Development of a novel sequence based real-time PCR assay for specific and sensitive detection of Burkholderia pseudomallei in clinical and environmental matrices

BACKGROUND

Melioidosis, caused by the category B biothreat agent Burkholderia pseudomallei, is a disease with a high mortality rate and requires an immediate culture-independent diagnosis for effective disease management. In this study, we developed a highly sensitive qPCR assay for specific detection of Burkholderia pseudomallei and melioidosis disease diagnosis based on a novel target sequence.

METHODS

An extensive in-silico analysis was done to identify a novel and highly conserved sequence for developing a qPCR assay. The specificity of the developed assay was analyzed with 65 different bacterial cultures, and the analytical sensitivity of the assay was determined with the purified genomic DNA of B. pseudomallei. The applicability of the assay for B. pseudomallei detection in clinical and environmental matrices was evaluated by spiking B. pseudomallei cells in the blood, urine, soil, and water along with suitable internal controls.

RESULTS

A novel 85-nucleotide-long sequence was identified using in-silico tools and employed for the development of the highly sensitive and specific quantitative real-time PCR assay S664. The assay S664 was found to be highly specific when evaluated with 65 different bacterial cultures related and non-related to B. pseudomallei. The assay was found to be highly sensitive, with a detection limit of 3 B. pseudomallei genome equivalent copies per qPCR reaction. The detection limit in clinical matrices was found to be 5 × 102 CFU/mL for both human blood and urine. In environmental matrices, the detection limit was found to be 5 × 101 CFU/mL of river water and 2 × 103 CFU/gm of paddy field soil.

CONCLUSIONS

The findings of the present study suggest that the developed assay S664 along with suitable internal controls has a huge diagnostic potential and can be successfully employed for specific, sensitive, and rapid molecular detection of B. pseudomallei in various clinical and environmental matrices.

A data-driven approach for simplifying the estimation of time for contaminant plumes to reach their maximum extent

Globally there exist a very large number of contaminated or possibly contaminated sites where a basic preliminary assessment has not been completed. This is largely, among others, due to limited simple methods/models available for estimating key site quantities such as the maximum plume length, further denoted as Lmax and the corresponding time T=TLmax, at which the plume reaches its maximum extent L=Lmax. An approach to easily obtain an estimate of TLmax in particular is presented in this work. Limited availability of high-quality field data, particularly of TLmax, necessitates the use of synthetic data, which constrains the overall model development works. Taking BIOSCREEN-AT (transient 3D model) as a base model, this work proposes second-order polynomial models, with only two parameters, for estimating Lmax and TLmax. This reformulation of the well established solution significantly reduces data requirement and workload for initial site assessment purposes. A global sensitivity analysis (Morris, 1991), using a large number of random synthetic data, identifies the first-order decay rate constants in the plume λEFF and at the source γ as dominantly most influential for TLmax. For Lmax, the first-order decay rate constant λEFF and groundwater velocity v are the two important parameters. The sensitivity analysis also identifies that these parameters non-linearly impact TLmax or Lmax. With this information, the proposed polynomial models (each for Lmax and TLmax) were trained to obtain model coefficients, using a large amount of synthetic data. For verification, the developed models were tested using four datasets comprising over 100 sample sets against the results obtained from BIOSCREEN-AT and the developed BIOSCREEN-AT-based steady-state model. Additionally, the developed models were evaluated against two well documented field sites. The proposed models largely simplify estimation, particularly, of TLmax, for which only very limited field or literature information is available.

Development of a Novel Internally Controlled HrpB1 Gene-Based Real-Time qPCR Assay for Detection of Burkholderia pseudomallei

BACKGROUND

Melioidosis, caused by category B bioterrorism agent Burkholderia pseudomallei, is a seasonal disease of tropical and subtropical regions with a high mortality rate. An early and culture-independent detection of B. pseudomallei is required for the appropriate disease management and prevention. The present study is designed to identify novel and unique sequences of B. pseudomallei and development of quantitative polymerase chain reaction (qPCR) assay.

METHODS

A novel B. pseudomallei-specific target sequence was identified by in silico analysis for the qPCR assay development. The specificity of the developed assay was assessed using purified DNA of 65 different bacterial cultures, and the sensitivity was estimated using a cloned target gene. Further, a type III secretion protein HrpB1 (HrpB1) gene-based duplex qPCR assay incorporating suitable extraction and amplification control was developed, and its viability was assessed in different clinical and environmental matrices for the detection of B. pseudomallei.

