Turnover of Lecanoroid Mycobionts and Their Trebouxia Photobionts Along an Elevation Gradient in Bolivia Highlights the Role of Environment in Structuring the Lichen Symbiosis

Shifts in climate along elevation gradients structure mycobiont–photobiont associations in lichens. We obtained mycobiont (lecanoroid Lecanoraceae) and photobiont (Trebouxia alga) DNA sequences from 89 lichen thalli collected in Bolivia from a ca. 4,700 m elevation gradient encompassing diverse natural communities and environmental conditions. The molecular dataset included six mycobiont loci (ITS, nrLSU, mtSSU, RPB1, RPB2, and MCM7) and two photobiont loci (ITS, rbcL); we designed new primers to amplify Lecanoraceae RPB1 and RPB2 with a nested PCR approach. Mycobionts belonged to Lecanora s.lat., Bryonora, Myriolecis, Protoparmeliopsis, the “Lecanora” polytropa group, and the “L.” saligna group. All of these clades except for Lecanora s.lat. occurred only at high elevation. No single species of Lecanoraceae was present along the entire elevation gradient, and individual clades were restricted to a subset of the gradient. Most Lecanoraceae samples represent species which have not previously been sequenced. Trebouxia clade C, which has not previously been recorded in association with species of Lecanoraceae, predominates at low- to mid-elevation sites. Photobionts from Trebouxia clade I occur at the upper extent of mid-elevation forest and at some open, high-elevation sites, while Trebouxia clades A and S dominate open habitats at high elevation. We did not find Trebouxia clade D. Several putative new species were found in Trebouxia clades A, C, and I. These included one putative species in clade A associated with Myriolecis species growing on limestone at high elevation and a novel lineage sister to the rest of clade C associated with Lecanora on bark in low-elevation grassland. Three different kinds of photobiont switching were observed, with certain mycobiont species associating with Trebouxia from different major clades, species within a major clade, or haplotypes within a species. Lecanoraceae mycobionts and Trebouxia photobionts exhibit species turnover along the elevation gradient, but with each partner having a different elevation threshold at which the community shifts completely. A phylogenetically defined sampling of a single diverse family of lichen-forming fungi may be sufficient to document regional patterns of Trebouxia diversity and distribution.

Participants’ characteristics and motivations to screen for HIV vaccine and monoclonal antibody trials in KwaZulu-Natal, South Africa

Background HIV is one of the greatest public health challenges in South Africa. Potential HIV vaccines and antibodies are thought to be cost-effective biomedical HIV prevention methods and are currently under investigation in phase I, II, and III trials. Consequently, current and future clinical trials need to ensure sufficient recruitment and retention. To achieve this goal, clinical trial staff need to understand the socio-demographic and behavioural characteristics of people volunteering to screen for these trials and their reasons for volunteering. Methods We conducted a secondary analysis of participant screening data across five vaccine and monoclonal antibody trials at four sites in KwaZulu-Natal, South Africa. Our study reviewed the demographic, behavioural, motivational, and health-related data from the case report forms and screening questionnaires. Descriptive statistics, chi-squared, and one-way ANOVA tests were used to analyse participants’ characteristics and motivation to participate in HIV vaccine and monoclonal antibody trials. Analyses were conducted using R version 3.5.2. Results Screening data from 1934 participants, including 79.2% of women, were obtained across all five trials (1034 enrolled, 900 screened out/declined). Screened participants predominately self-identified as black, heterosexual, cisgender women or men, many with lower educational backgrounds (43.9% did not complete secondary/high school), and several self-reported HIV-risk behaviours among themselves and their partners. 10.8% of the screened participants were living with HIV. Avoiding HIV risk was the main motivation to participate in clinical trials, followed by altruistic reasons such as a desire to help the community or helping to find a vaccine. Discussion The current recruitment approach of these trials attracts heterosexual participants who seek to reduce HIV risk and support their community. Hence, the data suggest the need for and potential acceptance of continued ongoing HIV prevention efforts. Current trials attract participants with lower educational levels, which may be driven by the site locations, current community mobilisation strategies and research site opening hours. The sites could consider more flexible working hours to accommodate working participants and find ways to connect participants to educational support and opportunities to upgrade education levels for the current clientele. Trial registration HVTN 100: A Safety and Immune Response Study of 2 Experimental HIV Vaccines, NCT02404311. Registered on March 17, 2015. HVTN 111: Safety and Immune Response to a Clade C DNA HIV Vaccine, NCT02997969. Registered on December 16, 2016. HVTN 108: Evaluating the Safety and Immunogenicity of HIV Clade C DNA Vaccine and MF59- or AS01B-Adjuvanted Clade C Env Protein Vaccines in Various Combinations in Healthy, HIV-Uninfected Adults, NCT02915016. Registered on September 22, 2016. HVTN 702: Pivotal Phase 2b/3 ALVAC/Bivalent gp120/MF59 HIV Vaccine Prevention Safety and Efficacy Study in South Africa, NCT02968849. Registered on November 1, 2016. HVTN 703/HPTN 081: Evaluating the Safety and Efficacy of the VRC01 Antibody in Reducing Acquisition of HIV-1 Infection in Women, NCT02568215. Registered on October 1, 2015.

