qPCR analysis of quorum sensing genes of pseudomonas aeruginosa: Primer design and qPCR efficiency

A well-designed and properly validated primer produces a specific and efficient qPCR assay. The primer’s melting temperature, G-C content, its size, as well as the amplicon’s size are the principal considerations while designing the primer for this study and it was in accordance with the MIQE guidelines. Subsequently, the designed primer was evaluated prior to the analysis to verify its efficiency and precision for the relative quantification of the gene transcription analysis. The validity of a qPCR assay is reliant on three elements; the qPCR efficiency (E) and the R2 as well as the slope, that were derived from constructed standard curve. The resulted E for the genes lasI, lasR, rhlI, rhlR and rplS are 92%, 93%, 96%, 92% and 94%, respectively. While the R2 and the slope value for these genes are 0.9991 and -3.523 for the lasI, 0.9991 and -3.501 for the lasR, 0.9989 and -3.434 for the rhlI, 0.9999 and -3.535 for the rhlR, and 0.9935 and -3.487 for the rplS. Melt curve analyses carried out post qPCR assay resulted in amplification of a single product. Resulted E, R2 and slope for all studied genes fell between the acceptable range, validating the use of designed primer for further analysis in the changes in transcription level of quorum sensing genes in treated Pseudomonas aeruginosa

Human Treated Dentin Matrix Hydrogel as a Drug Delivery Scaffold for Regenerative Endodontics

Introduction: The objective of the current study was to develop a human treated dentin matrix (hTDM) hydrogel for use as a scaffold to allow the controlled release of an antimicrobial agent for regenerative endodontics. Materials and Methods: Human extracted teeth were treated via chemical demineralization using ethylene diamine tetra-acetic acid solution to produce hTDM powder. Fourier transform infrared spectroscopy (FTIR) was conducted to determine the functional groups of hTDM, scanning electron microscopy (SEM) was used to define the morphology/particle size of hTDM, and energy dispersive X-ray analysis was performed to identify the superficial apatite groups. Prepared hTDM powder was added to the amoxicillin-clavulanate mixture with a mass ratio of 1:1. Then, the combination was dripped into a 5% (w/v) calcium chloride solution. Antibiotic release profiles were evaluated for 14 days via high performance liquid chromatography (HPLC). Hydrogel degradation properties were studied for 14 days using 10 mL of phosphate buffered saline (PBS). Encapsulation efficiency was determined by HPLC, while minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of amoxicillin-clavulanate were determined against Enterococcus faecalis (E. faecalis). The antibacterial activity of amoxicillin-clavulanate against E. faecalis was investigated for 14 days via agar diffusion test. Statistical analysis was performed with the Shapiro-Wilk test (P=0.05). Results: hTDM showed statistically a significant difference for percentage weight change (P=0.1). The encapsulation efficiencies for hTDM hydrogel with antibiotic and hydrogel with antibiotic was 96.08%±0.02 and 94.62%±0.11, respectively. MIC and MBC values of amoxicillin-clavulanate against E. faecalis were 2.4 µg/mL and 9.6 µg/mL, respectively. The antibacterial activity of antibiotic loaded hTDM hydrogels was significantly greater than loaded hydrogels alone by 31% after 4 and 100% at 14 days, respectively (P≤0.001). Conclusions: This in vitro study showed antibiotic-loaded injectable hTDM hydrogel could be an alternative system to transfer antibiotic-based intracanal medicaments for use in regenerative endodontics

Relative assessment of anti-quorum sensing in Piper betle leaves extract via pyoverdin assay

Anti-quorum sensing property has been a popular alternative approach over bactericidal/bacteriostatic property in combating bacterial infection while simultaneously tackling the dilemma of antibiotic resistance. We presented pyoverdin assay as an initial screening to qualitatively determine the anti-quorum sensing activity in Piper betle by measuring the loss of absorbance at wavelength 630 nm. Growth of Pseudomonas aeruginosa was proven to be unaffected by the presence of the P. betle leaves extract. The regression value (R2) of the quorum sensing (QS) activity in untreated supernatant of P. aeruginosa was 0.9636 and we presented the QS activity in fold-change, normalized to untreated sample for a fair comparison between batch of assays. We further assessed the QS activity in the extracts of P. betle leaves and found the QS activity of P. aeruginosa grown in the presence of ethyl acetate extract at 200 μg/ml was reduced to 0.6-fold. As the concentrations went lower, higher fold of QS activity was observed, suggesting that P. betle leaves extract is demonstrating anti-QS activity at a higher concentration. Further fractionate of ethyl acetate crude extracts resulted in three fractionates with high anti-QS activity with >50% reduction in QS activity and five fractionates with intermediate anti-QS activity. The use of pyoverdin assay to qualitatively portray the anti-QS activity could shorten the lengthiness of extracting and measuring the signaling molecule yet, produces reliable information to screen for anti-QS activity and guide for further fractionation and purification of bioactive compound

Deir el-Médina

La mission a débuté plus tard que prévu, car les autorisations de la Sécurité ont été délivrées fin janvier, deux semaines après la date du 15 janvier fixée pour l’ouverture de la mission. Faute de temps, certaines équipes n’ont pas réussi à atteindre leurs objectifs. La mission a poursuivi les travaux engagés en 2018 axés sur l’étude et la restauration des tombes de la nécropole de l’ouest et du mobilier conservé dans les magasins du site. Quatre équipes sont intervenues dans les TT 2, TT 2B..

