bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the Normal Mouse IGH Antibody Repertoire
Authors: Rettig Trisha A , Bye Bailey , Peacaut Michael J , Chapes Stephen K 
Published: January 2023

Abstract
While the process of antibody generation in response to pathogens and immunization is well understood, the normal antibody repertoire needs characterization to better understand the diversity of the antibody response. The antibody molecule is generated from multiple gene segments; variable (V), diversity (D), and joining (J). These segments rearrange (V, D, and J in the heavy chain, V and J in the light chain) and combine with a constant region, which determines the effector function within in the host. The V, D, and J gene segments are combined to form the complementary determining region 3 (CDR3), providing much of the variability within the B cell receptor repertoire. To address heavy chain rearrangement in the unstimulated antibody repertoire, we pooled and sequenced the total splenic RNA from three groups of normal C57BL/6J. V, D, J, and constant region usage and CDR3 formation were analyzed. We developed a bioinformatic workflow to analyze the most common usage and combinations of the V, D, and J gene segments and their pairings with constant regions. We examined length and composition of CDR3 along with the ontology of the observed antibodies. The preliminary screen identified over 33,000 sequences as possible antibodies; 5,743 were hypothesized to be productive sequences. The largest V-gene family represented was V1, followed by V2 and V6. The average CDR3 length was 11 amino acids and we identified a number of high-occurrence CDR3 amino acid sequences. These data provide a glimpse of the normal C57BL/6J heavy chain response and validate the bioinformatics needed for our future immunization studies. Supported by NASA grants NNX13AN34G and NNX15AB45G and NIH grant GM103418 and the Molecular Biology Core supported by CVM-KSU.
Epidemiologically characterized high and low transmission isolates of Mycobacterium tuberculosis induce distinct infection outcomes in mice
Authors: Verma Sheetal , Bhatt Kamlesh , Rodrigues Rodrigo Ribeiro , Jones-López Edward C. , Palaci Moises , Alland David , Dietze Reynaldo , Ellner Jerrold , Salgame Padmini 
Published: January 2023

Abstract
In a study of household contacts of infectious TB cases (HHC) conducted by us in Brazil, “index” cases were categorized into High (HT) and Low (LT) transmission groups based on the proportion of household contacts with a positive tuberculin skin test. In this study we wanted to determine whether Mycobacterium tuberculosis (Mtb) isolates with different transmission phenotypes diverged in their interaction with the host immune system. Initial in vitro analysis of 15 isolates from each group revealed significantly higher levels of TNF produced by macrophages infected with HT isolates. Two each of the HT and LT isolates were further characterized in vivo in the C3HeB/FeJ mice which develop lesions characteristic of human TB. Through the course of these infections, both the LT isolates exhibited a significantly higher bacterial burden and enhanced cellular recruitment to the lungs. Mice infected with the LT isolates exhibited early pulmonary inflammation that rapidly progressed to widespread consolidation of the granulomatous lesions. In contrast, mice infected with the two HT isolates formed organized cellular aggregates that contained abundant lymphocytes and foamy macrophages. Interestingly, pathological progression of the cellular aggregates into caseous fibrotic lesions, with abundant extracellular bacilli, was observed with one of the HT isolates. Furthermore, elevated levels of the pro-inflammatory cytokines IL-1β, IL-6 and IL-17 were found in the lungs of mice infected with the LT isolates. These results suggest that distinct interactions between microbe and host immunity might lead to differential trajectory in intracellular growth pattern and lung pathology that underlie differences in transmission potential.
Mycobacterium tuberculosis produces small noncoding RNAs during infections to regulate mycobacterial and eukaryotic gene expression
Authors: van Oers Nicolai S , Srivastava Shashikant , Raj Prithvi , Dozmorov Igor , Wakeland Edward K , Gumbo Tawanda 
Published: January 2023

