bluuebunny/crossref_metadata_2025_split huggingface dataset:
MHC II binds to multiple sites on H1N1 hemagglutinin protein
Authors: Becker Tynan A , Ferrante Andrea 
Published: January 2023

Abstract
The exact mechanisms of antigen processing within an antigen presenting cell (APC) are not well defined. The canonical pathway describes degradation of the antigenic proteins, competition between peptides for binding to MHC II, followed by presentation to T cells. Alternately, an entire protein might bind to MHC II first and be trimmed through the action of enzymes. Here we determined the binding affinity of HA to DR1, a human MHC II allele, in the presence and absence of the peptide-editing molecule DM and whether multiple DR1 can bind to a single HA. Binding affinities were determined by competitive binding assays with or without DM. Both native and denatured HA bind to DR1 with comparable affinities in the hundreds of nanomolar range. DM appears to decrease binding strength of HA irrespective of its state. Multiple binding events on individual HA were shown over time on blue native-PAGE gels. Bands of increasing molecular weight appear over a 24-hour time course in the blue native gels while amounts of HA and DR1 decrease over time. Taken together, these results support the hypothesis of an alternate pathway of antigen processing whereby the protein binds first to potentially multiple MHC II molecules and is then trimmed by enzymatic activity. Such MHC-mediated shielding mechanism may increase presentation of peptides by APCs that would be otherwise lost to cleavage.
Three unique interstitial macrophages in the murine lung at steady state
Authors: Gibbings Sophie L. , Thomas Stacey M. , Frasch Courtney S. , Atif Shaikh M. , McCubbrey Alexandra L. , Desch A. Nicole , Danhorn Thomas , Leach Sonia M , Bratton Donna L. , Henson Peter M. , Janssen William J. , Jakubzick Claudia V. 
Published: January 2023

Abstract

Rationale
The current paradigm in macrophage biology is that some tissues mainly contain macrophages from embryonic origin such as microglia in the brain, while other tissues contain postnatal-derived macrophages, such as the gut. However, in the lung and in other organs such as the skin, there are both embryonic and postnatal-derived macrophages.

Objectives
In this study, we demonstrate in the steady-state lung that the mononuclear phagocyte system is comprised of three newly identified interstitial macrophages (IMs), alveolar macrophages (AMs), dendritic cells and few extravascular monocytes.

Methods
We focused on similarities and differences between the three IM subtypes, specifically, their phenotype, location, transcriptional signature, phagocytic capacity, turnover and lack of survival dependency on CX3CR1.

Measurements and Main Results
Pulmonary IMs were located in the bronchial interstitium but not the alveolar interstitium. At the transcriptional level, all three IMs displayed a macrophage signature. All IMs expressed MerTK+CD64+ CD11b+ CX CR1+ and were furthermore distinguished by differences in cell surface protein expression of CD206, Lyve-1, CD11c, CCR2 and MHCII, along with the absence of Ly6C, Ly6G, and Siglec F. Ex vivo analysis revealed that all three IMs were highly phagocytic compared to AMs. Finally, similar phenotypic populations of IMs were present in other non-lymphoid organs, suggesting that these IMs may not be unique to the lung.

Conclusions
These findings promote future research to track four distinct pulmonary macrophages and decipher the division of labor that exists between them.
IgA You Assay? The Correlation between Sleep and Stress
Authors: Redmond Sarah , Biggs Erick , Blevins Kasey , Brimer Kelsey , Brown Cameron , Bryan Sandra , Burger Haley , George Anna , Hunt Mckenzie , Jannise Caitlin , Kesterson Melissa , Kwan Anthony , Marshall Jacob , Miller Kenzie , Mohamed Attia , Rajashekara Arpitha Mysore , Pagan Rachael , Peters Mary , Saenz Allison , Steeves Gregory , Stowers Samuel , Welch Nate , Williams Alexis , Williams Devonn , Wingfield Kyle , Zimmermann Krista 
Published: January 2023

