scholarly journals Identifications of immune-responsive genes for adaptative traits by comparative transcriptome analysis of spleen tissue from Kazakh and Suffolk sheep

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hua Yang ◽  
Yong-Lin Yang ◽  
Guo-Qing Li ◽  
Qian Yu ◽  
Jinzeng Yang
Keyword(s):  
High Throughput Sequencing ◽  
Killer Cell ◽  
Cell Lineage ◽  
Production Performance ◽  
Adaptive Traits ◽  
Spleen Tissue ◽  
Indigenous Sheep ◽  
Immunological Mechanisms ◽  
Iga Production ◽  
Suffolk Sheep

AbstractAridity and heat are significant environmental stressors that affect sheep adaptation and adaptability, thus influencing immunity, growth, reproduction, production performance, and profitability. The aim of this study was to profile mRNA expression levels in the spleen of indigenous Kazakh sheep breed for comparative analysis with the exotic Suffolk breed. Spleen histomorphology was observed in indigenous Kazakh sheep and exotic Suffolk sheep raised in Xinjiang China. Transcriptome sequencing of spleen tissue from the two breeds were performed via Illumina high-throughput sequencing technology and validated by RT-qPCR. Blood cytokine and IgG levels differed between the two breeds and IgG and IL-1β were significantly higher in Kazakh sheep than in Suffolk sheep (p < 0.05), though spleen tissue morphology was the same. A total of 52.04 Gb clean reads were obtained and the clean reads were assembled into 67,271 unigenes using bioinformatics analysis. Profiling analysis of differential gene expression showed that 1158 differentially expressed genes were found when comparing Suffolk with Kazakh sheep, including 246 up-regulated genes and 912 down-regulated genes. Utilizing gene ontology annotation and pathway analysis, 21 immune- responsive genes were identified as spleen-specific genes associated with adaptive traits and were significantly enriched in hematopoietic cell lineage, natural killer cell-mediated cytotoxicity, complement and coagulation cascades, and in the intestinal immune network for IgA production. Four pathways and up-regulated genes associated with immune responses in indigenous sheep played indispensable and promoting roles in arid and hot environments. Overall, this study provides valuable transcriptome data on the immunological mechanisms related to adaptive traits in indigenous and exotic sheep and offers a foundation for research into adaptive evolution.

A Review of the Natural Killer Cell Lineage in the Uterus of the Mouse and of the Pig

1994 ◽  
Vol 72 (suppl_3) ◽  
pp. 9-15 ◽  
Author(s):  
B. A. Croy ◽  
Z. M. Yu ◽  
G. J. King
Keyword(s):  
Natural Killer Cell ◽  
Natural Killer ◽  
Killer Cell ◽  
Cell Lineage

scholarly journals Harnessing Natural Killer Cell Innate and Adaptive Traits in HIV Infection

2020 ◽  
Vol 10 ◽  
Author(s):  
Aljawharah Alrubayyi ◽  
Ane Ogbe ◽  
Elia Moreno Cubero ◽  
Dimitra Peppa
Keyword(s):  
Natural Killer Cell ◽  
Hiv Infection ◽  
Natural Killer ◽  
Killer Cell ◽  
Adaptive Traits

scholarly journals tascCODA: Bayesian Tree-Aggregated Analysis of Compositional Amplicon and Single-Cell Data

2021 ◽  
Vol 12 ◽  
Author(s):  
Johannes Ostner ◽  
Salomé Carcy ◽  
Christian L. Müller
Keyword(s):  
Single Cell ◽  
Count Data ◽  
High Throughput Sequencing ◽  
Cell Lineage ◽  
Population Data ◽  
Amplicon Sequencing ◽  
Cell Type ◽  
Modeling And Analysis ◽  
Generative Modeling ◽  
Compositional Changes

