Characterizing the interactions that SARS-CoV-2 viral RNAs make with host cell proteins during infection can improve our understanding of viral RNA functions and the host innate immune response. ...Using RNA antisense purification and mass spectrometry, we identified up to 104 human proteins that directly and specifically bind to SARS-CoV-2 RNAs in infected human cells. We integrated the SARS-CoV-2 RNA interactome with changes in proteome abundance induced by viral infection and linked interactome proteins to cellular pathways relevant to SARS-CoV-2 infections. We demonstrated by genetic perturbation that cellular nucleic acid-binding protein (CNBP) and La-related protein 1 (LARP1), two of the most strongly enriched viral RNA binders, restrict SARS-CoV-2 replication in infected cells and provide a global map of their direct RNA contact sites. Pharmacological inhibition of three other RNA interactome members, PPIA, ATP1A1, and the ARP2/3 complex, reduced viral replication in two human cell lines. The identification of host dependency factors and defence strategies as presented in this work will improve the design of targeted therapeutics against SARS-CoV-2.
Magnetic nanoparticles (MNPs) have been adapted for many applications, e.g., bioassays for the detection of biomarkers such as antibodies, by controlled engineering of specific surface properties. ...Specific measurement of such binding states is of high interest but currently limited to highly sensitive techniques such as ELISA or flow cytometry, which are relatively inflexible, difficult to handle, expensive and time-consuming. Here we report a method named COMPASS (Critical-Offset-Magnetic-Particle-SpectroScopy), which is based on a critical offset magnetic field, enabling sensitive detection to minimal changes in mobility of MNP ensembles, e.g., resulting from SARS-CoV-2 antibodies binding to the S antigen on the surface of functionalized MNPs. With a sensitivity of 0.33 fmole/50 µl (≙7 pM) for SARS-CoV-2-S1 antibodies, measured with a low-cost portable COMPASS device, the proposed technique is competitive with respect to sensitivity while providing flexibility, robustness, and a measurement time of seconds per sample. In addition, initial results with blood serum demonstrate high specificity.
DNA damage response (DDR) involves dramatic transcriptional alterations, the mechanisms of which remain ill defined. Here, we show that following genotoxic stress, the RNA-binding motif protein 7 ...(RBM7) stimulates RNA polymerase II (Pol II) transcription and promotes cell viability by activating the positive transcription elongation factor b (P-TEFb) via its release from the inhibitory 7SK small nuclear ribonucleoprotein (7SK snRNP). This is mediated by activation of p38MAPK, which triggers enhanced binding of RBM7 with core subunits of 7SK snRNP. In turn, P-TEFb relocates to chromatin to induce transcription of short units, including key DDR genes and multiple classes of non-coding RNAs. Critically, interfering with the axis of RBM7 and P-TEFb provokes cellular hypersensitivity to DNA-damage-inducing agents due to activation of apoptosis. Our work uncovers the importance of stress-dependent stimulation of Pol II pause release, which enables a pro-survival transcriptional response that is crucial for cell fate upon genotoxic insult.
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•iCLIP identifies a genotoxic-stress-enhanced interaction of RBM7 with 7SK snRNA•RBM7 interacts with core subunits of 7SK snRNP to activate P-TEFb•Induced Pol II transcription through P-TEFb is a hallmark of the DNA damage response•The RBM7-P-TEFb axis promotes viability of genotoxic-stressed cells
Bugai et al. report that stimulation of Pol II pause release is central to the DNA damage response. Mechanistic studies uncover the vital role of RBM7 in the genotoxic-stress-induced release of P-TEFb from the inhibitory 7SK snRNP, which enables a transcriptional response that is crucial to the survival of stressed cells.
