bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of the B Cell Receptor Repertoire and Discovery of New Immunoglobulin Genes in the Domestic Ferret
Authors: Hebert Luke S , Lavinder Jason J , Soto Gabriel , Ross Ted , Moody Tony A , Ippolito Gregory C , Seeger Allison E 
Published: August 2023

Abstract
Mustela putorius furo uniquely reflects physiological and immunological changes in human aging such as immune imprinting from influenza infection, yet key ferret immunobiology knowledge gaps limit the scope of molecular analyses. First, ferret germline B cell receptor genes require identification. Additionally, the V, D, and J gene repertoire expressed by B cell receptors in antigen-experienced cells needs characterization.
Illumina NGS was used to generate B-cell receptor mRNA data sets. A candidate list of gene segments was assembled including ferret genomic accessions homologous to known immunoglobulin genes and previously-known ferret immunoglobulin genes. NGS reads were queried against the candidate list using IgBLAST. IgBLAST hits were focused into consensus sequences using principal components analysis and K-means clustering. To identify IgG subclasses, putative ferret genome sequences sharing human IgG C genes were used to query Oxford Nanopore data that covered the FR3 through C gene area of transcripts.
We report two new functional IGHV, two IGKV, and one IGLV gene segments in the ferret, with more sequences likely to surface in downstream analyses. We also corroborate most already-proposed functional V, D, and J gene segment sequences. Ferret orthologues to human IGHV subgroups commonly involved in stem-directed, broadly neutralizing antibody responses were identified. For the first time, productive IgG3 was described in the ferret model and distinguished from productive IgG1.
Our report of novel ferret immunoglobulin genes will disinhibit the ferret as a model organism for the study of infectious disease. Specifically, it will inform the immunogenicity of candidate HA antigens in preclinical vaccine studies.
Research reported in this abstract was supported by NIH NIAID contract 75N93019C00050.
Investigating the functional roles of TNFSF13 family members in Cartilaginous Fishes
Authors: Hill Thomas , Redmond Anthony , Dooley Helen 
Published: August 2023

Abstract
The TNFSF13 cytokines BAFF and APRIL along with their cognate receptors BAFFR, TACI, and BCMA play critical parts in the development, function, and maintenance of B cells in mammals. Despite the well-studied roles that BAFF and APRIL play in the immune systems of higher vertebrates, their evolutionary history and functions in non-mammalian organisms are not well understood. Recently, our lab has demonstrated that collectively the TNFSF is evolutionarily ancient, with most of its members having evolved over 450 million years ago in the jawed vertebrate ancestor. Interestingly, we found that despite the evolutionary ancient position of cartilaginous fishes, their repertoire of TNFSF is just as complex as higher vertebrates with evidence of lineage specific TNFSF members that are absent in more evolutionary recent taxa. Specifically, cartilaginous fishes possess two additional TNFSF13 family members, namely BALM (TNFSF13C) and a retrotransposed duplicate of BAFF (iBAFF). Thus, cartilaginous fishes possess four TNFSF13 members whose functional roles remain unexplored. Here we demonstrate the tissue specific expression of BAFF, iBAFF, BALM, and APRIL, as well as their anticipated receptors BAFFR, TACI, and BCMA in the nurse shark. Additionally, we explore receptor-ligand interactions using a yeast surface display assay aiming to understand the role(s) each plays in the development and maintenance of shark B cells. Such information is key to understanding the evolutionary history of this key cytokine family.
The biology and evolution of the unconventional γμ T cell in non-eutherian mammals
Authors: Morrissey Kimberly A , Stammnitz Maximilian , Miller Robert D 
Published: August 2023

