Pooled Polymerase Chain Reaction Research Articles

Low Rate of Asymptomatic Dengue Infection Detected in Coastal Kenya Using Pooled Polymerase Chain Reaction Testing.

Asymptomatic dengue virus (DENV) infections have important public health implications but are challenging to identify. We performed a cross-sectional study of reverse transcription quantitative polymerase chain reaction on pooled sera of asymptomatic individuals from the south coast of Kenya at two time periods to identify cases of asymptomatic viremia. Among 2,460 samples tested in pools of 9 or 10, we found only one positive case (0.04% incidence). Although pooling of samples has the potential to be a cost-effective and time-efficient method for asymptomatic DENV detection, mass cross-sectional pooled testing may not provide accurate data on rates of asymptomatic infection, likely owing to a decrease in the sensitivity with pooling of samples, a short period of viremia, or testing in the absence of an outbreak.

Influence parental- and child-related factors on the acceptance of SARS-CoV-2 test methods in schools and daycare facilities.

Rapid testing for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infections was an essential step in reducing the spread of the virus and monitoring pandemic development. Most mandatory standard pandemic testing in Germany has been performed in schools and daycare facilities. We investigated the influence of behavioral and attitudinal characteristics of children and caregivers on their acceptance of (i) antigen-based nasal swab rapid and (ii) oral saliva-based pooled Polymerase Chain Reaction (PCR) tests. Conducted through a cross-sectional survey between November and December 2021, with 1962 caregivers and 581 children/adolescents participating, the study evaluated the acceptability of each testing method on a six-point scale. Participants scored one test method conducted on their child at one of six levels with 1 and 6 denoting "excellent" (1) and "inadequate" (6), respectively. We considered demographic variables, vaccination status, child mental health (measured by the SDQ-questionnaire), and facility type (kindergarten, primary school, secondary school) as covariates. Results reveal a preference for saliva-based PCR tests over nasal swabs by about one grade, particularly among parents of unvaccinated children, especially if their child expressed future vaccination reluctance. Testing acceptance was lower among children with mental health issues, primary school-aged, and those with less-educated parents. Perception of test accuracy and convenience influenced attitudes, favoring saliva-based PCR tests. Moreover, children with mental health issues felt less secure during testing. To our knowledge, this is the first study to investigate the influence of different testing methods on testing acceptance for SARS-CoV-2 in children and caregivers. Our study identifies predictors of lower acceptance of public health surveillance measures and enables the development of educational programs on testing and vaccination tailored to the needs of specific target groups. Moreover, we demonstrate that test acceptance in vulnerable groups can be enhanced by careful choice of an appropriate testing method.

Acceptance of Different Self-sampling Methods for Semiweekly SARS-CoV-2 Testing in Asymptomatic Children and Childcare Workers at German Day Care Centers

Closure of day care centers (DCCs) to contain the COVID-19 pandemic has been associated with negative effects on children's health and well-being. To investigate the acceptance of self-sampling methods for continuous SARS-CoV-2 surveillance among asymptomatic children and childcare workers (CCWs) in DCCs. This nonrandomized pilot study included children and CCWs at 9 DCCs in Wuerzburg, Germany, from May to July 2021. Twice weekly testing for SARS-CoV-2 was conducted by self-sampled mouth-rinsing fluid (saliva sampling [SAL], with subsequent pooled polymerase chain reaction test) plus nasal rapid antigen self-test (RAgT) (group 1), SAL only (group 2), or RAgT only (group 3) in children and CCWs. Main outcomes were rates for initial acceptance and successful (≥60% of scheduled samples) long-term participation. The probability of SARS-CoV-2 introduction into DCCs was modeled as a function of age-adjusted background incidence and DCC size. Of 836 eligible children, 452 (54.1%; 95% CI, 50.7%-57.4%) participated (median [IQR] age: 4 [3-5] years; 213 [47.1%] girls), including 215 (47.6%) in group 1, 172 (38.1%) in group 2, and 65 (14.4%) in group 3. Of 190 CCWs, 139 (73.2%; 95% CI, 66.4%-79.0%) participated (median [IQR] age: 30 [25-46] years; 128 [92.1%] women), including 96 (69.1%) in group 1, 29 (20.9%) in group 2, and 14 (10.1%) in group 3. Overall, SARS-CoV-2 PCR tests on 5306 SAL samples and 2896 RAgTs were performed in children, with 1 asymptomatic child detected by PCR from SAL. Successful long-term participation was highest in group 2 (SAL only; children: 111 of 172 [64.5%]; CCWs: 18 of 29 [62.1%]). Weekly participation rates in children ranged from 54.0% to 83.8% for SAL and from 44.6% to 61.4% for RAgT. Participation rates decreased during the study course (P < .001). The probability of SARS-CoV-2 introduction into a DCC with 50 children was estimated to reach at most 5% for an age-adjusted SARS-CoV-2 incidence below 143. Self-sampling for continuous SARS-CoV-2 testing was well accepted, with SAL being the preferred method. Given the high number of negative tests, thresholds for initiating continuous testing should be established based on age-adjusted SARS-CoV-2 incidence rates. German Registry for Clinical Trials Identifier: DRKS00025546.

