bluuebunny/crossref_metadata_2025_split huggingface dataset:
Host responses to feline coronavirus are significantly different in primary macrophages compared to CRFK cells.
Authors: Drechsler Yvonne , Vasconcelos Elton J.R. , Griggs Lisa M , Diniz Pedro P.P.V. 
Published: February 2023

Abstract
Feline coronavirus (FCoV) is a highly contagious virus that exists as two pathotypes, with feline infectious peritonitis (FIP) caused by the pathogenic FIPV. The pathogenesis of FIPV remains poorly understood, and several different theories are still being discussed. A strong argument can be made for a role of the immune status and genetics of affected cats in pathogenesis. Most studies have focused on viral entry or differential replication instead of host responses. Considering the importance of genetics and host immune responses in viral infections, transcriptome studies to elucidate host pathogen interactions in primary macrophages and Crandell-Rees Feline Kidney cells (CRFK) were performed by next-generation sequencing of mRNA. CRFK and macrophages from healthy male cats infected with FIPV 79-1146 ex vivo displayed differential gene expression in response. While CRFK gene expression was enriched for many classical virally induced genes and pathway networks, gene expression in macrophages was quite different. Interestingly, some of the commonly downregulated genes in macrophages involved innate anti-viral factors, while upregulated genes fell within unexpected pathways, such as autophagy, cellular senescence and other cellular processes not directly linked to infection. Our results highlight how individual host responses play a strong role when exposed to the virus, consistent with the fact that cats developing feline infectious peritonitis are very young or old, immune suppressed or of a particular genetic background. This study will give more insight into interactions of FCoV with feline macrophages and contrast it with the responses of a cell line that readily replicates the virus.
Butyrate alters lipopolysaccharide-induced inflammatory response by porcine monocytes
Authors: Becker Sage R , Byrne Kristen , Loving Crystal L 
Published: February 2023

Abstract
Continuous, low-level inflammation can have a negative impact on intestinal health. Butyrate is a short-chain fatty acid produced in the lower intestinal tract by microbial fermentation of dietary fibers and modulates immune cell responses through various mechanisms. Blood monocytes migrate into the intestine and respond to signals, including potential modulation by butyrate or in response to microbial components, such as lipopolysaccharide (LPS). To investigate the impact of butyrate on inflammatory response to LPS, porcine monocytes were either cultured with a combination of LPS and varying butyrate concentrations or pre-treated with butyrate before LPS exposure. Independent of butyrate, LPS stimulation of monocytes induced IL-1β and TNF production. Monocytes cultured just three hours (h) prior to LPS stimulation had reduced overall cytokine production, suggesting rapid phenotypic changes in monocytes. Butyrate had varying effects on the amount of cytokine produced in response to LPS. Specifically, low butyrate concentrations (0.25 mM) limited IL-1β production, but did not impact TNF production. Higher butyrate concentrations (&gt; 4 mM) limited TNF production to LPS stimulation. Pre-treatment of monocytes with butyrate for 3 h prior to LPS stimulation altered IL-1β production. Pre-treatment with 0.25 mM butyrate did not limit IL-1β production, but concentrations &gt; 4 mM did. In conclusion, reduction of LPS-induced cytokine production by porcine monocytes was dependent on butyrate concentration and exposure time relative to LPS exposure. Further work is ongoing to understand the mechanism of butyrate modulation of pig monocytes and inflammatory response to LPS for potential application in vivo.
Purification, biotinylation, and testing of a monoclonal antibody to identify B cells in Trachemys scripta, the red-eared slider turtle
Authors: Paton Hanna D , Mool Allison , Green Whitney , Bowden Rachel , Vogel Laura A 
Published: February 2023

