scholarly journals Sequence variability ofChrysanthemum stunt viroidin different chrysanthemum cultivars

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e2933 ◽  
Author(s):  
Hoseong Choi ◽  
Yeonhwa Jo ◽  
Ju-Yeon Yoon ◽  
Seung-Kook Choi ◽  
Won Kyong Cho

Viroids are the smallest infectious agents, and their genomes consist of a short single strand of RNA that does not encode any protein.Chrysanthemum stunt viroid(CSVd), a member of the familyPospiviroidae, causes chrysanthemum stunt disease. Here, we report the genomic variations of CSVd to understand the sequence variability of CSVd in different chrysanthemum cultivars. We randomly sampled 36 different chrysanthemum cultivars and examined the infection of CSVd in each cultivar by reverse transcription polymerase chain reaction (RT-PCR). Eleven cultivars were infected by CSVd. Cloning followed by Sanger sequencing successfully identified a total of 271 CSVd genomes derived from 12 plants from 11 cultivars. They were further classified into 105 CSVd variants. Each single chrysanthemum plant had a different set of CSVd variants. Moreover, different single plants from the same cultivar had different sets of CSVd variants but identical consensus genome sequences. A phylogenetic tree using 12 consensus genome sequences revealed three groups of CSVd genomes, while six different groups were defined by the phylogenetic analysis using 105 variants. Based on the consensus CSVd genome, by combining all variant sequences, we identified 99 single-nucleotide variations (SNVs) as well as three nucleotide positions showing high mutation rates. Although 99 SNVs were identified, most CSVd genomes in this study were derived from variant 1, which is identical to known CSVd SK1 showing pathogenicity.

1994 ◽  
Vol 299 (1) ◽  
pp. 207-211 ◽  
Author(s):  
F Umenishi ◽  
E Kajii ◽  
S Ikemoto

To investigate the genetic basis of the Rh polypeptide gene, we attempted the isolation of cDNA clones for Rh polypeptide from a family with the RhD-positive and RhD-negative phenotypes using the reverse transcription (RT)-PCR method for each reticulocyte RNAs followed by subcloning. The isolated cDNAs showed the existence of another Rh-related clone (RhPII-1 cDNA, tentative designation) besides the RhPI and RhPII cDNA clones reported previously by us. The RhPII-1 cDNA had a single nucleotide substitution with one amino acid substitution compared with the RhPII cDNA:substitution C-->T in nucleotide 380, changing codon 127 from GCG to GTG (Ala->Val). The RhPI, RhPII, and RhPII-1 cDNA clones were detected in all individuals by the PCR experiment. This suggests that the Rh polypeptide genes have been inherited from parents and might be highly polymorphic. The PCR amplification of an RhPII-specific region from reticulocyte RNA and genomic DNA in all the family proved that the RhPII gene exists in both RhD-positive and RhD-negative individuals. By Southern-blot analysis of the DNAs from the family, two independent polymorphisms concerning the RhC/c and RhD/d phenotypes were observed. These results demonstrate that the RhPI and RhPII genes are also present in the RhD-negative donors, and the RhPII-related cDNAs encode not the RhD, but the RhC/c and/or E/e, polypeptides.


2020 ◽  
Vol 13 (9) ◽  
pp. 1764-1770
Author(s):  
Jorge Miranda ◽  
Lina Violet-Lozano ◽  
Samia Barrera ◽  
Salim Mattar ◽  
Santiago Monsalve-Buriticá ◽  
...  

Background and Aim: Wildlife animals are reservoirs of a large number of microorganisms pathogenic to humans, and ticks could be responsible for the transmission of these pathogens. Rickettsia spp. are the most prevalent pathogens found in ticks. This study was conducted to detect Rickettsia spp. in ticks collected from free-living and illegally trafficked reptiles from the Department of Córdoba, Colombia. Materials and Methods: During the period from October 2011 to July 2014, ticks belonging to the family Ixodidae were collected, preserved in 96% ethanol, identified using taxonomic keys, and pooled (between 1 and 14 ticks) according to sex, stage, host, and collected place for subsequent DNA extraction. Rickettsia detection was performed using real-time polymerase chain reaction (RT-PCR), followed by conventional PCR to amplify a larger fragment of the gltA and 16S rRNA genes. The amplicons were sequenced using the Sanger method, and the nucleotide sequences were subjected to BLAST analysis to identify homologous sequences in GenBank, after which phylogenetic analysis was performed using the MEGA X software. Results: In total, 21 specimens of nine species of reptiles were sampled, from which 805 Amblyomma dissimile ticks were collected, but only 180 ticks were selected to create 34 groups. The DNA of Rickettsia spp. was detected in 30/34 (88%) groups. The sequences of the gene gltA and 16S rRNA revealed a 100% identity with Candidatus Rickettsia colombianensi (GenBank: KF905456 and GenBank: KF691750). Conclusion: A. dissimile was the only tick found in all the sampled reptiles. The presence of Candidatus Rickettsia colombianensi in reptile ticks could represent a public health problem due to the risk of transmission to humans and the introduction of microorganisms to other geographical areas.


