Miracle-dz/UniFAR-FTUs huggingface dataset:
Ubiquitin Conjugation of Open Reading Frame F DNA Vaccine Leads to Enhanced Cell-Mediated Immune Response and Induces Protection against Both Antimony-Susceptible and -Resistant Strains of Leishmania donovani1

Resistance of Leishmania donovani to sodium antimony gluconate has become a critical issue in the current, prolonged epidemic in India. Hence, there is an urgent need for a vaccine that is protective against both antimony-susceptible and -resistant strains of L. donovani. The multigene LD1 locus located on chromosome 35 of Leishmania is amplified in ∼15% of the isolates examined. The open reading frame F (ORFF), a potential vaccine candidate against visceral leishmaniasis, is part of the multigene LD1 locus. ORFF was expressed as a chimeric conjugate of ubiquitin to elicit an Ag-specific cell-mediated immune response. Analysis of the cellular immune responses of ubiquitin-conjugated ORFF (UBQ-ORFF) DNA-immunized, uninfected BALB/c mice demonstrated that the vaccine induced enhanced IFN-γ-producing CD4+ and CD8+ T cells compared with nonubiquitinated ORFF DNA vaccine. Higher levels of IL-12 and IFN-γ and the low levels of IL-4 and IL-10 further indicated that the immune responses with UBQ-ORFF were mediated toward the Th1 rather than Th2 type. Infection of immunized mice with either the antimony-susceptible (AG83) or -resistant (GE1F8R) L. donovani strain showed that UBQ-ORFF DNA vaccine induced higher protection when compared with ORFF DNA. UBQ-ORFF DNA-immunized and -infected mice showed a significant increase in IL-12 and IFN-γ and significant down-regulation of IL-10. High levels of production of nitrite and superoxide, two macrophage-derived oxidants that are critical in controlling Leishmania infection, were observed in protected mice. The feasibility of using ubiquitinated-conjugated ORFF DNA vaccine as a promising immune enhancer for vaccination against both antimony-susceptible and -resistant strains of L. donovani is reported.
Hybrid knowledge and climate-resilient agriculture practices of the Tharu in the western Tarai, Nepal

Indigenous knowledge can function as a basis of innovation in agriculture because it is not only culturally accepted, but often also environmentally adaptive. The debates and misunderstandings regarding the relations between Indigenous and scientific knowledge are transforming into a trend to integrate all knowledge to deal with complex issues, such as climate change. In this study we explore the understandings of the Tharu people of their farming system in relation to adaptation and mitigation of climate change, based on mixed methods design using both ethnographic analysis of their specific agriculture practices from participant observation and a survey of 229 households in the western Tarai of Nepal. Among our findings is the fit of the traditional agricultural calendar of the Tharu with the labor regimen of agricultural seasons. We found that conservation tillage-oriented agricultural practices, such as relay cropping, including zero-tillage, remain important in the farming system. Although this practice is decreasing, particularly due to the low yield as compared to the conventional tillage system, relay sowing and zero-tillage in the lowlands and uplands remain important for timely crop sowing. Similarly, mixed cropping is prevalent, particularly among small holders, for subsistence-based farming, in part due to higher yield than sole cropping. We conclude that Indigenous knowledge regarding climate and agriculture practices assists making informed decisions for climate-resilient and low emission agriculture. Although some traditional climate-resilient agriculture practices may yield lower profit than those derived from scientific knowledge/methods, the Tharu have therefore embraced “hybrid knowledge”—a combination of Indigenous and scientific knowledge, technology and practice—to balance increased yield and profit maximization with concurrent decreased vulnerability to extreme weather events. We argue that it is not useful to make firm distinctions among traditional, Indigenous and local knowledge in the age of hybridity. This hybridity is evident in the complementarity of the use of improved varieties and scientific agricultural practices for the major grains and the continuing use of landraces for minor crops such as lentils, peas and mustard. However, further research on the sustainable productivity of such practices is required before their widespread dissemination.
The Adaptor Protein p62/SQSTM1 Targets Invading Bacteria to the Autophagy Pathway1