Therapeutic Efficacy of Artemether-Lumefantrine (Coartem®) for the Treatment of Uncomplicated Falciparum Malaria in Africa: A Systematic Review.

Background Africa still bears the largest burden of malaria as the majority of infections in the continent are caused by P. falciparum. Artemether-lumefantrine (AL, Coartem®) is the most widely used artemisinin-based combination therapy (ACT), for treating uncomplicated falciparum malaria globally. However, the development of resistance to antimalarial drugs is a major challenge for malaria control. In this review, the efficacy of AL for the treatment of uncomplicated falciparum malaria in Africa was evaluated. Methods Articles published between January 2015 and July 2019 were systematically searched using comprehensive search strings from PubMed/Medline, SCOPUS, and grey literature from Google Scholar. Interventional studies that followed patients for at least 28 days were included. Two reviewers independently assessed study eligibility, extracted data, and assessed risk of bias. All the included articles were measured to be good quality. While computing the efficacy of AL, polymerase chain reaction (PCR)–corrected cure rate (adequate clinical and parasitological response, ACPR) at day 28 was considered as the main endpoint. Meta-analysis was computed using STATA v 15 to calculate the pooled ACPR. Results In this review, 39 articles that reported the treatment outcome of 8,320 patients were included. After 28 days of follow-up, the pooled PCR uncorrected and corrected APCR was at 87% (95% CI: 85-90%) and 97.0% (95% CI: 96-98%), respectively. Moreover, the proportion of early treatment failure (ETF) was almost 0%, while most of the included articles reported <8% late treatment failures. The reinfection and recrudescence rate was less than 10% and 2.6%, respectively, within 28 days. We noted rapid fever and parasite clearance in which greater than 93% and 94% patients were parasite and fever free at day three following AL treatment. Conclusions This review discovered that despite more than a decade since its introduction, Coartem® remains effective and thus could continue to be the drug of choice for the treatment of uncomplicated falciparum malaria for all age groups in Africa. However, the risk of new emerging resistance for this combination warrants regular monitoring of its efficacy across the continent.

The Interruption of Transmission of Human Onchocerciasis by an Annual Mass Drug Administration Program in Plateau and Nasarawa States, Nigeria.

.Plateau and Nasarawa states in central Nigeria were endemic for onchocerciasis. The rural populations of these two states received annual ivermectin mass drug administration (MDA) for a period of 8–26 years (1992–2017). Ivermectin combined with albendazole was given for 8–13 of these years for lymphatic filariasis (LF); the LF MDA program successfully concluded in 2012, but ivermectin MDA continued in areas known to have a baseline meso-/hyperendemic onchocerciasis. In 2017, serological and entomological assessments were undertaken to determine if MDA for onchocerciasis could be stopped in accordance with the current WHO guidelines. Surveys were conducted in 39 sites that included testing 5- to < 10-year-old resident children by using ELISA for OV16 IgG4 antibodies, and Onchocerca volvulus O150 pooled polymerase chain reaction (PCR) testing of Simulium damnosum s.l. vector heads. Only two of 6,262 children were OV16 positive, and none of 19,056 vector heads were positive for parasite DNA. Therefore, both states were able to meet WHO stop-MDA thresholds of an infection rate in children of < 0.1% and a rate of infective blackflies of <1/2,000, with 95% statistical confidence. Transmission of onchocerciasis was declared interrupted in Plateau and Nasarawa states by the Federal Ministry of Health, and 2.2 million ivermectin treatments/year were stopped in 2018. Post-treatment Surveillance was launched focusing on entomological monitoring on borders with neighboring onchocerciasis-endemic states. An apparent positive impact of the LF MDA program on eliminating hypo-endemic onchocerciasis was observed. This is the first stop-MDA decision for onchocerciasis in Nigeria and the largest single stop-MDA decision for onchocerciasis yet reported. This achievement, along with the process used in adapting and implementing the 2016 WHO stop-MDA guidelines, will be important as a potential model for decision makers and national onchocerciasis elimination committees in other African countries that are charged with advancing their programs.

