Optimization of loop-mediated isothermal amplification (LAMP) assay for robust visualization in SARS-CoV-2 and emerging variants diagnosis

Loop-mediated isothermal amplification (LAMP) is widely used in detection of pathogenic microorganisms including SARS-CoV-2. However, the performance of LAMP assay needs further exploration in the emerging SARS-CoV-2 variants test. Here, we design serials of primers and select an optimal set for LAMP-based on SARS-CoV-2 N gene for a robust and visual assay in SARS-CoV-2 diagnosis. The limit of detectable template reaches 10 copies of N gene per 25 μL reaction at isothermal 58℃ within 40 min. Importantly, the primers for LAMP assay locate at 12 to 213 nt of N gene, a highly conservative region, which serves as a compatible test in emerging SARS-CoV-2 variants. Comparison to a commercial qPCR assay, this LAMP assay exerts the high viability in diagnosis of 41 clinical samples. Our study optimizes an advantageous LAMP assay for colorimetric detection of SARS-CoV-2 and emerging variants, which is hopeful to be a promising test in COVID-19 surveillance.

Reduced expression of carbonic anhydrase III in skeletal muscles could be linked to muscle fatigue: A rat muscle fatigue model

Background

Carbonic anhydrase III (CAIII) is expressed abundantly in slow skeletal muscles, adipocytes, and the liver. It plays a critical role in maintaining intracellular pH, antioxidation, and energy metabolism, which are further involved in fatigue. However, its function and mechanism in maintaining the physiological function of muscles or antifatigue are still ambiguous. We hypothesized that changes of CAIII in skeletal muscles might be related to the occurrence of muscle fatigue.

Method

After establishing a rat soleus muscle fatigue model, we measured the protein expression of the CAIII in muscles. And the muscle intracellular biochemical indices [malondialdehyde (MDA), adenosine triphosphate (ATP), and lactic acid] were also measured using assay kits. After transfected by CAIII-overexpressing and knockdown lentiviral vectors, the rat soleus muscles were induced to fatigue to investigate the effects and possible molecular mechanisms of CAIII in antifatigue.

Results

The expression of CAIII in fatigued soleus muscles was significantly decreased compared with that of the control group (P ​< ​0.001). Moreover, the ATP level in the fatigued muscle also significantly decreased, whereas lactic acid and MDA levels were significantly increased (P ​< ​0.001). After posttransfection for 21 days, CAIII levels in muscles were significantly reduced in the CAIII-interfering lentivirus group, but increased in the CAIII-overexpressed lentivirus group (P ​< ​0.001). In addition, CAIII knockdown muscles showed more reduction of the maximal muscle force and ATP levels ​and more increase of MDA and lactic acid levels during the fatigue test than the control group, (P ​< ​0.05). On the other hand, CAIII-overexpressed muscles showed less reduction of the maximal muscle force and ATP levels and less increase of MDA and lactic acid levels during muscle fatigue than the control group (P ​< ​0.05).

Conclusions

Our study showed that soleus muscle fatigue induced by electrical stimulation could result in downregulation of CAIII and ATP levels ​and accumulation of lactic acid and MDA. Further study showed that CAIII knockdown led to more reduction of the maximal muscle force, whereas CAIII overexpression showed less reduction of the maximal muscle force, which suggested that CAIII levels in muscles might be related to the occurrence of muscle fatigue.

Translational potential

CAIII plays an important role in muscle fatigue. Up-regulating the expression of CAIII might contribute to dissipating fatigue, which would provide a new method to solve the difficulties in eliminating muscular fatigue.

The Prognostic and Predictive Value of Melanoma-related MicroRNAs Using Tissue and Serum: A MicroRNA Expression Analysis

The overall 5-year survival for melanoma is 91%. However, if distant metastasis occurs (stage IV), cure rates are < 15%. Hence, melanoma detection in earlier stages (stages I–III) maximises the chances of patient survival. We measured the expression of a panel of 17 microRNAs (miRNAs) (MELmiR-17) in melanoma tissues (stage III; n = 76 and IV; n = 10) and serum samples (collected from controls with no melanoma, n = 130; and patients with melanoma (stages I/II, n = 86; III, n = 50; and IV, n = 119)) obtained from biobanks in Australia and Germany. In melanoma tissues, members of the ‘MELmiR-17’ panel were found to be predictors of stage, recurrence, and survival. Additionally, in a minimally-invasive blood test, a seven-miRNA panel (MELmiR-7) detected the presence of melanoma (relative to controls) with high sensitivity (93%) and specificity (≥ 82%) when ≥ 4 miRNAs were expressed. Moreover, the ‘MELmiR-7’ panel characterised overall survival of melanoma patients better than both serum LDH and S100B (delta log likelihood = 11, p < 0.001). This panel was found to be superior to currently used serological markers for melanoma progression, recurrence, and survival; and would be ideally suited to monitor tumour progression in patients diagnosed with early metastatic disease (stages IIIa–c/IV M1a–b) to detect relapse following surgical or adjuvant treatment.

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A seven-miRNA panel (MELmiR-7) detected the presence of melanoma with high sensitivity (93%) and specificity (≥ 82%).

