PCR inhibitors – occurrence,properties and removal

The polymerase chain reaction (PCR) is increasingly used as the standard method for detection and characterization of microorganisms and genetic markers in a variety of sample types. However, the method is prone to inhibiting substances, which may be present in the analysed sample and which may affect the sensitivity of the assay or even lead to false‐negative results. The PCR inhibitors represent a diverse group of substances with different properties and mechanisms of action. Some of them are predominantly found in specific types of samples thus necessitating matrix‐specific protocols for preparation of nucleic acids before PCR. A variety of protocols have been developed to remove the PCR inhibitors. This review focuses on the general properties of PCR inhibitors and their occurrence in specific matrices. Strategies for their removal from the sample and for quality control by assessing their influence on the individual PCR test are presented and discussed.     

The virobacterial agglutination test as a rapid means of detecting cocoa swollen shoot virus

The virobacterial agglutination (VBA) test was developed as a means of detection of cocoa swollen shoot virus (CSSV). Identification of CSSV-infected Theobroma cacao in the field has only been possible by visual examination of symptoms, by virus transmission using mealybugs and by grafting to induce symptom expression in Amelonado cocoa seedlings. Detection of latent infection has not been possible even using enzyme-linked immunosorbent assays (ELISA). The VBA test successfully detected CSSV in infected sap diluted to 1/2560. Antisera to a range of mild and severe CSSV isolates were tested, and the results suggest a close relationship between seven isolates (1A, Bosomtwi, Bosomuoso, Nkrankwanta, Nsaba, Seidi-Nkawie and SS365B) while the mild isolate N1 appears to be less closely related. The VBA test was compared with both direct and indirect ELISA in the field. Only VBA detected all the cocoa trees which were known to be infected and additionally identified infection in many symp-tomless trees.     

Extracellular pH Regulates Zinc Signaling via an Asp Residue of the Zinc-sensing Receptor (ZnR/GPR39)

Zinc activates a specific Zn²⁺-sensing receptor, ZnR/GPR39, and thereby triggers cellular signaling leading to epithelial cell proliferation and survival. Epithelial cells that express ZnR, particularly colonocytes, face frequent changes in extracellular pH that are of physiological and pathological implication. Here we show that the ZnR/GPR39-dependent Ca²⁺ responses in HT29 colonocytes were maximal at pH 7.4 but were reduced by about 50% at pH 7.7 and by about 62% at pH 7.1 and were completely abolished at pH 6.5. Intracellular acidification did not attenuate ZnR/GPR39 activity, indicating that the pH sensor of this protein is located on an extracellular domain. ZnR/GPR39-dependent activation of extracellular-regulated kinase (ERK)1/2 or AKT pathways was abolished at acidic extracellular pH of 6.5. A similar inhibitory effect was monitored for the ZnR/GPR39-dependent up-regulation of Na⁺/H⁺ exchange activity at pH 6.5. Focusing on residues putatively facing the extracellular domain, we sought to identify the pH sensor of ZnR/GPR39. Replacing the histidine residues forming the Zn²⁺ binding site, His¹⁷ or His¹⁹, or other extracellular-facing histidines to alanine residues did not abolish the pH dependence of ZnR/GPR39. In contrast, replacing Asp³¹³ with alanine resulted in similar Ca²⁺ responses triggered by ZnR/GPR39 at pH 7.4 or 6.5. This mutant also showed similar activation of ERK1/2 and AKT pathways, and ZnR-dependent up-regulation of Na⁺/H⁺ exchange at pH 7.4 and pH 6.5. Substitution of Asp³¹³ to His or Glu residues restored pH sensitivity of the receptor. This indicates that Asp³¹³, which was shown to modulate Zn²⁺ binding, is an essential residue of the pH sensor of GPR39. In conclusion, ZnR/GPR39 is tuned to sense physiologically relevant changes in extracellular pH that thus regulate ZnR-dependent signaling and ion transport activity.     

