomal aberrations were assessed. • Cytogenetic analysis was performed in human CD34+ HSPC by mFISH. • We report transmission of stable aberrations in irradiated, clonally expanded HSPC. • Unstable aberrations in clonally expanded HSPC occur independently of irradiation. • Carbon ions and X-rays bear a similar risk for propagation of cytogenetic changes. - Abstract: In radiation-induced acute myeloid leukemia (rAML), clonal chromosomal abnormalities are often observed in bone marrow cells of patients, suggesting that their formation is crucial in the development of the disease. Since rAML is considered to originate from hematopoietic stem and progenitor cells (HSPC), we investigated the frequency and spectrum of radiation-induced chromosomal abnormalities in human CD34{sup +} cells. We then measured stable chromosomal abnormalities, a possible biomarker of leukemia risk, in clonally expanded cell populations which were grown for 14 days in a 3D-matrix (CFU-assay). We compared two radiation qualities used in radiotherapy, sparsely ionizing X-rays and densely ionizing carbon ions (29 and 60–85 keV/μm, doses between 0.5 and 4 Gy). Only a negligible number of de novo arising, unstable aberrations (≤0.05 aberrations/cell, 97% breaks) were measured in the descendants of irradiated HSPC. However, stable aberrations were detected in colonies formed by irradiated HSPC. All cells of the affected colonies exhibited one or more identical aberrations, indicating their clonal origin. The majority of the clonal rearrangements (92%) were simple exchanges such as translocations (77%) and pericentric inversions (15%), which are known to contribute to the development of rAML. Carbon ions were more efficient in inducing cell killing (maximum of ∼30–35% apoptotic cells for 2 Gy carbon ions compared to ∼25% for X-rays) and chromosomal aberrations in the first cell-cycle after exposure (∼70% and

  8. On Longitudinal Spectral Coherence

    DEFF Research Database (Denmark)

    Kristensen, Leif

    1979-01-01

    It is demonstrated that the longitudinal spectral coherence differs significantly from the transversal spectral coherence in its dependence on displacement and frequency. An expression for the longitudinal coherence is derived and it is shown how the scale of turbulence, the displacement between ...... observation sites and the turbulence intensity influence the results. The limitations of the theory are discussed....

  9. CXCR4-using HIV variants in a cohort of Black men who have sex with men: HIV Prevention Trials Network 061.

    Science.gov (United States)

    Chen, Iris; Huang, Wei; Connor, Matthew B; Frantzell, Arne; Cummings, Vanessa; Beauchamp, Geetha G; Griffith, Sam; Fields, Sheldon D; Scott, Hyman M; Shoptaw, Steven; Del Rio, Carlos; Magnus, Manya; Mannheimer, Sharon; Tieu, Hong-Van; Wheeler, Darrell P; Mayer, Kenneth H; Koblin, Beryl A; Eshleman, Susan H

    2016-07-01

    To evaluate factors associated with HIV tropism among Black men who have sex with men (MSM) in the United States enrolled in a clinical study (HIV Prevention Trials Network 061). HIV tropism was analyzed using a phenotypic assay (Trofile assay, Monogram Biosciences). Samples were analyzed from 43 men who were HIV infected at enrollment and reported either exclusive insertive intercourse or exclusive receptive intercourse; samples were also analyzed from 20 men who were HIV uninfected at enrollment and seroconverted during the study. Clonal analysis of individual viral variants was performed for seroconverters who had dual/mixed (DM) viruses. DM viruses were detected in samples from 11 (26%) of the 43 HIV-infected men analyzed at the enrollment visit; HIV tropism did not differ between those reporting exclusive insertive vs receptive intercourse. DM viruses were also detected in five (25%) of the 20 seroconverters. DM viruses were associated with lower CD4 cell counts. Seroconverters with DM viruses had dual-tropic viruses only or mixed populations of CCR5- and dual-tropic viruses. DM viruses were frequently detected among Black MSM in this study, including seroconverters. Further studies are needed to understand factors driving transmission and selection of CXCR4- and dual-tropic viruses among Black MSM.

  10. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... of HIV in the United States, please visit: https://www.aids.gov/hiv-aids-basics/hiv-aids- ... HIV, STD, and TB Prevention. About HIV/AIDS. ( https://www.cdc.gov/actagainstaids/basics/whatishiv.html ). Atlanta, ...

  11. Retrivability in The Danish National Hospital Registry of HIV and hepatitis B and C coinfection diagnoses of patients managed in HIV centers 1995-2004

    DEFF Research Database (Denmark)

    Obel, N.; Reinholdt, H.; Omland, L.H.

    2008-01-01

    BACKGROUND: Hospital-based discharge registries are used increasingly for longitudinal epidemiological studies of HIV. We examined completeness of registration of HIV infections and of chronic hepatitis B (HBV) and hepatitis C (HCV) coinfections in the Danish National Hospital Registry (DNHR......) covering all Danish hospitals. METHODS: The Danish HIV Cohort Study (DHCS) encompasses all HIV-infected patients treated in Danish HIV clinics since 1 January 1995. All 2,033 Danish patients in DHCS diagnosed with HIV-1 during the 10-year period from 1 January 1995 to 31 December 2004 were included....... The positive predictive values of being registered with HBV and HCV in DHCS were thereby estimated to 0.88 and 0.97 and in DNHR to 0.32 and 0.54. CONCLUSION: The study demonstrates that secondary data from national hospital databases may be reliable for identification of patients diagnosed with HIV infection...

  12. Clonality, virulence and antimicrobial resistance of enteroaggregative Escherichia coli from Mirzapur, Bangladesh.

    Science.gov (United States)

    Chattaway, Marie Anne; Day, Michaela; Mtwale, Julia; White, Emma; Rogers, James; Day, Martin; Powell, David; Ahmad, Marwa; Harris, Ross; Talukder, Kaisar Ali; Wain, John; Jenkins, Claire; Cravioto, Alejandro

    2017-10-01

    This study investigates the virulence and antimicrobial resistance in association with common clonal complexes (CCs) of enteroaggregative Escherichia coli (EAEC) isolated from Bangladesh. The aim was to determine whether specific CCs were more likely to be associated with putative virulence genes and/or antimicrobial resistance. The presence of 15 virulence genes (by PCR) and susceptibility to 18 antibiotics were determined for 151 EAEC isolated from cases and controls during an intestinal infectious disease study carried out between 2007-2011 in the rural setting of Mirzapur, Bangladesh (Kotloff KL, Blackwelder WC, Nasrin D, Nataro JP, Farag TH et al.Clin Infect Dis 2012;55:S232-S245). These data were then analysed in the context of previously determined serotypes and clonal complexes defined by multi-locus sequence typing. Overall there was no association between the presence of virulence or antimicrobial resistance genes in isolates of EAEC from cases versus controls. However, when stratified by clonal complex (CC) one CC associated with cases harboured more virulence factors (CC40) and one CC harboured more resistance genes (CC38) than the average. There was no direct link between the virulence gene content and antibiotic resistance. Strains within a single CC had variable virulence and resistance gene content indicating independent and multiple gene acquisitions over time. In Bangladesh, there are multiple clonal complexes of EAEC harbouring a variety of virulence and resistance genes. The emergence of two of the most successful clones appeared to be linked to either increased virulence (CC40) or antimicrobial resistance (CC38), but increased resistance and virulence were not found in the same clonal complexes.

  13. High resolution melting analysis (HRM) for the assessment of clonality in feline B-cell lymphomas.

    Science.gov (United States)

    Henrich, Manfred; Scheffold, Svenja; Hecht, Werner; Reinacher, Manfred

    2018-06-01

    Analysis of clonality is gaining importance in diagnosing lymphomas in veterinary medicine. Usually, PCR for the analysis of antigen receptor rearrangement (PARR) is followed by electrophoretic separation of the PCR products. Aim of this study was to test the feasibility of HRM for the assessment of clonality in B-cell lymphomas of cats. High resolution melting analysis differentiates PCR products by their different melting point using the decrease in fluorescence of an intercalating dye during melting of the PCR product. Additionally, the method is easy to use with no post-PCR manipulation of the samples. Forty-seven feline B-cell lymphomas and 31 reactive lymphatic proliferations of cats were investigated by PARR followed either by capillary electrophoresis or an HRM assay. To objectify the interpretation of the HRM results a recently published mathematical approach was applied to the melting curve. To overcome discrepancies between the visual interpretation and the mathematical approach, the latter was modified to include testing of reproducibility and recognition of pseudoclonality. In 11 of 47 lymphoma cases clonal populations were detectable by HRM assay compared to 14 of 47 lymphomas in which clonal populations were detected by capillary electrophoresis assay. Neither of the methods showed a clonal pattern in any of the reactive samples. However, the HRM assay showed a unique pattern in cases of follicular lymphatic hyperplasia that had no corresponding pattern in capillary electrophoresis. The capillary electrophoresis assay could identify 3 lymphomas that were not detected by the HRM assay and is therefore regarded superior to the HRM assay. The comparison however, was hampered by the overall bad performance of the PARR, that might be the consequence of insufficient primer binding due to somatic hypermutation of the binding sites during antigen stimulated proliferation of the B lymphocytes. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.

    Directory of Open Access Journals (Sweden)

    Veronika Tchesnokova

    Full Text Available Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs, which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E. coli clonal-level antibiograms to improve empiric antibiotic selection. A novel PCR-based clonotyping assay was applied to fresh urine samples to rapidly detect E. coli and the urine strain's clonotype. Based on a database of clonotype-specific antibiograms, the acceptability of various antibiotics for empiric therapy was inferred using a 20%, 10%, and 30% allowed resistance threshold. The test's performance characteristics and possible effects on prescribing were assessed. The rapid test identified E. coli clonotypes directly in patients' urine within 25-35 minutes, with high specificity and sensitivity compared to culture. Antibiotic selection based on a clonotype-specific antibiogram could reduce the relative likelihood of antibiotic/pathogen mismatch by ≥ 60%. Compared to observed prescribing patterns, clonal diagnostics-guided antibiotic selection could safely double the use of trimethoprim/sulfamethoxazole and minimize fluoroquinolone use. In summary, a rapid clonotyping test showed promise for improving empiric antibiotic prescribing for E. coli UTI, including reversing preferential use of fluoroquinolones over trimethoprim/sulfamethoxazole. The clonal diagnostics approach merges epidemiologic surveillance, antimicrobial stewardship, and molecular diagnostics to bring evidence-based medicine directly to the point of care.

  15. Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.

    Science.gov (United States)

    Tchesnokova, Veronika; Avagyan, Hovhannes; Rechkina, Elena; Chan, Diana; Muradova, Mariya; Haile, Helen Ghirmai; Radey, Matthew; Weissman, Scott; Riddell, Kim; Scholes, Delia; Johnson, James R; Sokurenko, Evgeni V

    2017-01-01

    Despite the known clonal distribution of antibiotic resistance in many bacteria, empiric (pre-culture) antibiotic selection still relies heavily on species-level cumulative antibiograms, resulting in overuse of broad-spectrum agents and excessive antibiotic/pathogen mismatch. Urinary tract infections (UTIs), which account for a large share of antibiotic use, are caused predominantly by Escherichia coli, a highly clonal pathogen. In an observational clinical cohort study of urgent care patients with suspected UTI, we assessed the potential for E. coli clonal-level antibiograms to improve empiric antibiotic selection. A novel PCR-based clonotyping assay was applied to fresh urine samples to rapidly detect E. coli and the urine strain's clonotype. Based on a database of clonotype-specific antibiograms, the acceptability of various antibiotics for empiric therapy was inferred using a 20%, 10%, and 30% allowed resistance threshold. The test's performance characteristics and possible effects on prescribing were assessed. The rapid test identified E. coli clonotypes directly in patients' urine within 25-35 minutes, with high specificity and sensitivity compared to culture. Antibiotic selection based on a clonotype-specific antibiogram could reduce the relative likelihood of antibiotic/pathogen mismatch by ≥ 60%. Compared to observed prescribing patterns, clonal diagnostics-guided antibiotic selection could safely double the use of trimethoprim/sulfamethoxazole and minimize fluoroquinolone use. In summary, a rapid clonotyping test showed promise for improving empiric antibiotic prescribing for E. coli UTI, including reversing preferential use of fluoroquinolones over trimethoprim/sulfamethoxazole. The clonal diagnostics approach merges epidemiologic surveillance, antimicrobial stewardship, and molecular diagnostics to bring evidence-based medicine directly to the point of care.

  16. Longitudinal categorical data analysis

    CERN Document Server

    Sutradhar, Brajendra C

    2014-01-01

    This is the first book in longitudinal categorical data analysis with parametric correlation models developed based on dynamic relationships among repeated categorical responses. This book is a natural generalization of the longitudinal binary data analysis to the multinomial data setup with more than two categories. Thus, unlike the existing books on cross-sectional categorical data analysis using log linear models, this book uses multinomial probability models both in cross-sectional and longitudinal setups. A theoretical foundation is provided for the analysis of univariate multinomial responses, by developing models systematically for the cases with no covariates as well as categorical covariates, both in cross-sectional and longitudinal setups. In the longitudinal setup, both stationary and non-stationary covariates are considered. These models have also been extended to the bivariate multinomial setup along with suitable covariates. For the inferences, the book uses the generalized quasi-likelihood as w...

  17. Asymptomatic HIV infection

    Science.gov (United States)

    ... of HIV/AIDS during which there are no symptoms of HIV infection. During this phase, the immune system in someone with HIV slowly weakens, but the person has no symptoms. How long this phase lasts depends on how ...

  18. HIV and Pulmonary Hypertension

    Science.gov (United States)

    ... What do I need to know about pulmonary hypertension in connection with HIV? Although pulmonary hypertension and ... Should an HIV patient be tested for pulmonary hypertension? HIV patients know that medical supervision is critical ...

  19. Investigating signs of recent evolution in the pool of proviral HIV type 1 DNA during years of successful HAART

    DEFF Research Database (Denmark)

    Mens, Helene; Pedersen, Anders G; Jørgensen, Louise B

    2007-01-01

    In order to shed light on the nature of the persistent reservoir of human immunodeficiency virus type 1 (HIV-1), we investigated signs of recent evolution in the pool of proviral DNA in patients on successful HAART. Pro-viral DNA, corresponding to the C2-V3-C3 region of the HIV-1 env gene...... there were temporal trends indicating ongoing replication and evolution. In summary, it was not possible to detect definitive signs of ongoing evolution in either the bulk-sequenced or the clonal data with the methods employed here, but our results could be consistent with localized expression of archival...

  20. HIV coreceptor phenotyping in the clinical setting.

    Science.gov (United States)

    Low, Andrew J; Swenson, Luke C; Harrigan, P Richard

    2008-01-01

    The introduction of CCR5 antagonists increases the options available for constructing antiretroviral regimens. However, this option is coupled with the caveat that patients should be tested for HIV coreceptor tropism prior to initiating CCR5 antagonist-based therapy. Failure to screen for CXCR4 usage increases the risk of using an ineffective drug, thus reducing the likelihood of viral suppression and increasing their risk for developing antiretroviral resistance. This review discusses current and future methods of determining HIV tropism, with a focus on their utility in the clinical setting for screening purposes. Some of these methods include recombinant phenotypic tests, such as the Monogram Trofile assay, as well as genotype-based predictors, heteroduplex tracking assays, and flow cytometry based methods. Currently, the best evidence supports the use of phenotypic methods, although other methods of screening for HIV coreceptor usage prior to the administration of CCR5 antagonists may reduce costs and increase turnaround time over phenotypic methods. The presence of low levels of X4 virus is a challenge to all assay methods, resulting in reduced sensitivity in clinical, patient-derived samples when compared to clonally derived samples. Gaining a better understanding of the output of these assays and correlating them with clinical progression and therapy response will provide some indication on how both genotype-based, and phenotypic assays for determining HIV coreceptor usage can be improved. In addition, leveraging new technologies capable of detecting low-level minority species may provide the most significant advances in ensuring that individuals with low levels of dual/mixed tropic virus are not inadvertently prescribed CCR5 antagonists.

  1. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.

    Science.gov (United States)

    Chen, Yi; Gonzalez-Escalona, Narjol; Hammack, Thomas S; Allard, Marc W; Strain, Errol A; Brown, Eric W

    2016-10-15

    Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated that core genome MLST

  2. How clonal is clonal? Genome plasticity across multicellular segments of a "Candidatus Marithrix sp." filament from sulfidic, briny seafloor sediments in the Gulf of Mexico

    Directory of Open Access Journals (Sweden)

    Verena Salman-Carvalho

    2016-08-01

    Full Text Available Candidatus Marithrix is a recently described lineage within the group of large sulfur bacteria (Beggiatoaceae, Gammaproteobacteria. This group of bacteria comprises vacuolated, attached-living filaments that inhabit the sediment surface around vent and seep sites in the marine environment. A single filament is ca. 100 µm in diameter, several millimeters long, and consists of hundreds of clonal cells, which are considered highly polyploid. Based on these characteristics, Candidatus Marithrix was used as a model organism for the assessment of genomic plasticity along segments of a single filament using next generation sequencing to possibly identify hotspots of microevolution. Using six consecutive segments of a single filament sampled from a mud volcano in the Gulf of Mexico, we recovered ca. 90% of the Candidatus Marithrix genome in each segment. There was a high level of genome conservation along the filament with average nucleotide identities between 99.98-100%. Different approaches to assemble all reads into a complete consensus genome could not fill the gaps. Each of the six segment datasets encoded merely a few hundred unique nucleotides and 5 or less unique genes - the residual content was redundant in all datasets. Besides the overall high genomic identity, we identified a similar number of single nucleotide polymorphisms (SNPs between the clonal segments, which are comparable to numbers reported for other clonal organisms. An increase of SNPs with greater distance of filament segments was not observed. The polyploidy of the cells was apparent when analyzing the heterogeneity of reads within a segment. Here, a strong increase in single nucleotide variants, or 'intrasegmental sequence heterogeneity' (ISH events, was observed. These sites may represent hotspots for genome plasticity, and possibly microevolution, since two thirds of these variants were not co-localized across the genome copies of the multicellular filament.

  3. Copenhagen comorbidity in HIV infection (COCOMO) study

    DEFF Research Database (Denmark)

    Ronit, Andreas; Haissman, Judith Melchior; Kirkegaard-Klitbo, Ditte Marie

    2016-01-01

    BACKGROUND: Modern combination antiretroviral therapy (cART) has improved survival for people living with HIV (PLWHIV). Non-AIDS comorbidities have replaced opportunistic infections as leading causes of mortality and morbidity, and are becoming a key health concern as this population continues....../DESIGN: The Copenhagen comorbidity in HIV-infection (COCOMO) study is an observational, longitudinal cohort study. The study was initiated in 2015 and recruitment is ongoing with the aim of including 1500 PLWHIV from the Copenhagen area. Follow-up examinations after 2 and 10 years are planned. Uninfected controls...... (PBMC), urine, and stool samples are collected in a biobank for future studies. Data will be updated through periodical linking to national databases. DISCUSSION: As life expectancy for PLWHIV improves, it is essential to study long-term impact of HIV and cART. We anticipate that findings from...

  4. CONTRIBUTIONS OF SEXUAL AND ASEXUAL REPRODUCTION TO POPULATION STRUCTURE IN THE CLONAL SOFT CORAL, ALCYONIUM RUDYI.

    Science.gov (United States)

    McFadden, Catherine S

    1997-02-01

    Numerous studies of population structure in sessile clonal marine invertebrates have demonstrated low genotypic diversity and nonequilibrium genotype frequencies within local populations that are monopolized by relatively few, highly replicated genets. All of the species studied to date produce planktonic sexual propagules capable of dispersing long distances; despite local genotypic disequilibria, populations are often panmictic over large geographic areas. The population structure paradigm these species represent may not be typical of the majority of clonal invertebrate groups, however, which are believed to produce highly philopatric sexual propagules. I used allozyme variation to examine the population structure of the temperate soft coral, Alcyonium rudyi, a typical clonal species whose sexually produced larvae and asexually produced ramets both have very low dispersal capabilities. Like other clonal plants and invertebrates, the local population dynamics of A. rudyi are dominated by asexual reproduction, and recruitment of new sexually produced genets occurs infrequently. As expected from its philopatric larval stage, estimates of genetic differentiation among populations of A. rudyi were highly significant at all spatial scales examined (mean θ = 0.300 among 20 populations spanning a 1100-km range), suggesting that genetic exchange seldom occurs among populations separated by as little as a few hundred meters. Mapping of multilocus allozyme genotypes within a dense aggregation of A. rudyi ramets confirmed that dispersal of asexual propagules is also very limited: members of the same genet usually remain within invertebrates, populations of A. rudyi do not appear to be dominated by a few widespread genets: estimates of genotypic diversity (G o ) within 20 geographically distinct populations did not differ from expectations for outcrossing, sexual populations. Despite theoretical suggestions that philopatric dispersal combined with typically small effective

  5. Molecular HIV screening.

    Science.gov (United States)

    Bourlet, Thomas; Memmi, Meriam; Saoudin, Henia; Pozzetto, Bruno

    2013-09-01

    Nuclear acid testing is more and more used for the diagnosis of infectious diseases. This paper focuses on the use of molecular tools for HIV screening. The term 'screening' will be used under the meaning of first-line HIV molecular techniques performed on a routine basis, which excludes HIV molecular tests designed to confirm or infirm a newly discovered HIV-seropositive patient or other molecular tests performed for the follow-up of HIV-infected patients. The following items are developed successively: i) presentation of the variety of molecular tools used for molecular HIV screening, ii) use of HIV molecular tools for the screening of blood products, iii) use of HIV molecular tools for the screening of organs and tissue from human origin, iv) use of HIV molecular tools in medically assisted procreation and v) use of HIV molecular tools in neonates from HIV-infected mothers.

  6. Longitudinal beam dynamics

    International Nuclear Information System (INIS)

    Tecker, F

    2014-01-01

    The course gives a summary of longitudinal beam dynamics for both linear and circular accelerators. After discussing different types of acceleration methods and synchronism conditions, it focuses on the particle motion in synchrotrons

  7. Projecting Sexual and Injecting HIV Risks into Future Outcomes with Agent-Based Modeling

    Science.gov (United States)

    Bobashev, Georgiy V.; Morris, Robert J.; Zule, William A.

    Longitudinal studies of health outcomes for HIV could be very costly cumbersome and not representative of the risk population. Conversely, cross-sectional approaches could be representative but rely on the retrospective information to estimate prevalence and incidence. We present an Agent-based Modeling (ABM) approach where we use behavioral data from a cross-sectional representative study and project the behavior into the future so that the risks of acquiring HIV could be studied in a dynamical/temporal sense. We show how the blend of behavior and contact network factors (sexual, injecting) play the role in the risk of future HIV acquisition and time till obtaining HIV. We show which subjects are the most likely persons to get HIV in the next year, and whom they are likely to infect. We examine how different behaviors are related to the increase or decrease of HIV risks and how to estimate the quantifiable risk measures such as survival HIV free.

  8. Prevalence and clonal analysis of Porphyromonas gingivalis in primary endodontic infections.

    Science.gov (United States)

    Siqueira, José F; Rôças, Isabela N; Silva, Marlei G

    2008-11-01

    This study investigated the prevalence of Porphyromonas gingivalis in 62 teeth with primary endodontic infections by using a species-specific 16S rRNA gene-based nested polymerase chain reaction assay. P. gingivalis isolates recovered from 2 infected root canals were also analyzed for clonal diversity by using arbitrarily primed PCR. Overall, P. gingivalis was found in 48% of the samples. This species was specifically detected in 36% of canals of teeth with chronic apical periodontitis, in 46% of the cases of acute apical periodontitis, and in 67% of acute apical abscesses. P. gingivalis was significantly more frequent in abscess aspirates than in canals of teeth with chronic apical periodontitis (P abscesses, and demonstrated that different clonal types of this species can colonize the root canal in the same individual.

  9. Staphylococcus aureus clonal dynamics and virulence factors in children with atopic dermatitis

    DEFF Research Database (Denmark)

    Lomholt, Hans Bredsted; Andersen, KE; Kilian, Mogens

    2005-01-01

    A prospective cohort study was undertaken to determine the clonal dynamics of Staphylococcus aureus colonization and infection during 1 y in children with atopic dermatitis, and to correlate specific clones, accessory gene regulator (agr) groups, and production of virulence factors with eczema......, toxins, and were assigned to agr groups. S. aureus colonization patterns ranged from rare colonization over transient colonization to persistent colonization by a single clone or a dynamic exchange of up to five clones. Production of no single virulence factor including superantigens and toxins...... activity. Eleven children were examined every 6 wk with swaps taken from active eczema, anterior nose, axillae and perineum, and scoring of eczema activity by severity scoring of atopic dermatitis (SCORAD). Individual S. aureus clonal types were identified and examined for production of superantigens...

  10. Assessing T cell clonal size distribution: a non-parametric approach.

    Directory of Open Access Journals (Sweden)

    Olesya V Bolkhovskaya

    Full Text Available Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences like autoimmune diseases. Here we develop and make use of a non-parametric statistical approach to assess T cell clonal size distributions from recent next generation sequencing data. For 41 healthy individuals and a patient with ankylosing spondylitis, who undergone treatment, we invariably find power law scaling over several decades and for the first time calculate quantitatively meaningful values of decay exponent. It has proved to be much the same among healthy donors, significantly different for an autoimmune patient before the therapy, and converging towards a typical value afterwards. We discuss implications of the findings for theoretical understanding and mathematical modeling of adaptive immunity.

  11. Assessing T cell clonal size distribution: a non-parametric approach.

    Science.gov (United States)

    Bolkhovskaya, Olesya V; Zorin, Daniil Yu; Ivanchenko, Mikhail V

    2014-01-01

    Clonal structure of the human peripheral T-cell repertoire is shaped by a number of homeostatic mechanisms, including antigen presentation, cytokine and cell regulation. Its accurate tuning leads to a remarkable ability to combat pathogens in all their variety, while systemic failures may lead to severe consequences like autoimmune diseases. Here we develop and make use of a non-parametric statistical approach to assess T cell clonal size distributions from recent next generation sequencing data. For 41 healthy individuals and a patient with ankylosing spondylitis, who undergone treatment, we invariably find power law scaling over several decades and for the first time calculate quantitatively meaningful values of decay exponent. It has proved to be much the same among healthy donors, significantly different for an autoimmune patient before the therapy, and converging towards a typical value afterwards. We discuss implications of the findings for theoretical understanding and mathematical modeling of adaptive immunity.

  12. Clonality, virulence and antimicrobial resistance of enteroaggregative Escherichia coli from Mirzapur, Bangladesh

    DEFF Research Database (Denmark)

    Chattaway, Marie Anne; Day, Michaela; Mtwale, Julia

    2017-01-01

    Purpose. This study investigates the virulence and antimicrobial resistance in association with common clonal complexes (CCs) of enteroaggregative Escherichia coli (EAEC) isolated from Bangladesh. The aim was to determine whether specific CCs were more likely to be associated with putative...... virulence genes and/or antimicrobial resistance.Methodology. The presence of 15 virulence genes (by PCR) and susceptibility to 18 antibiotics were determined for 151 EAEC isolated from cases and controls during an intestinal infectious disease study carried out between 2007-2011 in the rural setting...... between the presence of virulence or antimicrobial resistance genes in isolates of EAEC from cases versus controls. However, when stratified by clonal complex (CC) one CC associated with cases harboured more virulence factors (CC40) and one CC harboured more resistance genes (CC38) than the average...

