bluuebunny/crossref_metadata_2025_split huggingface dataset:
The specific transcriptomic response of porcine intestinal epithelial cells to Escherichia coli and Salmonella enterica Typhimurium infections is modulated by bovine colostrum fractions
Authors: Blais Mylene , Bouchard Michael , Asselin Ckaude , Lessard Martin 
Published: January 2023

Abstract
Enterotoxigenic Escherichiacoli (ETEC) and Salmonella enterica Typhimurium are both enteric pathogens, but the mechanisms by which they infect intestinal epithelium are different. Recently, we observed that bovine colostrum (BC) increases protection against enteric infections in weaned piglets. In this study, we described the transcriptomic response of porcine intestinal epithelial cells IPEC-J2 infected by each pathogens, and we measured the specific effect of defatted BC, as well as bovine serocolostrum and casein fractions (SC and CAS respectively) on IPEC-J2 transcriptomic response to ETEC and Salmonella by microarray analysis. We also measured the impact of BC, SC and CAS on pathogen-induced epithelial integrity loss using transepithelial electrical resistance (TEER), and on NF-kB transcriptional activity by luciferase assays. Results showed that transcriptomic profile of cells challenged with ETEC and Salmonella both induced genes involved in inflammatory response, while ETEC specifically induced the expression of genes involved in morphogenesis and response to lipids, and Salmonella specifically regulated genes involved in oxidative stress, migration and apoptotic process. The ETEC induction of inflammatory genes was decreased by BC and SC, while Salmonella induction of inflammatory genes was specifically reduced by BC and CAS fraction. BC prevented epithelial integrity disruption caused by both pathogens, while SC only prevented the one caused by Salmonella. Finally, BC and SC decreased NF-kB activity induced by each pathogen. Altogether, these results indicated that BC fractions modulate in a specific manner cellular mechanisms involved in intestinal epithelial response to these pathogens.
Lattice light-sheet microscopy Multi-Dimensional Analyses (LaMDA) of T-cell receptor dynamics predict T-cell signaling states
Authors: Huang Jun 
Published: January 2023

Abstract
Cell surface receptors dynamically change in response to cell signaling, but a direct linkage between receptor dynamics and cell state has not been established. Here we report the development of lattice light-sheet microscopy multi-dimensional analyses (LaMDA), a pipeline that combines high spatiotemporal-resolution four-dimensional lattice light-sheet microscopy, machine learning, and diffusion maps to analyze T-cell receptor (TCR) dynamics and predict T-cell signaling states without the need for complex biochemical measurements. LaMDA images thousands of TCR microclusters on the surface of live primary cells to collect high-dimensional dynamic data for machine learning, which extracts key dynamic features to build predictive diffusion maps. LaMDA spatiotemporally reveals global changes of TCRs across the 3D cell surface, accurately differentiates stimulated cells from unstimulated cells, precisely predicts attenuated T-cell signaling after CD4 and CD28 receptor blockades, and reliably discriminates between structurally similar TCR ligands. We anticipate broad usage of this approach for other receptors and cells, as well as for guiding the design and development of future immunotherapies for cancer, infection, and autoimmunity.
IFN-γ control of metabolic stress response during T. gondii infection
Authors: Reyes JS B , Zhao Yanlin , Yap George S 
Published: January 2023

Abstract
IFN-γ is essential for host resistance against Toxoplasma gondii infection; however, overproduction of IFN-γ systemically results in increased host morbidity. During acute infection, mice lose weight due to anorexia and hypermetabolism and exhibit high levels of circulating IFN-γ. We wish to understand the role of IFN-γ in the host stress response during infection. We focused on two peptide stress hormones: GDF15 and FGF21. Growth differentiation factor 15, a member of the TGF-β family, is an anorexic agent while fibroblast growth factor 21 is a hormone that upregulates energy expenditure. Indeed, we observed increased levels of serum GDF15 and FGF21 during acute infection preceding weight loss. To investigate the contribution of IFN-γ in the regulation of GDF15 and FGF21, we transiently neutralized IFN-γ in T. gondii infected mice. We observed a decrease in serum GDF15 and FGF21 levels following IFN-γ blockade. Moreover, IFN-γ neutralization not only prevented further weight loss but also led to weight gain. However, there was no difference between control and treated mice in the tissue levels of GDF15. Altogether, these data suggest that IFN-γ contributes to the sickness response during infection by regulating the systemic levels of GDF15 and FGF21. Ongoing studies are focused on the role of IFN-γ in promoting the maturation and release to the circulation of these metabolism-regulating stress hormones during infection.
KLRG1+ Memory CD8 T cells Combine Properties of Short-lived Effectors and Long-lived Memory
Authors: Huggins Matthew A , Renkema Kristin R , da Silva Henrique Borges , Knutson Todd P , Henzler Christy M , Jameson Stephen C , Hamilton Sara E 
Published: January 2023

