SYBR Green Research Articles

Diverse Expression Patterns of EBV Oncogenes (LMP2A, EBV-Encoded microRNA, and EBV-encoded dUTPase) in EBV Associated Gastric Carcinoma and their Association with Viral Loads.

The chromogenic in situ hybridization (CISH) test is the gold standard for detecting Epstein-Barr virus (EBV)-associated gastric carcinoma (GC). Real-time (RT) PCR method is also a sensitive test that can detect the viral load in samples. As such, three EBV oncogenes were investigated in this study. RNA extraction and cDNA synthesis were performed on GC tissues of nine patients, who were previously confirmed to have EBVGC subtype. In addition, 44 patients that had positive RT-PCR but negative CISH results were also included as the control group. TaqMan RT-PCR analysis was performed to determine the expression of EBV-encoded microRNAs, and the expression of EBV-encoded dUTPase, as well as LMP2A, was analyzed by SYBR Green RT-PCR. EBV-encoded microRNAs and LMP2A were identified in 2 out of 9 (22%) EBVGC subtypes. In addition, EBV-encoded dUTPase was detected in 4 out of 9 (44.5%) EBVGC subtypes. EBV-encoded dUTPase was also expressed in a sample of the control group. The expression of LMP2A, EBV-encoded microRNAs, and EBV-encoded dUTPase viral oncogenes in patients with high EBV viral loads indicates that these expressions correlate with viral loads. Our findings indicate that the EBV-encoded dUTPase gene may have a role in EBVGC patients' non-response to treatment and might be considered a Biomarker-targeted therapy.

Surfactant-Assisted Label-Free Fluorescent Aptamer Biosensors and Binding Assays.

Using DNA staining dyes such as SYBR Green I (SGI) and thioflavin T (ThT) to perform label-free detection of aptamer binding has been performed for a long time for both binding assays and biosensor development. Since these dyes are cationic, they can also adsorb to the wall of reaction vessels leading to unstable signals and even false interpretations of the results. In this work, the stability of the signal was first evaluated using ThT and the classic adenosine aptamer. In a polystyrene microplate, a drop in fluorescence was observed even when non-binding targets or water were added, whereas a more stable signal was achieved in a quartz cuvette. Equilibrating the system can also improve signal stability. In addition, a few polymers and surfactants were also screened, and 0.01% Triton X-100 was found to have the best protection effect against fluorescence signal decrease due to dye adsorption. Three aptamers for Hg2+, adenosine, and cortisol were tested for their sensitivity and signal stability in the absence and presence of Triton X-100. In each case, the sensitivity was similar, whereas the signal stability was better for the surfactant. This study indicates that careful control experiments need to be designed to ensure reliable results and that the reliability can be improved by using Triton X-100 and a long equilibration time.

Antiplasmodial, Antioxidant and Cytotoxicity Activity of Ethanol and Aqueous Extracts of Khaya grandifoliola Stem Bark.

Malaria is a serious public health problem, especially in sub-Saharan Africa. The aim of this study was to scientifically provide baseline information on the use of Khaya grandifoliola stem bark as an antimalaria drug by traditional healers. The stem barks of K.grandifoliola were harvested and dried to obtain powder, and fifty grams of the powder were soaked in ethanol and hot distilled water respectively, for the preparation of ethanol and aqueous extracts, then dried in an oven at 40°C for the ethanol extract and 50°C for the aqueous extract. Plasmodium falciparum strains 3D7 sensitive and Dd2 resistant to chloroquine, were used to evaluate in vitro antiplasmodial activity using SYBR Green. The ability of the extracts to prevent oxidative stress was assessed by trapping 2, 2'-diphenyl-1-picrylhydrazyl (DPPH); nitric oxide, hydrogen peroxide and ferric reducing power. The cytotoxicity test of the extracts was carried out on RAW 264.7 cell lines and on erythrocytes. The data obtained were entered in the Excel software, then in Graph pad where the IC50 was calculated and the curves plotted. The fifty percent inhibition (IC50) of the antiplasmodial activity of the chloroquine-resistant strain PfDd2 were 54.27 ± 2.41 μg/mL and 31.19 ± 4.06 μg/mL respectively, for the aqueous and ethanol extracts. As for the Chloroquino-sensitive Pf3D7, IC50 of 53.06 μg/mL was obtained for the aqueous extract and 28.03 ± 1.90 μg/mL for ethanol. The DPPH radical scavenging activity presented IC50 of 104 μg/mL for the aqueous and 2.617 μg/mL for the ethanol extract; for the Nitric oxide (NO) presented an IC50 of 301 ± 21 μg/mL for the aqueous extract 140.7 ± 21 μg/mL for the ethanol; for hydrogen peroxide the ethanol and aqueous presented IC50 of 845.1 ± 21 μg/mL and 509.4 ± 21 μg/mL respectively. The cytotoxicity on RAW 264.7 cells presented High CC50 in particular >1000 μg/mL and 467.4 μg/mL respectively for the aqueous and ethanol extract. Extracts of Khaya grandifoliola exhibited antiplasmodial activity. The ability to inhibit oxidative stress as well as lower cell toxicity on RAW 264.7 and erythrocytes, is a good indicator. However, in vivo tests remain important in order to confirm the use of this plant for the treatment of malaria.