Filling reference gaps via assembling DNA barcodes using high-throughput sequencing-moving toward barcoding the world.

Over the past decade, biodiversity researchers have dedicated tremendous efforts to constructing DNA reference barcodes for rapid species registration and identification. Although analytical cost for standard DNA barcoding has been significantly reduced since early 2000, further dramatic reduction in barcoding costs is unlikely because Sanger sequencing is approaching its limits in throughput and chemistry cost. Constraints in barcoding cost not only led to unbalanced barcoding efforts around the globe, but also prevented high-throughput sequencing (HTS)–based taxonomic identification from applying binomial species names, which provide crucial linkages to biological knowledge. We developed an Illumina-based pipeline, HIFI-Barcode, to produce full-length Cytochrome c oxidase subunit I (COI) barcodes from pooled polymerase chain reaction amplicons generated by individual specimens. The new pipeline generated accurate barcode sequences that were comparable to Sanger standards, even for different haplotypes of the same species that were only a few nucleotides different from each other. Additionally, the new pipeline was much more sensitive in recovering amplicons at low quantity. The HIFI-Barcode pipeline successfully recovered barcodes from more than 78% of the polymerase chain reactions that didn’t show clear bands on the electrophoresis gel. Moreover, sequencing results based on the single molecular sequencing platform Pacbio confirmed the accuracy of the HIFI-Barcode results. Altogether, the new pipeline can provide an improved solution to produce full-length reference barcodes at about one-tenth of the current cost, enabling construction of comprehensive barcode libraries for local fauna, leading to a feasible direction for DNA barcoding global biomes.

Targeted deep resequencing of ALOX5 and ALOX5AP in patients with diabetes and association of rare variants with leukotriene pathways.

The aim of the present study was to investigate a possible association between the accumulation of rare coding variants in the genes for arachidonate 5-lipoxygenase (ALOX5) and ALOX5-activating protein (ALOX5AP), and corresponding production of leukotrienes (LTs) in patients with type 2 diabetes mellitus (T2DM) receiving acetylsalicylic therapy. Twenty exons and corresponding introns of the selected genes were resequenced in 303 DNA samples from patients with T2DM using pooled polymerase chain reaction amplification and next-generation sequencing, using an Illumina HiSeq 2000 sequencing system. The observed non-synonymous variants were further confirmed by individual genotyping of DNA samples comprising of all individuals from the original discovery pools. The association between the investigated phenotypes was based on LTB4 and LTE4 concentrations, and the accumulation of rare missense variants (genetic burden) in investigated genes was evaluated using statistical collapsing tests. A total of 10 exonic variants were identified for each resequenced gene, including 5 missense and 5 synonymous variants. The rare missense variants did not exhibit statistically significant differences in the accumulation pattern between the patients with low and high LTs concentrations. As the present study only included patients with T2DM, it is unclear whether the absence of observed association between the accumulation of rare missense variants in investigated genes and LT production is associated with diabetic populations only or may also be applied to other populations.

Pooled Nucleic Acid Testing to Detect Antiretroviral Treatment Failure in HIV-Infected Patients in Mozambique.