Abstract
Mycobacterium tuberculosis (Mtb) presently infects 1/3 of the World’s population, causing both active and latent pulmonary tuberculosis (TB). The pathogenic mechanisms used by Mtb remain poorly defined. We used a small RNA sequencing strategy on RNA extracted from Mtb-infected THP-1 macrophages to characterize the changes in eukaryotic microRNAs (miRs) and identify any mycobacterially-encoded small RNAs. A large number of mammalian microRNAs were differentially regulated during the infection course. Target prediction programs indicated that the mRNAs regulated by the miRs were involved in immune processes, metabolic pathways, cell communication, and developmental events. In addition, 35 Mtb-encoded small RNAs (18–30 nucleotides, mRs) were discovered. Several of the Mtb-encoded mRs were detected in lung tissue biopsies from TB infected monkeys. The 100–150 nucleotides surrounding the 35 Mtb-encoded small RNAs had extensive secondary RNA folding capabilities, including hairpins and antisense stretches more characteristic of eukaryotic pre-microRNAs. Two such small RNAs, Mtb-mR-1 and Mtb-mR-6 were transcribed in Mycobacterium avium complex and Mtb in a hairpin loop and antisense sequence-dependent manner. These mRs were not expressed in Mycobacterium smegmatis, revealing a restricted expression to pathogenic strains. Mtb-encoded mR-1 and mR-6 modulated both prokaryotic and eukaryotic gene expression. Taken together, our findings reveal potentially novel pathogenic processes utilized by Mtb during infections.
Role of secreted IgM in regulating the host response to Mycobacterium tuberculosis
Authors: Mehta Simren , Xu Jiayong , Wang Yanhua , Chan John 
Published: January 2023

Abstract
B cell aggregates, which display characteristics of germinal center reactions, are a prominent feature in the lungs of Mycobacterium tuberculosis (Mtb)-infected hosts. Using the B cell-deficient mouse strain μMT, we have previously shown that B cells are required for optimal protection against aerosol Mtb infection. μMT mice display exacerbated lung granulomatous inflammation during acute tuberculosis (TB), and this can be ameliorated by adoptive transfer of B cells or treatment with immune serum, suggesting a role for immunoglobulin in modulating the local lung response to Mtb. To investigate the role of antibody in a protective host response to Mtb, we utilized mice deficient in various immunoglobulins. Mice unable to secrete IgM (μS−/−) were more susceptible to aerosol Mtb infection than those lacking all other immunoglobulin isotypes, and displayed increased mortality during chronic TB. Relative to wild-type (WT) mice, Mtb-infected μS−/− mice had fewer lymphoid aggregates and a delayed granulomatous response in the lungs, despite having greater numbers of activated pulmonary CD4+ T cells. Treatment of μS−/− mice with immune serum (derived from Mtb-infected WT mice) during acute infection, led to increased lymphoid aggregates and plasma cells in the lungs, more pulmonary infiltrate, a concomitant decrease in the lung bacterial burden, and ultimately delayed the onset of death of μS−/− mice during chronic TB. These data suggest IgM plays an important role in controlling Mtb infection by orchestrating local granulomatous responses in the lungs, which leads to improved host survival during the chronic phase of infection.
Mycobacterium tuberculosis hijacks alveolar macrophages to translocate from the airway to the lung parenchyma.
Authors: Cohen Sara Beth , Adams Kristin , Urdahl Kevin 
Published: January 2023

Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, a chronic bacterial infection of the lung that affects one third of the world’s population. While lung alveolar macrophages (AM) are thought to be the first host cell infected with Mtb, it remains unclear how bacteria leave AM in the airway and disseminate to the lung parenchyma. Using fluorescent Mtb to identify infected cells and non-surgical intra-tracheal antibody delivery to label airway-resident cells, we found that airway-resident AM are indeed the first cells infected by Mtb. Interestingly, infected AM become increasingly resistant to airway labeling over time, with only 30% of infected AM localizing to the airway by Day 21 post-infection, suggesting that infected AM exit the airway and translocate to the lung parenchyma as infection progresses. In contrast, uninfected AM continue to predominantly label with the airway antibody, suggesting that migration of AM into the lung parenchyma is specific to infected cells. In the absence of the TLR adaptor MyD88, but not IL12R or type I IFN, infected AM are partially impaired in their ability to migrate, implicating MyD88 signaling in this trafficking pathway. Surprisingly, AM infected with the attenuated ΔdrrA strain that lacks the virulence lipid PDIM are impaired in translocation to the parenchyma, identifying a possible role for this lipid in promoting AM migration. Conversely, AM infected with the hypervirulent SA161 strain translocated to the lung parenchyma more rapidly 10 days post-infection. Combined, these studies provide insights into the cellular mechanisms of Mtb entry into the lung parenchyma following aerosol infection, a key step in the pathogenesis of tuberculosis.
Commensal E. coli induced colonization resistance against mucosal Salmonella infection
Authors: Lu Chunchi , Zhao Xiadan , Lai Marvin A , Lopez-Yglesias Americo H , Quarles Ellen K , Lo Chiata , Smith Kelly D 
Published: January 2023

