RNA Reverse Transcription-polymerase Chain Reaction Research Articles

First report of groundnut ringspot virus infecting Zinnia sp. in Brazil.

Zinnia sp. is a genus belonging to Asteraceae family, originated in Mexico and adapted to a warm-hot climate (Hemmati and Mehrnoosh, 2017). Several types of zinnias with different flower color and forms are cultivated in Brazil (Min et al., 2020 and Souza Jr. et al., 2020). Characteristic symptoms of infection caused by orthotospovirus, including chlorotic spots and concentric rings on the leaves, were observed in two plants of Zinnia sp. of a florist located in the city of Piracicaba, State of São Paulo, Brazil. Orthotospovirus-like particles were observed by transmission electron microscope in leaf extracts from both plants, stained negatively with 1% uranyl acetate. By analyzing ultrathin sections of infected leaf tissues, particles of 80-100 nm in diameter were found in the lumen of the endoplasmic reticulum and nucleocapsid aggregates in the cytoplasm. Total RNA extracted separately from the leaves of both samples, using the Purelink Viral DNA / RNA kit (Thermo Fisher Scientific), was used to detect the virus by reverse transcription polymerase chain reaction (RT-PCR), using the universal primers for orthotospovirus BR60, complementary to the 3' end of the non-translated region of the S RNA (position 1 to 15 nt), and BR65, matching the nucleocapsid gene (N) (position 433 to 453 nt), generating and amplicon of 453 nt (Eiras et al., 2001). Amplicons of the expected size were obtained for the two samples. An amplicon was purified with the Wizard SV Gel and PCR Clean-Up System kit (Promega) and sequenced in both directions at Macrogen Inc (South Korea). The nucleotide sequence (GenBank MW629018) showed 99.29-99.76% identity with nucleotide sequences of the orthotospovirus groundnut ringspot virus (GRSV) isolates (GenBank MH686229 and KY400110). Leaf extracts from symptomatic plants were also analyzed by plate-trapped antigen-enzyme-linked immunosorbent assay (PTA-ELISA), using polyclonal antiserum produced against the GRSV nucleocapsid protein (Esquivel et al., 2019). The absorbance values obtained for the extracts of the two symptomatic plants of Zinnia sp. (1.3 and 1.7) were twice as high as the value obtained for the healthy plant extract (0.5). Leaf extract of symptomatic Zinnia sp. was inoculated mechanically onto leaves of healthy plants of Zinnia sp., Capsicum annuum cv. Dara, Cucumis sativus, Cucurbita pepo cv. Caserta, Chenopodium amaranticolor, Datura stramonium, Nicotiana tabacum cv. Turkish and Solanum lycopersicum cv. Compack. At 5 days post inoculation (dpi), inoculated leaves of D. stramonium reacted with local lesions, and at 9 dpi, newly developed leaves of inoculated S. lycopersicum plants showed necrotic spot and concentric ring symptoms, whereas C. annuum exhibited concentric rings at 10 dpi. Inoculated zinnia plants showed systemic chlorotic spot and concentric ring symptoms at 20 dpi, indistinguishable from those observed under natural infection. The other inoculated plant species were not symptomatic, nor the virus was detected. PTA-ELISA and RT-PCR confirmed infection with GRSV in symptomatic plants. The amplicons generated by RT-PCR of total RNA extracted from an experimentally infected plant of C. annuum and D. stramonium, and two plants of Zinnia sp. were sent for nucleotide sequencing. The obtained nucleotide sequences (MW629019, MW629020, MW629021, MW629022) shares 100% identity with the nucleotide sequence corresponding to the original GRSV isolate (MW629018) identified in Zinnia sp. This is the first report of the natural occurrence of GRSV in Zinnia sp. in Brazil. Studies on incidence and damage are needed to recommend alternatives for management.

Evidence of Severe Acute Respiratory Syndrome Coronavirus 2 Replication and Tropism in the Lungs, Airways, and Vascular Endothelium of Patients With Fatal Coronavirus Disease 2019: An Autopsy Case Series.

