scholarly journals Quasispecies Composition of Small Ruminant Lentiviruses Found in Blood Leukocytes and Milk Epithelial Cells

Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2497
Author(s):  
Monika Olech ◽  
Arkadiusz Bomba ◽  
Jacek Kuźmak
Keyword(s):  
Epithelial Cells ◽  
Small Ruminant ◽  
Peripheral Blood Leukocytes ◽  
Blood Leukocytes ◽  
Single Nucleotide ◽  
Individual Host ◽  
Single Nucleotide Variations ◽  
Small Ruminant Lentiviruses ◽  
Double Immunolabeling

Small ruminant lentiviruses (SRLVs) exist as populations of closely related genetic variants, known as quasispecies, within an individual host. The privileged way of SRLVs transmission in goats is through the ingestion of colostrum and milk of infected does. Thus, characterization of SRLV variants transmitted through the milk, including milk epithelial cells (MEC), may provide useful information about the transmission and evolution of SRLVs. Therefore, the aim of this study was to detect SRLVs in peripheral blood leukocytes (PBLs) and milk epithelial cells of goats naturally infected with SRLVs and perform single nucleotide variations analysis to characterize the extent of genetic heterogeneity of detected SRLVs through comparison of their gag gene sequences. Blood and milk samples from 24 seropositive goats were tested in this study. The double immunolabeling against p28 and cytokeratin demonstrated that milk epithelial cells originated from naturally infected goats were infected by SRLVs. Moreover, PCR confirmed the presence of the integrated SRLVs proviral genome indicating that MECs may have a role as a reservoir of SRLVs and can transmit the virus through milk. The blood and MEC derived sequences from 7 goats were successfully sequenced using NGS and revealed that these sequences were genetically similar. The MEC and blood-derived sequences contained from 3 to 30 (mean, 10.8) and from 1 to 10 (mean, 5.4) unique SNVs, respectively. In five out of seven goats, SNVs occurred more frequent in MEC derived sequences. Non-synonymous SNVs were found in both, PBLs and MEC-derived sequences of analyzed goats and their total number differed between animals. The results of this study add to our understanding of SRLVs genomic variability. Our data provides evidence for the existence of SRLVs quasispecies and to our knowledge, this is the first study that showed quasispecies composition and minority variants of SRLVs present milk epithelial cells.

Molecular characterization of circulating strains of small ruminant lentiviruses in Brazil based on complete gag and pol genes

2019 ◽  
Vol 177 ◽  
pp. 160-166 ◽  
Author(s):  
Dalva Alana Aragão de Azevedo ◽  
Jomar Patrício Monteiro ◽  
Raymundo Rizaldo Pinheiro ◽  
Mauricio de Alvarenga Mudadu ◽  
Alice Andrioli ◽  
...  
Keyword(s):  
Molecular Characterization ◽  
Small Ruminant ◽  
Small Ruminant Lentiviruses

Serological characterization of small ruminant lentiviruses: A complete tool for serotyping lentivirus infection in goat

2019 ◽  
Vol 176 ◽  
pp. 42-46 ◽  
Author(s):  
Chiara Nogarol ◽  
Luigi Bertolotti ◽  
Siv Klevar ◽  
Margherita Profiti ◽  
Britt Gjerset ◽  
...  
Keyword(s):  
Small Ruminant ◽  
Serological Characterization ◽  
Small Ruminant Lentiviruses

scholarly journals Isolation, Synthesis, and Antimicrobial Activities of Naturally Occurring θ-Defensin Isoforms from Baboon Leukocytes

2008 ◽  
Vol 76 (12) ◽  
pp. 5883-5891 ◽  
Author(s):  
Angie E. Garcia ◽  
George Ösapay ◽  
Patti A. Tran ◽  
Jun Yuan ◽  
Michael E. Selsted
Keyword(s):  
Bone Marrow ◽  
Single Species ◽  
Antimicrobial Activities ◽  
Peripheral Blood Leukocytes ◽  
Blood Leukocytes ◽  
Naturally Occurring ◽  
Test Organisms ◽  
High Degree

ABSTRACT θ-Defensins are macrocyclic antimicrobial peptides that were previously isolated from leukocytes of a single species, the rhesus macaque. We now report the characterization of baboon θ-defensins (BTDs) expressed in bone marrow and peripheral blood leukocytes. Four cDNAs encoding θ-defensin precursors were characterized, allowing for the prediction of 10 theoretical θ-defensins (BTD-1 to BTD-10) produced by binary, head-to-tail splicing of nonapeptides excised from paired precursors. Five of the predicted θ-defensins were purified from baboon leukocytes, and synthetic versions of each were prepared. Anti-θ-defensin antibody localized the peptides in circulating neutrophils and monocytes and in immature and mature myeloid elements in bone marrow. Each of the BTDs possessed antimicrobial activity against bacterial and fungal test organisms in vitro. Peptide activities varied markedly despite a high degree of sequence conservation among the θ-defensins tested. Thus, baboons express numerous θ-defensins which appear to differentially contribute to host defense against diverse pathogens.