Autophagy, a cellular degradative pathway, plays a key role in protecting the cytosol from bacterial colonization, but the mechanisms of bacterial recognition by this pathway are unclear. Autophagy is also known to degrade cargo tagged by ubiquitinated proteins, including aggregates of misfolded proteins, and peroxisomes. Autophagy of ubiquitinated cargo requires p62 (also known as SQSTM1), an adaptor protein with multiple protein-protein interaction domains, including a ubiquitin-associated (UBA) domain for ubiquitinated cargo binding and an LC3 interaction region (LIR) for binding the autophagy protein LC3. Previous studies demonstrated that the intracellular bacterial pathogen Salmonella typhimurium is targeted by autophagy during infection of host cells. Here we show that p62 is recruited to S. typhimurium targeted by autophagy, and that the recruitment of p62 is associated with ubiquitinated proteins localized to the bacteria. Expression of p62 is required for efficient autophagy of bacteria, as well as restriction of their intracellular replication. Our studies demonstrate that the surveillance of misfolded proteins and bacteria occurs via a conserved pathway, and they reveal a novel function for p62 in innate immunity.
Inhibition of Thymic Adipogenesis by Caloric Restriction Is Coupled with Reduction in Age-Related Thymic Involution1

Aging of thymus is characterized by reduction in naive T cell output together with progressive replacement of lymphostromal thymic zones with adipocytes. Determining how calorie restriction (CR), a prolongevity metabolic intervention, regulates thymic aging may allow identification of relevant mechanisms to prevent immunosenescence. Using a mouse model of chronic CR, we found that a reduction in age-related thymic adipogenic mechanism is coupled with maintenance of thymic function. The CR increased cellular density in the thymic cortex and medulla and preserved the epithelial signatures. Interestingly, CR prevented the age-related increase in epithelial-mesenchymal transition (EMT) regulators, FoxC2, and fibroblast-specific protein-1 (FSP-1), together with reduction in lipid-laden thymic fibroblasts. Additionally, CR specifically blocked the age-related elevation of thymic proadipogenic master regulator, peroxisome proliferator activated receptor γ (PPARγ), and its upstream activator xanthine-oxidoreductase (XOR). Furthermore, we found that specific inhibition of PPARγ in thymic stromal cells prevented their adipogenic transformation in an XOR-dependent mechanism. Activation of PPARγ-driven adipogenesis in OP9-DL1 stromal cells compromised their ability to support T cell development. Conversely, CR-induced reduction in EMT and thymic adipogenesis were coupled with elevated thymic output. Compared with 26-mo-old ad libitum fed mice, the T cells derived from age-matched CR animals displayed greater proliferation and higher IL-2 expression. Furthermore, CR prevented the deterioration of the peripheral TCR repertoire diversity in older animals. Collectively, our findings demonstrate that reducing proadipogenic signaling in thymus via CR may promote thymopoiesis during aging.
Design of a performance measurement system for just-in-time production: a methodological framework

In this era of globalisation and fierce competition amongst businesses there is a need to implement new manufacturing strategies to enhance business performance. Time-based competition is a multidimensional approach and Just-in-Time (JIT) philosophy designed to achieve high volume production using minimum inventory at the right time based on planned elimination of all wastes and continuous improvement, now plays an increasingly prominent role in manufacturing environment. However, there is no evidence in the literature of any mechanism for quantitatively relating JIT techniques to measurable performance in manufacturing environment. This paper describes the methodological framework to understand the impact of key JIT drivers on performance and hence develop a generic model to identify and capture the strategic influences of JIT practices on performance. An application of this methodology in a JIT-enabled UK manufacturing company is presented.
Outside-In Signal Transmission by Conformational Changes in Integrin Mac-11

Intracellular signals associated with or triggered by integrin ligation can control cell survival, differentiation, proliferation, and migration. Despite accumulating evidence that conformational changes regulate integrin affinity to its ligands, how integrin structure regulates signal transmission from the outside to the inside of the cell remains elusive. Using fluorescence resonance energy transfer, we addressed whether conformational changes in integrin Mac-1 are sufficient to transmit outside-in signals in human neutrophils. Mac-1 conformational activation induced by ligand occupancy or activating Ab binding, but not integrin clustering, triggered similar patterns of intracellular protein tyrosine phosphorylation, including Akt phosphorylation, and inhibited spontaneous neutrophil apoptosis, indicating that global conformational changes are critical for Mac-1-dependent outside-in signal transduction. In neutrophils and myeloid K562 cells, ligand ICAM-1 or activating Ab binding promoted switchblade-like extension of the Mac-1 extracellular domain and separation of the αM and β2 subunit cytoplasmic tails, two structural hallmarks of integrin activation. These data suggest the primacy of global conformational changes in the generation of Mac-1 outside-in signals.
Skin and Peripheral Lymph Node Invariant NKT Cells Are Mainly Retinoic Acid Receptor-Related Orphan Receptor γt+ and Respond Preferentially under Inflammatory Conditions1