Abstract
There is a shortage of research in reptile immunity which is further hampered by lack of reptile-specific reagents. Evidence suggests there are important differences between reptile and mammalian immune strategies and our laboratory is interested in reptile B cell development and function. Our undergraduate research project involved the preparation of a previously developed monoclonal antibody (HL673) that recognizes turtle light chain protein. To begin, culture supernatant from the HL673 mAb murine cell line was received and was applied to a protein A affinity column. Unbound proteins were then washed away, and the bound proteins were removed from the column using low pH glycine-HCl buffer. The purified antibody proteins were collected in fractions, OD at 280nm measured, then positive fractions were pooled and dialyzed. The concentration of the purified antibodies was determined, and reactivity tested using an ELISA plate coated with dilute turtle serum. Dilutions of the purified HL673 were detected by anti-mouse IgG-horseradish peroxidase (HRP). Furthermore, some of the antibody preparation was conjugated to biotin. After dialysis, the HL673-biotin was tested by ELISA with dilute turtle serum and detected by streptavidin-HRP. The newly biotinylated antibody was incubated with blood and spleen samples from both adult and hatchling red-eared slider turtles. Bound antibodies were detected using streptavidin-fluorochrome and B cell populations identified using flow cytometry. Our results showed successful detection of turtle B cells using the labeled mAb in both hatchling and adult turtle cell samples. Future studies will use this reagent to investigate the distribution and function of B cells in reptile gut immunity.
Characterization of circulating porcine immune cells using single-cell RNA-sequencing and comparison to human datasets
Authors: Loving Crystal L , Wiarda Jayne E , Sivasankaran Sathesh K , Daharsh Lance , Liu Haibo , Byrne Kristen A , Tuggle Christopher K 
Published: February 2023

Abstract
Pigs are part of global food security and serve as a valuable human biomedical model. Immunoreagent unavailability limits resolution of pig leukocyte populations by protein markers; thus, single-cell RNA-sequencing (scRNA) was used to characterize pig peripheral blood mononuclear cell (PBMC) populations and infer function based on transcriptional profiles and comparison to human datasets. Across seven PBMC samples partitioned and sequenced, 28,810 cells distributed across 36 clusters were classified into 13 general cell types including plasmacytoid dendritic cells (DC), conventional DCs, monocytes, more than ten B cell clusters including plasmablasts, conventional CD4 and CD8 αβ T cells, NK cells, and four clusters of γδ T cells. Signature gene sets for a publicly available human bulk RNA-seq dataset were assessed for relative enrichment in genes expressed in pig cells and substantial overlap in gene expression between specific pig and human PBMC populations was detected. Integration of pig scRNA with a public human scRNA dataset provided further validation for similarity between human and pig. Of four pig γδ T cell clusters, two had high prediction and mapping scores with human γδ T cells. The other two pig γδ T cell clusters had gene expression profiles predictive of human γδ T cells, but also human CD4 T central memory (Tcm) and innate lymphoid cells, suggesting innate and adaptive function of some pig γδ T cells. Pigs have a population of circulating double-positive (DP) CD4+CD8αα+ αβ T cells, and putative DP clusters had high prediction scores to human CD4 Tcm cells, supporting their classification in literature as memory cells. Overall, the data provided the first single-cell atlas for porcine PBMCs and comparison to human datasets.
Comparative annotation of porcine bone marrow cell types using scRNAseq
Authors: Daharsh Lance N , Sivasankaran Sathesh K , Byrne Kristen A , Herrera-Uribe Juber , Loving Crystal L , Tuggle Christopher K 
Published: February 2023

Abstract
Pigs are important as a biomedical model and for worldwide meat production. Therefore, a better understanding of porcine hematopoiesis and immune system development could have a wide impact on human disease research and food production. The bone marrow represents a unique environment that is the major site of differentiation of stem cells and progenitors into mature blood cells. We performed scRNA-seq on bone marrow from healthy adult pigs and sequenced a total of 3,576 cells. After QC, 2,707 cells and 16,432 genes were used for downstream analysis. The porcine bone marrow cells were grouped into 15 distinct clusters and these relationships were mapped using non-linear dimensional reduction. To find markers that defined each cluster, we found a total of 3,335 differentially expressed genes using the non-parameteric Wilcoxon rank sum test. Further, pairwise differential expression testing and random forest models were used to evaluate the similarity between clusters and further define the unique features of each cluster. Using these defined markers, we were able to annotate the cell types for each cluster. The clusters represented a diverse set of cell types including myeloid and lymphoid cells, myeloid and lymphoid cell progenitors, and platelet and red blood cell progenitors. We validated these annotations using publicly available datasets including the CITE-seq database of human bone marrow mononuclear cells (Stuart et al., 2019). We also compared the expression profiles between similarly annotated cell types between human and pig. Our novel annotation of porcine bone marrow cells will be a resource for the study of porcine hematopoiesis and immune system development and help inform human translational biomedical research.
Genetic Variation in the RSV fusion protein controls strain-dependent inflammasome activation and the development of a pathogenic Th17 response
Authors: Waldstein Kody , Weiss Kayla , Hartwig Stacey , Varga Steven M 
Published: February 2023