scholarly journals Using Single Nucleotide Variations in Single-Cell RNA-Seq to Identify Subpopulations and Genotype-phenotype Linkage

2016 ◽  
Author(s):  
Olivier Poirion ◽  
Xun Zhu ◽  
Travers Ching ◽  
Lana X. Garmire
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Single Cells ◽  
Transcript Abundance ◽  
Rna Seq ◽  
Linear Modeling ◽  
Modeling Framework ◽  
Single Nucleotide ◽  
Single Nucleotide Variations

AbstractDespite its popularity, characterization of subpopulations with transcript abundance is subject to a significant amount of noise. We propose to use effective and expressed nucleotide variations (eeSNVs) from scRNA-seq as alternative features for tumor subpopulation identification. We developed a linear modeling framework, SSrGE, to link eeSNVs associated with gene expression. In all the datasets tested, eeSNVs achieve better accuracies than gene expression for identifying subpopulations. Previously validated cancer-relevant genes are also highly ranked, confirming the significance of the method. Moreover, SSrGE is capable of analyzing coupled DNA-seq and RNA-seq data from the same single cells, demonstrating its value in integrating multi-omics single cell techniques. In summary, SNV features from scRNA-seq data have merits for both subpopulation identification and linkage of genotype-phenotype relationship. The method SSrGE is available at https://github.com/lanagarmire/SSrGE.

scholarly journals The Characterization of peripheral blood leukocytes during the development of adjuvant arthritis in rats.

Ensho ◽  
1992 ◽  
Vol 12 (1) ◽  
pp. 55-61
Author(s):  
Yoshihide Segawa ◽  
Masakatsu Nozaki ◽  
Kaito Tsurumi ◽  
Shunro Kohbata
Keyword(s):  
Peripheral Blood ◽  
Adjuvant Arthritis ◽  
Peripheral Blood Leukocytes ◽  
Blood Leukocytes

scholarly journals Characterization of the novel clinical isolate X-4 containing a new tp0548 sequence-type

2019 ◽  
Author(s):  
Dan Liu ◽  
Man-Li Tong ◽  
Li-Li Liu ◽  
Li-Rong Lin ◽  
Yu Lin ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Clinical Isolate ◽  
Treponema Pallidum ◽  
Sequence Type ◽  
The Novel ◽  
Single Nucleotide ◽  
Single Nucleotide Variations ◽  
Chromosomal Loci

AbstractBackgroundA novel tp0548 sequence-type was identified in one clinical isolate (X-4) from a patient diagnosed with primary syphilis in Xiamen, China. To precisely define and characterize this new clinical isolate, we performed further genome-scale molecular analysis.Methodology/Principal findingsThe alignment of all published tp0548 genotypes revealed that this new genotype had a unique nucleotide substitution G->T at position 167, and the letter “ao” was assigned to the genotype. Phylogenetic analysis showed that the “ao” genotype belonged to the SS14-like clade of Treponema pallidum (TPA) strains. The genome of the X-4 isolate was then sequenced and analyzed, and the result of a multi-locus sequence analysis using a set of nine chromosomal loci showed that the X-4 isolate was clustered with a monophyletic group of TPA strains, which clearly identified the isolate as a TPA strain. Whole-genome phylogenetic analysis was subsequently conducted to corroborate the TPA strain classification of the X-4 isolate. And the isolate was genetically related to the SS14 strain, with 42 single nucleotide variations and 12 insertions/deletions. In addition, high intrastrain heterogeneity in the length of the poly G/C tracts was found in the TPAChi_0347 locus, which indicated that this gene was most likely involved in phase variation events. The first investigation of the length heterogeneity of the poly A/T tracts showed the variability of the ploy A/T was lower, and all the observed intrastrain variations fell within coding regions.Conclusions/SignificanceThe study demonstrated the X-4 isolate was a TPA isolate containing a novel tp0548 sequence-type. The identification of intrastrain genetic heterogeneity at poly G/C tracts and poly A/T tracts of the isolate could provide a snapshot of the genes that potentially involved in genotype-phenotype variations. These findings provide an unequivocal characterization for better understanding the molecular variation of this emerging isolate.Author summaryThree subspecies of Treponema pallidum (pallidum, pertenue, and endemicum) are increasingly showing overlap in terms of transmission and clinical manifestations. We recently identified a novel tp0548 genotype in the X-4 isolate, which was obtained from an adult male with genital lesions. The novel genotype contained a unique nucleotide substitution G->T at position 167 and belonged to the SS14-like clade of TPA strains, as determined by phylogenetic analysis. We conducted an in-depth exploration of the genome of the X-4 isolate using the pooled segment genome sequencing method followed by Illumina sequencing. Multi-locus sequence analysis of nine chromosomal loci demonstrated that the X-4 isolate was clustered within a monophyletic group of TPA strains, which identified the isolate as a TPA strain. Whole-genome phylogenetic analysis subsequently corroborated the TPA strain classification of the X-4 isolate and revealed that the isolate was very closely related to the SS14 strain, with 42 single nucleotide variations and 12 insertions/deletions. In addition, characterization of the intrastrain heterogeneity in the lengths of homopolymeric tracts in the X-4 isolate showed that the heterogeneity of the poly G/C tracts was greater than that of the poly A/T tracts, and high poly G/C tract diversity was observed in the TPAChi_0347 locus.