Lymph nodes (LNs) have been long considered as comprising few invariant NKT (iNKT) cells, and these cells have not been studied extensively. In this study, we unravel the existence of stable rather than transitional LN-resident NK1.1− iNKT cell populations. We found the one resident in peripheral LNs (PLNs) to comprise a major IL-17-producing population and to express the retinoic acid receptor-related orphan receptor γt (RORγt). These cells respond to their ligand α-galactosylceramide (α-GalCer) in vivo by expanding dramatically in the presence of LPS, providing insight into how this rare population could have an impact in immune responses to infection. PLN-resident RORγt+ NK1.1− iNKT cells express concomitantly CCR6, the integrin α-chain αE (CD103), and IL-1R type I (CD121a), indicating that they might play a role in inflamed epithelia. Accordingly, skin epithelia comprise a major RORγt+ CCR6+CD103+CD121a+ NK1.1− cell population, reflecting iNKT cell composition in PLNs. Importantly, both skin and draining PLN RORγt+ iNKT cells respond preferentially to inflammatory signals and independently of IL-6, indicating that they could play a nonredundant role during inflammation. Overall, our study indicates that RORγt+ iNKT cells could play a major role in the skin during immune responses to infection and autoimmunity.
Dynamic Development of Homing Receptor Expression and Memory Cell Differentiation of Infant CD4+CD25high Regulatory T Cells1

Migration of CD4+CD25+FOXP3+ regulatory T cells (Treg) is important for suppressing immune responses in different tissues. Previous studies show that the majority of Treg at birth express gut homing receptor α4β7 and that only few express CCR4, while the reverse pattern is found in adults. The age at which homing receptor switch occurs in vivo is not known. In this study, we show, in a prospective study of human infants from birth to 3 years of age, that homing receptor switch from α4β7 to CCR4 commences between 1 1/2 and 3 years of age and that Treg at that age also had started their switch to a memory phenotype. The majority of naive Treg express α4β7 in infants but not in adults, while the majority of memory Treg express CCR4 both infants and adults. The homing receptor expression on Treg corresponds to their actual migration properties, because Treg from cord blood migrate foremost toward the gut-associated chemokine CCL25. CD4+FOXP3+ T cell numbers increase rapidly in the circulation during the first days of life indicating conversion to suppressive Treg from CD25high Treg precursors. These findings suggest that the gut is the primary site of Treg stimulation to exogenous Ags during the first 18 mo of life and that homing receptor switch toward a more extra-intestinal phenotype occurs thereafter.
Fms-Like Tyrosine Kinase 3 Ligand Regulates Migratory Pattern and Antigen Uptake of Lung Dendritic Cell Subsets in a Murine Model of Allergic Airway Inflammation1

Fms-like tyrosine kinase 3 ligand (Flt3L) reverses the features of allergic airway inflammation and increases a Th2-suppressive regulatory lung CD11chighCD11blow dendritic cell (DC) subset in a mouse model. We examined the migratory pattern and Ag uptake efficiency of lung DC subsets in the therapeutic effect of Flt3L. Lung CD11chighCD11blow and CD11clowCD11bhigh DCs from PBS-treated, OVA-sensitized, and Flt3L-treated/OVA-sensitized BALB/c mice were sorted using MACS and FACS for phenotype analysis. Lymphatic chemokine expression in thoracic lymph nodes was determined by immunohistochemistry. Migration of two lung DC subsets to lymphatic chemokines was examined in vitro using a Transwell chemotaxis assay. Labeled Ag was intranasally delivered into mouse lung to track the migration and Ag uptake of lung DCs. The in vitro cytokine secretion of mediastinal lymph node cells was determined using ELISA. CD11clowCD11bhigh DCs have higher expression of CCR5, CCR6, and CCR7, but lower expression of CCR2 than CD11chighCD11blow DCs. CD11clowCD11bhigh DCs in Flt3L-treated/OVA-sensitized mice demonstrated a less mature phenotype, inefficiency in Ag uptake, and impaired migration in vitro to lymphatic chemokine than those in OVA-sensitized mice. Administration of Flt3L decreased the expression of CCR5 and CCR7 in CD11clowCD11bhigh DCs in OVA-sensitized mice. Fewer Ag-carrying cells were detected in the lungs and lymph nodes in Flt3L-treated/OVA-sensitized mice than OVA-sensitized mice with a greater decrease in CD11clowCD11bhigh DCs. Mediastinal lymph node cells from Flt3L-treated mice secreted higher levels of Th1 cytokines and IL-10 than OVA-sensitized mice in vitro. In conclusion, Flt3L-generated lung immunogenic CD11clowCD11bhigh DCs have a less mature phenotype, impaired Ag uptake, and impaired migration to draining lymph nodes.
Immunotherapy Can Reject Intracranial Tumor Cells without Damaging the Brain despite Sharing the Target Antigen