Symbiodinium diversity and potential hybridisation on the highly biodiverse coral reefs of Timor-Leste

<p>To persist in oligotrophic waters, reef-building corals rely on nutritional interactions with their intracellular symbionts: photosynthetic dinoflagellates of the genus Symbiodinium. This relationship is threatened by increasing environmental stress, which can stimulate loss of these symbionts from coral tissues (‘coral bleaching’). Members of the genus Symbiodinium display high levels of genetic diversity, and demonstrate a corresponding diversity in physiological responses to environmental change. However, the true diversity and potential for genetic adaptation in this genus remain poorly characterised. This thesis aimed to further the understanding of symbiont diversity and adaptive potential by conducting assessments of Symbiodinium at Atauro Island and the neighbouring Timor-Leste mainland. These sites have previously been shown to be of outstanding conservation value, with extremely high levels of coral diversity. Atauro Island also possibly hosts the highest diversity of reef fish in the world. However, the Symbiodinium communities at these sites have never been assessed. Two specific objectives were therefore addressed here. The first was to measure Symbiodinium diversity at Atauro Island (four sites) and Timor (three sites), using direct sequencing of three gene regions: cob gene, mitochondrion; ITS2 region, nucleus; and psbAncr region, chloroplast; in addition to Next Generation Sequencing of the ITS2 region. The second objective was to establish evidence for Symbiodinium hybridisation, a potentially rapid evolutionary mechanism that may facilitate adaptation to environmental stress, by looking for genetic incongruences between Symbiodinium organelles. Coral symbionts of Timor-Leste were found to be similar to those from other coral reefs of the Indo-Pacific, with several host generalist and multiple host specific types observed. However, there were also several novel Symbiodinium types found (C15p, C15q, C1x, C1z). Despite their geographic proximity, there were strong differences observed between the symbiont communities of Atauro Island and mainland Timor. In particular, the coral genus Pocillopora hosted clade C symbionts exclusively at Atauro Island, while it hosted clade D exclusively at Timor sites. Other symbiont types also showed geographic partitioning, and diversity was 1.25 times higher at Atauro Island, a figure consistent for the cob and ITS2 regions. While Timor sites have comparable Symbiodinium diversity to other reefs globally, Atauro has noticeably elevated Symbiodinium diversity. Next Generation Sequencing affirmed these patterns, with Atauro Island sites having much more diverse cryptic populations of Symbiodinium, largely driven by symbionts in clade C. The exception was clade D symbionts, which were proportionally far more diverse at Timor, a pattern consistent in multiple coral genera. There was strong evidence of genetic incongruence at two Atauro Island sites, with all testing procedures identifying genetic discordance between organellar and nuclear genomes, consistent with theoretical predictions of hybridisation. This study therefore presents strong evidence for Symbiodinium hybridisation, and its corroboration by multiple loci is significant. Putative hybrid Symbiodinium always had a common type as one of the possible parents, with a rarer symbiont as the other. For example, one putative hybrid had organellar genes of the common generalist Symbiodinium C40, while it was identified as the rare type C3z with the ITS2 region. Both of these Symbiodinium types were also found in congruent relationships, which strongly supports the possibility that they sexually reproduced to produce the incongruent putative hybrid. Environmental stressors, such as increased temperature, turbidity and sedimentation, are suggested reasons for lowered Symbiodinium diversity at Timor, as they may impose a selection pressure on corals to only keep highly beneficial symbionts. This reduction in diversity likely limits the potential for adaptive change through methods like hybridisation, and highlights the need to assess and conserve symbiont diversity to the same extent as coral diversity.</p>

