scholarly journals Optimization of RNA Extraction for PCR Quantification of Aromatic Compound Degradation Genes

2009 ◽  
Vol 76 (4) ◽  
pp. 1282-1284 ◽  
Author(s):  
Weidong Kong ◽  
Cindy H. Nakatsu
Keyword(s):  
Reverse Transcriptase ◽  
Quantitative Pcr ◽  
Aromatic Compound ◽  
Rna Extraction ◽  
Maximum Activity ◽  
Bacterial Strains ◽  
Aromatic Compound Degradation ◽  
Polluted Sites ◽  
Primer Sets ◽  
Mixed Community

ABSTRACT Seven different bacterial strains and primer sets and a mixed community were used to evaluate the use of reverse transcriptase quantitative PCR (Q-PCR) and Q-PCR of oxygenase genes to assess various approaches for monitoring the bioremediation of polluted sites. Differences in maximum activity were seen when different RNA extraction kits were compared.

Studies on antibacterial potential and phytochemical screening of different extract of Achyranthes aspera

2016 ◽  
Vol 5 (12) ◽  
pp. 5138
Author(s):  
Shyamji Shukla* ◽  
Priyanka Soni ◽  
Harish K. Kewat
Keyword(s):  
Methanolic Extract ◽  
Salmonella Typhi ◽  
Maximum Activity ◽  
Phytochemical Screening ◽  
Bacterial Strains ◽  
Antibacterial Compounds ◽  
Achyranthes Aspera ◽  
Biological Sources ◽  
Almost All ◽  
Antibacterial Potential

There is an alarming increase in the problem of resistance towards antibiotics amongst most of the pathogenic bacterial strains in recent years. This has drawn the attention of researchers around the world to search for novel and eco-friendly antibacterial compounds. Several biological sources have been explored in this respect but medicinal plants have taken a centre stage out of all. Plants have been known as a reservoir of number of bioactive compounds specially the antibacterial ones since time immemorial. Therefore, the present investigation was undertaken to analyze the antibacterial potential of the medicinal plant Achyranthes aspera. This study revealed that highest antibacterial activity was observed in the methanolic extract of stem against almost all test Bacteria. It showed maximum activity against E.coli (30 mm), followed by S. aureus (28 mm), Enterococcus sp.(25mm), Salmonella typhi ( 20 mm) and least activity was recorded in same extract against K.pneumoniae (6 mm). Four phytochemicals were screened in various solvent extracts. They are alkaloid, flavonoids, saponins and tannins.

scholarly journals One-step RNA extraction for RT-qPCR detection of 2019-nCoV

2020 ◽  
Author(s):  
Monica Sentmanat ◽  
Evguenia Kouranova ◽  
Xiaoxia Cui
Keyword(s):  
Real Time ◽  
Rna Extraction ◽  
Virus Transmission ◽  
Extraction Methods ◽  
Viral Rna ◽  
Taqman Probe ◽  
N Gene ◽  
Structural Protein ◽  
Diagnostic Panel ◽  
Primer Sets

ABSTRACTThe global outbreak of coronavirus disease 2019 (COVID-19) has placed an unprecedented burden on healthcare systems as the virus spread from the initial 27 reported cases in the city of Wuhan, China to a global pandemic in under three month[1]. Resources essential to monitoring virus transmission have been challenged with a demand for expanded surveillance. The CDC 2019-nCoV Real-Time Diagnostic Panel uses a real-time reverse transcription polymerase chain reaction (RT-PCR) consisting of two TaqMan probe and primer sets specific for the 2019-nCoV N gene, which codes for the nucleocapsid structural protein that encapsulates viral RNA, for the qualitative detection of 2019-nCoV viral RNA in respiratory samples. To isolate RNA from respiratory samples, the CDC lists RNA extraction kits from four manufacturers. In anticipation of a limited supply chain of RNA extraction kits and the need for test scalability, we sought to identify alternative RNA extraction methods. Here we show that direct lysis of respiratory samples can be used in place of RNA extraction kits to run the CDC 2019-nCoV Real-Time Diagnostic assay with the additional benefits of higher throughput, lower cost, faster turnaround and possibly higher sensitivity and improved safety.

scholarly journals Antibacterial Potential of Aloe weloensis (Aloeacea) Leaf Latex against Gram-Positive and Gram-Negative Bacteria Strains

2019 ◽  
Vol 2019 ◽  
pp. 1-4
Author(s):  
Yohannes Kelifa Emiru ◽  
Ebrahim Abdela Siraj ◽  
Tekleab Teka Teklehaimanot ◽  
Gedefaw Getnet Amare
Keyword(s):  
Antibacterial Activity ◽  
Bacterial Infections ◽  
Inhibition Zone ◽  
Antibacterial Activities ◽  
Maximum Activity ◽  
New Drugs ◽  
Diffusion Method ◽  
Bacterial Strains ◽  
Gram Positive ◽  
Gram Negative

Objective. To evaluate the antibacterial effects of the leaf latex of Aloe weloensis against infectious bacterial strains. Methods. The leaf latex of A. weloensis at different concentrations (400, 500, and 600 mg/ml) was evaluated for antibacterial activities using the disc diffusion method against some Gram-negative species such as Escherichia coli (ATCC 14700) and Pseudomonas aeruginosa (ATCC 35619) and Gram-positive such as Staphylococcus aureus (ATCC 50080) and Enterococcus fecalis (ATCC 4623). Results. The tested concentrations of the latex ranging between 400 and 600 mg·mL−1 showed significant antibacterial activity against bacterial strain. The highest dose (600 mg/ml) of A. weloensis leaf latex revealed the maximum activity (25.93 ± 0.066 inhibition zone) followed by the dose 500 mg/ml against S. aureus. The lowest antibacterial activity was observed by the concentration 400 mg/ml (5.03 ± 0.03) against E. coli. Conclusion. The results of the present investigation suggest that the leaf latex of A. weloensis can be used as potential leads to discover new drugs to control some bacterial infections.