BackgroundThe coronavirus disease 2019 (COVID-19) pandemic continues to produce substantial morbidity and mortality. To understand the reasons for the wide-spectrum complications and severe outcomes of COVID-19, we aimed to identify cellular targets of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) tropism and replication in various tissues.MethodsWe evaluated RNA extracted from formalin-fixed, paraffin-embedded autopsy tissues from 64 case patients (age range, 1 month to 84 years; 21 COVID-19 confirmed, 43 suspected COVID-19) by SARS-CoV-2 reverse-transcription polymerase chain reaction (RT-PCR). For cellular localization of SARS-CoV-2 RNA and viral characterization, we performed in situ hybridization (ISH), subgenomic RNA RT-PCR, and whole-genome sequencing.ResultsSARS-CoV-2 was identified by RT-PCR in 32 case patients (21 COVID-19 confirmed, 11 suspected). ISH was positive in 20 and subgenomic RNA RT-PCR was positive in 17 of 32 RT-PCR–positive case patients. SARS-CoV-2 RNA was localized by ISH in hyaline membranes, pneumocytes, and macrophages of lungs; epithelial cells of airways; and endothelial cells and vessel walls of brain stem, leptomeninges, lung, heart, liver, kidney, and pancreas. The D614G variant was detected in 9 RT-PCR–positive case patients.ConclusionsWe identified cellular targets of SARS-CoV-2 tropism and replication in the lungs and airways and demonstrated its direct infection in vascular endothelium. This work provides important insights into COVID-19 pathogenesis and mechanisms of severe outcomes.

Nanostring-based screening for tyrosine kinase fusions in inflammatory myofibroblastic tumors

Gene expression imbalances were measured for tyrosine kinase (TK) genes using Nanostring in 19 samples of inflammatory myofibroblastic tumor (IMT). All cases were immunohistochemically stained with anaplastic lymphoma kinase (ALK) and pan-tropomyosin-related-kinase (pan-Trk) antibodies. Five cases with imbalanced ALK expression, reported with Nanostring, were tested using fluorescence in situ hybridization (FISH); two cases with imbalanced neurotrophic tyrosine receptor kinase 3 (NTRK3) expression were tested using reverse transcription-polymerase chain reaction (RT-PCR). One case with imbalanced expression for ROS proto-oncogene 1 (ROS1) was tested using RNA sequencing and RT-PCR. TK fusions were detected in all cases with imbalanced TK expression. RNA sequencing detected a FN1–ROS1 fusion gene in an adult IMT case. IMT with ALK rearrangement showed myofibroblast-dominant features. IMT with ETV6–NTRK3 fusion showed prominent lymphoplasmacytic infiltration with scattered myofibroblasts. Pan-Trk IHC revealed only scattered positively stained cells in IMT with ETV6–NTRK3 fusion gene. ROS1-positive IMT showed myofibroblast-dominant features.

The Negative RT-PCR Test is Enough to Rule Out Covıd-19 in Cancer Patients or Not? Covıd-19 or Not?

At the end of 2019, a new coronavirus pneumonia turned into an epidemic in China and then spread to other countries around the world. This disease was identified as the COVID-19 (SARS-CoV-2) disease. SARS-CoV-2 RNA is detected by Reverse-Transcription Polymerase Chain Reaction (RT-PCR). A positive test for SARS-CoV-2 may confirm the diagnosis of COVID-19, but the results of false negativity and false positivity can be confusing. This article describes the negative COVID-19 RNA RT-PCR test results of four cancer patients with symptoms/clinical findings suggestive of COVID-19 and also computed tomography findings consistent with viral pneumonia.

Laboratory verification of an RT-PCR assay for SARS-CoV-2.

BackgroundReverse transcription‐polymerase chain reaction (RT‐PCR) is an extremely common clinical method for detecting pathogens, particularly for emerging infectious diseases such as the new coronavirus disease (COVID‐19). Currently, detection of the RNA from the novel coronavirus SARS‐CoV‐2 is the gold standard for establishing a COVID‐19 diagnosis. This study evaluates the characteristic performance of the analytical system in a clinical laboratory.MethodsA commercial SARS‐CoV‐2 RNA RT‐PCR Kit used in a clinical laboratory is assessed based on ISO 15189 verification requirements. A multiple real‐time RT‐PCR assay for the RdRP, N, and E genes in SARS‐CoV‐2 is verified.ResultsThe analytical system exhibits good analytical sensitivity (1000 copies/mL) and specificity (100%); however, the values of 86.7% and 100% for analytical accuracy deserved attention, compared with two other types of methods. Overall, the kit is potentially useful for SARS‐CoV‐2 diagnostic testing and meets the verification requirements.ConclusionCompliance with international standards, such as ISO 15189, is valuable for clinical laboratories and for improving laboratory medicine quality and safety. Normalization is essential for obtaining reliable results from the SARS‐CoV‐2 RNA RT‐PCR assay. This study aims to develop an improved SARS‐CoV‐2 verification framework compared with traditional molecular diagnostic methods, given the urgency of implementing new assays in clinical laboratories.

