scholarly journals Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques

2016 ◽  
Author(s):  
Trent M. Prall ◽  
Michael E. Graham ◽  
Julie A. Karl ◽  
Roger W. Wiseman ◽  
Adam J. Ericsen ◽  
...  
Keyword(s):  
Rhesus Macaques ◽  
Killer Cell ◽  
Full Length ◽  
Human Pathogens ◽  
New Genes ◽  
Target Capture ◽  
Cynomolgus Macaques ◽  
Novel Alleles ◽  
Sequencing Platforms ◽  
Allele Discovery

ABSTRACTKiller cell Immunoglobulin-like Receptors (KIRs) modulate disease progression of pathogens including HIV, malaria, and hepatitis C. Cynomolgus and rhesus macaques are widely used as nonhuman primate models to study human pathogens and so considerable effort has been put into characterizing their KIR genetics. However, previous studies have relied on cDNA cloning and Sanger sequencing that lacks the throughput of current sequencing platforms. In this study, we present a high throughput, full-length allele discovery method utilizing PacBio circular consensus sequencing (CCS). We also describe a new approach to Macaque Exome Sequencing (MES) and the development of the Rhexome1.0, an adapted target capture reagent that includes macaque-specific capture probesets. By using sequence reads generated by whole genome sequencing (WGS) and MES to inform primer design, we were able to increase the sensitivity of KIR allele discovery. We demonstrate this increased sensitivity by defining nine novel alleles within a cohort of Mauritian cynomolgus macaques (MCM), a geographically isolated population with restricted KIR genetics that was thought to be completely characterized. Finally, we describe an approach to genotyping KIRs directly from sequence reads generated using WGS/MES reads. The findings presented here expand our understanding of KIR genetics in MCM by associating new genes with all eight KIR haplotypes and demonstrating the existence of at least one KIR3DS gene associated with every haplotype.

scholarly journals Improved full-length killer cell immunoglobulin-like receptor transcript discovery in Mauritian cynomolgus macaques

2017 ◽  
Vol 69 (5) ◽  
pp. 325-339 ◽  
Author(s):  
Trent M. Prall ◽  
Michael E. Graham ◽  
Julie A. Karl ◽  
Roger W. Wiseman ◽  
Adam J. Ericsen ◽  
...  
Keyword(s):  
Killer Cell ◽  
Full Length ◽  
Cynomolgus Macaques ◽  
Transcript Discovery

scholarly journals Major histocompatibility complex haplotyping and long-amplicon allele discovery in cynomolgus macaques from Chinese breeding facilities

2016 ◽  
Author(s):  
Julie A. Karl ◽  
Michael E. Graham ◽  
Roger W. Wiseman ◽  
Katelyn E. Heimbruch ◽  
Samantha M. Gieger ◽  
...  
Keyword(s):  
Major Histocompatibility Complex ◽  
Mhc Class I ◽  
Mhc Class Ii ◽  
Cynomolgus Macaque ◽  
Full Length ◽  
Class I ◽  
Major Histocompatibility ◽  
Histocompatibility Complex ◽  
Cynomolgus Macaques ◽  
Allele Discovery

ABSTRACTVery little is currently known about the major histocompatibility complex (MHC) region of cynomolgus macaques (Macaca fascicularis; Mafa) from Chinese breeding centers. We performed comprehensive MHC class I haplotype analysis of 100 cynomolgus macaques from two different centers, with animals from different reported original geographic origins (Vietnamese, Cambodian, and Cambodian/Indonesian mixed-origin). Many of the samples were of known relation to each other (sire, dam, and progeny sets), making it possible to characterize lineage-level haplotypes in these animals. We identified 52 Mafa-A and 74 Mafa-B haplotypes in this cohort, many of which were restricted to specific sample origins. We also characterized full-length MHC class I transcripts using Pacific Biosciences (PacBio) RS II single-molecule real-time (SMRT) sequencing. This technology allows for complete read-through of unfragmented MHC class I transcripts (~1,100 bp in length), so no assembly is required to unambiguously resolve novel full-length sequences. Overall, we identified 313 total full-length transcripts in a subset of 72 cynomolgus macaques from these Chinese breeding facilities; 131 of these sequences were novel and an additional 116 extended existing short database sequences to span the complete open reading frame. This significantly expands the number of Mafa-A, Mafa-B, and Mafa-I full-length alleles in the official cynomolgus macaque MHC class I database. The PacBio technique described here represents a general method for full-length allele discovery and genotyping that can be extended to other complex immune loci such as MHC class II, killer immunoglobulin-like receptors, and Fc gamma receptors.