RESULTS

In this study, an 80-nucleotide-long B. pseudomallei-specific region within the gene HrpB1 was identified by computational analysis. The developed HrpB1-based qPCR assay was highly specific for B. pseudomallei detection when evaluated with 65 different bacterial cultures. The sensitivity of the qPCR assay with the HrpB1-recombinant plasmid was found to be five copies per qPCR reaction. The assay's detection limit was found to be 5 × 102 CFU/mL for human blood and urine, 5 × 101 CFU/mL in river water, and 2 × 103 CFU/gm in paddy field soil.

CONCLUSION

The results of the study showed the applicability of a novel HrpB1-based qPCR assay for sensitive and specific detection of B. pseudomallei in diverse clinical and environmental samples.

A rapid direct-differential agglutination assay for Brucella detection using antibodies conjugated with functionalized gold nanoparticles

Brucellosis is the most widespread and serious zoonotic disease worldwide which affects livestock, sylvatic wildlife, marine dwellers, and humans. It is acquired through Alphaproteobacteria which belong to the genus Brucella and is categorized as a potential bio-threat agent. In this study, we developed a rapid and direct differential whole cell (WC) agglutination-based assay for its on-field detection. The recombinant outer membrane (rOmp28) protein-derived specific mice IgG polyclonal antibodies (pAbs) of Brucella were purified using affinity chromatography and conjugated with functionalized gold nanoparticles (AuNPs) for rapid agglutination. A positive blot of 32 kDa protein revealed specific immuno-reactivity of rOmp28-pAbs using immunoblot analysis. For the synthesis of AuNPs, the conventional “Turkevich method” was optimized at a concentration < 1 mM of gold precursor for obtaining 50-nm-sized particles. Also, their physico-chemical characteristics were analyzed using UV-visible spectrophotometry, Fourier transform infra-red spectroscopy (FT-IR), Raman spectroscopy, X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), dynamic light scattering (DLS), zeta potential (ζ, ZP), and fluorescence spectroscopy. Furthermore, these AuNPs were functionalized with N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride (EDC) and N-hydroxysuccinimide (NHS) to prepare modified carboxylated AuNPs. For bioconjugation with Brucella rOmp28 IgG pAbs, antibody-conjugated functionalized AuNP constructs were prepared and characterized using FT-IR analysis with strong N–H deformations. Subsequently, these bioconjugated AuNPs were used to develop a direct-differential slide agglutination assay with a detection limit of 104 CFU mL−1. The sensitivity of this assay was compared with standard double-antibody sandwich ELISA (S-ELISA) using rOmp28 IgG pAbs with an LOD of 103 CFU mL−1 and a detection range of 102–108 CFU mL−1. No intraspecies cross-reactivity was observed based on evaluation of its specificity with a battery of closely related bacterial species. In conclusion, the increased sensitivity and specificity of the developed agglutination assay obtained using bioconjugated functionalized AuNPs is ≥ 98% for the detection of Brucella. Therefore, it can be used as an alternate rapid method of direct WC detection of bacteria as it is simple, robust, and cost-effective, with minimal time of reaction in the case of early disease diagnosis.

Carbon removal from a mirror-like gold surface by UV light, RF plasma, and IR laser exposure: a comparative study

A decrease in photon intensity due to carbon contamination on optical elements is a serious issue in synchrotron radiation (SR) beamlines. Photon intensity can be regained by refurbishment of optical elements using suitable techniques. In the literature, three suitable techniques [radio frequency (RF) plasma, ultraviolet (UV) radiation (λ=172nm), and infrared (IR) laser (λ=1064nm) exposure] are reported to remove carbon contaminations from optical elements. These techniques are used independently to remove carbon, and, to the best of our knowledge, no systematic study is available on their relative efficiencies and effects on a mirror surface. We have applied these techniques independently for removal of carbon contamination from a gold surface, and detailed surface characterizations are carried out using soft x-ray reflectivity, x-ray photoelectron spectroscopy, Raman spectroscopy, and atomic force microscopy techniques. Characterization results suggest that all three techniques are capable of removing carbon contamination with certain limitations. Here, detailed relative effects on a gold surface after cleaning experiments with three techniques are discussed.