Abstract
An effective memory CD8 T cell response must generate cells that respond robustly to antigen re-encounter to produce an effective recall response while also maintaining a stable pool of durable cells in the absence of antigen. During the effector response KLRG1+ CD127low cells are described predominantly as short-lived effectors that will undergo apoptosis during the contraction phase or downregulate KLRG1. However, we have shown that long-lived KLRG1+ CD127low T cells are still present at the memory phase, and that these T cells (termed long-lived effector cells or LLEC) display robust protective function during acute re-challenge with bacteria or viruses. Here, we find that LLEC are derived exclusively from KLRG1+ effector cells, and that this contributes a substantial fraction of the resulting memory pool. Our work challenges the concept that the KLRG1+ CD127low population is dominated by short-lived cells, shows that KLRG1 downregulation is not a prerequisite to become a long-lived protective memory T cell, and highlights the diversity within the memory compartment. Furthermore, using single-cell sequencing we demonstrate that LLEC are not simply a remnant effector population that has failed to undergo initial contraction, but rather a discrete population of T cells with a distinct transcriptional signature that shares characteristics of both early effectors (GzmA, GzmB, Klrg1, Cx3cr1, Zeb2), long-lived memory cells (Bcl2, Il7r, Aqp9, Dmrta1), and a pattern of inhibitory receptors associated with NK cell function (Klrc1, Klre1, Klrd1). Overall, the unique transcriptional profile of LLEC translates to an identity encompassing the hybrid characteristics of effector-like cytotoxicity paired with longevity.
Blimp-1 in adipose resident Tregs controls adipocyte beiging and obesity
Authors: Beppu Lisa , Qu Xiaoyao , Marrero Giovanni , Fooks Allen , Frias Adolfo , Helfrich Katherine , Sipula Ian , Xie Bingxian , Watkins Simon , Poholek Amanda , Jurczak Michael , D’Cruz Louise 
Published: January 2023

Abstract
Visceral adipose tissue regulatory T cells (VAT Tregs) protect against systemic inflammation and metabolic disease by limiting expansion of pro-inflammatory Th1 cells and M1 macrophages, and by preserving insulin sensitivity and glucose tolerance. Although their basic markers and roles have been studied, less is known about the transcriptional machinery regulating their differentiation and function.
B lymphocyte-induced maturation protein-1 (Blimp-1) is a transcriptional regulator known to be involved in the development, polarization, and maintenance of various immune cells including CD4+ T cells. Using Blimp-1 reporter mice, we discovered that Blimp-1 is constitutively expressed in a subset of VAT Tregs compared to lymphoid Tregs, and that Blimp-1+ VAT Tregs are phenotypically distinct from their Blimp-1− counterparts. Blimp-1 is not required for VAT Treg development, however Treg-specific deletion of Blimp-1 led to unique changes in VAT Treg markers in lean versus obese adipose tissue. In addition, Blimp-1 knockout mice fed high fat diet had fewer adipose-resident NK cells and increased CD8 T cells. Surprisingly, loss of Blimp-1+ Tregs led to less adipose tissue IL-10, increased expression of thermogenic genes, reduced body fat, decreased weight, and improved insulin sensitivity. Based on these data, we hypothesize that Blimp-1+ Treg dependent IL-10 production suppresses adipocyte beiging, and that loss of these cells results in increased thermogenesis, greater weight loss and improved insulin sensitivity in obese mice.
Using Electric Cell-Substrate Impedance Sensing (ECIS) as a novel method to evaluate bacterial urinary tract infections
Authors: Horseman Tim , Campbell Carmen , Gomes Grace , Fong Keith 
Published: January 2023