scholarly journals Full-length transcriptome analysis reveals the mechanism of acupuncture at PC6 improves cardiac function in myocardial ischemia model

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Jing Yuan ◽  
Jun-Meng Wang ◽  
Zhi-Wei Li ◽  
Cheng-Shun Zhang ◽  
Bin Cheng ◽  
...  
Keyword(s):  
Myocardial Ischemia ◽  
Cardiac Function ◽  
Acupuncture Treatment ◽  
Pathological Process ◽  
Full Length ◽  
The Novel ◽  
New Genes ◽  
Myocardial Infraction ◽  
Differential Expression Genes ◽  
Multi Level

Abstract Background The pathological process of myocardial ischemia (MI) is very complicated. Acupuncture at PC6 has been proved to be effective against MI injury, but the mechanism remains unclear. This study investigated the mechanism that underlies the effect of acupuncture on MI through full-length transcriptome. Methods Adult male C57/BL6 mice were randomly divided into control, MI, and PC6 groups. Mice in MI and PC6 group generated MI model by ligating the left anterior descending (LAD) coronary artery. The samples were collected 5 days after acupuncture treatment. Results The results showed that treatment by acupuncture improved cardiac function, decreased myocardial infraction area, and reduced the levels of cTnT and cTnI. Based on full-length transcriptome sequencing, 5083 differential expression genes (DEGs) and 324 DEGs were identified in the MI group and PC6 group, respectively. These genes regulated by acupuncture were mainly enriched in the inflammatory response pathway. Alternative splicing (AS) is a post-transcriptional action that contributes to the diversity of protein. In all samples, 8237 AS events associated with 1994 genes were found. Some differential AS-involved genes were enriched in the pathway related to heart disease. We also identified 602 new genes, 4 of which may the novel targets of acupuncture in MI. Conclusions Our findings suggest that the effect of acupuncture on MI may be based on the multi-level regulation of the transcriptome.

scholarly journals Structural and Functional Diversity among Five RING Finger Proteins from Carassius Auratus Herpesvirus (CaHV)

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 254
Author(s):  
Zi-Hao Wang ◽  
Fei Ke ◽  
Qi-Ya Zhang ◽  
Jian-Fang Gui
Keyword(s):  
Subcellular Localization ◽  
Carassius Auratus ◽  
Ring Finger ◽  
Structural Diversity ◽  
Full Length ◽  
Ring Domain ◽  
Whole Cells ◽  
Host Interaction ◽  
New Genes ◽  
Ring Finger Proteins

Carassius auratus herpesvirus (CaHV) has been identified as a high-virulence pathogenic virus that infects aquatic animals, but the key factor for virus–host interaction is still unclear. Five Really interesting new genes (RING) finger proteins (39L, 52L, 131R, 136L, and 143R) of CaHV were screened to determine structural diversity. RING finger proteins were also predicted in other known fish herpesviruses, with an arrangement and number similar to CaHV. We performed multifaceted analyses of the proteins, including protein sizes, skeleton structures, subcellular localizations, and ubiquitination activities, to determine their precise roles in virus–host interactions. The five proteins were overexpressed and detected different levels of ubiquitination activities, and 143R showed the highest activity. Then, the prokaryotic expressed and purified full-length proteins (131R and 136L), RING domain isolates (131R12–43 and 136L45–87), and RING domain-deleted mutants (131RΔ12–43 and 136LΔ45–87) were prepared to detect their activities through ubiquitination assays. The results indicate that both full-length proteins and their isolates have activities that catalyze ubiquitination, and the full-length proteins possess higher activity than the isolates, but RING domain-deleted mutants lose their activities. Furthermore, the activities of the five proteins were verified as E3 ubiquitin ligase activity, showing that the RING domains determine the ubiquitination activity. These proteins present different subcellular localization. RING domain-deleted mutants showed similar subcellular localization with their full-length proteins, and all the isolates diffused in whole cells. The current results indicate that the sequence outside the RING domain determines subcellular localization and the level of ubiquitination activity, suggesting that the RING finger proteins of fish herpesviruses might have diverse functions in virus–host interaction.