In resource-limited settings, viral load monitoring of HIV-infected patients receiving antiretroviral therapy (ART) is not readily available because of high costs. Here, we compared the accuracy and costs of quantitative and qualitative pooled methods with standard viral load testing. Blood was collected prospectively from 461 patients receiving first-line ART in Mozambique who had not been evaluated previously with viral load testing. Screening for virologic failure of ART was performed quantitatively (ie, standard viral loads) and qualitatively [one and 2 rounds of polymerase chain reaction (PCR)]. Individual samples and minipools of 5 samples were then analyzed using both methods. The relative efficiency, accuracy, and costs of each method were calculated based on viral load thresholds for ART failure. Standard viral load testing of individual samples revealed a high rate of ART failure (19%-23%) across all virologic failure thresholds, and the majority of the patients (93%) with viral loads >1500 copies per milliliter had genotypic resistance to drugs in their ART regimen. Pooled quantitative screening and deconvolution testing had positive and negative predictive values exceeding 95% with cost savings of $11,250 compared with quantitative testing of each sample individually. Pooled qualitative screening and deconvolution testing had a higher cost savings of $30,147 for 1 PCR round and $25,535 for 2 PCR rounds compared with quantitative testing each sample individually. Both pooled qualitative PCR methods had positive and negative predictive values ≥90%, but the pooled 1-round PCR method had a sensitivity of 64%. Given the high rate of undiagnosed ART failure and drug resistance in this cohort, it is clear that virologic monitoring is urgently needed in this population. Here, we compared alternative methods of virologic monitoring with standard viral load testing of individual samples and found these methods to be cost saving and accurate. The test characteristics of each method will likely need to be considered for each local population before it is adopted.

Estimating Community Prevalence of Ocular Chlamydia trachomatis Infection using Pooled Polymerase Chain Reaction Testing

Purpose: Trachoma is the leading cause of blindness from infection worldwide. Treatment programs require accurate Chlamydia trachomatis infection prevalence rates to guide decision making. The use of clinical examination is by far the most common way to monitor activity, but may yield overestimates of infection prevalence. Laboratory testing on individual specimens such as polymerase chain reaction (PCR) is highly sensitive and specific, but prohibitively expensive. Here we demonstrate simulations of pooled PCR results may estimate infection prevalence of an entire community yielding substantial cost savings if pool size is chosen correctly.Methods: Community infection prevalence was estimated using maximum likelihood estimation with data collected from a previously described study. Simulations for communities were performed to determine the accuracy of prevalence estimation using pooled results. The root mean squared error was then used to determine an acceptable inaccuracy in estimates allowing for a pooling strategy to be formed.Results: Results from simulations and empirical data suggest optimum pooling strategies to estimate community infection prevalence while keeping the root mean squared error of the estimate below 2%. Reduction of PCR testing which permits cost savings is shown to be between 5 and 80% given a community infection prevalence below 60%.Conclusions: Pooling specimens for PCR testing often provides enough data to accurately estimate infection prevalence at the community level.

Making a knockout mouse: From stem cells to embryos

Janet Rossant is a Senior Scientist and the Chief of Research at The Hospital for Sick Children, University of Toronto, 555 University Avenue, Toronto, Ontario, M5G 1X8, Canada. e-mail: janet.rossant@sickkids.ca the underlying principles and genetic pathways of development were conserved. I was very excited by the new research horizons opened by these developments. With Alex’s arrival, our labs started working together on the next challenges — testing the function of these newly identified genes in mouse development and finding more ways to identify other key developmental genes. We knew the answer must lie with ESCs. In 1981, Martin Evans and Matt Kaufman in Cambridge and Gail Martin in San Francisco had separately isolated pluripotent stem cells directly from the mouse blastocyst. Allan Bradley and Liz Robertson, in Martin Evans’s lab, and Achim Gossler in Rolf Kemler’s lab then provided proof-of-principle studies demonstrating that any genetic alteration introduced into these cells in culture could be transmitted through the germ line in chimaeras. Alex introduced ESC concepts to Toronto from San Francisco. When Achim Gossler joined my lab as a post-doc and brought germline-competent ESCs, we had the starting material for a major assault on gene functional analysis in the mouse. But how should we attack the problem? We knew about the promise of targeted mutagenesis by homologous recombination, developed in mammalian cells by Mario Capecchi and Oliver Smithies, but it had only been demonstrated to work in ESCs for genes such as Hprt, where one could select for mutation or correction of the gene. Would it be efficient enough to work for non-selectable genes such as engrailed? We pondered instead a random retroviral insertional approach, followed by a pooled polymerase chain reaction (PCR) assay to detect mutations in genes of interest. Achim and I also started to plan an enhancer trap approach, similarly to that developed in Drosophila melanogaster, to identify novel genes by expression of their associated enhancers in ESC chimaeras. However, when we heard from Oliver Smithies that he was developing a PCR-based approach to detect targeted mutations in non-selectable genes in ESCs, we abandoned the random insertional approach and put all our efforts into targeted mutagenesis with engrailed2 as the first target. We were fortunate to have Bill Skarnes join Alex’s lab as a graduate student at that time. He developed the targeting vector for En2, which was at the same time developed into a gene trap reporter vector, using the En2 splice acceptor to trap upstream exons in a lacZ fusion that would also disrupt the gene. Alex and I started the targeting experiments, picking portions of hundreds of individual neomycin-resistant colonies and assaying for targeted integrations using PCR. We began without a PCR machine — moving tubes by hand from waterbath to water-bath. Hints of success spurred us to purchase the second PCR machine ever sold in Canada, and, as they say, the rest is history. We published one of the first reports of successful targeting of a non-selectable gene in ESCs in Nature in 1989, and reported approaches for enhancer and gene-trap screens in ESCs in Science in the same year. The field of mammalian genetics was very rapidly transformed as more and more ways of manipulating the mouse germ line were developed by different groups. But it was a special time for me in Toronto, working in a great group of talented people, all with our own personalities and quirks, but all bringing our unique skills to make a successful team. The efforts of the International Knockout Mouse Consortium have made knockout mouse ESCs available off the shelf for almost the entire mouse genome, relegating the generation of a targeted mutation to supplementary material in most papers. And it seems that classical targeted mutagenesis in ESCs may be rapidly superseded by exciting new genome editing tools. Mammalian genetics moves on and new horizons await.