Abstract
The most well known fact about sleep is that humans need it - while we are asleep our metabolic processes slow down and during long periods of sleep our bodies repair the damage that the stress our bodies have undergone throughout the day. Throughout the day our bodies are bombarded by signals from the environment, and undergoes biological changes in response to external and internal stimuli. Sleep is a period of time to restore the body to optimum condition to continue the process all over again the next day. The human body regulates stress by producing glucocorticoid steroid hormones, which also function as immune response suppressants. During sleep cortisol levels are decreased as they inhibit the body’s period of restoration. The production of immunoglobulin A, an antibody associated with mucosal membranes, is inhibited by glucocorticoids, and thus shows a relationship with sleep and other factors associated with stress. This experiment focused on correlations between sleep and stress found on the campus of Radford University. Our groups recorded the amount of sleep participants acquired the previous night and how long they had been awake, and correlated these with the concentration of salivary IgA. According to our initial data collection there was no significant correlation between the amount of sleep (p=0.305) or hours awake (0.670) to IgA levels. Additional sampling later in the semester will be used to supplement this data set and mapped using geospatial coordinates.
Regulation of Immunomodulatory Cytokine Secretion by IFNb-1a is Mediated through Up-regulation of IRF7-SOCS1 Signaling in Monocytes from Patients with Relapsing-Remitting Multiple Sclerosis
Authors: Zhang Xin , Tao Yazhong , Markovic-Plese Silva 
Published: January 2023

Abstract

Objective
To explore the mechanism by which IFNb-1a modulates cytokine production in monocytes from patients with relapsing-remitting multiple sclerosis (RRMS).

Methods
91 RRMS patients and 77 control subjects were enrolled in the study. Magnetic resonance imaging (MRI) scans were used to detect the brain T2 and T1 lesion volume. Serum, cerebrospinal fluid (CSF) and peripheral blood CD14+ monocytes were collected for flow cytometry, RT-PCR, Western blotting and ELISA.

Results
As compared to the control subjects, IL-23 was increased in serum and CSF, while IL-27 was decreased in CSF of the RRMS patients. Serum IL-23 levels were positively correlated with brain MRI T2 and T1 lesion volumes in RRMS patients. CD14+ monocytes from RRMS patients showed decreased percentage of IL-27, IL-10 and IL-4, and increased percentage of IL-23; secreted lower levels of IL-27, IL-12p70 and IL-4, and higher levels of IL-23; and exhibited decreased gene expression of IFNb-1, IFNAR1, IFNAR2, SOCS1, TLR7 and MyD88. IFNb-1a in vitro treatment of monocytes from RRMS patients induced IL-27 and inhibited IL-23 production, increased gene expression of IRF7, MyD88 and SOCS1, and induced protein expression of IFNAR1, pSTAT1, IRF7, and SOCS1. STAT1 inhibitor diminished IFNb-1a-mediated STAT1 phosphorylation and up-regulation of IRF7 and SOCS1, while siRNA IRF7 abolished the IFNb-1a-mediated induction of SOCS1 in monocytes. Both STAT1 inhibitor and siRNA IRF7 impaired IFNb-1a-mediated regulation of IL-27 and IL-23.

Conclusion
Our study demonstrated that IRF7 is critical for the IFNb-mediated upregulation of SOCS1, which mediates IFNb-1a-induced up-regulation of IL-27 and down-regulation of IL-23 cytokine production in monocytes from RRMS patients.
Immune cross-reactivity between Dengue and Zika viruses in two pediatric studies in Nicaragua
Authors: Cruz Magelda Montoya , Puerta-Guardo Henry Nelson , Schildhauer Sam , Katzeltnick Leah , Balmaseda Angel Lazaro , Harris Eva 
Published: January 2023

Abstract
The 4 dengue virus (DENV) serotypes and Zika virus (ZIKV) are antigenically related mosquito-borne flaviviruses that cause human diseases of major medical and public health importance worldwide. The cross-reactivity between DENV and ZIKV has raised questions about cross-neutralization and concerns of cross-enhancement, yet few data exist characterizing the long-term antibody response. Here, we studied the extent of immunological cross-reactivity between DENV and ZIKV using samples from two long-term studies in Nicaragua: a hospital-based study with a longitudinal arm extending for 18 months and a 13-year ongoing community-based cohort study with annual healthy blood samples. We selected confirmed dengue cases, stratified by serotype (DENV1, 2, 3) and immune status (primary, secondary) (n=5/group), and analyzed plasma samples collected at acute, convalescent, 3-, 6-, 12- and 18-month time-points, as well as 1–3 years post-infection, using a Vero cell-based focus reduction neutralization assay. We found that primary DENV infections display lower levels of cross-neutralizing antibodies to ZIKV than secondary DENV infections, but that both maintain cross-reactivity over time. We noted differences by serotype, with less cross-neutralization in DENV1-immune plasma. However, when we compared these data with neutralization titers against DENV1-4, we found neutralizing antibody titers to ZIKV to be ~10-fold lower than to the homologous DENV. We are also testing Zika-positive samples with and without prior DENV exposure and samples negative for prior ZIKV or DENV infections. These findings improve our understanding of cross-neutralization over time between DENV and ZIKV, with implications for natural immunity and vaccines.
Effects of cell population rate of rat bone marrow derived mast cell on protein constituents analyzed by 2 dimensional electrophoresis
Authors: Cho Sung-Weon , Oh Haejin , Shin Kyung Sook 
Published: January 2023

