EXTENDED TUDOR-DOMAINS of the piRNA BIOGENESIS PATHWAY HAVE RNA-SPECIFIC NUCLEASE ACTIVITY

piRNAs are essential for transposon repression and protecting the germline from deleterious mutations. piRNA biogenesis comprises a primary and secondary pathway, and involves PIWI clade argonaute proteins and ancillary factors. Secondary piRNA biogenesis is tightly coupled to transposon repression. It requires processing of the 3-prime end of pre-piRNA during an amplification loop by an as yet unidentified endonuclease. Here, using crystallography, and biochemical assays, we discover that the Drosophila Qin protein, which is a critical member of the core amplification complex, has endonuclease activity. Qin contains five extended Tudor domains, which had been proposed to recognize methylated ligands. Instead, we show that these domains act as RNA-specific nucleases. This supports a role for Qin in the 3-prime end processing of Ago3-bound pre-piRNAs. Extended Tudor domains are frequent in piRNA-processing proteins, suggesting that the uncovered nuclease activity of this protein fold may be key to understanding the piRNA biogenesis.

Significance of a Tumor Microenvironment-Mediated P65-miR-30a-5p-BCL2L11 Amplification Loop in Multiple Myeloma

Despite significant progress in the treatment of myeloma, multiple myeloma (MM) remains an incurable hematological malignancy due to cell adhesion-mediated drug resistance (CAM-DR) phenotype. However, data on the molecular mechanisms underlying the CAM-DR remains scanty. Here, we identified a miRNA-mRNA regulatory network in myeloma cells that are directly adherent to bone marrow stromal cells (BMSCs). Our data showed that the BMSCs up-regulated miR-30a-5p and down-regulated BCL2L11 at both mRNA and protein level in the myeloma cells. Besides, luciferase reporter genes demonstrated direct interaction between miR-30a-5p and BCL2L11 gene. Moreover, the BMSCs activated NF-ΚB signaling pathway in myeloma cells and the NF-κB P65 was shown to directly bind the miR-30a-5p promoter region. Moreover, suppression of the miR-30a-5p or upregulation of the BCL2L11 promoted apoptosis of the myeloma cells independent of the BMSCs, thus suggesting clinical significance of miR-30a-5p inhibitor and PLBCL2L11 plasmid in CAM-DR. Together, our data demonstrated the role of P65-miR-30a-5p-BCL2L11 loop in CAM-DR myeloma cells. These findings give new insights into the role of tumor microenvironment in the treatment of patients with myeloma.

Two parallel sRNA amplification cycles contribute to RNAi inheritance in C. elegans

RNA-mediated interference (RNAi) is a conserved mechanism that uses small RNAs (sRNAs) to tune gene expression. In C. elegans, exposure to dsRNA induces the production of gene-specific sRNAs that are propagated to progeny not exposed to the dsRNA trigger. We present evidence that RNAi inheritance is mediated by two parallel sRNA amplification loops. The first loop, dependent on the nuclear Argonaute HRDE-1, targets nascent transcripts, and reduces but does not eliminate productive transcription at the locus. The second loop, dependent on the conserved helicase ZNFX-1, targets mature transcripts and concentrates them in perinuclear condensates (nuage). Each amplification loop generates a distinct class of sRNAs, with the ZNFX-1 loop responsible for the bulk of sRNA production on the region targeted by the trigger. By independently targeting nascent and mature transcripts, the HRDE-1 and ZNFX-1 loops ensure maximum silencing in progeny not exposed to the trigger.

Scalable Reporter Assays to Analyze the Regulation of stx2 Expression in Shiga Toxin-Producing Enteropathogens

Stx2 is the major virulence factor of EHEC and is associated with an increased risk for HUS in infected patients. The conditions influencing its expression in the intestinal tract are largely unknown. For optimal management and treatment of infected patients, the identification of environmental conditions modulating Stx2 levels in the human gut is of central importance. In this study, we established a set of chromosomal stx2 reporter assays. One system is based on superfolder GFP (sfGFP) using a T7 polymerase/T7 promoter-based amplification loop. This reporter can be used to analyze stx2 expression at the single-cell level using FACSs and fluorescence microscopy. The other system is based on the cytosolic release of the Gaussia princeps luciferase (gluc). This latter reporter proves to be a highly sensitive and scalable reporter assay that can be used to quantify reporter protein in the culture supernatant. We envision that this new set of reporter tools will be highly useful to comprehensively analyze the influence of environmental and host factors, including drugs, small metabolites and the microbiota, on Stx2 release and thereby serve the identification of risk factors and new therapies in Stx-mediated pathologies.