Abstract
Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in young children worldwide. RSV-induced disease ranges from mild to severe, with severe disease correlating with increased levels of pro-inflammatory cytokines, including the Th17-associated cytokine, IL-17. To understand the viral factors that influence the induction of a pathogenic Th17 response, we compared the inflammatory responses elicited by different RSV strains. In contrast to the commonly used RSV A2 strain, RSV 2–20 infection resulted in increased protein levels of IL-6 and IL-1β, which were required to induce a pathogenic Th17 response. RSV 2–20 infection increased mucus production and airway hyperreactivity indicating strain-specific disease induction. RSV 2–20 and A2 induced similar expression of caspase-1, however, 2–20 infection resulted in increased levels of pro-IL-1β suggesting differential activation of inflammasome signal 1. Increased production of IL-1β following RSV 2–20 infection was dependent on TLR4 expression and signaling, a canonical inflammasome signal 1 activator. A recombinant A2 virus expressing the 2–20 fusion (F) protein induced IL-1β to similar levels as wild-type 2–20 indicating the 2–20 F protein is sufficient to increase pro-inflammatory cytokine production. Reversion of three-point mutations in a region likely to interact with host cells in the RSV A2/2–20 F recombinant virus to the A2 sequence significantly reduced IL-6 and IL-1β protein production. Our results demonstrate that genetic variation in the RSV F protein plays a crucial role in the induction of pro-inflammatory cytokines and modulating disease severity in the animal model and may contribute to differential RSV pathogenesis.
Molecular insights into host-virus interaction of human and rhesus cytomegalovirus UL144 mediated by immune checkpoint BTLA and CD160
Authors: Nemcovicova Ivana , Lenhartová Simona , Škrabana Rostislav , Benko Mário , Nemčovič Marek 
Published: February 2023

Abstract
Cell-cell communication is a crucial mode for multi-cellular organisms to accomplish complex biological functions and various signaling molecules have evolved to meet ever complicated demands to communicate extracellular stimuli with intracellular components. Thus, signaling molecules, whose expression is responsive to local environments; balance the communication between host innate cells and viral pathogens. This intimate interaction between virus and the host immune system covers a wide range of contacts. HVEM, a member of the TNF receptor superfamily, is commonly recognized as a co-stimulatory receptor for LIGHT and LTα. Interestingly, HVEM was also found to interact with BTLA and CD160, and thus deliver a suppressive signal to T cells, therefore the complex molecular network between HVEM and its cellular partners makes bidirectional signaling feasible. Here, we study the viral glycoprotein UL144 of human and rhesus cytomegalovirus that is orthologous to cellular HVEM, thus resembling some of its promiscuity on the cell surface. This molecular network is quite well described, however, the engagement of CD160 by UL144 has not yet been satisfactorily studied. We measured both human and rhesus CMV UL144 binding to BTLA or CD160 using purified HVEM or UL144 proteins and their mutants. We confirmed that human CMV UL144 only bound BTLA and not CD160, whereas HVEM bound both BTLA and CD160. Surprisingly, we have observed binding between UL144-glycan free mutant not only to BTLA but also CD160. Moreover, considering that the ectodomain of UL144 is highly polymorphic across primate CMV we examined both human and rhesus CMV UL144 selectivity for its cellular receptors. We found rhesus CMV UL144 bound CD160 with lower KD when compared to BTLA.
NK cells exhibit memory and stem cell like features after Zika virus infection
Authors: Kujur Weshely , Gomez Oscar M , Adduri Raju S.R. , Vankayalapati Ramakrishna , Konduru Nagarjun V , Mulik Sachin 
Published: February 2023