  13. Fusion of remote sensing images based on pyramid decomposition with Baldwinian Clonal Selection Optimization

    Science.gov (United States)

    Jin, Haiyan; Xing, Bei; Wang, Lei; Wang, Yanyan

    2015-11-01

    In this paper, we put forward a novel fusion method for remote sensing images based on the contrast pyramid (CP) using the Baldwinian Clonal Selection Algorithm (BCSA), referred to as CPBCSA. Compared with classical methods based on the transform domain, the method proposed in this paper adopts an improved heuristic evolutionary algorithm, wherein the clonal selection algorithm includes Baldwinian learning. In the process of image fusion, BCSA automatically adjusts the fusion coefficients of different sub-bands decomposed by CP according to the value of the fitness function. BCSA also adaptively controls the optimal search direction of the coefficients and accelerates the convergence rate of the algorithm. Finally, the fusion images are obtained via weighted integration of the optimal fusion coefficients and CP reconstruction. Our experiments show that the proposed method outperforms existing methods in terms of both visual effect and objective evaluation criteria, and the fused images are more suitable for human visual or machine perception.

  14. Accounting for dropout reason in longitudinal studies with nonignorable dropout.

    Science.gov (United States)

    Moore, Camille M; MaWhinney, Samantha; Forster, Jeri E; Carlson, Nichole E; Allshouse, Amanda; Wang, Xinshuo; Routy, Jean-Pierre; Conway, Brian; Connick, Elizabeth

    2017-08-01

    Dropout is a common problem in longitudinal cohort studies and clinical trials, often raising concerns of nonignorable dropout. Selection, frailty, and mixture models have been proposed to account for potentially nonignorable missingness by relating the longitudinal outcome to time of dropout. In addition, many longitudinal studies encounter multiple types of missing data or reasons for dropout, such as loss to follow-up, disease progression, treatment modifications and death. When clinically distinct dropout reasons are present, it may be preferable to control for both dropout reason and time to gain additional clinical insights. This may be especially interesting when the dropout reason and dropout times differ by the primary exposure variable. We extend a semi-parametric varying-coefficient method for nonignorable dropout to accommodate dropout reason. We apply our method to untreated HIV-infected subjects recruited to the Acute Infection and Early Disease Research Program HIV cohort and compare longitudinal CD4 + T cell count in injection drug users to nonusers with two dropout reasons: anti-retroviral treatment initiation and loss to follow-up.

  15. Establishment of dna fingerprinting in clonal tea improved cultivars from yunnan of china using issr markers

    International Nuclear Information System (INIS)

    Liu, B.Y.; Zhao, C.M.; Sun, X.M.; Jiang, H.B.

    2015-01-01

    In this study, DNA fingerprints were constructed by using ISSR markers for 20 clonal improved varieties developed by two breeding institutes in Yunnan province. Seven core ISSR primers were selected from 15 primers. A total of 110 bands were generated by PAGE with seven core primers, 93 of which were polymorphic bands, the percentage of polymorphic band (PPB) was 84.54%, and the mean value of polymorphism information content (PIC) reached 0.417; the genetic similarity coefficient of the cultivars was 0.574-0.854. The two primers, UBC835 and ISSR2, had high PIC values, and could be used to distinguish all cultivars, presenting the most efficient single primers. Among the all of primer combinations from the seven core primers, the three combinations, UBC835/UBC811, UBC835/ISSR2, and UBC835/ISSR3 showed lower similar coefficients, and more efficient in identifying the 20 improved varieties than the other primer combinations. Then these three primer combinations were further scored in 15 traditional cultivars. The results showed that UBC835/ISSR2 was the optimal primer combination, which could be used to distinguish each material among the 20 clonal improved varieties and 15 traditional cultivals. Finally, the DNA fingerprints of the 20 clonal improved varieties were constructed based on country and region code, breeding institute, core primer name and ISSR marker data. The established fingerprints could provide reliable scientific base for the protection of intellectual property right for these clonal improved varieties, and the important molecular information contained in these fingerprints would be useful for the authenticity identification and genetic relationship analysis of tea varieties. (author)

  16. Invasion strategies in clonal aquatic plants: are phenotypic differences caused by phenotypic plasticity or local adaptation?

    Science.gov (United States)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit; Clayton, John S.; Brix, Hans; Sorrell, Brian K.

    2010-01-01

    Background and Aims The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions. Methods Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified. Key Results For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics. Conclusions The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained

  17. Transgenerational plasticity as an important mechanism affecting response of clonal species to changing climate

    OpenAIRE

    M?nzbergov?, Zuzana; Hadincov?, V?roslava

    2017-01-01

    Abstract In spite of the increasing number of studies on the importance of transgenerational plasticity for species response to novel environments, its effects on species ability to respond to climate change are still largely unexplored. We study the importance of transgenerational plasticity for response of a clonal species Festuca rubra. Individuals from four natural populations representing two levels of temperature and two levels of precipitation were cultivated in four growth chambers th...

  18. MIRU-VNTR allelic variability depends on Mycobacterium bovis clonal group identity.

    Science.gov (United States)

    Hauer, Amandine; Michelet, Lorraine; De Cruz, Krystel; Cochard, Thierry; Branger, Maxime; Karoui, Claudine; Henault, Sylvie; Biet, Franck; Boschiroli, María Laura

    2016-11-01

    The description of the population of M. bovis strains circulating in France from 1978 to 2013 has highlighted the discriminating power of the MLVA among predominant spoligotype groups. In the present study we aimed to characterize clonal groups via MLVA and to better understand the strain's population structure. MLVA was performed with eight MIRU-VNTR loci, most of them defined by the Venomyc European consortium. The discriminatory index of each MLVA loci was calculated for SB0120, SB0134, SB0121 and the "F4-family", the main spoligotype groups in France. Differences in global DI per spoligotype, but also by locus within each spoligotype, were observed, which strongly suggest the clonal complex nature of these major groups. These MLVA results were compared to those of other European countries where strain collections had been characterized (Spain, Portugal, Italy, Northern Ireland and Belgium). Overall, QUB 3232 and ETR D are respectively the most and the least discriminative loci, regardless of the strains geographical origin. However, marked DI differences are observed in the rest of the MIRU-VNTR loci, again highlighting that strain genetic variability in a country depends on the dominant existing clonal complexes. A web application for M. bovis, including spoligotyping and MIRU-VNTR typing data, was developed to allow inter-laboratory comparison of field isolates. In conclusion, combination of typing methods is required for M. bovis optimum discrimination and differentiation of groups of strains. Thus, the loci employed for MLVA in a country should be those which are the most discriminative for the clonal complexes which characterize their M. bovis population. Copyright © 2016 Elsevier B.V. All rights reserved.

  19. Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae)

    OpenAIRE

    Gaddis, Keith D.; Zukin, Helen L.; Dieterich, Inca A.; Braker, Elizabeth; Sork, Victoria L.

    2014-01-01

    The existence of monodominant forests on well-drained soils in tropical regions has been widely reported. Such forests most likely result from a combination of both ecological and evolutionary factors. Under conditions of high seed and seedling mortality, vegetative reproduction could create a reproductive advantage leading to forest dominance, and profoundly affect the distribution of genetic variation in a clonal species. We investigated these effects in a low diversity forest site in North...

  20. Against the odds: complete outcrossing in a monoecious clonal seagrass Posidonia australis (Posidoniaceae).

    Science.gov (United States)

    Sinclair, Elizabeth A; Gecan, Ilena; Krauss, Siegfried L; Kendrick, Gary A

    2014-06-01

    Seagrasses are marine, flowering plants with a hydrophilous pollination strategy. In these plants, successful mating requires dispersal of filamentous pollen grains through the water column to receptive stigmas. Approximately 40 % of seagrass species are monoecious, and therefore little pollen movement is required if inbreeding is tolerated. Outcrossing in these species is further impacted by clonality, which is variable, but can be extensive in large, dense meadows. Despite this, little is known about the interaction between clonal structure, genetic diversity and mating systems in hydrophilous taxa. Polymorphic microsatellite DNA markers were used to characterize genetic diversity, clonal structure, mating system and realized pollen dispersal in two meadows of the temperate, monoecious seagrass, Posidonia australis, in Cockburn Sound, Western Australia. Within the two sampled meadows, genetic diversity was moderate among the maternal shoots (R = 0·45 and 0·64) and extremely high in the embryos (R = 0·93-0·97). Both meadows exhibited a highly clumping (or phalanx) structure among clones, with spatial autocorrelation analysis showing significant genetic structure among shoots and embryos up to 10-15 m. Outcrossing rates were not significantly different from one. Pollen dispersal distances inferred from paternity assignment averaged 30·8 and 26·8 m, which was larger than the mean clone size (12·8 and 13·8 m). These results suggest highly effective movement of pollen in the water column. Despite strong clonal structure and moderate genetic diversity within meadows, hydrophilous pollination is an effective vector for completely outcrossed offspring. The different localized water conditions at each site (highly exposed conditions vs. weak directional flow) appear to have little influence on the success and pattern of successful pollination in the two meadows. © The Author 2014. Published by Oxford University Press on behalf of the Annals of Botany Company. All

  1. Clonal differences in generation times of GPK epithelial cells in monolayer culture.

    Science.gov (United States)

    Riley, P A; Hola, M

    1980-01-01

    Pedigrees of cells in eight clones of guinea pig keratocyte (GPK) cells in monolayer culture were analyzed from a time-lapse film. The generation times and the position in the field of observation were recorded up to the sixth generation when the cultures were still subconfluent. Statistical analysis of the results indicates that the position in the culture has less significance than the clonal origin of the cell in determining the interval between successive mitoses.

  2. Clonal structure and variable fertilization success in Florida Keys broadcast-spawning corals

    Science.gov (United States)

    Miller, M. W.; Baums, I. B.; Pausch, R. E.; Bright, A. J.; Cameron, C. M.; Williams, D. E.; Moffitt, Z. J.; Woodley, C. M.

    2018-03-01

    Keystone reef-building corals in the Caribbean are predominantly self-incompatible broadcast spawners and a majority are threatened due to both acute adult mortality and poor recruitment. As population densities decline, concerns about fertilization limitation and effective population size in these species increase and would be further exacerbated by either high clonality or gametic incompatibility of parental genotypes. This study begins to address these concerns for two Caribbean broadcasting species by characterizing clonal structure and quantifying experimental pairwise fertilization success. Orbicella faveolata showed surprisingly high and contrasting levels of clonality between two sampled sites; Acropora palmata was previously known to be highly clonal. Individual pairwise crosses of synchronously spawning genotypes of each species were conducted by combining aliquots of gamete bundles immediately after spawning, and showed high and significant variability in fertilization success. Over half of the individual crosses of O. faveolata and about one-third of A. palmata crosses yielded ≤ 40% fertilization. Total sperm concentration was quantified in only a subset of O. faveolata crosses (range of 1-6 × 107 mL-1), but showed no correlation with fertilization success. We interpret that both parental incompatibility and individual genotypes with low-quality gametes are likely to have contributed to the variable fertilization observed with important implications for conservation. Differential fertilization success implies effective population size may be considerably smaller than hoped and population enhancement efforts need to incorporate many more parental genotypes at the patch scale to ensure successful larval production than indicated by estimates based simply on preserving levels of standing genetic diversity.

  3. The Hayflick Limit May Determine the Effective Clonal Diversity of Naive T Cells.

    Science.gov (United States)

    Ndifon, Wilfred; Dushoff, Jonathan

    2016-06-15

    Having a large number of sufficiently abundant T cell clones is important for adequate protection against diseases. However, as shown in this paper and elsewhere, between young adulthood and >70 y of age the effective clonal diversity of naive CD4/CD8 T cells found in human blood declines by a factor of >10. (Effective clonal diversity accounts for both the number and the abundance of T cell clones.) The causes of this observation are incompletely understood. A previous study proposed that it might result from the emergence of certain rare, replication-enhancing mutations in T cells. In this paper, we propose an even simpler explanation: that it results from the loss of T cells that have attained replicative senescence (i.e., the Hayflick limit). Stochastic numerical simulations of naive T cell population dynamics, based on experimental parameters, show that the rate of homeostatic T cell proliferation increases after the age of ∼60 y because naive T cells collectively approach replicative senescence. This leads to a sharp decline of effective clonal diversity after ∼70 y, in agreement with empirical data. A mathematical analysis predicts that, without an increase in the naive T cell proliferation rate, this decline will occur >50 yr later than empirically observed. These results are consistent with a model in which exhaustion of the proliferative capacity of naive T cells causes a sharp decline of their effective clonal diversity and imply that therapeutic potentiation of thymopoiesis might either prevent or reverse this outcome. Copyright © 2016 by The American Association of Immunologists, Inc.

  4. Population genetics of Trypanosoma brucei rhodesiense: clonality and diversity within and between foci.

    Directory of Open Access Journals (Sweden)

    Craig W Duffy

    2013-11-01

    Full Text Available African trypanosomes are unusual among pathogenic protozoa in that they can undergo their complete morphological life cycle in the tsetse fly vector with mating as a non-obligatory part of this development. Trypanosoma brucei rhodesiense, which infects humans and livestock in East and Southern Africa, has classically been described as a host-range variant of the non-human infective Trypanosoma brucei that occurs as stable clonal lineages. We have examined T. b. rhodesiense populations from East (Uganda and Southern (Malawi Africa using a panel of microsatellite markers, incorporating both spatial and temporal analyses. Our data demonstrate that Ugandan T. b. rhodesiense existed as clonal populations, with a small number of highly related genotypes and substantial linkage disequilibrium between pairs of loci. However, these populations were not stable as the dominant genotypes changed and the genetic diversity also reduced over time. Thus these populations do not conform to one of the criteria for strict clonality, namely stability of predominant genotypes over time, and our results show that, in a period in the mid 1990s, the previously predominant genotypes were not detected but were replaced by a novel clonal population with limited genetic relationship to the original population present between 1970 and 1990. In contrast, the Malawi T. b. rhodesiense population demonstrated significantly greater diversity and evidence for frequent genetic exchange. Therefore, the population genetics of T. b. rhodesiense is more complex than previously described. This has important implications for the spread of the single copy T. b. rhodesiense gene that allows human infectivity, and therefore the epidemiology of the human disease, as well as suggesting that these parasites represent an important organism to study the influence of optional recombination upon population genetic dynamics.

  5. Prevalence of clonal complexes and virulence genes among commensal and invasive Staphylococcus aureus isolates in Sweden.

    Directory of Open Access Journals (Sweden)

    Gunlög Rasmussen

    Full Text Available Staphylococcus aureus encodes a remarkable number of virulence factors which may contribute to its pathogenicity and ability to cause invasive disease. The main objective of this study was to evaluate the association between S. aureus invasiveness and bacterial genotype, in terms of the presence of virulence genes and affiliation to clonal complexes. Also, the significance of different virulence genes, mainly adhesins, for the development of infective endocarditis was investigated. DNA microarray technology was used to analyze 134 S. aureus isolates, all methicillin-susceptible, derived from three groups of clinically well-characterized patients: nasal carriers (n=46, bacteremia (n=55, and bacteremia with infective endocarditis (n=33. Invasive isolates were dominant in four of the major clonal complexes: 5, 8, 15, and 25. Of the 170 virulence genes examined, those encoding accessory gene regulator group II (agr II, capsule polysaccharide serotype 5 (cap5, and adhesins such as S. aureus surface protein G (sasG and fibronectin-binding protein B (fnbB were found to be associated with invasive disease. The same was shown for the leukocidin genes lukD/lukE, as well as the genes encoding serine protease A and B (splA/splB, staphylococcal complement inhibitor (scn and the staphylococcal exotoxin-like protein (setC or selX. In addition, there was a trend of higher prevalence of certain genes or gene clusters (sasG, agr II, cap5 among isolates causing infective endocarditis compared to other invasive isolates. In most cases, the presence of virulence genes was linked to clonal complex affiliation. In conclusion, certain S. aureus clonal lineages harboring specific sets of virulence genes seem to be more successful in causing invasive disease.

  6. A novel genetic tool for clonal analysis of fourth chromosome mutations

    OpenAIRE

    Sousa-Neves, Rui; Schinaman, Joseph M.

    2012-01-01

    The fourth chromosome of Drosophila remains one of the most intractable regions of the fly genome to genetic analysis. The main difficulty posed to the genetic analyses of mutations on this chromosome arises from the fact that it does not undergo meiotic recombination, which makes recombination mapping impossible, and also prevents clonal analysis of mutations, a technique which relies on recombination to introduce the prerequisite recessive markers and FLP-recombinase recognition targets (FR...

  7. An efficient identification strategy of clonal tea cultivars using long-core motif SSR markers.

    Science.gov (United States)

    Wang, Rang Jian; Gao, Xiang Feng; Kong, Xiang Rui; Yang, Jun

    2016-01-01

    Microsatellites, or simple sequence repeats (SSRs), especially those with long-core motifs (tri-, tetra-, penta-, and hexa-nucleotide) represent an excellent tool for DNA fingerprinting. SSRs with long-core motifs are preferred since neighbor alleles are more easily separated and identified from each other, which render the interpretation of electropherograms and the true alleles more reliable. In the present work, with the purpose of characterizing a set of core SSR markers with long-core motifs for well fingerprinting clonal cultivars of tea (Camellia sinensis), we analyzed 66 elite clonal tea cultivars in China with 33 initially-chosen long-core motif SSR markers covering all the 15 linkage groups of tea plant genome. A set of 6 SSR markers were conclusively selected as core SSR markers after further selection. The polymorphic information content (PIC) of the core SSR markers was >0.5, with ≤5 alleles in each marker containing 10 or fewer genotypes. Phylogenetic analysis revealed that the core SSR markers were not strongly correlated with the trait 'cultivar processing-property'. The combined probability of identity (PID) between two random cultivars for the whole set of 6 SSR markers was estimated to be 2.22 × 10(-5), which was quite low, confirmed the usefulness of the proposed SSR markers for fingerprinting analyses in Camellia sinensis. Moreover, for the sake of quickly discriminating the clonal tea cultivars, a cultivar identification diagram (CID) was subsequently established using these core markers, which fully reflected the identification process and provided the immediate information about which SSR markers were needed to identify a cultivar chosen among the tested ones. The results suggested that long-core motif SSR markers used in the investigation contributed to the accurate and efficient identification of the clonal tea cultivars and enabled the protection of intellectual property.

  8. Genetic diversity of a clonal angiosperm near its range limit: The case of Cymodocea nodosa at the Canary Islands

    OpenAIRE

    Alberto, Filipe; Arnaud-Haond, Sophie; Duarte, Carlos M.; Serrao, Ester Álvares

    2006-01-01

    The seagrass Cymodocea nodosa forms a unique community in the Canary Islands, where it is classified as an endangered species. Biogeographic theory predicts that clonal species on islands near their distributional limits might show lower proportions of sexual (versus clonal) reproduction, lower genetic diversity, and higher differentiation. We addressed these hypotheses by comparing the genetic structure of C. nodosa from 10 meadows in the 4 main Canary Islands with 2 Iberian sites (Atlantic ...

  9. Spirituality and adherence to antiretroviral drugs among HIV positive ...

    African Journals Online (AJOL)

    Method: It was an observational, longitudinal study in which 215 consenting HIV positive patients aged 18 to 65 years who were on antiretroviral drugs were recruited through systematic random sampling technique. Socio-demographic characteristics, clinical history and physical examination findings were documented for ...

  10. Age-related mutations associated with clonal hematopoietic expansion and malignancies.

    Science.gov (United States)

    Xie, Mingchao; Lu, Charles; Wang, Jiayin; McLellan, Michael D; Johnson, Kimberly J; Wendl, Michael C; McMichael, Joshua F; Schmidt, Heather K; Yellapantula, Venkata; Miller, Christopher A; Ozenberger, Bradley A; Welch, John S; Link, Daniel C; Walter, Matthew J; Mardis, Elaine R; Dipersio, John F; Chen, Feng; Wilson, Richard K; Ley, Timothy J; Ding, Li

    2014-12-01

    Several genetic alterations characteristic of leukemia and lymphoma have been detected in the blood of individuals without apparent hematological malignancies. The Cancer Genome Atlas (TCGA) provides a unique resource for comprehensive discovery of mutations and genes in blood that may contribute to the clonal expansion of hematopoietic stem/progenitor cells. Here, we analyzed blood-derived sequence data from 2,728 individuals from TCGA and discovered 77 blood-specific mutations in cancer-associated genes, the majority being associated with advanced age. Remarkably, 83% of these mutations were from 19 leukemia and/or lymphoma-associated genes, and nine were recurrently mutated (DNMT3A, TET2, JAK2, ASXL1, TP53, GNAS, PPM1D, BCORL1 and SF3B1). We identified 14 additional mutations in a very small fraction of blood cells, possibly representing the earliest stages of clonal expansion in hematopoietic stem cells. Comparison of these findings to mutations in hematological malignancies identified several recurrently mutated genes that may be disease initiators. Our analyses show that the blood cells of more than 2% of individuals (5-6% of people older than 70 years) contain mutations that may represent premalignant events that cause clonal hematopoietic expansion.

  11. Genetic diversity in three invasive clonal aquatic species in New Zealand

    Directory of Open Access Journals (Sweden)

    Sorrell Brian K

    2010-06-01

    Full Text Available Abstract Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946 and L. major (1950. Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient.

  12. Ribosomal DNA sequence analysis of different geographically distributed Aloe Vera plants: Comparison with clonally regenerated plants

    International Nuclear Information System (INIS)

    Yagi, A.; Sato, Y.; Miwa, Y.; Kabbash, A.; Moustafa, S.; Shimomura, K.; El-Bassuony, A.

    2006-01-01

    A comparison of the sequences in an internally transcribed spacer (ITS) 1 region of rDNA between clonally regenerated A.vera and same species in Japan, USA and Egypt revealed the presence of two types of nucleotide sequences, 252 and 254 bps. Based on the findings in the ITS 1 region, A.vera having 252 and 254 bps clearly showed a stable sequence similarity, suggesting high conversation of the base peak sequence in the ITS 1 region. However, frequent base substitutions in the 252 bps samples leaves that came from callus tissue and micropropagated plants were observed around the regions of nucleotide positions 66, 99 and 199-201. The minor deviation in clonally regenerated A.vera may be due to the stage of regeneration and cell specification in cases of the callus tissue. In the present study, the base peak sequence of the Its 1 region of rDNA was adopted as a molecular marker for differentiating A.vera plants from geographically distributed and clonally regenerated A.vera plants and it was suggested that the base peak substitutions in the ITS 1 region may arise from the different nutritional and environmental factors in cultivation and plant growth stages. (author)

  13. Loss of heterozygosity drives clonal diversity of Phytophthora capsici in China.

    Directory of Open Access Journals (Sweden)

    Jian Hu

    Full Text Available Phytophthora capsici causes significant loss to pepper (Capsicum annum in China and our goal was to develop single nucleotide polymorphism (SNP markers for P. capsici and characterize genetic diversity nationwide. Eighteen isolates of P. capsici from locations worldwide were re-sequenced and candidate nuclear and mitochondrial SNPs identified. From 2006 to 2012, 276 isolates of P. capsici were recovered from 136 locations in 27 provinces and genotyped using 45 nuclear and 2 mitochondrial SNPs. There were two main mitochondrial haplotypes and 95 multi-locus genotypes (MLGs identified. Genetic diversity was geographically structured with a high level of genotypic diversity in the north and on Hainan Island in the south, suggesting outcrossing contributes to diversity in these areas. The remaining areas of China are dominated by four clonal lineages that share mitochondrial haplotypes, are almost exclusively the A1 or A2 mating type and appear to exhibit extensive diversity based on loss of heterozygosity (LOH. Analysis of SNPs directly from infected peppers confirmed LOH in field populations. One clonal lineage is dominant throughout much of the country. The overall implications for long-lived genetically diverse clonal lineages amidst a widely dispersed sexual population are discussed.

  14. Noise-Driven Phenotypic Heterogeneity with Finite Correlation Time in Clonal Populations.

    Directory of Open Access Journals (Sweden)

    UnJin Lee

    Full Text Available There has been increasing awareness in the wider biological community of the role of clonal phenotypic heterogeneity in playing key roles in phenomena such as cellular bet-hedging and decision making, as in the case of the phage-λ lysis/lysogeny and B. Subtilis competence/vegetative pathways. Here, we report on the effect of stochasticity in growth rate, cellular memory/intermittency, and its relation to phenotypic heterogeneity. We first present a linear stochastic differential model with finite auto-correlation time, where a randomly fluctuating growth rate with a negative average is shown to result in exponential growth for sufficiently large fluctuations in growth rate. We then present a non-linear stochastic self-regulation model where the loss of coherent self-regulation and an increase in noise can induce a shift from bounded to unbounded growth. An important consequence of these models is that while the average change in phenotype may not differ for various parameter sets, the variance of the resulting distributions may considerably change. This demonstrates the necessity of understanding the influence of variance and heterogeneity within seemingly identical clonal populations, while providing a mechanism for varying functional consequences of such heterogeneity. Our results highlight the importance of a paradigm shift from a deterministic to a probabilistic view of clonality in understanding selection as an optimization problem on noise-driven processes, resulting in a wide range of biological implications, from robustness to environmental stress to the development of drug resistance.

  15. Different rates of defense evolution and niche preferences in clonal and nonclonal milkweeds (Asclepias spp.).

    Science.gov (United States)

    Pellissier, Loïc; Litsios, Glenn; Fishbein, Mark; Salamin, Nicolas; Agrawal, Anurag A; Rasmann, Sergio

    2016-02-01

    Given the dual role of many plant traits to tolerate both herbivore attack and abiotic stress, the climatic niche of a species should be integrated into the study of plant defense strategies. Here we investigate the impact of plant reproductive strategy and components of species' climatic niche on the rate of chemical defense evolution in the milkweeds using a common garden experiment of 49 species. We found that across Asclepias species, clonal reproduction repeatedly evolved in lower temperature conditions, in species generally producing low concentrations of a toxic defense (cardenolides). Additionally, we found that rates of cardenolide evolution were lower for clonal than for nonclonal species. We thus conclude that because the clonal strategy is based on survival, long generation times, and is associated with tolerance of herbivory, it may be an alternative to toxicity in colder ecosystems. Taken together, these results indicate that the rate of chemical defense evolution is influenced by the intersection of life-history strategy and climatic niches into which plants radiate. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

  16. Clonal multiplication of Cymbidiums through tissue culture of the shoot meristem

    Energy Technology Data Exchange (ETDEWEB)

    Wimber, Donald E.

    1963-09-01

    The propagation of clonal varieties of some orchids is at times exasperatingly slow and occasionally an almost futile effort. Clonal multiplication is generally confined to dlvidlng mature plants and to starting plants from pseudobulbs. There is, of course, the specialized technique for obtaining Phalaenopsis plantlets from the aseptic culture of inflorescence nodes, but this is basically the same thing as propagating plants from pseudobulbs. In certain cases it is highly desirable to rapidly multiply certain clones of orchids. Awarded varieties could thereby be dispersed with great rapidity where now it may take decades for some clones to became fairly common. Commercial flower production would be very much enhanced if certain desirable clones could be multiplied ad infinitum within a short time. Orchid flower production could then be placed more on a par with many of the other cut flowers and the clonal peculiarities of some fo the current hybrids could be pampered instead of ignored. This paper describes a tissue culture method for the rapid propagation of Cymbidium clones.

