Connectivity and exploitation of Acanthurus triostegus and Acanthurus leucosternon in the Indian Ocean : Application of genetics and single stock assessment to aid coral reef management

Extrinsic/abiotic and intrinsic/biotic factors can influence the connectivity and exploitation of reef fish. Coral reef fish from the genus Acanthurus have evolved different life history characteristics that can affect their connectivity and exploitation. The aim of this thesis is to explore the population genetic structure and growth parameters of Acanthurus triostegus and Acanthurus leucosternon in the Indian Ocean, to determine the influence of biotic and abiotic factors on the connectivity and exploitation of coral reef species. First, a 491bp fragment of cytochrome b and microsatellite loci was used to show that the long pelagic larval duration of acanthurids can confer widespread genetic connectivity to A. leucosternon in the Eastern Africa region. Although the global AMOVA (Analysis of Molecular Variance) involving all A. leucosternon Eastern African population is significant, the hierarchical AMOVA and STRUCTURE does not show any genetic breaks consistent with known Eastern African oceanographic and biogeographical barriers to dispersal. Second, a mitochondrial DNA fragment spanning the ATPase8 and ATPase6 gene regions is used to demonstrate that the genetic differentiation of A. triostegus is correlated with geographic distance throughout the Indo-Pacific. In addition, this study shows that populations of A. triostegus are significantly differentiated in the Indian Ocean (Western Indian Ocean and East Indian Ocean), but not in the Pacific Ocean (West, Central, and East Pacific). Third, using syntopic sampling of the spawning aggregating A. triostegus and monogamous pairing A. leucosternon this study determined the influence of mating behaviour on the connectivity of these two Acanthurus species. Contrary to expectations, DAPC (discriminant analysis of principal components), hierarchical AMOVA, and pairwise comparisons showed that the divergent mating behaviour does not lead to differences in the connectivity patterns of A. leucosternon and A. triostegus, but the two species experienced differences in their demographic history. A detailed analysis in BEAST (Bayesian Evolutionary analysis Sampling Trees) showed iv that A. leucosternon which is often restricted to coral reef habitats had a faster and more recent demographic expansion than the habitat generalist A. triostegus. Finally, the growth parameters and mortality of A. triostegus and A. leucosternon were estimated, to determine whether differences in mating behaviour can lead to differences in exploitation rate. Consistent with expectations, the length-based stock assessment showed that the A. triostegus, the species that often forms spawning aggregation has a higher exploitation rate than the monogamous pairing A. leucosternon, supporting previous studies indicating that spawning aggregation may increase the susceptibility of coral reef fish to fishing

HIV-1 molecular diversity and drug resistance mutations amongst immuno-competent, therapy naïve infants/children and adults in Yaounde, Cameroon

Thesis (MScMedSc)--Stellenbosch University, 2017.Background: In Cameroon, HIV infections range between 550, 000 to 690, 000 for adults aged 15 to 49 years and a prevalence rate at 4.5%. In children of 0 – 14 years, HIV infections range between 34, 000 to 44, 000. The country harbors both HIV type 1 (HIV-1) and HIV type 2 (HIV-2). HIV groups found in Cameroon include M, N, O, P variants. Group M subtypes are the most prevalent, with CRF02_AG accounting for approximately 40% of all HIV infections. This is unlike other regions globally where other group M subtypes like C are the predominant ones. The high genomic diversity of HIV-1 and the emergence of drug resistant associated mutations (RAMs) continue to be a major challenge in designing standardized laboratory protocols for HIV testing, vaccine development and providing successful lifelong therapy to HIV infected patients. In Cameroon, drug resistance rates for therapy naïve individuals are currently at 3.8% in adults and 3.6% in children. This study aimed at identifying HIV-1 diversity and evaluate drug resistant mutations (DRMs) in two different cohorts of therapy-naïve infants/children and adults in Cameroon. Methods: A total of 180 plasma samples were collected from therapy naïve HIV positive patients that included: (1) 55 plasma samples from proxy-consented infants/children aged 9-72 months old with unknown prevention of mother-to-child transmission (PMTCT) exposure and (2) 125 plasma samples from adults of 15 to 50 years old. The CD4+ T-cell count was performed using standard methods following manufacturer’s instructions. To study the HIV-1 diversity and resistance in the two cohorts, partial pol Protease (PR), Reverse Transcriptase (RT) and Integrase (IN) regions of the HIV-1 genome were targeted for conventional PCR amplification and Sanger DNA sequencing. Phylogenetic inference using Neighbor-Joining (NJ) trees were used to cluster and infer subtypes. Results: In the infants/children cohort, the CD4+ T-cell count ranged between 500-2000 cells/m3 (a median of 33.0%) and the HIV-1 viral load between 3000-6000 copies/ml (a median of 4.96 RNA copies/ml). A total of 37/55 (67.3%) paediatric cohort samples were amplified for at least one of the HIV-1 pol fragments. These include 29/55 (52.0%) for the PR, 27/55 (49.0%) for the RT and 28/55 (51.0%) for IN. The most predominant HIV-1 strain was G/CRF02_AG at 62.5% (n = 15). Other subtypes detected include subtype A (20.8%; n = 5), C (8.3%; n = 2) and F2 (8.3%; n = 2). Three sequences (11.1%) could not be assigned to any subtype with confidence. Levels of DRMs to Protease inhibitors (PIs), nucleoside reverse transcriptase inhibitors (NRTIs) and non-NRTI were 27.6% (only minor DRMS were observed for PR), 3.7% and 40.7%, respectively. The NRTI mutations observed showed high-level resistance to Zidovudine (AZT), Tenofovir (TDF), Didanosine (DDI) and Stavudine (D4T), and low to intermediate-level resistance to Lamivudine (3TC), Abacavir (ABC), and Emtricitabine (FTC). The NNRTI mutations observed showed high level resistance to Nevirapine (NVP) and Efavirenz (EFV) with reduced susceptibility to Etravirine (ETR) and Rilpivirine (RPV). In the adult cohort, the RT fragment (n = 55) was used for phylogenetic analysis with majority of the sample sequences clustered with HIV-1 subtype G/CRF02_AG which accounted for 40% (n = 22), CRF22_01A1 (10.9%; n = 6), C (1.8%; n = 1), B (1.8%; n = 1), other complex forms – 37_cpx/11_cpx (3.6%; n = 2). Twenty three samples (41.8%) could not be assigned to any subtype with confidence. The levels of drug resistance for adults was 5.4% for both NRT and NNRT inhibitors - 4.0% had low level resistance to EFV, ETR, NVP and RPV while 1.4% had intermediate to high level resistance to ABC, FTC, TDF, EFV and NVP. Conclusion: Cameroon continues to harbor many HIV-1 subtypes and circulating recombinant forms (CRFs) as observed in both cohorts. Furthermore, rare group O and other group M subtypes like C were noticed within the study cohorts suggesting an improvement in sensitivity of detection methodologies currently used. Drug resistance is a major challenge to current antiretroviral drug regimens as illustrated by the detection of RAMS in both cohorts of this study. Continuous surveillance of the HIV diversity and drug resistance is therefore necessary to better manage the HIV-1 pandemic

