scholarly journals CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing

2020 ◽  
Author(s):  
Yongping Li ◽  
Tobias Fehlmann ◽  
Adam Borcherding ◽  
Snezana Drmanac ◽  
Sophie Liu ◽  
...  

Abstract Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.

2021 ◽  
Vol 11 (8) ◽  
pp. 3696
Author(s):  
Sohyeon Park ◽  
Yoonjin Park ◽  
Heejong Shin ◽  
Boyong Kim ◽  
Seunggwan Lee

Although Allium species are involved in bioactivity, to the best of our knowledge, there is no research on the effects of Allium senescens on drug resistance in hepatocarcinoma. Ultra-high performance liquid chromatography was used to determine the concentration of several bioactive compounds in A. senescens extract; flow cytometry, reverse transcription–quantitative polymerase chain reaction, and siRNA-mediated knockdown to estimate the levels of different markers in HepG2 cells. The quantity of p-coumaric acid in the extract was 4.7291 ± 0.06 μg/mL, and the protein of relevant evolutionary and lymphoid interest (PRELI) in the resistant cells decreased 2.1 times in the presence of p-coumaric acid. The resistant cells strongly downregulated the efflux transporters (ABCB1, ABCC2, and ABCG2) when exposed to the extract or p-coumaric acid and when PRELI was knocked down, in contrast to the influx proteins (OCT-1). Additionally, the extract induced mitochondrial apoptosis and suppressed autophagy. Consequently, the extract and p-coumaric acid attenuated drug resistance of HepG2 cells through the downregulation of PRELI, a key protein associated with the modulation of drug transporter expression, the activation of autophagy, and mitochondrial apoptosis. Our results indicate that A. senescens extract is beneficial in protecting cancer cells against drug resistance and sustaining the efficacy of sorafenib against liver cancer.


Molecules ◽  
2021 ◽  
Vol 26 (2) ◽  
pp. 465
Author(s):  
Omer Anis ◽  
Ajjampura C. Vinayaka ◽  
Nurit Shalev ◽  
Dvora Namdar ◽  
Stalin Nadarajan ◽  
...  

Cannabis sativa contains more than 500 constituents, yet the anticancer properties of the vast majority of cannabis compounds remains unknown. We aimed to identify cannabis compounds and their combinations presenting cytotoxicity against bladder urothelial carcinoma (UC), the most common urinary system cancer. An XTT assay was used to determine cytotoxic activity of C. sativa extracts on T24 and HBT-9 cell lines. Extract chemical content was identified by high-performance liquid chromatography (HPLC). Fluorescence-activated cell sorting (FACS) was used to determine apoptosis and cell cycle, using stained F-actin and nuclei. Scratch and transwell assays were used to determine cell migration and invasion, respectively. Gene expression was determined by quantitative Polymerase chain reaction (PCR). The most active decarboxylated extract fraction (F7) of high-cannabidiol (CBD) C. sativa was found to contain cannabichromene (CBC) and Δ9-tetrahydrocannabinol (THC). Synergistic interaction was demonstrated between CBC + THC whereas cannabinoid receptor (CB) type 1 and type 2 inverse agonists reduced cytotoxic activity. Treatments with CBC + THC or CBD led to cell cycle arrest and cell apoptosis. CBC + THC or CBD treatments inhibited cell migration and affected F-actin integrity. Identification of active plant ingredients (API) from cannabis that induce apoptosis and affect cell migration in UC cell lines forms a basis for pre-clinical trials for UC treatment.


2020 ◽  
Vol 10 (23) ◽  
pp. 8737
Author(s):  
Svetlana Pushkar

This study aims to assess the similarities and differences between Finland and Spain in terms of Leadership in Energy and Environmental Design for Existing Buildings (LEED-EB) Gold large office building-type projects transitioning from version 3 (v3) to version 4 (v4). The percentages of the average scores are used here to assess the achievements of the LEED-EB data. The natural logarithm of the odds ratio lnθ and Fisher′s exact 2 × 2 tests with a mid p-value are used to evaluate dichotomous data, while the exact Wilcoxon–Mann–Whitney and Cliff′s δ effect size tests are used to evaluate ordinary data. The results for LEED-EB Gold large offices demonstrate similar certification strategies in Finland and Spain. These results may be useful to LEED-EB practitioners in Finland and Spain for facilitating the selection of appropriate certification strategies in line with identified high-performance credits for large offices.


Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 770-770 ◽  
Author(s):  
Jean-Pierre Allain ◽  
Alex Owusu-Ofori ◽  
Sonny Michael Assennato ◽  
Susanne Marschner ◽  
Raymond P Goodrich ◽  
...  