Abstract
Natural Killer (NK) cells are the components of innate immune system known for their role in virus infection and tumor immunity. Their importance is appreciated from the case studies where lack of NK cells leads to life threatening herpes virus infection and increased host susceptibility to certain cancers. Recent development in the NK field have opened a new frontier bringing to light that innate immune cells can demonstrate memory features too. In line with the above-mentioned development, we report NK memory cell generation post Zika virus infection in mice. Our detailed transcriptomics, epigenetic and functional analysis revealed that CD27+ memory like NK cell that developed post Zika virus infection exhibited stem cell like properties and shared gene signatures with memory CD8 T cells, stem cells and stem like T cells from chronic infection and cancer. We termed these cells as “NK memory stem cells” which also possessed greater antiviral function when adoptively transferred into Zika infected mice. We next performed single cell RNA-seq on NK memory stem cells and identified multiple subpopulations which differed in gene expression profiles. Our work revealed NK cells with memory like and stemness features that are helpful in fighting viral infection. We also detected subpopulations in NK memory stem cells and efforts are ongoing to evaluate the role of these NK subpopulations in antiviral immunity.
Expression of Nutrient Transporters on NK Cells during Murine Cytomegalovirus Infection is MyD88-Dependent
Authors: Khan Abrar Ul Haq , Almutairi Saeedah Musaed , Ali Alaa Kassim , Salcedo Rosalba , Stewart C. Andrew , Lee Seung-Hwan 
Published: February 2023

Abstract
Natural killer (NK) cells are the predominant innate lymphocytes that provide the first line of defence without prior sensitization. In the inflammatory milieu, NK cells modify their metabolism to cope with the high energy demand required to support their proliferation, activation, and functional plasticity. This metabolic reprogramming is usually accompanied by the upregulated expression of nutrient transporters on the cell surface, leading to increased nutrient uptake needed for robust proliferation. The members of interleukin-1 family of inflammatory cytokines are critical in activating NK cells during infection; however, their function in NK cell metabolism is not fully elucidated. Previously, IL-18 has been shown to upregulate the expression of solute carrier transmembrane proteins and thereby induces a robust metabolic boost in NK cells. However, we demonstrated that IL-18 signaling is dispensable during viral infection in vivo whereas the expression of nutrient transporters on NK cells is primarily regulated by MyD88-pathway since NK cells from Myd88−/− mice displayed significantly reduced expression of nutrient receptors. Moreover, we identified that IL-33, another cytokine employing MyD88 signaling, can induce the expression of nutrient receptor but requires a sequential exposure to IL-12. Furthermore, signaling through NK cells activating receptor, Ly49H, can also promote the expression of nutrient transporters. In summary, our findings revealed multiple pathways that induce the expression of nutrient transporters on NK cells while highlighting the imperative role of MyD88 in NK cell metabolism during infection.
Murine Roseolovirus Induces Autoimmune Gastritis and Disrupts Thymic Antigen Presenting Cells.
Authors: Bigley Tarin , Yang Li-ping , Kang Liang-I , Saenz Jose B , Mills Jason C , Yokoyama Wayne M 
Published: February 2023

Abstract
Murine roseolovirus (MRV) is a beta-herpesvirus that is a natural murine pathogen and is genetically highly related to the human roseoloviruses, HHV6 and HHV7. The human roseoloviruses have been associated with autoimmune disease but demonstrating causality has been difficult due to the ubiquitous and chronic nature of roseolovirus infections. Neonatal MRV infection resulted in transient thymic and peripheral CD4+ T cell depletion, including CD4+Foxp3+ regulatory T cells (Tregs). We found that neonatal MRV infection induced autoimmune gastritis in adult mice. Our studies showed that autoimmune gastritis occurs in the absence of detectable virus in gastric mucosa. Ganciclovir (GCV) inhibited MRV replication as well as MRV-mediated CD4+ T cell depletion and development of autoimmune gastritis. This suggests that MRV replication is necessary for altering immunologic tolerance early in life. Interestingly, neonatal MRV infection resulted in the production of a wide array of autoantibodies in adult mice. The inflammatory infiltrate into the gastric mucosa was characterized by an increase in T cells, neutrophils and eosinophils. Furthermore, the CD4+ T cells in the gastric mucosa exhibited Th2 and Th17 differentiation. The development of autoimmune gastritis was CD4+ T cell and IL-17 dependent, while B cells were only necessary early in life. Neonatal MRV infection resulted in a transient decrease in medullary thymic epithelial and thymic dendritic cells numbers, as well as reduced expression of AIRE and tissue restricted self-antigens in the thymus. These findings strongly suggest that infection with a roseolovirus early in life results in disruption of central tolerance and development of autoimmune disease.
Novel Mechanisms of Innate Immune System Regulation Following SARS-CoV-2 Exposure
Authors: Allen Irving C , Ivester Hannah , Morrison Holly , Finkielstein Carla , Auguste Jonathan , Duggal Nisha , Smyth Jamie , Meng Xiang-Jin , Kehn-Hall Kylene , Weger James 
Published: February 2023