Although vaccines targeting tissue differentiation Ags represent a promising strategy for cancer immunotherapy, the risk of triggering autoimmune damage to normal tissues remains to be determined. Immunizing against a melanoma-associated Ag, dopachrome tautomerase (DCT), which normal melanocytes and glial cells also express, allowed concurrent analysis of autoimmune consequences in multiple tissues. We show that vaccination with recombinant adenovirus expressing DCT elicited a strong CTL response in C57BL/6 mice, leading to protection against intracranial challenge with B16-F10 melanoma cells. Both histological analysis and behavioral testing indicated that there was no evidence of neuropathology in vaccinated animals and long-term survivors. Although vitiligo or demyelination could be induced by additional stimuli (i.e., surgery or inflammation) in DCT-vaccinated mice, it did not extend beyond the inflammatory area, suggesting that there is self-regulatory negative feedback in normal tissues. These results demonstrate that it is possible to vaccinate against a tumor embedded in a vital organ that shares the target Ag.
Signalingand T Cell Activities Requiring IL-6R for Factor 1 to Form a Cytokine Regulating NK The IL-27 p28 Subunit Binds Cytokine-Like

IL-27 is formed by the association of a cytokine subunit, p28, with the soluble cytokine receptor EBV-induced gene 3 (EBI3). The IL-27R comprises gp130 and WSX-1. The marked difference between EBI3 (cid:1) / (cid:1) and WSX-1 (cid:1) / (cid:1) mice suggests that p28 has functions independent of EBI3. We have identiﬁed an alternative secreted complex formed by p28 and the soluble cytokine receptor cytokine-like factor 1 (CLF). Like IL-27, p28/CLF is produced by dendritic cells and is biologically active on human NK cells, increasing IL-12- and IL-2-induced IFN- (cid:2) production and activation marker expression. Experiments with Ba/F3 transfectants indicate that p28/CLF activates cells expressing IL-6R (cid:3) in addition to the IL-27R subunits. When tested on CD4 and CD8 T cells, p28/CLF induces IL-6R (cid:3) -dependent STAT1 and STAT3 phosphorylation. Furthermore, p28/CLF inhibits CD4 T cell proliferation and induces IL-17 and IL-10 secretion. These results indicate that p28/CLF may participate in the regulation of NK and T cell functions by dendritic cells. The p28/CLF complex engages IL-6R and may therefore be useful for therapeutic applications targeting hyper IL-6 (25), the cDNAs for IL-6R (cid:4) and IL-6 (IMAGE ID 5135770 Open Biosystems) were modiﬁed by PCR to generate a single- chain fusion protein encoding for the extracellular domain of IL-6R (cid:4) fused to the mature form of IL-6 by a GGG(SGGGG) 3 SHHHHHH linker. The inserts were recloned in the insect expression vector pIB/V5-His (Invitro-gen). Stable High Five (Invitrogen) transfectants were generated and ex- panded in Express Five Medium (Invitrogen) according to the supplier’s recommended procedure. The p28/CLF complex and hyper-IL-6 were pu- riﬁed by immobilized metal-afﬁnity chromatography on Ni-NTA agarose (Qiagen) following Qiagen protocol using LPS-free reagent and glassware. Puriﬁed proteins were dialyzed, quantiﬁed, and analyzed by Western blot for the presence of p28, CLF, or hyper-IL-6 and were tested for LPS con- tamination as described above for human p28/CLF. Western blot analysis of hyper-IL-6 was revealed using anti-penta His mAb (Qiagen). No CLF/ p28 unprocessed fusion protein contamination could be detected in the p28/CLF preparations. We examined whether CLF could substitute for EBI3 in forming an alternative complex activating IL-27R. To investigate the activation of cells expressing IL-27R by p28/CLF, we used the mouse pro-B cell line Ba/F3. This cell line expresses WSX-1 and can be rendered IL-27 responsive by solely introducing gp130 cDNA (2). Ba/F3 transfected with gp130 showed a partial response to p28/ CLF: incubation with the complex led to STAT3 phosphorylation but was insufﬁcient to induce STAT1 activation and resulted in minimal cell proliferation, suggesting that the receptor required an additional chain. In accordance with this hypothesis, p28/CLF binds to HEK-293 transfectants expressing IL-6R (cid:4) . Introduction of to to by using (cid:4) that two receptor of IL-6.
Ly49H Engagement Compensates for the Absence of Type I Interferon Signaling in Stimulating NK Cell Proliferation During Murine Cytomegalovirus Infection1