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In serially collected stage IV specimens, members of the ‘MELmiR-7’ panel confirmed tumour progression in 100% of cases.

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The ‘MELmiR-7’ panel is superior to currently used serological markers for melanoma progression, recurrence, and survival.

Preferential expression of cytochrome CYP CYP2R1 but not CYP1B1 in human cord blood hematopoietic stem and progenitor cells

Cytochrome P450 (CYP) enzymes metabolize numerous endogenous substrates, such as retinoids, androgens, estrogens and vitamin D, that can modulate important cellular processes, including proliferation, differentiation and apoptosis. The aim of this study is to characterize the expression of CYP genes in CD34+ human cord blood hematopoietic stem and early progenitor cells (CBHSPCs) as a first step toward assessment of the potential biological functions of CYP enzymes in regulating the expansion or differentiation of these cells. CD34+ CBHSPCs were purified from umbilical cord blood via antibody affinity chromatography. Purity of CD34+ CBHSPCs was assessed using fluorescence-activated cell sorting. RNA was isolated from purified CD34+ CBHSPCs and total mononuclear cells (MNCs) for RNA-PCR analysis of CYP expression. Fourteen human CYPs were detected in the initial screening with qualitative RT-PCR in CD34+ CBHSPCs. Further quantitative RNA-PCR analysis of the detected CYP transcripts yielded evidence for preferential expression of CYP2R1 in CD34+ CBHSPCs relative to MNCs; and for greater expression of CYP1B1 in MNCs relative to CD34+ CBHSPCs. These findings provide the basis for further studies on possible functions of CYP2R1 and CYP1B1 in CBHSPCs׳ proliferation and/or differentiation and their potential utility as targets for drugs designed to modulate CD34+ CBHSPC expansion or differentiation.

The role of autophagy in the intracellular survival of Campylobacter concisus

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Autophagy is involved in host clearance of Campylobacter concisus.

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C. concisus can be found within Campylobacter-containing vacuoles.

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Some C. concisus strains may subvert autophagy to survive intracellularly.

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Proteins specific to invasive C. concisus may be involved in autophagy subversion.

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Proteins of interest in C. concisus infection: ATG4B, ATG7, ATG9B, CTSD and LAMP1.

Campylobacter concisus is an emerging pathogen that has been associated with gastrointestinal diseases. Given the importance of autophagy for the elimination of intracellular bacteria and the subversion of this process by pathogenic bacteria, we investigated the role of autophagy in C. concisus intracellular survival. Gentamicin protection assays were employed to assess intracellular levels of C. concisus within Caco-2 cells, following autophagy induction and inhibition. To assess the interaction between C. concisus and autophagosomes, confocal microscopy, scanning electron microscopy, and transmission electron microscopy were employed. Expression levels of 84 genes involved in the autophagy process were measured using qPCR. Autophagy inhibition resulted in two- to four-fold increases in intracellular levels of C. concisus within Caco-2 cells, while autophagy induction resulted in a significant reduction in intracellular levels or bacterial clearance. C. concisus strains with low intracellular survival levels showed a dramatic increase in these levels upon autophagy inhibition. Confocal microscopy showed co-localization of the bacterium with autophagosomes, while transmission electron microscopy identified intracellular bacteria persisting within autophagic vesicles. Further, qPCR showed that following infection, 13 genes involved in the autophagy process were significantly regulated, and a further five showed borderline results, with an overall indication towards a dampening effect exerted by the bacterium on this process. Our data collectively indicates that while autophagy is important for the clearance of C. concisus, some strains may manipulate this process to benefit their intracellular survival.

Development of the gut microbiota in southern Indian infants from birth to 6 months: a molecular analysis

Acquisition of the gastrointestinal microbiota at birth may have long-term health impacts. We longitudinally characterised major microbial communities in the faeces of a cohort of infants using molecular methods. Faecal samples were prospectively obtained at several time points after birth from eighty-three infants. Real-time PCR using SYBR green and primers targeted at 16S rRNA gene sequences were used to quantify Bifidobacterium, Lactobacillus acidophilus group, Bacteroides–Prevotella group, Enterobacteriaceae, Enterococcus, Clostridium coccoides–Eubacterium rectale group, Clostridium leptum group and Staphylococcus. Microbial community abundance was expressed relative to amplification of sequences conserved universally for domain bacteria. Faecal copy number of 16S rRNA genes increased non-significantly from a mean of 4·1 × 10⁹/g on day 1 to 1·1 × 10¹⁰/g on day 4. All microbial communities were detected from day 1 after birth. Enterobacteriaceae and lactobacilli predominated on day 1, while bifidobacteria and staphylocci increased on day 4. Bacteroides–Prevotella and C. coccoides–E. rectale increased by day 180. C. leptum was detected in half of the cohort at birth and in a slightly larger percentage by 6 months. Caesarean section was associated with delayed colonisation by several bacterial communities. Higher socio-economic status was associated with more abundant lactobacilli and Bacteroides–Prevotella at 90 and 180 d. Supplemental feeding was associated with a reduction in Enterobacteriaceae. Microbial colonisation of the gut was well established on the first day of birth, and relative abundance of microbial communities was influenced by mode of delivery, socio-economic status and supplemental feeding. These findings may have relevance to infant nutrition and growth.