scholarly journals Characterization of full-length MHC class II sequences in Indonesian and Vietnamese cynomolgus macaques

2011 ◽  
Vol 63 (9) ◽  
pp. 611-618 ◽  
Author(s):  
Hannah M. Creager ◽  
Ericka A. Becker ◽  
Kelly K. Sandman ◽  
Julie A. Karl ◽  
Simon M. Lank ◽  
...  
Keyword(s):  
Mhc Class Ii ◽  
Class Ii ◽  
Full Length ◽  
Cynomolgus Macaques

scholarly journals Ultrasound-guided, Transabdominal, Intrauterine Artificial Insemination for Cynomolgus Macaques (Macaca fascicularis) Based on Estimated Timing of Ovulation

2021 ◽  
Vol 60 (2) ◽  
pp. 125-132
Author(s):  
Nobuhiro Shimozawa ◽  
Naohide Ageyama ◽  
Shunya Nakayama ◽  
Hiroshi Koie ◽  
Yasuhiro Yasutomi
Keyword(s):  
Artificial Insemination ◽  
Macaca Fascicularis ◽  
Rhesus Macaques ◽  
Complex Structure ◽  
Pregnancy Rates ◽  
Cervical Canal ◽  
Ultrasound Guided ◽  
Cynomolgus Macaques

Intrauterine sperm injection for artificial insemination is difficult in cynomolgus macaques (Macaca fascicularis) and rhesus macaques (M. mulatta) due to the complex structure of the cervical canal, which differs from that of humans. Despite the availability of several artificial insemination methods for macaques, pregnancy rates are inconsistent, and details regarding ovulation are unclear, thus warranting more effective methods. Therefore, we developed an effective, ultrasound-guided, transabdominal intrauterine artificial insemination method for cynomolgus macaques that involves timing sperm injection to coincide with the periovulation phase estimated according to rapid hormone measurement. We performed our intrauterine artificial insemination on 6 female macaques; 4 of the 5 animals that were predicted to have ovulated soon after insemination became pregnant, whereas the 1 macaque that was predicted not to have ovulated did not. Furthermore, we saw no evidence of injury, such as a conspicuous needle hole or bleeding on the surface of or inside the uterus, nor did our method result in any abnormalities in the mothers or their offspring. Thus, our ultrasound-guided, transabdominal, intrauterine artificial insemination method is rapid, safe, and effective in cynomolgus macaques.

scholarly journals Association of the killer immunoglobulin-like receptor genes KIR2DS1 and KIR2DS4 with pediatric autoimmune hepatitis type I in Egypt

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ola Galal Behairy ◽  
Ola Samir El-Shimi ◽  
Naglaa Hamed Shalan ◽  
Shaymaa Mohamed Baghdady
Keyword(s):  
Autoimmune Hepatitis ◽  
Matched Control ◽  
Killer Cell ◽  
Full Length ◽  
Type I ◽  
Egyptian Children ◽  
Human Natural Killer Cells ◽  
And Function ◽  
Control Study ◽  
Apparently Healthy

Abstract Background Killer cell immunoglobulin-like receptors (KIR) are considered to be the key receptors that control the development and function of human natural killer cells which play complex mechanisms in autoimmune diseases. We aimed in this study to assess possible associations between killer cell immunoglobulin-like receptors (KIR2DS1 and 2DS4) genes and susceptibility to autoimmune hepatitis type I in Egyptian children. Results In the case-control study conducted on eighty children diagnosed as autoimmune hepatitis (AIH) type I and eighty apparently healthy age and sex-matched control, we found that KIR2DS1, -2DS4, KIR2DS4-full length allele, and homozygous KIR2DS4-full/full variant were significantly associated with AIH-I, while the KIR1D allele and homozygous KIR2DS4-del/del variant were significantly observed in controls (P < 0.05 each). Absence of KIR2DS4 gene was significant among ANA positive AIH-I patients, patients on steroid therapy alone, and patients showing complete disease remission (P < 0.05 each). Higher activity and fibrosis indices were found significantly in patients lacking one or both studied genes. Conclusions Children carrying KIR2DS1, -2DS4 genes, KIR2DS4-full length allele, and homozygous KIR2DS4-full/full variant could be more susceptible to develop autoimmune hepatitis type I.

