BET bromodomain antagonist JQ1 reactivates HIV‐1, while suppressing T cell activation genes, and upregulating histone modification genes that favor increased Tat activity.
The persistence of latent ...HIV‐1 remains a major challenge in therapeutic efforts to eradicate infection. We report the capacity for HIV reactivation by a selective small molecule inhibitor of BET family bromodomains, JQ1, a promising therapeutic agent with antioncogenic properties. JQ1 reactivated HIV transcription in models of latent T cell infection and latent monocyte infection. We also tested the effect of exposure to JQ1 to allow recovery of replication‐competent HIV from pools of resting CD4+ T cells isolated from HIV‐infected, ART‐treated patients. In one of three patients, JQ1 allowed recovery of virus at a frequency above unstimulated conditions. JQ1 potently suppressed T cell proliferation with minimal cytotoxic effect. Transcriptional profiling of T cells with JQ1 showed potent down‐regulation of T cell activation genes, including CD3, CD28, and CXCR4, similar to HDAC inhibitors, but JQ1 also showed potent up‐regulation of chromatin modification genes, including SIRT1, HDAC6, and multiple lysine demethylases (KDMs). Thus, JQ1 reactivates HIV‐1 while suppressing T cell activation genes and up‐regulating histone modification genes predicted to favor increased Tat activity. Thus, JQ1 may be useful in studies of potentially novel mechanisms for transcriptional control as well as in translational efforts to identify therapeutic molecules to achieve viral eradication.
The CONSTANS-like ( COL ) gene plays important roles in plant growth, development, and abiotic stress. A total of 15 COL genes are unevenly distributed on eight chromosomes in the potato genome. The ...amino acid length of the family members was 347–453 aa, the molecular weight was 38.65–49.92 kD, and the isoelectric point was 5.13–6.09. The StCOL family can be divided into three subfamilies by evolutionary tree analysis, with conserved motifs and similar gene structure positions in each subfamily. The analysis of promoter cis-acting elements showed 17 cis-acting elements related to plant hormones, stress, and light response. Collinearity analysis of COL genes of tomato, potato, and Arabidopsis showed that 13 StCOL genes in the different species may have a common ancestor. A total of 10 conserved motifs and six kinds of post-translational modifications in the 15 StCOL proteins were identified. The 15 StCOL genes exhibit a genomic structure consisting of exons and introns, typically ranging from two to four in number. The results showed that 10 genes displayed significant expression across all potato tissues, while the remaining five genes were down-expressed in potato transcriptome data. The q uantitative reverse transcription polymerase chain reaction ( qRT-PCR) analysis exhibited differential expression of 8 StCOL genes in the potato leaves and tubers at different growth stages, as well as 7 StCOL genes under 2°C treatment conditions. These results suggested that the StCOL gene family may play an important role in regulating potato tuberization and responding to cold stress.
Summary
A literature review was undertaken to ascertain the molecular basis for tigecycline and colistin resistance mechanisms and the experimental basis for the detection and delineation of this ...resistance particularly in carbapenemase‐producing Gram‐negative bacteria. Pubmed, Google Scholar and Science Direct were searched with the keywords colistin, tigecycline, resistance mechanisms and detection methods. Trans‐complementation and comparative MIC studies, mass spectrometry, chromatography, spectrofluorometry, PCR, qRT‐PCR and whole genome sequencing (WGS) were commonly used to determine tigecycline and colistin resistance mechanisms, specifically modifications in the structural and regulatory efflux (acrAB, OqxAB, kpgABC adeABC‐FGH‐IJK, mexAB‐XY‐oprJM and soxS, rarA robA, ramRAB marRABC, adeLRS, mexRZ and nfxb) and lipid A (pmrHFIJFKLM, lpxA, lpxC lpxD and mgrB, pmrAB, phoPQ,) genes respectively. Mutations in the ribosomal 16S rRNA operon rrnBC, also yielded resistance to tigecycline through target site modifications. The mcr‐1 gene conferring resistance to colistin was identified via WGS, trans‐complementation and a murine thigh infection model studies. Common detection methods are mainly antibiotic sensitivity testing with broth microdilution while molecular identification tools are mostly PCR and WGS. Spectrofluorometry, MALDI‐TOF MS, micro‐array and real‐time multiplex PCR hold much promise for the future as new detection tools.