Incidence of norovirus in tropical seafood harbouring fecal indicator bacteria

The occurrence of human norovirus (HuNoV) in fresh seafood was studied by reverse transcription-polymerase chain reaction (RT-PCR). Samples (n = 104) comprising of oysters, clams, shrimps and finfish were collected from 3 retail markets, a landing center and a rocky intertidal zone. The samples were subjected to virus concentration, followed by RNA extraction and RT-PCR. Of these, 43 (41.34%) samples were positive for HuNoV Group II (GII). The fecal contamination status of the samples was determined by the Most Probable Number (MPN) method. All (100%) the samples were fecally contaminated, with the fecal coliform counts ranging from 10 to >1400 MPN/100 g. The study shows that fresh seafood, especially the bivalve mollusks, can act as vehicles for transmission and spread of HuNoV in the community. The high level of HuNoV contamination of seafood not only constitutes a health risk to the domestic consumers, but also compromises the microbiological qualities of seafood meant for international trade.

A sensitive haemadsorption technique based RT-PCR for concentration and detection of Newcastle disease virus from clinical samples and allantoic fluid.

The present study describes the exploitation of haemadsorption (HAd) property of the Newcastle disease virus (NDV) for the development of a novel sensitive HAd technique based RT-PCR for detection of NDV from clinical samples of virus infected experimental birds. The NDV propagated allantoic fluid from the infected embryonated chicken eggs or supernatant of the processed clinical samples (tissue triturate, cloaca and tracheal swabs) from the experimentally infected birds were added with chicken red blood cells (RBC) to adsorb the virus on RBC's surface. The virus adsorbed RBCs were subjected to trizol method of RNA extraction and reverse transcription-polymerase chain reaction (RT-PCR) for detection of NDV. The HAd based RNA extraction showed better yield of 700-900ng RNA and when subjected to RT-PCR detection revealed a 100 times higher sensitivity than the conventional RNA extraction and RT-PCR detection system. This could be an alternate technique which can be exploited in low NDV load situations in clinical samples.

Identifikasi Polerovirus Penyebab Klorosis pada Cabai Asal Bali, Indonesia

Based on the results of a survey conducted on chilipepper plants in Kertha Village, Payangan Subdistrict, Gianyar District, Bali Province, many chilipepper plants with chlorosis symptoms caused by the virus was observed. Infected plants showed yellowing of the lamina, but the veins remain green. Identification was focused on the Pepper vein yellows virus (PeVYV) through transmission using Aphis nasturtii, observation on the morphology of virus particles, total RNA detection by reverse transcription-polymerase chain reaction (RT-PCR), and nucleotide sequence. The results showed that the disease can be transmitted from infected plant to healthy plant using A. nasturtii. Viral particle has hexagonal shape with the diameter ~30 nm. RT-PCR of total RNA from severe, moderate, and mild symptomatic infected plants, using specific primer sets for coat protein gene of PeVYV successfully amplified DNA with size of ~650 bp. Coat protein gene sequence of PeVYV isolates Bali, Indonesia showing different chlorosis intensity had the highest homology with PeVYV isolates from Taiwan 95.1–96.6%. Based on the data, PeVYV has been confirmed as the cause of chlorosis in chilipepper plants in Bali, Indonesia.

Absence of detectable influenza RNA transmitted via aerosol during various human respiratory activities--experiments from Singapore and Hong Kong.

