Porcine endogenous retroviruses (PERVs) integrate into germline DNA as proviral genome that enables vertical transmission from parents to their offspring. The provirus usually survives as part of the host genome rather than as an infectious agent, but may become pathogenic if it crosses species barriers. Therefore, replication-competent PERV should be controlled through selective breeding or knockout technologies. Two microRNAs (miRNAs), dual LTR1 and LTR2, were selected to inhibit the expression of PERV in primary porcine kidney cells. The inhibition efficiency of the miRNAs was compared based on their inhibition of different PERV regions, specifically long terminal repeats (LTRs), gag, pol, and env. Gene expression was quantified using real-time polymerase chain reaction and the C-type reverse transcriptase (RT) activity was determined. The messenger RNA (mRNA) expression of the PERV LTR and env regions was determined in HeLa cells co-cultured with primary porcine kidney cells. The mRNA expression of the LTR, gag, pol, and env regions of PERV was dramatically inhibited by dual miRNA from 24 to 144 h after transfection, with the highest inhibition observed for the LTR and pol regions at 120 h. Additionally, the RT activity of PERV in the co-culture experiment of porcine and human cells was reduced by 84.4% at the sixth passage. The dual LTR 1+2 miRNA efficiently silences PERV in primary porcine kidney cells.
Coculture Techniques ; DNA ; Endogenous Retroviruses ; Gene Expression ; Genome ; HeLa Cells ; Humans ; Kidney ; MicroRNAs ; Parents ; Proviruses ; Real-Time Polymerase Chain Reaction ; RNA, Messenger ; RNA-Directed DNA Polymerase ; Selective Breeding ; Terminal Repeat Sequences ; Transfection

OBJECTIVE: Respiratory viral infection of the neonatal period is highly contagious. Rapid and accurate diagnosis is important for proper treatment and prevention. However, the existing diagnostic method, respiratory virus cell culture, takes a long time to diagnose. Recent development of rapid diagnostic methods such as multiplex reverse transcriptase polymerase chain reaction (RT-PCR) enable early detection and effective treatment of respiratory viral infections. We compared the efficiency of multiplex RT-PCR and R-mix virus culture for rapid detection of respiratory viruses. METHODS: We retrospectively analyzed the clinical features and results of R-mix virus culture and multiplex RT-PCR with nasopharyngeal aspiration specimens in 117 newborns admitted to neonatal intensive care unit suspected of infectious diseases. RESULTS: R-mix virus culture was positive in 29 cases (24.8%) and RT-PCR in 86 cases (73.5%). R-mix virus culture and multiplex RTPCR were identical in 54 cases (positive 26 cases, negative 28 cases). Among 75 cases that showed different results, 60 showed negative result in R-mix virus culture and positive result in multiplex RT-PCR, and three showed positive result in R-mix virus culture and negative result in multiplex RT-PCR. Different viruses were detected in the remaining 12 cases by both methods. CONCLUSION: Multiplex RT-PCR is faster than R-mix virus culture and has the advantage of identifying new respiratory viruses. On the other hand, Multiplex RT-PCR is more susceptible to false positives and mixed infections than R-mix virus culture, so more attention is required when interpreting test results.
Cell Culture Techniques ; Coinfection ; Communicable Diseases ; Diagnosis ; Hand ; Humans ; Infant, Newborn ; Intensive Care, Neonatal ; Methods ; Retrospective Studies ; Reverse Transcriptase Polymerase Chain Reaction* ; RNA-Directed DNA Polymerase*

The diagnostic criteria for sequential rapidly destructive coxarthrosis remain unclear and this condition is rarely reported in patients with human immunodeficiency virus (HIV). Here, we report a case of an HIV-infected 73-year old female who experienced hip joint destruction. The patient was diagnosed with HIV in 2012 (at age 68 years) and began continuous treatment with nucleoside reverse transcriptase and protease inhibitors. Twenty-nine months after her HIV diagnosis, the patient experienced osteonecrosis of the right hip and underwent a total hip arthroplasty (THA). Twelve months post right-hip THA, X-ray results showed good outcomes. Eight months later (20 months post THA), however, osteolysis of the left femoral head was detected upon radiological exam and THA of the left hip was performed; chronic inflammation and fibrosis were identified in the resultant biopsy. Favorable results were obtained at 3 months after the second surgery.
Arthroplasty, Replacement, Hip ; Biopsy ; Diagnosis ; Female ; Femur Head ; Fibrosis ; Head ; Hip ; Hip Joint ; HIV ; Humans ; Humans ; Inflammation ; Osteoarthritis, Hip ; Osteolysis ; Osteonecrosis ; Protease Inhibitors ; RNA-Directed DNA Polymerase