Abstract
Urinary tractinfections (UTIs) are commonly acquired bacterial infections that cause significant morbidity, worsened by the rise of antimicrobial resistance among uropathogenic bacteria. Understanding the dynamics of bacterial UTIs is essential to the proper use of antimicrobial therapies in patient treatment. In this study, Electric Cell-Substrate Impedance Sensing (ECIS) technology was used to monitor bacterial-mediated cytotoxicity in-vitro enabling evaluation of antibiotics. Using the ECIS system, real-time changes of barrier function were recorded for human bladder epithelial cells infected with either antibiotic sensitive or resistant bacteria. This study employed four common uropathogens: Pseudomonas aeruginosa, Escherichia coli, Enterococcus species, and Klebsiella pneumoniae. The effect of different antimicrobials, antibiotic titers, and organism concentrations were evaluated. The addition of an antibiotic helped confirm and differentiate sensitive and resistant bacterial strains. Antibiotic concentrations at sensitive and resistant breakpoints were not as effective at high organism concentrations but were completely effective at lower more clinically relevant bacterial loads. The data showed bacterial strains resistant to co-cultured antibiotic took longer on average to degrade the cell monolayer than sensitive strains. Overall, these results indicate that antibiotic resistance is often associated with a fitness cost. Our findings support the use of ECIS to augment routine susceptibility data allowing the direct phenotypic measurement of bacterial virulence and the effects of antibiotic treatment on these strains.
Development and organization of pulmonary lymphoid aggregates after Klebsiella pneumoniae infection of the murine respiratory tract
Authors: Wasbotten Rachel , Smith Catherine Diane Morffy , Rosen David A. 
Published: January 2023

Abstract
Klebsiella pneumoniae is a worrisome nosocomial pathogen given the widespread emergence of antibiotic resistant strains. Little is known about the host immune response to K. pneumoniae; however, it has recently been shown that aggregates of lymphoid cells can be found in murine lungs 4 weeks after surviving K. pneumoniae pulmonary infection. Others have characterized pulmonary collections of lymphoid cells in response to other pathogens and coined them induced bronchus-associated lymphoid tissue (iBALT). iBALT is believed to assist in protection against re-infection. In our nonlethal model of K. pneumoniae, mice that survive the primary infection and exhibit these structures are indeed protected from K. pneumoniae challenge. To further characterize the development and organization of these structures, pulmonary immune cell populations were analyzed post-infection by flow cytometry, histology, and immunofluorescence. As expected, pulmonary neutrophil populations increase over the first 10 days post-infection. T cells appear to rapidly expand between 7 and 10 days post-infection and both CD4+ and γδ T cell subsets make up the majority of this population. Immunofluorescent imaging of lymphoid aggregates demonstrate that CD4+ and γδ T cells are found within these structures at early time-points. Experiments using TCRβδ−/− mice lacking T cells reveals the absence of lymphoid aggregates 28 days post-infection, suggesting that T cells are essential in the initial formation and development of these structures.
Nanobody LAMPoles: Novel tools for dengue virus and Zika virus diagnosis
Authors: Grab Dennis J , Sharma Anuj , Burbulis Ian , Lehrer Axel T , Nerurkar Vivek , Magez Stefan 
Published: January 2023

Abstract
Detection of antibodies by ELISA for verifying exposure to dengue virus (DENV) and Zika virus (ZIKV) has been a challenge. Point-of-care (POC) diagnostics with detection of very low concentrations of viral antigens would improve critical disease staging and surveillance to reduce morbidity and mortality. LAMPoles are protein-DNA hybrids where a ‘DNA barcode’ is covalently linked to a single site on a protein. Recombinant camelid nanobodies (Nb), which are variable region of the heavy chain antigen binding domain (VHH), can be tailored to bind almost any molecular target to maximize assay sensitivity and specificity. LAMPole fusions displaying Nb that bind ZIKV and DENV antigens will improve the sensitivity and specificity of virus antigen measurement at the POC. Llama were vaccinated with recombinant DENV envelope or ZIKV NS1 proteins and VHH phagemid libraries constructed and screened for DENV and ZIKV antigen-specific Nb. For DENV 70 full-length Nb were identified, belonging to 26 different CDR3 groups. For ZIKV 63 full-length anti-ZIKV Nb were identified, belonging to 42 different CDR3 groups. Nb screened by surface plasmon resonance spectroscopy with Koff kinetics in the 10−3 sec range were conjugated to chalcone synthase specific DNA elements using psoralen-based photocross-linkers. In a pilot experiment, LAMP targeting the CHS DNA tail of one Nb-LAMPole detected less than 10 fg of Nb-LAMPole protein. Nb-LAMPole recognized DENV-2 E-protein antigen in sandwich ELISA and in DENV-2 infected cells by immunofluorescence. We assert that LAMPole fusions displaying Nb that bind viral antigens may improve the sensitivity and specificity of DENV and ZIKV antigen detection that will facilitate markedly improved POC diagnosis.
A therapeutic vaccine strategy to prevent Pneumocystis pneumonia in an immunocompromised host in a NHP model HIV and Pneumocystis co-infection
Authors: Rabacal Whitney , Rayens Emily , Jimenez Viviana Cobos , Schweitzer Finja , Kling Heather M , Norris Karen 
Published: January 2023