Abstract Background: Across sub-Saharan Africa, blood supplies are threatened by numerous pathogens. In some locations, Plasmodium parasitemia prevalence in donor blood is nearly 50%. Donor testing for malaria in these areas is not effective and the risk of transfusion-transmitted malaria (TTM) is high. The Mirasol® PRT System for Whole Blood (WB) is a medical device intended for extracorporeal pathogen reduction of WB. The current clinical study evaluated the ability of Mirasol-treated WB to reduce the incidence of TTM. Study Design/Methods: This was a prospective, randomized, double-blind, controlled, single-center study in Ghana, which is hyperendemic for malaria. The study had 90% power to demonstrate a 90% reduction in TTM. Hospitalized patients requiring WB transfusions were randomly allocated to receive ≤ 2 transfusions of standard (untreated) or Mirasol-treated WB. The primary endpoint was the incidence of TTM as measured by quantitative polymerase chain reaction and Plasmodium alleleic sequence homology between transfused and patient WB during 28 days of follow-up. Patient safety was assessed by monitoring treatment-emergent adverse events (TEAEs) and transfusion reactions.Clinical outcomes related to hemoglobin increments, hemostatic parameters, and clinical chemistries were monitored for 28 days post-transfusion. Results: Overall, 226 subjects (113 Mirasol, 113 Untreated) were enrolled; 223 subjects were included in the safety analysis. Sixty-five (65) subjects were non-parasitemic at pre-transfusion (28 Mirasol, 37 Untreated) and received at least 1 parasitemic WB transfusion. Of 16 cases of suspected TTM (3 Mirasol, 13 Untreated) with 2 consecutive days of parasitemia, 9 were confirmed by alleleic homology (1 Mirasol, 8 Untreated). Incidence of TTM was significantly reduced in patients receiving treated products. Hemoglobin (mean [standard deviation]) was similar between groups at baseline (6.71 g/dL; p = 1.0), and Day 1 following 1 transfusion (8.53 [2.0] vs 8.49 [1.5] g/dL; p = 0.93) or 2 transfusions (7.09 [1.5] vs 7.38 [1.6] g/dL; p = 0.33). Ninety-two subjects (48 Mirasol, 44 Untreated) reported 145 TEAEs (75 Mirasol, 70 Untreated). Transfusion reactions were observed in 8.1% and 13.4% of subjects receiving Mirasol-treated and untreated WB, respectively. Table. Incidence of TTM Mirasol n (%); 95% CI Untreated n (%); 95% CI P-Value 2 Consecutive days of ParasitemiaN = 65 3 (10.7); 2.3, 28.2 n = 28 13 (35.1); 20.2, 52.2n = 37 < 0.05 2 Consecutive days of Parasitemia and >2 Allele match by PCRN = 65 1 (3.6); 0.1, 18.3n = 28 8 (21.6); 9.8, 38.2n = 37 < 0.05 ITT PopulationN = 223 1 (0.9); 0.0, 4.9n = 111 8 (7.1); 3.1, 13.6n = 112 < 0.05 Abbreviation: CI = confidence interval, ITT = intent-to-treat, PCR = polymerase chain reaction. Conclusions: The primary endpoint of the study was met. Mirasol treatment of WB clinically and statistically reduced TTM infections in the study population. This was the first human clinical study demonstrating that a PRT system can reduce transmission of a bloodborne pathogen. No safety issues were related to the device or device-treated WB. Transfusion reactions did not differ between patients receiving Mirasol-treated or untreated WB. Hemoglobin increments and transfusion outcome parameters in transfused patients did not differ between the treatment groups. Disclosures Allain: Terumo BCT: Consultancy. Owusu-Ofori:Terumo BCT: Other: Clinical Study Sub-Investigator. Marschner:Terumo BCT: Employment. Goodrich:Terumo BCT: Employment. Owusu-Ofori:Terumo BCT: Other: Clinical Study Investigator.


2004 ◽  
Vol 08 (11) ◽  
pp. 1289-1292 ◽  
Author(s):  
Shiho Hirohara ◽  
Makoto Obata ◽  
Shun-ichiro Ogura ◽  
Ichiro Okura ◽  
Suguru Higashida ◽  
...  

Photodynamic therapy (PDT) is one of the most effective treatments for cancer. We synthesized and characterized a series of 16 glycoconjugated porphyrins using a modification of the Lindsey method in the presence of Zn ( OAc )2·2 H 2 O as a template. The Zn 2+ ion template strategy improved the yield about 3-fold in the case of meta-substituted tetraphenylporphyrins, and free-base porphyrins were obtaind almost quantitatively by demetalation with 4 M HCl . The hydrophobicity parameter (Log P) of these porphyrins was evaluated by reversed phase high-performance liquid chromatography (RP-HPLC). The Log P values ranged from +4.8 to +7.8, so that most of the compounds are amphiphilic. The effect of the glycopyranosyl unit on the hydrophobicity of these compounds is discussed on the basis of the Log P value.