Gap detection in the European starling (Sturnus vulgaris)

Summary Gap-detection thresholds were determined for single units in the cochlear ganglion and in auditory nerve fibres of the starling from responses to two broad-band noise bursts separated by a temporal gap of between 0.4 and 204.8 ms. All 35 units showed a threshold within the range of gap sizes tested. The median minimum-detectable gap was 12.8 ms with the minimum being 1.6 ms. A multiple regression analysis revealed that the size of the minimum-detectable gap was not significantly correlated with the neuron's CF, with its sharpness of tuning as given by its bandwidth 10 dB above threshold, or with its Q_10dB value. Only the level of stimulation above the neuron's threshold showed a significant negative correlation with the size of the minimum-detectable gap. These results are discussed with respect to theoretical considerations of limits posed on temporal resolution by the characteristics of peripheral filters. These findings are also discussed in the context of the coding of gaps at different levels of the starling's auditory system and in relation to psychoacoustic results in the starling on gap detection and time resolution described by temporal modulation transfer functions.     

Detection of groundnut rosette umbravirus infections with radioactive and non-radioactive probes to its satellite RNA

A cloned cDNA copy of the satellite RNA of groundnut rosette virus (GRV), labelled with either ³²P or digoxigenin, was used as a probe to detect the satellite RNA in infected leaves. The test was successfully applied to N. benthamiana and to groundnuts, infected with isolates of GRV from East and West Africa and with isolates which cause different types of symptom in groundnuts, including one which is almost symptomless. Although the probe did not react with extracts from plants infected with GRV isolates from which the satellite RNA had been artificially eliminated, all naturally occurring GRV isolates contain the satellite RNA. The test therefore provides a reliable indicator of infection by GRV.     

Evaluation of Harmonic Direction-Finding Systems for Detecting Locomotor Activity

Abstract: We conducted a physical simulation experiment to test the efficacy of harmonic direction finding for remotely detecting locomotor activity in animals. The ability to remotely detect movement helps to avoid disturbing natural movement behavior. Remote detection implies that the observer can sense only a change in signal bearing. In our simulated movements, small changes in bearing (<5.7°) were routinely undetectable. Detectability improved progressively with the size of the simulated animal movement. The average (±SD) of reflector tag movements correctly detected for 5 observers was 93.9 ± 12.8% when the tag was moved ≥11.5°; most observers correctly detected tag movements ≥20.1°. Given our data, one can assess whether the technique will be effective for detecting movements at an observation distance appropriate for the study organism. We recommend that both habitat and behavior of the organism be taken into consideration when contemplating use of this technique for detecting locomotion.     

Wood-based building components: what have we learned?

Wood has long played a part in sheltering humans from the elements, but many of its properties remain poorly understood. This paper reviews deterioration of wood in buildings and discusses methods for preventing, detecting, and arresting decay. Research needs for reducing losses to fungal and insect attack are also addressed.     

Spatial patch occupancy patterns of the Lower Keys marsh rabbit

Reliable estimates of presence or absence of a species can provide substantial information on management questions related to distribution and habitat use but should incorporate the probability of detection to reduce bias. We surveyed for the endangered Lower Keys marsh rabbit (Sylvilagus palustris hefneri) in habitat patches on 5 Florida Key islands, USA, to estimate occupancy and detection probabilities. We derived detection probabilities using spatial replication of plots and evaluated hypotheses that patch location (coastal or interior) and patch size influence occupancy and detection. Results demonstrate that detection probability, given rabbits were present, was <0.5 and suggest that naïve estimates (i.e., estimates without consideration of imperfect detection) of patch occupancy are negatively biased. We found that patch size and location influenced probability of occupancy but not detection. Our findings will be used by Refuge managers to evaluate population trends of Lower Keys marsh rabbits from historical data and to guide management decisions for species recovery. The sampling and analytical methods we used may be useful for researchers and managers of other endangered lagomorphs and cryptic or fossorial animals occupying diverse habitats. © 2011 The Wildlife Society.     

High-Sensitivity Detection of Fruit Tree Viruses Using Bacterial Magnetic Particles

Prunus necrotic ring spot virus (PNRSV) and grapevine fanleaf virus (GFLV) were detected by fluoroimmunoassay using bacterial magnetic particles (BMPs),and a double antibody sandwich enzyme linked immunosorbent assay (DAS-ELISA).For the fluoroimmunoassay,fluorescein isothiocyanate labeled anti-PNRSV antibody or anti-GFLV antibody was conjugated onto BMPs of Magnetospirillum gryphiswaldense MSR-I.With this method,a very low minimum antigen concentration (1 x 106 dilution of the original sample concentration) could be detected.Using DAS-ELISA,the minimum antigen detection concentration was the original sample concentration.Thus,comparing these two methods,a BMP-based method could increase the sensitivity up to six orders of magnitude (106) higher than an ELISA-based method of detection PNRSV and GFLV.