Abstract
Salmonella is the causative agent in Salmonellosis and is a leading cause of gastrointestinal bacterial infections worldwide. During mucosal Salmonella infection Salmonella must first establish a niche in the gastrointestinal tract in order to initiate infection. Colonization resistance (CR), defined as the ability of intestinal microbiota and host defenses to protect against pathogens, is the first line defense against intestinal infection. The mechanism for commensal bacteria mediated CR has been studied for a long time; however, only a few studies have explored how microbiota can induce CR against Salmonella infection. Herein we demonstrate that a mouse commensal E. coli strain mediates CR against mucosal Salmonella Typhimurium infection, and that this CR is independent of the inflammasome, TLR5, MyD88, adaptive immunity, and a complex microbiome. The commensal E. coli strain does not directly compete with Salmonella growth in vitro, and is only capable of inducing colonization resistance in vivo. Gene expression analysis demonstrates that colonization of mice by commensal E. coli induces a large number of host defense genes involved in the regulation of mucosal barriers, innate immune cells and arachidonic acid metabolism. Our studies demonstrate that commensal E. coli interacts with the host through a novel pathway to induce CR against mucosal Salmonella infection and illuminate the complex interactions between microbiota and the host that shape defenses and defend against enteric infections.
Modulation of TRAIL mediated apoptosis signaling by Helicobacter pylori
Authors: Hsu Ping-Ning , Lin Woan-Yu 
Published: January 2023

Abstract
Helicobacter pylori (H. pylori) infection is associated with chronic gastritis, peptic ulcer and gastric cancer. However, the mechanisms by which cause disease remain unclear. Apoptosis induced by microbial infections is implicated in the pathogenesis of H. pylori infection. Here we show that human gastric epithelial cells sensitized to H. pylori confer susceptibility to TRAIL-mediated apoptosis via modulation of death receptor signaling. Human gastric epithelial cells are intrinsically resistant to TRAIL-mediated apoptosis. The induction of TRAIL sensitivity by H. pylori is dependent on the activation of caspase-8 and its downstream pathway. H. pylori induces caspase-8 activation via enhanced assembly of the TRAIL death-inducing signaling complex (DISC) through down-regulation of cellular FLICE-inhibitory protein (FLIP). Our study thus demonstrates H. pylori induces sensitivity to TRAIL apoptosis by regulation of FLIP and assembly of DISC, which initiates caspase activation, resulting in the breakdown of resistance to apoptosis, and provides insight into the pathogenesis of gastric damage in Helicobacter infection. We further demonstrated that FLIPS expression was consistent with Akt activation. H. pylori induced reduced Akt phosphorylation and led to decreased FLIPS expression in human gastric epithelial cells. Modulation of host apoptosis signaling by bacterial interaction adds a new dimension to the pathogenesis of Helicobacter.
Development of Dictyostelium discoideum as a model to identify evolutionarily-conserved virulence factors in Escherichia coli
Authors: Snyder Michelle , Weichseldorfer Matthew , Parker Dominique , Qureshi Mohammed , Phan Philong , White Theresa , Leicht Benjamin , Alkharouf Nadim , Rasko David , Hemm Matthew 
Published: January 2023