Evaluation of Molecular Methods to Identify Chagas Disease and Leishmaniasis in Blood Donation Candidates in Two Brazilian Centers.

In Brazil, blood donation is regulated by the Brazilian Ministry of Health, and all States follow the same protocol for clinical and laboratory screening. Brazil is an endemic country for Chagas disease (CD), caused by Trypanosoma cruzi, and for leishmaniasis, caused by a species of Leishmania spp. Screening for leishmaniosis is not routinely performed by blood banks. Given the antigenic similarity between T. cruzi and Leishmania spp., cross-reactions in serological tests can occur, and inconclusive results for CD have been found. The objective of this study was to apply molecular techniques, e.g., nPCR, PCR, and qPCR, to clarify cases of blood donation candidates with non-negative serology for CD and to analyze the difference between the melting temperature during real-time PCR using SYBR Green. Thirty-seven cases that showed non-negative results for CD using chemiluminescent microparticle immunoassay (CMIA) tests from blood banks in Campo Grande, MS, and Campinas, SP, were analyzed. In the serum samples, 35 samples were evaluated by ELISA, and 24.3% (9/35) showed positive results for CD. nPCR was able to detect 12 positive results in 35 samples (34.28%). qPCR for T. cruzi was quantifiable in the samples that showed a value ≥0.002 par eq/mL (parasite equivalents per milliliter), and in 35 samples, 11 (31.42%) were positive. Of all evaluated samples using the described tests (CMIA, ELISA, nPCR, and qPCR), 18 (48.6%) were positive for CD. For MCA by qPCR, the melting temperature was 82.06 °C ± 0.46 for T. cruzi and 81.9 °C ± 0.24 for Leishmania infantum. The Mann-Whitney test showed a significant value of p < 0.0001. However, the differentiation between T. cruzi and L. infantum could not be considered due to temperature overlap. For leishmaniasis, of the 35 samples with non-negative serology for CD tested by the indirect fluorescent antibody test (IFAT), only one sample (2.85%) was positive (1:80). The PCR for Leishmania spp. was performed on 36 blood samples from donation candidates, and all were negative. qPCR for L. infantum showed 37 negative results for the 37 analyzed samples. The data presented here show the importance of performing two different tests in CD screening at blood banks. Molecular tests should be used for confirmation, thereby improving the blood donation system.

Development and application ofalow-priced duplex quantitative PCR assay based onSYBR GreenI for the simultaneous detection ofporcine deltacoronavirus and porcine sapelovirus.

Porcine deltacoronavirus (PDCoV) and porcine sapelovirus (PSV) are two viruses that can cause diarrhoea inpigs and bring great economic loss tothe pig industry. Inthis research, aduplex real-time quantitative polymerase chain reaction (qPCR) assay based onSYBR Green I was developed tosimultaneously detect PDCoV and PSV. Nospecific melting peaks were found inother porcine diarrhoea-associatedviruses, indicating that the method developed inthis study had good specificity. The detection limits ofPDCoV and PSV were 1.0×101copiesμl-1 and 1.0×102 copiesμl-1, respectively. The duplex real-time qPCR assay tested two hundred and three (203) intestinal and faecal samples collected from diarrhoeal and asymptomatic pigs. The positive rates ofPDCoV and PSV were 20.2% and 23.2%, respectively. The co-infection rate ofPDCoV and PSV was 13.8%. Toevaluate the accuracy ofthedeveloped method, conventional PCR and singular TaqMan real-time qPCR assays for PDCoV/PSV were also used todetect the samples. The results showed that the duplex real-time qPCR assay was consistent with thesingular assays, but its sensitivity was higher than conventional PCR methods. This duplex real-time qPCR assay provides arapid, sensitive and reliable method inaclinic tosimultaneously detect PDCoV and PSV.

