Taking qPCR to a higher level: Analysis of CNV reveals the power of high throughput qPCR to enhance quantitative resolution

This paper assesses the quantitative resolution of qPCR using copy number variation (CNV) as a paradigm. An error model is developed for real-time qPCR data showing how the precision of CNV determination varies with the number of replicates. Using samples with varying numbers of X chromosomes, experimental data demonstrates that real-time qPCR can readily distinguish four copes from five copies, which corresponds to a 1.25-fold difference in relative quantity. Digital PCR is considered as an alternative form of qPCR. For digital PCR, an error model is shown that relates the precision of CNV determination to the number of reaction chambers. The quantitative capability of digital PCR is illustrated with an experiment distinguishing four and five copies of the human gene MRGPRX1. For either real-time qPCR or digital PCR, practical application of these models to achieve enhanced quantitative resolution requires use of a high throughput PCR platform that can simultaneously perform thousands of reactions. Comparing the two methods, real-time qPCR has the advantage of throughput and digital PCR has the advantage of simplicity in terms of the assumptions made for data analysis.

High-throughput single nucleotide polymorphism genotyping using nanofluidic Dynamic Arrays

BACKGROUND

Single nucleotide polymorphisms (SNPs) have emerged as the genetic marker of choice for mapping disease loci and candidate gene association studies, because of their high density and relatively even distribution in the human genomes. There is a need for systems allowing medium multiplexing (ten to hundreds of SNPs) with high throughput, which can efficiently and cost-effectively generate genotypes for a very large sample set (thousands of individuals). Methods that are flexible, fast, accurate and cost-effective are urgently needed. This is also important for those who work on high throughput genotyping in non-model systems where off-the-shelf assays are not available and a flexible platform is needed.

RESULTS

We demonstrate the use of a nanofluidic Integrated Fluidic Circuit (IFC) - based genotyping system for medium-throughput multiplexing known as the Dynamic Array, by genotyping 994 individual human DNA samples on 47 different SNP assays, using nanoliter volumes of reagents. Call rates of greater than 99.5% and call accuracies of greater than 99.8% were achieved from our study, which demonstrates that this is a formidable genotyping platform. The experimental set up is very simple, with a time-to-result for each sample of about 3 hours.

CONCLUSION

Our results demonstrate that the Dynamic Array is an excellent genotyping system for medium-throughput multiplexing (30-300 SNPs), which is simple to use and combines rapid throughput with excellent call rates, high concordance and low cost. The exceptional call rates and call accuracy obtained may be of particular interest to those working on validation and replication of genome- wide- association (GWA) studies.

Re-excretion of infectious bronchitis virus in chickens induced by cyclosporin

Following inoculation of day-old chicks with Moroccan strain 'G' of infectious bronchitis virus (IBV) which has a predilection for the gut, virus was recovered from the trachea up to day 7 and from the cloaca up to day 35. After this no virus could be detected, even following the natural stress of re-housing with unfamiliar birds at 9 weeks. When the birds were 12.5 weeks old, they were injected with cyclosporin, a selective T-cell suppressor. Four of the five birds re-excreted virus very erratically, as did two of five contacts. This was accompanied by the appearance of IBV-specific IgM in the sera of both groups. The results suggest that in long-term infections with IBV, virus persistence is controlled by T lymphocytes.

A comparison of direct electron microscopy, virus isolation and a DNA amplification method for the detection of avian infectious laryngotracheitis virus in field material

Seventy-two post-mortem samples of mainly tracheal tissue from commercial chickens from 25 commercial chicken flocks with suspected infectious laryngotracheitis (ILT) were examined for the presence of the virus using direct electron microscopy (EM), virus isolation (VI) in primary chick embryo liver cell culture and a DNA amplification method (polymerase chain reaction; PCR). ILT virus was identified in 22 outbreaks, and in 58 of the 72 specimens. PCR detected virus in 52 of the 72 specimens and VI was positive in 48. In five instances, VI was positive where the other methods were negative and in three, PCR was the only test positive. Direct EM examination detected virus in only 19 of the 58 positive samples and in no case was EM the only method positive. An advantage of PCR was that it could sometimes detect virus in samples that were too heavily contaminated with bacteria for virus to be isolated and on other occasions it was positive for ILT virus when the only virus that could be detected by growth in tissue culture was adenovirus.

