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Additional File 1.

Additional file 1: Supplementary Figure S1. Sequential gating approach for the measurement of CCR2 expression by CD14+ monocytes. The sequential gating approached used was as follows: First, the viable (7-AAD negative; region ‘Viable”) cells were identified using a 7-AAD vs SS Log density plot. A “Viable” region was created around the 7-AAD negative cells. Gated on the “Viable”cells, a SSLog vs FS plot was used to capture intact cells in the “E” region. CD14+ monocytes were identified (“CD14+” region) using a CD14 vs SS Log density plot that were gated on viable, intact cells (“E” region). CD14+ monocytes that express CCR2 were quantified using a CD192 (CCR2) vs SS Log plot. The proportion of CD14+/CCR2+ cells were captured in the “CD14+ CCR2+” region. The gating strategy followed to quantify CCR2 expression by CD16+ neutrophils was similar to what was described for CD14+ monocytes, but instead of identifying CD14+ monocytes, CD16+ neutrophils were identified (“CD16+” region) using a CD16 vs SS Log density plot that were gated on viable, intact cells (“E” region). CD16+ neutrophils that express CCR2 were quantified using a CD192 (CCR2) vs SS Log plot. The proportion of CD14+/CCR2+ cells was captured in the “CD16+ CCR2+” region.

With the advent of antiretroviral therapy (ART), HIV-infected individuals are now living longer and healthier lives. However, ART does not completely restore health and treated individuals are experiencing increased rates of noncommunicable diseases such as dyslipidemia, insulin resistance, type 2 diabetes, cardiovascular disease, and nonalcoholic fatty liver disease. While it is well known that persistent immune activation and inflammation contribute to the development of these comorbid diseases, the mechanisms underlying this chronic activation remain incompletely understood. In this review, we will discuss emerging evidence that suggests that alterations in cellular metabolism may play a central role in driving this immune dysfunction in HIV patients on ART.

Macrophages are terminally differentiated cells of the mononuclear phagocyte system that also encompasses dendritic cells, circulating blood monocytes, and committed myeloid progenitor cells in the bone marrow. Both macrophages and their monocytic precursors can change their functional state in response to microenvironmental cues exhibiting a marked heterogeneity. However, there are still uncertainties regarding distinct expression patterns of surface markers that clearly define macrophage subsets, particularly in the case of human macrophages. In addition to their tissue distribution, macrophages can be functionally polarized into M1 (proinflammatory) and M2 (alternatively activated) as well as regulatory cells in response to both exogenous infections and solid tumors as well as by systems biology approaches.

Three decades into the HIV-1 pandemic, it is increasingly apparent that generalized immune activation is a key pathogenic determinant of AIDS. Studies of immune activation, in the setting of HIV-1, have focused primarily on the adaptive immune response despite the role of monocytes and macrophages as key regulators of inflammatory responses. In this thesis, I focused on the relationships between mononuclear phagocyte activation and HIV-1 pathogenesis, both in vitro using model systems and in vivo in African patients with AIDS, Using a monocyte-derived macrophage (MDM) model of Ml and M2a polarization, I found that activation transiently altered the capacity of macrophages to support productive HIV-1 infection and that the level of viral inhibition was dependant on the polarization phenotype. Ml and M2a polarized MDM also differed in the capacity to transmit virus to CD4+ T cells with M2a cells efficiently transmitting HIV-1 via a DC-SIGN dependant mechanism. In a cohort of treatment-naive AIDS patients, in vivo activation of circulating monocytes and intestinal macrophages was strongly associated with HIV-1 pathogenesis. Monocyte activation in these patients was differentially regulated by HIV-1 and circulating LPS (marker of microbial translocation) and was associated with two clearly distinct activation profiles. At the tissue level, HIV-1 was associated with alterations in intestinal macrophage distribution, frequency and phenotype. In the colon, macrophage activation was negatively correlated with viral load and positively correlated with microbial translocation suggesting that, although inflammatory macrophages in the intestine may contribute to the control viral replication, they may also enhance microbial translocation and systemic activation.