Case report

There are several different methods of testing cattle for persistent infection with bovine viral diarrhea virus (PI-BVDV), including immunohistochemistry (IHC), polymerase chain reaction (PCR), virus isolation, and antigen capture enzyme-linked immunosorbent assay (ACE). The purpose of this report is to describe a case in which a pooled PCR test (28 specimens/pool) was compared for sensitivity against an ACE test (tested as single specimens). Ear notch specimens (fresh) were collected from beef calves purchased by a stocker operation. From January through March 2010, this stocker operation received 2,424 calves and took two ear-notch specimens from each calf for PI-BVDV testing. One specimen from each calf was sent to a commercial PI-BVDV testing laboratory that utilizes real-time PCR technology in specimen pools of 28 (Laboratory A), and a second specimen was sent to a commercial PI-BVDV testing laboratory that utilizes ACE (NS23) technology using non-pooled specimens (Laboratory B). Laboratory A detected four positive specimens out of the 2,424 specimens submitted (0.165% PI prevalence), while Laboratory B detected 12 positive specimens out of the 2,424 specimens submitted (0.495% PI prevalence). The 12 specimens detected by Laboratory B included the same four detected by Laboratory A, as well as eight additional positive specimens. Upon receiving these discordant results, the attending veterinarian requested that the 12 positive specimens detected by Laboratory B be re-tested using the original specimens. These original 12 ACE-positive specimens were then re-tested as single specimens at Laboratory B using a commercially available ACE test (Erns) and real-time PCR technology. The 12 original ACE-positive specimens were again positive by these different tests. Follow-up testing on the 12 calves was conducted more than 30 days after initial testing with a second set of samples from the eight surviving calves (four of the 12 calves died between the original and the second collection). The second set of samples from the eight surviving calves initially ACE-positive by Laboratory B were tested using serum, formalin-fixed ear notches, and fresh ear notches in phosphate buffered saline. All specimens were positive by gel-based reverse transcriptase PCR on serum and ear notches (non-pooled), and all eight formalin-fixed notches were also positive by IHC.

Trends in export of dairy Holstein heifers from the United States

A general overview of the export and testing requirements is given for bred female dairy cattle from the United States (US) to Turkey, Mexico, and Russia, the top three export markets. Disease-by-disease serologic test results are presented for 7,339 Holstein dairy heifers tested in quarantine in southeastern Chester County, Pennsylvania for export to Turkey from June 2010 to October 2011. Management practices to decrease the prevalence of diseases of importance to the export market are reviewed. Prevalence rates of serologically positive heifers tested during the quarantine period using the enzyme linked-immunosorbent assay were: bluetongue virus (BTV) 4.9%, Mycobacterium avium subsp. paratuberculosis (MAP) 0.65%, and bovine leukemia virus (BLV) 5.7%. Prevalence rate of bovine viral diarrhea virus - persistently infected (BVDV PI) heifers using pooled polymerase chain reaction was 0.68%. Because of the high prevalence of BLV in US cattle, most if not all heifers are routinely screened for BLV prior to purchase and entry into quarantine. Some of the heifers in this data set originating from endemic BTV states were pre-screened for BTV. Because of pre-screening for BLV prior to purchase for export, the prevalence of BLV reported was lower than would be expected in the general population of heifers in the US. The prevalence of BTV would depend on whether heifers came from BTV free or endemic states. Dairy herds wanting to market heifers for export should apply management practices known to decrease the prevalence of BTV, BLV, MAP, and BVDV PI.