Comparison of cultural methods for primary isolation of infectious laryngotracheitis virus from field material

Primary isolation of infectious laryngotracheitis virus (ILT) from tracheal samples from 11 suspected field outbreaks was attempted using a variety of avian cell cultures, Vero cells and embryonated chicken eggs. Tracheal smears of each field sample were also examined by electron microscopy (EM) for the presence of herpesvirus particles. Chick embryo liver cells (CELi) appeared to be the most rapid and sensitive isolation system of those examined with chick kidney (CK) a satisfactory alternative, both demonstrating virus in all 11 samples on first passage. Chick embryo kidney, chick embryo lung and the dropped chorioallantoic membrane of eggs were all less sensitive. Chick embryo fibroblasts and Vero cells were of no particular value for the primary isolation of ILT virus. EM was a useful method of rapid virus identification and confirmation but at least 3.51og10/0.1ml of infectious virus was required to be detected by this method.

A reverse transcriptase-polymerase chain reaction survey of infectious bronchitis virus genotypes in Western Europe from 2002 to 2006

A survey of infectious bronchitis virus (IBV) genotypes in poultry flocks in selected countries in Western Europe was carried out between March 2002 and December 2006. Identification of IBV was by reverse transcriptase-polymerase chain reaction of RNA extracted from oropharyngeal swabs taken from poultry flocks exhibiting signs of clinical disease thought to be attributable to IBV. Part of the hypervariable S1 gene of IBV was sequenced to differentiate between the various genotypes. During the survey, 4103 samples were processed, of which 2419 (59%) were positive for IBV. The predominant IBV genotypes detected were 793B and Massachusetts. The third and fourth most common genotypes were two new economically important field types: Italy02, and a virus similar to genotypes originally detected in China called QX. Analysis of the partial S1 sequences of the genotypes detected suggested that approximately 50% of all 793B, Massachusetts types and D274 IBVs were identical to the homologous commercially available live vaccines. Since 2004 the prevalence of Italy02 (present in all countries from which samples were received) has been declining in all countries except Spain, where it appeared to be the predominant genotype. Since 2004 an IBV genotype has been detected in Holland, Germany, Belgium and France similar to QX and the incidence has increased. QX was not detected in the United Kingdom or Spain. When detections thought to be attributable to vaccines were removed, the dominant genotype in France and Europe overall was 793B; in Germany, Holland and Belgium, it was QX-like IBV; and in the United Kingdom and Spain the dominant genotype was Italy02. The present study is the first to identify the prevalence of both Italy02 and QX field-type variants in poultry flocks in Western Europe. Several novel genotypes have also been detected.

The isolation and characterisation of six avian infectious bronchitis viruses isolated in Morocco

The first isolation and characterisation of infectious bronchitis (IB) viruses from poultry flocks in Morocco are reported. Five isolates designated D, E, F, H and M were related serologically to the Massachusetts serotype, while the sixth, isolate G, was found to be different from any previously reported serotype of IB virus. Neutralising antibodies to isolate G have been detected in sera collected from commercial flocks in Britain, although the virus has not been isolated. While all six isolates caused respiratory disease typical of IB in experimentally infected 3-week-old specified pathogen-free (SPF) chickens, isolate G was unusual in that it could be isolated from several parts of the alimentary tract for up to 21 days post inoculation, and from the duodenum up to 28 days. H120 vaccines protected chicks challenged with isolates E and F but not isolate G.