Screening of food allergens in cereals using real-time PCR

Allergen is a substance that induces hypersensitivity reactions. Most of the food allergens are protein in nature and cause life-threatening allergies as well as influencing the quality of life. The present study was designed to evaluate the screening of major allergens in commercially available processed food commodities of wheat, soybean species and the cross reactivity of peanut in tree nuts using real-time PCR. Analysis of the results demonstrates that the SYBER Green qPCR assay is a quick and reliable method for screening of allergens. A total of 42 food samples were collected for these studies and analyzed results. Peanut allergen was detected in tree nuts of walnut, coconut, almond, and hazelnut, wheat allergen was detected in rice, oat, barely and buckwheat, while soybean allergen was detected in the species of pea, broad bean, bean seed, and kidney bean. This study will provide information for affected consumers and to do meaningful risk assessment.

Ultrasensitive fluorescence detection of multiple DNA methyltransferases based on DNA walkers and hyperbranched rolling circle amplification

The accurate and ultrasensitive detection of multiple methyltransferases was in great request for clinical diagnosis and epigenetic therapy. Here, a novel fluorescence assay was proposed for ultrasensitive CpG methyltransferase (M.SssI) and DNA adenine methyltransferase (Dam) activity detection based on hyperbranched rolling circle amplification (HRCA) and DNA walkers. The biosensor showed an extremely high sensitivity due to the dual-amplification strategy of HRCA and DNA walker. The LOD of the biosensor for M.SssI and Dam methyltransferase was estimated at 0.0004 U/mL and 0.001 U/mL, respectively. Without the presence of M.SssI methyltransferase, the corresponding recognition site of hairpin HM was cleaved by HpaII endonuclease, generating a DNA fragment (T-DNA) and inducing the DNA walker-HRCA reaction. Since the HRCA products contained numerous double-strand DNA (dsDNA), SYBR Green I could be embedded in the dsDNA, leading to a high fluorescent signal. In the presence of M.SssI methyltransferase, the corresponding recognition site of hairpin HM was methylated and the HpaII endonuclease-catalyzed stem of hairpin HM dissociation was hindered, leading to no DNA fragment (T-DNA) present. Hence, the DNA walker-HRCA reaction was not initiated and the fluorescent signal of SYBR Green I remained at a low level. Similarly, DNA adenine methyltransferase (Dam) and its inhibitors could also be detected by redesigning hairpin HD with the Dam recognition sequences. Furthermore, the sensing system was applied to analyze the endogenic Dam methyltransferase in the real samples such as E. coli cell lysate.

Abstract P2-18-02: Promoter hypomethylation associated upregulation of MEN1 mRNA expression and its correlation with pathological parameters in Indian breast cancer patients

