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Many factors impact the onset and progression of infectious and autoimmune diseases within a given population, and the COVID-19 pandemic has magnified the health disparities experienced within susceptible communities, revealing poor disease outcomes and high mortality. Reported differences in infectious disease outcomes of different demographic groups have mostly highlighted environmental and socioeconomic factors as the presumed primary drivers. In this study, circulating IgG levels reactive to proteins from eight different viruses and 20 self-antigens from cohorts of 100 and 40 subjects were compared, respectively. Subjects within the cohorts were stratified by demographic differences, including race, sex, age, HIV status, and date of sample collection (pre- vs. during the COVID-19 pandemic). Across all subjects, EBV-specific IgG was highest, on average, as compared to antibody levels reactive with all other viruses. Black/AA participants possess higher anti-EBV GP 350, lower anti-Sm, and higher anti-CENP-B antibodies as compared to white individuals, the former indicating that viral reactivation is more frequent in minority populations and may lead to impaired cellular immunity. Females exhibited a higher level of SARS-CoV-2 wildtype (WT) spike and anti-proteinase 3 IgG than male counterparts. Anti-viral OC43, Flu, and EBV IgG were higher and the autoimmune antibodies anti-Sm and anti-C1q lower in older individuals compared with younger counterparts. In ART-suppressed HIV+ individuals, eCoV and CMV-reactive IgG was lower and EBV antibody levels higher compared with uninfected participants; and antibodies to CMV and proteinase 3 were higher in samples collected after the start of the pandemic as compared to earlier time points. To investigate links between virus-specific IgG and autoantibodies within subjects, linear regression and Spearman’s correlation tests were performed on the collected dataset. Ribosomal P autoantibody levels positively correlated EBV GP 350-specific antibodies, and CENP-B and CMV-specific IgG tracked positively as well. Also, CMV- and EBV- specific antibody levels were positively associated with one another. Further examination of these trends is required to define links between chronic infections and predisposition to certain autoimmune diseases. Overall, these results illuminate novel serological information among differing demographics to provide new insight into drivers of health disparities and association between chronic infections (i.e. EBV, CMV) and autoimmune diseases.

Mycobacterium tuberculosis (Mtb) is proven to augment protection against unrelated pathogens through enhanced antibody responses and epigenetic remodeling of innate immune cells. Although the role of Mtb on HIV-1 specific antibody responses has not been explored, the recognition of highly immunogenic antigens on Mtb may trigger a cascade of events culminating in an increased HIV-1 antigen presentation and specific B cell responses. Here, we compared HIV-1-specific antibody responses among people with HIV-1 either with or without active Mtb and simulated immune responses to HIV-1 infection and Mtb antigens using a tonsil organoid model. We examined HIV-1 specific neutralization and antibody-dependent cellular cytotoxicity (ADCC) breadth and potency (BP) among people with HIV-1 either with or without active Mtb (PWH/Active Mtb, PWH/Treated Mtb, and PWH/No Mtb). Before antiretroviral treatment (ART) and Mtb treatment, PWH/Active Mtb as compared to PWH/No Mtb demonstrated higher neutralization BP. During ART, PWH who developed new Mtb disease (PWH/Active Mtb) as compared to PWH/Treated Mtb and PWH/No Mtb had the highest fold increase in neutralization and ADCC BP. Neutralization BP did not associate with previously described determinants like HIV-1 virus levels, envelope diversity, and IgG concentrations, but associated with B cell cytokines (BAFF, APRIL, and IL-6) and ADCC BP. Our data suggest that active Mtb is associated with the augmentation of HIV-1 specific B cell responses before and during ART. Broad and potent anti-HIV-1 antibodies emerge from the germinal center activity in the lymph node. Mtb disease potentially exerts a bystander effect through cytokines on HIV-1 specific B and T cells. Additionally, Mtb disease may be broadening B cell responses by enhancing HIV-1 envelope expression. We used Mtb-derived antigens to simulate Mtb co-infection in HIV-1 infected human tonsils. HIV-1 infected as compared to HIV-1 infected and Mtb-antigen stimulated tonsil organoids had similar proportions of B and T cell subsets over 1 week in culture. HIV-1 infection led to the loss of CD4 T and T follicular helper cells in both groups. The tonsil organoid model may allow us to explore mechanisms underlying Mtb mediated enhancement of HIV-1 specific antibody responses in future studies. / 2025-11-02T00:00:00Z