Abstract
Pneumocystis (Pc) is a ubiquitious fungal pathogen that causes pneumonia (PCP) and Pc-related pulmonary sequelae in HIV-infected individuals and other immunocompromised populations. Deficiencies in CD4 T cell populations and immunologic dysfunction can limit humoral immunity and vaccine efficacy in Pc-susceptible populations. The ultimate goal of the field is to develop an effective vaccine that can overcome immune deficits in at risk populations and induce long-lasting protective immunity to Pc. Toward this goals, our laboratory has established a model of PCP co-infection in simian immunodeficiency virus (SIV)-infected non-human primates (NHP). We have previously identified a recombinant protein sub-unit vaccine, KEX1, that induces robust anti-Pc immunity in immune-competent macaques that is durable and prevents Pc pneumonia following simian immunodeficiency virus (SIV)-induced immunosuppression and subsequent Pc challenge (Kling and Norris, 2016). In the present study, we used the SIV model of HIV infection to address whether therapeutic vaccination with KEX1 can be effective following virus-induced immunosuppression. Type I, or invariant natural killer T (iNKT) cells have the potential to provide CD4-independent B cell help. When activated, iNKT cells are capable of rapidly expressing a wide array of cytokines and co-stimulatory molecules that can enhance humoral responses. The central hypothesis of this study is that a therapeutic vaccination strategy can induce invariant natural killer (iNKT) cell-B cell help to boost anti-KEX1 titers and enhance immunity to Pc during virus-induced immunosuppression.
Effective clearance of Chlamydia from the female reproductive tract in the absence of T-bet+ Th1 cells
Authors: Rixon Jordan , McSorley Stephen J 
Published: January 2023

Abstract
Protective immune responses to Chlamydia infection within the female reproductive tract (FRT) are incompletely understood. MHC class II-restricted CD4 Th1 responses are thought to be vital for bacterial clearance, due to their capacity to secrete IFN-γ. However, other studies suggest protective or pathogenic roles for additional CD4 T helper subsets. We used a variety of gene-deficient mice to re-examine bacterial clearance following primary genital infection of C57BL/6 mice with Chlamydia muridarum. As seen previously, IFN-γ-, and IFN-γR-deficient mice resolved much of FRT infection, but experienced systemic dissemination and 100% mortality with an average median survival of approximately 4 weeks. Mice lacking the Th1 subset defining transcription factor T-bet or the Th2 transcription factor STAT6 both effectively cleared infection from the reproductive tract, suggesting that neither Th1 nor Th2 cells are essential for local bacterial control. In contrast, RORγt mutant mice selectively deficient in Th17 responses exhibited a week delay in clearance compared to wild-type mice. Th17 subset markers were not observed to be upregulated in T-bet−/− mice and markers of Th1 subsets were minimally upregulated in RORγt mutant mice, indicating that compensation between these subsets does not explain bacterial clearance. In conclusion, timely local clearance of Chlamydia muridarum from the reproductive tract requires Th17 CD4 T cells, but will ultimately clear independent of classical T-bet+ Th1 and RORγt+ Th17 cells individually. Studies are underway to examine which alternative CD4 T cell mechanisms contribute to bacterial clearance within the FRT.
Development and characterization of first ever panels of human helminth-specific IgE monoclonal antibodies (mAb)
Authors: Hadadianpour Azadeh , Daniel Jacob Luke , Smith Scott Alan , Bogdan Olivia 
Published: January 2023