Abstract Background: Breast cancer in the recent years has accounted to be most frequently reported cancer across the globe. Nearly 11.7% of total cancer cases were of breast cancer and 6,84,996 deaths were reported in the year 2020. Multiple endocrine neoplasia type 1 gene that encodes for menin protein is known be involved in numerous signaling pathways and is also reported to show its interactions with histone modifiers. MEN1 is frequently reported to be dysregulated in the cancer including neuroendocrine tumors, lung cancer and melanoma. However, the role of MEN1 in case of Breast cancer has not been well understood. Lifestyle, environmental conditions and ethnicity play crucial role in epigenetic modulation of gene expression. In the current scenario with high increase in number of cancer cases, there is need to develop more personalized course of treatment rather than generalized approach. Thus, discovery of new biomarkers will aid in designing better diagnostic and therapeutic strategy to treat cancer. Aims and Objective: In this study we aim to find MEN1 mRNA expression and its connection with the MEN1 promoter methylation in case of Indian breast cancer patients and to correlate our findings with the pathological parameters of the patients to understand the role of MEN1 gene in breast cancer progression. Material and methods: The ethical approval for the study was procured from Institutional ethical committee of AIIMS,New Delhi and Jamia Millia Islamia, New Delhi. The study comprises of 44 pair of Breast tissue samples including cancer and adjacent normal tissue collected at department of surgical oncology AIIMS, New Delhi and were stored in RNA later and PBS at -80˚C for RNA and DNA extraction respectively. DNA was extracted through PCI (Phenol-Chloroform-Isoamyl alcohol) method and was further confirmed by Agarose gel electrophoresis. TRIZOL method was used to extract RNA from tissue samples and was quantified using nanodrop. Moreover, cDNA synthesis was carried out using Verso cDNA synthesis kit. To investigate the MEN1 mRNA expression, RT- PCR was carried out with LightCycler96 SYBR Green I Master (Roche) using specific primers. To analyze the promoter methylation status of MEN1 promoter region, CT- conversion was done and MS-PCR was performed using Methylation and Unmethylation specific primers. Statistical analysis was done using Graph Pad and SPSS to correlate our findings with clinical parameters. Results: In our study we found 27 out of 44 patients to exhibit up-regulation of MEN1 mRNA in the breast cancer tissue as compared with the normal tisuue. MEN1 promoter unmethylation was detected in 25 out of 44 cases, which revealed its significant correlation with the upregulated MEN1 gene. Further on correlation of our data with the clinical parameters, we found its significant association with the estrogen receptor status and age of menopause of the patients. Conclusion: Our results of the MEN1 mRNA expression study and its association with MEN1 promoter methylation in case of breast cancer suggests the tumorigenic role of MEN1 in breast cancer. Our findings thereby indicate the possible role of MEN1 gene in progression of the disease. Further study on large sample size will aid in better understanding the role of MEN1 gene in Breast carcinoma. Citation Format: Sheersh Massey, Aasif Khan, Asifa Khan, SVS Deo, Syed Akhtar Husain. Promoter hypomethylation associated upregulation of MEN1 mRNA expression and its correlation with pathological parameters in Indian breast cancer patients [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P2-18-02.

Abstract P6-04-18: Rapid diagnosis of breast biopsies with open-top light-sheet microscopy

Abstract Intro: Detection of breast cancer is achieved through a diagnostic work-up that involves specialized breast imaging, image-guided biopsy, and pathological assessment. Pathology results typically require ~ 3 business days before a diagnosis is rendered, creating avoidable anxiety in women presenting with a breast abnormality. We describe a solution to deliver a rapid preliminary diagnosis within 30 minutes of biopsy. This rapid preliminary diagnosis has the potential to reduce anxiety, streamline patient care workflows, and reduce healthcare costs. Methods: Fresh 14 gauge breast biopsies in normal saline were received directly from the breast imaging clinic and immediately stained using the nuclear marker SYBR Gold (Invitrogen) and pan-protein marker Atto 655 NHS Ester (Sigma) prepared in dimethyl sulfoxide, washed, and cleared for imaging at a refractive index of 1.46 using 2,2’-Thiodiethanol (Sigma). The full process requires approximately 14 minutes for staining and clearing. After staining, we placed the biopsy in a custom-built specimen holder and imaged a 100-micron cross section along the full length of the biopsy using our custom open-top light-sheet microscope. Images were subsequently converted computationally to a standard hematoxylin and eosin (H&amp;E) color format using Fiji and Aivia (Leica) software and were ready for evaluation by a pathologist on the same day they were collected. Results: Using the protocol above, we demonstrated the ability to stain, clear, image, and visualize needle core biopsies within 30 minutes of receiving the tissue sample. Processing the data and converting to the H&amp;E color palette required additional time, often requiring 60-90 minutes, surpassing the overall 30 minute turnaround time goal. The images contained identifiable stroma, epithelial cells, immune cells, and duct structures to a depth of 100 microns. Discussion: We describe a method to obtain a microscopic image for preliminary diagnosis within 30 minutes of receipt of tissue. The quality of the images produced by the method shows promise for preliminary diagnosis. Additional optimization is needed in sample preparation and data processing to meet the 30 minute turnaround time requirement. This optimization can be achieved by parallelization of the data processing on a cluster or cloud to reduce the time by an order of magnitude, which is currently under investigation by our team. The imaging and data processing will also be accelerated by multi-resolution imaging, which will decrease the time of imaging and dataset size for processing. A diagnostic study, comparing the preliminary light-sheet-based diagnosis to the final formalin fixed paraffin embedded (FFPE) pathology, is underway. Citation Format: Brandy E. Olin Pope, Suzanne Dintzis, Elizabeth U. Parker, Rebeca Alvarez, Alexandra Alvarsson, Habib Rahbar, Nicholas Reder. Rapid diagnosis of breast biopsies with open-top light-sheet microscopy [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-04-18.