  17. Clonal expansion under the microscope: studying lymphocyte activation and differentiation using live-cell imaging.

    Science.gov (United States)

    Polonsky, Michal; Chain, Benjamin; Friedman, Nir

    2016-03-01

    Clonal expansion of lymphocytes is a hallmark of vertebrate adaptive immunity. A small number of precursor cells that recognize a specific antigen proliferate into expanded clones, differentiate and acquire various effector and memory phenotypes, which promote effective immune responses. Recent studies establish a large degree of heterogeneity in the level of expansion and in cell state between and within expanding clones. Studying these processes in vivo, while providing insightful information on the level of heterogeneity, is challenging due to the complex microenvironment and the inability to continuously track individual cells over extended periods of time. Live cell imaging of ex vivo cultures within micro fabricated arrays provides an attractive methodology for studying clonal expansion. These experiments facilitate continuous acquisition of a large number of parameters on cell number, proliferation, death and differentiation state, with single-cell resolution on thousands of expanding clones that grow within controlled environments. Such data can reveal stochastic and instructive mechanisms that contribute to observed heterogeneity and elucidate the sequential order of differentiation events. Intercellular interactions can also be studied within these arrays by following responses of a controlled number of interacting cells, all trapped within the same microwell. Here we describe implementations of live-cell imaging within microwell arrays for studies of lymphocyte clonal expansion, portray insights already gained from these experiments and outline directions for future research. These tools, together with in vivo experiments tracking single-cell responses, will expand our understanding of adaptive immunity and the ways by which it can be manipulated.

  18. Genetic diversity in three invasive clonal aquatic species in New Zealand

    Science.gov (United States)

    2010-01-01

    Background Elodea canadensis, Egeria densa and Lagarosiphon major are dioecious clonal species which are invasive in New Zealand and other regions. Unlike many other invasive species, the genetic variation in New Zealand is very limited. Clonal reproduction is often considered an evolutionary dead end, even though a certain amount of genetic divergence may arise due to somatic mutations. The successful growth and establishment of invasive clonal species may be explained not by adaptability but by pre-existing ecological traits that prove advantageous in the new environment. We studied the genetic diversity and population structure in the North Island of New Zealand using AFLPs and related the findings to the number of introductions and the evolution that has occurred in the introduced area. Results Low levels of genetic diversity were found in all three species and appeared to be due to highly homogeneous founding gene pools. Elodea canadensis was introduced in 1868, and its populations showed more genetic structure than those of the more recently introduced of E. densa (1946) and L. major (1950). Elodea canadensis and L. major, however, had similar phylogeographic patterns, in spite of the difference in time since introduction. Conclusions The presence of a certain level of geographically correlated genetic structure in the absence of sexual reproduction, and in spite of random human dispersal of vegetative propagules, can be reasonably attributed to post-dispersal somatic mutations. Direct evidence of such evolutionary events is, however, still insufficient. PMID:20565861

  19. A Clonal Lineage of Fusarium oxysporum Circulates in the Tap Water of Different French Hospitals.

    Science.gov (United States)

    Edel-Hermann, Véronique; Sautour, Marc; Gautheron, Nadine; Laurent, Julie; Aho, Serge; Bonnin, Alain; Sixt, Nathalie; Hartemann, Philippe; Dalle, Frédéric; Steinberg, Christian

    2016-11-01

    Fusarium oxysporum is typically a soilborne fungus but can also be found in aquatic environments. In hospitals, water distribution systems may be reservoirs for the fungi responsible for nosocomial infections. F. oxysporum was previously detected in the water distribution systems of five French hospitals. Sixty-eight isolates from water representative of all hospital units that were previously sampled and characterized by translation elongation factor 1α sequence typing were subjected to microsatellite analysis and full-length ribosomal intergenic spacer (IGS) sequence typing. All but three isolates shared common microsatellite loci and a common two-locus sequence type (ST). This ST has an international geographical distribution in both the water networks of hospitals and among clinical isolates. The ST dominant in water was not detected among 300 isolates of F. oxysporum that originated from surrounding soils. Further characterization of 15 isolates by vegetative compatibility testing allowed us to conclude that a clonal lineage of F. oxysporum circulates in the tap water of the different hospitals. We demonstrated that a clonal lineage of Fusarium oxysporum inhabits the water distribution systems of several French hospitals. This clonal lineage, which appears to be particularly adapted to water networks, represents a potential risk for human infection and raises questions about its worldwide distribution. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

  20. Clonal stability of latex yield in eleven clones of Hevea brasiliensis Muell. Arg.

    Directory of Open Access Journals (Sweden)

    K.O. Omokhafe

    2003-01-01

    Full Text Available Eleven Hevea brasiliensis clones were evaluated for clonal stability of latex yield. A randomized complete block design was used with four replicates, two locations, seven years and three periods per year. Stability analysis was based on clone x year and clone x year x location interactions. Five stability parameters viz environmental variance, shukla's stability variance, regression of clonal latex yield on environmental index, variance due to regression and variance due to deviation from regression were applied. There was significant clone x environment effect at the two levels of interaction. Among the eleven clones, C 162 was outstanding for clonal stability and it can serve as donor parent for stability alleles. Three clones (C 76, C 150 and C 154 were also stable. The four stable clones (C 76, C 150, C 154 and C 162 are suitable for broad-spectrum recommendation for latex yield. Five clones (C 83, C 143, C 163, C 202 and RRIM 600 will require environment-specific recommendation because of their unstable phenotype. The stability feature of two clones (C 145 and C 159 was not clear and this will be investigated in subsequent studies.

  1. Gamma irradiation effect on the formation of Clonal variation from catharantus roseus plant

    International Nuclear Information System (INIS)

    Syukur, Sumaryati

    2000-01-01

    Clonal variation have been found in Catharantus roseus plant after gamma irradiation. Several doses have been used to produce clonal variation. The most effective doses used to perform better clonal variation was 20 krad. About 103 seeds irradiated for every radiation treatment, but only several clones were grown better than wild type. We have success to get (M) seeds the expected mutant. The seeds from selected mutant are bigger when compare to the wild type and growth better on medium containing 5-methyl Tryptophan (5-MT). The chlorophyll content is higher (almost twice) as compared to the wild type. Fulther experiment continue to do in vitro culture in order to develop embryonic callus from leaf tip and leaf base. Several manipulation of auxin and cytokini have been used to differentiate the callus formation. Modified MS medium with kinetin and cytokinin (10:1) can induce globular embryo like structure. Dragendrof alkaloid reagent were used to determine high alkaloid clones from the expected mutant. TLC analysis from callus mutant shows 3 clear bands with subsequence Rf about 0.22, 0.58 while control shows two smearing bands at 0.21 and 0.52

  2. Secondary immunization generates clonally related antigen-specific plasma cells and memory B cells.

    Science.gov (United States)

    Frölich, Daniela; Giesecke, Claudia; Mei, Henrik E; Reiter, Karin; Daridon, Capucine; Lipsky, Peter E; Dörner, Thomas

    2010-09-01

    Rechallenge with T cell-dependent Ags induces memory B cells to re-enter germinal centers (GCs) and undergo further expansion and differentiation into plasma cells (PCs) and secondary memory B cells. It is currently not known whether the expanded population of memory B cells and PCs generated in secondary GCs are clonally related, nor has the extent of proliferation and somatic hypermutation of their precursors been delineated. In this study, after secondary tetanus toxoid (TT) immunization, TT-specific PCs increased 17- to 80-fold on days 6-7, whereas TT-specific memory B cells peaked (delayed) on day 14 with a 2- to 22-fold increase. Molecular analyses of V(H)DJ(H) rearrangements of individual cells revealed no major differences of gene usage and CDR3 length between TT-specific PCs and memory B cells, and both contained extensive evidence of somatic hypermutation with a pattern consistent with GC reactions. This analysis identified clonally related TT-specific memory B cells and PCs. Within clusters of clonally related cells, sequences shared a number of mutations but also could contain additional base pair changes. The data indicate that although following secondary immunization PCs can derive from memory B cells without further somatic hypermutation, in some circumstances, likely within GC reactions, asymmetric mutation can occur. These results suggest that after the fate decision to differentiate into secondary memory B cells or PCs, some committed precursors continue to proliferate and mutate their V(H) genes.

  3. Morphological response to competition for light in the clonal Trifolium repens (Fabaceae).

    Science.gov (United States)

    Bittebiere, Anne-Kristel; Renaud, Nolwenn; Clément, Bernard; Mony, Cendrine

    2012-04-01

    Plant communities in temperate zones are dominated by clonal plants that can plastically modify their growth characteristics in response to competition. Given that plants compete with one another, and the implications this has for species coexistence, we conducted a study to assess how clonal species morphologically respond to competition for light depending on its intensity and heterogeneity, which are determined by the competitor species. We assessed the morphological response to competition for light of the clonal species Trifolium repens L. by measuring its growth performance, and vertical and horizontal growth traits. We used five competitive environments, i.e., one without competitor and four differing by their competitor species creating different conditions of competition intensity and heterogeneity. The morphological response of Trifolium repens to competition for light depended on the competitor identity. Competition intensity and heterogeneity, determined by competitor identity, had an interactive effect on most traits. The increase in petiole elongation and specific leaf area due to increased competition intensity was observed only at low to intermediate competition heterogeneity. Competition heterogeneity promoted the elongation of clone connections allowing space exploration. Our results demonstrated that the intensity and heterogeneity of competition, which depended on competitor identity, are of primary importance in determining the plastic response of Trifolium repens. This emphasizes that it is important to consider the fine-scale spatial distribution of individuals when studying their interactions within plant communities.

  4. Spatial heterogeneity in light supply affects intraspecific competition of a stoloniferous clonal plant.

    Directory of Open Access Journals (Sweden)

    Pu Wang

    Full Text Available Spatial heterogeneity in light supply is common in nature. Many studies have examined the effects of heterogeneous light supply on growth, morphology, physiology and biomass allocation of clonal plants, but few have tested those effects on intraspecific competition. In a greenhouse experiment, we grew one (no competition or nine ramets (with intraspecific competition of a stoloniferous clonal plant, Duchesnea indica, in three homogeneous light conditions (high, medium and low light intensity and two heterogeneous ones differing in patch size (large and small patch treatments. The total light in the two heterogeneous treatments was the same as that in the homogeneous medium light treatment. Both decreasing light intensity and intraspecific competition significantly decreased the growth (biomass, number of ramets and total stolon length of D. indica. As compared with the homogeneous medium light treatment, the large patch treatment significantly increased the growth of D. indica without intraspecific competition. However, the growth of D. indica with competition did not differ among the homogeneous medium light, the large and the small patch treatments. Consequently, light heterogeneity significantly increased intraspecific competition intensity, as measured by the decreased log response ratio. These results suggest that spatial heterogeneity in light supply can alter intraspecific interactions of clonal plants.

  5. Somatically Acquired LINE-1 Insertions in Normal Esophagus Undergo Clonal Expansion in Esophageal Squamous Cell Carcinoma.

    Science.gov (United States)

    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.

  6. HIV Structural Database

    Science.gov (United States)

    SRD 102 HIV Structural Database (Web, free access)   The HIV Protease Structural Database is an archive of experimentally determined 3-D structures of Human Immunodeficiency Virus 1 (HIV-1), Human Immunodeficiency Virus 2 (HIV-2) and Simian Immunodeficiency Virus (SIV) Proteases and their complexes with inhibitors or products of substrate cleavage.

  7. HIV Viral Load

    Science.gov (United States)

    ... PF4 Antibody Hepatitis A Testing Hepatitis B Testing Hepatitis C Testing HER2/neu Herpes Testing High-sensitivity C-reactive Protein (hs-CRP) Histamine Histone Antibody HIV Antibody and HIV Antigen (p24) HIV Antiretroviral Drug Resistance Testing, Genotypic HIV Viral Load HLA Testing HLA- ...

  8. National HIV Testing Day

    Centers for Disease Control (CDC) Podcasts

    Dr. Kevin A. Fenton, Director of CDC's National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, discusses National HIV Testing Day, an annual observance which raises awareness of the importance of knowing one's HIV status and encourages at-risk individuals to get an HIV test.

  9. Eliminating Perinatal HIV Transmission

    Centers for Disease Control (CDC) Podcasts

    In this podcast, CDC’s Dr. Steve Nesheim discusses perinatal HIV transmission, including the importance of preventing HIV among women, preconception care, and timely HIV testing of the mother. Dr. Nesheim also introduces the revised curriculum Eliminating Perinatal HIV Transmission intended for faculty of OB/GYN and pediatric residents and nurse midwifery students.

  10. HIV-related social intolerance and risky sexual behavior in a high HIV prevalence environment.

    Science.gov (United States)

    Delavande, Adeline; Sampaio, Mafalda; Sood, Neeraj

    2014-06-01

    Although most countries state that fighting social intolerance against persons with HIV is part of their national HIV strategy, the impact of reducing intolerance on risky sexual behavior is largely unknown. In this paper, we estimate the effect of social intolerance against HIV+ persons on risky sexual behavior in rural Malawi using data from roughly 2000 respondents from the 2004 and 2006 waves of the Malawi Longitudinal Study of Families and Health (MLSFH). The effect of social intolerance on risky behavior is a priori ambiguous. On the one hand, higher social intolerance or stigma can lead people to disassociate from the stigmatized group and hence promote risky behavior. On the other hand, intolerance can be viewed as a social tax on being HIV+ and thus higher intolerance may reduce risky behavior. We find that a decrease in social intolerance is associated with a decrease in risky behavior, including fewer partners and a lower likelihood of having extra-marital relations. This effect is mainly driven by the impact of social intolerance on men. Overall the results suggests that reducing social intolerance might not only benefit the HIV positive but might also forestall the spread of HIV. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. National HIV Testing Day

    Centers for Disease Control (CDC) Podcasts

    2011-06-09

    Dr. Kevin A. Fenton, Director of CDC's National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, discusses National HIV Testing Day, an annual observance which raises awareness of the importance of knowing one's HIV status and encourages at-risk individuals to get an HIV test.  Created: 6/9/2011 by National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention (NCHHSTP).   Date Released: 6/9/2011.

  12. Eliminating Perinatal HIV Transmission

    Centers for Disease Control (CDC) Podcasts

    2012-11-26

    In this podcast, CDC’s Dr. Steve Nesheim discusses perinatal HIV transmission, including the importance of preventing HIV among women, preconception care, and timely HIV testing of the mother. Dr. Nesheim also introduces the revised curriculum Eliminating Perinatal HIV Transmission intended for faculty of OB/GYN and pediatric residents and nurse midwifery students.  Created: 11/26/2012 by Division of HIV/AIDS Prevention.   Date Released: 11/26/2012.

  13. Normal telomere lengths in naive and memory CD4+ T cells in HIV type 1 infection: a mathematical interpretation

    NARCIS (Netherlands)

    Wolthers, K. C.; Noest, A. J.; Otto, S. A.; Miedema, F.; de Boer, R. J.

    1999-01-01

    To study CD4+ T cell productivity during HIV-1 infection, CD4+ T cell telomere lengths were measured. Cross-sectional and longitudinal analysis of HIV-1-infected individuals with CD4+ T cells counts >300 cells/mm3 showed normal average telomeric restriction fragment (TRF) length and normal

  14. Normal telomere lengths in naive and memory CD4 T cells in HIV type 1 infection : a mathematical interpretation

    NARCIS (Netherlands)

    Wolthers, K.C.; Noest, A.J.; Otto, S.A.; Miedema, F.; Boer, R.J. de

    1999-01-01

    To study CD4+ T cell productivity during HIV-1 infection, CD4+ T cell telomere lengths were measured. Cross-sectional and longitudinal analysis of HIV-1-infected individuals with CD4+ T cells counts >300 cells/mm3 showed normal average telomeric restriction fragment (TRF) length and normal

  15. Differences in HIV Type 1 RNA Plasma Load Profile of Closely Related Cocirculating Ethiopian Subtype C Strains: C and C '

    NARCIS (Netherlands)

    Ayele, Workenesh; Mekonnen, Yared; Messele, Tsehaynesh; Mengistu, Yohannes; Tsegaye, Aster; Bakker, Margreet; Berkhout, Ben; Dorigo-Zetsma, Wendelien; Wolday, Dawit; Goudsmit, Jaap; Coutinho, Roel; de Baar, Michel; Paxton, William A.; Pollakis, Georgios

    2010-01-01

    Two HIV-1 subtype C subclusters have been identified in Ethiopia (C and C') with little knowledge regarding their biological or clinical differences. We longitudinally monitored HIV-1 viral loads and CD4(+) T cell counts for 130 subtype C-infected individuals from Ethiopia over 5 years. The genetic

  16. Care of HIV-exposed and HIV-infected neonates

    African Journals Online (AJOL)

    However, further reduction in MTCT may be possible if newborns at high risk of acquiring HIV ... infants of breastfeeding mothers with newly diagnosed HIV infection, dual NVP/ .... birth HIV DNA PCR testing for HIV-exposed low birth weight.

  17. Side Effects of HIV Medicines: HIV and Diabetes

    Science.gov (United States)

    ... Children and Adolescents HIV and Women HIV and Gay and Bisexual Men HIV and Older Adults HIV ... throughout the body. A hormone called insulin helps move the glucose into the cells. Once in the ...

  18. Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae).

    Science.gov (United States)

    Gaddis, Keith D; Zukin, Helen L; Dieterich, Inca A; Braker, Elizabeth; Sork, Victoria L

    2014-06-01

    The existence of monodominant forests on well-drained soils in tropical regions has been widely reported. Such forests most likely result from a combination of both ecological and evolutionary factors. Under conditions of high seed and seedling mortality, vegetative reproduction could create a reproductive advantage leading to forest dominance, and profoundly affect the distribution of genetic variation in a clonal species. We investigated these effects in a low diversity forest site in Northeastern Costa Rica dominated by the species Pentaclethra macroloba, which sprouts from the root mass of fallen trees and from snapped trunks. We examined the population structure of juvenile P. macroloba growing in different soil types and across an elevational gradient. Using seven molecular markers, we genotyped 173 juvenile P. macroloba from 18 plots (six plots in seasonally inundated swamps, and 12 plots in upland non-swamp) spanning 50-300m in elevation at La Selva Biological Station and the adjacent Reserva Ecológica Bijagual in Northeastern Costa Rica. We answered two specific questions: (1) How extensive is clonal reproduction? and (2) what is the distribution of genetic diversity and structure? We found that clonal reproduction occurred exclusively within inundated swamp areas. However, there was no significant difference between genetic diversity measures in swamp and non-swamp plots, which were both generally low when compared with other tropical forest species. Genetic structure was significant across all plots (F(ST) = -0.109). However, genetic structure among swamp plots (F(ST) = 0.128) was higher than among non-swamp upland plots (F(ST) = 0.093). Additionally, spatial autocorrelation among individuals within non-swamp upland plots was significant from the 25 to 100m spatial scale, but not within swamp plots. The degree of overall genetic structure we found in P. macroloba is high for a tropical forest tree. The incidence of clonal reproduction is a contributing

  19. Effect of clonal reproduction on genetic structure in Pentaclethra macroloba (Fabaceae: Mimosoideae

    Directory of Open Access Journals (Sweden)

    Keith D. Gaddis

    2014-08-01

    Full Text Available The existence of monodominant forests on well-drained soils in tropical regions has been widely reported. Such forests most likely result from a combination of both ecological and evolutionary factors. Under conditions of high seed and seedling mortality, vegetative reproduction could create a reproductive advantage leading to forest dominance, and profoundly affect the distribution of genetic variation in a clonal species. We investigated these effects in a low diversity forest site in Northeastern Costa Rica dominated by the species Pentaclethra macroloba, which sprouts from the root mass of fallen trees and from snapped trunks. We examined the population structure of juvenile P. macroloba growing in different soil types and across an elevational gradient. Using seven molecular markers, we genotyped 173 juvenile P. macroloba from 18 plots (six plots in seasonally inundated swamps, and 12 plots in upland non-swamp spanning 50-300m in elevation at La Selva Biological Station and the adjacent Reserva Ecológica Bijagual in Northeastern Costa Rica. We answered two specific questions: (1 How extensive is clonal reproduction? and (2 what is the distribution of genetic diversity and structure?. We found that clonal reproduction occurred exclusively within inundated swamp areas. However, there was no significant difference between genetic diversity measures in swamp and non-swamp plots, which were both generally low when compared with other tropical forest species. Genetic structure was significant across all plots (F ST=0.109. However, genetic structure among swamp plots (F ST=0.128 was higher than among non-swamp upland plots (F ST=0.093. Additionally, spatial autocorrelation among individuals within non-swamp upland plots was significant from the 25 to 100m spatial scale, but not within swamp plots. The degree of overall genetic structure we found in P. macroloba is high for a tropical forest tree. The incidence of clonal reproduction is a

  20. Clonal expansion of CD4+ Cytotoxic T Lymphocytes in IgG4-related disease

    Science.gov (United States)

    Mattoo, Hamid; Mahajan, Vinay S.; Maehara, Takashi; Deshpande, Vikram; Della-Torre, Emanuel; Wallace, Zachary S.; Kulikova, Maria; Drijvers, Jefte M.; Daccache, Joe; Carruthers, Mollie N.; Castellino, Flavia; Stone, James R.; Stone, John H.; Pillai, Shiv

    2016-01-01

    Background IgG4-related disease (IgG4-RD) is a systemic condition of unknown etiology, characterized by highly fibrotic lesions with dense lymphoplasmacytic infiltrates. CD4+ T cells constitute the major inflammatory cell population in IgG4-RD lesions. Objective We used an unbiased approach to characterize CD4+ T cell subsets in IgG4-RD subjects based on their clonal expansion and their ability to infiltrate affected tissue sites. Methods We used flow cytometry to identify CD4+ effector/memory T cells (TEM) in a cohort of 101 IgG4-related disease (IgG4-RD) patients. These expanded cells were characterized by gene expression analysis and flow cytometry. Next-generation sequencing of the T cell receptor β chain gene was performed on CD4+SLAMF7+ CTLs and CD4+GATA3+ TH2 cells in a subset of patients to identify their clonality. Tissue infiltration by specific T cells was examined using quantitative multi-color imaging. Results CD4+ effector/memory T cells with a cytolytic phenotype were expanded in IgG4-RD patients. Next-generation sequencing revealed prominent clonal expansions of these CD4+CTLs but not CD4+GATA3+ memory TH2 cells in subjects with IgG4-RD. The dominant T cells infiltrating a range of inflamed IgG4-RD tissue sites were clonally-expanded CD4+CTLs that expressed SLAMF7, granzyme A, IL-1β, and TGF-β1. Clinical remission induced by rituximab-mediated B cell depletion was associated with a reduction in disease-associated CD4+ CTLs Conclusions IgG4-RD is prominently linked to clonally-expanded, IL-1β, and TGF- β1 secreting, CD4+ CTLs in peripheral blood as well as in inflammatory tissue lesions. These active, terminally-differentiated, cytokine-secreting effector CD4+ T cells are now linked to a human disease characterized by chronic inflammation and fibrosis. PMID:26971690

  1. Bone health in HIV-infected children and adolescents.

    Science.gov (United States)

    Eckard, Allison R; Mora, Stefano

    2016-05-01

    Chronic HIV infection and exposure to antiretroviral therapy compromises bone health in children and adolescents, potentially impacting their long-term quality of life. Thus, the purpose of this article is to review the most recent literature on this topic in HIV-infected children and adolescents. Recent studies continue to demonstrate bone abnormalities in HIV-infected children and adolescents, whether HIV is acquired perinatally or during adolescence. Researchers have employed new modalities, both high tech and those that can be utilized in resource-limited settings, to better assess bone health. New data suggest that this population may also be experiencing an increase incidence of fractures, and they may not acquire the same peak bone mass as their HIV-uninfected counterparts. Reassuringly, however, in-utero tenofovir exposure does not appear to have a significant impact on bone health in HIV-exposed, uninfected infants. HIV-infected children and adolescents are exposed to HIV and antiretroviral therapy for many decades starting early in life and during the most critical time for skeletal growth and bone mass accrual. Recent findings underscore the need for further research on bone in this population. Longitudinal studies are especially needed to evaluate long-term risk of osteoporosis and fracture.

  2. Progenitor strain introduction of Mycobacterium bovis at the wildlife-livestock interface can lead to clonal expansion of the disease in a single ecosystem

    KAUST Repository

    Dippenaar, Anzaan

    2017-04-13

    Mycobacterium bovis infects multiple wildlife species and domesticated cattle across South Africa, and negatively impacts on livestock trade and movement of wildlife for conservation purposes. M. bovis infection was first reported in the Kruger National Park (KNP) in South Africa during the 1990s, and has since spread to infect numerous animal host species throughout the park and across South Africa. Whole genome sequencing data of 17 M. bovis isolates were analyzed to investigate the genomic diversity among M. bovis isolates causing disease in different animal host species from various locations in South Africa. M. bovis strains analyzed in this study are geographic rather than host species-specific. The clonal expansion of M. bovis in the KNP highlights the effect of an introduction of a transmissible infectious disease leading to a rising epidemic in wildlife, and emphasizes the importance of disease control and movement restriction of species that serve as disease reservoirs. In conclusion, the point source introduction of a single M. bovis strain type in the KNP ecosystem lead to an M. bovis outbreak in this area that affects various host species and poses an infection risk in neighboring rural communities where HIV prevalence is high.

  3. Risk Behaviors Among HIV-Positive Gay and Bisexual Men at Party-Oriented Vacations

    Science.gov (United States)

    Fisher, Michael P.; Ramchand, Rajeev; Bana, Sarah; Iguchi, Martin Y.

    2013-01-01

    Objective: This study examined substance use (intended and actual), unprotected sex, and HIV disclosure practices (disclosure and questioning) among HIV-positive men who have sex with men (MSM) at two party-oriented vacations, where substance use and sexual risk may be heightened. Method: A random sample of 489 MSM attending one of two party-oriented vacations participated in PartyIntents, a short-term longitudinal survey. Nearly half (47%) completed a follow-up assessment at the event or online for up to 2 weeks after the event. We examined rates of baseline intentions to use substances, actual substance use, and unprotected intercourse among HIV-positive men in attendance.Rates among HIV-negative men were estimated for comparison. Multiple logistic regression was used to assess the impact of illegal drug use and HIV status on unprotected anal intercourse (UAI). Results: HIV-positive attendees (17%) were significantly more likely than HIV-negative attendees to use nitrite inhalants (or “poppers”) (24.3% vs. 10.7%). HIV-positive attendees were also significantly more likely to have insertive UAI (64.3% vs. 34.1%) and receptive UAI (68.8% vs. 22.2%). Multivariate models showed associations between HIV status and illegal drug use with UAI (for HIV status, odds ratio [OR] = 4.5, p = .001; for any illegal drug use, OR = 16.4, p < .001). There was no evidence that the influence of drug use moderated risk by HIV status. Rates of HIV disclosure and questioning did not differ by HIV status. Conclusions: HIV-positive men attending these events engaged in higher rates of illegal drug use and sexual risk than HIV-negative men. Prevention campaigns targeting MSM at high-risk events should include messages geared toward HIV-positive men. PMID:23200162

  4. Associations of the vaginal microbiota with HIV infection, bacterial vaginosis, and demographic factors.

    Science.gov (United States)

    Chehoud, Christel; Stieh, Daniel J; Bailey, Aubrey G; Laughlin, Alice L; Allen, Shannon A; McCotter, Kerrie L; Sherrill-Mix, Scott A; Hope, Thomas J; Bushman, Frederic D

    2017-04-24

    We sought to investigate the effects of HIV infection on the vaginal microbiota and associations with treatment and demographic factors. We thus compared vaginal microbiome samples from HIV-infected (HIV+) and HIV-uninfected (HIV-) women collected at two Chicago area hospitals. We studied vaginal microbiome samples from 178 women analyzed longitudinally (n = 324 samples) and collected extensive data on clinical status and demographic factors. We used 16S rRNA gene sequencing to characterize the bacterial lineages present, then UniFrac, Shannon diversity, and other measures to compare community structure with sample metadata. Differences in microbiota measures were modest in the comparison of HIV+ and HIV- samples, in contrast to several previous studies, consistent with effective antiretroviral therapy. Proportions of healthy Lactobacillus species were not higher in HIV- patients overall, but were significantly higher when analyzed within each hospital in isolation. Rates of bacterial vaginosis were higher among African-American women and HIV+ women. Bacterial vaginosis was associated with higher frequency of HIV+. Unexpectedly, African-American women were more likely to switch bacterial vaginosis status between sampling times; switching was not associated with HIV+ status. The influence of HIV infection on the vaginal microbiome was modest for this cohort of well suppressed urban American women, consistent with effective antiretroviral therapy. HIV+ was found to be associated with bacterial vaginosis. Although bacterial vaginosis has previously been associated with HIV transmission, most of the women studied here became HIV+ many years before our test for bacterial vaginosis, thus implicating additional mechanisms linking HIV infection and bacterial vaginosis.