Additional file 4: Supplementary Figure S4. Cooccurrence of maternal HIV and food insecurity may increase risk of stunting at birth. Amongst infants whose mothers report worrying about food runout, risk of stunting at birth is greater for HEU compared to HUU infants (e; RR=4.90 [0.76, 31.5], ARD=0.56 [0.17, 0.94], p=0.0498). The red line represents the proportion of infants who had stunting at birth or 12 weeks PP. Mosaic plots are proportion (%) of HUU or HEU infants who have stunting (

Additional file 3: Supplementary Figure S3. Maternal intake of estimated average requirements for macronutrients, vitamins and minerals for mothers who report on household food security circumstances. Maternal reports of food insecurity did not associate with intake levels of macronutrients or minerals. Maternal reports of experiencing food runout or inability to afford balanced meals associated with lower intake of vitamin B12 (p=0.01; p=0.04). Many women, irrespective of food security reports, are at risk of inadequate macronutrient, vitamin and mineral intakes. Percent intake of EARs for 36 nutrients were calculated for lactating women 14-18, 19-30 or 31-50 years of age [37]. Calculations for EAR for total protein considered maternal weight at time of dietary recall. Data are % intake of EAR reported in maternal dietary recall for macronutrients, *p

Additional file 6: Supplementary Table S1. Flow cytometry reagent list (including lasers and detectors used). Supplementary Table S2. Flow cytometry compensation matrix. Supplementary Table S3. Maternal nutrient intakes from one 24-hour dietary recall for mothers with and without HIV who attended follow up. Supplementary Table S4. Maternal nutrient intake from one 24-hour dietary recall for mothers who report experiencing food insecurity compared to those who do not experience food insecurity.

Additional file 5: Supplementary Figure S5. Food insecurity may associate with low attainment of GMCD milestones for HUU and HEU infants. Infants whose mothers reported household food insecurity did not attain 1-3 month GMCD milestones (A, C, E) for receptive language, large movement, relating and response behaviour or play activities, or 3-5 month GMCD milestones (B, D, F) for fine movement or relating and response behaviour in the same proportion as the international standardization sample. Maternal reports of food insecurity did not associate with risk of not attaining all 1-3 month or 3-5 month GMCD milestones (A-F, [p>0.05], Fisher’s exact 2-Tail). Data are proportion (%) of infants who attained all age-appropriate GMCD milestones. The horizontal dotted line represents the GMCD standardised international sample proportion (85%) of infants who attained all milestones in that age category, when they were in that age range. The numbers underneath the bars represent the number of infants attaining all milestones for each milestone. GMCD = Guide for monitoring child development; HUU = HIV-unexposed, uninfected infant; HEU = HIVexposed, uninfected infant.

Additional file 6: Supplementary Table S1. Flow cytometry reagent list (including lasers and detectors used). Supplementary Table S2. Flow cytometry compensation matrix. Supplementary Table S3. Maternal nutrient intakes from one 24-hour dietary recall for mothers with and without HIV who attended follow up. Supplementary Table S4. Maternal nutrient intake from one 24-hour dietary recall for mothers who report experiencing food insecurity compared to those who do not experience food insecurity.

Additional file 4: Supplementary Figure S4. Cooccurrence of maternal HIV and food insecurity may increase risk of stunting at birth. Amongst infants whose mothers report worrying about food runout, risk of stunting at birth is greater for HEU compared to HUU infants (e; RR=4.90 [0.76, 31.5], ARD=0.56 [0.17, 0.94], p=0.0498). The red line represents the proportion of infants who had stunting at birth or 12 weeks PP. Mosaic plots are proportion (%) of HUU or HEU infants who have stunting (

Additional file 3: Supplementary Figure S3. Maternal intake of estimated average requirements for macronutrients, vitamins and minerals for mothers who report on household food security circumstances. Maternal reports of food insecurity did not associate with intake levels of macronutrients or minerals. Maternal reports of experiencing food runout or inability to afford balanced meals associated with lower intake of vitamin B12 (p=0.01; p=0.04). Many women, irrespective of food security reports, are at risk of inadequate macronutrient, vitamin and mineral intakes. Percent intake of EARs for 36 nutrients were calculated for lactating women 14-18, 19-30 or 31-50 years of age [37]. Calculations for EAR for total protein considered maternal weight at time of dietary recall. Data are % intake of EAR reported in maternal dietary recall for macronutrients, *p

Additional file 5: Supplementary Figure S5. Food insecurity may associate with low attainment of GMCD milestones for HUU and HEU infants. Infants whose mothers reported household food insecurity did not attain 1-3 month GMCD milestones (A, C, E) for receptive language, large movement, relating and response behaviour or play activities, or 3-5 month GMCD milestones (B, D, F) for fine movement or relating and response behaviour in the same proportion as the international standardization sample. Maternal reports of food insecurity did not associate with risk of not attaining all 1-3 month or 3-5 month GMCD milestones (A-F, [p>0.05], Fisher’s exact 2-Tail). Data are proportion (%) of infants who attained all age-appropriate GMCD milestones. The horizontal dotted line represents the GMCD standardised international sample proportion (85%) of infants who attained all milestones in that age category, when they were in that age range. The numbers underneath the bars represent the number of infants attaining all milestones for each milestone. GMCD = Guide for monitoring child development; HUU = HIV-unexposed, uninfected infant; HEU = HIVexposed, uninfected infant.