Two independent studies by two separate research teams (from Hong Kong and Singapore) failed to detect any influenza RNA landing on, or inhaled by, a life-like, human manikin target, after exposure to naturally influenza-infected volunteers. For the Hong Kong experiments, 9 influenza-infected volunteers were recruited to breathe, talk/count and cough, from 0.1 m and 0.5 m distance, onto a mouth-breathing manikin. Aerosolised droplets exhaled from the volunteers and entering the manikin’s mouth were collected with PTFE filters and an aerosol sampler, in separate experiments. Virus detection was performed using an in-house influenza RNA reverse-transcription polymerase chain reaction (RT-PCR) assay. No influenza RNA was detected from any of the PTFE filters or air samples. For the Singapore experiments, 6 influenza-infected volunteers were asked to breathe (nasal/mouth breathing), talk (counting in English/second language), cough (from 1 m/0.1 m away) and laugh, onto a thermal, breathing manikin. The manikin’s face was swabbed at specific points (around both eyes, the nostrils and the mouth) before and after exposure to each of these respiratory activities, and was cleaned between each activity with medical grade alcohol swabs. Shadowgraph imaging was used to record the generation of these respiratory aerosols from the infected volunteers and their impact onto the target manikin. No influenza RNA was detected from any of these swabs with either team’s in-house diagnostic influenza assays. All the influenza-infected volunteers had diagnostic swabs taken at recruitment that confirmed influenza (A/H1, A/H3 or B) infection with high viral loads, ranging from 105-108 copies/mL (Hong Kong volunteers/assay) and 104–107 copies/mL influenza viral RNA (Singapore volunteers/assay). These findings suggest that influenza RNA may not be readily transmitted from naturally-infected human source to susceptible recipients via these natural respiratory activities, within these exposure time-frames. Various reasons are discussed in an attempt to explain these findings.

Molecular epidemiology and putative origin of hepatitis C virus in random volunteers from Argentina

To study the subtype prevalence and the phylogenetic relatedness of hepatitis C virus (HCV) sequences obtained from the Argentine general population, a large cohort of individuals was analyzed. Healthy Argentinian volunteers (n = 6251) from 12 provinces representing all geographical regions of the country were studied. All parents or legal guardians of individuals younger than 18 years provided informed written consent for participation. The corresponding written permission from all municipal authorities was obtained from each city or town where subjects were to be included. HCV RNA reverse transcription-polymerase chain reaction products were sequenced and phylogenetically analyzed. The 5' untranslated region (5'UTR) was used for RNA detection and initial genotype classification. The NS5B polymerase region, encompassing nt 8262-8610, was used for subtyping. An unexpectedly low prevalence of HCV infection in the general population (0.32%) was observed. Our data contrasted with previous studies that reported rates ranging from 1.5% to 2.5%, mainly performed in selected populations of blood donors or vulnerable groups. The latter values are in keeping with the prevalence reported by the 2007 Argentinian HCV Consensus (approximately 2%). HCV subtypes were distributed as follows: 1a (25%), 1b (25%), 2c (25%), 3a (5%), and 2j (5%). Two isolates ascribed either to genotype 1 (5%) or to genotype 3 (5%) by 5'UTR phylogenetic analysis could not be subtyped. Subtype 1a sequences comprised a highly homogeneous population and clustered with United States sequences. Genotype 1b sequences represented a heterogeneous population, suggesting that this genotype might have been introduced from different sources. Most subtype 2c sequences clustered close to the 2c reported from Italy and Southern France. HCV has a low prevalence of 0.32% in the studied general population of Argentina. The pattern of HCV introduction and transmission in Argentina appears to be a consequence of multiple events and different for each subtype.

Cloning and expression of genes enocoding antimicrobial peptides and bradykinin from the skin and brain of Oki Tago's brown frog, Rana tagoi okiensis

