Molecular detection and characterization of Potato spindle tuber viroid (PSTVd) infecting Tomato (Solanum lycopersicum L.) in Karnataka State of India

Potato Spindle Tuber Viroid (PSTVd) is a non-coding, infectious, small, circular RNA known to cause disease in agricultural and horticultural plants. In the present work, an investigation was conducted in the southern districts of Karnataka state to assess the possible pospiviroid infections on tomato plants that are considered natural hosts for viroids. A total of 83 tomato samples showing disease symptoms (virus or viroid-like) along with healthy ones were collected and subjected to viroid detection by conventional Reverse Transcriptase Polymer Chain Reaction (RT-PCR) using universal (Pospi1-RE/Pospi1-FW) and a specific set of primers (3H1/2H1). The study confirmed the presence of PSTVd in one of the samples of tomato collected from Banghatta village of Mandy District, with an expected amplicon of ~ 361 bp. The bioassay conducted on tomato plants (cv. Rutgers) proved the association of PSTVd, which was further confirmed by RT-PCR. The amplicons were cloned, sequenced, and the representative sequences were deposited in the NCBI GenBank. The sequence alignment and secondary structure analysis of the isolated viroid with other reference sequences revealed the variations in the pathogenicity, central conserved region, and Terminal right domains. The variations observed between the isolated PSTVd with that of other Indian isolates support that viroid may have been transmitted among the crop plants, possibly through seed or mechanical means.

Pooling samples: a testing option for SARS-CoV-2 during a supply shortage

Pooling of 1 positive sample with up to 5 negative samples prior to testing with the Cepheid GenXpert SARS-CoV-2 assay did not adversely impact detection of positive samples. At our current prevalence of 2%, it could save up to 70% of the test kits.

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Validation of sample pooling to conserve reagents during COVID-19 testing

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Benefits and limitations of sample pooling during a COVID-19 test reagent shortage

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Low SARS coronavirus-2 samples detected in pools with 3 negative samples

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Pooling 4 COVID-19 samples saves 63% of test kits when the prevalence is 3%.

COVID-19: Current Trends in Invitro Diagnostics

The novel coronavirus SARS-CoV-2 is the seventh known species of coronavirus, infectious to human beings. The pandemic COVID-19 spread all over the world with an unprecedented spreading rate after its first appearance in Wuhan, China. As a novel viral disease there in no antiviral treatment or vaccine for the COVID-19. At present, the early detection and the quarantine of infected patients are the ways to stop the spreading of the disease. This review will discuss about the current invitro diagnostic methods used worldwide for the early and accurate diagnosis of COVID-19. Currently the nucleic acid based polymerase chain reaction is used as the reliable diagnostic platform and antigen/antibody detection immunoassays are playing the role of screening tests for early detection and prognosis in COVID-19 treatment.

Development of TaqMan real-time RT-PCR for sensitive detection of diverse Raspberry ringspot virus isolates

Raspberry ringspot virus (RpRSV) is an important virus that infects horticultural crops including grapevine, cherry, berry fruit and rose. The genome sequences of RpRSV are highly diverse between isolates and this makes the design of a PCR-based detection method difficult. In this study, a TaqMan real-time RT-PCR assay was developed for the rapid and sensitive detection of RpRSV. Primers and probes targeting the most conserved region of the movement protein gene were designed to amplify a 229 bp fragment of RpRSV RNA-2. The assay was able to amplify all RpRSV isolates tested. The detection limit of the RpRSV target region was estimated to be 61-98 copies, depending on the RpRSV strain. The sensitivity was about 100 times greater than the conventional RT-PCR assay using the same primers as the real-time RT-PCR assay. A comparison with published conventional RT-PCR assays indicated that both published assays lacked reliability and sensitivity, as neither were able to amplify all RpRSV isolates tested, and both were at least 1000 times less sensitive than the novel TaqMan real-time RT-PCR assay. The assay can also be run as a duplex reaction with the nad5 plant internal control primers and probe to simultaneously verify the PCR competency of the samples. The amplicon obtained with the real-time RT-PCR assay is suitable for direct sequencing if it is necessary to further confirm the RpRSV identity or determine the RpRSV strain.