Pseudomonas aeruginosa is a Gram-negative environmental and human opportunistic pathogen highly adapted to many different environmental conditions. It can cause a wide range of serious infections, including wounds, lungs, the urinary tract, and systemic infections. The high versatility and pathogenicity of this bacterium is attributed to its genomic complexity, the expression of several virulence factors, and its intrinsic resistance to various antimicrobials. However, to thrive and establish infection, P. aeruginosa must overcome several barriers. One of these barriers is the presence of oxidizing agents (e.g., hydrogen peroxide, superoxide, and hypochlorous acid) produced by the host immune system or that are commonly used as disinfectants in a variety of different environments including hospitals. These agents damage several cellular molecules and can cause cell death. Therefore, bacteria adapt to these harsh conditions by altering gene expression and eliciting several stress responses to survive under oxidative stress. Here, we used PubMed to evaluate the current knowledge on the oxidative stress responses adopted by P. aeruginosa. We will describe the genes that are often differently expressed under oxidative stress conditions, the pathways and proteins employed to sense and respond to oxidative stress, and how these changes in gene expression influence pathogenicity and the virulence of P. aeruginosa. Understanding these responses and changes in gene expression is critical to controlling bacterial pathogenicity and developing new therapeutic agents.

Urokinase-type plasminogen activator (uPA), an inducer of macrophage adhesion, inhibits HIV-1 expression in PMA-stimulated, chronically infected U1 cells. We investigated whether uPA-dependent cell adhesion played a role in uPA-dependent inhibition of HIV-1 replication in these cells. Monocyte-derived macrophages (MDM) were generated from monocytes of HIV-infected individuals or from cells of seronegative donors infected acutely in vitro. U1 cells were stimulated in the presence or absence of uPA in standard tissue culture (TC) plates, allowing firm cell adhesion or ultra-low adhesion (ULA) plates. Moreover, U1 cells were also maintained in the presence or absence of vitronectin (VN)-containing sera or serum from VN-/- mice. Virus production was evaluated by RT activity in culture supernatants, whereas cell adhesion was by crystal violet staining and optical microscopy. uPA inhibited HIV replication in MDM and PMA-stimulated U1 cells in TC plates but not in ULA plates. uPA failed to inhibit HIV expression in U1 cells stimulated with IL-6, which induces virus expression but not cell adhesion in TC plates. VN, known to bind to the uPA/uPA receptor complex, was crucial for these adhesion-dependent, inhibitory effects of uPA on HIV expression, in that they were not observed in TC plates in the presence of VN-/- mouse serum. HIV production in control cell cultures was increased significantly in ULA versus TC plates, indicating that macrophage cell adhesion per se curtails HIV replication. In conclusion, uPA inhibits HIV-1 replication in macrophages via up-regulation of cell adhesion to the substrate mediated by VN. Urokinase-type plasminogen activator (uPA), an inducer of macrophage adhesion, inhibits HIV-1 expression in PMA-stimulated, chronically infected U1 cells. We investigated whether uPA-dependent cell adhesion played a role in uPA-dependent inhibition of HIV-1 replication in these cells. Monocyte-derived macrophages (MDM) were generated from monocytes of HIV-infected individuals or from cells of seronegative donors infected acutely in vitro. U1 cells were stimulated in the presence or absence of uPA in standard tissue culture (TC) plates, allowing firm cell adhesion or ultra-low adhesion (ULA) plates. Moreover, U1 cells were also maintained in the presence or absence of vitronectin (VN)-containing sera or serum from VN-/- mice. Virus production was evaluated by RT activity in culture supernatants, whereas cell adhesion was by crystal violet staining and optical microscopy. uPA inhibited HIV replication in MDM and PMA-stimulated U1 cells in TC plates but not in ULA plates. uPA failed to inhibit HIV expression in U1 cells stimulated with IL-6, which induces virus expression but not cell adhesion in TC plates. VN, known to bind to the uPA/uPA receptor complex, was crucial for these adhesion-dependent, inhibitory effects of uPA on HIV expression, in that they were not observed in TC plates in the presence of VN-/- mouse serum. HIV production in control cell cultures was increased significantly in ULA versus TC plates, indicating that macrophage cell adhesion per se curtails HIV replication. In conclusion, uPA inhibits HIV-1 replication in macrophages via up-regulation of cell adhesion to the substrate mediated by VN.