Experimental reovirus infection in chickens: observations on early viraemia and virus distribution in bone marrow, liver and enteric tissues

The nature of viraemia and tissue distribution of reovirus were studied in the early phase after oral infection of 1-day-old specific-pathogen-free (SPF) White Leghorn chicks with the R2 strain of avian reovirus. A range of tissues collected up to 3 weeks after infection was titrated for their viral content. Virus was present in the plasma, erythrocyte and mononuclear fractions of the blood within 30 hours post-inoculation (p.i.) and was widely distributed in tissues, including the bone marrow by 3 to 5 days p.i. A greater part of the viraemia was associated with plasma, virus in the blood mononuclear fraction being detected only occasionally. There was more infectious virus in the duodenum than the liver and the highest virus titres were found in cloacal swabs taken 1 to 5 days p.i. It was also evident that virus reached the liver within a very short time after infection (<6 hours p.i.) although the source of this early hepatic virus was considered to be residual inoculum absorbed directly into the portal blood. Viraemic virus titres could not be correlated either with duodenal or hepatic virus titre alone.

Reovirus-induced tenosynovitis in chickens: the effect of breed

The effect of breed of chicken on infection with an arthrotropic avian reovirus strain R2 was studied by oral or footpad inoculation of 1-day-old chicks of the following breeds: (1) specific pathogen-free (SPF) light-hybrid, (2) commercial White Leghorn egg-layer, and (3) commercial Ross I broiler, and observed to 12 weeks of age. Although most inoculated birds of all three breeds developed swelling of one or both legs below the hock joint at 3 to 4 weeks of age, gross lesions of tenosynovitis became progressively more severe and extended above the joints only in broilers, whereas in most orally-infected SPF and commercial light chickens gross lesions were intermittently severe and regressed with time. Cloacal virus shedding continued up to 2 weeks in the lighter breeds and 3 weeks after infection in broilers. From a small proportion of infected chickens, reovirus was also reisolated from heart, pancreas and caecal tonsils. In all breeds, the tissue in which virus persisted longest was the hock joint/tendon. There was a poor correlation between isolation of virus and the presence of gross lesions in chickens of 12 weeks of age, especially in broilers. Virus-neutralisation tests demonstrated that seroconversion in the lighter breeds occurred predominantly at 3 weeks and in broilers at 4 weeks after infection. In all three breeds the footpad infection gave significantly lower growth rates than were found in the control and oral-infection groups. Oral infection had no apparent effect on growth rates. The greater susceptibility of broilers to reovirus infection is discussed.

Reproductive biology in egg-laying mammals

The duck-billed platypus and short-beaked echidna are iconic species in Australia. Their morphology and physiology have puzzled scientists all over the world for more than 200 years. Recent genetic studies, particularly the platypus whole-genome sequencing project, have revealed the molecular basis of some of the extraordinary characteristics of monotremes. This and other works demonstrate the great value of research on our most distantly related mammalian relatives for comparative genomics and developmental biology. In this review we focus on the reproductive biology of monotremes and discuss works that unravel genes involved in lactation, testicular descent, gamete biology and fertilization, and early development. In addition we discuss works on the evolution of the complex sex chromosome system in platypus and echidna, which has also significant impact on our general understanding of mammalian sex chromosomes and sex determination.

Reovirus-induced tenosynovitis in chickens the influence of age at infection

Groups of specific pathogen-free (SPF) light hybrid chickens were infected with an arthrotropic reovirus at 1 day old, or at 2, 4, 6 or 9 weeks of age. In each group, approximately 20 were infected orally and 6 via the footpad. For each age group clinical signs of tenosynovitis, gross and microscopic lesions in the legs, virus excretion in the faeces, virus persistence in the joints, and precipitin response to reovirus were observed over a period of 9 weeks post infection (p.i.). For both routes of infection an age-limited susceptibility was shown, the most serious effects, both in numbers of affected birds and severity of gross lesions including tendon rupture, being seen in the youngest group. Gross lesions were rarely seen after oral infection of 6- and 9-week-old chickens. Footpad inoculation of virus had a more severe effect overall, and extended the age susceptibility, mild leg swellings being seen in some birds infected at 6 and 9 weeks of age. After oral infection, higher virus titres in the faeces and a more prolonged persistence in the gut and hock joint were recorded in chicks infected at 1 day old compared with the other age groups. Also, compared with the older groups, a delayed precipitin response was found in those infected at 1 day old. Footpad inoculation provoked earlier virus replication in the gut and a more rapid precipitin response.