Flaviviruses are a genus of arboviruses, including dengue virus (DENV), Zika virus, yellow fever virus, and West Nile virus, that have the potential to cause severe disease in humans and represent a tremendous and growing threat to public health. Like all arboviruses, flavivirus infection is contracted upon the bite of an infected vector, a process during which the virus and saliva are injected into the host skin. A large body of work has already reported the infection-enhancing ability of proteins derived from vector saliva, suggesting the existence of selective pressures on the vector-to-host viral transmission process. Through the work described herein, we demonstrated that flavivirus infection of Aedes aegypti modulates the protein cargo of extracellular vesicles, a potential avenue for the delivery of pro-viral factors during transmission. In doing so, we identified one protein, AAEL002675 (ARGIL1- Aedes aegypti Arginase-like 1 Protein), a putative arginase, within specific fractions of Aedes aegypti saliva that displayed infection-enhancing activity. We also observed this ARGIL1 protein within extracellular vesicles derived from dengue-infected Aedes aegypti cells. Importantly, treatment of cells with ARGIL1 resulted in an arginase-dependent enhanced level of DENV infection in vitro. In mammals, arginase is an important regulator of excessive cellular inflammation. It catalyzes production of collagen and polyamines from L-arginine, therefore reducing the pool of L-arginine substrate available for inducible nitric oxide synthase (iNOS) to produce nitric oxide. Consistently, cells treated with ARGIL1 displayed decreased levels of iNOS upon DENV infection, suggesting that ARGIL1 treatment reshapes the cellular environment to be more permissive to viral replication upon mosquito bite. These findings provide further evidence that ARGIL1 is an arginase-like pro-viral factor enhancing vector-to-host DENV transmission. Altogether, a better understanding of the molecular processes driving DENV transmission, such as those described here, will be instrumental for the development of innovative preventative antiviral strategies against flaviviruses and arboviruses, including vaccines that target vector proteins.

PLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you. / The purpose of this research project was to examine the capacity of anti-idiotypic antibodies and anti-idiotypic-like antibodies to regulate normal and malignant B-cell populations. Out of this project stemmed two new findings. The first was a technique for the rapid comparison of the primary amino acid sequences of antibody molecules. This method was applied to studying a panel of antibodies derived from an immune response characterized by a dominant idiotype where it was able to quickly distinguish between idiotype positive antibodies that differed by only a few amino acids. The technique was also applied to the analysis of monoclonal antibodies derived from fusions between human B-cell tumor containing tissue and mouse myeloma cells in order to identify which hybridomas were derived from the malignant B-cell population. The second finding involved techniques for growing non-murine antibody secreting hybridomas in immunosuppressed mice. Human x mouse and rat x mouse heterohybridomas grew readily in mice treated with cortisone and radiation but completely xenogeneic (rat x rat) hybrids did not. This was overcome by developing a ouabain resistant variant of the SP-2 mouse myeloma cell line and fusing it to the (rat x rat) hybridomas forming a "second generation" hybridoma cell lines that grew readilly in immunosuppressed mice. As an outgrowth of the human anti-idiotype project came an idiotype-like regulation model system. The idiotype-like regulation project was an attempt to extend the idiotype specific regulation effects of anti-idiotypic antibodies to the entire antigen binding antibody response. An antibody construct was made by covalently coupling antibodies specific for photoligand moiety to a peptide consisting of a photoligand attached to a hapten. The resulting complex had a single hapten specifically bound to each antigen binding region of the monoclonal antibody and was expected to influence antigen binding B-cells in much the same way as an anti-idiotypic antibody. However, when these complexes were injected into mice it was found that they did not modulate the subsequent antibody response. This lack of effect was due to a greatly decreased circulation time of the antibody-photoligand-hapten complex.

The effects of various culture parameters were investigated to optimize pigment production by Monascus purpureus ATCC 16365 in solid-state fermentations with emphasis on the effects of oxygen and carbon dioxide. The Monascus strain was selected because it showed the highest pigment production among strains tested which lacked antibiotic activity. Polished long rice was found to be the best substrate. Optimum relative humidity and initial moisture content were 97-100% and 45-50%, respectively. A moderate hand mixing of the culture gave a stimulatory effect on pigment yield. Optimum pH and temperature were 5.0-6.0 and 30$\sp\circ$C, respectively. Zinc supplementation at 1.5 $\times$ 10$\sp{-2}$ M gave maximum red pigment productivity, which reached 6016 OD units per gram of dry fermented solid after 6 days. Moderate forced aeration gave maximum pigment yields in packed-bed fermentations. Levels of oxygen and carbon dioxide in gas environments were found to significantly influence pigment production. Maximum pigment yields were observed at 0.5 atm oxygen in closed pressure vessels. However, high carbon dioxide pressures inhibited pigment production significantly, with complete inhibition at 1.0 atm. In a closed aeration system with a packed-bed fermentor, oxygen pressures ranging 0.05 to 0.5 atm at constant 0.02 atm of carbon dioxide partial pressure gave high pigment yields with a maximum at 0.50 atm of oxygen, whereas lower carbon dioxide pressures at constant 0.21 atm of oxygen partial pressure gave higher pigment yields. Maximum oxygen uptake rate and carbon dioxide evolution rate were observed at about 70-90 hr and 60-80 hr, respectively, depending on the gas environment. Respiratory quotients were close to 1.0, except at 0.05 atm oxygen and 0.02 atm carbon dioxide partial pressures, suggesting that anaerobic metabolism played a significant role under oxygen limiting conditions. Ethanol also appears to be subject to the Crabtree effect. Finally, optimum conditions for pigment formation were generally not the same as those for biomass formation.