The advent of oral antiviral agents has revolutionized hepatitis B treatment. It has led to decreased incidence and mortality related to hepatocellular carcinoma. However, although nucleos(t)ide analogs (NA) are fast and potent in inhibiting hepatitis B virus (HBV) polymerase and reverse transcriptase activity, complete cure of the virus is not possible. The complete eradication of HBV requires the covalently-closed-circular DNA (cccDNA) to be eliminated. Novel gene editing methods, such as zing finger nucleases, transcription activator-like effector nucleases, and the clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9) system, designed to target specific DNA sequences has great potential for therapeutic application. Among these, the CRISPR/Cas9 system may be the most feasible approach to eradicate HBV cccDNA. Further studies are needed to develop a more efficient and safer method of delivery using the CRISPR/Cas9 system to achieve complete cure of chronic hepatitis B.
Antiviral Agents ; Base Sequence ; Carcinoma, Hepatocellular ; Clustered Regularly Interspaced Short Palindromic Repeats ; DNA ; DNA, Circular ; Fingers ; Hepatitis B virus* ; Hepatitis B* ; Hepatitis B, Chronic ; Hepatitis* ; Incidence ; Methods ; Mortality ; RNA-Directed DNA Polymerase

There are high levels of co-incidence of porcine reproductive and respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) in porcine tissue. This study established a duplex nested reverse transcriptase polymerase chain reaction (RT-PCR) method that targets the genomic RNA of type 2 PRRSV and the mRNA of PCV2 in infected tissues. The method amplified discriminative bands of 347 bp and 265 bp specific for type 2 PRRSV and PCV2, respectively. The limits of detection of the duplex nested RT-PCR were 10(1.5) TCID₅₀/mL for type 2 PRRSV and 10² infected cells/mL for PCV2. The kappa statistic, which measures agreement between methods, was 0.867, indicating a good level of agreement. This RNA-based duplex RT-PCR approach can be another way to detect type 2 PRRSV and PCV2 simultaneously and with improved convenience.
Circovirus ; Limit of Detection ; Methods ; Porcine Reproductive and Respiratory Syndrome* ; Porcine respiratory and reproductive syndrome virus* ; Reverse Transcriptase Polymerase Chain Reaction* ; RNA ; RNA, Messenger ; RNA-Directed DNA Polymerase*

BACKGROUND: Abacavir is a widely-used nucleoside reverse transcriptase inhibitor for the treatment of human immunodeficiency virus (HIV) infection. Mandatory postmarketing surveillance was conducted in Korea to monitor the safety and evaluate the effectiveness of Ziagen® (abacavir sulfate 300 mg; ViiV Healthcare, Middlesex, UK). MATERIALS AND METHODS: An open-label, multi-center, non-interventional postmarketing surveillance study was conducted from June 2010 to June 2016 to monitor the safety and effectiveness of Ziagen across 12 hospitals in Korea. Subjects older than 18 years taking Ziagen according to prescribing information were enrolled. The primary outcome was defined as the occurrence of any adverse events after Ziagen administration. Secondary outcomes included the occurrence of adverse drug reactions, occurrence of serious adverse events, and effectiveness of Ziagen administration. RESULTS: A total of 669 patients were enrolled in this study, with a total observation period of 1047.8 person-years. Of these, 90.7% of patients were male. The mean age of patients was 45.8±11.9 years. One-hundred ninety-six (29.3%) patients reported 315 adverse events, and four patients reported seven serious adverse events, without any fatal events. There was one potential case of an abacavir hypersensitivity reaction. Among the 97 adverse drug reactions that were reported from 75 patients, the most frequent adverse drug reactions included diarrhea (12 events), dyspepsia (10 events), and rash (9 events). No ischemic heart disease was observed. In the effectiveness analysis, 91% of patients achieved HIV-1 RNA under 50 copies/mL after 24 months of observation with abacavir administration. CONCLUSION: Our data showed the safety and effectiveness of Ziagen in a real-world setting. During the study period, Ziagen was well-tolerated, with one incident of a clinically suspected abacavir hypersensitivity reaction. The postmarketing surveillance of Ziagen did not highlight any new safety information. These data may be helpful in understanding abacavir and the HIV treatment practices in Korea.
Delivery of Health Care ; Diarrhea ; Drug-Related Side Effects and Adverse Reactions ; Dyspepsia ; Exanthema ; HIV ; HIV-1 ; Humans ; Hypersensitivity ; Korea ; Male ; Myocardial Ischemia ; Pharmacoepidemiology ; RNA ; RNA-Directed DNA Polymerase