Pathogenicity of latent infectious laryngotracheitis virus in chickens

Groups of specific pathogen-free chickens were inoculated with the same dose of a field strain of infectious laryngotracheitis virus that had either been isolated from tracheal swabs taken from infected birds during acute phase shedding, or that had been isolated during an episode of virus shedding after a latent period of 12 to 17 weeks. Birds in both groups developed characteristic clinical signs of ILT including difficulty in breathing, rales and sneezing. Thus, ILT virus shed after a latent period is capable of causing disease in susceptible birds similar to that seen in the field.

Further studies on the development of a live attenuated vaccine against turkey rhinotracheitis

Turkey rhinotracheitis (TRT) virus attenuated by passaging in Vero cells was tested at two different passage levels (15 or 25 passages) and two dose levels [10(3) or 10(4) TCID50 (50% tissue culture infectious doses) per bird] to determine the efficacy in protecting turkey poults against experimental challenge with virulent TRT virus. Following administration by the eyedrop route at 10 days of age, all four preparations proved successful in providing protection against clinical disease and establishment of challenge virus in the trachea when challenged with virulent virus 3 weeks later. Twelve-day-old poults given the 25th Vero passage TRT virus at a dose of 10(3.5) TCID50 per bird were protected against experimental challenge with virulent virus for at least 22 weeks post-primary inoculation. The 25th passage virus was tested for safety by administering ten times the dose (10(4.5) TCID50 per bird) used in the previous trial to a group of 10-day-old turkey poults. None of the birds showed any clinical signs during 21 days post-inoculation. Attempts to back-passage the virus from bird to bird were unsuccessful.

Exacerbation of Mycoplasma gallisepticum infection in turkeys by rhinotracheitis virus

Groups of 1-day-old turkey poults from a parent flock free of antibodies to turkey rhinotracheitis virus (TRTV) and the pathogenic mycoplasmas, were infected by eyedrop with virulent TRTV, with Mycoplasma gallisepticum (Mg) or with both agents together. Dual infection resulted in increased morbidity compared with those groups given single infections. The presence of the Mg in the dual infection had no apparent effect on the pathogenesis of the virus, but the virus caused the Mycoplasma to be more invasive. Mg infection caused a transient depression in TRTV ELISA antibody titres at 29 days post-inoculation. At 14 days post-infection Mg haemagglutination inhibition (HI) and rapid serum agglutination (RSA) titres were higher (P <0.01) in the mixed infection group compared with those infected with Mg alone, but there was no significant difference between ELISA antibody titres of these two groups.

Development of a live attenuated vaccine against turkey rhinotracheitis

Three preparations of a strain of turkey rhinotracheitis (TRT) virus were tested for their ability to protect turkey poults against challenge with virulent virus given 3 weeks later. The preparations were as follows: one had been passaged in turkey embryo tracheal organ culture (TOC) 98 times, another had been passaged in primary chick embryo fibroblast (CEF) monolayers 28 times and the third had undergone 17 passages in Vero cell monolayers. Each was administered by the eyedrop route to groups of 21-day-old TRT-seronegative turkey poults. The TOC preparation caused clinical signs consistent with TRT infection, indicating the virus had not been attenuated. The CEF and Vero preparations produced no clinical effects. Following challenge with virulent TRT virus at 21 days post-inoculation, the CEF group developed clinical signs consistent with TRT but the TOC and Vero virus groups showed none. All other parameters correlated with these findings. All groups showed an increase in specific SN and ELISA antibodies following challenge. These results indicated that after relatively few passages in Vero cells, this strain of TRT virus became satisfactorily attenuated and was able to offer protection against clinical disease following experimental challenge. Two of the three virus preparations (TOC and Vero) were also shown to spread from the inoculated birds to uninoculated contact birds, introduced into the groups at 5 days post-inoculation, and they induced protection in these contacts against virulent virus challenge.