Abstract
Mast cells are the immune cells for defense from infecting organism including helminthes. Rat bone marrow dervied mast cells (rBMMC) are the proliferating cells that are induced from rat hematopoietic stem cells (rHSC) cultured in the presence of both IL-3 and stem cell factor (SCF). rBMMC are suggested as the useful cells for the treatment of clonorchiaiss with the results of rBMMC effects on rat clonorchiasis in vivo. The effects of cell population rate on rHSC for rBMMC preparation were investigated by analysing protein constituents using two dimensional electrophoresis (2-DE) with silver staining visualization. The cells in 4 cell population rate conditions were analyzed with ordinary cell population rate (1.1 × 105/ml, O-CPR), high cell population rate (2.2 × 105/ml, H-CPR), very high cell population rate (5.5 × 105/ml, VH-CPR), and very high heavy cell population rate (11.1 × 105/ml, VHH-CPR). The spot ditribution were described as the patterns that have two main group regions with spot dozens, high molecular weight and low pH (HL), and low molecular weight and high pH (LH). The patterns were comparable among the four conditions of cell population rate. However, in comparison between individual spot, the density of each spot was observed in remarkable difference. The results were suggested that the treatment effects of rBMMC on rat clonorchiasis would be dependent on culture condition of cell population rate.
Lymphocyte aggregates accumulate in the skin of melanoma associated autoimmune vitiligo
Authors: Vella Jennifer L , Huang Yina H 
Published: January 2023

Abstract
While melanoma is not the most common form of skin cancer, it is responsible for the majority of skin cancer related deaths. A small percentage of people that develop melanoma simultaneously develop autoimmune vitiligo, resulting in a favorable prognosis for these individuals. Melanoma associated vitiligo is a CD8+ T cell mediated disease that results in the death of healthy melanocytes. The destruction of melanocytes generates the self antigen(s) required for memory CD8 T cells that persist long term and provide protection from melanoma. Although the link between autoimmune vitiligo and anti-melanoma immunity has long been established and well studied, the mechanisms driving vitiligo and tumor protection still remain unknown. Using a mouse model of melanoma-associated vitiligo we are investigating this intimate relationship. Using multiparameter immunohistochemistry, we have identified large aggregates of lymphocytes clustered throughout the initial site of depigmentation. These lymphoid aggregates are comprised of a number of different lymphocyte subsets including CD4 and CD8 T cells, dendritic cells and macrophages. However, they are distinct in composition, duration and location from tertiary lymphoid organs and other lymphocyte clusters identified in the setting of HSV infection. Only vitiligo-affected mice develop these aggregates suggesting they may be important in the vitiligo development or dissemination and/or tumor protection. Understanding the role these lymphocyte aggregates play in vitiligo will give us a better understanding on the mechanisms required for both autoimmune vitiligo and anti-melanoma immunity.
Factors controlling the tolerogenic phenotype of lymphatic endothelial cells.
Authors: McKenna Nicole , Berendam Stella , Rouhani Sherin , Turner Stephen , Koeppal Alex , Cummings Kara , Dekoter Rodney , Engelhard Victor H 
Published: January 2023