Previous studies led to the isolation from skin extracts of Oki Tago's brown frog, Rana tagoi okiensis of five antimicrobial peptides belonging to the brevinin-1 (brevinin-1TOa), temporin (temporin-TOa and -TOb), and ranatuerin-2 (ranatuerin-2TOa and -2TOb) families, and bradykinin (BK) identical to mammalian BK. Using the reverse-transcription polymerase chain reaction (RT-PCR), we have now cloned from skin total RNA preparations cDNAs encoding biosynthetic precursors of brevinin-1TOa and brevinin-1TOb (containing the substitution Gly 1 → Val), temporin-TOa and -TOb, and ranatuerin-2TOa and -2TOb. In addition, three cDNA clones encoding preprobradykinins were obtained that contained either one, two, or three tandem repeats of the sequence of BK followed by the sequence of [Thr 6]-BK. In tissue expression analyses, preprobrevinin-1, preprotemporin, and preproranatuerin-2 gene transcripts were detected at higher levels in brain compared with peripheral tissues (heart, small intestine, kidney, liver lung, skeletal muscle, stomach, and testis). RT-PCR of brain RNA resulted in the amplification of cDNAs encoding ranatuerin-2TOc and ranatuerin-2TOd that contained the amino acid substitutions Lys 6 → Arg and Ala 14 → Thr, respectively compared with ranatuerin-2TOb. cDNAs encoding preprobrevinin-1TOa and preprotemporin-TOa were amplified from brain RNA as well as a second preprotemporin cDNA that contained a 10-nucleotide insertion that introduced a frame shift resulting in a premature stop codon. A cDNA encoding a novel peptide, DK25 (DVNDLKNLCAKTHNLLPMCAMFGKK) was amplified from brain RNA but neither DK25 nor its putative post-translationally modified form, DF22-amide (DVNDLKNLCAKTHNLLPMCAMF·NH 2) displayed antimicrobial or hemolytic activities.

Detecting Carcinoma Cells in Peripheral Blood of Patients With Hepatocellular Carcinoma by Immunomagnetic Beads and RT-PCR

Increasing the sensitivity and specificity of detecting circulating carcinoma cells of patients with hepatocellular carcinoma (HCC) is very important for monitoring recurrence. To establish a novel method of detecting circulating carcinoma cells. For method development, 3 sets of controls using HCC cell line HepG2 cells were used. (A): Serial dilutions of HepG2 cells were directly used to extract total RNA for nested reverse transcription-polymerase chain reaction (RT-PCR). (B): Five milliliter of healthy blood was spiked with a serial dilution of HepG2 cells and was used for Ficoll density gradient centrifugation to recover cells. The cells were used to extract total RNA for RT-PCR. (C): After cell recovery with the same procedure as B, the cells were sorted sequentially by CD45 and Ber-EP4 immunomagnetic beads and used for RNA extraction and RT-PCR. For clinical samples, 44 patients with HCC and 7 healthy subjects were included. The alpha-fetoprotein mRNA was amplified using nested RT-PCR technique. The spiking experiments using HepG2 cells showed that 10 cells in 5 mL blood could be detected by method C and an excellent dose-response to the number of spiked cells. Whereas, method B lacked any dose-response and would yield high false-positive rates. In clinical samples, the improved method led to a positive detection rate of 52.9%, 76.9%, and 92.9% in Child-Plug class A, B, and C, respectively. There was significant difference between class A and class C (P<0.05). The total positive detection rate was 72.7%. Combining negative and positive immunomagnetic beads with RT-PCR technique may improve the sensitivity and specificity of detecting circulating HCC cells.

Matrix and gene expression in the rat cranial base growth plate

Recent data have shown that the proliferation and differentiation of the cranial base growth plate (CBGP) chondrocytes are modulated by mechanical stresses. However, little is known about the expression of genes and matrix molecules in the CBGP during development or under mechanical stresses. The objective of the present study was to determine whether several cartilage- and bone-related molecules are expressed in the CBGP and whether their expression is modulated by cyclic loading. The CBGP of normal 8-day-old rats (n=8) were isolated immediately after death, followed by extraction of total RNA and reverse transcription/polymerase chain reaction (RT-PCR) analysis. All studied genes, including type II and X collagens, biglycan, versican, osteocalcin, osteopontin, and fetal liver kinase 1, were expressed in the CBGP with a reproducible absence of decorin mRNA. In age- and sex-matched rats (n=10), exogenous cyclic forces were applied to the maxilla at 500 mN and 4 Hz for 20 min/day over 2 days, followed by RNA isolation and RT-PCR analysis. This exogenous cyclic loading consistently induced the expression of the decorin gene, which was non-detectable, by the current RT-PCR approach, in control neonatal CBGPs without loading. Immunolocalization of several of the above-studied gene products demonstrated their remarkable site-specific expression. Decorin proteoglycan was primarily expressed in the perichondrium instead of various cartilage growth zones, especially upon mechanical loading. These findings serve as baseline data for the expression of several genes and gene products in the neonatal CBGP. Mechanical modulation of decorin expression is consistent with recent reports of its susceptibility to mechanical loading in several connective tissues.