Symbiodinium diversity and potential hybridisation on the highly biodiverse coral reefs of Timor-Leste

<p>To persist in oligotrophic waters, reef-building corals rely on nutritional interactions with their intracellular symbionts: photosynthetic dinoflagellates of the genus Symbiodinium. This relationship is threatened by increasing environmental stress, which can stimulate loss of these symbionts from coral tissues (‘coral bleaching’). Members of the genus Symbiodinium display high levels of genetic diversity, and demonstrate a corresponding diversity in physiological responses to environmental change. However, the true diversity and potential for genetic adaptation in this genus remain poorly characterised. This thesis aimed to further the understanding of symbiont diversity and adaptive potential by conducting assessments of Symbiodinium at Atauro Island and the neighbouring Timor-Leste mainland. These sites have previously been shown to be of outstanding conservation value, with extremely high levels of coral diversity. Atauro Island also possibly hosts the highest diversity of reef fish in the world. However, the Symbiodinium communities at these sites have never been assessed. Two specific objectives were therefore addressed here. The first was to measure Symbiodinium diversity at Atauro Island (four sites) and Timor (three sites), using direct sequencing of three gene regions: cob gene, mitochondrion; ITS2 region, nucleus; and psbAncr region, chloroplast; in addition to Next Generation Sequencing of the ITS2 region. The second objective was to establish evidence for Symbiodinium hybridisation, a potentially rapid evolutionary mechanism that may facilitate adaptation to environmental stress, by looking for genetic incongruences between Symbiodinium organelles. Coral symbionts of Timor-Leste were found to be similar to those from other coral reefs of the Indo-Pacific, with several host generalist and multiple host specific types observed. However, there were also several novel Symbiodinium types found (C15p, C15q, C1x, C1z). Despite their geographic proximity, there were strong differences observed between the symbiont communities of Atauro Island and mainland Timor. In particular, the coral genus Pocillopora hosted clade C symbionts exclusively at Atauro Island, while it hosted clade D exclusively at Timor sites. Other symbiont types also showed geographic partitioning, and diversity was 1.25 times higher at Atauro Island, a figure consistent for the cob and ITS2 regions. While Timor sites have comparable Symbiodinium diversity to other reefs globally, Atauro has noticeably elevated Symbiodinium diversity. Next Generation Sequencing affirmed these patterns, with Atauro Island sites having much more diverse cryptic populations of Symbiodinium, largely driven by symbionts in clade C. The exception was clade D symbionts, which were proportionally far more diverse at Timor, a pattern consistent in multiple coral genera. There was strong evidence of genetic incongruence at two Atauro Island sites, with all testing procedures identifying genetic discordance between organellar and nuclear genomes, consistent with theoretical predictions of hybridisation. This study therefore presents strong evidence for Symbiodinium hybridisation, and its corroboration by multiple loci is significant. Putative hybrid Symbiodinium always had a common type as one of the possible parents, with a rarer symbiont as the other. For example, one putative hybrid had organellar genes of the common generalist Symbiodinium C40, while it was identified as the rare type C3z with the ITS2 region. Both of these Symbiodinium types were also found in congruent relationships, which strongly supports the possibility that they sexually reproduced to produce the incongruent putative hybrid. Environmental stressors, such as increased temperature, turbidity and sedimentation, are suggested reasons for lowered Symbiodinium diversity at Timor, as they may impose a selection pressure on corals to only keep highly beneficial symbionts. This reduction in diversity likely limits the potential for adaptive change through methods like hybridisation, and highlights the need to assess and conserve symbiont diversity to the same extent as coral diversity.</p>