Influence of recharge rates on steady-state plume lengths

A large number of potentially contaminated sites reported worldwide require cost- and time-effective assessment of the extent of contamination and the threats posed to the water resources. A significant risk assessment metric for these sites can be the determination of the maximum (i.e., steady-state) contaminant plume length (L_max). Analytical approaches in the literature provide an option for such an assessment, but they include a certain degree of uncertainty. Often, the causes of such uncertainties are the simplifications in the analytical models, e.g., not considering the influence of hydrogeological stresses such as recharge, which impact the plume development significantly. This may lead to an over- or underestimation of L_max. This work includes the influence of the recharge for the effective estimation of L_max. For that, several two-dimensional (2D) numerical simulations have been performed by considering different aquifer thicknesses (1 m- 4 m) and recharge rates (ranging from 0 to 3.6 mm/day). From the numerical results of this work, it has been deduced that 1) the application of the recharge shortens L_max, and the recharge entering the aquifer top causes the plume to tilt, 2) the reduction percentage in L_max depends on the recharge rate applied and the aquifer thickness, and 3) the reduction percentage varies in a non-linear manner with respect to the recharge rate for a fixed aquifer thickness. Based on these results, a hybrid analytical-empirical solution has been developed for the estimation of L_max with the inclusion of the recharge rate. The proposed hybrid analytical-empirical solution superimposes an empirically obtained correction factor onto an analytical solution. Although extensive confirmation steps of the developed model are required for including the effect of the recharge on aquifer hydraulics, the proposed expression improves the estimation of the L_max significantly. The hybrid analytical-empirical solution has also been confirmed with a selection of limited field contamination sites data. The hybrid model result (L_hyb) provides a significant improvement in the estimation, i.e., an order of magnitude lower mean relative error compared to the analytical model.

Biocompatibility analysis of PLA based candidate materials for cardiovascular stents in a rat subcutaneous implant model

Modification of Polylactic acid (PLA), a biopolymer, is a strategy still to be fully explored for the next generation of bioresorbable vascular stent (BVS) biomaterials. With this focus, inclusions upto 5% of Polycaprolactone (PCL) and Magnesium in PLA were tested in the rat subcutaneous model and their cellular and tissue interactions characterized, specifically with respect to inflammatory response, angiogenesis and capsularization. The cytokines IL6, TNF Alpha and IL-1Beta were estimated in the peri-implant tissue, all of which showed a non-significant difference between the non-implanted animals and those containing PLA by 8 weeks, speaking to the benign nature of PLA as an implant biomaterial. Both modified materials, had increased macrophage counts and cytokine levels, except IL6 at 8 weeks. Vascularization only at 8 weeks in PLA PCL containing tissue was significantly higher than pure PLA, which may be more carefully controlled along with the material hydrophobicity for possible efforts towards therapeutic angiogenesis. Capsule thickness, measured by staining with both Hematoxylin & Eosin and Masson's Trichome did not show any differences between materials, including PLA.

Influence of the core-hole effect on optical properties of magnesium oxide (MgO) near the Mg L-edge region

The influence of the core-hole effect on optical properties of magnesium oxide (MgO) is established through experimental determination of optical constants and first-principles density functional theory studies. Optical constants (δ and β) of MgO thin film are measured in the spectral region 40-300 eV using reflectance spectroscopy techniques at the Indus-1 synchrotron radiation source. The obtained optical constants show strong core exciton features near the Mg L-edge region, causing significant mismatch with Henke's tabulated values. On comparing the experimentally obtained optical constants with Henke's tabulated values, an edge shift of ∼3.0 eV is also observed. Distinct evidence of effects of core exciton on optical constants (δ and β) in the near Mg L-edge absorption spectra are confirmed through first-principles simulations.