Evaluation of conventional PCR for detection of Strongylus vulgaris on horse farms

Strongyle parasites are ubiquitous in grazing horses. Of these, the bloodworm Strongylus vulgaris is regarded as most pathogenic. Increasing levels of anthelmintic resistance in strongyle parasites has led to recommendations of decreased treatment intensities, and there is now a pronounced need for reliable tools for detection of parasite burdens in general and S. vulgaris in particular. The only method currently available for diagnosing S. vulgaris in practice is the larval culture, which is laborious and time-consuming, so veterinary practitioners most often pool samples from several horses together in one culture to save time. Recently, molecular tools have been developed to detect S. vulgaris in faecal samples. The aim of this study was to compare the performance of a conventional polymerase chain reaction (PCR) assay with the traditional larval culture and furthermore test the performance of pooled versus individual PCR for farm screening purposes. Faecal samples were obtained from 331 horses on 18 different farms. Farm size ranged from 6 to 56 horses, and horses aged between 2 months and 31 years. Larval cultures and PCR were performed individually on all horses. In addition, PCR was performed on 66 faecal pools consisting of 3–5 horses each. Species-specific PCR primers previously developed were used for the PCR. PCR and larval culture detected S. vulgaris in 12.1 and 4.5% of individual horses, respectively. On the farm level, eight farms tested positive with the larval culture, while 13 and 11 farms were positive with the individual and pooled PCRs, respectively. The individual PCR method was statistically superior to the larval culture, while no statistical difference could be detected between pooled and individual PCR for farm screening. In conclusion, pooled PCR appears to be a useful tool for farm screening for S. vulgaris.

Functional screening using a microRNA virus library and microarrays: a new high-throughput assay to identify tumor-suppressive microRNAs

MicroRNA (miRNA) is a class of non-coding RNAs that represses expression of target messenger RNAs posttranscriptionally. A growing body of evidence supports their roles in various normal cellular processes, as well as in pathological conditions, such as cancer. We established a functional screening assay that enables high-throughput identification of miRNAs that have a role in cancer phenotypes of interest, via the combination of pooled lentivirus vectors expressing several hundred miRNA precursors and a custom-made microarray. Self versus self-hybridization analysis using pooled polymerase chain reaction products generated highly linear and reproducible results. To test the feasibility of the assay, we focused on miRNAs that control proliferation of pancreatic cancer cells and successfully identified five miRNAs that negatively control cell proliferation, including miRNA-34a that was previously identified as a representative tumor-suppressive miRNA. The results were further validated using lentivirus vectors expressing each of the five miRNAs or synthetic miRNAs. The function-based nature of the assay enabled identification of miRNAs that were strongly linked to cell proliferation, but the relative ease and flexibility of the assay allow for future studies of cancer stem cells, metastasis and other cancer phenotypes of interest.

Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing

Discovering single nucleotide polymorphisms (SNPs) in specific genes in a heterozygous polyploid plant species, such as sugarcane, is challenging because of the presence of a large number of homologues. To discover SNPs for mapping genes of interest, 454 sequencing of 307 polymerase chain reaction (PCR) amplicons (> 59 kb of sequence) was undertaken. One region of a four-gasket sequencing run, on a 454 Genome Sequencer FLX, was used for pooled PCR products amplified from each parent of a quantitative trait locus (QTL) mapping population (IJ76-514 x Q165). The sequencing yielded 96,755 (IJ76-514) and 86,241 (Q165) sequences with perfect matches to a PCR primer used in amplification, with an average sequence depth of approximately 300 and an average read length of 220 bases. Further analysis was carried out on amplicons whose sequences clustered into a single contig using an identity of 80% with the program cap3. In the more polymorphic sugarcane parent (Q165), 94% of amplicons (227/242) had evidence of a reliable SNP--an average of one every 35 bases. Significantly fewer SNPs were found in the pure Saccharum officinarum parent--with one SNP every 58 bases and SNPs in 86% (213/247) of amplicons. Using automatic SNP detection, 1632 SNPs were detected in Q165 sequences and 1013 in IJ76-514. From 225 candidate SNP sites tested, 209 (93%) were validated as polymorphic using the Sequenom MassARRAY system. Amplicon re-sequencing using the 454 system enables cost-effective SNP discovery that can be targeted to genes of interest and is able to perform in the highly challenging area of polyploid genomes.