Diversity of Three Small Type’s Giant Clams and Their Associated Endosymbiotic Symbiodiniaceae at Hainan and Xisha Islands, South China Sea

Giant clams are found in a mutualistic association with Symbiodiniaceae dinoflagellates, however, the diversity of the giant clams, as well as the diversity and distribution of Symbiodiniaceae in different Tridacnine species remain relatively poorly studied in the South China Sea. In this study, a total of 100 giant clams belonging to small type’s giant clams, Tridacna maxima, T. crocea, and T. noae, were collected from Hainan and Xisha Islands. Based on mtDNA cytochrome c oxidase subunit 1 gene (COI) and 16S rRNA fragments, T. maxima and T. crocea showed a closer phylogenetic relationship than T. noae. All the three species of giant clams hosted Symbiodiniaceae including genera Symbiodinium (formerly Clade A) and Cladocopium (formerly Clade C). Geographically, symbionts in Cladocopium are restricted to Xisha Islands, probably because Cladocopium prefers to inhabit in waters with higher mean temperatures. The endosymbiont specificity among the three giant clam species was also detected. T. noae and T. crocea are found to harbor Symbiodinium preferentially, compared with Cladocopium. These results could provide important information to understand various endosymbionts occurring in giant clams in the South China Sea.

Comprehensive Comparative Genomics and Phenotyping of Methylobacterium Species

The pink-pigmented facultative methylotrophs (PPFMs), a major bacterial group found in the plant phyllosphere, comprise two genera: Methylobacterium and Methylorubrum. They have been separated into three major clades: A, B (Methylorubrum), and C. Within these genera, however, some species lack either pigmentation or methylotrophy, which raises the question of what actually defines the PPFMs. The present study employed a comprehensive comparative genomics approach to reveal the phylogenetic relationship among the PPFMs and to explain the genotypic differences that confer their different phenotypes. We newly sequenced the genomes of 29 relevant-type strains to complete a dataset for almost all validly published species in the genera. Through comparative analysis, we revealed that methylotrophy, nitrate utilization, and anoxygenic photosynthesis are hallmarks differentiating the PPFMs from the other Methylobacteriaceae. The Methylobacterium species in clade A, including the type species Methylobacterium organophilum, were phylogenetically classified into six subclades, each possessing relatively high genomic homology and shared phenotypic characteristics. One of these subclades is phylogenetically close to Methylorubrum species; this finding led us to reunite the two genera into a single genus Methylobacterium. Clade C, meanwhile, is composed of phylogenetically distinct species that share relatively higher percent G+C content and larger genome sizes, including larger numbers of secondary metabolite clusters. Most species of clade C and some of clade A have the glutathione-dependent pathway for formaldehyde oxidation in addition to the H4MPT pathway. Some species cannot utilize methanol due to their lack of MxaF-type methanol dehydrogenase (MDH), but most harbor an XoxF-type MDH that enables growth on methanol in the presence of lanthanum. The genomes of PPFMs encode between two and seven (average 3.7) genes for pyrroloquinoline quinone-dependent alcohol dehydrogenases, and their phylogeny is distinctly correlated with their genomic phylogeny. All PPFMs were capable of synthesizing auxin and did not induce any immune response in rice cells. Other phenotypes including sugar utilization, antibiotic resistance, and antifungal activity correlated with their phylogenetic relationship. This study provides the first inclusive genotypic insight into the phylogeny and phenotypes of PPFMs.