Glucose dehydrogenase-deficient (Gcd$\sp-$) mutants of Pseudomonas cepacia 249 accumulated copious amounts of exopolymer on solid media containing 0.2% yeast extract supplemented with excess glucose. The majority of P. cepacia strains isolated from the pulmonary tracts of patients with cystic fibrosis were Gcd$\sp+$ indicating there was no correlation between glucose dehydrogenase-deficiency and the capacity of this bacterium to colonize the respiratory tract. Activities of glucokinase, phosphoglucomutase, glucose-6-phosphate dehydrogenase, and enzymes of the Entner-Doudoroff pathway were significantly lower in Gcd$\sp+$ than in Gcd$\sp-$ bacteria. The decrease in the levels of these enzymes in the Gcd$\sp+$ strains was associated with a dramatic drop in the pH of the culture medium due to conversion of glucose to gluconic and 2-ketogluconic acids. Both Gcd$\sp+$ and Gcd$\sp-$ strains accumulated polymer when gluconate, mannitol or fructose were substituted for glucose. Strain 249 and most other P. cepacia strains examined failed to form exopolymer in liquid medium. However, P. cepacia 389, a Gcd$\sp-$ clinical isolate accumulated large amounts of exopolymer in liquid and on solid media. When grown on media containing 0.2% yeast extract, 1% gluconate and 0.02% calcofluor white, this strain formed an exopolymer which reacted with the dye and fluoresced bright-green under UV-light. The exopolymers produced by strains 249 and 389 were distinct from alginic acid formed by Pseudomonas aeruginosa. Exopolymer of P. cepacia 249 contained galactose, glucose, rhamnose, mannose and uronic acid. However, strain 389 formed an exopolymer composed of glucose and galactose. When strain 389 was grown with excess gluconate the polymer also contained succinate. Thus the fluorescence phenotype of this strain in the presence of calcofluor white appeared to depend upon succinylation of its polymer. Synthesis of the exopolymer presumably involved the conversion of glucose-6-phosphate to glucose-1-phosphate, UDP-glucose and UDP-galactose by the enzymes phosphoglucomutase, UDP-glucose pyrophosphorylase and UDP-glucose-4-epimerase. Extracts of P. cepacia strains 389 and 249 contained significant levels of these enzymes. Mutants of strain 389 that either overproduced or failed to produce exopolymer were isolated. One Exo$\sp-$ mutant had only 10% of the normal level of phosphoglucomutase suggesting that exopolymer formation depended upon conversion of G6P to G1P.

The nucleotide sequence of IS402, from Pseudomonas cepacia, was determined. This transposable element was isolated previously from P. cepacia on the basis of its ability to increase expression of the Tn1 bla gene on plasmid pRP1. The IS402-containing region of pTGL52 (pRP1::IS402) was cloned into the Escherichia coli vector pBLUEKSP. Recombinant derivatives of pBLUEKSP carrying different regions of IS402 were constructed and were utilized for dideoxynucleotide sequence analysis of the element and flanking Tn1 DNA. IS402 (914-bp) had 17-bp terminal inverted repeat sequences with one mismatch, and three major open-reading-frames (ORFs) of 633, 441, and 264 nucleotides. It inserted into Tn1 170-bp upstream of its bla gene causing the direct duplication of 3-bp of target DNA. Comparison of IS402 with sequences in the GenBank and EMBL databases indicated that is was not closely related to previously described IS-elements. However the predicted amino acid sequence of the 441-nt ORF of IS402 exhibited 54% similarity with the putative transposase of IS427 from Agrobacterium tumefaciens. An effort was made to construct marked derivatives of IS402 suitable for testing whether its transposition might be triggered in response to nutrient starvation. For this purpose I cloned the fol gene of plasmid pR388 which confers resistance to trimethoprim (Tp) into the DraII site of IS402 adjacent to IR-L. The resulting element, IS402.2, was cloned into pTGL133, a broad-host-range plasmid which confers resistance to tetracycline and is temperature-sensitive with respect to its replication. The resulting plasmid, pTGL154, was transferred into P. cepacia and the transconjugants were propagated at 47$\sp\circ$C to isolate Tp$\sp{\rm R}$ transposants carrying IS402.2 in their chromosomes. Comparison of the extent of transposition of IS402.2 and of Tn5-751, a derivative of transposon Tn5 carrying a Tp$\sp{\rm R}$ marker, indicated that IS402.2 transposed at a relatively high rate. The orientation of the fol gene of IS402.2 was the same as the major ORFs of IS402 raising the possibility that the high frequency of transposition was due to increased transposase production caused by read-through transcription from the fol gene promoter. The high frequency of transposition of IS402.2 under normal conditions of growth makes it unsuitable for analysis of the influence of nutrient starvation on transposition. However, the results demonstrate the feasibility of constructing marked elements which may be suitable for this purpose.