Molecular Diversity of the Rumen Microbiome of Norwegian Reindeer on Natural Summer Pasture

The molecular diversity of the rumen microbiome was investigated in five semi-domesticated adult female Norwegian reindeer (Rangifer tarandus tarandus) grazing on natural summer pastures on the coast of northern Norway (71.00 degrees N, 25.30 degrees E). Mean population densities (numbers per gram wet weight) of methanogenic archaea, rumen bacteria and ciliate protozoa, estimated using quantitative real-time polymerase chain reaction (PCR), were 3.17x10(9), 5.17x10(11) and 4.02x10(7), respectively. Molecular diversity of rumen methanogens was revealed using a 16S rRNA gene library (54 clones) constructed using pooled PCR products from the whole rumen contents of the five individual reindeer. Based upon a similarity criterion of <97%, a total of 19 distinct operational taxonomic units (OTUs) were identified, nine of which are potential new species. The 16S rRNA sequences generated from the reindeer rumen exhibited a high degree of sequence similarity to methanogens affiliated with the families Methanobacteriaceae (14 OTUs) and Methanosarcinaceae (one OTU). Four of the OTUs detected belonged to a group of uncultivated archaea previously found in domestic ruminants and thought to be dominant in the rumen together with Methanobrevibacter spp. Denaturing gradient gel electrophoresis profiling of the rumen bacterial 16S rRNA gene and the protozoal 18S rRNA gene indicated a high degree of animal variation, although some bands were common to all individuals. Automated ribosomal intergenic spacer analysis (ARISA) profiling of the ruminal Neocallimastigales population indicated that the reindeer are likely to contain more than one type of anaerobic fungus. The ARISA profile from one animal was distinct from the other four. This is the first molecular investigation of the ruminal methanogenic archaea in reindeer, revealing higher numbers than expected based on methane emission data available. Also, many of the reindeer archaeal 16S rRNA gene sequences were similar to those reported in domesticated ruminants in Australia, Canada, China, New Zealand and Venezuela, supporting previous findings that there seems to be no host type or geographical effect on the methanogenic archaea community structure in ruminants.

Integrated cytogenetic map of mitotic metaphase chromosome 9 of maize: resolution, sensitivity, and banding paint development

To study the correlation of the sequence positions on the physical DNA finger print contig (FPC) map and cytogenetic maps of pachytene and somatic maize chromosomes, sequences located along the chromosome 9 FPC map approximately every 10 Mb were selected to place on maize chromosomes using fluorescent in situ hybridization (FISH). The probes were produced as pooled polymerase chain reaction products based on sequences of genetic markers or repeat-free portions of mapped bacterial artificial chromosome (BAC) clones. Fifteen probes were visualized on chromosome 9. The cytological positions of most sequences correspond on the pachytene, somatic, and FPC maps except some probes at the pericentromeric regions. Because of unequal condensation of mitotic metaphase chromosomes, being lower at pericentromeric regions and higher in the arms, probe positions are displaced to the distal ends of both arms. The axial resolution of FISH on somatic chromosome 9 varied from 3.3 to 8.2 Mb, which is 12-30 times lower than on pachytene chromosomes. The probe collection can be used as chromosomal landmarks or as a "banding paint" for the physical mapping of sequences including transgenes and BAC clones and for studying chromosomal rearrangements.

Sensitivity of Polymerase Chain Reaction for Detection of Bovine Viral Diarrhea Virus in Pooled Serum Samples and Use of Pooled Polymerase Chain Reaction to Determine Prevalence of Bovine Viral Diarrhea Virus in Auction Market Cattle

Two reverse transcription-nested polymerase chain reaction tests, 1 quantitative (qRT-nPCR) and 1 standard (RT-nPCR), were evaluated to assess sensitivity for detection of bovine viral diarrhea virus (BVDV) of a single positive serum sample in a pool of 30. The RT-nPCR and qRT-nPCR each detected 95 of 100 known positives. The RT-nPCR was used to estimate the prevalence of BVDV in adult beef cows. Serum samples were obtained from the US Department of Agriculture brucellosis testing laboratories in 3 Midwestern states. Samples originated from auction markets and private treaty sales throughout the 3 states. A total of 2,990 serum samples were collected and randomly pooled into 100 pools for testing. Two of the 100 pools of field samples were positive, and each positive pool had a single positive individual sample upon confirmation. The estimate of BVDV prevalence in adult cows in this study was 0.07%. This study estimates the diagnostic sensitivity of RT-nPCR for BVDV and confirms that it is a useful diagnostic tool for pools of 30 serum samples and that prevalence of BVDV in adult cattle from auction markets is low.