Early pathogenesis of experimental reovirus infection in chickens

One-day-old specific-pathogen-free, light hybrid chickens were infected orally with an avian arthrotropic reovirus and examined at intervals from 2 h until 12 days after infection. Entry, primary replication and spread of virus were studied by infectivity assay, immunohistochemical study and electron microscopy in a wide range of tissues. These showed viral entry and primary replication in the epithelium of intestine and bursa of Fabricius within 12 h after oral infection. These were followed by a rapid and pantropic distribution of virus which reached most tissues within 24 to 48 h after infection.

Studying copy number variations using a nanofluidic platform

Copy number variations (CNVs) in the human genome are conventionally detected using high-throughput scanning technologies, such as comparative genomic hybridization and high-density single nucleotide polymorphism (SNP) microarrays, or relatively low-throughput techniques, such as quantitative polymerase chain reaction (PCR). All these approaches are limited in resolution and can at best distinguish a twofold (or 50%) difference in copy number. We have developed a new technology to study copy numbers using a platform known as the digital array, a nanofluidic biochip capable of accurately quantitating genes of interest in DNA samples. We have evaluated the digital array's performance using a model system, to show that this technology is exquisitely sensitive, capable of differentiating as little as a 15% difference in gene copy number (or between 6 and 7 copies of a target gene). We have also analyzed commercial DNA samples for their CYP2D6 copy numbers and confirmed that our results were consistent with those obtained independently using conventional techniques. In a screening experiment with breast cancer and normal DNA samples, the ERBB2 gene was found to be amplified in about 35% of breast cancer samples. The use of the digital array enables accurate measurement of gene copy numbers and is of significant value in CNV studies.

Molecular characterization of infectious bronchitis virus strains isolated from the enteric contents of Brazilian laying hens and broilers

Infectious bronchitis virus (IBV) is the causative agent of avian infectious bronchitis, which is characterized by respiratory, reproductive, and renal signs. However, the role of IBV as an enteric pathogen in still controversial. In Brazil, antigenic groups of IBV divergent from the Massachusetts serotype used for vaccination schedules in that country have already been demonstrated. The present study aimed to assess the different genotypes of IBV in Brazilian commercial poultry flocks by partial sequencing of the S1 amino-terminus coding region using enteric contents as samples and examine their relationship with the vaccine serotype currently in use. Samples of enteric contents were taken as pools of five birds from each of 18 poultry farms (17 broiler and one laying farm) from five Brazilian states between 2002 and 2006. Birds were presenting watery diarrhea and poor general condition but were without respiratory, renal, or reproductive signs. Conventional antibacterial and anticoccidial therapies were unsuccessful and, furthermore, all samples proved negative for rotavirus, reovirus, and astrovirus. Eleven IBV samples were isolated in embryonated eggs and resulted in S1 sequences. Phylogenetic analysis showed that these segregated into an exclusive cluster, close to serotype D274, but distant from Massachusetts. Mean amino acid identity amongst these Brazilian strains was 94.07%; amongst these and serotypes D274, 4/91, and Massachusetts, mean amino acid identity was 77.17%, 69.94%, and 68.93%, respectively. In conclusion, the presence of genotype variant strains of IBV in Brazilian poultry flocks has been demonstrated and might be the reason for the unsuccessful control of IBV in Brazil. Furthermore, these results also strengthen the implications of IBV in enteric diseases of poultry.

High throughput gene expression measurement with real time PCR in a microfluidic dynamic array

We describe a high throughput gene expression platform based on microfluidic dynamic arrays. This system allows 2,304 simultaneous real time PCR gene expression measurements in a single chip, while requiring less pipetting than is required to set up a 96 well plate. We show that one can measure the expression of 45 different genes in 18 tissues with replicates in a single chip. The data have excellent concordance with conventional real time PCR and the microfluidic dynamic arrays show better reproducibility than commercial DNA microarrays.

Methicillin-resistant Staphylococcus aureus infections among healthy full-term newborns

OBJECTIVE

Methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged in the community, causing disease among healthy people lacking traditional risk factors for MRSA infection. This article describes an outbreak of MRSA among healthy full-term newborns.

DESIGN

Cases were identified and corresponding medical information collected. Telephone interviews were conducted with mothers of cases and surveillance cultures from mothers and newborns were performed. MRSA isolates were genotyped.

SETTING

Hospital in Chicago, Illinois, USA.