The biochemistry and bioenergetics of the dissimilatory iron-reducing bacterium GS-15, proposed name Geobacter metallireducens gen. nov., sp. nov., were studied by identifying enzymes and electron transfer components. Enzymes of the citric acid cycle were found in detergent-treated, whole-cell suspensions, and cell-free extracts while enzymes of the carbon monoxide dehydrogenase were not. This was true whether nitrate or ferric ion acted as the terminal electron acceptor. Menaquinone and cytochrome c were extracted from cells. 2-Oxoglutarate and NADPH oxidation were coupled to methyl viologen reduction. 2-Oxoglutarate also reduced clostridial ferredoxin, and evidence for ferredoxin in GS-15 is given. A soluble, low-midpoint-potential cytochrome c was obtained having 3.1 mol heme c per MW of 12900 kD. Nutritional studies indicated: (1) that growth, as measured increase in cell protein, was coupled to iron reduction with a doubling time of 33 h and a yield of 2 g of cell protein per mol acetate; (2) penicillin-G completely growth at 100 $\mu$g per ml and iron reduction did not occur in cultures with 10 $\mu$g per ml; (3) pimelate was identified as a growth substrate; (4) cells contained in vivo hydrogenase activity and iron reduction was inhibited by hydrogen at high concentration. These data were used to construct a model for the transfer of electrons from the citric acid cycle to the terminal electron acceptor ferric iron. The low growth rate and yield of GS-15 is discussed with regards to energy conservation in this model for electron transfer. The presence of the citric acid cycle, 2-oxoglutarate synthase, menaquinone, and a multiheme cytochrome c are all consistent with members of the delta subgroup of the proteobacteria. Corroborating 16S rRNA sequence and lipid analysis data obtained elsewhere are included in the appendix. The relation of this iron-reducing bacterium to the sulfur- and sulfate-reducing bacteria is discussed. The similarities and differences with Shewanella putrefaciens, another dissimilatory iron-reducing bacterium, are also presented.

Microbial communities, through their metabolism, drive carbon cycling in marine environments. Marine heterotrophic bacteria are crucial players in this process, but the diversity of their metabolic preferences, evolved to match specific environmental conditions and inter-species partnerships, are still poorly understood. The emergent properties of microbial ecosystems make the challenge of predicting how heterotroph metabolisms influence the carbon cycle impossible with conventional approaches; teasing apart the mechanisms requires an intimate understanding of the organisms and organic matter involved. The primary goal of my dissertation research was to reduce the complexity of the ocean microbiome and organic matter to a tractable set of variables capable of reproducing basic principles of the heterotroph-organic matter relationship in a meaningful way. This challenge was addressed in multiple ways: First, I generated a phenotypic atlas for the growth capability of 63 heterotrophic marine strains across eight different classes of carbon compounds, which are representative of key components of marine dissolved organic matter. By computationally exploring the relationships between this atlas of phenotypes and the genomes of the different strains, I obtained new insight into the metabolic diversity of these marine bacteria and uncovered surprising patterns that can help understand the role of heterotrophs in the oceans. Second, I applied to this phenotypic atlas a new machine learning approach aimed at identifying subsets of environments that are informative about the whole dataset. This approach, which in this specific case study provided biologically interpretable metabolic axes for strain discrimination, is broadly applicable to high-throughput phenotypic data and can help map and understand complex biological systems. Third, I conducted a pilot study that integrates observations from laboratory and field experiments to explore the effect of microbe-microbe interactions on heterotrophic metabolic phenotypes in a highly complex natural ecosystem. Ultimately, in addition to helping understand the importance of heterotrophs under different conditions, the phenotypic fingerprints I obtained can help build higher resolution quantitative models of global microbial activity and biogeochemical cycles in the oceans. / 2025-06-16T00:00:00Z