Identification of Arabidopsis thaliana transformants without selection reveals a high occurrence of silenced T‐DNA integrations

Several recent investigations of T-DNA integration sites in Arabidopsis thaliana have reported 'cold spots' of integration, especially near centromeric regions. These observations have contributed to the ongoing debate over whether T-DNA integration is random or occurs preferentially in transcriptionally active regions. When transgenic plants are identified by selecting or screening for transgenic activity, transformants with integrations into genomic regions that suppress transcription, such as heterochromatin, may not be identified. This phenomenon, which we call selection bias, may explain the perceived non-random distribution of T-DNA integration in previous studies. In order to investigate this possibility, we have characterized the sites of T-DNA integration in the genomes of transgenic plants identified by pooled polymerase chain reaction (PCR), a procedure that does not require expression of the transgene, and is therefore free of selection bias. Over 100 transgenic Arabidopsis plants were identified by PCR and compared with kanamycin-selected transformants from the same T(1) seed pool. A higher perceived transformation efficiency and a higher frequency of transgene silencing were observed in the PCR-identified lines. Together, the data suggest approximately 30% of transformation events may result in non-expressing transgenes that would preclude identification by selection. Genomic integration sites in PCR-identified lines were compared with those in existing T-DNA integration databases. In PCR-identified lines with silenced transgenes, the integration sites mapped to regions significantly underrepresented by T-DNA integrations in studies where transformants were identified by selection. The data presented here suggest that selection bias can account for at least some of the observed non-random integration of T-DNA into the Arabidopsis genome.

Detection of Clonally Restricted Immunoglobulin Heavy Chain Gene Rearrangements in Normal and Lesional Skin: Analysis of the B Cell Component of the Skin-Associated Lymphoid Tissue and Implications for the Molecular Diagnosis of Cutaneous B Cell Lymphomas

A monoclonal B cell population is the hallmark of B cell neoplasms including cutaneous B cell lymphomas (CBCLs). We modified and tested several polymerase chain reaction (PCR)-based assays involving amplification of immunoglobulin heavy chain (IgH) gene rearrangements to optimize assays specifically for cutaneous lymphoid infiltrates. We achieved greatest sensitivity with an assay employing IgH consensus primers complementary to the framework 3 portion of the upstream variable region and the downstream joining region. We studied 12 CBCLs, 6 nodal lymphomas and 7 cell lines. In 17/25 of these B cell neoplasms (84%), we detected one or two dominant bands, consistent with one or both IgH alleles being rearranged in the neoplastic B cell clone. As expected, IgH PCR assays produced diffuse smears in agarose gels or complex ladders in polyacrylamide gels when polyclonal B cell controls (blood and tonsil) were analyzed. However, in normal skin and non-CBCL skin lesions, one or a small number of discrete bands were sometimes detected. In certain cases, this made it difficult to distinguish true positives (monoclonal CBCL) from false positives (clonally restricted benign B cells). Correlation with immunophenotyping confirmed that false positive results were confined to samples with sparse or immunohistologically undetectable B cell infiltrates. Pseudoclonal bands showed variable sizes in repeat PCR reactions and could be distinguished from monoclonal bands by polyacrylamide gel electrophoresis of pooled triplicate PCR products. These findings suggest that molecular diagnosis using IgH PCR assays is best suited for B-cell-rich infiltrates, and can be problematic when applied to suspected T-cell-rich CBCLs, cutaneous T cell lymphomas, or other lesions containing only few B cells unless one is cognizant of the potential pitfalls. Furthermore, these results demonstrate the presence of rare B cells in normal skin and immunohistologically defined cutaneous T cell infiltrates. This correlates with recent reports of sparse B cells within the lymph draining from normal skin and may represent molecular evidence for a trafficking B cell component of the skin-associated lymphoid tissue (SALT). It also suggests a candidate B cell subset for the pathogenesis of cutaneous lymphoid hyperplasia and CBCLs.