The levels of miR‐93, miR‐191, and miR‐499 have been reported to be up‐regulated in the tissues of experimental traumatic brain injury (TBI) rat models. However, the clinical diagnostic and ...prognostic values of the serum signatures of these 3 miRNAs in TBI remain unclear. The purpose of this study was to determine the expression levels of these 3 microRNAs (miRNAs) in the sera of TBI patients and to evaluate their relationships with the severity and clinical outcome of TBI. The serum levels of these miRNAs were assessed in TBI patients (n = 76) and healthy controls (n = 38) by quantitative reverse‐transcription PCR. The severities and clinical outcomes of the TBI patients were evaluated with the Glasgow coma scale and the Glasgow outcome scale. The serum miR‐93, miR‐191, and miR‐499 levels were significantly increased in the TBI patients compared with the controls at all examined time points, and these levels were significantly higher in the patients with severe TBI than in those with moderate or mild TBI (p < 0.05). The serum miR‐93, miR‐191, and miR‐499 levels were significantly higher in the patients with a poor outcome than in those with a good outcome (p < 0.05). The AUCs of miR‐93, miR‐191, and miR‐499 for distinguishing the TBI patients from the healthy controls were 1.000 (p < 0.001), 0.727 (p < 0.001) and 0.801 (p < 0.001), respectively. Interestingly, the AUCs of miR‐93, miR‐191, and miR‐499 for distinguishing the mild TBI patients from the healthy controls were 1.000 (p < 0.001), 0.742 (p < 0.001) and 0.819 (p < 0.001), respectively. Taken together, these results indicate that miR‐93, miR‐191, and miR‐499 are potentially valuable indicators of the diagnosis, severity, and prognosis of TBI.
Our study showed that the serum levels of miR‐93, miR‐191, and miR‐499 are all increased in traumatic brain injury (TBI) patients. Their serum levels are associated with TBI severity and outcome, which suggest that these miRNAs play important roles in the pathogenesis and progression of TBI. We think these findings should provide a new strategy for the diagnostic, prognostic, and treatment of TBI.
Our study showed that the serum levels of miR‐93, miR‐191, and miR‐499 are all increased in traumatic brain injury (TBI) patients. Their serum levels are associated with TBI severity and outcome, which suggest that these miRNAs play important roles in the pathogenesis and progression of TBI. We think these findings should provide a new strategy for the diagnostic, prognostic, and treatment of TBI.
Long noncoding RNA (lncRNA) NEAT1 has been reported to play critical roles in various human tumor entities and related to the survival of patients with malignancies. However, little is known about ...the role of lncRNA NEAT1 in glioma patients. The aim of this study was to investigate the expression of NEAT1 in human glioma and its correlation with clinicopathological features and prognosis in human glioma; we analyzed the relationship of lncRNA NEAT1 expression with clinicopathological characteristics and prognosis in glioma patients. In our results, the relative level of NEAT1 expression was higher in cancer tissues compared with adjacent noncancerous tissues (p < 0.001). High NEAT1 expression was observed to be closely correlated with larger tumor size (p = 0.023), higher WHO grade (p = 0.005), and recurrence (p = 0.011). Kaplan–Meier curves showed that patients with high NEAT1 expression showed unfavorable overall survival (OS) than the low NEAT1 expression group (p = 0.002). Multivariate analysis results revealed that NEAT1 overexpression was an independent prognostic factor for OS in addition to postoperative chemoradiotherapy and WHO grade. Moreover, high NEAT1 expression in patients with stage III~IV disease and postoperative chemoradiotherapy conferred unfavorable OS (stage III~IV p = 0.002, postoperative chemoradiotherapy p = 0.000). This study supports NEAT1 as a potential prognostic predictor with its high expression in cancer tissues and its association with carcinogenesis and progression in glioma.
Rapid and sensitive screening of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to limit the spread of the global pandemic we are facing. Quantitative real-time reverse ...transcription-polymerase chain reaction (qRT-PCR) is currently used for the clinical diagnosis of SARS-CoV-2 infection using nasopharyngeal swabs, tracheal aspirates, or bronchoalveolar lavage (BAL) samples. Despite the high sensitivity of the qRT-PCR method, false negative outcomes might occur, especially in patients with a low viral load. Here, we developed a multiplex qRT-PCR methodology for the simultaneous detection of SARS-CoV-2 genome (N gene) and of the human RNAse P gene as internal control. We found that multiplex qRT-PCR was effective in detecting SARS-Cov-2 infection in human specimens with 100% sensitivity. Notably, patients with few copies of SARS-CoV-2 RNA (<5 copies/reaction) were successfully detected by the novel multiplex qRT-PCR method. Finally, we assessed the efficacy of multiplex qRT-PCR on human nasopharyngeal swabs without RNA extraction. Collectively, our results provide evidence of a novel and reliable tool for SARS-CoV-2 RNA detection in human specimens, which allows the testing capacity to be expanded and the RNA extraction step to be bypassed.
