Biopolitical precarity in the permeable body: the social lives of people, viruses and their medicines

This article is based on multi-sited ethnography that traced a dynamic network of actors (activists, policy-makers, health care systems, pharmaceutical companies) and actants (viruses and medicines) that shaped South African women’s access to, and embodiment of, antiretroviral therapies (ARVs). Using actor network theory and post-humanist performativity as conceptual tools, the article explores how bodies become the meeting place for HIV and ARVs, or non-human actants. The findings centre around two linked sets of narratives that draw the focus out from the body to situate the body in relation to South Africa’s shifting biopolitical landscape. The first set of narratives articulate how people perceive the intra-action of HIV and ARVs in their sustained vitality. The second set of narratives articulate the complex embodiment of these actants as a form biopolitical precarity. These narratives flow into each other and do not represent a totalising view of the effects of HIV and ARVs in the lives of the people with whom I worked. The positive effects of ARVs (as unequivocally essential for sustaining life) were implicit and the precarious vitality of the people in this ethnography was fundamental. However, a related and emergent set of struggles become salient during the study that complicate a view of ARVs as a ‘technofix’. These emergent struggles were biopolitical, and they related first to the intra-action of HIV and ARVs ‘within’ the body; and second, to the ‘outside’ socio-economic context in which people’s bodies were situated

Rosa26-GFP Direct Repeat (RaDR-GFP) Mice Reveal Tissue- and Age-Dependence of Homologous Recombination in Mammals In Vivo

Homologous recombination (HR) is critical for the repair of double strand breaks and broken replication forks. Although HR is mostly error free, inherent or environmental conditions that either suppress or induce HR cause genomic instability. Despite its importance in carcinogenesis, due to limitations in our ability to detect HR in vivo, little is known about HR in mammalian tissues. Here, we describe a mouse model in which a direct repeat HR substrate is targeted to the ubiquitously expressed Rosa26 locus. In the Rosa26 Direct Repeat-GFP (RaDR-GFP) mice, HR between two truncated EGFP expression cassettes can yield a fluorescent signal. In-house image analysis software provides a rapid method for quantifying recombination events within intact tissues, and the frequency of recombinant cells can be evaluated by flow cytometry. A comparison among 11 tissues shows that the frequency of recombinant cells varies by more than two orders of magnitude among tissues, wherein HR in the brain is the lowest. Additionally, de novo recombination events accumulate with age in the colon, showing that this mouse model can be used to study the impact of chronic exposures on genomic stability. Exposure to N-methyl-N-nitrosourea, an alkylating agent similar to the cancer chemotherapeutic temozolomide, shows that the colon, liver and pancreas are susceptible to DNA damage-induced HR. Finally, histological analysis of the underlying cell types reveals that pancreatic acinar cells and liver hepatocytes undergo HR and also that HR can be specifically detected in colonic somatic stem cells. Taken together, the RaDR-GFP mouse model provides new understanding of how tissue and age impact susceptibility to HR, and enables future studies of genetic, environmental and physiological factors that modulate HR in mammals.National Institutes of Health (U.S.) (Program Project Grant P01-CA026731)National Institutes of Health (U.S.) (R33-CA112151)National Institute of Environmental Health Sciences (P30-ES002109)Singapore-MIT Alliance for Research and Technology CenterNational Institutes of Health (U.S.) (P41-EB015871)National Cancer Institute (U.S.) (P30-CA014051

MIGHTEE-HI: the HI Size-Mass relation over the last billion years

We present the observed HI size-mass relation of $204$ galaxies from the MIGHTEE Survey Early Science data. The high sensitivity of MeerKAT allows us to detect galaxies spanning more than 4 orders of magnitude in HI mass, ranging from dwarf galaxies to massive spirals, and including all morphological types. This is the first time the relation has been explored on a blind homogeneous data set which extends over a previously unexplored redshift range of $0 < z < 0.084$, i.e. a period of around one billion years in cosmic time. The sample follows the same tight logarithmic relation derived from previous work, between the diameter ($D_{\rm HI}$) and the mass ($M_{\rm HI}$) of HI discs. We measure a slope of $0.501\pm 0.008$, an intercept of $-3.252^{+0.073}_{-0.074}$, and an observed scatter of $0.057$ dex. For the first time, we quantify the intrinsic scatter of $0.054 \pm 0.003$ dex (${\sim} 10 \%$), which provides a constraint for cosmological simulations of galaxy formation and evolution. We derive the relation as a function of galaxy type and find that their intrinsic scatters and slopes are consistent within the errors. We also calculate the $D_{\rm HI} - M_{\rm HI}$ relation for two redshift bins and do not find any evidence for evolution with redshift. These results suggest that over a period of one billion years in lookback time, galaxy discs have not undergone significant evolution in their gas distribution and mean surface mass density, indicating a lack of dependence on both morphological type and redshift.Comment: 10 pages, 5 figures, accepted for publication in MNRA

Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects

Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications. </p

Food security risk level assessment : a fuzzy logic-based approach

A fuzzy logic (FL)-based food security risk level assessment system is designed and is presented in this article. Three inputs—yield, production, and economic growth—are used to predict the level of risk associated with food supply. A number of previous studies have related food supply with risk assessment for particular types of food, but none of the work was specifically concerned with how the wider food chain might be affected. The system we describe here uses the Mamdani method. The resulting system can assess risk level against three grades: severe, acceptable, and good. The method is tested with UK (United Kingdom) cereal data for the period from 1988 to 2008. The approach is discussed on the basis that it could be used as a starting point in developing tools that may either assess current food security risk or predict periods or regions of impending pressure on food supply