Transfection Efficacy and Cellular Uptake of Lipid-Modified Polyethyleneimine Derivatives for Anionic Nanoparticles as Gene Delivery Vectors.

Cationic polyethylenimine (PEI)-based nonviral gene carriers have been desirable to overcome the limitations of viral vectors in gene therapy. A range of PEI derivatives were designed, synthesized, and evaluated for nonviral delivery applications of plasmid DNA (pDNA). Linolenic acid, lauric acid, and oleic acid were covalently conjugated with low-molecular-weight PEI (Mw ∼ 1200 Da) via two different linkers, gallic acid (GA) and p-hydroxybenzoic acid (PHPA), that allows a differential loading of lipids per modified amine (3 vs 1, respectively). 1H NMR spectrum confirmed the expected structure of the conjugates as well as the level of lipid substitution. SYBR Green binding assay performed to investigate the 50% binding concentration (BC50) of lipophilic polymers to pDNA revealed increased BC50 with an increased level of lipid substitution. The particle analysis determined that GA- and PHPA-modified lipopolymers gave pDNA complexes with ∼300 and ∼100 nm in size, respectively. At the polymer/pDNA ratio of 5.0, the ζ-potentials of the complexes were negative (-6.55 to -10.6 mV) unlike the complexes with the native PEI (+11.2 mV). The transfection experiments indicated that the prepared lipopolymers showed higher transfection in attachment-dependent cells than in suspension cells based on the expression of the reporter green fluorescent protein (GFP) gene. When loaded with Cy3-labeled pDNA, the lipopolymers exhibited effective cellular uptake in attachment-dependent cells while the cellular uptake was limited in suspension cells. These results demonstrate the potential of lipid-conjugated PEI via GA and PHPA linkers, which are promising for the modification of anchorage-dependent cells.

Implementation of helicase-dependent amplification with SYBR Green I for prompt naked-eye detection of bacterial contaminants in platelet products

Platelet transfusions may lead to more significant risks of infection and septic transfusion reactions that can be fatal to the recipient. Platelet products should be screened to limit or detect bacterial contamination before application to patients to minimise any adverse reactions. This study aimed to develop a helicase-dependent amplification (HDA) technique targeting a universal highly conserved bacterial gene, 16S rRNA, in combination with naked-eye detection using SYBR Green I (HDA/SYBR Green I) to detect bacterial contamination in platelet products. Thirty positive samples were obtained from spiked platelet products by five transfusion-relevant bacterial strains and were screened for bacterial contamination by HDA/SYBR Green I. HDA/SYBR Green I showed an enhanced yield of bacterial contaminant detection when performed with medium to late shelf life, Day 2 of storage or later platelet products (98.67% sensitivity and 100% specificity compared to the BACT/ALERT culture system). The limit of detection of HDA/SYBR Green I was 1 ng, and there was no cross-reaction with other organisms that could likely contaminate platelet products. The developed HDA/SYBR Green I assay is rapid and simplistic and only requires an easy-to-find heat box, available in general blood bank laboratories, for the amplification step. This technique is suitable for further development as an alternative method to detect bacterial contamination in platelet products in the near future.

Expression profile of miRNAs computationally predicted to target PDL-1 in cervical tissues of different histology groups.