Abstract
There are three lineages of T cells in mammals, αβ, γδ and γμ T cells, classified by the composition of their T cell receptors (TCR). γμ T cells are present only in marsupials and monotremes. The γμTCR has a number of unique features, most distinctly is the three extracellular-domain TCRμ chain. In this study we investigate the evolution of the TCRμ genes and characteristics of γμ T cells in different species. γμ T cells appear to have tissue specific residency. In adult opossums, Monodelphis domestica, they are restricted to the spleen, liver, throughout the gut, and mesenteric lymph nodes. By comparison, in the Tasmanian devil, Sarcophilus harrisii, there was also tissue specific residency in liver, spleen, bone marrow, and skin. In opossums and Tasmanian devils, the TRM locus is organized as discrete, tandem clusters, and there is evidence of lineage specific cluster duplication. In a monotreme, the platypus, TRM is less organized, although there is evidence of ancestral cluster-like patterns. Our results support conserved patterns of tissue specific residency of the unconventional γμ T cell in marsupials and help to reconstruct the evolution of this unique T cell type.
NSF IOS-2103367 DGE-1939267
Changes in MMΦ Phenotype Influence Early Life Development of the Enteric Nervous System
Authors: Joyce Elisabeth L , Schill Ellen M , Gaddipati Shreya , Floyd Alexandria N , Rusconi Brigida , McDonald Keely G , Newberry Rodney D 
Published: August 2023

Abstract
Vancomycin is a common medication given to premature infants. While protective, this treatment is associated with increased risk of developing disease later in life, including late-onset sepsis and necrotizing enterocolitis (NEC). Previous studies demonstrated that neonatal mice exposed to vancomycin in the early life period exhibit disruptions in the structure and function of the enteric nervous system (ENS). It remains unclear whether these disruptions are a direct consequence of dysbiosis or an indirect result achieved via crosstalk with immune cells. Muscularis macrophages (MMΦs) are a subset of intestinal macrophages identified to interact closely with enteric neurons. We hypothesized that vancomycin impacts ENS structure and function in early life by altering the phenotype of MMΦs. Neonatal mice were fed vancomycin (83mg/kg/day) or water daily from day of life (DOL) 1–10 and sacrificed for analysis on DOL 10. Single cell RNA sequencing performed on isolated MMΦs (CD45+ CXCR1+CD11c−/lo) demonstrated that vancomycin-treated mice had macrophages with a more inflammatory phenotype. Consistent with our RNA seq, MMΦs in mice treated with vancomycin had changes in their morphology consistent with activated macrophages/microglia. Flow cytometry revealed that vancomycin treatment significantly altered the proportion of MMΦs that were yolk sac derived compared to the bone marrow. To investigate how early life bone marrow derived MMΦs contribute to postnatal ENS development, we utilized CCR2 minus;/minus; mice, which cannot recruit macrophages to the colon. These mice exhibited significantly fewer neural cell bodies, suggesting that antibiotic-driven changes in MMΦ origin may influence early postnatal development of the ENS.
Rapid adipose tissue expansion induces proliferation of memory adipose tissue T cells
Authors: Jacks Ramiah , Lumeng Carey N 
Published: August 2023

Abstract
Obesity is recognized as a pro-inflammatory state featuring immune dysregulation and metabolic disease. Obesity-induced inflammation is observed in the adipose tissue of humans and mice. Adipose tissue T cells (ATTs) are dynamically shifted from Th2 cells in the lean state to an influx of CD8+ and Th1 T cells that promote adipose tissue inflammation in the obese state. Knowing this, many gaps remain in our understanding of ATT generation, maintenance, expansion, and regulation in adipose tissue. Specifically, it is unknown if naïve T cells are recruited to and stimulated within adipose tissue or if resident memory ATTs, which are abundant in the lean state, are stimulated during the initiation of the obese state. We hypothesized that memory ATTs respond to the early fat expansion elicited upon obesity induction. To test this, we used a short-term DIO male mouse model and assessed ATT proliferation during high-fat diet (HFD) feeding. Mice on HFD gained significantly more total body, epidydimal white adipose tissue (eWAT), and inguinal WAT (iWAT) weight compared to normal diet mice. We observed no increase in frequency or proliferation of naïve ATTs with HFD. Conversely, we observed significant proliferation of memory ATTs with 1 week of HFD in the eWAT, iWAT and omental WAT. This proliferation was restored to normal diet levels by 2 weeks of HFD. These data suggest that memory ATTs uniquely and intensely respond to signals present during HFD-induced rapid adipose tissue expansion. Ongoing studies seek to determine if there are sex differences by examining ATT dynamics in female mice. Further, we seek to determine which signal(s) drive memory ATT proliferation to identify targets to suppress ATT initiation of obesity-associated inflammation.
Supported by grants from NIH (K12 GM111725, R01 DK090262).
Immunotherapy of melanoma using TRP2 peptide-loaded biodegradable nanoparticles combined with poly-IC
Authors: Park Ji-Hyun , Lee Hee-Sung , Kim Sang-Hyun , Park Chan-Su , Lee Chong-Kil 
Published: August 2023