A 3-month-old male cat in the animal facility was presented for investigation of anorexia and occasional vomiting. We collected the specimens from gastroscopic biopsy and stool collection. The gastroscopic biopsy specimens were tested using a rapid urease test, CLO Helicobacter-detection kits. Stool specimens were gathered and evaluated using the commercially available SD Bioline H. pylori Ag kit according to the manufacturer's instructions. Genomic DNAs from gastroscopic biopsy and stool specimens of the cat were extracted and submitted to the consensus PCR to amplify Helicobacter rpoB gene. Then the DNAs from gastroscopic biopsy and stool specimens were conducted a multiplex species-specific PCR to amplify urease B gene for H. heilmannii, H. pylori and H. felis. As the results, the rapid urease test with gastroscopic biopsy was revealed positive reaction. The result of H. pylori Stool Ag assay was one red line, negative for H. pylori. The gastroscopic biopsy and stool specimen were positive reactions by the consensus PCR reaction using the RNA polymerase beta-subunit-coding gene (rpoB) to detect Helicobacter species. By multiplex species-specific PCR with gastroscopic biopsy and stool specimens, no amplification products corresponding to either H. heilmannii or H. pylori were detected, but the specimens tested were positive for H. felis. This case was confirmed as gastroenteric disease induced by H. felis infection. On our knowledge, this is a very rare report about H. felis-induced gastroenteric disease in cat and may provide a valuable data on the study of feline Helicobacter infection.
Animals ; Animals, Laboratory* ; Anorexia ; Biopsy ; Cats* ; Consensus ; DNA ; DNA-Directed RNA Polymerases ; Felis ; Helicobacter felis* ; Helicobacter Infections ; Helicobacter* ; Humans ; Infant ; Male ; Polymerase Chain Reaction ; Stomach Diseases* ; Urease ; Vomiting

A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and applied it to scan National Center for Biotechnology Information (NCBI) RefSeq bacterial genome sequences. Among 16,844 bacterial sequences possessing a retron-type RT domain, we identified 48 unique types of msDNA. Currently, the biological role of msDNA is not well understood. Our work will be a useful tool in studying the distribution, evolution, and physiological role of msDNA.
Biotechnology ; Chimera ; DNA ; DNA, Single-Stranded* ; Genome, Bacterial* ; Retroelements ; Reverse Transcription ; RNA ; RNA-Directed DNA Polymerase

The C-terminal domain of RNA polymerase II is an unusual series of repeated residues appended to the C-terminus of the largest subunit and serves as a flexible binding scaffold for numerous nuclear factors. The binding of these factors is determined by the phosphorylation patterns on the repeats in the domain. In this study, we generated a synthetic antibody library by replacing the third heavy chain complementarity-determining region of an anti-HER2 (human epidermal growth factor receptor 2) antibody (trastuzumab) with artificial sequences of 7–18 amino-acid residues. From this library, antibodies were selected that were specific to serine phosphopeptides that represent typical phosphorylation patterns on the functional unit (YSPTSPS)₂ of the RNA polymerase II C-terminal domain (CTD). Antibody clones pCTD-1stS2 and pCTD-2ndS2 showed specificity for peptides with phosphoserine at the second residues of the first or second heptamer repeat, respectively. Additional clones specifically reacted to peptides with phosphoserine at the fifth serine of the first repeat (pCTD-1stS5), the seventh residue of the first repeat and fifth residue of the second repeat (pCTD-S7S5) or the seventh residue of either the first or second repeat (pCTD-S7). All of these antibody clones successfully reacted to RNA polymerase II in immunoblot analysis. Interestingly, pCTD-2ndS2 precipitated predominately RNA polymerase II from the exonic regions of genes in genome-wide chromatin immunoprecipitation sequencing analysis, which suggests that the phosphoserine at the second residue of the second repeat of the functional unit (YSPTSPS)2 is a mediator of exon definition.
Antibodies ; Chromatin Immunoprecipitation ; Clone Cells ; Complementarity Determining Regions ; DNA-Directed RNA Polymerases* ; Exons* ; Peptides ; Phosphopeptides ; Phosphorylation* ; Phosphoserine ; Receptor, Epidermal Growth Factor ; RNA Polymerase II* ; RNA* ; Sensitivity and Specificity ; Serine

The purpose of this study was to develop Streptococcus sobrinus-specific qPCR primers based on the nucleotide sequence of the RNA polymerase β-subunit gene (rpoB). The specificity of the primers was determined by conventional polymerase chain reaction (PCR) with 12 strains of S. sobrinus and 50 strains (50 species) of non-S. sobrinus bacteria. The sensitivity of the primers was determined by quantitative real-time PCR (qPCR) with serial dilutions of the purified genomic DNAs (40 ng to 4 fg) of S. sobrinus ATCC 33478(T). The specificity data showed that the S. sobrinus-specific qPCR primers (RTSsob-F4/RTSsob-R4) detected only the genomic DNAs of S. sobrinus strains with a detection limit of up to 4 fg of S. sobrinus genomic DNA. Our results suggest that the RTSsob-F4/RTSsob-R4 primers are useful in detecting S. sobrinus with high sensitivity and specificity for epidemiological studies of dental caries.
Bacteria ; Base Sequence ; Dental Caries ; DNA ; DNA-Directed RNA Polymerases ; Epidemiologic Studies ; Limit of Detection ; Polymerase Chain Reaction ; Real-Time Polymerase Chain Reaction* ; Sensitivity and Specificity ; Streptococcus sobrinus* ; Streptococcus*