Background: Human papilloma virus (HPV) is considered a successful pathogen as it has the ability to evade host immune responses and establish long-term persistent infection. It has been reported that programmed death ligand 1 (PDL-1) expression is correlated with HPV-positivity and is increased with lesion progression or tumor metastasis in cervical cancer. The expression of microRNAs (miRNAs) is often deregulated in cancer, and their potential targets are affected. Methods: RNA was extracted from formalin-fixed paraffin-embedded (FFPE) cervical samples of different histological types, previously typed for the presence of HPV. A specific quantitative polymerase chain reaction (qPCR) protocol with SYBR Green was used to check for the expression of four miRNAs that were computationally predicted to target PDL-1. Results and conclusion: hsa-miR-20a-5p and hsa-miR-106b-5p showed an expression increase with the severity of the lesions, while hsa-miR-125b-5p depicted a significant decrease in its expression in cancerous samples when compared to normal samples.

Antimalarial and Cytotoxic Activity of Native Plants Used in Cabo Verde Traditional Medicine.

Medicinal plants have historically been a source of drugs in multiple applications, including the treatment of malaria infections. The Cabo Verde archipelago harbors a rich diversity of native plants, most of which are used for medicinal purposes. The present study investigated the in vitro antiplasmodial activities of four native plants from Cabo Verde (i.e., Artemisia gorgonum, Lavandula rotundifolia, Sideroxylon marginatum, and Tamarix senegalensis). Traditional preparations of these medicinal plants, namely aqueous extracts (infusions) and ethanolic extracts, were tested against both chloroquine-sensitive (3D7) and chloroquine-resistant (Dd2) Plasmodium falciparum strains using the SYBR Green detection method. The in vitro cytotoxicity was evaluated in Caco-2 and PLP2 cells using a sulforhodamine B colorimetric assay. An ethanolic extract of A. gorgonum and infusions of T. senegalensis exhibited high antiplasmodial activities (EC50 < 5 μg/mL) without cytotoxicity (GI50 > 400 μg/mL). Extracts of L. rotundifolia and S. marginatum exhibited moderate activities, with EC50 values ranging from 10-30 μg/mL. The A. gorgonum ethanolic extract showed activity toward early ring stages, and parasites treated with the T. senegalensis infusions progressed to the early trophozoite stage, although did not develop further to the late trophozoite or schizont stages. Antimalarial activities and the lack of cytotoxicity of the extracts are reported in the present study and support previous claims by traditional practitioners for the use of these plants against malaria while suggesting their ethnopharmacological usefulness as future antimalarials.

Diminazene aceturate and imidocarb dipropionate-based combination therapy for babesiosis - a new paradigm.

In the present study, the effect of a combination therapy consisting of diminazene aceturate (DA) and imidocarb dipropionate (ID) on the in vitro growth of several parasitic piroplasmids, and on Babesia microti in BALB/c mice was evaluated using a fluorescence-based SYBR Green I test. We evaluated the structural similarities between the regularly used antibabesial medications, DA and ID, and the recently found antibabesial drugs, pyronaridine tetraphosphate, atovaquone, and clofazimine, using atom pair fingerprints (APfp). The Chou-Talalay approach was used to determine the interactions between the two drugs. A Celltac MEK-6450 computerized hematology analyzer was used to detect hemolytic anemia every 96h in mice infected with B. microti and in those treated with either mono- or combination therapy. According to the APfp results, DA and ID have the most structural similarities (MSS). DA and ID had synergistic and additive interactions against the in vitro growth of Babesia bigemina and Babesia bovis, respectively. Low dosages of DA (6.25mg kg-1) and ID (8.5mg kg-1) in conjunction with each other inhibited B. microti growth by 16.5, 32, and 4.5% more than 25mg kg-1 DA, 6.25mg kg-1 DA, and 8.5mg kg-1 ID monotherapies, respectively. In the blood, kidney, heart, and lung tissues of mice treated with DA/ID, the B. microti small subunit rRNA gene was not detected. The obtained findings suggest that DA/ID could be a promising combination therapy for treating bovine babesiosis. Also, such combination may overcome the potential problems of Babesiaresistance and host toxicity induced by utilizing full doses of DA and ID.