PARTICIPANTS

Newborns, their mothers and hospital healthcare workers.

INTERVENTION

Nursery infection control practices were enhanced. The MRSA-colonised healthcare workers received intranasal mupirocin.

MAIN OUTCOME

Within 4-23 days of birth, 11 newborns were identified with pustules, vesicles or blisters located on the head, groin, perineum, ears, legs, chin and trunk. All received antimicrobials and recovered without incident.

RESULTS

None of 432 peripartum women, one of 399 newborns, and two of 135 healthcare workers were nasal MRSA carriers. Available isolates from six patients, two healthcare workers, and one from an MRSA-colonised newborn were similar by pulsed-field gel electrophoresis. Other than contact with the hospital, no common exposures of MRSA transmission were identified.

CONCLUSIONS

MRSA strains that initially emerged in the community are now causing disease in healthcare settings. Providers should be aware that MRSA can cause skin infections among healthy newborns. Adherence to standard infection control practices is important to prevent transmission of MRSA in nurseries.

Protection in specific pathogen free chickens with live avian metapneumovirus and Newcastle disease virus vaccines applied singly or in combination

This paper describes two experiments. In each experiment, 1-day-old specific pathogen free chicks were divided into three groups. In Experiment 1 - [avian metapneumo virus (aMPV) challenge] - one group served as unvaccinated controls; the second group was vaccinated with live aMPV (subtype B) vaccine only, and the third group received the aMPV vaccine in combination with live Newcastle disease virus (NDV) vaccine (VG/GA strain). Oropharyngeal swabs, tissues and blood samples were collected before and after challenge with a virulent subtype aMPV at 21 days post vaccination. Chicks were monitored for post-challenge clinical signs. Swabs and tissues were examined for the detection of challenge aMPV by virus isolation and by reverse-transcriptase polymerase-chain reaction. Sera were assayed for antibodies against aMPV and NDV. The single and combined vaccinated chicks were all protected against clinical signs and no challenge virus was isolated from either of the vaccinated-challenged groups. In Experiment 2 (NDV challenge), as in Experiment 1, chicks were divided into three groups where one group remained as unvaccinated control and the other two groups were vaccinated as above, except that the second group received live NDV vaccine only, instead of aMPV. At 21 days post vaccination, 15 chicks from each of the three groups were removed to a different site and challenged with a virulent NDV (Texas GB strain). Re-isolation of the challenge virus was not attempted. All chicks in both NDV-vaccinated challenged groups were protected against clinical signs and mortality. These results show that, based on parameters monitored for the respective challenge virus, simultaneous application of live aMPV and NDV vaccines did not affect the efficacy of either vaccine.

Interaction between a live avian pneumovirus vaccine and two different Newcastle disease virus vaccines in broiler chickens with maternal antibodies to Newcastle disease virus

Broiler chicks with maternal antibodies to Newcastle disease virus (NDV) but none to avian metapneumovirus (APV) were divided into six groups. One group was kept as an unvaccinated control group. Three of the other groups were vaccinated at 1 day old with live APV vaccine or one of two live NDV vaccines (VG/GA or HB1). The remaining two groups received the APV vaccine in combination with either of the two NDV vaccines at 1 day old. At intervals after vaccination for up to 42 days, distribution of the viruses in the tissues was monitored, together with humoral antibody responses. Few NDV isolations were made from any NDV-vaccinated chicks, probably due to the presence of NDV maternal antibodies. In both dual-vaccinated groups, APV persisted longer (up to 21 days post vaccination (d.p.v.)) than in the single vaccinates (up to 14 d.p.v.). After 14 d.p.v., antibody titres against APV in both dual-vaccinated groups remained higher than the single APV vaccinates. For NDV haemagglutination inhibition antibodies, similar titres were found in the single and dual NDV VG/GA vaccinates. However, for chickens dually vaccinated with NDV HB1 and APV, the haemagglutination inhibition titres were significantly higher at 21 and 28 d.p.v. than the single HB1 vaccinates. These differences reflect the fact that NDV haemagglutination inhibition titres may depend on the NDV vaccine used.