The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans

Copyright © 2021 Elsevier Inc.Eukaryotic cells regulate 50-triphosphorylated RNAs (ppp-RNAs) to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the g phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR-1 (phosphatase that interacts with RNA and ribonucleoprotein particle 1) family of RNA polyphosphatases remove both the b and g phosphates from ppp-RNAs. Here, we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RNA-dependent RNA polymerases (RdRPs) and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in both somatic and germline development. Our findings suggest that PIR-1 modulates both Dicer-dependent and Dicer-independent Argonaute pathways and provide insight into how cells and viruses use a conserved RNA phosphatase to regulate and respond to ppp-RNA species.info:eu-repo/semantics/publishedVersio

On the Optimization of a Centrifugal Maglev Blood Pump Through Design Variations

Centrifugal blood pumps are usually designed with secondary flow paths to avoid flow dead zones and reduce the risk of thrombosis. Due to the secondary flow path, the intensity of secondary flows and turbulence in centrifugal blood pumps is generally very high. Conventional design theory is no longer applicable to centrifugal blood pumps with a secondary flow path. Empirical relationships between design variables and performance metrics generally do not exist for this type of blood pump. To date, little scientific study has been published concerning optimization and experimental validation of centrifugal blood pumps with secondary flow paths. Moreover, current hemolysis models are inadequate in an accurate prediction of hemolysis in turbulence. The purpose of this study is to optimize the hydraulic and hemolytic performance of an inhouse centrifugal maglev blood pump with a secondary flow path through variation of major design variables, with a focus on bringing down intensity of turbulence and secondary flows. Starting from a baseline design, through changing design variables such as blade angles, blade thickness, and position of splitter blades. Turbulent intensities have been greatly reduced, the hydraulic and hemolytic performance of the pump model was considerably improved. Computational fluid dynamics (CFD) combined with hemolysis models were mainly used for the evaluation of pump performance. A hydraulic test was conducted to validate the CFD regarding the hydraulic performance. Collectively, these results shed light on the impact of major design variables on the performance of modern centrifugal blood pumps with a secondary flow path

The RNA phosphatase PIR-1 regulates endogenous small RNA pathways in C. elegans [preprint]

Eukaryotic cells regulate 5\u27 triphosphorylated (ppp-) RNAs to promote cellular functions and prevent recognition by antiviral RNA sensors. For example, RNA capping enzymes possess triphosphatase domains that remove the γ phosphates of ppp-RNAs during RNA capping. Members of the closely related PIR1 family of RNA polyphosphatases remove both the β and γ phosphates from ppp-RNAs. Here we show that C. elegans PIR-1 dephosphorylates ppp-RNAs made by cellular RdRPs and is required for the maturation of 26G-RNAs, Dicer-dependent small RNAs that regulate thousands of genes during spermatogenesis and embryogenesis. PIR-1 also regulates the CSR-1 22G-RNA pathway and has critical functions in both somatic and germline development. Our findings suggest that PIR-1 modulates both Dicer-dependent and -independent Argonaute pathways, and provide insight into how cells and viruses use a conserved RNA phosphatase to regulate and respond to ppp-RNA species

HVEM Promotes the Osteogenesis of allo-MSCs by Inhibiting the Secretion of IL-17 and IFN-γ in Vγ4T Cells

Bone defects are a common orthopaedic concern, and an increasing number of tissue-engineered bones (TEBs) are used to repair bone defects. Allogeneic mesenchymal stem cells (allo-MSCs) are used as seed cells in many approaches to develop TEB constructs, but the immune response caused by allogeneic transplantation may lead to transplant failure. V gamma 4 T (Vγ4T) cells play an important role in mediating the immune response in the early stage after transplantation; therefore, we wanted to verify whether suppressing Vγ4T cells by herpesvirus entry mediator (HVEM)/B and T lymphocyte attenuator (BTLA) signalling can promote MSCs osteogenesis in the transplanted area. In vitro experiments showed that the osteogenic differentiation of MSCs and Vγ4T cells was weakened after co-culture, and an increase in interleukin-17 (IL-17) and interferon-γ (IFN-γ) levels was detected in the culture supernatant. HVEM-transfected MSCs (MSCs-HVEM) still exhibited osteogenic differentiation activity after co-culture with Vγ4T cells, and the levels of IL-17 and IFN-γ in the co-culture supernatant were significantly reduced. In vivo experiments revealed that inflammation in the transplanted area was reduced and osteogenic repair was enhanced after Vγ4T cells were removed. MSCs-HVEM can also consistently contribute to reduced inflammation in the transplanted area and enhanced bone repair in wild-type (WT) mice. Therefore, our experiments verified that HVEM can promote the osteogenesis of allo-MSCs by inhibiting IL-17 and IFN-γ secretion from Vγ4T cells

