Tertiary Mutations Stabilize CD8+ T Lymphocyte Escape-Associated Compensatory Mutations following Transmission of Simian Immunodeficiency Virus

Compensatory mutations offset fitness defects resulting from CD8⁺ T lymphocyte (CD8_TL)-mediated escape, but their impact on viral evolution following transmission to naive hosts remains unclear. Here, we investigated the reversion kinetics of Gag_181–189CM9 CD8_TL escape-associated compensatory mutations in simian immunodeficiency virus (SIV)-infected macaques. Preexisting compensatory mutations did not result in acute-phase escape of the SIVmac239 CD8TL epitope Gag181-189CM9 and instead required a tertiary mutation for stabilization in the absence of Gag_181–189CM9 escape mutations. Therefore, transmitted compensatory mutations do not necessarily predict rapid CD8_TL escape.     

Small heat shock proteins are necessary for heart migration and laterality determination in zebrafish

Small heat shock proteins (sHsps) regulate cellular functions not only under stress, but also during normal development, when they are expressed in organ-specific patterns. Here we demonstrate that two small heat shock proteins expressed in embryonic zebrafish heart, hspb7 and hspb12, have roles in the development of left–right asymmetry. In zebrafish, laterality is determined by the motility of cilia in Kupffer's vesicle (KV), where hspb7 is expressed; knockdown of hspb7 causes laterality defects by disrupting the motility of these cilia. In embryos with reduced hspb7, the axonemes of KV cilia have a 9+0 structure, while control embyros have a predominately 9+2 structure. Reduction of either hspb7 or hspb12 alters the expression pattern of genes that propagate the signals that establish left–right asymmetry: the nodal-related gene southpaw (spaw) in the lateral plate mesoderm, and its downstream targets pitx2, lefty1 and lefty2. Partial depletion of hspb7 causes concordant heart, brain and visceral laterality defects, indicating that loss of KV cilia motility leads to coordinated but randomized laterality. Reducing hspb12 leads to similar alterations in the expression of downstream laterality genes, but at a lower penetrance. Simultaneous reduction of hspb7 and hspb12 randomizes heart, brain and visceral laterality, suggesting that these two genes have partially redundant functions in the establishment of left–right asymmetry. In addition, both hspb7 and hspb12 are expressed in the precardiac mesoderm and in the yolk syncytial layer, which supports the migration and fusion of mesodermal cardiac precursors. In embryos in which the reduction of hspb7 or hspb12 was limited to the yolk, migration defects predominated, suggesting that the yolk expression of these genes rather than heart expression is responsible for the migration defects.     

Preventing horticultural introductions of invasive plants: potential efficacy of voluntary initiatives

Although prevention is the most cost-effective way to avoid the enormous expenses associated with plant invasions, invasive plants continue to be imported as trade commodities for horticultural use. With very little government regulation of horticultural imports of invasive plants, efforts have turned toward fostering voluntary initiatives to encourage self-regulation by the horticulture trade. Our study takes the first step toward evaluating the potential success of these voluntary initiatives. We conducted a survey of nursery professionals to gauge their perceptions of invasive species, the role of the horticulture trade in invasive plant introductions, and their participation—potential and actual—in preventive measures outlined in the St Louis Voluntary Codes of Conduct for nursery professionals. We found nursery professionals to be highly aware of invasive plants and to accept responsibility as a trade for horticultural introductions. Although only 7% of respondents had heard of the St Louis Voluntary Codes of Conduct, the majority (57%) reported having participated in at least two of seven preventive measures, and most (78%) reported willingness to engage in the majority of preventive measures. We found that several factors significantly predict increased participation in preventive measures, particularly awareness of invasive plants and involvement in trade associations. We also identified incentives and obstacles to participating in preventive behaviors, including “concern for the environment” and “lack of information,” respectively. Our results suggest that participation in voluntary initiatives will improve through increased outreach, and we provide specific recommendations for improving participation in voluntary programs in the horticulture trade.     

Gag-specific CD8+ T lymphocytes recognize infected cells before AIDS-virus integration and viral protein expression

CD8(+) T cells are a key focus of vaccine development efforts for HIV. However, there is no clear consensus as to which of the nine HIV proteins should be used for vaccination. The early proteins Tat, Rev, and Nef may be better CD8(+) T cell targets than the late-expressed structural proteins Gag, Pol, and Env. In this study, we show that Gag-specific CD8(+) T cells recognize infected CD4(+) T lymphocytes as early as 2 h postinfection, before proviral DNA integration, viral protein synthesis, and Nef-mediated MHC class I down-regulation. Additionally, the number of Gag epitopes recognized by CD8(+) T cells was significantly associated with lower viremia (p = 0.0017) in SIV-infected rhesus macaques. These results suggest that HIV vaccines should focus CD8(+) T cell responses on Gag.     