MIGHTEE-HI: The first MeerKAT HI mass function from an untargeted interferometric survey

We present the first measurement of the HI mass function (HIMF) using data from MeerKAT, based on 276 direct detections from the MIGHTEE Survey Early Science data covering a period of approximately a billion years ($0 \leq z \leq 0.084$). This is the first HIMF measured using interferometric data over non-group or cluster field, i.e. a deep blank field. We constrain the parameters of the Schechter function which describes the HIMF with two different methods: $1/\rm V_{\rm max}$ and Modified Maximum Likelihood (MML). We find a low-mass slope $\alpha=-1.29^{+0.37}_{-0.26}$, `knee' mass $\log_{10}(M_{*}/{\rm M_{\odot}}) = 10.07^{+0.24}_{-0.24}$ and normalisation $\log_{10}(\phi_{*}/\rm Mpc^{-3})=-2.34^{+0.32}_{-0.36}$ ($H_0 = 67.4$ kms$^{-1}$ Mpc$^{-1}$) for $1/\rm V_{\rm max}$ and $\alpha=-1.44^{+0.13}_{-0.10}$, `knee' mass $\log_{10}(M_{*}/{\rm M_{\odot}}) = 10.22^{+0.10}_{-0.13}$ and normalisation $\log_{10}(\phi_{*}/\rm Mpc^{-3})=-2.52^{+0.19}_{-0.14}$ for MML. When using $1/\rm V_{\rm max}$ we find both the low-mass slope and `knee' mass to be consistent within $1\sigma$ with previous studies based on single-dish surveys. The cosmological mass density of HI is found to be slightly larger than previously reported: $\Omega_{\rm HI}=5.46^{+0.94}_{-0.99} \times 10^{-4}h^{-1}_{67.4}$ from $1/\rm V_{\rm max}$ and $\Omega_{\rm HI}=6.31^{+0.31}_{-0.31} \times 10^{-4}h^{-1}_{67.4}$ from MML but consistent within the uncertainties. We find no evidence for evolution of the HIMF over the last billion years.Comment: 13 pages, 9 figures, accepted for publication in MNRA

BioTIME: A database of biodiversity time series for the Anthropocene.

MotivationThe BioTIME database contains raw data on species identities and abundances in ecological assemblages through time. These data enable users to calculate temporal trends in biodiversity within and amongst assemblages using a broad range of metrics. BioTIME is being developed as a community-led open-source database of biodiversity time series. Our goal is to accelerate and facilitate quantitative analysis of temporal patterns of biodiversity in the Anthropocene.Main types of variables includedThe database contains 8,777,413 species abundance records, from assemblages consistently sampled for a minimum of 2 years, which need not necessarily be consecutive. In addition, the database contains metadata relating to sampling methodology and contextual information about each record.Spatial location and grainBioTIME is a global database of 547,161 unique sampling locations spanning the marine, freshwater and terrestrial realms. Grain size varies across datasets from 0.0000000158 km2 (158 cm2) to 100 km2 (1,000,000,000,000 cm2).Time period and grainBioTIME records span from 1874 to 2016. The minimal temporal grain across all datasets in BioTIME is a year.Major taxa and level of measurementBioTIME includes data from 44,440 species across the plant and animal kingdoms, ranging from plants, plankton and terrestrial invertebrates to small and large vertebrates.Software format.csv and .SQL

Herpes Simplex Virus Type 2, Genital Ulcers and HIV-1 Disease Progression in Postpartum Women

Co-infection with herpes simplex virus type 2 (HSV-2) has been associated with increased HIV-1 RNA levels and immune activation, two predictors of HIV-1 progression. The impact of HSV-2 on clinical outcomes among HIV-1 infected pregnant women is unclear.HIV-1 infected pregnant women in Nairobi were enrolled antenatally and HSV-2 serology was obtained. HIV-1 RNA and CD4 count were serially measured for 12-24 months postpartum. Survival analysis using endpoints of death, opportunistic infection (OI), and CD4<200 cells µL, and linear mixed models estimating rate of change of HIV-1 RNA and CD4, were used to determine associations between HSV-2 serostatus and HIV-1 progression.Among 296 women, 254 (86%) were HSV-2-seropositive. Only 30 (10%) women had prior or current genital ulcer disease (GUD); median baseline CD4 count was 422 cells µL. Adjusting for baseline CD4, women with GUD were significantly more likely to have incident OIs (adjusted hazard ratio (aHR) 2.79, 95% CI: 1.33-5.85), and there was a trend for association between HSV-2-seropositivity and incident OIs (aHR 3.83, 95% CI: 0.93-15.83). Rate of change in CD4 count and HIV-1 RNA did not differ by HSV-2 status or GUD, despite a trend toward higher baseline HIV-1 RNA in HSV-2-seropositive women (4.73 log10 copies/ml vs. 4.47 log10 copies/ml, P = 0.07).HSV-2 was highly prevalent and pregnant HIV-1 infected women with GUD were significantly more likely to have incident OIs than women without GUD, suggesting that clinically evident HSV-2 is a more important predictor of HIV-1 disease progression than asymptomatic HSV-2