Abstract
Vaccination with tumor epitopes associated with MHC-I is an attractive approach directed at inducing tumor-specific CTLs. However, challenges remain in improving the therapeutic efficacy of peptide epitope vaccines, including the low immunogenicity of peptide epitopes and insufficient stimulation of innate immune components in vivo. Herein, we report an innovative strategy to overcome the limitations. The essential feature of this strategy is vaccination using tumor epitope-loaded biodegradable nanoparticles (NPs) in combination with poly-IC. Carboxylated NPs were prepared using poly(lactic-co-glycolic acid), covalently conjugated with anti-H-2Kb mAb, and then attached with H-2Kb molecules. Native peptides associated with the H-2Kb molecules of H-2Kb-attached NPs were exchanged with melanoma-specific peptide TRP2(180–188). TRP2 peptide-loaded NPs in combination with poly-IC efficiently induced TRP2-specific CTLs when immunized into melanoma-bearing mice as well as normal mice. Accordingly, TRP2 peptide-loaded NPs in combination with poly-IC exerted significant anti-tumor activity in mice implanted with B16-F10 melanoma cells. In addition, TRP2 peptide-loaded NPs in combination with poly-IC exerted potent anti-metastatic activity in mice i.v. injected with B16-F10 melanoma cells. These findings show that TRP2 peptide-loaded NPs combined with poly-IC could be an effective means in treating melanoma via the induction of TRP2-specific CTLs.
IAV/bacteria coinfection causes changes in pathology in an in vitro model of the lung epithelium
Authors: Zambrano Raphael Angelo I , Fitzgerald Ethan , Jamieson Amanda 
Published: August 2023

Abstract
Infection by the Influenza A Virus (IAV) remains a persistent issue contributing to increased risk of morbidity and mortality, especially for susceptible individuals. IAV infection can lead to increased susceptibility to bacterial infections, which further exacerbate disease. Therapeutics targeting pathogens are often ineffective as pathogens can mutate to avoid potential vaccines and antimicrobials. Improving our understanding of IAV/bacteria-host interactions can allow us to improve host-specific approaches to tackle potential morbidity and mortality brought on by coinfections that are primarily found in epithelial cells. Lung epithelial cells not only serve as an integral part of the respiratory system, but are also crucial in host defense against respiratory infections. Therefore, we adopted an Air-Liquid Interface (ALI) strategy for the culture of human bronchial epithelial cells (HBEC) to mimic the structure and function of respiratory epithelial tissue. ALI cultures were then subjected to single and coinfections by IAV and Streptococcus pneumoniae to assess the resulting pathology. We discovered that the specific type of infection influenced the type of programmed cell death that occurred, ranging from apoptotic to necroptotic. Additionally, coinfection with IAV and bacteria caused a unique gene expression profile. These findings demonstrate that the presence of specific pathogens causes a significant change in the cell death characteristics as well as transcriptional profile of lung epithelial cells. We hope that the progress of our investigation further elucidates consequences of host-pathogen interactions that can contribute to developing novel therapeutic strategies for complex lung infections.
Supported by grants from the NIH, NHLBI R01HL126887 (A.J.), P20GM121344 Pilot Project (A.J.), and under award number RL5GM118975 (R.Z.) of NIGMS.
Mosquito saliva alters draining LN architecture and function
Authors: Brisse Morgan E , Valenzuela Jesus , Olivera Fabiano , Hickman Heather D 
Published: August 2023