Normal move-out correction in anisotropic and laterally heterogeneous media using simultaneous velocity variation with offset

In this paper, we present a new method of normal move-out (NMO) correction that works on a trace by trace basis technique rather than the current conventional sample by sample semblance analysis. The method corrects the pre-stack seismic data due to the NMO effect in both anisotropic and laterally heterogeneous mediums and simultaneously provides a full NMO velocity field that covers every single offset/azimuth in a common depth point (CDP). Also, we introduce a new computational method to recover the anisotropy effect from the extracted NMO velocity field. The presented method gives every single primary seismic reflector in a CDP, three different corrections; Positive correction (where the NMO velocity increases), Negative correction (where NMO velocity decreases) and zero correction (where NMO velocity doesn't change). The first two corrections (positive and negative) work only in case of anisotropy or laterally heterogeneous mediums while the last correction is applicable in case of the seismic reflector is isotropic. The method starts by picking the NMO velocity for each seismic reflector using the conventional semblance plot, then we use these picked NMO velocities as an initial input to our method and since every seismic reflector has three different possibilities, getting all the possible combinations is crucial. To get these combinations, we simply use the combination with repetition mathematical method. To control the degree of the increasing and the decreasing of the NMO velocity correction, we use two parameters called the Anisotropy range parameter(A(r)) and its increment. The Ar parameter is used to modify the picked NMO velocity of the primary seismic reflector N times (by adding and subtracting a correction value) based on the number of combinations. The total number of times where initial NMO velocities are modified is based on both the Ar parameter and the number of the seismic reflectors. After all the picked NMO velocities are modified then, we use each of the modified NMO velocity traces (after the interpolation between the modified NMO velocities) to correct the corresponding seismic trace due to the NMO effect then, measure the similarity/semblance between the pilot trace (e.g. Zero offset trace but it dynamically changes) and that seismic trace under the NMO correction. This corresponding seismic trace is corrected due to the NMO effect N times and at each time we measure the semblance value. The modified NMO velocity trace that gives the highest semblance measure is selected. The process is repeated for all the other seismic traces in a CDP. We tested the method on different real and synthetic examples; Isotropic, anisotropic and laterally heterogeneous mediums synthetic examples are presented. Furthermore, we tested the method on a pre-stack CDP real example using Alaska dataset. The results show an excellent flattening to the seismic reflectors and provides a reasonably accurate normal move-out velocity field that covers every offset in a CDP. (C|) 2017 Elsevier B.V. All rights reserved

Air quality predictions using log normal distribution functions of particulate matter in Kuala Lumpur

Malaysia’s capital city of Kuala Lumpur has been developed from a small settlement at the confluence of the Klang and Gombak rivers into a vibrant and bustling metropolis. The associated rapid economic growths have started to impose costs in terms of industrial pollution and the degradation of urban environment. Air pollution is a major issue in this city that has been affecting human health, agricultural crops, forest species, and ecosystems. This paper reports findings of a research aimed at developing a tool needed to analyze the statistical characters of air quality data in Kuala Lumpur, Malaysia. In this study, the theoretical distribution Log Normal was used to fit the parent distribution of PM10 for 1998 and 2002 for Kuala Lumpur. Two estimating methods namely method of maximum likelihood and method of moments, were used to estimate the parameters of the theoretic distributions. From the statistical properties of air pollutants, the probabilities of air pollutant concentration exceeding Malaysia Ambient Quality Standards can be predicted. The results of this work provide useful information for air quality management, and can also be used to develop the corresponding air pollution control strateg

Automatic NMO correction and full common depth point NMO velocity field estimation in anisotropic media

We present a new computational method of automatic normal moveout (NMO) correction that not only accurately flattens and corrects the far offset data, but simultaneously provides NMO velocity (v) for each individual seismic trace. The method is based on a predefined number of NMO velocity sweeps using linear vertical interpolation of different NMO velocities at each seismic trace. At each sweep, we measure the semblance between the zero offset trace (pilot trace) and the next seismic trace using a trace-by-trace rather than sample-by-sample based semblance measure; then after all the sweeps are done, the one with the maximum semblance value is chosen, which is assumed to be the most suitable NMO velocity trace that accurately flattens seismic reflection events. Other traces follow the same process, and a final velocity field is then extracted. Isotropic, anisotropic and lateral heterogenous synthetic geological models were built to test the method. A range of synthetic background noise, ranging from 10 to 30\ua0%, was applied to the models. In addition, the method was tested on Hess’s VTI (vertical transverse isotropy) model. Furthermore, we tested our method on a real pre-stack seismic CDP gathered from a gas field in Alaska. The results from the presented examples show an excellent NMO correction and extracted a reasonably accurate NMO velocity field

Piper betle leaves extract adversely affect motility of pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen that orchestrate its disease manifestation via a complex communication system known as quorum sensing (QS). Under the regulation of this complex network of QS system, is a myriad of virulence factors including the flagella and pili that contribute to its motility. To establish an infection in a host, P. aeruginosa must first attach itself to host cells with the assistance of flagella and pili and it would be a mere impossible for P. aeruginosa to initiate and establish an infection in the host without those features. In this study, we investigated the motility of P. aeruginosa under the influence of Piper betle leaves extract by growing the bacteria on a semi solid medium and compared the growth spread of the pathogen against the untreated sample. There are three types of motilities that were being investigated, which were swimming, swarming and twitching. In all three assays, a fraction of ethyl acetate extract of P. betle leaves were found to reduce the motility of P. aeruginosa with greatest defect in swimming at more than 80% reduction as compared to the untreated sample. Meanwhile, the fraction partially decreased the swarming and twitching of P. aeruginosa by 58% and 50% reduction respectively, in comparison to the untreated sample. The exhibited defect in the motility of P. aeruginosa proves the anti-QS property of the fraction of ethyl acetate extract of P. betle leaves and could be developed as a potential therapeutic agent against the pathogen