scholarly journals Draft Genome Sequence of Labrenzia sp. Strain EL143, a Coral-Associated Alphaproteobacterium with Versatile Symbiotic Living Capability and Strong Halogen Degradation Potential

2018 ◽  
Vol 6 (10) ◽  
Author(s):  
Gisele Nunes Rodrigues ◽  
Asunción Lago-Lestón ◽  
Rodrigo Costa ◽  
Tina Keller-Costa
Keyword(s):  
Heavy Metals ◽  
Aromatic Compound ◽  
Genome Sequence ◽  
Draft Genome ◽  
Draft Genome Sequence ◽  
Gorgonian Coral ◽  
Toxic Compounds ◽  
Content Type ◽  
Multiple Genes ◽  
Aromatic Compound Degradation

ABSTRACT We report here the genome sequence of Labrenzia sp. EL143, an alphaproteobacterium isolated from the gorgonian coral Eunicella labiata that possesses various genes involved in halogen and aromatic compound degradation, as well as polyketide synthesis. The strain also maintains multiple genes that confer resistance to toxic compounds such as heavy metals and antibiotics.

Equilibrium studies of cadmium biosorption by presumed non-viable bacterial strains isolated from polluted sites

2014 ◽  
Vol 91 ◽  
pp. 37-44 ◽  
Author(s):  
Ganiyu Oladunjoye Oyetibo ◽  
Matthew Olusoji Ilori ◽  
Oluwafemi Sunday Obayori ◽  
Olukayode Oladipo Amund
Keyword(s):  
Bacterial Strains ◽  
Equilibrium Studies ◽  
Polluted Sites

Reverse Transcription with a Random Pentadecamer Primer Increases the Sensitivity of Quantitative PCR for BCR-ABL.

Blood ◽  
2006 ◽  
Vol 108 (11) ◽  
pp. 2339-2339
Author(s):  
David M. Ross ◽  
Timothy P. Hughes ◽  
Susan Branford
Keyword(s):  
Reverse Transcriptase ◽  
Quantitative Pcr ◽  
Reverse Transcription ◽  
Limit Of Detection ◽  
Negative Control ◽  
Gene Copy ◽  
Imatinib Treatment ◽  
Control Gene ◽  
Simple Modification ◽  
Number Of Patients

Abstract Real-time quantitative reverse transcriptase PCR for BCR-ABL (RQ-PCR) is used to monitor treatment response in chronic myeloid leukaemia (CML). BCR-ABL levels continue to decline over several years of imatinib treatment and increasing numbers of patients have BCR-ABL levels at or below the limit of detection. The sensitivity of current RQ-PCR assays limits our ability to identify patients who have a continuing decline in BCR-ABL levels; or to assess the effects of novel therapies to improve outcome in patients who have a good response to ABL kinase inhibitors, but harbour minimal residual disease. Improvements in therapy for these patients will be hard to assess without more sensitive monitoring of BCR-ABL. BCR-ABL levels are usually reported relative to a control gene. The control gene value gives an indication of the sensitivity achieved within each RNA sample; this varies with sample quality and efficiency of reverse transcription (RT). Control gene copy number below a defined value indicates that the analysis may be unreliable. We investigated the use of a random pentadecamer (RP; 15mer) primer in the RT reaction to improve the sensitivity of RQ-PCR. The RP primer is reported to be more efficient than the random hexamer (RH; 6mer) which is commonly used for RQ-PCR. BCR-ABL and BCR control gene transcripts were measured in 30 peripheral blood samples. After Trizol extraction 2μg RNA and 400U Superscript II reverse transcriptase were added to two RT reactions using RP or RH at a final concentration of 25μM. Each RT and quantitative PCR was performed 2–3 times and results compared using the Wilcoxon signed rank test or paired t-test. A more efficient RT is indicated by higher transcript levels. The table shows that BCR-ABL and BCR control gene values were significantly higher with RP primers. There was a proportionate increase in all transcripts so that the change in BCR-ABL/BCR% was not significant. BCR-ABL and control gene values with pentadecamer or hexamer primers No. of Samples Primer Median 25th Percentile 75th Percentile P value (RP v HP) * missing values due to inclusion of samples with undetectable BCR-ABL BCR transcripts 30 RH 438900 241800 1090000 < 0.001 RP 1203700 836500 2125000 BCR-ABL transcripts 16* RH 280 110 11340 < 0.001 RP 390 220 32910 BCR-ABL/BCR ratio 16* RH 0.10% 0.06% 5.6% =0.083 RP 0.08% 0.05% 4.2% We tested samples with undetectable BCR-ABL including 10 from CML patients on imatinib, and 10 from BCR-ABL negative control subjects. Each RNA was tested in two independent RTs and Q-PCRs. If the results were discordant a third RQ-PCR was performed and a consensus result determined. Using RP primers 6/10 patient samples were positive; 2/10 were positive with RH. None of the BCR-ABL negative control samples was positive with either primer. Sensitivity was calculated using the lower limit of detection and the standardised baseline value for untreated CML patients.The median calculated sensitivity increased from 4.5-log with RH to 5.0-log with RP. The use of pentadecamer primer made possible the detection of BCR-ABL in a small number of patients who had undetectable BCR-ABL with random hexamer RQ-PCR. This initial analysis suggests that the sensitivity of BCR-ABL detection may be improved 2–3-fold with a simple modification to RT methodology. This also has the potential to reduce the number of samples deemed unsatisfactory due to low control gene levels.

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