Prognostic Significance of DNA Aneuploidy and p21ras Oncoprotein Expression in Colorectal Cancer and Their Role in the Determination of Treatment Modalities

The purpose of the present study was to investigate the prognostic significance of DNA ploidy, S-phase fraction and p21ras oncoprotein expression in patients with colorectal cancer and to correlate these factors with the clinical behavior of the tumors and their response to therapy. Of 79 patients with colorectal cancer 57% (45/79) had early stage disease. Forty-one percent (32/79) had aneuploid tumors while 30% (24/79) of the tumors had a high (>10%) S-phase fraction. p21ras oncoprotein expression was detected in 38% (30/79) of tumors. Patients with aneuploid tumors had a worse prognosis than patients with diploid tumors (p=0.0002). Similarly, patients with high S-phase fraction tumors had a shorter survival than those with low S-phase fraction tumors (p=0.005). No such difference was found between p21ras-positive and p21ras-negative tumor subgroups. In early stage colorectal cancer, aneuploidy was closely correlated with disease outcome (p=0.029). Early stage patients with diploid tumors who received radiotherapy and chemotherapy had a better prognosis than patients with aneuploid tumors. In conclusion, DNA ploidy is a significant and independent prognostic factor in colorectal cancer. Aneuploidy and genetic alteration of the p21ras oncoprotein are important in determining the biological aggressiveness of colorectal cancer. Furthermore, DNA ploidy may identify those subgroups of patients with early stage disease who may benefit from more aggressive treatment.

Structural variation in a synchrotron-induced contamination layer (a-C:H) deposited on a toroidal Au mirror surface

A carbon layer deposited on an optical component is the result of complex interactions between the optical surface, adsorbed hydrocarbons, photons and secondary electrons (photoelectrons generated on the surface of optical elements). In the present study a synchrotron-induced contamination layer on a 340 mm × 60 mm Au-coated toroidal mirror has been characterized. The contamination layer showed a strong variation in structural properties from the centre of the mirror to the edge region (along the long dimension of the mirror) due to the Gaussian distribution of the incident photon beam intensity/power on the mirror surface. Raman scattering measurements were carried out at 12 equidistant (25 mm) locations along the length of the mirror. The surface contamination layer that formed on the Au surface was observed to be hydrogenated amorphous carbon film in nature. The effects of the synchrotron beam intensity/power distribution on the structural properties of the contamination layer are discussed. The I(D)/I(G) ratio, cluster size and disordering were found to increase whereas the sp²:sp³ ratio, G peak position and H content decreased with photon dose. The structural parameters of the contamination layer in the central region were estimated (thickness ≃ 400 Å, roughness ≃ 60 Å, density ≃ 72% of bulk graphitic carbon density) by soft X-ray reflectivity measurements. The amorphous nature of the layer in the central region was observed by grazing-incidence X-ray diffraction.

Chemomodulation of carcinogen metabolising enzymes, antioxidant profiles and skin and forestomach papillomagenesis by Spirulina platensis

Numerous reports have revealed an inverse association between consumption of some selective natural products and risk of developing cancer. In the present study the effect of 250 and 500 mg/kg body wt. of Spirulina was examined on drug metabolising phase I and phase II enzymes, antioxidant enzymes, glutathione content, lactate dehydrogenase and lipid peroxidation in the liver of 7-week-old Swiss albino mice. The implications of these biochemical alterations have been further evaluated adopting the protocol of benzo(a)pyrene induced forestomach and 7,12 dimethylbenz(a)anthracene (DMBA) initiated and croton oil promoted skin papillomagenesis. Our primary findings reveal the 'Monofunctional' nature of Spirulina as deduced from its potential to induce only the phase II enzyme activities associated mainly with carcinogen detoxification. The glutathione S-transferase and DT-diaphorase specific activities were induced in hepatic and all the extrahepatic organs examined (lung, kidney and forestomach) by Spirulina pretreatment (significance level being from p < 0.05 to p < 0.005) except for the low dose treatment in forestomach. With reference to antioxidant enzymes viz., superoxide dismutase, catalase, glutathione reductase, glutathione peroxidase and reduced glutathione were increased significantly by both the chosen doses of Spirulina from p < 0.01 to p < 0.005. Chemopreventive response was quantitated by the average number of papillomas per effective mouse (tumor burden) as well as percentage of tumor bearing animals. There was a significant inhibition of tumor burden as well as tumor incidence in both the tumor model systems studied. In the skin tumor studies tumor burden was reduced from 4.86 to 1.20 and 1.15 by the low and high dose treatment respectively. In stomach tumor studies tumor burden was 2.05 and 1.73 by the low and high doses of Spirulina treatment against 3.73 that of control.