HIV-1 establishes a persistent proviral reservoir by integrating into the genome of infected host cells. Current antiretroviral treatments do not target this persistent population of proviruses which include latently infected cells that upon treatment interruption can be reactivated to contribute to HIV-1 rebound. Deep sequencing of persistent HIV proviruses has revealed that greater than 90% of integrated HIV genomes are defective and unable to produce infectious virions. We hypothesized that intragenic elements in the HIV genome support transcription of aberrant HIV-1 RNAs from defective proviruses that lack long terminal repeats (LTRs). Using an intact provirus detection assay, we observed that resting CD4+ T cells and monocyte-derived macrophages (MDMs) are biased towards generating defective HIV-1 proviruses. Multiplex reverse transcription droplet digital PCR identified env and nef transcripts which lacked 5’ untranslated regions (UTR) in acutely infected CD4+ T cells and MDMs indicating transcripts are generated that do not utilize the promoter within the LTR. 5’UTR-deficient env transcripts were also identified in a cohort of people living with HIV (PLWH) on ART, suggesting that these aberrant RNAs are produced in vivo. Using 5’ rapid amplification of cDNA ends (RACE), we mapped the start site of these transcripts within the Env gene. This region bound several cellular transcription factors and functioned as a transcriptional regulatory element that could support transcription and translation of downstream HIV-1 RNAs. These studies provide mechanistic insights into how defective HIV-1 proviruses are persistently expressed to potentially drive inflammation in PLWH.

Climate change models often assume similar responses to temperatures across the range of a species, but local adaptation or phenotypic plasticity can lead plants and animals to respond differently to temperature in different parts of their range. To date, there have been few tests of this assumption at the scale of continents, so it is unclear if this is a large‐scale problem. Here, we examined the assumption that insect taxa show similar responses to temperature at 96 sites in grassy habitats across North America. We sampled insects with Malaise traps during 2019–2021 (N = 1041 samples) and examined the biomass of insects in relation to temperature and time of season. Our samples mostly contained Diptera (33%), Lepidoptera (19%), Hymenoptera (18%), and Coleoptera (10%). We found strong regional differences in the phenology of insects and their response to temperature, even within the same taxonomic group, habitat type, and time of season. For example, the biomass of nematoceran flies increased across the season in the central part of the continent, but it only showed a small increase in the Northeast and a seasonal decline in the Southeast and West. At a smaller scale, insect biomass at different traps operating on the same days was correlated up to ~75 km apart. Large‐scale geographic and phenological variation in insect biomass and abundance has not been studied well, and it is a major source of controversy in previous analyses of insect declines that have aggregated studies from different locations and time periods. Our study illustrates that large‐scale predictions about changes in insect populations, and their causes, will need to incorporate regional and taxonomic differences in the response to temperature.

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People living with HIV suffer from a variety of co-morbidities including neurological deficits and cardiovascular disease even while on antiretroviral therapy (ART). Chronic inflammation has been implicated in these co-morbidities and has long been described in HIV patients. Characterization of the HIV DNA (provirus) reservoir in CD4 T cells from HIV patients on ART has revealed that more than 90% are defective and unable to complete the viral life cycle. Macrophages are susceptible to HIV infection and are positioned at the nexus of pathogen detection, inflammation, and priming of adaptive immune responses. We hypothesized that HIV-infected macrophages harbor defective HIV proviruses which remain transcriptionally competent and affect adaptive immune responses. To test this, we examined the status of HIV proviruses in primary human monocyte-derive macrophages (MDMs) and their expression of HIV transcripts. MDMs were infected with HIV in vitro and using an intact provirus detection assay we observed that roughly half of HIV proviruses were defective. Reverse transcription droplet-digital PCR (RT-ddPCR) detected a distribution of HIV transcripts, many of which lack the full 5′ LTR sequence consistent with transcription starting from an intragenic site. When CD8 T cells were co-cultured with autologous HIV-infected MDMs, they increased their expression of CD107a, a degranulation marker, indicating that infected macrophages could trigger CD8+ activation. Together, these results support that alternative transcriptional mechanisms, which persist in the absence of a fully functional LTR, are active during HIV infection in macrophages, contributing to macrophage dysfunction and persistent HIV-associated diseases.