High-Throughput Sequencing for Diagnosis, Prognosis and Monitoring of Lymphoid Malignancies

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 3779-3779
Author(s):  
Scott D Boyd ◽  
Jason D. Merker ◽  
James L. Zehnder ◽  
Andrew Z Fire
Keyword(s):  
High Throughput ◽  
Peripheral Blood ◽  
Read Length ◽  
Peripheral Blood Leukocytes ◽  
Blood Leukocytes ◽  
Normal Peripheral Blood ◽  
Dilution Series ◽  
Lymphoid Malignancies ◽  
Immune Receptors

Abstract New high-throughput DNA sequencing methods have many advantages for the analysis of rearranged immunoglobulin (Ig) and T cell receptor (TCR) loci in suspected lymphoid malignancies. Instead of primarily analyzing the size distribution of rearranged immune receptors using gel or capillary electrophoresis, sequencing complex nucleic acid pools provides much more complete characterization of the receptor sequences present. Currently, separate assays are used to evaluate Ig and TCR clonality, Ig hypermutation status, and to test for residual malignant cells after treatment. We used multiplexed PCR amplification of immunoglobulin heavy chain loci for high-throughput pyrosequencing with the Roche 454 platform to evaluate the detection of clonal IgH sequences, determination of hypermutation status, and sensitivity of detection of low levels of a known clonal receptor. Our method also evaluated the feasibility of physical “bar-coding” of DNA molecules derived from different samples to enable cost-effective sequencing of sample pools. 23 pooled specimens were sequenced including: known lymphoma specimens (4); peripheral blood leukocytes from normal individuals (4); specimens with indeterminate or discordant results by conventional clonality assays (7); and a dilution series of a clonal CLL/SLL specimen into normal peripheral blood leukocytes. Our initial experiment characterized 522,099 IgH sequences from these specimens, with a mean read length of 242 base pairs. We have employed IgBlast (NCBI) for initial alignment of rearranged IgH sequences to germline V, D and J gene segments. Our data demonstrate that clonal IgH populations can be readily detected and characterized as to their germline or hypermutated status and unique V-D and D-J junctions with this approach. In our dilution series experiment, the clonal receptor sequence could be reliably observed after 1000-fold dilution. Normal patient specimens show expected extensive sequence diversity, and we are exploring methods for optimally summarizing and representing these data. Some PCR artifacts, as well as non-immunoglobulin sequences commonly amplified by current IgH primer sets were also detected, and suggest avenues for further improvement of the methods used for detection and characterization of clonal immune receptors. More broadly, these methods also offer a novel approach to monitoring normal immune responses such as the response of patients to vaccination, and of characterizing the immune system in patients with autoimmune diseases.

Functional characterization of NBC4: a new electrogenic sodium-bicarbonate cotransporter

2002 ◽  
Vol 282 (2) ◽  
pp. C408-C416 ◽  
Author(s):  
Pejvak Sassani ◽  
Alexander Pushkin ◽  
Eitan Gross ◽  
Alla Gomer ◽  
Natalia Abuladze ◽  
...  
Keyword(s):  
Sodium Bicarbonate ◽  
Mammalian Cells ◽  
Functional Characterization ◽  
Amino Acid Level ◽  
Peripheral Blood Leukocytes ◽  
Blood Leukocytes ◽  
Bicarbonate Transporter ◽  
Sodium Bicarbonate Cotransporter ◽  
Protein Variants

Sodium-bicarbonate cotransporters are homologous membrane proteins mediating the electrogenic or electroneutral transport of sodium and bicarbonate. Of the functionally characterized sodium-bicarbonate cotransporters (NBC), NBC1proteins are known to be electrogenic. Here we report the cloning and functional characterization of NBC4c, a new splice variant of the NBC4 gene. At the amino acid level, NBC4c is 56% identical to NBC1 protein variants and 40% identical to electroneutral NBC3. When expressed in mammalian cells, NBC4c mediates electrogenic sodium-bicarbonate cotransport. The transport of sodium and bicarbonate is chloride independent and is completely inhibited by DIDS. NBC4c transcripts were detected in several tissues including brain, heart, kidney, testis, pancreas, muscle, and peripheral blood leukocytes. The data indicate that NBC4c is an electrogenic sodium-bicarbonate cotransporter. The finding that both NBC1 and NBC4c proteins function as electrogenic sodium-bicarbonate cotransporters will aid in determining the structural motifs responsible for this unique functional property, which distinguishes these transporters from other members of the bicarbonate transporter superfamily.

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