Author(s):  
SHAHNAZ USMAN ◽  
M. BASSAM ISMAIL SHEHADA ◽  
ANAB USMAN ◽  
QUAMRUL ISLAM

Objective: The main objective of the study was to assess the quality attribute of generic brands and newly formulated tablet of glimepiride and compare their drug release profile with innovator brand. Methods: Different brands were purchased from different markets of UAE. The validated high-performance liquid chromatography method was used to assess the quantitative analysis of glimepiride. The linearity of curve (r² = 0.9999) indicated the accuracy and precision of the analytical method. Comparative dissolution of newly formulated and generic tablets was carried out using USP dissolution apparatus II. Study was accomplished in phosphate buffer (pH = 7.8), the paddle speed was adjusted at 75 rpm. F1 and F2 factor among the brands and kinetic assessment were done to obtain the order of release. Results: Dissolution profiles of formulated tablets were almost same as that of innovator, 91.53 and 94.9, respectively, in 15 min. The statistical value between the different brands (F = 3.698) indicated that there were some differences among the few groups of tablets and p-value (0.002154) indicated that it supported H1 hypothesis. First-order and Weibull models described the drug release with r2 value of 0.9981–0.927210 and 0.9992– 0.9835, respectively. Stability of optimized formulated batch was also examined. Conclusion: It was concluded that the formulated tablets are stable and pharmaceutically as good as the innovators; however, all the selected brands could not be used interchangeably in the clinical practice. It was also concluded that the scrutiny and screening of the drug products, available in the markets, can help to build a better health-care setup.


2021 ◽  
Vol 9 (B) ◽  
pp. 1092-1097
Author(s):  
Nermine Mahfouz ◽  
Ebtissam Salah ◽  
Ayman Armaneous ◽  
Mai M. Youssef ◽  
Mones Mahmoud Abu Shady ◽  
...  

 The glomerulus is the accessible window to visualize the endothelial status of the whole body. Minimal level of albuminuria even below the cutoff point of microalbuminuria might be a marker of endothelial dysfunction. Exposure to Bisphenol A may be a risk factor of developing low-grade albuminuria in pediatrics. Aim: This study investigated the association of exposure to Bisphenol A and the presence of low-grade albuminuria. Methods: A cross-sectional study enrolling 158 children; 91 boys and 67 girls. Children with hepatic disease, kidney disease and endocrinopathies were excluded from the study. Urinary albumin and creatinine were measured in a first morning urine specimen. Urinary albumin/creatinine ratio was calculated in mg/gm and was stratified into: macroalbuminuria of ˃300mg/gm, microalbuminuria of 30-300mg/gm and low grade albuminuria of ˂30mg/gm. Urinary Bisphenol A was measured by high performance liquid chromatography using florescent detector. Results: Low grade albuminuria was detected in 141 participants (89.24%), while microalbuminuria and macroalbuminuria were detected in 15 (9.5%) and 2 (1.26%) participants, respectively. The total urinary Bisphenol A in candidates with low grade albuminuria was categorized into four quartiles (<0.285, 0.285–0.599, 0.600–1.215, >1.215) ng/mL and similarly their low grade albuminuria into (<2.0404, 2.0404–4.0385, 4.0386–7.3870, >7.3870) mg/gm. Children with the highest compared to the lowest quartile of urinary Bisphenol A had comparable mean of low grade albuminuria with insignificant P value. Conclusion: low grade albuminuria was found in 141 out of 158 children. A direct cause effect of exposure to Bisphenol A could not be proved. Further studies are needed to investigate the pathophysiology of low grade   albuminuria and its significance                                                                                      


2020 ◽  
Vol 19 ◽  
pp. 153303382095702
Author(s):  
Lisong Heng ◽  
Zhen Jia ◽  
Jian Sun ◽  
Yitong Zhao ◽  
Kun Zhang ◽  
...  