Abstract
The prevailing model of peripheral tolerance necessitates tissue-resident dendritic cells migrating to lymph nodes and cross presenting self-antigen to T cells, resulting in their deletion or anergy. Our lab has identified a novel mechanism of peripheral tolerance involving a subset of lymph node stromal cells called lymphatic endothelial cells (LEC). LEC in the lymph node induce peripheral tolerance by presenting epitopes derived from peripheral tissue antigens (PTAs) in conjunction with expression of PD-L1, leading to CD8 T cell deletion. However, PTAs and PD-L1 are not expressed on LEC in the colon or diaphragm. We performed RNAseq analysis on LEC from lymph node and diaphragm to identify differences in expression of transcription factors that might control expression of PD-L1 and PTA. We found that Spi-B is the most differentially expressed transcription factor in the lymph node compared to the diaphragm, with a fold change of over 500. Spi-B has been implicated in the development and function of medullary thymic epithelial cells, a key cell type in central tolerance. Lymph node LEC harvested from Spi-B deficient mice have a significant shift in markers associated with LEC tolerogenicity. Expression levels of PD-L1, ICAM-1, MAdCAM-1, and LTbR delineate different lymph node LEC subpopulations that vary in their ability to express PTAs and tolerize CD8 T cells. LEC from Spi-B deficient mice have decreased MAdCAM-1 expression and increased LTbR and ICAM-1 expression suggesting a population shift of non-tolerogenic lymph node LEC to tolerogenic lymph node LEC. This data suggests Spi-B may be involved in a negative feedback mechanism to limit the number of tolerogenic LEC during development.
TET2 deficiency promotes CD8+ T cell memory differentiation
Authors: Jordan Martha S , Carty Shannon A , Gohil Mercy , Cotton Renee , Johnson Matthew , Stelekati Erietta , Wells Andrew D , Wherry E. John , Koretzky Gary A 
Published: January 2023

Abstract
DNA methylation contributes to T cell differentiation. The ten-eleven translocation (TET) family of methylcytosine dioxygenases mediates active DNA demethylation. Here we demonstrate that TET2 regulates CD8+ T cell differentiation in vivo following acute viral infection. At steady-state, mice with a T-cell specific deletion of TET2 have intact thymic and peripheral T cell populations. However, following infection, TET2 loss promotes early acquisition of a memory CD8+ T cell fate in a cell-intrinsic manner without disrupting antigen-driven T cell expansion or effector function. Upon re-challenge, TET2-deficient memory CD8+ T cells exhibit superior pathogen control. Genome-wide methylation analysis of TET2-deficient versus WT CD8+ T cells identified multiple differentially methylated regions (DMRs). Analyses of DMRs suggest TET2 regulates T cell differentiation at regulatory genes, opposed to individual loci of differentially expressed memory markers. One hypermethyated region was the PRDM1 loci (encoding Blimp-1). This finding was associated with an increased Bcl6 to Blimp-1 ratio in vitro, a pattern predicted to favor memory cell fate. Taken together, our data indicate that TET2 is an important regulator of CD8+ T cell fate decisions.
Recombinantly engineered antibodies for reproducible and background free flow cytometry analysis
Authors: Fleischer Johannes , Singh Kalpana , Nölle Volker , Hellmer Jens , Schmitz Jürgen 
Published: January 2023

Abstract
Antibodies are key reagents for numerous cell analysis applications. Therefore, the contribution of antibodies in experimental irreproducibility is being critically looked at. The majority of antibodies used in basic research are still derived from hybridoma technology established in 1975. As highlighted during recent debates, hybridoma-based antibodies are prone to quality issues, i.e., lot-to-lot variability and lack of specificity. In addition, the technology itself doesn’t allow any improvements in the quality and the properties of the antibodies.
Recombinantly generated antibodies possess highly defined characteristics and are produced under standardized culture conditions leading to products that are reproducible in nature. This saves users the time associated with standardizing analysis and decreases the financial burden associated with working with inconsistent reagents. Recombinant technology also opens up myriads of possibilities to improve antibody properties. REAfinity™ Antibodies provided by Miltenyi Biotec are recombinantly engineered to lack background binding and share a single isotype. This solves the two common problems associated with flow cytometry: non-specific signals and complicated experiment planning with multiple antibody isotypes.
Fast isolation of mouse XCR-1+ dendritic cells
Authors: Huang Yi-Ju , Morrissey-Wettey Frank , Andreoni Cristina Conforti , Dzionek Andrzej 
Published: January 2023