In their article 'An index-based framework for assessing patterns and trends in river fragmentation and flow regulation by global dams at multiple scales' (2015 Environ. Res. Lett. 10 015001), Grill ...et al utilized a graph-based river routing model to simultaneously assess flow regulation and fragmentation by dams at multiple scales. Using global dam data they developed the river fragmentation index and the river regulation index, both based on river volume. Their results indicate that, on a global basis, 48% of river volume is moderately to severely impacted by either flow regulation, fragmentation, or both. Assuming completion of all dams planned and under construction in their future scenario, Grill et al find this number would rise to 93%, an effect they attribute largely to dam construction in the Amazon Basin. They also provide evidence for the importance of considering small- to medium-sized dams. We find this approach interesting and the analysis straightforward, but in this response note some limitations to the Asia-specific data on which the analysis is based. China and India are not only the two most populous countries, but are home to the vast majority of the world's largest dams and reservoirs, numbers which will rapidly increase in the future. Grill et al however, limit their modeling and subsequent basin assessment (flow regulation and river fragmentation) to less than ten percent of existing and forthcoming dams in those two countries. While we suspect this is due to data limitations, it results in what we feel are significant misinterpretations of the future of dams and rivers across much of Asia.
Hand hygiene is a crucial measure for the prevention of healthcare-associated infections (HAIs). The Hand Hygiene Excellence Award (HHEA) is an international programme acknowledging healthcare ...facilities for their leadership in implementing hand hygiene improvement programmes, including the World Health Organisation's Multimodal Improvement Strategy. This study aimed at summarising the results of the HHEA campaign between 2010 and 2021 and investigating the relationship between different hand hygiene parameters based on data from participating healthcare facilities.
A retrospective analysis was performed on datasets from HHEA forms, including data on hand hygiene compliance, alcohol-based handrub (ABHR) consumption, and Hand Hygiene Self-Assessment Framework (HHSAF) scores. Descriptive statistics were reported for each variable. The correlation between variables was inspected through Kendall's test, while possible non-linear relationships between hand hygiene compliance, ABHR consumption and HHSAF scores were sought through the Locally Estimated Scatterplot Smoothing or logistic regression models. A tree-structured partitioning model was developed to further confirm the obtained findings.
Ninety-seven healthcare facilities from 28 countries in three world regions (Asia-Pacific, Europe, Latin America) were awarded the HHEA and thus included in the analysis. HHSAF scores indicated an advanced hand hygiene promotion level (median 445 points, IQR 395-480). System change (100 95-100 points) and institutional safety climate (85 70-95 points) showed the highest and lowest score, respectively. In most cases, hand hygiene compliance was above 70%, with heterogeneity between countries. ABHR consumption above 20 millilitres per patient-day (ml/PD) was widely reported, with overall increasing trends. HHSAF scores were positively correlated with hand hygiene compliance (τ = 0.211, p = 0.007). We observed a positive correlation between compliance rates and ABHR consumption (τ = 0.193, p < 0.001), although the average predicted consumption was stable around 55-60 ml/PD for compliance rates above 80-85%. Logistic regression and partitioning tree analyses revealed that higher HHSAF scores were more likely in the high-ABHR consumption group at cut-offs around 57-59 ml/PD.
Ten years after its inception, the HHEA proves to be a valuable hand hygiene improvement programme in healthcare facilities worldwide. Consistent results were provided by the different hand hygiene indicators and the HHSAF score represents a valuable proxy measure of hand hygiene compliance.
Surgical hand preparation is an essential part of modern surgery. Both alcohol-based and antiseptic detergent-based hand preparation are recommended practices, with a trend towards use of alcohol ...based handrubs. However, discussion has arisen whether chlorhexidine is a required ingredient in highly efficacious alcohol-based formulations, in view of providing sustained antimicrobial efficacy.
One alcohol-only formulation (product A), containing ethanol and n-propanol, and one formulation containing a chlorhexidine-ethanol combination (product B) were directly compared with each other using a modified test protocol based on European standard EN 12791 (2016) with 25 volunteers. The alcohol-only formulation (product A) was applied for only 90 s, the chlorhexidine-alcohol formulation (product B) for 180 s. Microbial log reduction factors were determined and statistically compared immediately after application and at 6 h under surgical gloves.
The alcohol-only formulation (product A) achieved mean log reduction factors of 1.96 ± 1.06 immediately after application and 1.67 ± 0.71 after 6 h. The chlorhexidine-alcohol combination (product B) achieved mean log reduction factors of 1.42 ± 0.79 and 1.24 ± 0.90 immediately and after 6 h, respectively. The values for product A were significantly greater than those for product B at both measured time points (
≤ 0.025 immediately after application and
≤ 0.01 after 6 h).