  5. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... Drugs and HIV Learn the Link - Drugs and HIV Email Facebook Twitter 2005 –Ongoing Behaviors associated with ... Send the Message . Get the Facts What are HIV and AIDS? HIV (human immunodeficiency virus) is the ...

  6. Global HIV/AIDS Epidemic

    Science.gov (United States)

    ... Policy The Global HIV/AIDS Epidemic The Global HIV/AIDS Epidemic Published: Nov 29, 2017 Facebook Twitter ... 2001-FY 2018 Request The Global Response to HIV/AIDS International efforts to combat HIV began in ...

  7. HIV/AIDS in Women

    Science.gov (United States)

    HIV stands for human immunodeficiency virus. It harms your immune system by destroying the white blood cells ... It is the final stage of infection with HIV. Not everyone with HIV develops AIDS. HIV often ...

  8. HIV / AIDS: An Unequal Burden

    Science.gov (United States)

    Skip Navigation Bar Home Current Issue Past Issues HIV / AIDS HIV / AIDS: An Unequal Burden Past Issues / Summer 2009 ... high-risk category, emphasizes Dr. Cargill. Photo: iStock HIV and Pregnancy Are there ways to help HIV- ...

  9. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... contracting or transmitting HIV/AIDS or other infectious diseases. Research Reports: HIV/AIDS : Explores the link between drug misuse and HIV/AIDS, populations most at risk, trends in HIV/AIDS, and ...

  10. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... help us Send the Message . Get the Facts What are HIV and AIDS? HIV (human immunodeficiency virus) ... hiv-aids-101/statistics/ . Reference Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, National ...

  11. Serodiagnostic profiles of HIV and HIV pathogenesis in vivo

    NARCIS (Netherlands)

    Goudsmit, J.; Lange, J. M.; Smit, L.; Bakker, M.; Klaver, B.; Danner, S. A.; Coutinho, R. A.

    1988-01-01

    Different stages of HIV infection are marked by expression of HIV genes, production of HIV antibodies, formation of antigen/antibody complexes and clearance of such complexes. Transient HIV antigenemia appearing generally 6-8 weeks prior to HIV antibody (HIV-Ab) seroconversion and lasting 3-4 months

  12. LIA longitudinal coupling impedance

    International Nuclear Information System (INIS)

    Faltens, A.

    1980-01-01

    The beam generated fields enter into the problems of waveform generation and longitudinal stability. In the former, provision must be made for the longitudinally defocusing forces due to the space charge and the beam loading effects on the accelerating voltage due to the current of a presumably known bunch. In the latter, the concern is for the growth of unintentional perturbations to unacceptably large values through the interaction of the charge and current fluctuations with the rest of the beam and the surrounding structures. These beam generated electric fields may be related to the beam current through a coupling impedance

  13. Living with HIV/AIDS - Multiple Languages

    Science.gov (United States)

    ... HIV - Newly diagnosed with HIV, part 5 - English MP3 Children and HIV - Newly diagnosed with HIV, part 5 - 简体中文 (Chinese, Simplified (Mandarin dialect)) MP3 Children and HIV - Newly diagnosed with HIV, part ...

  14. Structural drivers and social protection: mechanisms of HIV risk and HIV prevention for South African adolescents.

    Science.gov (United States)

    Cluver, Lucie Dale; Orkin, Frederick Mark; Meinck, Franziska; Boyes, Mark Edward; Sherr, Lorraine

    2016-01-01

    Social protection is high on the HIV-prevention agenda for youth in sub-Saharan Africa. However, questions remain: How do unconditional cash transfers work? What is the effect of augmenting cash provision with social care? And can "cash plus care" social protection reduce risks for adolescents most vulnerable to infection? This study tackles these questions by first identifying mediated pathways to adolescent HIV risks and then examining potential main and moderating effects of social protection in South Africa. This study was a prospective observational study of 3515 10-to-17-year-olds (56.7% female; 96.8% one-year retention). Within randomly selected census areas in four rural and urban districts in two South African provinces, all homes with a resident adolescent were sampled between 2009/2010 and 2011/2012. Measures included 1) potential structural drivers of HIV infection such as poverty and community violence; 2) HIV risk behaviours; 3) hypothesized psychosocial mediating factors; and 4) types of social protection involving cash and care. Using gender-disaggregated analyses, longitudinal mediation models were tested for potential main and moderating effects of social protection. Structural drivers were associated with increased onset of adolescent HIV risk behaviour (psocial protection were associated with reductions in HIV risk behaviour and psychosocial deprivations. In addition, cash social protection moderated risk pathways: for adolescent girls and boys experiencing more acute structural deprivation, social protection had the greatest associations with HIV risk prevention (e.g. moderation effects for girls: B=-0.08, psocial protection has the greatest prevention effects for the most vulnerable. Social protection comprising unconditional cash plus care was associated with reduced risk pathways through moderation and main effects, respectively. Our findings suggest the importance of social protection within a combination package of HIV

  15. Sexual Behaviors and HIV Status: A Population-Based Study Among Older Adults in Rural South Africa

    Science.gov (United States)

    Gómez-Olivé, Francesc X.; Rohr, Julia K.; Houle, Brian C.; Kabudula, Chodziwadziwa W.; Wagner, Ryan G.; Salomon, Joshua A.; Kahn, Kathleen; Berkman, Lisa F.; Tollman, Stephen M.; Bärnighausen, Till

    2017-01-01

    Objective: To identify the unmet needs for HIV prevention among older adults in rural South Africa. Methods: We analyzed data from a population-based sample of 5059 men and women aged 40 years and older from the study Health and Aging in Africa: Longitudinal Studies of INDEPTH Communities (HAALSI), which was carried out in the Agincourt health and sociodemographic surveillance system in the Mpumalanga province of South Africa. We estimated the prevalence of HIV (laboratory-confirmed and self-reported) and key sexual behaviors by age and sex. We compared sexual behavior profiles across HIV status categories with and without age–sex standardization. Results: HIV prevalence was very high among HAALSI participants (23%, 95% confidence interval [CI]: 21 to 24), with no sex differences. Recent sexual activity was common (56%, 95% CI: 55 to 58) across all HIV status categories. Condom use was low among HIV-negative adults (15%, 95% CI: 14 to 17), higher among HIV-positive adults who were unaware of their HIV status (27%, 95% CI: 22 to 33), and dramatically higher among HIV-positive adults who were aware of their status (75%, 95% CI: 70 to 80). Casual sex and multiple partnerships were reported at moderate levels, with slightly higher estimates among HIV-positive compared to HIV-negative adults. Differences by HIV status remained after age–sex standardization. Conclusions: Older HIV-positive adults in an HIV hyperendemic community of rural South Africa report sexual behaviors consistent with high HIV transmission risk. Older HIV-negative adults report sexual behaviors consistent with high HIV acquisition risk. Prevention initiatives tailored to the particular prevention needs of older adults are urgently needed to reduce HIV risk in this and similar communities in sub-Saharan Africa. PMID:27926667

  16. Sexual Behaviors and HIV Status: A Population-Based Study Among Older Adults in Rural South Africa.

    Science.gov (United States)

    Rosenberg, Molly S; Gómez-Olivé, Francesc X; Rohr, Julia K; Houle, Brian C; Kabudula, Chodziwadziwa W; Wagner, Ryan G; Salomon, Joshua A; Kahn, Kathleen; Berkman, Lisa F; Tollman, Stephen M; Bärnighausen, Till

    2017-01-01

    To identify the unmet needs for HIV prevention among older adults in rural South Africa. We analyzed data from a population-based sample of 5059 men and women aged 40 years and older from the study Health and Aging in Africa: Longitudinal Studies of INDEPTH Communities (HAALSI), which was carried out in the Agincourt health and sociodemographic surveillance system in the Mpumalanga province of South Africa. We estimated the prevalence of HIV (laboratory-confirmed and self-reported) and key sexual behaviors by age and sex. We compared sexual behavior profiles across HIV status categories with and without age-sex standardization. HIV prevalence was very high among HAALSI participants (23%, 95% confidence interval [CI]: 21 to 24), with no sex differences. Recent sexual activity was common (56%, 95% CI: 55 to 58) across all HIV status categories. Condom use was low among HIV-negative adults (15%, 95% CI: 14 to 17), higher among HIV-positive adults who were unaware of their HIV status (27%, 95% CI: 22 to 33), and dramatically higher among HIV-positive adults who were aware of their status (75%, 95% CI: 70 to 80). Casual sex and multiple partnerships were reported at moderate levels, with slightly higher estimates among HIV-positive compared to HIV-negative adults. Differences by HIV status remained after age-sex standardization. Older HIV-positive adults in an HIV hyperendemic community of rural South Africa report sexual behaviors consistent with high HIV transmission risk. Older HIV-negative adults report sexual behaviors consistent with high HIV acquisition risk. Prevention initiatives tailored to the particular prevention needs of older adults are urgently needed to reduce HIV risk in this and similar communities in sub-Saharan Africa.

  17. Retrivability in The Danish National Hospital Registry of HIV and hepatitis B and C coinfection diagnoses of patients managed in HIV centers 1995–2004

    Directory of Open Access Journals (Sweden)

    Sørensen Henrik T

    2008-04-01

    Full Text Available Abstract Background Hospital-based discharge registries are used increasingly for longitudinal epidemiological studies of HIV. We examined completeness of registration of HIV infections and of chronic hepatitis B (HBV and hepatitis C (HCV coinfections in the Danish National Hospital Registry (DNHR covering all Danish hospitals. Methods The Danish HIV Cohort Study (DHCS encompasses all HIV-infected patients treated in Danish HIV clinics since 1 January 1995. All 2,033 Danish patients in DHCS diagnosed with HIV-1 during the 10-year period from 1 January 1995 to 31 December 2004 were included in the current analysis. We used the DHCS as a reference to examine the completeness of HIV and of HBV and HCV coinfections recorded in DNHR. Cox regression analysis was used to estimate hazard ratios of time to diagnosis of HIV in DNHR compared to DHCS. Results Of the 2,033 HIV patients in DHCS, a total of 2,006 (99% were registered with HIV in DNHR. Of these, 1,888 (93% were registered in DNHR within one year of their first positive HIV test. A CD4 = 100,000 copies/ml and being diagnosed after 1 January 2000, were associated with earlier registration in DNHR, both in crude and adjusted analyses. Thirty (23% HIV patients registered with chronic HBV (n = 129 in DHCS and 126 (48% of HIV patients with HCV (n = 264 in DHCS were registered with these diagnoses in the DNHR. Further 17 and 8 patients were registered with HBV and HCV respectively in DNHR, but not in DHCS. The positive predictive values of being registered with HBV and HCV in DHCS were thereby estimated to 0.88 and 0.97 and in DNHR to 0.32 and 0.54. Conclusion The study demonstrates that secondary data from national hospital databases may be reliable for identification of patients diagnosed with HIV infection. However, the predictive value of co-morbidity data may be low.

  18. Association of Internalized and Social Network Level HIV Stigma With High-Risk Condomless Sex Among HIV-Positive African American Men.

    Science.gov (United States)

    Wagner, Glenn J; Bogart, Laura M; Klein, David J; Green, Harold D; Mutchler, Matt G; McDavitt, Bryce; Hilliard, Charles

    2016-08-01

    We examined whether internalized HIV stigma and perceived HIV stigma from social network members (alters), including the most popular and most similar alter, predicted condomless intercourse with negative or unknown HIV status partners among 125 African American HIV-positive men. In a prospective, observational study, participants were administered surveys at baseline and months 6 and 12, with measures including sexual behavior, internalized HIV stigma, and an egocentric social network assessment that included several measures of perceived HIV stigma among alters. In longitudinal multivariable models comparing the relative predictive value of internalized stigma versus various measures of alter stigma, significant predictors of having had condomless intercourse included greater internalized HIV stigma (in all models), the perception that a popular (well-connected) alter or alter most like the participant agrees with an HIV stigma belief, and the interaction of network density with having any alter that agrees with a stigma belief. The interaction indicated that the protective effect of greater density (connectedness between alters) in terms of reduced risk behavior dissipated in the presence of perceived alter stigma. These findings call for interventions that help people living with HIV to cope with their diagnosis and reduce stigma, and inform the targets of social network-based and peer-driven HIV prevention interventions.

  19. The impact of HIV status, HIV disease progression, and post-traumatic stress symptoms on the health-related quality of life of Rwandan women genocide survivors.

    Science.gov (United States)

    Gard, Tracy L; Hoover, Donald R; Shi, Qiuhu; Cohen, Mardge H; Mutimura, Eugene; Adedimeji, Adebola A; Anastos, Kathryn

    2013-10-01

    We examined whether established associations between HIV disease and HIV disease progression on worse health-related quality of life (HQOL) were applicable to women with severe trauma histories, in this case Rwandan women genocide survivors, the majority of whom were HIV-infected. Additionally, this study attempted to clarify whether post-traumatic stress symptoms were uniquely associated with HQOL or confounded with depression. The Rwandan Women's Interassociation Study and Assessment was a longitudinal prospective study of HIV-infected and uninfected women. At study entry, 922 women (705 HIV+ and 217 HIV-) completed measures of symptoms of post-traumatic stress and HQOL as well as other demographic, clinical, and behavioral characteristics. Even after controlling for potential confounders and mediators, HIV+ women, in particular those with the lowest CD4 counts, scored significantly worse on HQOL and overall quality of life (QOL) than did HIV- women. Even after controlling for depression and HIV disease progression, women with more post-traumatic stress symptoms scored worse on HQOL and overall QOL than women with fewer post-traumatic stress symptoms. This study demonstrated that post-traumatic stress symptoms were independently associated with HQOL and overall QOL, independent of depression and other confounders or potential mediators. Future research should examine whether the long-term impact of treatment on physical and psychological symptoms of HIV and post-traumatic stress symptoms would generate improvement in HQOL.

  20. Therapeutic HIV Peptide Vaccine

    DEFF Research Database (Denmark)

    Fomsgaard, Anders

    2015-01-01

    Therapeutic vaccines aim to control chronic HIV infection and eliminate the need for lifelong antiretroviral therapy (ART). Therapeutic HIV vaccine is being pursued as part of a functional cure for HIV/AIDS. We have outlined a basic protocol for inducing new T cell immunity during chronic HIV-1...... infection directed to subdominant conserved HIV-1 epitopes restricted to frequent HLA supertypes. The rationale for selecting HIV peptides and adjuvants are provided. Peptide subunit vaccines are regarded as safe due to the simplicity, quality, purity, and low toxicity. The caveat is reduced immunogenicity...

  1. A lipid storage-like disorder contributes to cognitive decline in HIV-infected subjects.

    Science.gov (United States)

    Bandaru, Veera Venkata Ratnam; Mielke, Michelle M; Sacktor, Ned; McArthur, Justin C; Grant, Igor; Letendre, Scott; Chang, Linda; Wojna, Valerie; Pardo, Carlos; Calabresi, Peter; Munsaka, Sody; Haughey, Norman J

    2013-10-22

    In this multicenter cohort study, we sought to identify prognostic and associative metabolic indicators for HIV-associated neurocognitive disorders (HAND). A quantitative lipidomic analysis was conducted on 524 longitudinal CSF samples collected from 7 different performance sites across the mainland United States, Hawaii, and Puerto Rico. Subjects included HIV-infected individuals with longitudinal clinical and cognitive testing data and cognitively normal HIV-negative healthy controls. At baseline, HIV+ subjects could be differentiated from HIV- controls by reductions in a single ceramide species and increases in multiple forms of cholesterol. Perturbations in cholesterol metabolism and ceramide were influenced by combined antiretroviral therapy (cART) use. There were no cross-sectional baseline differences in any lipid metabolite when HIV+ subjects were grouped according to cognitive status. However, a single sphingolipid metabolite and reduced levels of esterified cholesterols were prognostic indicators of incident cognitive decline. Longitudinal patterns of these disturbances in sphingolipid and sterol metabolism suggest that a progressive disorder of lipid metabolism that is similar to disorders of lipid storage may contribute to the pathogenesis of HAND. These findings suggest that HIV infection and cART are independently associated with a CNS metabolic disturbance, identify surrogate markers that are prognostic for cognitive decline, and implicate a lipid storage-like disorder in the progression of HAND.

  2. Longitudinal joint specifications and performance.

    Science.gov (United States)

    2012-08-01

    Deterioration of longitudinal joints is widely recognized as one of the major factors contributing to failure of asphalt pavements. Finding : ways to improve the durability of longitudinal joints will lead to improved service lives and lower life cyc...

  3. Identification of genuine primary pulmonary NK cell lymphoma via clinicopathologic observation and clonality assay.

    Science.gov (United States)

    Gong, Li; Wei, Long-Xiao; Huang, Gao-Sheng; Zhang, Wen-Dong; Wang, Lu; Zhu, Shao-Jun; Han, Xiu-Juan; Yao, Li; Lan, Miao; Li, Yan-Hong; Zhang, Wei

    2013-08-19

    Extranodal natural killer (NK)/T-cell lymphoma, nasal type, is an uncommon lymphoma associated with the Epstein-Barr virus (EBV). It most commonly involves the nasal cavity and upper respiratory tract. Primary pulmonary NK/T cell lymphoma is extremely rare. If a patient with a NK or T-cell tumor has an unusual reaction to treatment or an unusual prognosis, it is wise to differentiate NK from T-cell tumors. The clinicopathologic characteristics, immunophenotype, EBV in situ hybridization, and T cell receptor (TCR) gene rearrangement of primary pulmonary NK cell lymphoma from a 73-year-old Chinese woman were investigated and the clonal status was determined using female X-chromosomal inactivation mosaicism and polymorphisms at the phosphoglycerate kinase (PGK) gene. The lesion showed the typical histopathologic characteristics and immunohistochemical features of NK/T cell lymphoma. However, the sample was negative for TCR gene rearrangement. A clonality assay demonstrated that the lesion was monoclonal. It is concluded that this is the first recorded case of genuine primary pulmonary NK cell lymphoma. The purpose of the present work is to recommend that pathologists carefully investigate the whole lesion to reduce the likelihood that primary pulmonary NK cell lymphoma will be misdiagnosed as an infectious lesion. In addition, TCR gene rearrangement and clonal analysis, which is based on female X-chromosomal inactivation mosaicism and polymorphisms at PGK and androgen receptor (AR) loci, were found to play important roles in differentiating NK cell lymphoma from T cell lymphoma. The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/5205300349457729.

  4. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

    Science.gov (United States)

    Dale, Julia; Price, Erin P; Hornstra, Heidie; Busch, Joseph D; Mayo, Mark; Godoy, Daniel; Wuthiekanun, Vanaporn; Baker, Anthony; Foster, Jeffrey T; Wagner, David M; Tuanyok, Apichai; Warner, Jeffrey; Spratt, Brian G; Peacock, Sharon J; Currie, Bart J; Keim, Paul; Pearson, Talima

    2011-12-01

    Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST). These populations correlate with the major foci of endemicity (Australia and Southeast Asia). Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs). Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic characteristics

  5. Epidemiological tracking and population assignment of the non-clonal bacterium, Burkholderia pseudomallei.

    Directory of Open Access Journals (Sweden)

    Julia Dale

    2011-12-01

    Full Text Available Rapid assignment of bacterial pathogens into predefined populations is an important first step for epidemiological tracking. For clonal species, a single allele can theoretically define a population. For non-clonal species such as Burkholderia pseudomallei, however, shared allelic states between distantly related isolates make it more difficult to identify population defining characteristics. Two distinct B. pseudomallei populations have been previously identified using multilocus sequence typing (MLST. These populations correlate with the major foci of endemicity (Australia and Southeast Asia. Here, we use multiple Bayesian approaches to evaluate the compositional robustness of these populations, and provide assignment results for MLST sequence types (STs. Our goal was to provide a reference for assigning STs to an established population without the need for further computational analyses. We also provide allele frequency results for each population to enable estimation of population assignment even when novel STs are discovered. The ability for humans and potentially contaminated goods to move rapidly across the globe complicates the task of identifying the source of an infection or outbreak. Population genetic dynamics of B. pseudomallei are particularly complicated relative to other bacterial pathogens, but the work here provides the ability for broad scale population assignment. As there is currently no independent empirical measure of successful population assignment, we provide comprehensive analytical details of our comparisons to enable the reader to evaluate the robustness of population designations and assignments as they pertain to individual research questions. Finer scale subdivision and verification of current population compositions will likely be possible with genotyping data that more comprehensively samples the genome. The approach used here may be valuable for other non-clonal pathogens that lack simple group-defining genetic

  6. Clonal mutations in primary human glial tumors: evidence in support of the mutator hypothesis

    Directory of Open Access Journals (Sweden)

    Sarkar Chitra

    2007-10-01

    Full Text Available Abstract Background A verifiable consequence of the mutator hypothesis is that even low grade neoplasms would accumulate a large number of mutations that do not influence the tumor phenotype (clonal mutations. In this study, we have attempted to quantify the number of clonal mutations in primary human gliomas of astrocytic cell origin. These alterations were identified in tumor tissue, microscopically confirmed to have over 70% neoplastic cells. Methods Random Amplified Polymorphic DNA (RAPD analysis was performed using a set of fifteen 10-mer primers of arbitrary but definite sequences in 17 WHO grade II astrocytomas (low grade diffuse astrocytoma or DA and 16 WHO grade IV astrocytomas (Glioblastoma Multiforme or GBM. The RAPD profile of the tumor tissue was compared with that of the leucocyte DNA of the same patient and alteration(s scored. A quantitative estimate of the overall genomic changes in these tumors was obtained by 2 different modes of calculation. Results The overall change in the tumors was estimated to be 4.24% in DA and 2.29% in GBM by one method and 11.96% and 6.03% in DA and GBM respectively by the other. The difference between high and lower grade tumors was statistically significant by both methods. Conclusion This study demonstrates the presence of extensive clonal mutations in gliomas, more in lower grade. This is consistent with our earlier work demonstrating that technique like RAPD analysis, unbiased for locus, is able to demonstrate more intra-tumor genetic heterogeneity in lower grade gliomas compared to higher grade. The results support the mutator hypothesis proposed by Loeb.

  7. Identification and clonal characterisation of a progenitor cell sub-population in normal human articular cartilage.

    Directory of Open Access Journals (Sweden)

    Rebecca Williams

    Full Text Available BACKGROUND: Articular cartilage displays a poor repair capacity. The aim of cell-based therapies for cartilage defects is to repair damaged joint surfaces with a functional replacement tissue. Currently, chondrocytes removed from a healthy region of the cartilage are used but they are unable to retain their phenotype in expanded culture. The resulting repair tissue is fibrocartilaginous rather than hyaline, potentially compromising long-term repair. Mesenchymal stem cells, particularly bone marrow stromal cells (BMSC, are of interest for cartilage repair due to their inherent replicative potential. However, chondrocyte differentiated BMSCs display an endochondral phenotype, that is, can terminally differentiate and form a calcified matrix, leading to failure in long-term defect repair. Here, we investigate the isolation and characterisation of a human cartilage progenitor population that is resident within permanent adult articular cartilage. METHODS AND FINDINGS: Human articular cartilage samples were digested and clonal populations isolated using a differential adhesion assay to fibronectin. Clonal cell lines were expanded in growth media to high population doublings and karyotype analysis performed. We present data to show that this cell population demonstrates a restricted differential potential during chondrogenic induction in a 3D pellet culture system. Furthermore, evidence of high telomerase activity and maintenance of telomere length, characteristic of a mesenchymal stem cell population, were observed in this clonal cell population. Lastly, as proof of principle, we carried out a pilot repair study in a goat in vivo model demonstrating the ability of goat cartilage progenitors to form a cartilage-like repair tissue in a chondral defect. CONCLUSIONS: In conclusion, we propose that we have identified and characterised a novel cartilage progenitor population resident in human articular cartilage which will greatly benefit future cell

  8. Clonal mutations in primary human glial tumors: evidence in support of the mutator hypothesis

    International Nuclear Information System (INIS)

    Misra, Anjan; Chattopadhyay, Parthaprasad; Chosdol, Kunzang; Sarkar, Chitra; Mahapatra, Ashok K; Sinha, Subrata

    2007-01-01

    A verifiable consequence of the mutator hypothesis is that even low grade neoplasms would accumulate a large number of mutations that do not influence the tumor phenotype (clonal mutations). In this study, we have attempted to quantify the number of clonal mutations in primary human gliomas of astrocytic cell origin. These alterations were identified in tumor tissue, microscopically confirmed to have over 70% neoplastic cells. Random Amplified Polymorphic DNA (RAPD) analysis was performed using a set of fifteen 10-mer primers of arbitrary but definite sequences in 17 WHO grade II astrocytomas (low grade diffuse astrocytoma or DA) and 16 WHO grade IV astrocytomas (Glioblastoma Multiforme or GBM). The RAPD profile of the tumor tissue was compared with that of the leucocyte DNA of the same patient and alteration(s) scored. A quantitative estimate of the overall genomic changes in these tumors was obtained by 2 different modes of calculation. The overall change in the tumors was estimated to be 4.24% in DA and 2.29% in GBM by one method and 11.96% and 6.03% in DA and GBM respectively by the other. The difference between high and lower grade tumors was statistically significant by both methods. This study demonstrates the presence of extensive clonal mutations in gliomas, more in lower grade. This is consistent with our earlier work demonstrating that technique like RAPD analysis, unbiased for locus, is able to demonstrate more intra-tumor genetic heterogeneity in lower grade gliomas compared to higher grade. The results support the mutator hypothesis proposed by Loeb

  9. Clonal integration supports the expansion from terrestrial to aquatic environments of the amphibious stoloniferous herb Alternanthera philoxeroides.

    Science.gov (United States)

    Wang, N; Yu, F-H; Li, P-X; He, W-M; Liu, J; Yu, G-L; Song, Y-B; Dong, M

    2009-05-01

    Effects of clonal integration on land plants have been extensively studied, but little is known about the role in amphibious plants that expand from terrestrial to aquatic conditions. We simulated expansion from terrestrial to aquatic habitats in the amphibious stoloniferous alien invasive alligator weed (Alternanthera philoxeroides) by growing basal ramets of clonal fragments in soils connected (allowing integration) or disconnected (preventing integration) to the apical ramets of the same fragments submerged in water to a depth of 0, 5, 10 or 15 cm. Clonal integration significantly increased growth and clonal reproduction of the apical ramets, but decreased both of these characteristics in basal ramets. Consequently, integration did not affect the performance of whole clonal fragments. We propose that alligator weed possesses a double-edged mechanism during population expansion: apical ramets in aquatic habitats can increase growth through connected basal parts in terrestrial habitats; however, once stolon connections with apical ramets are lost by external disturbance, the basal ramets in terrestrial habitats increase stolon and ramet production for rapid spreading. This may contribute greatly to the invasiveness of alligator weed and also make it very adaptable to habitats with heavy disturbance and/or highly heterogeneous resource supply.

  10. Confirmation of the reported association of clonal chromosomal mosaicism with an increased risk of incident hematologic cancer.