Diabetes Mellitus and COVID-19: Associations and Possible Mechanisms

Coronavirus disease 2019 (COVID-19) is a recently emerged disease with formidable infectivity and high mortality. Emerging data suggest that diabetes is one of the most prevalent comorbidities in patients with COVID-19. Although their causal relationship has not yet been investigated, preexisting diabetes can be considered as a risk factor for the adverse outcomes of COVID-19. Proinflammatory state, attenuation of the innate immune response, possibly increased level of ACE2, along with vascular dysfunction, and prothrombotic state in people with diabetes probably contribute to higher susceptibility for SARS-CoV-2 infection and worsened prognosis. On the other hand, activated inflammation, islet damage induced by virus infection, and treatment with glucocorticoids could, in turn, result in impaired glucose regulation in people with diabetes, thus working as an amplification loop to aggravate the disease. Therefore, glycemic management in people with COVID-19, especially in those with severe illness, is of considerable importance. The insights may help to reduce the fatality in the effort against COVID-19.

LAMP amplification of nucleic acids. I. Two decades of development and improvement.

Over the two decades that have passed since the development of loop amplification (Loop AMPlification, LAMP), that carry out to detect specific nucleic acid under isothermal conditions, it has undergone quite a lot of improvements. This review presents data represented methodological bases of about a hundred variations of the LAMP, classified according to the methods of detecting both target DNA products (lamplicons) and by-products (pyrophosphate and protons), taking into account the specificity of the processes, and according to the purpose of certain LAMP options and implementation, including microfluidics. Particular attention is paid to quantitative LAMP amplification and promising digital LAMP. The prospects for the development of the method are presented.

Research work undertaken in the Inokuchi Laboratory – Chronic inflammation & chronic disease research including diabetes and metabolic diseases.

Today, type 2 diabetes is typically treated by lowering sugar in the blood and increasing the sensitivity of muscle cells to insulin. However, novel discoveries could allow future treatments to target the molecular mechanisms in our bodies that generate insulin resistance – effectively preventing the biological chain of events that causes chronic inflammation and disease to initially occur. Professor Jin-ichi Inokuchi heads the Glycopathology Laboratory at Tohoku Medical and Pharmaceutical University, Japan. Situated within the Institute of Molecular Biomembrane and Glycobiology, the Laboratory focuses on gangliosides and their roles in inflammatory cycles. The scientists are particularly interested in GM3 ganglioside species, as their previous research has indicated that the increased presence of anti-inflammatory GM3 species and decreased presence of pro-inflammatory GM3 species have the power to alter inflammatory cycles in the body, thus contributing to chronic inflammation and associated diseases. Recently, Inokuchi and his colleagues' research revealed some interesting insights regarding GM3. Namely, they discovered that GM3 plays an important role in an inflammation amplification loop that affects diseases involving chronic inflammation, such as type 2 diabetes and metabolic diseases closely linked with obesity. 'Collectively, we propose a novel inflammation loop triggered by GM3 molecular species,' asserts Inokuchi. Inokuchi's research provides an avenue for tackling these conditions from the inside out. By focusing on the biological processes involved in these lifestyle-related chronic diseases, it may be possible to treat type 2 diabetes and metabolic diseases more efficiently.

Learning from House Prices: Amplification and Business Fluctuations

We formalize the idea that house price changes may drive rational waves of optimism and pessimism in the economy. In our model, a house price increase caused by aggregate disturbances may be misinterpreted as a sign of higher local permanent income, leading households to demand more consumption and housing. Higher demand reinforces the initial price increase in an amplification loop that drives comovement in output, labor, residential investment, land prices, and house prices even in response to aggregate supply shocks. The qualitative implications of our otherwise frictionless model are consistent with observed business cycles and it can explain the economic impact of apparently autonomous changes in sentiment without resorting to non-fundamental shocks or nominal rigidity.