Tenofovir Disoproxil Fumarate and an Optimized Background Regimen of Antiretroviral Agents as Salvage Therapy for Pediatric HIV Infection

Highly active antiretroviral therapy has altered the course of HIV infection among children, but new antiretroviral agents are needed for treatment-experienced children with drug-resistant virus. Tenofovir disoproxil fumarate (DF) is a promising agent for use in pediatric salvage therapy, because of its tolerability, efficacy, and resistance profile. We designed this study to provide preliminary pediatric safety and dosing information on tenofovir DF, while also providing potentially efficacious salvage therapy for heavily treatment-experienced, HIV-infected children. Tenofovir DF, alone and in combination with optimized background antiretroviral regimens, was studied among 18 HIV-infected children (age range: 8.3-16.2 years) who had progressive disease with > or = 2 prior antiretroviral regimens, in a single-center, open-label trial. Tenofovir DF monotherapy for 6 days was followed by the addition of individualized antiretroviral regimens. Subjects were monitored with HIV RNA reverse transcription-polymerase chain reaction, flow cytometry, and routine laboratory studies; monitoring for bone toxicity included measurement of lumbar spine bone mineral density (BMD) with dual-energy x-ray absorptiometry. Subjects were monitored through 48 weeks. Two subjects developed grade 3 elevated hepatic transaminase levels during monotherapy and were removed from the study. The remaining 16 subjects had a median of 4 antiretroviral agents (range: 3-5 agents) added to tenofovir DF. HIV plasma RNA levels decreased from a median pretreatment level of 5.4 log10 copies per mL (range: 4.1-5.9 log10 copies per mL) to 4.21 log10 copies per mL at week 48 (n = 15), with 6 subjects having < 400 copies per mL, including 4 with < 50 copies per mL. The overall median increases in CD4+ T cell counts were 58 cells per mm3 (range: -64 to 589 cells per mm3) at week 24 and 0 cells per mm3 (range: -274 to 768 cells per mm3) at week 48. The CD4+ cell responses among the virologic responders were high and sustained. The major toxicity attributed to tenofovir DF was a >6% decrease in BMD for 5 of 15 subjects evaluated at week 48, necessitating the discontinuation of tenofovir DF therapy for 2; all 5 subjects experienced >2 log10 copies per mL decreases in HIV plasma RNA levels. Tenofovir DF-containing, individualized, highly active antiretroviral therapy regimens were well tolerated and effective among heavily treatment-experienced, HIV-infected children. Loss of BMD may limit tenofovir DF use among prepubertal patients.

Expression of Estrogen Receptor ESR1 and Its 46-kDa Variant in the Gubernaculum Testis1

Testicular descent corresponds to migration of the testis from the abdominal cavity to the scrotum and is essential for proper functioning of the testis. Recent advances in the characterization of estrogen receptor (ESR) subtypes and isoforms in various tissues prompted us to study ESRs within the gubernaculum testis, a structure involved in testicular descent. In the rat gubernaculum, we searched for ESR alpha (Esr1) and beta (Esr2) and for the androgen receptor (Ar), androgens being known to regulate testicular descent. Reverse transcription-polymerase chain reaction (RT-PCR) revealed that Esr1, Esr2, and Ar mRNAs were all expressed in the gubernaculum. Using PEETA (Primer extension, Electrophoresis, Elution, Tailing, and Amplification), we established that all Esr1 leader exons, previously identified in other organs, such as the uterus and pituitary, were transcribed in the gubernaculum, with the major form being O/B. The RNA protection assays, RT-PCR, and Western blot experiments revealed that isoform-specific mRNA transcripts generated by alternative splicing of the C-leader sequence on coding exons 1 and 2 of the Esr1 gene gave the 46- and 66-kDa ESR1 proteins. The ESR1 and AR proteins were found to colocalize in the parenchymal cells of the gubernaculum early in development, whereas AR also was strongly expressed in the muscular cells, both during fetal and postnatal life. The ESR2 protein was weakly expressed, principally in the muscular cells, but only once testicular descent had occurred. The levels of the 46-kDa ESR1 variant (ER46) exceeded those of the 66-kDa ESR1 form (ER66) at periods when the gubernaculum developed. Conversely, the 66-kDa form appears to predominate clearly when the gubernaculum growth was low or completed. The possible role of estrogens on the modulation of the androgen-dependent growth of the gubernaculum and, more widely, on testicular descent is discussed.