    Directory of Open Access Journals (Sweden)

    Ursula M Schick

    Full Text Available Chromosomal abnormalities provide clinical utility in the diagnosis and treatment of hematologic malignancies, and may be predictive of malignant transformation in individuals without apparent clinical presentation of a hematologic cancer. In an effort to confirm previous reports of an association between clonal mosaicism and incident hematologic cancer, we applied the anomDetectBAF algorithm to call chromosomal anomalies in genotype data from previously conducted Genome Wide Association Studies (GWAS. The genotypes were initially collected from DNA derived from peripheral blood of 12,176 participants in the Group Health electronic Medical Records and Genomics study (eMERGE and the Women's Health Initiative (WHI. We detected clonal mosaicism in 169 individuals (1.4% and large clonal mosaic events (>2 mb in 117 (1.0% individuals. Though only 9.5% of clonal mosaic carriers had an incident diagnosis of hematologic cancer (multiple myeloma, myelodysplastic syndrome, lymphoma, or leukemia, the carriers had a 5.5-fold increased risk (95% CI: 3.3-9.3; p-value = 7.5×10(-11 of developing these cancers subsequently. Carriers of large mosaic anomalies showed particularly pronounced risk of subsequent leukemia (HR = 19.2, 95% CI: 8.9-41.6; p-value = 7.3×10(-14. Thus we independently confirm the association between detectable clonal mosaicism and hematologic cancer found previously in two recent publications.

  11. Evidence for Within-Host Genetic Recombination among the Human Pegiviral Strains in HIV Infected Subjects.

    Science.gov (United States)

    Wu, Haoming; Padhi, Abinash; Xu, Junqiang; Gong, Xiaoyan; Tien, Po

    2016-01-01

    The non-pathogenic Human Pegivirus (HPgV, formerly GBV-C/HGV), the most prevalent RNA virus worldwide, is known to be associated with reduced morbidity and mortality in HIV-infected individuals. Although previous studies documented its ubiquity and important role in HIV-infected individuals, little is known about the underlying genetic mechanisms that maintain high genetic diversity of HPgV within the HIV-infected individuals. To assess the within-host genetic diversity of HPgV and forces that maintain such diversity within the co-infected hosts, we performed phylogenetic analyses taking into account 229 HPgV partial E1-E2 clonal sequences representing 15 male and 8 female co-infected HIV patients from Hubei province of central China. Our results revealed the presence of eleven strongly supported clades. While nine clades belonged to genotype 3, two clades belonged to genotype 2. Additionally, four clades that belonged to genotype 3 exhibited inter-clade recombination events. The presence of clonal sequences representing multiple clades within the HIV-infected individual provided the evidence of co-circulation of HPgV strains across the region. Of the 23 patients, six patients (i.e., five males and one female) were detected to have HPgV recombinant sequences. Our results also revealed that while male patients shared the viral strains with other patients, viral strains from the female patients had restricted dispersal. Taken together, the present study revealed that multiple infections with divergent HPgV viral strains may have caused within-host genetic recombination, predominantly in male patients, and therefore, could be the major driver in shaping genetic diversity of HPgV.

  12. Clonal relationship among Vibrio cholerae O1 El Tor strains isolated in Somalia.

    Science.gov (United States)

    Scrascia, Maria; Pugliese, Nicola; Maimone, Francesco; Mohamud, Kadigia A; Grimont, Patrick A D; Materu, Sadiki F; Pazzani, Carlo

    2009-03-01

    One hundred and three Vibrio cholerae O1 strains, selected to represent the cholera outbreaks which occurred in Somalia in 1998-1999, were characterized by random amplified polymorphic DNA patterns, ribotyping, and antimicrobial susceptibility. All strains showed a unique amplified DNA pattern and 2 closely related ribotypes (B5a and B8a), among which B5a was the more frequently identified. Ninety-one strains were resistant to ampicillin, chloramphenicol, spectinomycin, streptomycin, sulfamethoxazole, and trimethoprim, conferred, except for spectinomycin, by a conjugative plasmid IncC. These findings indicated that the group of strains active in Somalia in the late 1990s had a clonal origin.

  13. Clonal propagation of Stevia rebaudiana Bertoni by stem-tip culture.

    Science.gov (United States)

    Tamura, Y; Nakamura, S; Fukui, H; Tabata, M

    1984-10-01

    Clonal propagation of Stevia rebaudiana has been established by culturing stem-tips with a few leaf primordia on an agar medium supplemented with a high concentration (10 mg/l) of kinetin. Anatomical examination has suggested that these multiple shoots originate from a number of adventitious buds formed on the margin of the leaf. Innumerable shoots can be obtained by repeating the cycle of multiple-shoot formation from a single stem-tip of Stevia. These shoots produce roots when transferred to a medium containing NAA (0.1 mg/l) without kinetin. The regenerated plantlets can be transplanted to soil.

  14. Demographic variability and heterogeneity among individuals within and among clonal bacteria strains

    DEFF Research Database (Denmark)

    Jouvet, Lionel; Rodriguez-Rojas, Alexandro; Steiner, Ulrich

    2018-01-01

    to accurately decompose the drivers of heterogeneity among individuals as genetically fixed or selectively neutral. Rather than working on wild populations we present here data from a simple bacterial system in the lab, Escherichia coli. Our system, based on cutting-edge microfluidic techniques, provides high...... control over the genotype and the environment. It therefore allows to unambiguously decompose and quantify fixed genetic variability and dynamic stochastic variability among individuals. We show that within clonal individual variability (dynamic heterogeneity) in lifespan and lifetime reproduction...

  15. Clonal outbreaks of [ Pasteurella] pneumotropica biovar Heyl in two mouse colonies

    DEFF Research Database (Denmark)

    Adhikary, Sadhana; Bisgaard, Magne; Dagnæs-Hansen, Frederik

    2017-01-01

    The aim of this study was to document the pathogenic role of biovar Heyl of [Pasteurella] pneumotropica in mouse colonies. Fifty-three isolates associated with mastitis and orbital, cutaneous and vaginal abscesses as well as isolates from the nose and vagina of healthy mice were investigated...... strains with the same rpoB sequence type, as shown by the PFGE profiles. The investigation documented that members of biovar Heyl of [P.] pneumotropica caused disease outbreaks in mouse colonies since the clonality indicated a primary role of [P.] pneumotropica biovar Heyl in the infections observed....

  16. Probable clonal origin of acute myeloblastic leukemia following radiation and chemotherapy of colon cancer

    International Nuclear Information System (INIS)

    Wiggans, R.G.; Jacobson, R.J.; Fialkow, P.J.; Woolley, P.V. III; Macdonald, J.S.; Schein, P.S.

    1978-01-01

    A 64-yr-old female developed acute myeloblastic leukemia following radiation and drug therapy for colon carcinoma. The patient was heterozygous for glucose-6-phosphate dehydrogenase [G-6-PD) and displayed types A and B isoenzymes in nonhematopoietic tissue. In contrast, only type B G-6-PD was observed in peripheral blood white cells. In addition, a karyotypic abnormality was found in peripheral blood and marrow cells but not in skin fibroblasts. The data are consistent with a clonal origin of this leukemia

  17. HIV-infected Children in Malawi Have Decreased Performance on the 6-minute Walk Test With Preserved Cardiac Mechanics Regardless of Antiretroviral Treatment Status.

    Science.gov (United States)

    Sims Sanyahumbi, Amy E; Hosseinipour, Mina C; Guffey, Danielle; Hoffman, Irving; Kazembe, Peter N; McCrary, Madeline; Minard, Charles G; van der Horst, Charles; Sable, Craig A

    2017-07-01

    The aims of this study were to 1) determine if cardiac disease can be detected in HIV-infected children by strain imaging and 2) to evaluate differences in exercise performance between HIV-infected children on antiretroviral therapy (ART) and HIV-infected children not yet on ART and in HIV-uninfected children by 6-minute walk tests (6MWTs). This cross-sectional study evaluated cardiac function by echocardiogram and exercise performance by 6MWT in HIV-infected and HIV-uninfected children 4-18 years of age in Lilongwe, Malawi. Analyses compared HIV uninfected, HIV infected not yet on ART, and HIV infected on ART. Comparisons used χ test, t test, analysis of variance and multiple linear regression. No differences were found in ejection fraction, shortening fraction or strain in 73 children not yet on ART, 149 on ART and 77 HIV-uninfected controls. As viral load increased, children had worse circumferential strain. In addition, children receiving ART had better circumferential strain than those not yet on ART. Increased CD4 percentage was associated with better longitudinal strain and farther 6MWT distance. As longitudinal strain worsened, the 6MWT distance decreased. HIV-infected children not yet on ART walked a mean of 25.8 m less than HIV-uninfected children, and HIV-infected children on ART walked 25.9 m less (P = 0.015 comparing 3 groups). HIV-uninfected children performed better on the 6MWT than HIV-infected children. Lower viral load, being on ART, and higher CD4 percentage were associated with better strain measures. Better longitudinal strain was associated with a farther 6MWT distance. Overall, ejection fraction, shortening fraction and strain measures between groups were similar, so cardiac strain did not detect cardiac dysfunction in this young population.

  18. Association between HIV status and psychological symptoms in perimenopausal women.

    Science.gov (United States)

    Looby, Sara E; Psaros, Christina; Raggio, Greer; Rivard, Corinne; Smeaton, Laura; Shifren, Jan; Grinspoon, Steven; Joffe, Hadine

    2018-01-29

    HIV-infected women are burdened by depression and anxiety, which may impact adherence to antiretroviral therapy and overall quality of life. Yet, little is known about the scope of psychological symptoms in the growing number of HIV-infected women reaching menopause, when affective symptoms are more prevalent in the general population. We conducted a longitudinal study to compare affective symptoms between perimenopausal HIV-infected and non-HIV-infected women. The Center for Epidemiologic Studies Depression Scale (CES-D), and the Generalized Anxiety Disorder scale (GAD-7) were completed at baseline and 12 months among 33 HIV-infected and 33 non-HIV-infected perimenopausal women matched by race, age, menstrual patterns, and BMI. Linear regression models estimated the relationship of baseline GAD-7 and CES-D scores with clinical factors. All women were perimenopausal at baseline, and the vast majority remained perimenopausal throughout follow-up. HIV status was associated with higher baseline CES-D scores (median [interquartile range] 21 [12, 29] vs 10 [5, 14]; P = 0.03) and GAD-7 scores (7 [5, 15] vs 2 [1, 7]; P = 0.01), controlling for smoking, substance use, and antidepressant use. Depressive symptoms and anxiety remained significantly higher in the HIV-infected women at 12 months (P ≤ 0.01). Significant relationships of depressive symptoms (P = 0.048) and anxiety (P = 0.02) with hot flash severity were also observed. Perimenopausal HIV-infected women experienced a disproportionately high level of affective symptom burden over a 12-month observation period. Given the potential for these factors to influence adherence to HIV clinical care and quality of life, careful assessment and referral for treatment of these symptoms is essential.

  19. Longitudinal analysis of HIV risk behaviour patterns and their ...

    African Journals Online (AJOL)

    2018-02-06

    Feb 6, 2018 ... their predictors among public primary care patients with tuberculosis in South ... Keywords: sexual risk behaviour, TB patients, health status, mental ..... High prevalence and partner correlates of physical and sexual violence.

  20. HIV and Hepatitis C

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content HIV and Opportunistic Infections, Coinfections, and Conditions Home Understanding ... 4 p.m. ET) Send us an email HIV and Hepatitis C Last Reviewed: July 25, 2017 ...

  1. HIV/AIDS Basics

    Science.gov (United States)

    ... Partner Spotlight Awareness Days Get Tested Find an HIV testing site near you. Enter ZIP code or ... AIDS Get Email Updates on AAA Anonymous Feedback HIV/AIDS Media Infographics Syndicated Content Podcasts Slide Sets ...

  2. HIV and Tuberculosis (TB)

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content HIV and Opportunistic Infections, Coinfections, and Conditions Home Understanding ... 4 p.m. ET) Send us an email HIV and Tuberculosis (TB) Last Reviewed: June 14, 2018 ...

  3. HIV and Hepatitis B

    Science.gov (United States)

    ... AIDS Drugs Clinical Trials Apps skip to content HIV and Opportunistic Infections, Coinfections, and Conditions Home Understanding ... 4 p.m. ET) Send us an email HIV and Hepatitis B Last Reviewed: July 24, 2017 ...

  4. Thrombocytopenia in HIV

    African Journals Online (AJOL)

    2007-06-15

    infected community and can severely hamper thrombopoietin production, due to liver damage. HIV and platelets. Thrombocytopenia in HIV was first described in 1982. The prevalence is more or less 40%, depending on which ...

  5. HIV Resistance Testing

    Science.gov (United States)

    ... 14, 2016 Select a Language: Fact Sheet 126 HIV Resistance Testing WHAT IS RESISTANCE? HOW DOES RESISTANCE ... ARVs. If you miss doses of your medications, HIV will multiply more easily. More mutations will occur. ...

  6. HIV: Treatment and Comorbidity

    NARCIS (Netherlands)

    C. Rokx (Casper)

    2016-01-01

    markdownabstractClinicians worldwide strive to improve HIV care for their patients. Antiretroviral therapy prevents HIV related mortality and is lifelong. A clinical evaluation of these treatment strategies is necessary to identify strategies that may jeopardize treatment effectiveness and patient

  7. Testing for HIV

    Science.gov (United States)

    ... Medical Devices Radiation-Emitting Products Vaccines, Blood & Biologics Animal & Veterinary Cosmetics Tobacco Products Vaccines, Blood & Biologics Home Vaccines, Blood & Biologics Safety & Availability (Biologics) HIV Home Test Kits Testing for HIV Share Tweet Linkedin Pin it More ...

  8. Pregnancy and HIV

    Science.gov (United States)

    ... 17, 2014 Select a Language: Fact Sheet 611 Pregnancy and HIV HOW DO BABIES GET AIDS? HOW CAN WE ... doses due to nausea and vomiting during early pregnancy, giving HIV a chance to develop resistance The risk of ...

  9. Comprehensive knowledge of HIV among women in rural Mozambique: development and validation of the HIV knowledge 27 scale.

    Directory of Open Access Journals (Sweden)

    Philip J Ciampa

    Full Text Available The relationship between HIV knowledge and HIV-related behaviors in settings like Mozambique has been limited by a lack of rigorously validated measures.A convenience sample of women seeking prenatal care at two clinics were administered an adapted, orally-administered, 27 item HIV-knowledge scale, the HK-27. Validation analyses were stratified by survey language (Portuguese and Echuabo. Kuder-Richardson (KR-20 coefficients estimated internal reliability. Construct validity was assessed with bivariate associations between HK-27 scores (% correct and selected participant characteristics. The association between knowledge, self-reported HIV testing, and HIV infection were evaluated with multivariable logistic regression.Participants (N = 348 had a median age of 24; 188 spoke Portuguese, and 160 spoke Echuabo. Mean HK-27 scores were higher for Portuguese-speaking participants than Echuabo-speaking participants (68% correct vs. 42%, p0.8 for scales in both languages. Higher HK-27 scores were significantly (p≤0.05 correlated with more education, more media items in the home, a history of HIV testing, and participant work outside of the home for women of both languages. HK-27 scores were independently associated with completion of HIV testing in multivariable analysis (per 1% correct: aOR:1.02, 95%CI:0.01-0.03, p = 0.01, but not with HIV infection.HK-27 is a reliable and valid measure of HIV knowledge among Portuguese and Echuabo-speaking Mozambican women. The HK-27 demonstrated significant knowledge deficits among women in the study, and higher scores were associated with higher HIV testing probability. Future studies should evaluate the role of the HK-27 in longitudinal studies and in other populations.

  10. Comprehensive knowledge of HIV among women in rural Mozambique: development and validation of the HIV knowledge 27 scale.

    Science.gov (United States)

    Ciampa, Philip J; Skinner, Shannon L; Patricio, Sérgio R; Rothman, Russell L; Vermund, Sten H; Audet, Carolyn M

    2012-01-01

    The relationship between HIV knowledge and HIV-related behaviors in settings like Mozambique has been limited by a lack of rigorously validated measures. A convenience sample of women seeking prenatal care at two clinics were administered an adapted, orally-administered, 27 item HIV-knowledge scale, the HK-27. Validation analyses were stratified by survey language (Portuguese and Echuabo). Kuder-Richardson (KR-20) coefficients estimated internal reliability. Construct validity was assessed with bivariate associations between HK-27 scores (% correct) and selected participant characteristics. The association between knowledge, self-reported HIV testing, and HIV infection were evaluated with multivariable logistic regression. Participants (N = 348) had a median age of 24; 188 spoke Portuguese, and 160 spoke Echuabo. Mean HK-27 scores were higher for Portuguese-speaking participants than Echuabo-speaking participants (68% correct vs. 42%, p0.8) for scales in both languages. Higher HK-27 scores were significantly (p≤0.05) correlated with more education, more media items in the home, a history of HIV testing, and participant work outside of the home for women of both languages. HK-27 scores were independently associated with completion of HIV testing in multivariable analysis (per 1% correct: aOR:1.02, 95%CI:0.01-0.03, p = 0.01), but not with HIV infection. HK-27 is a reliable and valid measure of HIV knowledge among Portuguese and Echuabo-speaking Mozambican women. The HK-27 demonstrated significant knowledge deficits among women in the study, and higher scores were associated with higher HIV testing probability. Future studies should evaluate the role of the HK-27 in longitudinal studies and in other populations.

  11. Recreational Drug Use and T Lymphocyte Subpopulations in HIV-uninfected and HIV-infected Men

    Science.gov (United States)

    Chao, Chun; Jacobson, Lisa P; Tashkin, Donald; Martínez-Maza, Otoniel; Roth, Michael D; Margolick, Joseph B; Chmiel, Joan S; Rinaldo, Charles; Zhang, Zuo-Feng; Detels, Roger

    2009-01-01

    The effects of recreational drugs on CD4 and CD8 T cells in humans are not well understood. We conducted a longitudinal analysis of men who have sex with men (MSM) enrolled in the Multicenter AIDS Cohort Study to define associations between self-reported use of marijuana, cocaine, poppers and amphetamines, and CD4 and CD8 T cell parameters in both HIV-uninfected and HIV-infected MSM. For the HIV-infected MSM, we used clinical and laboratory data collected semiannually before 1996 to avoid potential effects of antiretroviral treatment. A regression model that allowed random intercepts and slopes as well as autoregressive covariance structure for within subject errors was used. Potential confounders adjusted for included length of follow-up, demographics, tobacco smoking, alcohol use, risky sexual behaviors, history of sexually transmitted infections, and antiviral therapy. We found no clinically meaningful associations between use of marijuana, cocaine, poppers, or amphetamines and CD4 and CD8 T cell counts, percentages, or rates of change in either HIV-uninfected or -infected men. The regression coefficients were of minimum magnitude despite some reaching statistical significance. No threshold effect was detected for frequent (at least weekly) or continuous substance use in the previous year. These results indicate that use of these substances does not adversely affect the numbers and percentages of circulating CD4 or CD8 T cells in either HIV-uninfected or -infected MSM. PMID:18180115

  12. Clonal Propagation of Khaya senegalensis: The Effects of Stem Length, Leaf Area, Auxins, Smoke Solution, and Stockplant Age

    Directory of Open Access Journals (Sweden)

    Catherine Ky-Dembele

    2011-01-01

    Full Text Available Khaya senegalensis is a multipurpose African timber species. The development of clonal propagation could improve plantation establishment, which is currently impeded by mahogany shoot borer. To examine its potential for clonal propagation, the effects of cutting length, leaf area, stockplant maturation, auxin, and smoke solution treatments were investigated. Leafy cuttings rooted well (up to 80% compared to leafless cuttings (0%. Cuttings taken from seedlings rooted well (at least 95%, but cuttings obtained from older trees rooted poorly (5% maximum. The rooting ability of cuttings collected from older trees was improved (16% maximum by pollarding. Auxin application enhanced root length and the number of roots while smoke solution did not improve cuttings' rooting ability. These results indicate that juvenile K. senegalensis is amenable to clonal propagation, but further work is required to improve the rooting of cuttings from mature trees.

  13. The HIV Airway

    African Journals Online (AJOL)

    Adele

    dren living with HIV/AIDS. Annual national antenatal surveil- lance shows an HIV prevalence of 26.5% among pregnant women. Anaesthetists are confronted with an increasing number of HIV infected patients, presenting for both emergency and elective sur- gery. They range from having asymptomatic infection to end stage.

  14. HIV/AIDS

    Science.gov (United States)

    ... Key populations are groups who are at increased risk of HIV irrespective of epidemic type or local context. They include: men who have sex with men, ... HIV testing and counselling; HIV treatment and care; risk-reduction ... management of STIs, tuberculosis and viral hepatitis. Elimination of ...

  15. HIV Antibody Test

    Science.gov (United States)

    ... 65 in the case of the USPSTF) and pregnant women be screened for HIV at least once. The CDC and American College ... to make sure she is not infected with HIV before getting pregnant may opt to get tested (see Pregnancy: HIV .) ...

  16. 24-month HIV-free survival among infants born to HIV-positive women enrolled in Option B+ program in Kigali, Rwanda: The Kabeho Study.

    Science.gov (United States)

    Gill, Michelle M; Hoffman, Heather J; Ndatimana, Dieudonne; Mugwaneza, Placidie; Guay, Laura; Ndayisaba, Gilles F; Bobrow, Emily A; Asiimwe, Anita; Mofenson, Lynne M

    2017-12-01

    Lifelong antiretroviral therapy (ART) provision to all pregnant HIV-positive women ("Option B+") has been recommended by the World Health Organization since 2013, but there remain limited data on the effects of Option B+ on long-term HIV-free survival in breastfeeding HIV-exposed infants. The Kigali Antiretroviral and Breastfeeding Assessment for the Elimination of HIV (Kabeho) study enrolled HIV-positive women from the third trimester of pregnancy to 2 weeks postpartum in 14 heath facilities implementing Option B+ in Kigali, Rwanda. Mother-child pairs in the longitudinal observational cohort were followed until 24 months postpartum, with HIV diagnostic testing at 6 weeks, and 9, 18 and 24 months. The Kaplan-Meier method was used to estimate HIV transmission, survival, and HIV-free survival through 24 months. We enrolled 608 HIV-positive women in 2013-2014; birth outcome data were available for 600 women and 597 live-born infants. By 6 weeks, 11 infants had died and 3 infants had confirmed HIV infection (0.5% transmission; 95% confidence interval [CI] 0.2-1.6). At 9 months, there were 9 additional deaths and 2 new infections (cumulative transmission 0.9%, 95% CI 0.4-2.2). At 18 months, there were 6 additional deaths and no new infant infections. At 24 months, there were no additional child deaths and 1 new infection (cumulative 2.2%, 95% CI 0.7-7.0), for an overall 24-month HIV-free survival of 93.2% (95% CI 89.5-95.6). Low transmission rates and high HIV-free survival at 24 months were achieved in breastfeeding infants of HIV-positive mothers receiving universal ART in urban health facilities in Rwanda, though vigilance on maintaining viral suppression for ART-experienced women is needed. Copyright © 2017 The Authors. Published by Wolters Kluwer Health, Inc. All rights reserved.

  17. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

    Directory of Open Access Journals (Sweden)

    Kiwako S Araki

    Full Text Available In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals. We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers. We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms

  18. Genet-specific DNA methylation probabilities detected in a spatial epigenetic analysis of a clonal plant population.

    Science.gov (United States)

    Araki, Kiwako S; Kubo, Takuya; Kudoh, Hiroshi

    2017-01-01

    In sessile organisms such as plants, spatial genetic structures of populations show long-lasting patterns. These structures have been analyzed across diverse taxa to understand the processes that determine the genetic makeup of organismal populations. For many sessile organisms that mainly propagate via clonal spread, epigenetic status can vary between clonal individuals in the absence of genetic changes. However, fewer previous studies have explored the epigenetic properties in comparison to the genetic properties of natural plant populations. Here, we report the simultaneous evaluation of the spatial structure of genetic and epigenetic variation in a natural population of the clonal plant Cardamine leucantha. We applied a hierarchical Bayesian model to evaluate the effects of membership of a genet (a group of individuals clonally derived from a single seed) and vegetation cover on the epigenetic variation between ramets (clonal plants that are physiologically independent individuals). We sampled 332 ramets in a 20 m × 20 m study plot that contained 137 genets (identified using eight SSR markers). We detected epigenetic variation in DNA methylation at 24 methylation-sensitive amplified fragment length polymorphism (MS-AFLP) loci. There were significant genet effects at all 24 MS-AFLP loci in the distribution of subepiloci. Vegetation cover had no statistically significant effect on variation in the majority of MS-AFLP loci. The spatial aggregation of epigenetic variation is therefore largely explained by the aggregation of ramets that belong to the same genets. By applying hierarchical Bayesian analyses, we successfully identified a number of genet-specific changes in epigenetic status within a natural plant population in a complex context, where genotypes and environmental factors are unevenly distributed. This finding suggests that it requires further studies on the spatial epigenetic structure of natural populations of diverse organisms, particularly for

  19. Effects of Cu Pollution on the Expansion of an Amphibious Clonal Herb in Aquatic-Terrestrial Ecotones.

    Directory of Open Access Journals (Sweden)

    Liang Xu

    Full Text Available Physiological integration can enhance the performance of clonal plants in aquatic and terrestrial heterogeneous habitats and associated ecotones. Similar to nutrients, pollutants may be transported among connected ramets via physiological integration. Few studies have examined the expansion of amphibious clonal plants from terrestrial to aquatic environments, particularly when the local water supply is polluted with heavy metals. A greenhouse experiment was conducted using the amphibious plant Alternanthera philoxeroides to determine whether Cu can spread among clonal plants and examine the corresponding effects of this pollution on the expansion of clonal plants in aquatic-terrestrial ecotones. Ramets from the same clonal fragments were rooted in unpolluted soil and polluted water at five different levels. The responses of the ramets in terrestrial and aquatic habitats were quantified via traits associated with growth, morphology and Cu accumulation. The results indicated that ramets in soil and water significantly differed in nearly all of these traits. The expansion of populations from terrestrial to polluted aquatic habitats was facilitated by stem elongation rather than new ramet production. The accumulated Cu in polluted ramets can be horizontally transported to other ramets in soil via connected stolons. In terms of clonal growth patterns, variations in Cu pollution intensity were negatively correlated with variations in the morphological and growth traits of ramets in polluted aquatic habitats and unpolluted soil. We concluded that Cu ions are distributed among the clones and accumulated in different ramet tissues in heterogeneous habitats. Therefore, we suggest that Cu pollution of aquatic-terrestrial ecotones, especially at high levels, can affect the growth and expansion of the whole clones because Cu ions are shared between integrated ramets.

  20. Effects of Cu Pollution on the Expansion of an Amphibious Clonal Herb in Aquatic-Terrestrial Ecotones.

    Science.gov (United States)

    Xu, Liang; Zhou, Zhen-Feng

    2016-01-01

    Physiological integration can enhance the performance of clonal plants in aquatic and terrestrial heterogeneous habitats and associated ecotones. Similar to nutrients, pollutants may be transported among connected ramets via physiological integration. Few studies have examined the expansion of amphibious clonal plants from terrestrial to aquatic environments, particularly when the local water supply is polluted with heavy metals. A greenhouse experiment was conducted using the amphibious plant Alternanthera philoxeroides to determine whether Cu can spread among clonal plants and examine the corresponding effects of this pollution on the expansion of clonal plants in aquatic-terrestrial ecotones. Ramets from the same clonal fragments were rooted in unpolluted soil and polluted water at five different levels. The responses of the ramets in terrestrial and aquatic habitats were quantified via traits associated with growth, morphology and Cu accumulation. The results indicated that ramets in soil and water significantly differed in nearly all of these traits. The expansion of populations from terrestrial to polluted aquatic habitats was facilitated by stem elongation rather than new ramet production. The accumulated Cu in polluted ramets can be horizontally transported to other ramets in soil via connected stolons. In terms of clonal growth patterns, variations in Cu pollution intensity were negatively correlated with variations in the morphological and growth traits of ramets in polluted aquatic habitats and unpolluted soil. We concluded that Cu ions are distributed among the clones and accumulated in different ramet tissues in heterogeneous habitats. Therefore, we suggest that Cu pollution of aquatic-terrestrial ecotones, especially at high levels, can affect the growth and expansion of the whole clones because Cu ions are shared between integrated ramets.

