Integration Sites in the Persistence of Latent HIV-1

Human immunodeficiency virus (HIV-1), the pathogen that causes acquired immune deficiency syndrome (AIDS), remains one of the world’s most pressing health issues. Since the beginning of the HIV/AIDS epidemic, over 32M people have succumbed to AIDS-related illnesses. Despite remarkable advances in HIV-1 biology, neither a vaccine or cure have been achieved. While antiretroviral therapy (ART) has significantly improved disease outcomes for people with HIV-1 and reduced transmission, treatment is often accompanied by long-term side effects or stigma, or impeded by limited access to health care. Furthermore, because viral load quickly rebounds upon treatment interruption, ART is required to be a life-long medication. The major barrier to HIV cure is the persistence of long-lived latently infected CD4+ T cells. Collectively known as the latent reservoir, these cells carry integrated HIV-1 proviruses that are transcriptionally quiescent and are thus able to evade host immunity and virus-induced cell death. Cellular and molecular characterization of the latent reservoir is challenging because latently infected cells are exceedingly rare and express no known surface marker. Moreover, the infected cell pool is dominated by cells containing defective proviruses which cannot contribute to rebound viremia. The work herein elucidates the contribution of proviral integration site to HIV-1 latency and the maintenance of the replication-competent, or intact, reservoir. Using an innovative single-cell sequencing technique that provides paired proviral sequence and integration site information, as well as enables selective analysis of replication-competent HIV-1, I interrogate the integration landscape of HIV infected individuals whose reservoirs are dominated by a small number of large expanded clones. By performing viral outgrowth assays, I also show that replication-competent proviruses harbored in the expanded clones readily produce infectious virion upon stimulation. I report an integrative analysis of the clonal dynamics, inducibility, and genomic position of intact proviruses in ARTsuppressed individuals, and demonstrate that proviruses in expanded clones across patients are significant more likely to be mapped to Krüppel-associated box (KRAB) domain-containing zinc finger (ZNF) genes on chromosome 19. Transcriptional and epigenetic meta-analysis of primary CD4+ T cells reveal that these specific chromosomal locations harboring integrated provirus are associated with genes downregulated upon cellular activation. Taken together, the data indicate that selected sites in the genome, including ZNF genes, can be especially permissive for maintaining HIV-1 latency during memory CD4+ T cell clonal expansion. These findings demonstrate that gene activity at the integration site impacts the survival and persistence of intact, expanded HIV proviruses in infected cells, and provide evidence that the quality, not only the quantity, of the latent reservoir must a key consideration in HIV-1 cure strategies

Quantum phase transition in ultrahigh mobility SiGe/Si/SiGe two-dimensional electron system

The metal-insulator transition (MIT) is an exceptional test bed for studying strong electron correlations in two dimensions in the presence of disorder. In the present study, it is found that in contrast to previous experiments on lower-mobility samples, in ultra-high mobility SiGe/Si/SiGe quantum wells the critical electron density, $n_{\text{c}}$, of the MIT becomes smaller than the density, $n_{\text{m}}$, where the effective mass at the Fermi level tends to diverge. Near the topological phase transition expected at $n_{\text{m}}$, the metallic temperature dependence of the resistance should be strengthened, which is consistent with the experimental observation of more than an order of magnitude resistance drop with decreasing temperature below $\sim1$ K.Comment: Misprints corrected. As publishe

Peptide nanofiber hydrogel adjuvanted live virus vaccine enhances cross-protective immunity to porcine reproductive and respiratory syndrome virus