Physiological characteristic changes and full-length transcriptome of rose (Rosa chinensis) roots and leaves in response to drought stress

2020 ◽  
Author(s):  
Wei Li ◽  
Lufeng Fu ◽  
Ziwen Geng ◽  
Xiaojuan Zhao ◽  
Qinghua Liu ◽  
...  
Keyword(s):  
Acetic Acid ◽  
Drought Stress ◽  
Posttranscriptional Regulation ◽  
Regulatory Networks ◽  
Average Length ◽  
Physiological Characteristic ◽  
Full Length ◽  
Rosa Chinensis ◽  
New Genes ◽  
Leaves And Roots

Abstract Rose (Rosa chinensis) is the most important ornamental crops worldwide. However, the physiological and molecular mechanism of rose under drought stress remains elusive. In this study, we analyzed the changes of photosynthetic and phytohormone levels in the leaves and roots of rose seedlings grown under control (no drought/ND), mild (MD), and severe (SD) drought stress. The total chlorophyll content and water use efficiency were significantly enhanced under MD in rose leaves. In addition, the concentration of abscisic acid (ABA) was higher in the leaves compared to the roots, whereas the roots accumulated more indole-3-acetic acid (IAA), methylindole-3-acetic acid (Me-IAA) and indole-3-propionic acid (IPA). We also constructed the first full-length transcriptome for rose, and identified 96,201,862 full-length reads of average length 1,149 bp that included 65,789 novel transcripts. A total of 3,657 and 4,341 differentially expressed genes (DEGs) were identified in rose leaves and roots respectively. KEGG pathway analysis showed enrichment of plant hormone, signal transduction, and photosynthesis are among the DEGs. 42,544 alternatively spliced isoforms were also identified, and alternative 3ʹ splice site was the major alternative splicing (AS) event among the DEGs. Variations in the AS patterns of three genes between leaves and roots indicated the possibility of tissue-specific posttranscriptional regulation in response to drought stress. Furthermore, 2,410 novel long non-coding RNAs were detected that may participate in regulating the drought-induced DEGs. Our findings identified previously unknown splice sites and new genes in the rose transcriptome, and elucidated the drought stress-responsive genes as well as their intricate regulatory networks.

scholarly journals Extracellular Cystatin F Is Internalised by Cytotoxic T Lymphocytes and Decreases Their Cytotoxicity

Cancers ◽  
2020 ◽  
Vol 12 (12) ◽  
pp. 3660
Author(s):  
Mateja Prunk ◽  
Milica Perišić Nanut ◽  
Tanja Jakoš ◽  
Jerica Sabotič ◽  
Urban Švajger ◽  
...  
Keyword(s):  
T Lymphocytes ◽  
Cytotoxic T Lymphocytes ◽  
Cathepsin L ◽  
Killer Cell ◽  
Full Length ◽  
Cytotoxic T Cell ◽  
Target Cells ◽  
Natural Killer Cell Cytotoxicity ◽  
Cathepsin C ◽  
Cysteine Cathepsins

Cystatin F is a protein inhibitor of cysteine cathepsins, peptidases involved in the activation of the effector molecules of the perforin/granzyme pathway. Cystatin F was previously shown to regulate natural killer cell cytotoxicity. Here, we show that extracellular cystatin F has a role in regulating the killing efficiency of cytotoxic T lymphocytes (CTLs). Extracellular cystatin F was internalised into TALL-104 cells, a cytotoxic T cell line, and decreased their cathepsin C and H activity. Correspondingly, granzyme A and B activity was also decreased and, most importantly, the killing efficiency of TALL-104 cells as well as primary human CTLs was reduced. The N-terminally truncated form of cystatin F, which can directly inhibit cathepsin C (unlike the full-length form), was more effective than the full-length inhibitor. Furthermore, cystatin F decreased cathepsin L activity, which, however, did not affect perforin processing. Cystatin F derived from K-562 target cells could also decrease the cytotoxicity of TALL-104 cells. These results clearly show that, by inhibiting cysteine cathepsin proteolytic activity, extracellular cystatin F can decrease the cytotoxicity of CTLs and thus compromise their function.

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