Blood ◽  
1995 ◽  
Vol 86 (6) ◽  
pp. 2146-2155 ◽  
Author(s):  
S Pearson-White ◽  
D Deacon ◽  
R Crittenden ◽  
G Brady ◽  
N Iscove ◽  
...  

The ski/sno protooncogenes encode nuclear proteins that may act as transcription factors. We examined ski and sno mRNA expression in hemolymphopoietic lineages. The ski protooncogene is expressed in B- and T-lineage cells, mature macrophages, and mast cells. In normal murine marrow-derived progenitors analyzed by single-cell reverse transcription-polymerase chain reaction (RT-PCR), ski expression is limited to dual-lineage megakaryocyte/erythrocyte colony-starts. Expression of sno is more limited than ski in mature cells; it is expressed in T lymphopoietic cells, but not in B-lineage cells. The sno protooncogene is expressed more widely than ski in myeloid progenitors, as it is found consistently in tri-, dual-, and single-lineage progenitors. Both ski and sno are cell cycle-regulated in synchronized factor-dependent mouse myeloid cells. Expression of ski mRNA peaks in mid G1 in cells synchronized by isoleucine deprivation in the presence of growth factor, but falls off rapidly when growth factor is withdrawn. Expression of sno mRNA is maximal in early to mid G1 and then oscillates as the cells continue through cycle. These results suggest that the ski/sno protooncogenes play a role in hematopoiesis, growth factor responses, and cell cycle-regulation, with the two members of the family showing differing properties.


Author(s):  
Scott C. Roberts ◽  
Teresa R. Zembower ◽  
Egon A. Ozer ◽  
Chao Qi

Whole-genome sequences of Candida auris isolates from nosocomial and non-nosocomial infections were compared. The average number of single nucleotide variations were different between the two groups. The small amount of genetic variability between intra- or inter-host isolates suggests recovering all colonizing or infecting genomes for comparison is required for outbreaks.


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 2319-2319
Author(s):  
Benjamin Kim ◽  
Zachary A. Hing ◽  
Andrew Wu ◽  
Tal Schiller ◽  
Evi B. Struble ◽  
...  