VISA - Vector Integration Site Analysis server: a web-based server to rapidly identify retroviral integration sites from next-generation sequencing

Background

Analyzing the integration profile of retroviral vectors is a vital step in determining their potential genotoxic effects and developing safer vectors for therapeutic use. Identifying retroviral vector integration sites is also important for retroviral mutagenesis screens.

Results

We developed VISA, a vector integration site analysis server, to analyze next-generation sequencing data for retroviral vector integration sites. Sequence reads that contain a provirus are mapped to the human genome, sequence reads that cannot be localized to a unique location in the genome are filtered out, and then unique retroviral vector integration sites are determined based on the alignment scores of the remaining sequence reads.

Conclusions

VISA offers a simple web interface to upload sequence files and results are returned in a concise tabular format to allow rapid analysis of retroviral vector integration sites.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-015-0653-6) contains supplementary material, which is available to authorized users.     

The Social Life of Death on Delhi's Streets: Unclaimed Souls,Pollutive Bodies,Dead Kin and the Kinless Dead

ABSTRACT

How does the status of ‘street children’ in life inflect the narrative representation of their deaths? Street-dwelling children's interactions with death in North India reveal much about how their identities are produced in public domains. In this paper, I examine several instances of ‘homeless child’ death to illuminate the place of such subjects in society and urban space, and to interrogate the degree to which they can be rendered ‘recognizable’ or ‘grievable’, in Butler's (2010) terminology. In particular, I explore the presence or absence of kin in the ways that child death is narrated. I also explore the related question of how living ‘vagabond (aawara) children’ situate their status in narratives of death and loss. I conclude with discussions of how children negotiate their orientations towards death through ghost narratives, and of the space-, economy- and age-bound assignment of pollutive tasks once reserved for low castes to street-dwelling children.     

Resource selection and its implications for wide-ranging mammals of the brazilian cerrado

Conserving animals beyond protected areas is critical because even the largest reserves may be too small to maintain viable populations for many wide-ranging species. Identification of landscape features that will promote persistence of a diverse array of species is a high priority, particularly, for protected areas that reside in regions of otherwise extensive habitat loss. This is the case for Emas National Park, a small but important protected area located in the Brazilian Cerrado, the world's most biologically diverse savanna. Emas Park is a large-mammal global conservation priority area but is too small to protect wide-ranging mammals for the long-term and conserving these populations will depend on the landscape surrounding the park. We employed novel, noninvasive methods to determine the relative importance of resources found within the park, as well as identify landscape features that promote persistence of wide-ranging mammals outside reserve borders. We used scat detection dogs to survey for five large mammals of conservation concern: giant armadillo (Priodontes maximus), giant anteater (Myrmecophaga tridactyla), maned wolf (Chrysocyon brachyurus), jaguar (Panthera onca), and puma (Puma concolor). We estimated resource selection probability functions for each species from 1,572 scat locations and 434 giant armadillo burrow locations. Results indicate that giant armadillos and jaguars are highly selective of natural habitats, which makes both species sensitive to landscape change from agricultural development. Due to the high amount of such development outside of the Emas Park boundary, the park provides rare resource conditions that are particularly important for these two species. We also reveal that both woodland and forest vegetation remnants enable use of the agricultural landscape as a whole for maned wolves, pumas, and giant anteaters. We identify those features and their landscape compositions that should be prioritized for conservation, arguing that a multi-faceted approach is required to protect these species.     

Impact of sex and chronic resistance training on human patellar tendon dry mass, collagen content, and collagen cross-linking

Collagen content and cross-linking are believed to be major determinants of tendon structural integrity and function. Sex and chronic resistance training have been shown to alter tendon function and may also alter the key structural features of tendon. Patellar tendon biopsies were taken from untrained men [n = 8, 1 repetition maximum (RM) = 53 +/- 3 kg], untrained women (n = 8, 1 RM = 29 +/- 2 kg), and resistance-trained (10 +/- 1 yr of training) men (n = 8, 1 RM = 71 +/- 6 kg). Biopsies were analyzed for dry mass, collagen content, and collagen cross-linking (hydroxylysylpyridinoline). We hypothesized that these elements of tendon structure would be lower in women than men, whereas chronic resistance training would increase these parameters in men. Tendon dry mass was significantly lower in women than men (343 +/- 5 vs. 376 +/- 8 microg dry mass/mg tendon wet wt, P < 0.01) and was not influenced by chronic resistance training (P > 0.05). The lower tendon dry mass in women tended to reduce (P = 0.08) collagen content per tendon wet weight. Collagen content of the tendon dry mass was not influenced by sex or resistance training (P > 0.05). Similarly, cross-linking of collagen was unaltered (P > 0.05) by sex or training. Although sex alters the water content of patellar tendon tissue, any changes in tendon function with sex or chronic resistance training in men do not appear to be explained by alterations in collagen content or cross-linking of collagen within the dry mass component of the tendon.