  1. Unexpected heterogeneity derived from Cas9 ribonucleoprotein-introduced clonal cells at the HPRT1 locus.

    Science.gov (United States)

    Sakuma, Tetsushi; Mochida, Keiji; Nakade, Shota; Ezure, Toru; Minagawa, Sachi; Yamamoto, Takashi

    2018-04-01

    Single-cell cloning is an essential technique for establishing genome-edited cell clones mediated by programmable nucleases such as CRISPR-Cas9. However, residual genome-editing activity after single-cell cloning may cause heterogeneity in the clonal cells. Previous studies showed efficient mutagenesis and rapid degradation of CRISPR-Cas9 components in cultured cells by introducing Cas9 ribonucleoproteins (RNPs). In this study, we investigated how the timing for single-cell cloning of Cas9 RNP-transfected cells affected the heterogeneity of the resultant clones. We carried out transfection of Cas9 RNPs targeting several loci in the HPRT1 gene in HCT116 cells, followed by single-cell cloning at 24, 48, 72 hr and 1 week post-transfection. After approximately 3 weeks of incubation, the clonal cells were collected and genotyped by high-resolution microchip electrophoresis and Sanger sequencing. Unexpectedly, long-term incubation before single-cell cloning resulted in highly heterogeneous clones. We used a lipofection method for transfection, and the media containing transfectable RNPs were not removed before single-cell cloning. Therefore, the active Cas9 RNPs were considered to be continuously incorporated into cells during the precloning incubation. Our findings provide a warning that lipofection of Cas9 RNPs may cause continuous introduction of gene mutations depending on the experimental procedures. © 2018 Molecular Biology Society of Japan and John Wiley & Sons Australia, Ltd.

  2. Wind power forecast using wavelet neural network trained by improved Clonal selection algorithm

    International Nuclear Information System (INIS)

    Chitsaz, Hamed; Amjady, Nima; Zareipour, Hamidreza

    2015-01-01

    Highlights: • Presenting a Morlet wavelet neural network for wind power forecasting. • Proposing improved Clonal selection algorithm for training the model. • Applying Maximum Correntropy Criterion to evaluate the training performance. • Extensive testing of the proposed wind power forecast method on real-world data. - Abstract: With the integration of wind farms into electric power grids, an accurate wind power prediction is becoming increasingly important for the operation of these power plants. In this paper, a new forecasting engine for wind power prediction is proposed. The proposed engine has the structure of Wavelet Neural Network (WNN) with the activation functions of the hidden neurons constructed based on multi-dimensional Morlet wavelets. This forecast engine is trained by a new improved Clonal selection algorithm, which optimizes the free parameters of the WNN for wind power prediction. Furthermore, Maximum Correntropy Criterion (MCC) has been utilized instead of Mean Squared Error as the error measure in training phase of the forecasting model. The proposed wind power forecaster is tested with real-world hourly data of system level wind power generation in Alberta, Canada. In order to demonstrate the efficiency of the proposed method, it is compared with several other wind power forecast techniques. The obtained results confirm the validity of the developed approach

  3. Limpeza clonal de mudas de videira infectadas por Xanthomonas campestris pv. viticola

    Directory of Open Access Journals (Sweden)

    Adriano Márcio Freire Silva

    2013-03-01

    Full Text Available O cancro bacteriano da videira é causado por Xanthomonas campestris pv. viticola (Xcv. Visando à limpeza clonal de mudas de 'Red Globe', foram estudados: tamanho ideal de ápices e gemas axilares para cultivo em meio de Galzy modificado (MGM; efeito da termoterapia (38ºC/30 dias; e ação de antibióticos na eliminação de Xcv em videiras infectadas. Os percentuais de contaminação por Xcv e de regeneração foram analisados, e as plantas obtidas foram indexadas em meio ágar nutritivo-dextrose-extrato de levedura-ampicilina (NYDAM, seguindo-se teste de patogenicidade. O cultivo de explantes com 3 mm possibilitou a obtenção de plantas livres da bactéria, com regeneração 14,3 vezes maior que explantes com 1 mm. A termoterapia de mudas infectadas, associada ao cultivo in vitro, não eliminou o patógeno. O cultivo de explantes com 10 mm, durante 40 dias em MGM + cefotaxima (300 mg L-1, proporcionou limpeza clonal das mudas. A indexação de plantas de videira regeneradas in vitro, quanto à infecção por Xcv utilizando NYDAM, seguida de teste de patogenicidade, é uma alternativa econômica e eficiente para produção de mudas de alta qualidade fitossanitária.

  4. Brake fault diagnosis using Clonal Selection Classification Algorithm (CSCA – A statistical learning approach

    Directory of Open Access Journals (Sweden)

    R. Jegadeeshwaran

    2015-03-01

    Full Text Available In automobile, brake system is an essential part responsible for control of the vehicle. Any failure in the brake system impacts the vehicle's motion. It will generate frequent catastrophic effects on the vehicle cum passenger's safety. Thus the brake system plays a vital role in an automobile and hence condition monitoring of the brake system is essential. Vibration based condition monitoring using machine learning techniques are gaining momentum. This study is one such attempt to perform the condition monitoring of a hydraulic brake system through vibration analysis. In this research, the performance of a Clonal Selection Classification Algorithm (CSCA for brake fault diagnosis has been reported. A hydraulic brake system test rig was fabricated. Under good and faulty conditions of a brake system, the vibration signals were acquired using a piezoelectric transducer. The statistical parameters were extracted from the vibration signal. The best feature set was identified for classification using attribute evaluator. The selected features were then classified using CSCA. The classification accuracy of such artificial intelligence technique has been compared with other machine learning approaches and discussed. The Clonal Selection Classification Algorithm performs better and gives the maximum classification accuracy (96% for the fault diagnosis of a hydraulic brake system.

  5. Genetic surveillance detects both clonal and epidemic transmission of malaria following enhanced intervention in Senegal.

    Directory of Open Access Journals (Sweden)

    Rachel Daniels

    Full Text Available Using parasite genotyping tools, we screened patients with mild uncomplicated malaria seeking treatment at a clinic in Thiès, Senegal, from 2006 to 2011. We identified a growing frequency of infections caused by genetically identical parasite strains, coincident with increased deployment of malaria control interventions and decreased malaria deaths. Parasite genotypes in some cases persisted clonally across dry seasons. The increase in frequency of genetically identical parasite strains corresponded with decrease in the probability of multiple infections. Further, these observations support evidence of both clonal and epidemic population structures. These data provide the first evidence of a temporal correlation between the appearance of identical parasite types and increased malaria control efforts in Africa, which here included distribution of insecticide treated nets (ITNs, use of rapid diagnostic tests (RDTs for malaria detection, and deployment of artemisinin combination therapy (ACT. Our results imply that genetic surveillance can be used to evaluate the effectiveness of disease control strategies and assist a rational global malaria eradication campaign.

  6. Using BOX-PCR to exclude a clonal outbreak of melioidosis

    Directory of Open Access Journals (Sweden)

    Ward Linda

    2007-06-01

    Full Text Available Abstract Background Although melioidosis in endemic regions is usually caused by a diverse range of Burkholderia pseudomallei strains, clonal outbreaks from contaminated potable water have been described. Furthermore B. pseudomallei is classified as a CDC Group B bioterrorism agent. Ribotyping, pulsed-field gel electrophoresis (PFGE and multilocus sequence typing (MLST have been used to identify genetically related B. pseudomallei isolates, but they are time consuming and technically challenging for many laboratories. Methods We have adapted repetitive sequence typing using a BOX A1R primer for typing B. pseudomallei and compared BOX-PCR fingerprinting results on a wide range of well-characterized B. pseudomallei isolates with MLST and PFGE performed on the same isolates. Results BOX-PCR typing compared favourably with MLST and PFGE performed on the same isolates, both discriminating between the majority of multilocus sequence types and showing relatedness between epidemiologically linked isolates from various outbreak clusters. Conclusion Our results suggest that BOX-PCR can be used to exclude a clonal outbreak of melioidosis within 10 hours of receiving the bacterial strains.

  7. Clonal heterogeneity and chromosomal instability at disease presentation in high hyperdiploid acute lymphoblastic leukemia.

    Science.gov (United States)

    Talamo, Anna; Chalandon, Yves; Marazzi, Alfio; Jotterand, Martine

    2010-12-01

    Although aneuploidy has many possible causes, it often results from underlying chromosomal instability (CIN) leading to an unstable karyotype with cell-to-cell variation and multiple subclones. To test for the presence of CIN in high hyperdiploid acute lymphoblastic leukemia (HeH ALL) at diagnosis, we investigated 20 patients (10 HeH ALL and 10 non-HeH ALL), using automated four-color interphase fluorescence in situ hybridization (I-FISH) with centromeric probes for chromosomes 4, 6, 10, and 17. In HeH ALL, the proportion of abnormal cells ranged from 36.3% to 92.4%, and a variety of aneuploid populations were identified. Compared with conventional cytogenetics, I-FISH revealed numerous additional clones, some of them very small. To investigate the nature and origin of this clonal heterogeneity, we determined average numerical CIN values for all four chromosomes together and for each chromosome and patient group. The CIN values in HeH ALL were relatively high (range, 22.2-44.7%), compared with those in non-HeH ALL (3.2-6.4%), thus accounting for the presence of numerical CIN in HeH ALL at diagnosis. We conclude that numerical CIN may be at the origin of the high level of clonal heterogeneity revealed by I-FISH in HeH ALL at presentation, which would corroborate the potential role of CIN in tumor pathogenesis. Copyright © 2010 Elsevier Inc. All rights reserved.

  8. How old are you? Genet age estimates in a clonal animal.

    Science.gov (United States)

    Devlin-Durante, M K; Miller, M W; Precht, W F; Baums, I B

    2016-11-01

    Foundation species such as redwoods, seagrasses and corals are often long-lived and clonal. Genets may consist of hundreds of members (ramets) and originated hundreds to thousands of years ago. As climate change and other stressors exert selection pressure on species, the demography of populations changes. Yet, because size does not indicate age in clonal organisms, demographic models are missing data necessary to predict the resilience of many foundation species. Here, we correlate somatic mutations with genet age of corals and provide the first, preliminary estimates of genet age in a colonial animal. We observed somatic mutations at five microsatellite loci in rangewide samples of the endangered coral, Acropora palmata (n = 3352). Colonies harboured 342 unique mutations in 147 genets. Genet age ranged from 30 to 838 years assuming a mutation rate of 1.195 -04 per locus per year based on colony growth rates and 236 to 6500 years assuming a mutation rate of 1.542 -05 per locus per year based on sea level changes to habitat availability. Long-lived A. palmata genets imply a large capacity to tolerate past environmental change, and yet recent mass mortality events in A. palmata suggest that capacity is now being frequently exceeded. © 2016 John Wiley & Sons Ltd.

  9. Clonal selection in xenografted TAM recapitulates the evolutionary process of myeloid leukemia in Down syndrome.

    Science.gov (United States)

    Saida, Satoshi; Watanabe, Ken-ichiro; Sato-Otsubo, Aiko; Terui, Kiminori; Yoshida, Kenichi; Okuno, Yusuke; Toki, Tsutomu; Wang, RuNan; Shiraishi, Yuichi; Miyano, Satoru; Kato, Itaru; Morishima, Tatsuya; Fujino, Hisanori; Umeda, Katsutsugu; Hiramatsu, Hidefumi; Adachi, Souichi; Ito, Etsuro; Ogawa, Seishi; Ito, Mamoru; Nakahata, Tatsutoshi; Heike, Toshio

    2013-05-23

    Transient abnormal myelopoiesis (TAM) is a clonal preleukemic disorder that progresses to myeloid leukemia of Down syndrome (ML-DS) through the accumulation of genetic alterations. To investigate the mechanism of leukemogenesis in this disorder, a xenograft model of TAM was established using NOD/Shi-scid, interleukin (IL)-2Rγ(null) mice. Serial engraftment after transplantation of cells from a TAM patient who developed ML-DS a year later demonstrated their self-renewal capacity. A GATA1 mutation and no copy number alterations (CNAs) were detected in the primary patient sample by conventional genomic sequencing and CNA profiling. However, in serial transplantations, engrafted TAM-derived cells showed the emergence of divergent subclones with another GATA1 mutation and various CNAs, including a 16q deletion and 1q gain, which are clinically associated with ML-DS. Detailed genomic analysis identified minor subclones with a 16q deletion or this distinct GATA1 mutation in the primary patient sample. These results suggest that genetically heterogeneous subclones with varying leukemia-initiating potential already exist in the neonatal TAM phase, and ML-DS may develop from a pool of such minor clones through clonal selection. Our xenograft model of TAM may provide unique insight into the evolutionary process of leukemia.

  10. BRAF inhibition is associated with increased clonality in tumor-infiltrating lymphocytes

    Science.gov (United States)

    Cooper, Zachary A; Frederick, Dennie T; Juneja, Vikram R; Sullivan, Ryan J; Lawrence, Donald P; Piris, Adriano; Sharpe, Arlene H; Fisher, David E; Flaherty, Keith T; Wargo, Jennifer A

    2013-01-01

    There have been significant advances with regard to BRAF-targeted therapies against metastatic melanoma. However, the majority of patients receiving BRAF inhibitors (BRAFi) manifest disease progression within a year. We have recently shown that melanoma patients treated with BRAFi exhibit an increase in melanoma-associated antigens and in CD8+ tumor-infiltrating lymphocytes in response to therapy. To characterize such a T-cell infiltrate, we analyzed the complementarity-determining region 3 (CDR3) of rearranged T-cell receptor (TCR) β chain-coding genes in tumor biopsies obtained before the initiation of BRAFi and 10–14 d later. We observed an increase in the clonality of tumor-infiltrating lymphocytes in 7 of 8 patients receiving BRAFi, with a statistically significant 21% aggregate increase in clonality. Over 80% of individual T-cell clones detected after initiation of BRAFi treatment were new clones. Interestingly, the comparison of tumor infiltrates with clinical responses revealed that patients who had a high proportion of pre-existing dominant clones after the administration of BRAFi responded better to therapy than patients who had a low proportion of such pre-existing dominant clones following BRAFi. These data suggest that although the inhibition of BRAF in melanoma patients results in tumor infiltration by new lymphocytes, the response to treatment appears to be related to the presence of a pre-existing population of tumor-infiltrating T-cell clones. PMID:24251082

  11. Cryptosporidium,Giardia, Cryptococcus, Pneumocystis genetic variability: cryptic biological species or clonal near-clades?

    Directory of Open Access Journals (Sweden)

    Michel Tibayrenc

    2014-04-01

    Full Text Available An abundant literature dealing with the population genetics and taxonomy of Giardia duodenalis, Cryptosporidium spp., Pneumocystis spp., and Cryptococcus spp., pathogens of high medical and veterinary relevance, has been produced in recent years. We have analyzed these data in the light of new population genetic concepts dealing with predominant clonal evolution (PCE recently proposed by us. In spite of the considerable phylogenetic diversity that exists among these pathogens, we have found striking similarities among them. The two main PCE features described by us, namely highly significant linkage disequilibrium and near-clading (stable phylogenetic clustering clouded by occasional recombination, are clearly observed in Cryptococcus and Giardia, and more limited indication of them is also present in Cryptosporidium and Pneumocystis. Moreover, in several cases, these features still obtain when the near-clades that subdivide the species are analyzed separately ("Russian doll pattern". Lastly, several sets of data undermine the notion that certain microbes form clonal lineages simply owing to a lack of opportunity to outcross due to low transmission rates leading to lack of multiclonal infections ("starving sex hypothesis". We propose that the divergent taxonomic and population genetic inferences advanced by various authors about these pathogens may not correspond to true evolutionary differences and could be, rather, the reflection of idiosyncratic practices among compartmentalized scientific communities. The PCE model provides an opportunity to revise the taxonomy and applied research dealing with these pathogens and others, such as viruses, bacteria, parasitic protozoa, and fungi.

  12. Clonal deletion: A mechanism of tolerance in mixed bone marrow chimeras

    International Nuclear Information System (INIS)

    Yu, J.C.; Webster, M.; Fox, I.J.

    1990-01-01

    The mechanism of antigen-specific immunologic unresponsiveness which results from lethal irradiation and mixed (syngeneic-allogeneic) bone marrow cell (BMC) reconstitution is unknown. To determine whether clonal deletion is the mechanism of tolerance in this model, monoclonal antibody (Mab) RR-4-4, specific for a T-cell receptor (V beta 6) reactive against the minor alloantigen MLsa, was employed. Six-week-old B10 mice (H-2b, Mlsb, Thyl.2) were tolerized to AKR antigens (H-2k, Mlsa, Thyl.1) by whole body irradiation (950 R) and iv infusion of T-cell-depleted (TCD) B10 BMC + non-TCD AKR BMC. Chimerism and antigen-specific tolerance were documented by flow microfluorometry (FMF), skin grafting, mixed lymphocyte reaction, and cell-mediated lympholysis. When tolerant B10 mice (n = 15) had accepted AKR skin grafts for greater than 100 days, these animals were studied for the presence of host V beta 6+ T cells using Mab RR-4-4. FMF revealed that 0-5% of host (B10) lymph node and spleen cells from chimeras were V beta 6+ while 15-20% of lymph node and spleen cells from control B10 mice expressed V beta 6. These data demonstrate that clonal deletion occurs in the lethal irradiation-mixed reconstitution model as evidenced by the near total elimination of Mlsa-reactive V beta 6+ T cells and suggest that it maybe a mechanism responsible for tolerance in adult mice

  13. Clonality and distribution of clinical Ureaplasma isolates recovered from male patients and infertile couples in China.

    Directory of Open Access Journals (Sweden)

    Zhi Ruan

    Full Text Available Ureaplasma spp. have gained increasing recognition as pathogens in both adult and neonatal patients with multiple clinical presentations. However, the clonality of this organism in the male population and infertile couples in China is largely unknown. In this study, 96 (53 U. parvum and 43 U. urealyticum of 103 Ureaplasma spp. strains recovered from genital specimens from male patients and 15 pairs of infertile couples were analyzed using multilocus sequence typing (MLST/expanded multilocus sequence typing (eMLST schemes. A total of 39 sequence types (STs and 53 expanded sequence types (eSTs were identified, with three predominant STs (ST1, ST9 and ST22 and eSTs (eST16, eST41 and eST82. Moreover, phylogenetic analysis revealed two distinct clusters that were highly congruent with the taxonomic differences between the two Ureaplasma species. We found significant differences in the distributions of both clusters and sub-groups between the male and female patients (P 0.80. However, this concordance was observed only for the detection of U. urealyticum within the infertile couples. In conclusion, the distributions of the clusters and sub-groups significantly differed between the male and female patients. U. urealyticum is more likely to transmit between infertile couples and be associated with clinical manifestations by the specific epidemic clonal lineages.

  14. Unforeseen clonal evolution of tumor cell population in recurrent and metastatic dermatofibrosarcoma protuberans.

    Directory of Open Access Journals (Sweden)

    Ensel Oh

    Full Text Available Dermatofibrosarcoma protuberans (DFSP is a very rare soft tissue sarcoma, generally of low-grade malignancy. DFSP is locally aggressive with a high recurrence rate, but metastasis occurs rarely. To investigate the mechanism of metastasis in DFSP, we analyzed the whole exome sequencing data of serial tumor samples obtained from a patient who had a 10-year history of recurrent and metastatic DFSP. Tracking various genomic alterations, namely somatic mutations, copy number variations, and chromosomal rearrangements, we observed a dramatic change in tumor cell population during the occurrence of metastasis in this DFSP case. The new subclone that emerged in metastatic DFSP harbored a completely different set of somatic mutations and new focal amplifications, which had not been observed in the primary clone before metastasis. The COL1A1-PDGFB fusion, characteristic of DFSP, was found in all of the serial samples. Moreover, the break position on the fusion gene was identical in all samples. Based on these observations, we suggest a clonal evolution model to explain the mechanism underlying metastasis in DFSP and identified several candidate target genes responsible for metastatic DFSP by utilizing The Cancer Genome Atlas database. This is the first study to observe clonal evolution in metastatic DFSP and provide insight for a possible therapeutic strategy for imatinib-resistant or metastatic DFSP.

  15. Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

    Science.gov (United States)

    Honsa, Erin; Fricke, Thomas; Stephens, Alex J; Ko, Danny; Kong, Fanrong; Gilbert, Gwendolyn L; Huygens, Flavia; Giffard, Philip M

    2008-08-19

    Streptococcus agalactiae (Group B Streptococcus (GBS)) is an important human pathogen, particularly of newborns. Emerging evidence for a relationship between genotype and virulence has accentuated the need for efficient and well-defined typing methods. The objective of this study was to develop a single nucleotide polymorphism (SNP) based method for assigning GBS isolates to multilocus sequence typing (MLST)-defined clonal complexes. It was found that a SNP set derived from the MLST database on the basis of maximization of Simpsons Index of Diversity provided poor resolution and did not define groups concordant with the population structure as defined by eBURST analysis of the MLST database. This was interpreted as being a consequence of low diversity and high frequency horizontal gene transfer. Accordingly, a different approach to SNP identification was developed. This entailed use of the "Not-N" bioinformatic algorithm that identifies SNPs diagnostic for groups of known sequence variants, together with an empirical process of SNP testing. This yielded a four member SNP set that divides GBS into 10 groups that are concordant with the population structure. A fifth SNP was identified that increased the sensitivity for the clinically significant clonal complex 17 to 100%. Kinetic PCR methods for the interrogation of these SNPs were developed, and used to genotype 116 well characterized isolates. A five SNP method for dividing GBS into biologically valid groups has been developed. These SNPs are ideal for high throughput surveillance activities, and combining with more rapidly evolving loci when additional resolution is required.

  16. Genotypic diversity and clonal structure of Erigeron annuus (Asteraceae in Lithuania

    Directory of Open Access Journals (Sweden)

    Tunaitienė, Virginija

    2014-02-01

    Full Text Available This study was conducted to assess the clonal structure and genetic diversity of alien herbaceous plant species Erigeron annuus. The global warming and changes in agriculture practice in the past few decades were favourable for the expansion of this species in Lithuania. We used RAPD and ISSR assays to assess genetic variation within and among 29 populations of E. annuus. A total of 278 molecular markers were revealed. Our study detected reduced level of genetic diversity of invasive populations of E. annuus. Significant differences in DNA polymorphism among populations of E. annuus were also found. Some populations of this species are composed of genetically identical plants, while others were polymorphic. Clonal diversity of study populations ranged from 0.083 to 0.4 for both DNA marker systems. The Simpsons diversity index values ranged from 0.0 to 0.636. The average number of genotypes per population established using both assays was about 1.7. Out of 328 E. annuus individuals only 16 showed unique RAPD and 14 unique ISSR banding patterns. The remaining plants were clones of different size. The most common genotype of E. annuus identified in our study was represented by predominate in nine populations.

  17. Clonal origins of cells in the pigmented retina of the zebrafish eye

    International Nuclear Information System (INIS)

    Streisinger, G.; Coale, F.; Taggart, C.; Walker, C.; Grunwald, D.J.

    1989-01-01

    Mosaic analysis has been used to study the clonal basis of the development of the pigmented retina of the zebrafish, Brachydanio rerio. Zebrafish embryos heterozygous for a recessive mutation at the gol-1 locus were exposed to gamma-irradiation at various developmental stages to create mosaic individuals consisting of wild-type pigmented cells and a clone of pigmentless (golden) cells in the eye. The contribution of individual embryonic cells to the pigmented retina was measured and the total number of cells in the embryo that contributed descendants to this tissue was determined. Until the 32-cell stage, almost every blastomere has some descendants that participate in the formation of the pigmented retina of the zebrafish. During subsequent cell divisions, up to the several thousand-cell stage, the number of ancestral cells is constant: approximately 40 cells are present that will give rise to progeny in the pigmented retina. Analysis of the size of clones in the pigmented retina indicates that the cells of this tissue do not arise through a rigid series of cell divisions originating in the early embryo. The findings that each cleavage stage cell contributes to the pigmented retina and yet the contribution of such cells is highly variable are consistent with the interpretation that clonal descendants of different blastomeres normally intermix extensively prior to formation of the pigmented retina

  18. Effects of clonal fragmentation on intraspecific competition of a stoloniferous floating plant.

    Science.gov (United States)

    Wang, P; Xu, Y-S; Dong, B-C; Xue, W; Yu, F-H

    2014-11-01

    Disturbance is common and can fragment clones of plants. Clonal fragmentation may affect the density and growth of ramets so that it could alter intraspecific competition. To test this hypothesis, we grew one (low density), five (medium density) or nine (high density) parent ramets of the floating invasive plant Pistia stratiotes in buckets, and newly produced offspring ramets were either severed (with fragmentation) or remained connected to parent ramets (no fragmentation). Increasing density reduced biomass of the whole clone (i.e. parent ramet plus its offspring ramets), showing intense intraspecific competition. Fragmentation decreased biomass of offspring ramets, but increased biomass of parent ramets and the whole clone, suggesting significant resource translocation from parent to offspring ramets when clones were not fragmented. There was no interaction effect of density x fragmentation on biomass of the whole clone, and fragmentation did not affect competition intensity index. We conclude that clonal fragmentation does not alter intraspecific competition between clones of P. stratiotes, but increases biomass production of the whole clone. Thus, fragmentation may contribute to its interspecific competitive ability and invasiveness, and intentional fragmentation should not be recommended as a measure to stop the rapid growth of this invasive species. © 2014 German Botanical Society and The Royal Botanical Society of the Netherlands.

  19. Multiplex polymerase chain reaction on FTA cards vs. flow cytometry for B-lymphocyte clonality.

    Science.gov (United States)

    Dictor, Michael; Skogvall, Ingela; Warenholt, Janina; Rambech, Eva

    2007-01-01

    Two-colour flow cytometry was compared with multiplex PCR with capillary electrophoresis for clonality determination in specific categories of B-cell lymphoma. FTA cards were evaluated for preserving DNA from node imprints and expediting molecular analysis. A single-tube multiplex PCR targeted IGH and lymphoma-specific translocations in DNA extracted from 180 frozen lymphoid tissues and DNA bound to FTA cards from 192 fresh tissues and 137 aspirates. PCR results were compared with flow cytometry in the extracted and aspirated samples. Overall, single-tube multiplex PCR sensitivity was equivalent in the sample groups (intergroup range 79%-91%). False negatives were associated with tumour origin in the follicle centre. Multiplex PCR and flow cytometry were equally sensitive and together detected 98% of B-cell lymphomas. Additional two-tube targeting of IGK suggested an overall molecular sensitivity >90%. False positive (pseudoclonal) single-tube multiplex PCR was associated with necrosis and sparse lymphocytes. Multiplex PCR using template DNA bound to an FTA card effectively detects B-lymphocyte clonality, obviates DNA extraction and refrigeration, and can be used without diminished sensitivity in fine needle aspirates or node imprints as a replacement for or complement to flow cytometry at any point in the diagnostic work-up.