Abstract
Cross-presenting CD8-+ conventional dendritic cells (cDCs) are important for the eradication of cancers and viral infections due to their ability to induce cytotoxic T lymphocyte (CTL) responses. Cross presenting DCs are a very rare subset and in the past, studies of these cells have been limited by their scarcity of specific cell surface markers. Therefore, methods for the detection and isolation of these cells were commonly based on a multitude of immunophenotypic criteria, such as the expression of CD11c and CD8- and the absence of CD3, CD4, SIRP-- and CD11b. Recently, it was demonstrated that crosspresenting cDCs in lymphoid and non-lymphoid tissues specifically express XCR1, which correlates with the ability to take up and cross-present exogenous antigens. Combining our recombinant REAfinity™ Anti-XCR1 mouse mAb with MACS® Technology based on UltraPure MicroBeads, we developed a new method for the fast and easy isolation of cross-presenting DCs. Using this method XCR1+ DCs can be routinely enriched with high recovery and purity without the need for time-consuming laborious flow sorting. This will facilitate the study of cross-presenting DC subset, which will ultimately help to develop new therapeutic strategies employing DCs in the future.
Regulatory T cells exert differential functions during the early and late stages of the immune response to respiratory virus infection
Authors: Rogers Meredith C , Lamens Kristina D , Shafagati Nazly , Williams John V 
Published: January 2023

Abstract
Human metapneumovirus (HMPV) is the second leading cause of viral lower respiratory illness in children, and can be severe in premature infants, immunocompromised persons, and the elderly. Clearance of HMPV is predominantly mediated by cytotoxic CD8+ T lymphocytes (CTLs). HMPV and other respiratory viruses induce CTL impairment, where virus-specific CTLs are unable to function for an optimal antiviral immune response. We recently demonstrated that the inhibitory receptor Programmed Cell Death-1 (PD-1) mediates early functional impairment of the CTL response to HMPV, influenza, and other respiratory viruses early in infection. However, CTLs became impaired by day 10 post-infection in PD-1-deficient mice, indicating that other immunoregulatory cells or molecules may be acting during HMPV infection. CD4+ regulatory T cells (Tregs) are suppressive in cancer and some infections. We found that Tregs were increased in both number and percentage and activated during HMPV infection. Treg depletion throughout infection significantly increased CTL functionality and reduced peak virus titer. Early depletion of Tregs led to reduced recruitment of HMPV-specific CTLs to the lung, while depletion late after infection maintained the proportion of HMPV-specific CTLs and accelerated virus clearance. These data suggest that Tregs may perform distinct functions at different stages of lung infection. Tregs may be beneficial during the priming stage of the immune response, but are overall detrimental in the setting of HMPV infection and could be a target for therapeutics.
Noncytopathic bovine viral diarrhea virus 2 impairs virus control in a mouse model
Authors: Kyoung-Seong Choi , Seong Giyong , Shin Seung-Uk 
Published: January 2023

Abstract

Objective
Bovine viral diarrhea virus (BVDV) is an economically important viral pathogen. BVDV is classified into two distinct species: BVDV1 and BVDV2. Both these species consist of two biotypes: cytopathic (cp) and non-cytopathic (ncp), differing in their ability to induce cytopathogenic effects in cultured cells. In this study, we investigated the immunological differences between ncp BVDV1 and ncp BVDV2 infections.

Materials and methods
Specific pathogen-free BALB/c mice (6–8 wk old) were used. The challenge was performed by IP injection of 5 ′ 105 TCID50 of ncp BVDV1 or ncp BVDV2. Each BVDV strains- and mock-inoculated mice were sacrificed on days 4, 7, 10, and 14 post-inoculation (pi). Each tissues and blood were harvested. BVDV antigen detection, immunohistochemical staining was performed on mouse tissues. Spleens were used for flow cytometry. Cytokines and chemokines were detected separately by using a mouse CBA inflammation kit.

Results
Viral antigens were detected in the spleens of all infected mice from days 4 through 14 and also found in the mesenteric lymph nodes, GALT, heart, kidney, intestine, and BALT of some infected mice. In ncp BVDV2-infected mice, flow cytometric analysis revealed markedly fewer CD4+ and CD8+ T lymphocytes and lower expression of CD80/CD86 and I-A/I-E than those in ncp BVDV1-infected mice. IL-6 and MCP-1 was higher in the plasma of ncp BVDV2- than that in the plasma of ncp BVDV1-infected mice.

Discussion
Our results demonstrate that ncp BVDV1 and ncp BVDV2 interact differently with the host innate immune response in vivo. These findings highlight an important distinction between ncp BVDV1 and ncp BVDV2, and suggest that ncp BVDV2 impairs host’s virus control and enhances virus dissemination.