Abstract
Escherichia coli are a typical component of mammalian gut microbiota; however, a number of pathogenic strains remain a health concern for developing countries. Identification and disruption of virulence factors that promote infection could lead to reduction in infection. To identify novel bacterial virulence factors, we are using the soil amoeba, Dictyostelium discoideum, which preys upon bacteria, including E. coli, in the soil, as a model for mammalian phagocytic cells. Using random mutagenesis, we have created mutant stocks of MG1655 E. coli. These stocks were fed to D. discoideum, enriching the culture and selecting for mutants that were resistant to killing upon phagocytosis. After several rounds of selection, resistant mutant strains were isolated, and we found that some strains showed up to 100-fold increase in survival over a 2 h period. Once isolated, the genomes of the resistant mutant strains were sequenced and the sequences compared to that of the initial WT strain using Illumina’s MiSeq technology. While analyzing the sequences from these mutant strains, we found mutations in several potential genes of interest and are working to characterize their roles in the cell. We are testing E. coli strains reconstituted with specific mutations to identify particular mutations that are associated with phagocytosis-resistant phenotypes. These studies are aimed at identifying particular bacterial genes that may be involved in regulation of virulence. In addition, given that the development of mechanisms to resist D. discoideum predation may have contributed to the selection and maintenance of bacterial virulence factors against mammalian hosts, these studies may provide insight on the evolution of host-pathogen interactions.
Peripheral Francisella tularensis infection results in neural invasion and pathologic inflammation.
Authors: Ramos Muniz Mireya G , Pon Alexandra , Jones Devin , Spencer Charles T 
Published: January 2023

Abstract
Francisella tularensis infection triggers an overactive inflammatory response by stimulating production of host pro-inflammatory cytokines. Human tularemia, caused by F. tularensis, is a zoonotic disease transmitted by aerosol particles, direct contact, and via arthropod vectors, particularly ticks. Curiously, during peripheral inoculation in a mouse model of tularemia, F. tularensis was unexpectedly found in brain homogenates, though there is no prior evidence suggesting neural tropism. In the periphery, macrophages provide innate immune defense against foreign material, including bacteria. Microglial cells are resident macrophages of the brain and spinal cord and previously have been reported to rapidly respond to pathological changes in the central nervous system, serving a similar function as macrophages. Their rapid activation is an important factor in guarding the neural parenchyma against infectious diseases, inflammation, and neurodegeneration while maintaining and facilitating the return to tissue homeostasis. Therefore, we hypothesized that, having invaded the brain by an unknown mechanism, F. tularensis may be capable of eliciting an immune response following infection of microglial cells. Since macrophage infection leads to elicitation of inflammation, infection of microglia similarly stimulate inflammation leading to neural pathology. Mice were inoculated on the rear flank with fluorescently labeled bacteria. Using fluorescent confocal microscopy, labeled F. tularensis was localized in the brains of infected mice. We analyzed brain homogenates for production of inflammatory cytokines at these sites through Milliplex and qPCR.
Modulation of Gut Inflammation by Dietary Fibers in Murine Chronic Colitis
Authors: Singh Vishal , Yeoh Beng San , Saha Piu , Vijay-Kumar Matam 
Published: January 2023

Abstract
Natural dietary fiber serves as a substrate for gut microbiotal fermentation generating short chain fatty acids, which are thought to offer protection against inflammatory bowel disease (IBD). However, certain fibers are known to cause moderate to severe intestinal side effects in IBD patients. We hypothesize that soluble fibers (inulin & pectin) which are more accessible for microbiotal fermentation may offer pronounced gut protective effects than insoluble fiber (cellulose). To demonstrate this, chronic colitis was induced in dietary cellulose, inulin or pectin fed C57BL/6 mice by administering three weekly injections of α-IL-10R neutralizing antibody. Mice were euthanized two weeks after the last injection and colitis development was examined by serological, biochemical, histological and immunological parameters.
WT mice receiving dietary cellulose along with α-IL-10R mAb exhibited robust colitis as characterized by splenomegaly, colomegaly, elevated colonic MPO activity, pro-inflammatory cytokines (Kc, Il-1β & iNos), systemic and fecal Lcn2 levels (an inflammatory marker) and colon histology score when compared to control mice. Similar results were observed in toll-like receptor 5 knockout (Tlr5KO) mice which are prone to develop microbiota-dependent spontaneous colitis. Surprisingly, prebiotic fiber inulin failed to protect against α-IL-10R neutralization-induced chronic colitis in both WT and Tlr5KO mice. Interestingly, pectin ameliorates colitis development, supporting the notion that not all dietary fibers are created equal in modulating host gut inflammation. Further mechanistic study on how pectin dampens gut inflammation may yield development of novel dietary therapeutics to treat human IBD.
Group 2 innate lymphoid cells collaborate with dendritic cells to potentiate memory Th2 cell responses.
Authors: Halim Timotheus You Fu , Hwang You Yi , Scanlon Seth , Garbi Natalio , Zaghouani Habib , Fallon Padraic G , McKenzie Andrew 
Published: January 2023