Real-time RT-PCR for the detection and quantitation of Oropouche virus

Oropouche virus (OROV) causes an acute, systemic febrile illness, and in certain regions of South America, this represents the second most common human arboviral infection after dengue virus. A new real-time RT-PCR was developed for OROV and reassortant species. The new OROV rRT-PCR proved linear across 6-7 orders of magnitude with a lower limit of 95% detection of 5.6-10.8 copies/μL. Upon testing dilutions of OROV and Iquitos virus reference genomic RNA, all dilutions with >10 copies/μL were detected in both the OROV rRT-PCR and a comparator molecular assay, but the OROV rRT-PCR detected more samples with ≤10 copies/μL (8/14 vs 0/13, respectively, P = 0.002). In a set of 100 acute-phase clinical samples from Paraguay patients with a suspected arboviral illness, no patients tested positive for OROV RNA using either assay. The OROV rRT-PCR provides a sensitive molecular assay for the study of this important yet neglected tropical arboviral infection.

Heterologous expression, purification and biochemical characterization of a new xylanase from Myceliophthora heterothallica F.2.1.4

Myceliophthora heterothallica is a thermophilic fungus potentially relevant for the production of enzymes involved in the degradation of plant biomass. A xylanase encoding gene of this species was identified by means of RT-PCR using primers designed based on a xylanase coding sequence (GH11) of the fungus M. thermophila. The obtained gene was ligated to the vector pET28a(+) and the construct was transformed into Escherichia coli cells. The recombinant xylanase (r-ec-XylMh) was heterologously expressed, and the highest activity was observed at 55 °C and pH 6. The enzyme stability was greater than 70% between pH 4.5 and 9.5 and the inclusion of glycerol (50%) resulted in a significant increase in thermostability. Under these conditions, the enzyme retained more than 50% residual activity when incubated at 65 °C for 1 h, and approximately 30% activity when incubated at 70 °C for the same period. The tested cations did not increase xylanolytic activity, and the enzyme indicated significant tolerance to several phenolic compounds after 24 h, as well as high specificity for xylan, with no activity for other substrates such as CMC (carboxymethylcellulose), Avicel, pNPX (p-nitrophenyl-β-D-xylopyranoside) and pNPA (p-nitrophenyl-α-L-arabinofuranoside), and is thus, of potential relevance in pulp bleaching.

Evaluation of a commercially available synthetic RNA lipid enveloped control molecule

Detection of viral ribonucleic acid with RT PCR is a useful tool for viral detection. One of the drawbacks of this technique is the difficulty in including an internal control molecule to ensure the validity of the extraction and amplification process. In this study the potential usefulness of a novel lipid enveloped commercially available RNA control molecule is investigated. Initial optimisation of the detection assay was performed by amplification of IC (internal control) spiked into PCR water. Thirty-two clinical respiratory samples were spiked with the IC before and after extraction and RT PCR was then performed. Inefficient extraction was simulated. Inhibition of the RT PCR was achieved by serial dilution of heparin sulfate into samples post extraction. No Targets that matched the IC (Internal Control) primers were identified in 32 extracted sputum samples as determined by the absence of non specific amplification curves. The unextracted IC had an increased CT (cycle threshold) value compared to IC that had been extracted. Inefficient extraction was detected by an increased CT. Increasing concentrations of heparin inhibited the PCR in a predictable fashion. The Bioline IC molecule provides a stable RNA IC that has acceptable performance characteristics.