  20. Clonal diversity and clone formation in the parthenogenetic Caucasian rock Lizard Darevskia dahli [corrected].

    Science.gov (United States)

    Vergun, Andrey A; Martirosyan, Irena A; Semyenova, Seraphima K; Omelchenko, Andrey V; Petrosyan, Varos G; Lazebny, Oleg E; Tokarskaya, Olga N; Korchagin, Vitaly I; Ryskov, Alexey P

    2014-01-01

    The all-female Caucasian rock lizard species Darevskia dahli and other parthenogenetic species of this genus reproduce normally via true parthenogenesis. Previously, the genetic diversity of this species was analyzed using allozymes, mitochondrial DNA, and DNA fingerprint markers. In the present study, variation at three microsatellite loci was studied in 111 specimens of D. dahli from five populations from Armenia, and new information regarding clonal diversity and clone formation in D. dahli was obtained that suggests a multiple hybridization origin. All individuals but one were heterozygous at the loci studied. Based on specific allele combinations, 11 genotypes were identified among the individuals studied. Individuals with the same genotypes formed distinct clonal lineages: one major clone was represented by 72 individuals, an intermediate clone was represented by 21 individuals, and nine other clones were rare and represented by one or several individuals. A new approach based on the detection and comparison of genotype-specific markers formed by combinations of parental-specific markers was developed and used to identify at least three hybridization founder events that resulted in the initial formation of one major and two rare clones. All other clones, including the intermediate and seven rare clones, probably arose through postformation microsatellite mutations of the major clone. This approach can be used to identify hybridization founder events and to study clone formation in other unisexual taxa.

  1. Molecular analysis of immunoglobulin genes reveals frequent clonal relatedness in double monoclonal gammopathies.

    Science.gov (United States)

    Tschumper, R C; Dispenzieri, A; Abraham, R S; Henderson, K J; Jelinek, D F

    2013-04-19

    Monoclonal gammopathies (MGs) are hematological diseases characterized by high levels of a monoclonal immunoglobulin (Ig) or M-protein. Within this group are patients with more than one M-protein, referred to as double MGs (DMGs). The M-proteins in DMG patients may have different heavy chain (HC) isotypes that are associated with different light chains (LCs), or different HCs that are LC matched. In this study, we examined the clonal relatedness of the M-proteins in the latter type in a cohort of 14 DMG patients. By using PCR, we identified 7/14 DMG patients that expressed two Ig HC isotypes with identical Ig HC variable (IGHV), diversity (IGHD), joining (IGHJ), and complementarity determining region (HCDR3) sequences. Two additional DMG patients had two Ig transcripts using the same IGHV, IGHD and IGHJ genes but with slight differences in variable region or HCDR3 mutations. LC analysis confirmed that a single LC was expressed in 3/7 DMG patients with identical HC transcripts and in the two DMGs with highly similar transcripts. The PCR findings were confirmed by immunofluorescence for HC and LC expression. Clonally related HC-dissimilar/LC-matched DMGs may occur often and defines a new subtype of MG that may serve as a tool for studies of disease pathogenesis.

  2. Molecular analysis of immunoglobulin genes reveals frequent clonal relatedness in double monoclonal gammopathies

    International Nuclear Information System (INIS)

    Tschumper, R C; Dispenzieri, A; Abraham, R S; Henderson, K J; Jelinek, D F

    2013-01-01

    Monoclonal gammopathies (MGs) are hematological diseases characterized by high levels of a monoclonal immunoglobulin (Ig) or M-protein. Within this group are patients with more than one M-protein, referred to as double MGs (DMGs). The M-proteins in DMG patients may have different heavy chain (HC) isotypes that are associated with different light chains (LCs), or different HCs that are LC matched. In this study, we examined the clonal relatedness of the M-proteins in the latter type in a cohort of 14 DMG patients. By using PCR, we identified 7/14 DMG patients that expressed two Ig HC isotypes with identical Ig HC variable (IGHV), diversity (IGHD), joining (IGHJ), and complementarity determining region (HCDR3) sequences. Two additional DMG patients had two Ig transcripts using the same IGHV, IGHD and IGHJ genes but with slight differences in variable region or HCDR3 mutations. LC analysis confirmed that a single LC was expressed in 3/7 DMG patients with identical HC transcripts and in the two DMGs with highly similar transcripts. The PCR findings were confirmed by immunofluorescence for HC and LC expression. Clonally related HC-dissimilar/LC-matched DMGs may occur often and defines a new subtype of MG that may serve as a tool for studies of disease pathogenesis

  3. Clonality and distribution of clinical Ureaplasma isolates recovered from male patients and infertile couples in China.

    Science.gov (United States)

    Ruan, Zhi; Yang, Ting; Shi, Xinyan; Kong, Yingying; Xie, Xinyou; Zhang, Jun

    2017-01-01

    Ureaplasma spp. have gained increasing recognition as pathogens in both adult and neonatal patients with multiple clinical presentations. However, the clonality of this organism in the male population and infertile couples in China is largely unknown. In this study, 96 (53 U. parvum and 43 U. urealyticum) of 103 Ureaplasma spp. strains recovered from genital specimens from male patients and 15 pairs of infertile couples were analyzed using multilocus sequence typing (MLST)/expanded multilocus sequence typing (eMLST) schemes. A total of 39 sequence types (STs) and 53 expanded sequence types (eSTs) were identified, with three predominant STs (ST1, ST9 and ST22) and eSTs (eST16, eST41 and eST82). Moreover, phylogenetic analysis revealed two distinct clusters that were highly congruent with the taxonomic differences between the two Ureaplasma species. We found significant differences in the distributions of both clusters and sub-groups between the male and female patients (P Ureaplasma spp. The present study also attained excellent agreement of the identification of both Ureaplasma species between paired urine and semen specimens from the male partners (k > 0.80). However, this concordance was observed only for the detection of U. urealyticum within the infertile couples. In conclusion, the distributions of the clusters and sub-groups significantly differed between the male and female patients. U. urealyticum is more likely to transmit between infertile couples and be associated with clinical manifestations by the specific epidemic clonal lineages.

  4. Limpeza clonal de mudas de videira infectadas por Xanthomonas campestris pv. viticola Clonal cleaning of grapevine plants infected by Xanthomonas campestris pv. viticola

    Directory of Open Access Journals (Sweden)

    Adriano Márcio Freire Silva

    2013-03-01

    Full Text Available O cancro bacteriano da videira é causado por Xanthomonas campestris pv. viticola (Xcv. Visando à limpeza clonal de mudas de 'Red Globe', foram estudados: tamanho ideal de ápices e gemas axilares para cultivo em meio de Galzy modificado (MGM; efeito da termoterapia (38ºC/30 dias; e ação de antibióticos na eliminação de Xcv em videiras infectadas. Os percentuais de contaminação por Xcv e de regeneração foram analisados, e as plantas obtidas foram indexadas em meio ágar nutritivo-dextrose-extrato de levedura-ampicilina (NYDAM, seguindo-se teste de patogenicidade. O cultivo de explantes com 3 mm possibilitou a obtenção de plantas livres da bactéria, com regeneração 14,3 vezes maior que explantes com 1 mm. A termoterapia de mudas infectadas, associada ao cultivo in vitro, não eliminou o patógeno. O cultivo de explantes com 10 mm, durante 40 dias em MGM + cefotaxima (300 mg L-1, proporcionou limpeza clonal das mudas. A indexação de plantas de videira regeneradas in vitro, quanto à infecção por Xcv utilizando NYDAM, seguida de teste de patogenicidade, é uma alternativa econômica e eficiente para produção de mudas de alta qualidade fitossanitária.Bacterial canker is caused by Xanthomonas campestris pv. viticola (Xcv. In order to eliminate Xcv from 'Red Globe' plants it was studied: optimal size of meristem tips and axillary buds for cultivation in modified Galzy's medium (MGM; effects of thermotherapy (38ºC/30 days; and action of antibiotics in the elimination of Xcv in infected grapevines. The percentages of contamination by Xcv and regeneration were analyzed and plants obtained were indexed using the semi-selective culture medium nutrient agar-dextrose-yeast extract-ampicilin (NYDAM followed by a pathogenicity test. The cultivation of 3 mm explants permitted to obtain plants free of bacteria with regeneration 14.3 times higher than 1 mm explants. The thermotherapy of infected plants associated to the in vitro culture

  5. HIV tropism and decreased risk of breast cancer.

    Directory of Open Access Journals (Sweden)

    Nancy A Hessol

    2010-12-01

    Full Text Available During the first two decades of the U.S. AIDS epidemic, and unlike some malignancies, breast cancer risk was significantly lower for women with human immunodeficiency virus (HIV infection compared to the general population. This deficit in HIV-associated breast cancer could not be attributed to differences in survival, immune deficiency, childbearing or other breast cancer risk factors. HIV infects mononuclear immune cells by binding to the CD4 molecule and to CCR5 or CXCR4 chemokine coreceptors. Neoplastic breast cells commonly express CXCR4 but not CCR5. In vitro, binding HIV envelope protein to CXCR4 has been shown to induce apoptosis of neoplastic breast cells. Based on these observations, we hypothesized that breast cancer risk would be lower among women with CXCR4-tropic HIV infection.We conducted a breast cancer nested case-control study among women who participated in the WIHS and HERS HIV cohort studies with longitudinally collected risk factor data and plasma. Cases were HIV-infected women (mean age 46 years who had stored plasma collected within 24 months of breast cancer diagnosis and an HIV viral load≥500 copies/mL. Three HIV-infected control women, without breast cancer, were matched to each case based on age and plasma collection date. CXCR4-tropism was determined by a phenotypic tropism assay. Odds ratios (OR and 95% confidence intervals (CI for breast cancer were estimated by exact conditional logistic regression. Two (9% of 23 breast cancer cases had CXCR4-tropic HIV, compared to 19 (28% of 69 matched controls. Breast cancer risk was significantly and independently reduced with CXCR4 tropism (adjusted odds ratio, 0.10, 95% CI 0.002-0.84 and with menopause (adjusted odds ratio, 0.08, 95% CI 0.001-0.83. Adjustment for CD4+ cell count, HIV viral load, and use of antiretroviral therapy did not attenuate the association between infection with CXCR4-tropic HIV and breast cancer.Low breast cancer risk with HIV is specifically linked

  6. The Impact of Married Individuals Learning HIV Status in Malawi: Divorce, Number of Sexual Partners, and Condom Use With Spouses.

    Science.gov (United States)

    Fedor, Theresa M; Kohler, Hans-Peter; Behrman, Jere R

    2015-02-01

    This article assesses how married individuals' knowledge of HIV status gained through HIV testing and counseling (HTC) affects divorce, the number of sexual partners, and the use of condoms within marriage. This study improves upon previous studies on this topic because the randomized incentives affecting the propensity to be tested for HIV permit control for selective testing. Instrumental variable probit and linear models are estimated, using a randomized experiment administered as part of the Malawi Longitudinal Study of Families and Health (MLSFH). The results indicate that knowledge of HIV status (1) does not affect chances of divorce for either HIV-negative or HIV-positive respondents; (2) reduces the number of reported sexual partners among HIV-positive respondents; and (3) increases reported condom use with spouses for both HIV-negative and HIV-positive respondents. These results imply that individuals actively respond to information about their HIV status that they learn during HTC, invoking protective behavior against future risk of HIV/AIDS for themselves and their actual and potential sexual partners. Some limitations of this study are a small sample size for those who are HIV-positive and dependence on self-reported sexual behaviors.

  7. HIV antibodies for treatment of HIV infection.

    Science.gov (United States)

    Margolis, David M; Koup, Richard A; Ferrari, Guido

    2017-01-01

    The bar is high to improve on current combination antiretroviral therapy (ART), now highly effective, safe, and simple. However, antibodies that bind the HIV envelope are able to uniquely target the virus as it seeks to enter new target cells, or as it is expressed from previously infected cells. Furthermore, the use of antibodies against HIV as a therapeutic may offer advantages. Antibodies can have long half-lives, and are being considered as partners for long-acting antiretrovirals for use in therapy or prevention of HIV infection. Early studies in animal models and in clinical trials suggest that such antibodies can have antiviral activity but, as with small-molecule antiretrovirals, the issues of viral escape and resistance will have to be addressed. Most promising, however, are the unique properties of anti-HIV antibodies: the potential ability to opsonize viral particles, to direct antibody-dependent cellular cytotoxicity (ADCC) against actively infected cells, and ultimately the ability to direct the clearance of HIV-infected cells by effector cells of the immune system. These distinctive activities suggest that HIV antibodies and their derivatives may play an important role in the next frontier of HIV therapeutics, the effort to develop treatments that could lead to an HIV cure. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

  8. Powerful strategy for polymerase chain reaction-based clonality assessment in T-cell malignancies Report of the BIOMED-2 Concerted Action BHM4 CT98-3936

    NARCIS (Netherlands)

    Brüggemann, M.; White, H.; Gaulard, P.; Garcia-Sanz, R.; Gameiro, P.; Oeschger, S.; Jasani, B.; Ott, M.; Delsol, G.; Orfao, A.; Tiemann, M.; Herbst, H.; Langerak, A. W.; Spaargaren, M.; Moreau, E.; Groenen, P. J. T. A.; Sambade, C.; Foroni, L.; Carter, G. I.; Hummel, M.; Bastard, C.; Davi, F.; Delfau-Larue, M.-H.; Kneba, M.; van Dongen, J. J. M.; Beldjord, K.; Molina, T. J.

    2007-01-01

    Polymerase chain reaction (PCR) assessment of clonal T-cell receptor (TCR) and immunoglobulin (Ig) gene rearrangements is an important diagnostic tool in mature T-cell neoplasms. However, lack of standardized primers and PCR protocols has hampered comparability of data in previous clonality studies.

  9. Early and Middle Adolescents’ Autonomy Development: Impact of Maternal HIV/AIDS

    OpenAIRE

    Murphy, Debra A.; Greenwell, Lisa; Resell, Judith; Brecht, Mary-Lynn; Schuster, Mark A.

    2008-01-01

    Progression toward autonomy is considered of central importance during the adolescent period. For young adolescents with an HIV-infected parent, there may be additional challenges. This study investigated current autonomy among early and middle adolescents affected by maternal HIV (N = 108), as well as examined longitudinally the children’s responsibility taking when they were younger (age 6 - 11; N = 81) in response to their mother’s illness and their current autonomy as early/middle adolesc...

  10. Sexual risk behaviour trajectories among men who have sex with menat risk for HIV in Amsterdam, the Netherlands: a 10 year follow-up study.

    NARCIS (Netherlands)

    Basten, Maartje; Heijne, Janneke Cornelia Maria; Geskus, Ronald; Daas, Chantal Den; Kretzschmar, Mirjam; Matser, Amy

    2018-01-01

    Sexual risk behaviour changes during a person's life course. Insights in sexual risk behaviour trajectories of MSM may provide starting points for the timing of HIV prevention methods. We aimed to study longitudinal trajectories of sexual risk behaviour predictive of HIV acquisition from sexual

  11. NIMH Project Accept (HPTN 043: results from in-depth interviews with a longitudinal cohort of community members.

    Directory of Open Access Journals (Sweden)

    Suzanne Maman

    Full Text Available NIMH Project Accept (HPTN 043 is a community- randomized trial to test the safety and efficacy of a community-level intervention designed to increase testing and lower HIV incidence in Tanzania, Zimbabwe, South Africa and Thailand. The evaluation design included a longitudinal study with community members to assess attitudinal and behavioral changes in study outcomes including HIV testing norms, HIV-related discussions, and HIV-related stigma.A cohort of 657 individuals across all sites was selected to participate in a qualitative study that involved 4 interviews during the study period. Baseline and 30-month data were summarized according to each outcome, and a qualitative assessment of changes was made at the community level over time.Members from intervention communities described fewer barriers and greater motivation for testing than those from comparison communities. HIV-related discussions in intervention communities were more grounded in personal testing experiences. A change in HIV-related stigma over time was most pronounced in Tanzania and Zimbabwe. Participants in the intervention communities from these two sites attributed community-level changes in attitudes to project specific activities.The Project Accept intervention was associated with more favorable social norms regarding HIV testing, more personal content in HIV discussions in all study sites, and qualitative changes in HIV-related stigma in two of five sites.

  12. NIMH Project Accept (HPTN 043): results from in-depth interviews with a longitudinal cohort of community members.

    Science.gov (United States)

    Maman, Suzanne; van Rooyen, Heidi; Stankard, Petra; Chingono, Alfred; Muravha, Tshifhiwa; Ntogwisangu, Jacob; Phakathi, Zipho; Srirak, Namtip; F Morin, Stephen

    2014-01-01

    NIMH Project Accept (HPTN 043) is a community- randomized trial to test the safety and efficacy of a community-level intervention designed to increase testing and lower HIV incidence in Tanzania, Zimbabwe, South Africa and Thailand. The evaluation design included a longitudinal study with community members to assess attitudinal and behavioral changes in study outcomes including HIV testing norms, HIV-related discussions, and HIV-related stigma. A cohort of 657 individuals across all sites was selected to participate in a qualitative study that involved 4 interviews during the study period. Baseline and 30-month data were summarized according to each outcome, and a qualitative assessment of changes was made at the community level over time. Members from intervention communities described fewer barriers and greater motivation for testing than those from comparison communities. HIV-related discussions in intervention communities were more grounded in personal testing experiences. A change in HIV-related stigma over time was most pronounced in Tanzania and Zimbabwe. Participants in the intervention communities from these two sites attributed community-level changes in attitudes to project specific activities. The Project Accept intervention was associated with more favorable social norms regarding HIV testing, more personal content in HIV discussions in all study sites, and qualitative changes in HIV-related stigma in two of five sites.

  13. Genomic analyses of dominant U.S. clonal lineages of Phytophthora infestans reveals a shared common ancestry for clonal lineages US11 and US18 and a lack of recently shared ancestry among all other U.S. lineages

    Science.gov (United States)

    The populations of the potato and tomato late blight pathogen, Phytophthora infestans, in the US are well known for emerging repeatedly as novel clonal lineages. These successions of dominant clones have historically been named US1-US24, in order of appearance, since their first characterization usi...

  14. A Pluralistic, Longitudinal Method

    DEFF Research Database (Denmark)

    Evers, Winie; Marroun, Sana; Young, Louise

    2017-01-01

    There is recognition in business markets of the need for connected relationships to enable the survival and growth of firms. Finding new ways to collaborate enables firms to better seek opportunities and challenges and enhance network capability. However the traditional methods used to research...... and analysis. Longitudinal research considers a Danish advertising and communication firm looking for new ideas by involving their network in order to help them to compete in their environment of rapid globalization and emergence of new technologies. A five stage research design considered how network...

  15. A longitudinal study

    OpenAIRE

    Kristen, Astrid

    2010-01-01

    Does playing violent video games increase aggressive behavior over time or is it aggressive children who increasingly seek out (and play) these violent video games? To study such long-term effects a longitudinal design is necessary. Within a field study in a large German city (Kinder, Computer, Hobby, Lernen – KUHL, Freie Universtität Berlin) about 115 elementary school boys attending in the beginning (t1) classrooms of the third and fourth grade and twelve months later (t2) classrooms of the...

  16. Correlates of HIV infection among people visiting public HIV ...

    African Journals Online (AJOL)

    Correlates of HIV infection among people visiting public HIV counseling and testing clinics in Mpumalanga, ... Background: HIV voluntary counselling and testing (VCT) reduces high-risk sexual behaviour. ... AJOL African Journals Online.

  17. HIV/AIDS in Women - Multiple Languages

    Science.gov (United States)

    ... medicines and women - HIV medicines, part 7 - English MP3 HIV medicines and women - HIV medicines, part 7 - 简体中文 (Chinese, Simplified (Mandarin dialect)) MP3 HIV medicines and women - HIV medicines, part 7 - ...

  18. Acinetobacter baumannii Isolated from Lebanese Patients: Phenotypes and Genotypes of Resistance, Clonality, and Determinants of Pathogenicity.

    Science.gov (United States)

    Dahdouh, Elias; Hajjar, Micheline; Suarez, Monica; Daoud, Ziad

    2016-01-01

    Introduction: Acinetobacter baumannii is a nosocomial pathogen that usually affects critically ill patients. High mortality rates have been associated with MDR A. baumannii infections. Carbapenem resistance among these isolates is increasing worldwide and is associated with certain International Clones (ICs) and oxacillinases (OXAs). Moreover, this organism possesses a wide range of virulence factors, whose expression is not yet fully understood. In this study, clinical A. baumannii isolates are characterized in terms of antibiotic resistance, mechanisms of carbapenem resistance, clonality, and virulence. Materials and Methods: A. baumannii clinical isolates ( n = 90) where obtained from a tertiary care center in Beirut, Lebanon. API 20NE strips in addition to the amplification of bla OXA-51-like were used for identification. Antibiotic susceptibility testing by disk diffusion was then performed in addition to PCRs for the detection of the most commonly disseminated carbapenemases. Clonality was determined by tri-locus PCR typing and doubling times were determined for isolates with varying susceptibility profiles. Biofilm formation, hemolysis, siderophore production, proteolytic activity, and surface motility was then determined for all the isolates. Statistical analysis was then performed for the determination of associations. Results and Discussion: 81 (90%) of the isolates were resistant to carbapenems. These high rates are similar to other multi-center studies in the country suggesting the need of intervention on a national level. 74 (91.3%) of the carbapenem resistant isolates harbored bla OXA-23-like including two that also harbored bla OXA-24-like . 88.9% of the A. baumannii isolates pertained to ICII and three other international clones were detected, showing the wide dissemination of clones into geographically distinct locations. Virulence profiles were highly diverse and no specific pattern was observed. Nevertheless, an association between motility

  19. Selection and Clonal Propagation of High Artemisinin Genotypes of Artemisia annua

    Science.gov (United States)

    Wetzstein, Hazel Y.; Porter, Justin A.; Janick, Jules; Ferreira, Jorge F. S.; Mutui, Theophilus M.

    2018-01-01

    Artemisinin, produced in the glandular trichomes of Artemisia annua L. is a vital antimalarial drug effective against Plasmodium falciparum resistant to quinine-derived medicines. Although work has progressed on the semi-synthetic production of artemisinin, field production of A. annua remains the principal commercial source of the compound. Crop production of artemisia must be increased to meet the growing worldwide demand for artemisinin combination therapies (ACTs) to treat malaria. Grower artemisinin yields rely on plants generated from seeds from open-pollinated parents. Although selection has considerably increased plant artemisinin concentration in the past 15 years, seed-generated plants have highly variable artemisinin content that lowers artemisinin yield per hectare. Breeding efforts to produce improved F1 hybrids have been hampered by the inability to produce inbred lines due to self-incompatibility. An approach combining conventional hybridization and selection with clonal propagation of superior genotypes is proposed as a means to enhance crop yield and artemisinin production. Typical seed-propagated artemisia plants produce less than 1% (dry weight) artemisinin with yields below 25 kg/ha. Genotypes were identified producing high artemisinin levels of over 2% and possessing improved agronomic characteristics such as high leaf area and shoot biomass production. Field studies of clonally-propagated high-artemisinin plants verified enhanced plant uniformity and an estimated gross primary productivity of up to 70 kg/ha artemisinin, with a crop density of one plant m-2. Tissue culture and cutting protocols for the mass clonal propagation of A. annua were developed for shoot regeneration, rooting, acclimatization, and field cultivation. Proof of concept studies showed that both tissue culture-regenerated plants and rooted cutting performed better than plants derived from seed in terms of uniformity, yield, and consistently high artemisinin content. Use of

  20. Sequential Dysfunction and Progressive Depletion of Candida albicans-Specific CD4 T Cell Response in HIV-1 Infection

    Science.gov (United States)

    Liu, Fengliang; Fan, Xiuzhen; Auclair, Sarah; Ferguson, Monique; Sun, Jiaren; Soong, Lynn; Hou, Wei; Redfield, Robert R.; Birx, Deborah L.; Ratto-Kim, Silvia; Robb, Merlin L.; Kim, Jerome H.; Michael, Nelson L.; Hu, Haitao

    2016-01-01

    Loss of immune control over opportunistic infections can occur at different stages of HIV-1 (HIV) disease, among which mucosal candidiasis caused by the fungal pathogen Candida albicans (C. albicans) is one of the early and common manifestations in HIV-infected human subjects. The underlying immunological basis is not well defined. We have previously shown that compared to cytomegalovirus (CMV)-specific CD4 cells, C. albicans-specific CD4 T cells are highly permissive to HIV in vitro. Here, based on an antiretroviral treatment (ART) naïve HIV infection cohort (RV21), we investigated longitudinally the impact of HIV on C. albicans- and CMV-specific CD4 T-cell immunity in vivo. We found a sequential dysfunction and preferential depletion for C. albicans-specific CD4 T cell response during progressive HIV infection. Compared to Th1 (IFN-γ, MIP-1β) functional subsets, the Th17 functional subsets (IL-17, IL-22) of C. albicans-specific CD4 T cells were more permissive to HIV in vitro and impaired earlier in HIV-infected subjects. Infection history analysis showed that C. albicans-specific CD4 T cells were more susceptible to HIV in vivo, harboring modestly but significantly higher levels of HIV DNA, than CMV-specific CD4 T cells. Longitudinal analysis of HIV-infected individuals with ongoing CD4 depletion demonstrated that C. albicans-specific CD4 T-cell response was preferentially and progressively depleted. Taken together, these data suggest a potential mechanism for earlier loss of immune control over mucosal candidiasis in HIV-infected patients and provide new insights into pathogen-specific immune failure in AIDS pathogenesis. PMID:27280548

  1. Emerging Trends of HIV Drug Resistance in Chinese HIV-Infected Patients Receiving First-Line Highly Active Antiretroviral Therapy: A Systematic Review and Meta-Analysis

    Science.gov (United States)

    Liu, Huixin; Ma, Ye; Su, Yingying; Smith, M. Kumi; Liu, Ying; Jin, Yantao; Gu, Hongqiu; Wu, Jing; Zhu, Lin; Wang, Ning

    2014-01-01

    Background. Highly active antiretroviral therapy (HAART) has led to a dramatic decrease in AIDS-related morbidity and mortality through sustained suppression of human immunodeficiency virus (HIV) replication and reconstitution of the immune response. Settings like China that experienced rapid HAART rollout and relatively limited drug selection face considerable challenges in controlling HIV drug resistance (DR). Methods. We conducted a systematic review and meta-analysis to describe trends in emergent HIV DR to first-line HAART among Chinese HIV-infected patients, as reflected in the point prevalence of HIV DR at key points and fixed intervals after treatment initiation, using data from cohort studies and cross-sectional studies respectively. Results. Pooled prevalence of HIV DR from longitudinal cohorts studies was 10.79% (95% confidence interval [CI], 5.85%–19.07%) after 12 months of HAART and 80.58% (95% CI, 76.6%–84.02%) after 72 months of HAART. The HIV DR prevalence from cross-sectional studies was measured in treatment intervals; during the 0–12-month HAART treatment interval, the pooled prevalence of HIV DR was 11.1% (95% CI, 7.49%–16.14%), which increased to 22.92% at 61–72 months (95% CI, 9.45%–45.86%). Stratified analyses showed that patients receiving a didanosine-based regimen had higher HIV DR prevalence than those not taking didanosine (15.82% vs 4.97%). Patients infected through former plasma donation and those receiving AIDS treatment at village clinics had higher HIV DR prevalence than those infected through sexual transmission or treated at a county-level hospital. Conclusions. Our findings indicate higher prevalence of HIV DR for patients with longer cumulative HAART exposure, highlighting important subgroups for future HIV DR surveillance and control. PMID:25053721

  2. HIV prevalence is strongly associated with geographical variations in male circumcision and foreskin cutting in Papua New Guinea: an ecological study.