Abstract
According to WHO estimates, more than 1.5 billion people (&gt;24% worldwide) are living with some type of helminth infection and there is no FDA-approved anti-helminth vaccine available. The type 2 immune response is understood to be involved in our defense against helminth infection. In developing countries, elevated serum IgE level is a hallmark of parasitic disease. However, many aspects of the human immune response to helminth infection are still unknown; including, the identity of helminth proteins targeted by IgE antibodies and the size and complexity of the functional IgE repertoire. In this study, we have generated and characterized first ever panels of full-length naturally occurring human helminth specific IgE mAbs. We isolated IgE B cells from individuals with helminth infection and used human hybridoma technology to generate IgE mAbs. ELISA and Western blot techniques were used to test binding of purified IgE mAbs to helminth lysate. The helminth proteins targeted by IgE mAbs were determined using immunoprecipitation, mass spectrometry and de novo peptide sequencing techniques. The information obtained regarding IgE targets and their immune dominance will assist in our basic understanding of the role IgE plays in defending us against helminth infection and will ultimately aid in the rational design of anti-helminth vaccines. Lastly, we analyzed IgE mAb sequences and found remarkable variation in antibody variable region gene usage as well as mutation frequency.
The influence of the lung virome on pulmonary B cells
Authors: Aihara Fumiaki , Feng Feng , Wang Yu Mei , Breen Michael , Elledge Stephen J. , Mizgerd Joseph P. , Fearns Rachel , Kepler Thomas B. 
Published: January 2023

Abstract
The human microbiome is a complex and diverse environment that is implicated in human health and disease. Major locations that host a microbiome include the gut, respiratory system, and the urogenital tracts. While there have been steady advances of the effect of our commensal flora in regions such as the gut, the impact of the pulmonary microbiome, specifically the viral arm of the microbiome (virome), remains under-researched. Studies that have addressed this field provided insight into a complex interplay between viruses and the immune system. On one hand, there are reports of viruses inducing protection from other microorganisms, while on the other, they are correlated with increased risk towards other diseases. Despite this growing body of work on how the lung virome influences human health through the immune system, the immunological mechanisms that underlie this interaction remains unclear.
We hypothesize that constant exposure to pulmonary virus will generate a unique B cell repertoire distinct from peripheral B cells that is adapted specifically to pulmonary viruses. To address this hypothesis, we compared memory B cells from patent-paired lung and blood samples by flow cytometry as well as their secreted antibody affinity towards viral epitopes. Our results show B cell population distributions unique in the lung relative to blood. Secreted antibodies collected from cultured B cells have also shown specificity towards human viral pathogens. We believe our results will provide insight into the influence of a unique and chronic viral presence on pulmonary immunity.
Zinc supplementation modulates T helper 17 cells via its effect on gut microbiome
Authors: Gordon Sarah R , Vaishnava Shipra 
Published: January 2023

Abstract
Zinc is an essential micronutrient involved in many cellular functions in both humans and bacteria. In the gut, the availability of zinc may impact survival and pathogenicity of the gut microbiota. Recent studies show that changes in levels of dietary zinc can alter the composition of the gut microbiota, however how this impacts mucosal immune responses is not known. Here, we show that supplementing mice with zinc sulfate in drinking water for a week resulted in significant changes in gut microbial composition, as well drastic reduction in microbial diversity. More importantly we saw that zinc supplementation attenuated the T helper 17 cell number and activity in murine small intestine. Th17 induction via adherent microbes is mediated by upregulation of Serum Amyloid A (SAA) from epithelial cells. We see a reduction in SAA in zinc-supplemented mice. Furthermore, T regulatory cell numbers and IL-10 cytokine levels, which are known to antagonizes Th17 induction, is unchanged during zinc supplementation. Using 16S rRNA sequencing, we found major shifts in community composition of the mucosal-associated microbiota upon zinc supplementation. To determine if zinc-dependent changes in gut microbiota are sufficient to limit Th17 response, we transplanted microbiome from zinc treated mice into germ-free mice. We saw that germ-free mice that received cecal contents from zinc treated mice have reduced Th17 response thus establishing that dietary zinc changes immune potential of gut microbiome. Th17 cells mediate antimicrobial response in the gut and are involved in the pathogenesis of many autoimmune diseases. Our work thus provides a novel nutritional approach for remodeling microbiota to dampen inflammatory immune response in the gut.