Hematopoietic progenitor cell transplantation from a donor with indeterminate human immunodeficiency virus antibody status

A 53-year-old woman with acute myeloid leukemia achieved remission after two courses of induction chemotherapy. Allogeneic hematopoietic progenitor cell transplantation (HPCT) was planned. HLA typing of three siblings identified a 49-year-old fully matched sister. The potential donor’s test result for human immunodeficiency virus (HIV-1 and -2) antibody, however, was “indeterminate” by two commercial kits (VIDAS HIV DUO, bioMerieux, France, which detects antibodies against gp41, gp36, subtype group O, and p24 antigen; and AxSYM HIV-1/-2 assay, Abbott Laboratories, Wiesbaden, Germany, which detects antibodies against HIV-group M envelope, HIV-group O envelope, HIV-core, and HIV-2 envelope), as well as by Western blot (HIV blot 2.2 Western blot assay, Genelabs Diagnostics, Singapore). The same results were obtained when repeated after 4 and 8 months. Neither the potential donor nor her spouse had high-risk HIV exposures. Her physical examination and laboratory screening, including lymphocyte count, were normal. Results for HIV RNA reverse transcription-polymerase chain reaction (PCR, Amplicor HIV-1 Monitor, Version 1.5, Roche Diagnostics, Branchburg, NJ), as well as for HIV proviral DNA PCR (LabCorp, Burlington, NC), were negative. With informed consent, a myeloablative marrow transplantation was performed, and the patient engrafted on Day 26. After 6 months’ follow-up, the recipient’s HIV antibody test results were negative whereas the donor’s remained indeterminate. We believe that this is the first report of an HPCT using a donor with an indeterminate test result for HIV antibody. Indeterminate HIV antibody status can have many causes, including interfering antibodies from autoimmune diseases, transfusion, pregnancy, or animal exposure. Typically, these results are transient and the samples seroconvert to negative with time. Not all indeterminate HIV antibody results will seroconvert to negative, however. Low-level viremia 1 and viral clearance may be associated with HIV antibody‐indeterminate results and, reportedly, 0.4 to 7.3 percent of these cases convert to HIV seropositivity. 1-3

TIPIFICACIÓN MOLECULAR DEL VIRUS DENGUE 3 DURANTE EL BROTE EPIDÉMICO DE DENGUE CLÁSICO EN LIMA, PERÚ, 2005

Objectives: To identify the causative agent of the outbreak that occurred in Comas, Lima in April 2005 using reverse transcription-polymerase chain reaction (RT-PCR) and specific restriction site-PCR (RSS-PCR). Materials and methods: 20 serum samples collected during the dengue outbreak were assessed using RT-PCR for identifying serotypes, this technique was performed in a single step. Later, the RSS-PCR method was used to identify the circulating serotypes, and the results were corroborated by viral isolation and sequencing. Results: RT-PCR of viral RNA taken from the samples showed a 290-pb amplified product corresponding to dengue virus serotype 3 (DEN 3). RSS-PCR product analysis of RNA from DEN 3 isolates corresponded to pattern C, included in genotype III. Dengue 3 virus isolates in C6/36 cell lines identified using indirect immunofluorescence and gene sequencing confirmed the results obtained using the aforementioned tests. Conclusion: During the classic dengue fever outbreak in Lima, DEN 3 genotype III circulated.

Aspirin-mediated COX-2 transcript stabilization via sustained p38 activation in human intestinal myofibroblasts.