Assessment of artemisinin tolerance in Plasmodium falciparum clinical isolates in children with uncomplicated malaria in Ghana

BackgroundArtemisinin-based combination therapy (ACT) is the first-line treatment for uncomplicated malaria in Ghana. Artemisinin (ART) tolerance in Plasmodium falciparum has arisen in Southeast Asia and recently, in parts of East Africa. This is ascribed to the survival of ring-stage parasites post treatment. The present study sought to assess and characterize correlates of potential ART tolerance based on post-treatment parasite clearance, ex vivo and in vitro drug sensitivity, and molecular markers of drug resistance in P. falciparum isolates from children with uncomplicated malaria in Ghana.MethodsSix months to fourteen years old children presenting with acute uncomplicated malaria (n = 115) were enrolled in two hospitals and a Health Centre in Ghana’s Greater Accra region and treated with artemether-lumefantrine (AL) according to body weight. Pre- and post-treatment parasitaemia (day 0 and day 3) was confirmed by microscopy. The ex vivo ring-stage survival assay (RSA) was used to detect percent ring survival while the 72 h SYBR Green I assay was used to measure the 50% inhibition concentration (IC50s) of ART and its derivatives and partner drugs. Genetic markers of drug tolerance /resistance were evaluated using selective whole genome sequencing.ResultsOf the total of 115 participants, 85 were successfully followed up on day 3 post-treatment and 2/85 (2.4%) had parasitaemia. The IC50 values of ART, artesunate (AS), artemether (AM), dihydroartemisinin (DHA), amodiaquine (AQ), and lumefantrine (LUM) were not indicative of drug tolerance. However, 7/90 (7.8%) pre-treatment isolates had > 10% ring survival rates against DHA. Of the four isolates (2 RSA positive and 2 RSA negative) with high genomic coverage, P. falciparum (Pf) kelch 13 K188* and Pfcoronin V424I mutations were only present in the two RSA positive isolates with > 10% ring survival rates.ConclusionsThe observed low proportion of participants with day-3 post-treatment parasitaemia is consistent with rapid ART clearance. However, the increased rates of survival observed in the ex vivo RSA against DHA, maybe a pointer of an early start of ART tolerance. Furthermore, the role of two novel mutations in PfK13 and Pfcoronin genes, harboured by the two RSA positive isolates that had high ring survival in the present study, remains to be elucidated.

Distinction of Male and Female Trees of Ginkgo biloba Using LAMP.

Ginkgo biloba is utilized as food, medicine, wood, and street trees among other things. The objective of this study was to develop a loop-mediated isothermal amplification (LAMP) assay for gender distinction of G. biloba. Male-specific SCAR gene can be utilized to identify G. biloba gender using LAMP. The optimized LAMP conditions, temperature 60°C, 2-mM MgSO4, and [F3/B3]:[FIP/BIP] primer ratio of 1:4 were selected as final conditions. The G. biloba SCAR LAMP displayed a sensitivity of 10ng when amplified by concentration under the optimum conditions. Additionally, it demonstrated a particular response in male with SYBR Green I in LAMP analysis that can be a more powerful tool for field and scale-up applications. Our work represents a first attempt to identify G. biloba gender using LAMP and offers an efficient and reliable tool for roadside landscaping.

Culture of leukocyte-derived cells from human peripheral blood: Increased expression of pluripotent genes OCT4, NANOG, SOX2, self-renewal gene TERT and plasticity.

There are few stem cells in human peripheral blood (PB). Increasing the population and plasticity of stem cells in PB and applying it to regenerative medicine require suitable culture methods. In this study, leukocyte populations 250 mL of PB were collected using a blood separator before that were cultured in optimal cell culture medium for 4 to 7 days. After culturing, stemness characteristics were analyzed, and red blood cells were removed from the cultured cells. In our results, stemness markers of the leukocyte populations Sca-1+ CD45+, CD117+ CD45+, and very small embryonic-like stem cells CD34+ Lin- CD45- and CXCR4+ Lin- CD45- were significantly increased. Furthermore, the expression of stem cell genes OCT4 (POU5F1), NANOG, SOX2, and the self-renewal gene TERT was analyzed by quantitative real-time polymerase chain reaction in these cells, and it showed a significant increase. These cells could be candidates for multi-potential cells and were further induced using trans-differentiation culture methods. These cells showed multiple differentiation potentials for osteocytes, nerve cells, cardiomyocytes, and hepatocytes. These results indicate that appropriate culture methods can be applied to increase expression of pluripotent genes and plasticity. Leukocytes of human PB can be induced to trans-differentiate into pluripotent potential cells, which will be an important breakthrough in regenerative medicine.