The purpose of this work was to extract key players such as mRNAs and long non-coding RNA (lncRNAs) in the etiopathogenesis of osteosarcoma (OS). The sequencing analyses (mRNAs and lncRNAs) of OS were conducted followed by differentially expressed mRNAs and lncRNAs (DEmRNAs and DElncRNAs) identification between U-2OS cells with has-miR-590-5p overexpression and negative control cells. Following this, the co-expression and functional enrichment analyses of DEmRNAs and DElncRNAs were carried out. Also, the miRNAs-DElncRNAs-DEmRNAs regulatory network was constructed with DElncRNAs-miRNAs and DElncRNAs-DEmRNAs pairs after the target gene analysis of miRNA. In addition, the ceRNA-has-miR-590-5p was further extracted based on the has-miR-590-5p-DElncRNAs and DElncRNAs-DEmRNAs interactions. Finally, the results of the bioinformatics analysis was verified by reverse-transcription polymerase chain reaction (RT-PCR). Totally, 980 DEmRNAs (539 up-regulated DEmRNAs and 441 down-regulated DEmRNAs) and 682 DElncRNAs (352 up-regulated DElncRNAs and 330 down-regulated DElncRNAs) were extracted between cells with hsa-miR-590-5p overexpression and normal cells. The functional analyses suggested that up-regulated genes were significantly enriched in several GO terms such as signal transduction and cytokine-cytokine receptor interaction pathway while down-regulated genes ( SCUBE3, HIST1H4E and EDIL3) were associated with calcium ion binding, cell surface function and nucleosome assembly. Additionally, the miRNAs-DEmRNAs-DEmRNAs network represented 220 pairs among 41 miRNAs, 38 DElncRNAs and 61 DEmRNAs. Furthermore, the ceRNA-hsa-miR-590-5p network consisted of 70 interaction pairs including hsa-miR-590-5p- SCUBE3-CTB-113D17.1, hsa-miR-590-5p- EDIL3-CTB-113D17.1 and hsa-miR-590-5p- HIST1H4E-CTB-113D17.1) among hsa-miR-590-5p, 30 DEmRNAs and 4 down-regulated DElncRNAs. Meanwhile, the RT-PCR results incidated that compared with the blank (KB) and negative control (NC) group, the mRNA expression of SCUBE3, HIST1H4E, and EDIL3 were significantly descreased in mimics group (P value <0.05). The lncRNA CTB-113D17.1 might implicate with OS development probably via serving as a hsa-miR-590-5p sponge to regulate gene targets ( SCUBE3, EDIL3 and HIST1H4E), which will facilitate the deep understandings of OS progression.


2020 ◽  
Vol 52 (12) ◽  
pp. 1337-1347
Author(s):  
Jianhong Wu ◽  
Lingge Jin ◽  
Yudi Zhang ◽  
Aihong Duan ◽  
Juhong Liu ◽  
...  

Abstract Homeobox transcript antisense RNA (HOTAIR) is a long non-coding RNA associated with a number of fibrosis-related diseases. The aim of this study was to investigate the specific role of HOTAIR in the development of endometrial fibrosis and to identify the molecular mechanisms underlying this process. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was used to determine the expression levels of HOTAIR in samples of intrauterine adhesion (IUA) tissue and in endometrial stromal cells (ESCs) that had been treated with transforming growth factor beta 1 (TGF-β1). Additionally, we transfected ESCs with either overexpression plasmid (pcDNA-HOTAIR) or silencing construct (si-HOTAIR) and then treated these cells with TGF-β1. We then performed RT-qPCR and western blot analysis, along with cell proliferation and apoptosis assays, to investigate the effects of HOTAIR on the transdifferentiation of ESCs into myofibroblasts. The results showed that the expression levels of HOTAIR were significantly elevated in IUA tissue and in ESCs that had been treated with TGF-β1. The overexpression of HOTAIR had a pro-fibrotic effect on ESCs, while the silencing of HOTAIR exerted an anti-fibrotic effect. Most importantly, the protein expression levels of p-Smad2 and p-Smad3 were significantly upregulated in TGF-β1-treated ESCs transfected with pcDNA-HOTAIR and were downregulated after transfection with si-HOTAIR constructs. These data indicate that HOTAIR promotes endometrial fibrosis by activating the TGF-β1/Smad signaling pathway, suggesting that the inhibition of HOTAIR may represent a promising therapeutic option for suppressing endometrial fibrosis.


2013 ◽  
Vol 23 (03) ◽  
pp. 1350008 ◽  
Author(s):  
DI ZHAO ◽  
SHENGHUA NI

In this paper, by the novel idea of integrating multiple-proposal algorithm and multiple-chain algorithm by parallel computing, we develop a highly efficient sampler for approximating statistical distributions: parallel Multi-proposal and Multi-chain Markov Chain Monte Carlo (pMPMC3), and we illustrate the high performance of this sampler by calculating P-value (odds ratio significance) for Genome Wide Association Study (GWAS). Computational results show that, by setting the convergence condition as the standard deviation of P-value is less than 10−3, pMPMC3 with 4 proposals and 4 chains obtains a convergent P-value within 106 iterations, while the conventional method Monte Carlo simulation does not obtain convergent P-values even in 107 iterations. We also test pMPMC3 by changing the number of chains, the number of proposals and the size of the dataset on a cluster with maximum 600 processes, the algorithm scales well.


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