Acetylsalicylic acid (aspirin) is a cyclooxygenase (COX) inhibitor, yet some of its therapeutic effects are thought to derive from mechanisms unrelated to prostaglandin synthesis inhibition. In human intestinal myofibroblasts, aspirin, at therapeutic doses, had the unexpected effect of inducing prolonged COX-2 expression. This induction was especially pronounced when cells were treated with interleukin-1alpha (IL-1) plus aspirin for 24 h. Sodium salicylate, a poor COX inhibitor, likewise enhanced IL-1-mediated COX-2 gene expression whereas 5-aminosalicylic acid (5-ASA) or indomethacin had no effect. The COX-2 transcriptional rate, measured by nuclear runoff analysis and heterogeneous nuclear RNA reverse transcription-polymerase chain reaction, was only modestly elevated by aspirin treatment. In contrast, aspirin treatment dramatically stabilized the COX-2 message. The COX-2 mRNA half-life in IL-1 treated cells was 1 h and was increased in excess of 5 h in IL-1 + aspirin-treated cells. Phosphorylation of p38 MAPK was enhanced in aspirin-treated cells (but not in cells treated with 5-ASA or indomethacin) for up to 24 h after treatment. Inhibition of p38 activity negated aspirin-mediated COX-2 mRNA stabilization and the resultant increase in COX-2 mRNA and protein levels. The modest transcriptional response seen in aspirin treated cells was also abolished by p38 inhibition. We conclude that aspirin enhances COX-2 expression via sustained activation of p38, which results in prolonged stabilization of the COX-2 message and a slightly elevated transcription rate. Aspirin also enhanced steady-state mRNA levels of other IL-1 modulated genes (IL-1beta, IL-6, groalpha, and TNFalpha) that are likewise regulated at the level of message stability via p38 activation.

Detection of Fusion Gene Transcripts in Fresh-Frozen and Formalin-Fixed Paraffin-Embedded Tissue Sections of Soft-Tissue Sarcomas After Laser Capture Microdissection and RT-PCR

The diagnosis of small round cell sarcomas is often very difficult, especially when only small biopsy specimens are available for examination. Recent studies have shown that some sarcomas have specific recurrent chromosomal translocations producing chimeric gene fusions, which can be detected by reverse transcription-polymerase chain reaction (RT-PCR), fluorescent in situ hybridization (FISH), or cytogenetic analysis. In this study, 12 cases of well-defined sarcomas including Ewings sarcoma/primitive neuroectodermal tumors (ES/PNET), synovial sarcoma (SS), alveolar rhabdomyosarcoma (ARMS), and desmoplastic small round cell tumors (DSRCT) were used to collect specific numbers of cells by laser capture microdissection (LCM), subsequently used for RT-PCR to detect specific chimeric gene transcripts. Tumor cells from fresh-frozen (FS) tissue sections and paraffin-embedded (PS) tissue sections from the same cases were compared directly to evaluate the sensitivity of FS and PS sections as the starting material for analysis. Samples were used for RNA extraction, RT-PCR analysis, and Southern hybridization with fluorescein-labeled internal probes followed by enhance chemiluminescence (ECL) detection. The fusion gene transcripts could be detected using 50 cells from FS materials in all cases and from 1 cell in 9 of 12 cases. For PS, a positive signal could be detected using 200 to 1000 cells in all cases, while weaker signals were detected using 50 cells in most cases. These results indicate that the fusion gene products from small round cell sarcomas can be detected by RT-PCR with 10 to 200 cells from FS and PS tissues. The sensitivity of RT-PCR with FS was 10- to 50-fold greater than with PS. These results also suggest that RT-PCR analysis for sarcoma fusion gene products can be successfully performed when only a few cells are available for analysis, although this is not recommended for routine clinical use.

Expression and localization of heat shock factor (Hsf) 1 in the rodent cochlea

Activation of heat shock factors (Hsfs) is one of the potential mechanisms for regulating the transcription of the heat shock proteins (Hsps) and certain other stress-responsive genes. Reverse transcription polymerase chain reaction (RT-PCR), Western blot and immunocytochemistry were used to examine the expression and localization of Hsf1, the stress-responsive member of the Hsf family, in the rat and mouse cochlea. Cerebellum was used as a positive control. Semi-quantitative RT-PCR of cochlear RNA revealed that Hsf1 was more highly expressed in a subfraction containing sensorineural epithelium and lateral wall than in a subfraction containing modiolus, with the α splice form predominant over the β in both subfractions. Immunocytochemistry showed selective staining in the rodent cochlea. Hsf1 immunostaining was found in the nuclei of inner and outer hair cells in the organ of Corti, spiral ganglion cells in the modiolus, and cells in the marginal and intermediate layers of the stria vascularis. This is largely consistent with where Hsp70 induction is reported. Hsf1 activation following heat shock was examined by Western blot. Hyperthermia resulted in stress-induced Hsf1 hyperphosphorylation in cochlea as well as cerebellum. This hyperphosphorylation as well as the correlation of its localization with Hsp70 induction supports a role for Hsf1 in the cochlear stress response.