HIV positive men as fathers: Accounts of displacement, ir/responsibility and paternal emergence

It is now apparent that socio-cultural constructions of masculinity variously impact men’s experiences of their HIV positive status, yet how being a father can feature in this mix remains under-researched. This study employed in-depth semi-structured interviews and Foucauldian-informed discourse analysis to explore the accounts of six self-identifying heterosexual fathers (four black African migrants, two white European) who had been living with HIV from five to 24 years. While the HIV-related literature calls for the need to subvert ‘traditional’ expressions of masculinity as a means of promoting HIV prevention and HIV health, we argue that the lived experience for HIV positive men as fathers is more socially, discursively and thus more psychologically nuanced. We illustrate this by highlighting ways in which HIV positive men as fathers are not simply making sense of themselves as a HIV positive man for whom the modern (new) man and father positions are useful strategies for adapting to HIV and combating associated stigma. Discourses of modern and patriarchal fatherhoods, a gender-specific discourse of irresponsibility, and the neoliberal conflation of heath and self-responsibility are also at work in the sense making frames that HIV positive men, who are also fathers, can variously deploy. Our analysis shows how this discursive mix can underpin possibilities of often conflicted meaning and identity when living as a man and father with HIV in the UK, and specifically how discourses of fatherhood and HIV ‘positive’ health can complicate these men’s expressions and inhabitations of masculinity

Annotation Error in Public Databases: Misannotation of Molecular Function in Enzyme Superfamilies

Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%–63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with “overprediction” of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation

A process model of the formation of spatial presence experiences

In order to bridge interdisciplinary differences in Presence research and to establish connections between Presence and “older” concepts of psychology and communication, a theoretical model of the formation of Spatial Presence is proposed. It is applicable to the exposure to different media and intended to unify the existing efforts to develop a theory of Presence. The model includes assumptions about attention allocation, mental models, and involvement, and considers the role of media factors and user characteristics as well, thus incorporating much previous work. It is argued that a commonly accepted model of Spatial Presence is the only solution to secure further progress within the international, interdisciplinary and multiple-paradigm community of Presence research

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

BackgroundTrunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.ResultsThe integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.ConclusionsThis study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management

Abstracts from the 8th International Conference on cGMP Generators, Effectors and Therapeutic Implications

This work was supported by a restricted research grant of Bayer AG

What makes Elysia viridis tick? Fitness Consequences of Diet Selection and Kleptoplasty

ABSTRACT Understanding the mechanisms involved in resource use by an organism is pivotal to understanding its ecology. A conspecific population that as a whole demonstrates a generalist pattern of resource use may in fact consist of relatively specialized individuals. Elysia viridis, a sacoglossan opisthobranch mollusc, tends to demonstrate this type of sympatric variation in diet, although to differing extents depending on the ontogenetic stage. However, the mechanisms underlying this inter-individual variation are poorly understood. Utilizing the basic framework of optimal diet theory, this thesis investigated the prevalence of individual specialization and its effects on energy assimilation in E. viridis on different algal diets and the mechanisms that underpin or constrain diet selection. This was assessed through a combination of laboratory experiments addressing how E. viridis' original algal host affected algal diet choice, handling efficiency, growth, and the retention of functional chloroplasts (kleptoplasty) in the lab and relating conclusions from these experiments to observations of abundance and size of the sea slug in the study area. Assessments of abundance and size distributions of E. viridis on different algal hosts demonstrated that the sea slug commonly colonized the co-occuring algal species Codium fragile, Cladophora rupestris, and Cladophora sericea in the field. Abundance was generally highest on Cladophora hosts compared to C. fragile hosts, and C. rupestris tended to accommodate larger individuals compared to the other hosts (paper I). In the lab E. viridis tended to select algal diets that had a similar morphology (filamentous septate vs. planar siphonaceous) to their original host, which related to increased handling efficiency through previous experience of feeding techniques required for different algal morphologies. This indicated that short-term diet selection was influenced by differences in feeding efficiency, suggesting E. viridis were specialised to feed on particular diets. However, diet selection did not correlate to the long-term fitness value of a diet, indicating that factors other than nutrition are important for host/diet selection in E. viridis. However, positive growth by E. viridis on all algal diets irrespective of their original algal host indicated that slugs were capable of effectively switching to non-host algae (paper II). Furthermore, E. viridis derived functional kleptoplasts from three different genera of algae (Chaetomorpha, Codium, and Cladophora), refuting claims that members of Cladophorales were unsuitable sources of functional kleptoplasts to E. viridis (paper III). However, kleptoplast functionality varied within the genus Cladophora. Finally we provided evidence that E. viridis receives a substantial fitness benefit under satiation by retaining functional kleptoplasts through increased growth efficiency via phototrophy (paper IV). Overall this thesis contributes substantially to understanding the fitness trade-offs E. viridis faces through diet selection. Furthermore, it emphasizes that assessing energy assimilation in polyphagous sacoglossans requires not only an understanding of the fitness contributions of nutritional and morphological traits of different algal diets but also their role as a source of functional kleptoplasts to the slug. However, many conclusions reached in the lab did not concur with field patterns, indicating a need for further study on biotic (e.g. predation) and abiotic (e.g. wave force) pressures on E. viridis populations and assessment of the roles algal hosts play in circumventing these pressures