Influenza A virus preferentially snatches noncoding RNA caps

Influenza A virus (IAV) lacks the enzyme for adding 5\u27 caps to its RNAs and snatches the 5\u27 ends of host capped RNAs to prime transcription. Neither the preference of the host RNA sequences snatched nor the effect of cap-snatching on host processes is completely defined. Previous studies of influenza cap-snatching used poly(A)-selected RNAs from infected cells or relied on annotated host genes to define the snatched host RNAs, and thus lack details on many noncoding host RNAs including snRNAs, snoRNAs, and promoter-associated capped small (cs)RNAs, which are made by paused Pol II during transcription initiation. In this study, we used a nonbiased technique, CapSeq, to identify host and viral-capped RNAs including nonpolyadenylated RNAs in the same samples, and investigated the substrate-product correlation between the host RNAs and the viral RNAs. We demonstrated that noncoding host RNAs, particularly U1 and U2, are the preferred cap-snatching source over mRNAs or pre-mRNAs. We also found that csRNAs are highly snatched by IAV. Because the functions of csRNAs remain mostly unknown, especially in somatic cells, our finding reveals that csRNAs at least play roles in the process of IAV infection. Our findings support a model where nascent RNAs including csRNAs are the preferred targets for cap-snatching by IAV and raise questions about how IAV might use snatching preferences to modulate host-mRNA splicing and transcription

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Childlessness and Development

This paper leverages harmonized micro-data consisting of 82 million females from 164 household surveys covering 72 unique countries from all income levels to investigate the relationship between childlessness and development. Empirically, I find that childlessness rates display a U-shaped pattern with development at country, subgroups and individual levels, which contribute to 1/3 of heterogeneity of aggregate fertility across countries. Moreover, females in richer countries and those are more educated delay their fertility, suggested by the life- cycle childlessness rates. Combining these novel empirical findings, I construct a two-period model under a parsimonious set of assumptions to speak to the empirical finding: when the wage growth effect dominates the wage level effect, females choose to delay fertility; childlessness is driven by natural sterilization and different preference for number of children

Small RNA Plays Important Roles in Virus–Host Interactions

Non-coding small RNAs play important roles in virus–host interactions. For hosts, small RNAs can serve as sensors in antiviral pathways including RNAi and CRISPR; for viruses, small RNAs can be involved in viral transcription and replication. This paper covers several recent discoveries on small RNA mediated virus–host interactions, and focuses on influenza virus cap-snatching and a few important virus sensors including PIR-1, RIG-I like protein DRH-1 and piRNAs. The paper also discusses recent advances in mammalian antiviral RNAi

Strategies and Best Practice in Cloning Small RNAs.

High-throughput sequencing has become a standard and powerful tool for analyzing nucleic acids primarily due to its sensitivity and convenience. Small RNAs play important roles in regulating cellular and viral genes. The conventional methods for small RNA analyses are tedious and often lack accuracy, specificity and sensitivity for many small RNA species. Therefore, high-throughput sequencing becomes an indispensable tool for analyzing small RNAs. However, it is challenging to generate a reliable and representative small RNA library for high-throughput sequencing since small RNAs are usually expressed at extremely low levels and often contain modifications which affect library construction, usually causing biased readouts. This review compares various strategies for generating small RNA libraries of high quality and reliability, and provides recommendations on best practice in preparing high-throughput sequencing RNA libraries