Simultaneous detection and identification of Peste des petits ruminants Virus Lineages II and IV by MCA-Based real-time quantitative RT-PCR assay within single reaction

BackgroundPeste des petits ruminants (PPR) disease is a cross-species infectious disease that severely affects small ruminants and causes great losses to livestock industries in various countries. Distinguishing vaccine-immunized animals from naturally infected animals is an important prerequisite for the eradication of PPR. At present PPRV are classified into lineages I through IV, and only one vaccination strain, Nigeria/75/1, belongs to lineage II, but all of the epidemic strains in China at present are from lineage IV.ResultsTo achieve this goal, we developed an SYBR Green I real-time qRT-PCR method for rapid detection and identification of PPRV lineages II and IV by analyzing different melting curve analyses. The negative amplification of other commonly circulating viruses such as orf virus, goat poxvirus, and foot-and-mouth disease virus demonstrated that primers targeting the L gene of PPRV were extremely specific. The sensitivity of the assay was assessed based on plasmid DNA and the detection limit achieved was 100 copies of PPRV lineages II and IV.ConclusionSince the method has high sensitivity, specificity, and reproducibility, it will be effectively differentiated PPRV lineages II from PPRV lineages IV in PPRV infected animals.

Nanoplate digital PCR assays for detection and quantification of Xylella fastidiosa

Xylella fastidiosa is a fastidious Gram-negative bacterium that is associated with several important plant diseases, and is regulated as a quarantine pest in many countries where strategies are implemented to prevent its introduction and spread. To enact efficient quarantine measures, effective and early detection of the pathogen are essential, especially because global trade of goods increases the risks of introduction of alien pathogens. this study aimed to adapt two qPCR-based diagnostic methods (SYBR Green and Probe based qPCR), already in use to detect X. fastidiosa, for use with a nanoplate based digital PCR assay. Detection of the pathogen using the two digital PCR assays (EvaGreen- and Probe-based) was similar to standard qPCR, giving 100% sensitivity, specificity, and accuracy, while providing accurate absolute quantification of the pathogen when using experimental samples that had low concentrations of host DNA. Using undiluted plant DNA added with low concentrations of X. fastidiosa, only the TaqMan method maintained satisfactory performance and quantification, and is therefore preferred. These results are a first step demonstrating the usefulness of nanoplate-based digital PCR for detection of plant pathogens, which allows greater throughput than qPCR, reducing the time and cost of diagnostic assays.

Imidazo[1,2-a]pyridine: a Highly Potent Therapeutic Agent Clears Piroplasm Infection In Vitro.

The imidazo[1,2-a] pyridines have huge applications in medicinal chemistry with potent activity against wide spectrum of infectious agents. The efficacy of imidazo[1,2-a]pyridine on the in vitro growth of different piroplasms, including Babesia bovis, B. bigemina, B. divergens, B. caballi, and Theileria equi, was investigated in this study. The anti-piroplasm efficacy of imidazo[1,2-a] pyridines was assessed using a fluorescence-based SYBR Green I assay. Furthermore, efficacy of imidazo[1,2-a]pyridine against piroplasms following discontinuation of treatment was also assessed using a viability assay. In vitro cultures of B. bovis and T. equi were used to assess the imidazo[1,2-a]pyridine and diminazene aceturate (DA) interaction. In vitro, imidazo[1,2-a]pyridine inhibited the growth of B. bovis, B. bigemina, B. caballi, and T. equi in a dose-dependent manner. The highest inhibitoryeffects of imidazo[1,2-a]pyridine were detected on the growth of B. caballi with IC50 value of 0.47 ± 0.07. Interestingly, the efficacy of imidazo[1,2-a]pyridine was higher against B. bigemina (IC50: 1.37 ± 0.15) compared to the positive-control DA (IC50: 2.29 ± 0.06). The viability test findings indicate that imidazo[1,2-a]pyridine had a long-lasting inhibitory effect on bovine Babesia parasites in vitro growth up to 4days after treatment. Notably, when coupled with DA at 0.75 or 0.50 IC50, a high concentration (0.75 IC50) of imidazo[1,2-a]pyridine produced additive suppression of B. bovis growth which suggest that imidazo[1,2-a]pyridine/DA could be a promising combination therapy for the treatment of B. bovis. The obtained encouraging findings pave the way for in vitro and in vivo efficacy trials of imidazo[1,2-a]pyridine derivatives against several piroplasmids.