Xun Xiang

Background/Objectives: Bovine heat-stress RNA-seq studies differ in tissue, age, physiological state, and exposure design. We asked which responses recur across these contexts and which depend on the evidence base. Methods: We reprocessed 107 libraries from five in vivo Bos taurus studies and synthesized within-study heat-minus-control log₂ fold changes using restricted maximum-likelihood random-effects models with modified Knapp–Hartung inference. Eight tissue- and age-aware scenarios tested the cross-context estimate. A six-component heat-stress transcriptomic stability index (HSTSI) was benchmarked against five simpler rankings, and an independent mammary single-nucleus dataset provided cell-resolved comparison. Results: Of 266 FDR-significant pathways, 259 retained direction across all five study deletions and 21 remained significant in every deletion. Translation, ribosome, protein folding, endoplasmic-reticulum processing, proteasome, and heat-response programs formed the most recurrent axis. Four principal sensitivity scenarios retained 0.920–0.932 gene-direction agreement and 0.957–0.981 effect-rank correlation with the five-study analysis. In the single-nucleus dataset, leading-edge genes from the principal proteostasis programs showed 89.4–100% pooled-nucleus direction agreement and 94.7–100% agreement among published cluster-level differentially expressed genes. HSTSI had the highest mean top-200 held-out direction agreement (0.583 versus 0.516–0.562), with variation among folds. None of 16,756 genes met a modified Knapp–Hartung FDR below 0.10. IL1R2 and SDCBP2 were externally concordant, whereas GZMK and CD8A were context-dependent. Conclusions: A coordinated proteostasis program was the most transferable heat-stress signal. Energy remodeling, immune-associated bulk signals, and individual genes showed greater context dependence and define priorities for tissue-matched follow-up.

Introduction: Newcastle disease virus (NDV) can spread across regions via migratory wild birds, posing potential threats to livestock breeding and public health security. Systematic information on the genetic characteristics, immunoregulatory functions, and antiviral activity of IFN-γ in the migratory wild bird Larus ridibundus remains limited. Methods: In this study, the complete coding sequence of L. ridibundus IFN-γ was cloned and analyzed bioinformatically. A prokaryotic expression system was used to produce purified recombinant IFN-γ, and specific polyclonal antibodies were prepared for protein identification. Peripheral blood lymphocytes were exposed to graded NDV doses, serial concentrations of recombinant IFN-γ, or combined IFN-γ and NDV treatment. Quantitative real-time PCR was used to measure NDV NP transcripts and the transcription of TLR7, MyD88, IRF7, IFN-α, IFN-γ, and Mx. Results: NDV infection was associated with increased transcription of TLR7 pathway-related genes. Among the tested IFN-γ concentrations, 200 ng/mL produced the strongest TLR7 transcriptional response. IFN-γ intervention significantly reduced intracellular NDV NP transcript abundance, and this reduction coincided with lower transcription of TLR7 pathway-related genes under combined treatment. Discussion: These findings indicate that L. ridibundus IFN-γ has in vitro anti-NDV activity and that this activity is associated with transcriptional modulation of the TLR7-MyD88-IRF7 pathway. Direct pathway dependence remains to be established by pathway-inhibition experiments.

Newcastle disease virus (NDV) is an important avian pathogen that can circulate in migratory birds, including Larus ridibundus. This study examined the transcriptional responses and anti-NDV activities associated with recombinant IFN-α and Mx proteins from L. ridibundus. The IFN-α and Mx open reading frames were cloned (GenBank: OP263971 and OP263970), expressed using a pET32a(+)/E. coli system, and assessed using chicken embryos, DF-1 cells, and primary gull lymphocytes. qRT-PCR analysis showed that NDV infection increased IFN-α and Mx transcript abundance in gull lymphocytes, with peak levels at 48 h post-infection (p < 0.01). In chicken embryos, recombinant IFN-α was associated with higher embryo survival and lower NDV NP transcript abundance than recombinant Mx under the tested conditions. In DF-1 cells and primary gull lymphocytes, 0.25 mg/mL recombinant IFN-α was associated with reduced NDV NP transcript abundance, and morphological inspection suggested less severe cytopathic effects in DF-1 cells. IFN-α treatment was also accompanied by lower transcription of TLR7, MyD88, IRF7, and Mx compared with the NDV group at 48 h. These data support a role for gull IFN-α in limiting NDV-associated transcriptional responses in vitro, while further protein-level and infectious-virus assays are required to define the underlying mechanism.

Background/Objectives: Heat stress compromises cattle production, health, and welfare, but bovine transcriptomic studies span tissues and experimental settings. We sought gene-level effects and biological programs that recur across in vivo studies while preserving each study design. Methods: We uniformly reprocessed 107 bulk RNA-seq libraries from five Bos taurus studies, estimated heat-versus-control effects within study, and integrated log2 fold changes using restricted maximum-likelihood random-effects models. Modified Knapp–Hartung inference, prediction intervals, and Benjamini–Hochberg correction calibrated small-study uncertainty. A six-component heat-stress transcriptomic stability index (HSTSI), ten score definitions, five complete leave-one-study-out analyses, and directional enrichment assessed recurrence. Results: Among 16,756 genes, normal-approximation inference identified 19 at false-discovery rate (FDR) < 0.05, whereas none met FDR < 0.10 under modified Knapp–Hartung inference. IL1R2 ranked first by HSTSI (meta log2 fold change =0.82; 95% prediction interval, 0.31–1.33). Study deletion retained 68–117 of the top 200, and every estimable member preserved direction. IL1R2, SDCBP2, and GZMK were retained under all ten definitions and CD8A under nine. Proteostasis, translation, oxidative phosphorylation, and heat-response programs shifted positively; T-cell signaling, antigen presentation, cytotoxicity, cell-cycle, and small-GTPase programs shifted negatively. Of 266 full-data FDR-significant pathways, 259 retained direction in all five deletions and 21 remained FDR-significant throughout. Conclusions: Recurrence was strongest for coordinated biological programs. The graded candidate set supports tissue-matched validation without treating ranking as statistical significance.