    Science.gov (United States)

    MacLaren, David J; McBride, W John H; Kelly, Gerard C; Muller, Reinhold; Tommbe, Rachael; Kaldor, John M; Vallely, Andrew J

    2015-11-01

    To examine the correlation between HIV prevalence and male circumcision and other foreskin cutting practices across the four regions of Papua New Guinea (PNG). An ecological substudy using unique data from an interdisciplinary research programme to evaluate the acceptability, sociocultural context and public health impact of male circumcision for HIV prevention in PNG. Published data describing (a) self-reported circumcision status by region from the 'Acceptability and Feasibility of Male Circumcision for HIV prevention in PNG' study and (b) HIV prevalence by region from PNG National Department of Health were used to correlate male circumcision and other foreskin cutting practices and HIV prevalence. Maps were constructed to visually represent variations across the four regions of PNG. Regions of PNG with the highest HIV prevalence had the lowest prevalence of male circumcision and other forms of foreskin cutting and vice versa. Male circumcision and dorsal longitudinal cuts were strongly associated with HIV prevalence and able to explain 99% of the observed geographical variability in HIV prevalence in PNG (pPNG appears to be closely correlated with the regional distribution of male circumcision and dorsal longitudinal foreskin cuts. Further research is warranted to investigate causality of this correlation as well as the potential of dorsal longitudinal cuts to confer protection against HIV acquisition in heterosexual men. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

  3. Implications of extreme life span in clonal organisms: millenary clones in meadows of the threatened seagrass Posidonia oceanica.

    Directory of Open Access Journals (Sweden)

    Sophie Arnaud-Haond

    Full Text Available The maximum size and age that clonal organisms can reach remains poorly known, although we do know that the largest natural clones can extend over hundreds or thousands of metres and potentially live for centuries. We made a review of findings to date, which reveal that the maximum clone age and size estimates reported in the literature are typically limited by the scale of sampling, and may grossly underestimate the maximum age and size of clonal organisms. A case study presented here shows the occurrence of clones of slow-growing marine angiosperm Posidonia oceanica at spatial scales ranging from metres to hundreds of kilometres, using microsatellites on 1544 sampling units from a total of 40 locations across the Mediterranean Sea. This analysis revealed the presence, with a prevalence of 3.5 to 8.9%, of very large clones spreading over one to several (up to 15 kilometres at the different locations. Using estimates from field studies and models of the clonal growth of P. oceanica, we estimated these large clones to be hundreds to thousands of years old, suggesting the evolution of general purpose genotypes with large phenotypic plasticity in this species. These results, obtained combining genetics, demography and model-based calculations, question present knowledge and understanding of the spreading capacity and life span of plant clones. These findings call for further research on these life history traits associated with clonality, considering their possible ecological and evolutionary implications.

  4. Testing for disconnection and distance effects on physiological self-recognition within clonal fragments of Potentilla reptans

    NARCIS (Netherlands)

    Chen, Bin; Vermeulen, Peter; During, Heinjo; Anten, Niels

    2015-01-01

    Evidence suggests that belowground self-recognition in clonal plants can be disrupted between sister ramets by the loss of connections or long distances within a genet. However, these results may be confounded by severing connections between ramets in the setups. Using Potentilla reptans, we

  5. Clonal mobility and its implications for spatio-temporal patterns of plant communities: what do we need to know next?

    Czech Academy of Sciences Publication Activity Database

    Zobel, M.; Moora, M.; Herben, Tomáš

    2010-01-01

    Roč. 119, č. 5 (2010), s. 802-806 ISSN 0030-1299 Institutional research plan: CEZ:AV0Z60050516 Keywords : clonal mobility * spatio-temporal patterns * plant communities Subject RIV: EF - Botanics Impact factor: 3.393, year: 2010

  6. Genetic variation within clonal lineages of Phytophthora infestans revealed through genotyping-by-sequencing, and implications for late blight epidemiology

    Science.gov (United States)

    Genotyping-by-sequencing (GBS) was performed on 257 Phytophthora infestans isolates belonging to four clonal lineages to study within-lineage diversity. The four lineages used in the study included US-8 (n=28), US-11 (n=27), US-23 (n=166), and US-24 (n=36), with isolates originating from 23 of the U...

  7. Genomic Analysis of the Emergence and Rapid Global Dissemination of the Clonal Group 258 Klebsiella pneumoniae Pandemic.

    Directory of Open Access Journals (Sweden)

    Jolene R Bowers

    Full Text Available Multidrug-resistant Klebsiella pneumoniae producing the KPC carbapenemase have rapidly spread throughout the world, causing severe healthcare-associated infections with limited antimicrobial treatment options. Dissemination of KPC-producing K. pneumoniae is largely attributed to expansion of a single dominant strain, ST258. In this study, we explore phylogenetic relationships and evolution within ST258 and its clonal group, CG258, using whole genome sequence analysis of 167 isolates from 20 countries collected over 17 years. Our results show a common ST258 ancestor emerged from its diverse parental clonal group around 1995 and likely acquired blaKPC prior to dissemination. Over the past two decades, ST258 has remained highly clonal despite diversity in accessory elements and divergence in the capsule polysaccharide synthesis locus. Apart from the large recombination event that gave rise to ST258, few mutations set it apart from its clonal group. However, one mutation occurs in a global transcription regulator. Characterization of outer membrane protein sequences revealed a profile in ST258 that includes a truncated OmpK35 and modified OmpK37. Our work illuminates potential genomic contributors to the pathogenic success of ST258, helps us better understand the global dissemination of this strain, and identifies genetic markers unique to ST258.

  8. Marked heterogeneity in growth characteristics of myoblast clonal cultures and myoblast mixed cultures obtained from the same individual.

    Science.gov (United States)

    Maier, Andrea B; Cohen, Ron; Blom, Joke; van Heemst, Diana; Westendorp, Rudi G J

    2012-01-01

    Sarcopenia is defined as an age-related decrease in skeletal muscle mass and function while adjacent satellite cells are unable to compensate for this loss. However, myoblast cultures can be established even in the presence of sarcopenia. It is yet unknown whether satellite cells from failing muscle in older age are equally affected, as human satellite cells have been assessed using myoblast mixed cultures and not by using myoblast clonal cultures. We questioned to what extent myoblast mixed cultures reflect the in vivo characteristics of single satellite cells from adult skeletal muscle. We established a myoblast mixed culture and three myoblast clonal cultures out of the same muscle biopsy and cultured these cells for 100 days. Replicative capacity and oxidative stress resistance were compared. We found marked heterogeneity between the myoblast clonal cultures that all had a significantly lower replicative capacity when compared to the mixed culture. Replicative capacity of the clonal cultures was inversely related to the β-galactosidase activity after exposure to oxidative stress. Addition of L-carnosine enhanced the remaining replicative capacity in all cultures with a concomitant marginal decrease in β-galactosidase activity. It is concluded that myoblast mixed cultures in vitro do not reflect the marked heterogeneity between single isolated satellite cells. The consequences of the heterogeneity on muscle performance remain to be established. Copyright © 2011 S. Karger AG, Basel.

  9. Critical analysis of the stringent complete response in multiple myeloma: contribution of sFLC and bone marrow clonality.

    Science.gov (United States)

    Martínez-López, Joaquín; Paiva, Bruno; López-Anglada, Lucía; Mateos, María-Victoria; Cedena, Teresa; Vidríales, María-Belén; Sáez-Gómez, María Auxiliadora; Contreras, Teresa; Oriol, Albert; Rapado, Inmaculada; Teruel, Ana-Isabel; Cordón, Lourdes; Blanchard, María Jesús; Bengoechea, Enrique; Palomera, Luis; de Arriba, Felipe; Cueto-Felgueroso, Cecilia; Orfao, Alberto; Bladé, Joan; San Miguel, Jesús F; Lahuerta, Juan José

    2015-08-13

    Stringent complete response (sCR) criteria are used in multiple myeloma as a deeper response category compared with CR, but prospective validation is lacking, it is not always clear how evaluation of clonality is performed, and is it not known what the relative clinical influence is of the serum free light chain ratio (sFLCr) and bone marrow (BM) clonality to define more sCR. To clarify this controversy, we focused on 94 patients that reached CR, of which 69 (73%) also fulfilled the sCR criteria. Patients with sCR displayed slightly longer time to progression (median, 62 vs 53 months, respectively; P = .31). On analyzing this contribution to the prognosis of sFLCr or clonality, it was found that the sFLCr does not identify patients in CR at distinct risk; by contrast, low-sensitive multiparametric flow cytometry (MFC) immunophenotyping (2 colors), which is equivalent to immunohistochemistry, identifies a small number of patients (5 cases) with high residual tumor burden and dismal outcome; nevertheless, using traditional 4-color MFC, persistent clonal BM disease was detectable in 36% of patients, who, compared with minimal residual disease-negative cases, had a significantly inferior outcome. These results show that the current definition of sCR should be revised. © 2015 by The American Society of Hematology.

  10. CLO-PLA: a database of clonal and bud-bank traits of the Central European flora

    Czech Academy of Sciences Publication Activity Database

    Klimešová, Jitka; Danihelka, J.; Chrtek, Jindřich; de Bello, Francesco; Herben, Tomáš

    2017-01-01

    Roč. 98, č. 4 (2017), s. 1179 ISSN 0012-9658 R&D Projects: GA ČR GB14-36079G Institutional support: RVO:67985939 Keywords : Clonal traits * Central Europe * CLO-PLA database * bud-bank traits Subject RIV: EH - Ecology, Behaviour OBOR OECD: Ecology Impact factor: 4.809, year: 2016

  11. In vivo clonal analysis reveals lineage-restricted progenitor characteristics in mammalian kidney development, maintenance, and regeneration

    NARCIS (Netherlands)

    Rinkevich, Y.; Montoro, D.T.; Contreras-Trujillo, H.; Harari-Steinberg, O.; Newman, A.M.; Tsai, J.M.; Lim, X.; van Amerongen, R.; Bowman, A.; Januszyk, M.; Pleniceanu, O.; Nusse, R.; Longaker, M.T.; Weissman, I.L.; Dekel, B.

    2014-01-01

    The mechanism and magnitude by which the mammalian kidney generates and maintains its proximal tubules, distal tubules, and collecting ducts remain controversial. Here, we use long-term in vivo genetic lineage tracing and clonal analysis of individual cells from kidneys undergoing development,

  12. Vegetative regeneration of invasive Ludwigia cytotypes from clonal bud banks across resource gradients: colonizing diploid outperforms polyploid

    Science.gov (United States)

    Understanding functional traits that underlie the colonization of invasive plants is key to developing sustainable management strategies to curtail invasions at the establishment phase. Although common, recruitment of clonal plant species from bud banks is often overlooked but may be a key transiti...

  13. Modeling of genetic gain for single traits from marker-assisted seedling selection in clonally propagated crops

    Science.gov (United States)

    Ru, Sushan; Hardner, Craig; Carter, Patrick A; Evans, Kate; Main, Dorrie; Peace, Cameron

    2016-01-01

    Seedling selection identifies superior seedlings as candidate cultivars based on predicted genetic potential for traits of interest. Traditionally, genetic potential is determined by phenotypic evaluation. With the availability of DNA tests for some agronomically important traits, breeders have the opportunity to include DNA information in their seedling selection operations—known as marker-assisted seedling selection. A major challenge in deploying marker-assisted seedling selection in clonally propagated crops is a lack of knowledge in genetic gain achievable from alternative strategies. Existing models based on additive effects considering seed-propagated crops are not directly relevant for seedling selection of clonally propagated crops, as clonal propagation captures all genetic effects, not just additive. This study modeled genetic gain from traditional and various marker-based seedling selection strategies on a single trait basis through analytical derivation and stochastic simulation, based on a generalized seedling selection scheme of clonally propagated crops. Various trait-test scenarios with a range of broad-sense heritability and proportion of genotypic variance explained by DNA markers were simulated for two populations with different segregation patterns. Both derived and simulated results indicated that marker-based strategies tended to achieve higher genetic gain than phenotypic seedling selection for a trait where the proportion of genotypic variance explained by marker information was greater than the broad-sense heritability. Results from this study provides guidance in optimizing genetic gain from seedling selection for single traits where DNA tests providing marker information are available. PMID:27148453

  14. Novel types of staphylococcal cassette chromosome mec elements identified in clonal complex 398 methicillin-resistant Staphylococcus aureus strains.

    NARCIS (Netherlands)

    Li, S.; Skov, R.L.; Han, X.; Larsen, A.R.; Larsen, J.; Sorum, M.; Wulf, M.; Voss, A.; Hiramatsu, K.; Ito, T.

    2011-01-01

    The structures of staphylococcal cassette chromosome mec (SCCmec) elements carried by 31 clonal complex 398 (CC398) methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from the participants at a conference were analyzed. The SCCmecs were classified into novel types, namely, IX, X,

  15. Case Report: HIV test misdiagnosis

    African Journals Online (AJOL)

    Case Study: HIV test misdiagnosis 124. Case Report: HIV ... A positive rapid HIV test does not require ... 3 College of Medicine - Johns Hopkins Research Project, Blantyre,. Malawi ... test results: a pilot study of three community testing sites.

  16. HIV/AIDS and Alcohol

    Science.gov (United States)

    ... Psychiatric Disorders Other Substance Abuse HIV/AIDS HIV/AIDS Human immunodeficiency virus (HIV) targets the body’s immune ... and often leads to acquired immune deficiency syndrome (AIDS). The U.S. CDC reported that in 2015, 39, ...

  17. Living with HIV/AIDS

    Science.gov (United States)

    ... destroying the white blood cells that fight infection. AIDS stands for acquired immunodeficiency syndrome. It is the final stage of infection with HIV. Not everyone with HIV develops AIDS. Infection with HIV is serious. But thanks to ...

  18. HIV, AIDS, and the Future

    Science.gov (United States)

    Skip Navigation Bar Home Current Issue Past Issues HIV / AIDS HIV, AIDS, and the Future Past Issues / Summer 2009 ... turn Javascript on. Photo: The NAMES Project Foundation HIV and AIDS are a global catastrophe. While advances ...

  19. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... hiv-aids-101/statistics/ . Reference Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, National ... not just injection) can put a person at risk for getting HIV. Drug and alcohol intoxication affect ...

  20. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... What are HIV and AIDS? HIV (human immunodeficiency virus) is the virus that causes AIDS (acquired immune deficiency syndrome). AIDS ... but no cure, at the present time. The virus (HIV) and the disease it causes (AIDS) are ...

  1. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... the Link - Drugs and HIV Learn the Link - Drugs and HIV Email Facebook Twitter 2005 –Ongoing Behaviors ... GA: CDC, DHHS. Retrieved November 2017. How are Drug Misuse and HIV Related? Drug misuse and addiction ...

  2. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... Consequences of Drug Misuse Hepatitis (Viral) HIV/AIDS Mental Health Military Opioid Overdose Reversal with Naloxone (Narcan, ... hiv-aids-101/statistics/ . Reference Centers for Disease Control and Prevention, Division of HIV/AIDS Prevention, National ...

  3. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... can suppress the virus and prevent or decrease symptoms of illness. To learn about current statistics of HIV in the United States, please visit: https://www.aids.gov/hiv-aids-basics/hiv-aids-101/statistics/ . ...

  4. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... please visit: https://www.aids.gov/hiv-aids-basics/hiv-aids-101/statistics/ . Reference Centers for Disease ... About HIV/AIDS. ( https://www.cdc.gov/actagainstaids/basics/whatishiv.html ). Atlanta, GA: CDC, DHHS. Retrieved November ...

  5. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... causes (AIDS) are often linked and referred to as "HIV/AIDS." HIV can be transferred between people ... years, HIV is no longer a death sentence, as it was when the epidemic began. This is ...

  6. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... of HIV infection in the United States. Drugs can change the way the brain works, disrupting the ... linked and referred to as "HIV/AIDS." HIV can be transferred between people if an infected person's ...

  7. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... the spread of HIV infection in the United States. Drugs can change the way the brain works, ... about current statistics of HIV in the United States, please visit: https://www.aids.gov/hiv-aids- ...

  8. Drugs + HIV, Learn the Link

    Medline Plus

    Full Text Available ... in the spread of HIV infection in the United States. Drugs can change the way the brain works, ... learn about current statistics of HIV in the United States, please visit: https://www.aids.gov/hiv-aids- ...

  9. Variable effects of dexamethasone on protein synthesis in clonal rat osteosarcoma cells

    International Nuclear Information System (INIS)

    Hodge, B.O.; Kream, B.E.

    1988-01-01

    We examined the effects of dexamethasone on protein synthesis in clonal rat osteoblastic osteosarcoma (ROS) cell lines by measuring the incorporation of [ 3 H]proline into collagenase-digestible and noncollagen protein in the cell layer and medium of the cultures. In ROS 17/2 and subclone C12 of ROS 17/2.8, dexamethasone decreased collagen synthesis with no change in DNA content of the cultures. In ROS 17/2.8 and its subclone G2, dexamethasone stimulated collagen and noncollagen protein synthesis, with a concomitant decrease in the DNA content of the cells. These data indicate that ROS cell lines are phenotypically heterogeneous and suggest that in normal bone there may be distinct subpopulations of osteoblasts with varying phenotypic traits with respect to the regulation of protein synthesis

  10. Genetic structure of farmer-managed varieties in clonally-propagated crops.

    Science.gov (United States)

    Scarcelli, N; Tostain, S; Vigouroux, Y; Luong, V; Baco, M N; Agbangla, C; Daïnou, O; Pham, J L

    2011-08-01

    The relative role of sexual reproduction and mutation in shaping the diversity of clonally propagated crops is largely unknown. We analyzed the genetic diversity of yam-a vegetatively-propagated crop-to gain insight into how these two factors shape its diversity in relation with farmers' classifications. Using 15 microsatellite loci, we analyzed 485 samples of 10 different yam varieties. We identified 33 different genotypes organized in lineages supported by high bootstrap values. We computed the probability that these genotypes appeared by sexual reproduction or mutation within and between each lineage. This allowed us to interpret each lineage as a product of sexual reproduction that has evolved by mutation. Moreover, we clearly noted a similarity between the genetic structure and farmers' classifications. Each variety could thus be interpreted as being the product of sexual reproduction having evolved by mutation. This highly structured diversity of farmer-managed varieties has consequences for the preservation of yam diversity.

  11. Characterisation of free and glycosidically bound odourant compounds of Aragonez clonal musts by GC-O.

    Science.gov (United States)

    Botelho, Goreti; Mendes-Faia, Arlete; Clímaco, Maria Cristina

    2010-01-11

    To evaluate the potential aroma of Aragonez clonal red musts, several free and glycosidically bound odourant compounds were extracted. Then, the gas chromatography-olfactometry (GC-O) posterior intensity method was used to evaluate their odour intensity and the compounds were identified by gas chromatography-mass spectrometry (GC-MS). A group of eight sniffers evaluated free and bound fractions of Aragonez musts and perceived forty-three and twenty-two odourant peaks respectively. Furaneol (burnt sugar, candy-cotton) and vanillin (vanilla, sweet) were identified in both free and bound fractions of Aragonez musts, indicating their grape-derived origin. Principal component analysis (PCA) was applied to the posterior intensity method data and a relationship between the different odourant compound variables and the free fractions was established. Two principal components (PCs) were found which together explained 100% of the total variance. A large number of potentially important but yet unknown odourants was detected by the GC-O analysis.

  12. Invasion strategies in clonal aquatic plants: Are phenotypic differences caused by phenotypic plasticity or local adaptation?

    DEFF Research Database (Denmark)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit

    2010-01-01

    conditions and plant morphological characteristics. Conclusions: The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between......Background and Aims: The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important....... Methods: Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity...

  13. Cell proliferation in the Drosophila adult brain revealed by clonal analysis and bromodeoxyuridine labelling

    Directory of Open Access Journals (Sweden)

    Brand Andrea H

    2009-03-01

    Full Text Available Abstract Background The production of new neurons during adulthood and their subsequent integration into a mature central nervous system have been shown to occur in all vertebrate species examined to date. However, the situation in insects is less clear and, in particular, it has been reported that there is no proliferation in the Drosophila adult brain. Results We report here, using clonal analysis and 5'-bromo-2'-deoxyuridine (BrdU labelling, that cell proliferation does occur in the Drosophila adult brain. The majority of clones cluster on the ventrolateral side of the antennal lobes, as do the BrdU-positive cells. Of the BrdU-labelled cells, 86% express the glial gene reversed polarity (repo, and 14% are repo negative. Conclusion We have observed cell proliferation in the Drosophila adult brain. The dividing cells may be adult stem cells, generating glial and/or non-glial cell types.

  14. Clonal dominance between subpopulations of mixed small cell lung cancer xenografts implanted ectopically in nude mice

    DEFF Research Database (Denmark)

    Aabo, K; Vindeløv, L L; Spang-Thomsen, M

    1995-01-01

    Clonal evolution of neoplastic cells during solid tumour growth leads to the emergence of new tumour cell subpopulations with diverging phenotypic characteristics which may alter the behaviour of a malignant disease. Cellular interaction was studied in mixed xenografts in nude mice and during...... clone 54B was found to dominate the parent 54A clone when grown as mixed subcutaneous xenografts in nude mice, whereas no dominance was exerted during in vitro growth. The in vivo dominance could not be explained by differences in growth kinetics between the two tumour cell lines, and the interaction...... was not dependent on 54B being in excess in mixed tumours. The dominance was dependent on close in vivo contact as no remote effect on the growth of 54A was found when the dominating 54B cells were growing in the opposite flank of tumour-bearing mice. Irradiation inactivated 54B cells were unable to exert...

  15. Clonal Occurrence of Salmonella Weltevreden in Cultured Shrimp in the Mekong Delta, Vietnam

    Science.gov (United States)

    Noor Uddin, Gazi Md.; Larsen, Marianne Halberg; Barco, Lisa; Minh Phu, Tran; Dalsgaard, Anders

    2015-01-01

    This study investigated the occurrence, serovar and antimicrobial resistance of Salmonella spp. in shrimp samples from intensive and extensive farms located in three different provinces in the Mekong Delta, Vietnam. Shrimp from 11 of the 48 farms all contained S. Weltevreden, except for one farm yielding S. Agona, with no difference in Salmonella occurrence between the two production systems. Pulsed field gel electrophoresis (PFGE) of S. Weltevreden showed closely related XbaI pulse types, suggesting a clonal relationship despite the farms and shrimp samples being epidemiologically unrelated. S. Weltevreden was susceptible to most antimicrobials tested, with a few strains being resistant to florfenicol, chloramphenicol, sulfamethoxazole or trimethoprim. Future studies of the ecology of S. Weltevreden should establish if this serovar may survive better and even multiply in warm-water shrimp farm environments compared to other Salmonella serovars. PMID:26222547

  16. ROOT HYDRAULIC CONDUCTIVITY AND PHOTOSYNTHETIC CAPACITY OF EUCALYPT CLONAL CUTTINGS WITH ROOT MALFORMATION INDUCTIONS

    Directory of Open Access Journals (Sweden)

    Fábio Afonso Mazzei Moura de Assis Figueiredo

    2014-06-01

    Full Text Available http://dx.doi.org/10.5902/1980509814566The gain reduction of wood biomass in trees has been assigned to root deformations even in the nursery phase. The objective of this work was the evaluation of the root system hydraulic conductivity, gas exchanges and photochemical efficiency of eucalypt clonal cuttings with and without root deformation inductions. The treatments were: 1 operational cuttings without root malformation inductions (grown according to the used methodology of Fibria Cellulose S.A.; 2 root deformation inductions. These inductions did not promote decrease in the root volume. However, the deformations brought reduction of the root system hydraulic conductivity. Lower photosynthetic rates were also observed along the day in the cuttings in the root deformed cuttings. This decreasing rate is connected to stomatal and non stomatal factors.

  17. Clonal Occurrence of Salmonella Weltevreden in Cultured Shrimp in the Mekong Delta, Vietnam.

    Directory of Open Access Journals (Sweden)

    Gazi Md Noor Uddin

    Full Text Available This study investigated the occurrence, serovar and antimicrobial resistance of Salmonella spp. in shrimp samples from intensive and extensive farms located in three different provinces in the Mekong Delta, Vietnam. Shrimp from 11 of the 48 farms all contained S. Weltevreden, except for one farm yielding S. Agona, with no difference in Salmonella occurrence between the two production systems. Pulsed field gel electrophoresis (PFGE of S. Weltevreden showed closely related XbaI pulse types, suggesting a clonal relationship despite the farms and shrimp samples being epidemiologically unrelated. S. Weltevreden was susceptible to most antimicrobials tested, with a few strains being resistant to florfenicol, chloramphenicol, sulfamethoxazole or trimethoprim. Future studies of the ecology of S. Weltevreden should establish if this serovar may survive better and even multiply in warm-water shrimp farm environments compared to other Salmonella serovars.

  18. A Robust Single Primate Neuroepithelial Cell Clonal Expansion System for Neural Tube Development and Disease Studies

    Directory of Open Access Journals (Sweden)

    Xiaoqing Zhu

    2016-02-01

    Full Text Available Developing a model of primate neural tube (NT development is important to promote many NT disorder studies in model organisms. Here, we report a robust and stable system to allow for clonal expansion of single monkey neuroepithelial stem cells (NESCs to develop into miniature NT-like structures. Single NESCs can produce functional neurons in vitro, survive, and extensively regenerate neuron axons in monkey brain. NT formation and NESC maintenance depend on high metabolism activity and Wnt signaling. NESCs are regionally restricted to a telencephalic fate. Moreover, single NESCs can turn into radial glial progenitors (RGPCs. The transition is accurately regulated by Wnt signaling through regulation of Notch signaling and adhesion molecules. Finally, using the “NESC-TO-NTs” system, we model the functions of folic acid (FA on NT closure and demonstrate that FA can regulate multiple mechanisms to prevent NT defects. Our system is ideal for studying NT development and diseases.

  19. Clonal spread of Staphylococcus aureus with reduced susceptibility to oxacillin in a dermatological hospital unit

    DEFF Research Database (Denmark)

    Thomsen, Marianne Kragh; Rasmussen, Mads; Fuursted, Kurt

    2006-01-01

    transmission routes in order to intervene and prevent further spread. Clonality of the isolates was confirmed by pulsed field gel electrophoresis. Several breaches in infection control procedures were revealed suggesting both direct and indirect transmission between patients. Defective skin barriers, high...... carrier rates of S. aureus in dermatological patients and high consumption rates of dicloxacillin in the department might facilitate transmission. Following improvement of the general infection control measures, and after reassessment of the antibiotic policy in the department, the outbreak has......In November 2000, we became aware of isolates of Staphylococcus aureus with borderline resistance to oxacillin (BORSA) from patients in the Department of Dermatology, Aarhus University Hospital. The objective was to describe the isolates phenotypically and genotypically and to assess possible...

  20. Brief Training of HIV Medical Providers Increases Their Frequency of Delivering Prevention Counselling to Patients at Risk of Transmitting HIV to Others

    Science.gov (United States)

    Patel, Shilpa N.; Marks, Gary; Gardner, Lytt; Golin, Carol E.; Shinde, Sanjyot; O'Daniels, Christine; Wilson, Tracey E.; Quinlivan, E. Byrd; Banderas, Julie W.

    2013-01-01

    Objective: The aim of this study was to examine whether brief training of human immunodeficiency virus (HIV) medical providers increased the frequency with which they routinely delivered prevention counselling to patients, and whether patient characteristics were associated with receipt of that counselling. Design: Longitudinal. Setting: Seven HIV…