Abstract
The SARS-CoV-2 pandemic has wreaked havoc on our public health system and economy. The outcome of SARS-CoV-2 infection is determined by host-virus interactions and anti-viral immune responses. A delicate balance must be struck between mounting a vigorous immune response to eradicate the virus and quelling overactive inflammation to protect the host. Indeed, overzealous inflammation is associated with the “cytokine storm” reported in an alarming number of COVID-19 patients and underlies the Multisystem Inflammatory Syndrome reported in pediatric cases. Initial studies have suggested that SARS-CoV-2 is capable of inhibiting type-I interferon signaling, hijacking cell death processes, and inducing robust pro-inflammatory cytokine production in patients with poor outcomes. Here, we confirm many of these previous findings using whole genome transcriptomics approaches in human patients and complementary mechanistic studies using SARS-CoV-2 infection in K18-hACE2 mice. Using these approaches, we further identify 12 critical cytokines that appear to be associated with the overzealous immune response in COVID-19 patients. Further studies and pathway analysis identified members of the NBD-LRR (NLR) family of pattern recognition receptors that regulate distinct mechanisms underlying overzealous inflammation. Together, these data provide insight into novel mechanisms of immune system regulation that appear responsible for modulating several aspects of SARS-CoV-2 pathobiology.
Platelet-rich neutrophil-platelet micro-emboli contribute to cigarette smoke induced flu severity.
Authors: Kaminski Tomasz W. , Brzoska Tomasz , Li Xiuyang , Vats Ravi , Tutuncouglu Egemen , Robinson Keven , Nyuonya Toru , Sundd Prithu 
Published: February 2023

Abstract
Epidemiological evidence suggests that prior exposure to cigarette smoke (CS) or habitual smoking increases the risk of influenza A virus (IAV)-triggered respiratory failure. Although emerging evidence supports the role of thrombo-inflammation in the development of CS and IAV-triggered lung injury, the innate immune mechanism remains poorly understood. We have developed a two-hit model of CS-induced severe flu in mice. Mice were exposed to four weeks of room air (air) or CS followed by intra-nasal administration of A/PR/8/34 IAV. The body weight was measured every day for two weeks after IAV administration followed by assessment of lung injury at day 7. Lungs were harvested for histological assessment and viral titration by qPCR. Quantitative fluorescence intravital lung microscopy (qFILM) was conducted at 2-, 3- and 4-days post IAV-infection to visualize dynamics of neutrophil and platelet recruitment in the lung of mice IV administered with fluorescent dextran, anti-Ly6G Ab and anti-CD49Abs. Mice exposed to CS+IAV manifested significantly more weight loss, lung injury, lung congestion, hemorrhage and hypoxemia compared to mice administered IAV only. QFILM revealed that severity of lung injury was associated with significantly larger area with impaired blood flow and more vascular leakage secondary to vascular occlusion by platelet-rich neutrophil-platelet aggregates in the lung of CS+IAV than IAV administered mice. These initial results suggest that CS primes innate immune signaling in neutrophils and platelets to promote their recruitment in the lung following flu, leading to severe acute lung injury. Currently, studies are underway to identify innate immune pathways that drive hyper thrombo-inflammatory response.