Porcine reproductive and respiratory syndrome virus (PRRSV) is prevalent in swine farms worldwide and is a major source of economic loss and animal suffering. Rapid genetic variation of PRRSV makes it difficult for current vaccines to confer protection against newly emerging strains. We recently demonstrated that a novel peptide nanofiber hydrogel (H9e) could act as a potent adjuvant for killed H1N1 vaccines. Therefore, the objective of this study was to evaluate H9e as an adjuvant for PRRSV modified live virus (MLV) vaccines. Pigs were vaccinated with Ingelvac PRRSV MLV with or without H9e adjuvant before being challenged with the VR-2332 (parental vaccine strain) or MN184A (genetically diverse strain) PRRSV. Pigs vaccinated with MLV+H9e had higher levels of circulating vaccine virus. More importantly, pigs vaccinated with MLV+H9e had improved protection against challenge by both PRRSV strains, as demonstrated by reduced challenge-induced viremia compared with pigs vaccinated with MLV alone. Pigs vaccinated with MLV+H9e had lower frequency of T-regulatory cells and IL-10 production but higher frequency of Th/memory cells and IFN-γ secretion than that in pigs vaccinated with MLV alone. Taken together, our studies suggest that the peptide nanofiber hydrogel H9e, when combined with the PRRSV MLV vaccine, can enhance vaccine efficacy against two different PRRSV strains by modulating both host humoral and cellular immune responses

Visualization of lithium-ion transport and phase evolution within and between manganese oxide nanorods.

Multiple lithium-ion transport pathways and local phase changes upon lithiation in silver hollandite are revealed via in situ microscopy including electron diffraction, imaging and spectroscopy, coupled with density functional theory and phase field calculations. We report unexpected inter-nanorod lithium-ion transport, where the reaction fronts and kinetics are maintained within the neighbouring nanorod. Notably, this is the first time-resolved visualization of lithium-ion transport within and between individual nanorods, where the impact of oxygen deficiencies is delineated. Initially, fast lithium-ion transport is observed along the long axis with small net volume change, resulting in two lithiated silver hollandite phases distinguishable by orthorhombic distortion. Subsequently, a slower reaction front is observed, with formation of polyphase lithiated silver hollandite and face-centred-cubic silver metal with substantial volume expansion. These results indicate lithium-ion transport is not confined within a single nanorod and may provide a paradigm shift for one-dimensional tunnelled materials, particularly towards achieving high-rate capability

Novel components of the Toxoplasma inner membrane complex revealed by BioID.

UNLABELLED:The inner membrane complex (IMC) of Toxoplasma gondii is a peripheral membrane system that is composed of flattened alveolar sacs that underlie the plasma membrane, coupled to a supporting cytoskeletal network. The IMC plays important roles in parasite replication, motility, and host cell invasion. Despite these central roles in the biology of the parasite, the proteins that constitute the IMC are largely unknown. In this study, we have adapted a technique named proximity-dependent biotin identification (BioID) for use in T. gondii to identify novel components of the IMC. Using IMC proteins in both the alveoli and the cytoskeletal network as bait, we have uncovered a total of 19 new IMC proteins in both of these suborganellar compartments, two of which we functionally evaluate by gene knockout. Importantly, labeling of IMC proteins using this approach has revealed a group of proteins that localize to the sutures of the alveolar sacs that have been seen in their entirety in Toxoplasma species only by freeze fracture electron microscopy. Collectively, our study greatly expands the repertoire of known proteins in the IMC and experimentally validates BioID as a strategy for discovering novel constituents of specific cellular compartments of T. gondii. IMPORTANCE:The identification of binding partners is critical for determining protein function within cellular compartments. However, discovery of protein-protein interactions within membrane or cytoskeletal compartments is challenging, particularly for transient or unstable interactions that are often disrupted by experimental manipulation of these compartments. To circumvent these problems, we adapted an in vivo biotinylation technique called BioID for Toxoplasma species to identify binding partners and proximal proteins within native cellular environments. We used BioID to identify 19 novel proteins in the parasite IMC, an organelle consisting of fused membrane sacs and an underlying cytoskeleton, whose protein composition is largely unknown. We also demonstrate the power of BioID for targeted discovery of proteins within specific compartments, such as the IMC cytoskeleton. In addition, we uncovered a new group of proteins localizing to the alveolar sutures of the IMC. BioID promises to reveal new insights on protein constituents and interactions within cellular compartments of Toxoplasma

How Do Perceptions of Risk Communicator Attributes Affect Emergency Response? An Examination of a Water Contamination Emergency in Boston, USA