Abstract Background Although autosomal recessive hematologic disorders are individually rare and difficult to ascertain, studies involving one or more homozygous affected children and their unaffected heterozygous parents have led to expanded understanding of known and discovery of previously unknown processes. The son and daughter of two Salvadoran parents were diagnosed with congenital thrombotic thrombocytopenic purpura (cTTP) at 6 and 2 years of age, respectively, after presenting with fever, respiratory symptoms, hemolytic anemia, and thrombocytopenia and being found to have ADAMTS13 activities <1% without neutralizing IgG antibodies. They remain without long-term neurologic or renal sequelae following prophylactic infusions of fresh plasma (10 mL/kg every 2.5-weeks). The purpose of this study was to characterize and correlate single-nucleotide variations (SNVs) in each parent's, non-mutant ADAMTS13 allele with its mRNA and protein expression, activity, and enzyme kinetics. Methods Prior to a plasma infusion, blood samples were collected from the children and parents. Genomic DNA was isolated for polymerase chain reaction (PCR), and direct Sanger sequencing of all ADAMTS13 exons and flanking intronic segments was performed; all variants identified were confirmed by bidirectional sequencing of a second, independently generated amplicon. Total RNA was isolated and the steady-state level of ADAMTS13 mRNA was measured using a quantitative real-time PCR (q-RT-PCR)-based assay. ADAMTS13 was characterized enzymatically using the fluorogenic FRETS-VWF73 substrate and antigenically by ELISA. Results Both children were found to be homozygous and parents to be heterozygous for the previously described, cTTP-causing ADAMTS13 single-base-substitution mutation 20506C>T, a missense mutation that encodes cDNA-nucleotide 2518 (c.2518C>T) and ADAMTS13 residue 692 (692Arg>Cys [692R>C]) (Fig. A). As expected, the children's ADAMTS13 antigen and activity levels were undetectable, although notably, steady-state levels of the ADAMTS13 mRNA were >2.5-fold higher in the daughter than in the son. The re-sequenced regions of the ADAMTS13 loci segregating within this family contained 26 additional SNVs, seven of which were nonsynonymous (ns) including two previously unreported ns-SNVs: 27852C>T (c.3362C>T; 972Arg>Trp) and 33325G>A (c.3733G>A; 1096Arg>His) (Fig. A, left panel). The parents' genotypes differed at nine positions, including three ns-SNVs, creating two distinct, non-mutant haplotypes (designated I and III) at the gene, mRNA and protein levels. The q-RT-PCR assay revealed >4-fold higher steady-state mRNA levels in the father compared to the mother (p<0.001; Fig. B). Plasma ADAMTS13 activity and antigen levels were ∼2-fold greater in the father than in the mother (p=0.00164 and p=0.0633, respectively), but the specific activities of these structurally distinct ADAMTS13 proteins were notably almost identical (253.5 vs. 256.2 U/μg). Moreover, initial velocity kinetic analysis using the Michelis-Menten equation demonstrated that the Vmax of the father's ADAMTS13 was twice that of the mother's (1.4 vs. 0.7; p < 0.0001) while its affinity for substrate was one-third that of her ADAMTS13 (Km = 0.3 vs. 0.1; p = 0.0585). Discussion We capitalized on the fortuitous finding of children with complete homozygosity across ancestrally-related ADAMTS13 alleles harboring a null-type, loss-of-function mutation, as this enabled the substantially different levels of gene expression and function observed in the parents to be attributed to their two previously unreported, SNV-based, ADAMTS13 haplotypes. Additional investigation at the molecular, biochemical, cellular, and organismal levels will be necessary to determine which of the myriad potential individual SNV- and/or haplotype-based mechanisms are responsible for the observed parental differences in circulating ADAMTS13 antigen and activity. Disclosures: Kim: Haplomics, Inc.: Membership on an entity’s Board of Directors or advisory committees; Baxter: Honoraria. Marder:Baxter: Research Funding. Howard:Haplomics, Inc.: Equity Ownership, Membership on an entity’s Board of Directors or advisory committees; Baxter: Research Funding.


2018 ◽  
Vol 6 (25) ◽  
Author(s):  
Alisha A. Mullen ◽  
Ciara D. Lynch ◽  
Shannon M. Hill ◽  
Cian P. Holohan ◽  
Tadhg Ó Cróinín ◽  
...  

ABSTRACT No genome sequence of a species from Barnettozyma, a yeast genus in the family Phaffomycetaceae, is currently available. We isolated two B. californica strains from soils in Ireland and generated draft sequences of their 11.7-Mb genomes. Single nucleotide polymorphism (SNP) analysis showed 20,490 differences between the strains and suggests that B. californica is haploid.


2017 ◽  
Vol 61 (3) ◽  
pp. 5-11 ◽  
Author(s):  
Z. Mojžišová ◽  
P. Drzewnioková ◽  
E. Bocková ◽  
B. Vargová ◽  
V. Majláthová ◽  
...  

AbstractThe tick-borne encephalitis virus (TBEV) and West Nile virus (WNV) are arboviruses of the genusFlavivirusin the familyFlaviviridae. Their hosts are vertebratesof which rodents are the reservoirs of TBEV and birds are the reservoirs of WNV. Both viruses are transmitted from reservoirs to mammals by vectors. TBEV is transmitted by ticks (mostlyIxodesspp.) and WNV by mosquitoes (mostlyCulexspp.). Both viruses are capable of infecting mammals, including man. TBEV and WNV are neurotropic, however infection is, in most cases, subclinical or accompanied by only moderate general signs. However, in some cases they can cause serious disturbances of the CNS. Our study focused on the detection of the genomes of TBEV and WNV in vectors by means of the reverse-transcription polymerase chain reaction (RT-PCR). The flavivirus genome was detected by means of oligonucleotides delineating the sequence in NS5 gene that encodes viral RNA-dependent RNA-polymerase. For the detection of TBEV, we used the oligonucleotide pair detecting the structural envelope protein. The positive samples were subjected to the sequence and phylogenetic analysis. The WNV was not detected in any of the pooled samples prepared from 616 mosquitoes captured in the vicinity of the village Drienovec, district Košice-surroundings. The investigation of 676 ticks demonstrated the presence of one strain of TBEV. One blood-fedI. ricinusfemale was obtained from a goat grazing in a pasture in the Dúbrava area close to Prešov. The genetic analysis revealed the presence of a strain close to the endemic strainsof TBEV Hypr and Neudörfl. The results of our study can become a motivation for additional studies in model locations oriented on ecology and circulation of these important zoonotic flaviviruses.


Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 966
Author(s):  
Eleonora Chelli ◽  
Luca De Sabato ◽  
Gabriele Vaccari ◽  
Fabio Ostanello ◽  
Ilaria Di Bartolo

Porcine sapelovirus (PSV) belongs to the genus Sapelovirus of the family Picornaviridae. PSV infects pigs asymptomatically, but it can also cause severe neurologic, enteric, and respiratory symptoms or reproductive failure. Sapelovirus infections have been reported worldwide in pigs. The objective of this study was to investigate the presence and the prevalence of PSV in Italian swine farms in animals of different ages to clarify the occurrence of the infection and the genetic characteristics of circulating strains. In the present study, 92 pools of fecal samples, collected from pigs across three farms, were analyzed by Reverse Transcriptase-polymerase Chain Reaction-PCR (RT-PCR). Fecal pools from young growers (63/64) were found positive for Sapelovirus in all farms while detection in sows (4/28) was observed in only one farm. Phylogenetic analyses of the 19 partial capsid protein nucleotide sequences (VP1) (6–7 each farm) enable the classification of the virus sequences into three distinct clades and highlighted the high heterogeneity within one farm. The whole genome sequence obtained from one strain showed the highest correlation with the Italian strain detected in 2015. The study adds novel information about the circulation and heterogeneity of PSV strains in Italy and considering the movement of pigs across Europe would also be informative for other countries.


2018 ◽  
Vol 46 (05) ◽  
pp. 304-308 ◽  
Author(s):  
Svenja Funcke ◽  
Michael Lierz ◽  
Susanne Paries

Summary Objective: Tortoise picornavirus (ToPV) has been speculated to play an important role in the frequently seen disease pattern of juvenile shell softening. This study aimed to determine ToPV prevalence among German tortoise collections. Material and methods: A total of 334 animals selected from 27 different collections were included. Seven species of four genera of the family Testudinidae (Testudo graeca, T. hermanni, T. marginata, T. horsfieldii, Centrochelys sulcata, Stigmochelys pardalis, Chelonoidis carbonarius) were sampled. The tortoises were clinically investigated and none of the adults showed any signs of shell softening. Seven hatchlings of a ToPV-positive T. graeca breeding pair showed retarded growth and a progressive shell weakness that resulted in death. Each animal was sampled by conjunctival, pharyngeal and cloacal swabs (990 swabs in total) and blood sampling (293 in total). All three swabs of one animal were pooled and tested by reverse transcriptase polymerase chain reaction (RT-PCR) for tortoise picornavirus RNA. Blood samples were investigated by virus neutralisation test (VNT) for specific anti ToPV antibodies. All titres equal to or higher than log2 = 2 were considered positive. Results: In total, 35 adult and 11 juvenile animals were tested positive for ToPV RNA. The serological investigation did detect specific antibodies against ToPV in 44 adult tortoises and one juvenile. In total, 76 animals were tested positive in either one of the investigations, 16 animals in both. The highest number of ToPV-positive animals was found for T. graeca, with a prevalence of 32 %. No specimens of C. carbonarius, C. sulcata, or S. pardalis were tested positive. Conclusion and clinical relevance: The results propose a predisposition in T. graeca, as well as a high prevalence of ToPV in T. graeca, whereas other species showed only single or no positive animals, but may function as virus carriers.


2002 ◽  
Vol 129 (1) ◽  
pp. 113-117 ◽  
Author(s):  
K. STENE-JOHANSEN ◽  
P. A. JENUM ◽  
T. HOEL ◽  
H. BLYSTAD ◽  
H. SUNDE ◽  
...  

Several outbreaks of hepatitis A occurred in Norway in 1995–8. Molecular epidemiology was used to follow the spread of hepatitis A virus in the population. Distinct strains of hepatitis A virus (HAV) were detected by reverse transcriptase–polymerase chain reaction (RT–PCR) and subsequent sequencing in serum from patients in different communities at risk of infection. Two HAV strains were detected in an outbreak among 26 men having sexual contact with other men. One of these strains was also detected in a geographically limited family outbreak. The family outbreak was first believed to be acquired abroad. The sequence information linked the two outbreaks, and epidemiological and serological analyses revealed the transmission route. This study demonstrates the importance of molecular epidemiology in outbreak investigation, surveillance and monitoring of hepatitis A in the population.


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