NK cells vigorously proliferate during viral infections, resulting in an expanded pool of innate lymphocytes that are able to participate in early host defense. The relative contributions of cytokines and activation receptors in stimulating NK cell proliferation during viral infections are not well characterized. In this study, we demonstrated that signaling through the NK cell activation receptor Ly49H was able to compensate for the absence of cytokine stimulation in the preferential phase of viral-induced proliferation during murine cytomegalovirus infection. In the absence of type I IFN stimulation, NK cell proliferation was strongly biased toward cells expressing the Ly49H receptor, even at early time points when minimal preferential Ly49H-mediated proliferation was observed in wild-type mice. In the absence of effective Ly49H signaling or following infection with virus that did not express the ligand for Ly49H, no difference was observed in the proliferation of subsets of NK cells that either express or lack expression of Ly49H, although the overall proliferation of NK cells in IFNαβR−/− mice was substantially reduced. These results highlight the contribution of NK cell activation receptors in stimulating proliferation and subsequent expansion of NK cells that are able to recognize virally infected cells.
Potential biomarkers and immune cell infiltration involved in aortic valve calcification identified through integrated bioinformatics analysis

Background: Calcific aortic valve disease (CAVD) is the most common valvular heart disease in the aging population, resulting in a significant health and economic burden worldwide, but its underlying diagnostic biomarkers and pathophysiological mechanisms are not fully understood. Methods: Three publicly available gene expression profiles (GSE12644, GSE51472, and GSE77287) from human Calcific aortic valve disease (CAVD) and normal aortic valve samples were downloaded from the Gene Expression Omnibus database for combined analysis. R software was used to identify differentially expressed genes (DEGs) and conduct functional investigations. Two machine learning algorithms, least absolute shrinkage and selection operator (LASSO) and support vector machine-recursive feature elimination (SVM-RFE), were applied to identify key feature genes as potential biomarkers for Calcific aortic valve disease (CAVD). Receiver operating characteristic (ROC) curves were used to evaluate the discriminatory ability of key genes. The CIBERSORT deconvolution algorithm was used to determine differential immune cell infiltration and the relationship between key genes and immune cell types. Finally, the Expression level and diagnostic ability of the identified biomarkers were further validated in an external dataset (GSE83453), a single-cell sequencing dataset (SRP222100), and immunohistochemical staining of human clinical tissue samples, respectively. Results: In total, 34 identified DEGs included 21 upregulated and 13 downregulated genes. DEGs were mainly involved in immune-related pathways such as leukocyte migration, granulocyte chemotaxis, cytokine activity, and IL-17 signaling. The machine learning algorithm identified SCG2 and CCL19 as key feature genes [area under the ROC curve (AUC) = 0.940 and 0.913, respectively; validation AUC = 0.917 and 0.903, respectively]. CIBERSORT analysis indicated that the proportion of immune cells in Calcific aortic valve disease (CAVD) was different from that in normal aortic valve tissues, specifically M2 and M0 macrophages. Key genes SCG2 and CCL19 were significantly positively correlated with M0 macrophages. Single-cell sequencing analysis and immunohistochemical staining of human aortic valve tissue samples showed that SCG2 and CCL19 were increased in Calcific aortic valve disease (CAVD) valves. Conclusion: SCG2 and CCL19 are potential novel biomarkers of Calcific aortic valve disease (CAVD) and may play important roles in the biological process of Calcific aortic valve disease (CAVD). Our findings advance understanding of the underlying mechanisms of Calcific aortic valve disease (CAVD) pathogenesis and provide valuable information for future research into novel diagnostic and immunotherapeutic targets for Calcific aortic valve disease (CAVD).