Konnektivität und Nutzung zweier Acanthurus Arten im Indischen Ozean : Anwendung von Genetik und Bestandsabschätzungen im Hinblick auf Management Entscheidungen

Extrinsic/abiotic and intrinsic/biotic factors can influence the connectivity and exploitation of reef fish. Coral reef fish from the genus Acanthurus have evolved different life history characteristics that can affect their connectivity and exploitation. The aim of this thesis is to explore the population genetic structure and growth parameters of Acanthurus triostegus and Acanthurus leucosternon in the Indian Ocean, to determine the influence of biotic and abiotic factors on the connectivity and exploitation of coral reef species. First, a 491bp fragment of cytochrome b and microsatellite loci was used to show that the long pelagic larval duration of acanthurids can confer widespread genetic connectivity to A. leucosternon in the Eastern Africa region. Although the global AMOVA (Analysis of Molecular Variance) involving all A. leucosternon Eastern African population is significant, the hierarchical AMOVA and STRUCTURE does not show any genetic breaks consistent with known Eastern African oceanographic and biogeographical barriers to dispersal. Second, a mitochondrial DNA fragment spanning the ATPase8 and ATPase6 gene regions is used to demonstrate that the genetic differentiation of A. triostegus is correlated with geographic distance throughout the Indo-Pacific. In addition, this study shows that populations of A. triostegus are significantly differentiated in the Indian Ocean (Western Indian Ocean and East Indian Ocean), but not in the Pacific Ocean (West, Central, and East Pacific). Third, using syntopic sampling of the spawning aggregating A. triostegus and monogamous pairing A. leucosternon this study determined the influence of mating behaviour on the connectivity of these two Acanthurus species. Contrary to expectations, DAPC (discriminant analysis of principal components), hierarchical AMOVA, and pairwise comparisons showed that the divergent mating behaviour does not lead to differences in the connectivity patterns of A. leucosternon and A. triostegus, but the two species experienced differences in their demographic history. A detailed analysis in BEAST (Bayesian Evolutionary analysis Sampling Trees) showed iv that A. leucosternon which is often restricted to coral reef habitats had a faster and more recent demographic expansion than the habitat generalist A. triostegus. Finally, the growth parameters and mortality of A. triostegus and A. leucosternon were estimated, to determine whether differences in mating behaviour can lead to differences in exploitation rate. Consistent with expectations, the length-based stock assessment showed that the A. triostegus, the species that often forms spawning aggregation has a higher exploitation rate than the monogamous pairing A. leucosternon, supporting previous studies indicating that spawning aggregation may increase the susceptibility of coral reef fish to fishing

Genetic diversity of the WIO population.

<p>Genetic diversity of the WIO population.</p

Sample sites, number of sequences (n) and number of haplotypes (N_hp) for <i>Linckia laevigata</i> in the Indo-Malay-Philippine Archipelago (IMPA).

<p>Sample sites, number of sequences (n) and number of haplotypes (N_hp) for <i>Linckia laevigata</i> in the Indo-Malay-Philippine Archipelago (IMPA).</p

Saying No to Forced Early Retirement from Sex: Time to broaden the scope of HIV prevention in Kenya

HIV prevention messages have an impact on people's sexualities in ways that are unimaginable. In Kenya, consultations with HIV positive people under the Maanisha programme reveal that HIV prevention messages work to regulate and stigmatize sexual expressions among people already infected with HIV. Regrettably, these stereotypical strategies are promoted by health experts and HIV/AIDS service providers. Interventions must break with stereotypes and create spaces for behaviour change strategies that begin with positive peoples lived experiences, acknowledging their complexities and working with them in a more equitable and mutually respectful interaction. Development (2009) 52, 105–108. doi:10.1057/dev.2008.78