Accurate generative statistical modeling of count data is of critical relevance for the analysis of biological datasets from high-throughput sequencing technologies. Important instances include the modeling of microbiome compositions from amplicon sequencing surveys and the analysis of cell type compositions derived from single-cell RNA sequencing. Microbial and cell type abundance data share remarkably similar statistical features, including their inherent compositionality and a natural hierarchical ordering of the individual components from taxonomic or cell lineage tree information, respectively. To this end, we introduce a Bayesian model for tree-aggregated amplicon and single-cell compositional data analysis (tascCODA) that seamlessly integrates hierarchical information and experimental covariate data into the generative modeling of compositional count data. By combining latent parameters based on the tree structure with spike-and-slab Lasso penalization, tascCODA can determine covariate effects across different levels of the population hierarchy in a data-driven parsimonious way. In the context of differential abundance testing, we validate tascCODA’s excellent performance on a comprehensive set of synthetic benchmark scenarios. Our analyses on human single-cell RNA-seq data from ulcerative colitis patients and amplicon data from patients with irritable bowel syndrome, respectively, identified aggregated cell type and taxon compositional changes that were more predictive and parsimonious than those proposed by other schemes. We posit that tascCODA1 constitutes a valuable addition to the growing statistical toolbox for generative modeling and analysis of compositional changes in microbial or cell population data.

scholarly journals CD94 1A transcripts characterize lymphoblastic lymphoma/leukemia of immature natural killer cell origin with distinct clinical features

Blood ◽  
2005 ◽  
Vol 106 (10) ◽  
pp. 3567-3574 ◽  
Author(s):  
Chung-Wu Lin ◽  
Ting-Yun Liu ◽  
Shee-Uan Chen ◽  
Kun-Teng Wang ◽  
L. Jeffrey Medeiros ◽  
...  
Keyword(s):  
T Cells ◽  
T Cell ◽  
Nk Cells ◽  
Natural Killer ◽  
Nk Cell ◽  
Killer Cell ◽  
Cell Lineage ◽  
Lymphoid Cells ◽  
Terminal Deoxynucleotidyl Transferase ◽  
Gene Rearrangements

AbstractMost lymphoblastic lymphomas (LBLs) are regarded as neoplasms of immature T cells because they express cytoplasmic CD3 and frequently carry T-cell receptor (TCR) gene rearrangements. Immature natural killer (NK) and T cells, however, have a common bipotent T/NK-cell precursor in the thymus, and NK cells also express cytoplasmic CD3. Thus, some LBLs could arise from immature NK cells. Mature NK cells express 2 CD94 transcripts: 1A, induced by interleukin 15 (IL-15), and 1B constitutively. Because immature NK cells require IL-15 for development, CD94 1A transcripts could be a marker of NK-LBL. To test this hypothesis, we used laser capture microdissection to isolate IL-15 receptor α+ lymphoid cells from the thymus and showed that these cells contained CD94 1A transcripts. We then assessed for CD94 transcripts in 21 cases of LBL that were cytoplasmic CD3+, nuclear terminal deoxynucleotidyl transferase positive (TdT+), and CD56-, consistent with either the T-cell or NK-cell lineage. We found that 7 LBLs expressed CD94 1A transcripts without TCR gene rearrangements, suggesting NK-cell lineage. Patients with NK-LBL were younger than patients with T-LBL (15 years versus 33 years; P = .11) and had a better 2-year survival (100% versus 27%; P &lt; .01). These results improve the current classification of LBL and contribute to our understanding of NK-cell differentiation.

scholarly journals Identification of a Human Natural Killer Cell Lineage-Restricted Progenitor in Fetal and Adult Tissues

Immunity ◽  
2015 ◽  
Vol 43 (2) ◽  
pp. 394-407 ◽  
Author(s):  
Virginie M. Renoux ◽  
Alya Zriwil ◽  
Claudia Peitzsch ◽  
Jakob Michaëlsson ◽  
Danielle Friberg ◽  
...  
Keyword(s):  
Natural Killer Cell ◽  
Natural Killer ◽  
Killer Cell ◽  
Cell Lineage ◽  
Human Natural Killer Cell ◽  
Adult Tissues
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