Abstract
Rapid memory CD4+ T helper 2 (Th2) cell activation during allergic inflammation requires their recruitment into the affected tissue. Tissue-resident innate immune cells such as dendritic cells (DC) are essential for orchestrating local memory Th2 cell responses. We now know that tissue-resident group 2 innate lymphoid cells (ILC2) are an important innate source of type-2 cytokines in barrier sites. However, it is currently not known if ILC2 remain functionally important after the generation of adaptive Th2 cells. Here we demonstrate that group 2 innate lymphoid cells (ILC2) play a critical role in memory Th2 cell responses. By targeted ILC2 depletion, using ILC2-specific diphtheria toxin receptor expressing iCOS-T mice, we show a profound impairment in Th2 cell localization to the lungs and skin of sensitized mice after allergen re-challenge. Mechanistically, ILC2-derived IL-13 is critical for eliciting IRF4+CD11b+CD103− DCs to produce the Th2 cell-attracting chemokine CCL17. Consequently, the sentinel function of DCs is contingent on ILC2s for the generation of an efficient memory Th2 cell response. These results elucidate a key new innate mechanism in the regulation of the adaptive memory immune response to allergens.
R970, A Selective Activator of Nrf2, is Efficacious in a Murine Model of Multiple Sclerosis
Authors: Owyang Alexander , Masuda Esteban S , Payan Donald G , Park Gary , Lau David , Torneros Allan , Pablo Florentino San , Bhamidipati Somasekhar , Singh Rajinder , Duncton Matthew A. J. 
Published: January 2023

Abstract
The transcription factor Nrf2 (nuclear factor erythroid-derived-2-like 2) is a key mediator of the anti-oxidant response. Nrf2 can be activated by alkylating its chaperone, Keap-1, resulting in a retardation of Nrf2 degradation, and increased Nrf2 in the cytoplasm. Upon translocation to the nucleus, Nrf2 binds an Antioxidant Response Element (ARE), which leads to the transcription of antioxidant gene products, many of which may be cytoprotective. Activation of the Nrf2 pathway may be useful against a wide-range of disorders, such as multiple sclerosis, psoriasis, and Huntington’s Disease, among others. For example, monomethylfumarate (MMF), the active component of the multiple sclerosis drug, dimethylfumarate (DMF), has been shown to activate the Nrf2-pathway at therapeutic concentrations. However, MMF also serves as an agonist of the niacin receptor, which is likely responsible for the flushing side-effect seen in patients taking DMF.
We have discovered a novel class of molecules that are potent activators of Nrf2 and are inactive at the niacin receptor, yet are efficacious in vivo in a model of multiple sclerosis. Lead candidate R970 is an orally-bioavailable small molecule activator of Nrf2 (EC50 = 1 uM; MMF EC50 = 127 uM), which is inactive at the niacin receptor (0% activity at 500 uM; MMF EC50 ca. 1 uM). Additionally, R970 is selective against a range of kinase, G-protein-coupled receptor, ion-channel, and transporter targets. When dosed orally in a murine model of multiple sclerosis, R970 delayed the onset and also suppressed clinical disease. Further exploration with R970 and other selective activators of Nrf2 is ongoing and may yield a next-generation Nrf2-therapeutic, with an improved side-effect profile.