Structurally related but genetically unrelated antibody lineages converge on an immunodominant HIV-1 Env neutralizing determinant following trimer immunization

Understanding the molecular mechanisms by which antibodies target and neutralize the HIV-1 envelope glycoprotein (Env) is critical in guiding immunogen design and vaccine development aimed at eliciting cross-reactive neutralizing antibodies (NAbs). Here, we analyzed monoclonal antibodies (mAbs) isolated from non-human primates (NHPs) immunized with variants of a native flexibly linked (NFL) HIV-1 Env stabilized trimer derived from the tier 2 clade C 16055 strain. The antibodies displayed neutralizing activity against the autologous virus with potencies ranging from 0.005 to 3.68 μg/ml (IC50). Structural characterization using negative-stain EM and X-ray crystallography identified the variable region 2 (V2) of the 16055 NFL trimer to be the common epitope for these antibodies. The crystal structures revealed that the V2 segment adopts a β-hairpin motif identical to that observed in the 16055 NFL crystal structure. These results depict how vaccine-induced antibodies derived from different clonal lineages penetrate through the glycan shield to recognize a hypervariable region within V2 (residues 184–186) that is unique to the 16055 strain. They also provide potential explanations for the potent autologous neutralization of these antibodies, confirming the immunodominance of this site and revealing that multiple angles of approach are permissible for affinity/avidity that results in potent neutralizing capacity. The structural analysis reveals that the most negatively charged paratope correlated with the potency of the mAbs. The atomic level information is of interest to both define the means of autologous neutralization elicited by different tier 2-based immunogens and facilitate trimer redesign to better target more conserved regions of V2 to potentially elicit cross-neutralizing HIV-1 antibodies.

Molecular analysis of mitochrondrial cytb of Pediculus humanus capitis in Thailand revealed potential historical connection with South Asia

Background Pediculus humanus capitis or head louse is an obligate ectoparasite and its infestation remains a major public health issue worldwide. Molecular analysis divides head lice into six clades and intra-clade genetic differences have been identified. Several hypotheses have been formulated to elucidate the discrepancies of the variety of head lice among different regions of the world. It is currently concluded that head lice distribution might be associated with human migration history. This study aims to investigate genetic data of human head lice in Thailand. We believe that the analysis could help establish the correlation between local and global head lice populations. Method We investigated mitochondrial cytochrome b (cytb) gene of the collected 214 head lice to evaluate genetic diversity from 15 provinces among 6 regions of Thailand. The head lice genes were added to the global pool for the phylogenetic tree, Bayesian tree, Skyline plot, and median joining network construction. The biodiversity, neutrality tests, and population genetic differentiation among the 6 Thailand geographic regions were analyzed by DNAsp version 6. Results The phylogenetic tree analysis of 214 collected head lice are of clade A and clade C accounting for roughly 65% and 35% respectively. The Bayesian tree revealed a correlation of clade diversification and ancient human dispersal timeline. In Thailand, clade A is widespread in the country. Clade C is confined to only the Central, Southern, and Northeastern regions. We identified 50 novel haplotypes. Statistical analysis showed congruent results between genetic differentiation and population migration especially with South Asia. Conclusions Pediculosis remains problematic among children in the rural areas in Thailand. Cytb gene analysis of human head lice illustrated clade distribution and intra-clade diversity of different areas. Our study reported novel haplotypes of head lice in Thailand. Moreover, the statistic calculation provided a better understanding of their relationship with human, as an obligate human parasite and might help provide a better insight into the history of human population migration. Determination of the correlation between phylogenetic data and pediculicide resistance gene as well as residing bacteria are of interest for future studies.