Abstract
Current murine models of most arbovirus infections result in the development of viremia and antiviral adaptive immune responses. However, delivery of virus by injection via syringe does not fully encompass all aspects of the response that develops after viral delivery via mosquito bite. One reason for this is likely to be the lack of additional immunomodulatory responses specifically induced by mosquito saliva as previous studies have demonstrated profound proviral and immunosuppressive properties of saliva. While the adaptive antiviral response develops in the lymph node draining the site of infection, the impact of mosquito saliva on this critical lymphoid organ has not been extensively explored. Further, the lymphatic system acts both as centralized hubs for immune cell activation and as dissemination pathways to distal tissues, meaning that immunomodulation of the lymphatic system likely affects infection and immunity systemically. Therefore, we explored the effect of mosquito saliva on the structure and function of the draining lymph node in the presence of absence of the mosquito borne arbovirus Zika virus (ZIKV). Preliminary confocal microscopic analyses of lymph nodes after saliva injection into the skin revealed changes in nodal architecture and specific cellular populations. Future studies will explore the impact of saliva specifically on lymphatic endothelial cells within the lymph node. These studies should provide additional insight into the mechanisms of bite-induced immunomodulation in secondary lymphoid organs and the impact on the developing antiviral response.
Supported by the Intramural Research Program of NIAID, NIH (H.D.H.)
Design and Characterization of Bivalent Molecules Against SARS-CoV2
Authors: Ahmad Javeed dhobi , Jiang Jiansheng , Perks Richard W , Lafont Bernard , Burdette Tracey , Reed Johnson , Muslinkina Lisa , Boyd Lisa , Natarajan Kannan , Margulies David 
Published: August 2023

Abstract
The pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has compelled extraordinary attention to the development of therapeutic reagents. The favorable physical properties of nanobodies make them attractive candidates for investigations of their ability to block viral entry. By X-ray crystallography we determined the structural basis of the interaction of a panel of synthetic nanobodies (Sb14, Sb16, Sb45 and Sb68) with the SARS-CoV-2 receptor binding domain (RBD): binary complexes of Sb16–RBD and Sb45–RBD; a ternary complex of Sb14–RBD–Sb68, and Sb45–RBD–Sb68. Sb16 and Sb45 bind the RBD with identical footprints with ACE2, but their complementarity determining regions (CDR)2 and CDR3 are oriented diametrically oppositely. The ternary structure of the Sb45-RBD-Sb68 complex indicates that Sb45 binds squarely at the ACE2 interface, whereas Sb68 attaches toward the ACE2 interface’s perimeter. The ternary configuration suggests that several sybodies may capture a sizable portion of the RBD’s surface. These sybody structures provided structural insights that were used to create novel, highly potent biparatopic nanobodies and bivalent molecules with ACE2 and ACE2 binding scaffold mimicking miniproteins that bind the RBD with high affinity and neutralize SARS-CoV-2 and variants.
Supported by the Intramural research program of the NIAID/NIH
Altered epithelial function in the stria vascularis and hearing loss in a mouse model of congenital cytomegalovirus infection associated hearing loss
Authors: Smith Matthew , Britt William 
Published: August 2023

Abstract
Congenital Human Cytomegalovirus (HCMV) infection is a leading cause of sensorineural hearing loss (SNHL) in children. The mechanism of HCMV damage to the developing auditory system that leads to SNHL is not understood and effective treatments are lacking. We developed a murine model of HCMV infection that results in neurodevelopmental abnormalities and SNHL, thus providing a useful model to study the mechanisms of SNHL associated with cCMV infection. We have shown that MCMV induces expression of proinflammatory molecules and immune cell activation in the cochlea associated with histopathologic changes and SNHL. The stria vascularis (SV) plays a critical role in hearing by; (1) maintaining an epithelial barrier needed for generation of the high electrical potential of endocochlear fluid surrounding the hair cells; (2) expression of a system of ion channels that create a high K+ concentration in the endocochlear fluid; and (3) generation of a blood labyrinth barrier (BLB) that surrounds the vasculature in the SV and functions like the blood brain barrier. Utilizing several assays, our studies showed that MCMV infection altered each of these functions. The transcription and protein expression in the SV required for tight junctions in the epithelial barrier and ion channels were decreased early after infection and in SV from infected mice with SNHL compared to those without SNHL. In addition, the resident macrophages that contribute to the BLB had altered phenotypes. Functionally, penetration of a cell-impermeable tracer into the SV could be demonstrated in MCMV infected mice. In all, our data show that MCMV dysregulates expression of key proteins in the SV that in turn impact the capacity of the SV to maintain the cochlea’s unique environment.
Rab27-dependent extracellular vesicle releasing participates in dengue virus non-structural protein 1 secretion
Authors: Wan Shu-Wen , Cheng Miao-Huei , Lee Yan-Hua 
Published: August 2023