Mesenchymal stem cell secreted platelet derived growth factor exerts a pro-migratory effect on resident Cardiac Atrial appendage Stem Cells

Mesenchymal stem cells (MSCs) modulate cardiac healing after myocardial injury through the release of paracrine factors, but the exact mechanisms are still unknown. One possible mechanism is through mobilization of endogenous cardiac stem cells (CSCs). This study aimed to test the pro-migratory effect of MSC conditioned medium (MSC-CM) on endogenous CSCs from human cardiac tissue. By using a three-dimensional collagen assay, we found that MSC-CM improved migration of cells from human cardiac tissue. Cell counts, perimeter and area measurements were utilized to quantify migration effects. To examine whether resident stem cells were among the migrating cells, specific stem cell properties were investigated. The migrating cells displayed strong similarities with resident Cardiac Atrial appendage Stem Cells (CASCs), including a clonogenic potential of ~21.5% and expression of pluripotency associated genes like Oct-4, Nanog, c-Myc and Klf-4. Similar to CASCs, migrating cells demonstrated high aldehyde dehydrogenase activity and were able to differentiate towards cardiomyocytes. Receptor tyrosine kinase analysis and collagen assays performed with recombinant platelet derived growth factor (PDGF)-AA and Imatinib Mesylate, a PDGF receptor inhibitor, suggested a role for the PDGF-AA/PDGF receptor α axis in enhancing the migration process of CASCs. In conclusion, our findings demonstrate that factors present in MSC-CM improve migration of resident stem cells from human cardiac tissue. These data open doors towards future therapies in which MSC secreted factors, like PDGF-AA, can be utilized to enhance the recruitment of CASCs towards the site of myocardial injury.

Development of a novel reverse transcriptase polymerase chain reaction to determine the Gram reaction and viability of bacteria in clinical specimens

OBJECTIVE

To develop a novel RNA based assay to determine the Gram reaction and viability of bacteria in clinical specimens.

MATERIALS AND METHODS

Reverse transcriptase PCR (RT-PCR) targeting 16SrRNA region was optimized using Staphylococcus aureus ATCC 25923 and Pseudomonas aeruginosa ATCC 27853 by using two novel sets of primers. Sixty clinical specimens consisting of 31 intraocular specimens (19 vitreous fluids and 12 aqueous humor), 11 peripheral blood specimens and 18 other clinical specimens were subjected to standard microbiological culture and RT-PCR to determine the Gram reaction and viability of bacteria. The amplified products were subjected to DNA sequencing to identify the bacterium.

RESULTS

The sensitivity of RT-PCR was 0.4fg and the primers amplified bacterial cDNA. RT-PCR detected the presence of bacteria in 60 clinical specimens indicating the presence of viable bacteria. Concordant results were obtained with both primer sets. Seventy five bacterium comprising 52 single (69.3%) and 23 mixed bacteria (30.6%), both Gram positive and Gram negative were detected. These results correlated with the bacterial identity by PCR based DNA sequencing.

CONCLUSION

RT-PCR is a reliable tool to identify the presence of viable bacteria and to precisely determine Gram reaction.

Expression of bone morphogenetic protein 2 and 6 and clinical significance in liver carcinoma

AIM: To investigate the expression of bone morphogenetic protein 2 and 6 (BMP-2, 6) mRNA in human liver cancer, and to explore its relationship with biologic action in liver cancer.

METHODS: The expressions of BMP-2 and BMP-6 in 30 carcinoma liver tissue samples and 30 normal liver tissue samples were detected and analyzed by reverse transcriptase PCR and Western blot.

RESULTS: The relative level of BMP-2 and BMP-6 mRNA was significantly lower in the normal liver tissue samples than in the liver carcinoma tissue samples (0.3245 ± 0.1127 vs 0.8298 ± 0.1187, 0.2947 ± 0.1853 vs 0.7145 ± 0.1373, both P < 0.05). The relative level of BMP-2 and BMP-6 mRNA in III, IV stages of liver cancer was significantly higher than that in I, II stages (0.92431 ± 0.1234 vs 0.69355 ± 0.1925, 0.8354 ± 0.1423 vs 0.6043 ± 0.1234, both P < 0.05). The expression level of BMP-2 and BMP-6 protein were significantly higher in the metastatic liver cancer compared with that without metastasis (0.9854 ± 0.2888 vs 0.6244 ± 0.3087, 0.9076 ± 0.1276 vs 0.5678 ± 0.2493, both P < 0.01).

CONCLUSION: Up-regulated expressions of BMP-2 and BMP-6 play an important role in liver cancer. It may have the active role in invasion and metastasis of liver cancer.