Rose (Rosa chinensis) is subjected to various biotic and abiotic stresses. In this study, rose leaves with blight symptoms were collected and based on microscopic, morphological, and genetic ...analyses, the disease-causing pathogen was identified as Aspergillus niger. To our knowledge, this is the first report of leaf blight of R. chinensis in Pakistan. To control this disease, iron oxide nanoparticles (Fe2O3 NPs) were synthesized in the seed extract of Trachyspermum ammi. Suitable formation of synthesized Fe2O3 NPs was tested using reliable techniques. Fourier transformed infrared (FTIR) spectrum of Fe2O3 NPs determined the presence of reducing agent like alcohol, alkyl halide and amine on the surface of NPs. X-Ray diffraction (XRD) analysis depicted crystal-like nature and size (41 nm) of NPs, while scanning electron microscopy (SEM) depicted their spherical shape. Sharp Fe and O peaks were observed by energy dispersive X-ray (EDX) analysis. All concentrations of Fe2O3 NPs (0.25, 0.5, 0.75, 1 and 1.5 mg/ mL) inhibited mycelial growth, in vitro and the greatest inhibition (88.9 %) was observed at 1.0 mg/ mL concentration. SEM micrographs showed severe shrinking and structural decomposition of mycelia at this concentration. In pot experiment, Fe2O3 NPs adeptly controlled blight disease of rose leaves by improving various physiological and biochemical attributes and superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities. Findings of Real-Time Quantitative Reverse Transcription PCR (qRT-PCR) showed the higher expression of RcWRKY29 by the application of Fe2O3 NPs, depicting its probable role in plant defense mechanism. These results proved that the application of Fe2O3 NPs can efficiently prevent the spread of blight disease.
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•Fe2O3 nanoparticles were used to control leaf blight of Rosa chinensis.•Application of NPs increased the activity of antioxidant enzymes.•Interaction of NPs also up-regulated the expression of RcWRKY29.•qRT-PCR and KEGG pathway demonstrated plant-defense mechanism.•These NPs can efficiently prevent the spread of blight disease.s.
Control of the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic requires accurate laboratory testing to identify infected individuals while also clearing essential staff ...to continue to work. At the current time, a number of quantitative real-time PCR (qRT-PCR) assays have been developed to identify SARS-CoV-2, targeting multiple positions in the viral genome. While the mutation rate of SARS-CoV-2 is moderate, given the large number of transmission chains, it is prudent to monitor circulating viruses for variants that might compromise these assays. Here, we report the identification of a C-to-U transition at position 26340 of the SARS-CoV-2 genome that is associated with failure of the cobas SARS-CoV-2 E gene qRT-PCR in eight patients. As the cobas SARS-CoV-2 assay targets two positions in the genome, the individuals carrying this variant were still called SARS-CoV-2 positive. Whole-genome sequencing of SARS-CoV-2 showed all to carry closely related viruses. Examination of viral genomes deposited on GISAID showed this mutation has arisen independently at least four times. This work highlights the necessity of monitoring SARS-CoV-2 for the emergence of single-nucleotide polymorphisms that might adversely affect RT-PCRs used in diagnostics. Additionally, it argues that two regions in SARS-CoV-2 should be targeted to avoid false negatives.
Aims
Kluyveromyces marxianus dairy strains were tested for γ‐aminobutyric acid (GABA) production. The genes involved in GABA catabolism (UGA1 and UGA2) and anabolism (GAD1) were found in K. marxianus ...genome. Their relative expression was evaluated with primer designed ad hoc.
Methods and Results
Strains were grouped on the basis of GAD1 gene sequence. Representative strains for each group were tested for GABA production by high‐performance liquid chromatography. All strains produced it at low levels. qRT‐PCR showed the absence of a relation between GABA production and GAD1 gene expression. UGA1 and UGA2 genes were not upregulated and low amounts of succinic acid were detected.
Conclusions
All strains released a low amount of GABA suggesting that probably it was stored within cells. The different behaviour of strains in terms of GABA and succinic acid production as well as gene expression highlighted the genetic and phenotypic biodiversity of this species.
Significance and Impact of the Study
GABA production and genes involved in its catabolism and anabolism were described in a population of dairy K. marxianus for the first time. The variability observed in terms of genetic and phenotypic biodiversity is important especially to exploit this non‐conventional yeast as microbial platform.
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