Abstract
Dengue disease is one of important arthropod-borne disease in the world and causes around 20,000 deaths annually. Dengue virus (DENV) non-structural protein 1 (NS1) is the major secreted non-structural protein from infected cells and highly associated with the pathogenesis of severe dengue. Several studies have shown that the secreted NS1 contribute to increase of vascular permeability, coagulopathy, activation of immune cells as well as inflammation. These findings strongly indicate the pathological roles of secreted NS1; however, the secretory pathway is not fully clear. Accumulating evidence have shown that virus-associated extracellular vesicles (EVs) not only contain viral components including viral proteins, genetic material or virion particle but also host components. Rab27 is one of several GTPases essential to regulate EV releasing by affecting docking of multivesicular body (MVB) to the target plasma membrane. Here, we show that NS1 can be exported from DENV-infected cells by EVs. NS1 as well as EV biogenesis-associated proteins ALG-2-interacting protein X (ALIX) and neutral sphingomyelinase2 (nSMase2) co-accumulate in extracellular vesicles. We next determine the topology of NS1 and demonstrate that NS1 is associated at the surface of EVs. In addition, the secretion of DENV NS1 is regulated by Rab27. The EV biogenesis and secretion inhibitor, Tipifarnib treatment decreases the levels of NS1 and nSMase 2 but not the levels of ALIX in the EVs. Taken together, this study not only provide the new insights of mechanisms in DENV NS1 secretion through Rab27-mediated vesicle trafficking but also valuable therapeutic targets to dengue disease.
Supported by grants from Ministry of Science and Technology of Taiwan (MOST 111-2320-B-006 -051 -MY3)
Long-term metabolomic alterations during post-acute sequelae of COVID-19
Authors: Wong Andrea C , Devason Ashwarya , Umana Iboro C , Cox Timothy , Dohnalová Lenka , Meyer Nuala J , Abramoff Benjamin , Cherry Sara , Thaiss Christoph , Levy Maayan 
Published: August 2023

Abstract
A large fraction of COVID-19 patients does not fully recover from the acute infection with SARS-CoV-2 but develops long-term symptoms that persist for several months. The pathobiology of such post-acute sequelae of COVID-19 (PASC, “long COVID”) remains largely enigmatic. This project is based on a discovery made by a plasma metabolomics exploration of individuals with acute SARS-CoV-2 infection, post-COVID patients that have fully recovered from the disease, and PASC patients that have persistent manifestations across a wide range of organ systems. We have found key metabolites that are altered by acute SARS-CoV-2 infection and do not recover in individuals with PASC, while returning to normal levels in post-COVID individuals who do not develop long-term symptoms. These metabolites offer a pathway-level hypothesis for a new molecular etiology underlying PASC. We have shown that viral RNA is sufficient to alter these metabolites and suggest that this can explain some of the symptoms reported by patients with long covid.
A.C.W. is supported by training grant T32-AI-055400-19. C.T. is a Pew biomedical scholar and a Kathryn W. Davis Aging Brain scholar and is supported by the NIH Director’s New Innovator Award (DP2-AG-067492), the Agilent Early Career Professor Award, and grants from the Edward Mallinckrodt Jr Foundation, the IDSA Foundation, the Thyssen Foundation, PennCHOP Microbiome Program, Penn Institute for Immunology, Penn Center for Molecular Studies in Digestive and Liver Diseases (P30-DK-050306), Penn Skin Biology and Diseases Resource-based Center (P30-AR-069589), Penn Diabetes Research Center (P30-DK-019525), Penn Institute on Aging and the Borrelli Family Pilot Grant in Lynch Syndrome. M.L. is supported by the NIH Director’s New Innovator Award (DP2-AG-067511), an American Cancer Society Scholar Award, The Pew Scholar Award, the Searle Scholar program, the Edward Mallinckrodt Jr Foundation and grants from the Abramson Cancer Center, The Penn-CHOP microbiome program, Penn Coronavirus Center Pilot, Penn Institute for Immunology, Penn Center for Molecular Studies in Digestive and Liver Diseases, Penn Center for Precision Medicine, Penn Institute on Aging, Penn Center of Excellence in Environmental Toxicology (P30-ES-013508) and the Borrelli Family Pilot Grant in Lynch Syndrome.