A water main break that contaminated the Boston area\u27s water distribution system prompted a four-day “boil water” order. To understand risk communication during this incident, 600 randomly sampled residents were mailed questionnaires, yielding 110 valid responses. This article describes how perceptions of different social stakeholders influenced whether respondents complied with the Protective Action Recommendation—PAR (i.e., drank boiled water), took alternative protective actions (i.e., drank bottled water or/and self-chlorinated water), or ignored the threat (i.e., continued to drink untreated tap water). Respondents perceived technical authorities (i.e., water utility, public health, and emergency management) to be higher on three social influence attributes (hazard expertize, trustworthiness, and protection responsibility) than public (i.e., news media, elected officials) and private (i.e., self/family, peers, and personal physicians) intermediate sources. Furthermore, respondents were most likely to comply with the PAR if they perceived authorities and public intermediates to be high on all three attributes and if they had larger households and lower income. Contrarily, they were more likely to take alternative actions if they were younger and had higher levels of income, risk perception, and emergency preparedness. These results underscore the need for technical authorities to develop credibility with their potential audiences before a crisis occurs

Compartmentalization of neutrophils in the kidney and lung following acute ischemic kidney injury

During renal ischemia-reperfusion, local and distant tissue injury is caused by an influx of neutrophils into the affected tissues. Here we measured the kinetics of margination and transmigration of neutrophils in vivo in the kidney and lungs following renal ischemia-reperfusion. After bilateral renal injury, kidney neutrophil content increased threefold at 24 h. The neutrophils were found primarily in the interstitium and to a lesser degree marginated to the vascular endothelium. These interstitial neutrophils had significantly lower levels of intracellular IFN-γ, IL-4, IL-6, and IL-10 a tendency for decreased amounts of IL-4 and TNF-α compared to the marginated neutrophils. Localization of the neutrophils to the kidney interstitium was confirmed by high resolution microscopy and these sites of transmigration were directly associated with areas of increased vascular permeability. Activation of the adenosine 2A receptor significantly decreased both kidney neutrophil transmigration by about half and vascular permeability by about a third. After unilateral renal ischemia-reperfusion, the unclipped kidney and lungs did not accumulate interstitial neutrophils or have increased vascular permeability despite a marked increase of neutrophil margination in the lungs. Our findings suggest there is a sequential recruitment and transmigration of neutrophils from the vasculature into the kidney interstitium at the site of tissue injury following renal ischemia-reperfusion

Inhibition of αvβ5 Integrin Attenuates Vascular Permeability and Protects against Renal Ischemia-Reperfusion Injury

Ischemia-reperfusion injury (IRI) is a leading cause of AKI. This common clinical complication lacks effective therapies and can lead to the development of CKD. The αvβ5 integrin may have an important role in acute injury, including septic shock and acute lung injury. To examine its function in AKI, we utilized a specific function-blocking antibody to inhibit αvβ5 in a rat model of renal IRI. Pretreatment with this anti-αvβ5 antibody significantly reduced serum creatinine levels, diminished renal damage detected by histopathologic evaluation, and decreased levels of injury biomarkers. Notably, therapeutic treatment with the αvβ5 antibody 8 hours after IRI also provided protection from injury. Global gene expression profiling of post-ischemic kidneys showed that αvβ5 inhibition affected established injury markers and induced pathway alterations previously shown to be protective. Intravital imaging of post-ischemic kidneys revealed reduced vascular leak with αvβ5 antibody treatment. Immunostaining for αvβ5 in the kidney detected evident expression in perivascular cells, with negligible expression in the endothelium. Studies in a three-dimensional microfluidics system identified a pericyte-dependent role for αvβ5 in modulating vascular leak. Additional studies showed αvβ5 functions in the adhesion and migration of kidney pericytes in vitro Initial studies monitoring renal blood flow after IRI did not find significant effects with αvβ5 inhibition; however, future studies should explore the contribution of vasomotor effects. These studies identify a role for αvβ5 in modulating injury-induced renal vascular leak, possibly through effects on pericyte adhesion and migration, and reveal αvβ5 inhibition as a promising therapeutic strategy for AKI