An optimized alcohol-only formulation tested according to a modified EN 12791 protocol in 25 healthy volunteers outperformed a chlorhexidine-alcohol formulation both immediately after application and at 6 h under surgical gloves, despite a much shorter application time. Thus, optimized alcohol-only formulations do not require chlorhexidine to achieve potent immediate and sustained efficacy. In conclusion, chlorhexidine is not an essential component for alcohol-based surgical hand preparation.
Infection by viruses, including herpes simplex virus-1 (HSV-1), and cellular stresses cause widespread disruption of transcription termination (DoTT) of RNA polymerase II (RNAPII) in host genes. ...However, the underlying mechanisms remain unclear. Here, we demonstrate that the HSV-1 immediate early protein ICP27 induces DoTT by directly binding to the essential mRNA 3' processing factor CPSF. It thereby induces the assembly of a dead-end 3' processing complex, blocking mRNA 3' cleavage. Remarkably, ICP27 also acts as a sequence-dependent activator of mRNA 3' processing for viral and a subset of host transcripts. Our results unravel a bimodal activity of ICP27 that plays a key role in HSV-1-induced host shutoff and identify CPSF as an important factor that mediates regulation of transcription termination. These findings have broad implications for understanding the regulation of transcription termination by other viruses, cellular stress and cancer.
The Ayeyarwady basin, one of Asia's largest transnational river basins, shared by Myanmar, China and India, has an immense theoretical hydropower potential of 45GW. Currently hydropower projects with ...an approximate capacity of 33GW are already in various stages of development. Projects include some of the world's largest and most controversial endeavours (e.g. Myitsone). Of these projects 6.4GW are already installed in 187 hydropower projects (≥1MW). Despite its huge relevance, the transnational Ayeyarwady basin still belongs to the less known basins, which is largely attributed to its small Chinese section. However, the current knowledge is limited to Myanmar's segment where a limited number of 16 projects exist. In contrast, there are a multitude of projects −174 (18 large and 156 small) - in the Chinese section, including the basins largest one (Daying-4: 875MW). The combination of small and large projects makes the Chinese section one of the most dense (small) hydropower catchments worldwide. About half of the entire basin's hydropower output is exported to the energy starved Guangdong province (from both countries) and almost another quarter is used for energy intensive industries in the tiny Chinese section; hence currently only about 30% of the basin's generated (hydro-)electricity is used there for households, industry, etc. This results in a complex water-energy nexus that is complicated by a tangled geopolitical setting directly in the border region, where many projects are located. This paper describes that nexus based on Darrin Magee's powershed approach.
During lytic infection, herpes simplex virus (HSV) 1 induces a rapid shutoff of host RNA synthesis while redirecting transcriptional machinery to viral genes. In addition to being a major human ...pathogen, there is burgeoning clinical interest in HSV as a vector in gene delivery and oncolytic therapies, necessitating research into transcriptional control. This review summarizes the array of impacts that HSV has on RNA Polymerase (Pol) II, which transcribes all mRNA in infected cells. We discuss alterations in Pol II holoenzymes, post-translational modifications, and how viral proteins regulate specific activities such as promoter-proximal pausing, splicing, histone repositioning, and termination with respect to host genes. Recent technological innovations that have reshaped our understanding of previous observations are summarized in detail, along with specific research directions and technical considerations for future studies.
The herpes simplex virus 1 (HSV-1) virion host shut-off (vhs) protein cleaves both cellular and viral mRNAs by a translation-initiation-dependent mechanism, which should spare circular RNAs ...(circRNAs). Here, we show that vhs-mediated degradation of linear mRNAs leads to an enrichment of circRNAs relative to linear mRNAs during HSV-1 infection. This was also observed in influenza A virus (IAV) infection, likely due to degradation of linear host mRNAs mediated by the IAV PA-X protein and cap-snatching RNA-dependent RNA polymerase. For most circRNAs, enrichment was not due to increased circRNA synthesis but due to a general loss of linear RNAs. In contrast, biogenesis of a circRNA originating from the long isoform (NEAT1_2) of the nuclear paraspeckle assembly transcript 1 (NEAT1) was induced both in HSV-1 infection-in a vhs-independent manner-and in IAV infection. This was associated with induction of novel linear splicing of NEAT1_2 both within and downstream of the circRNA. NEAT1_2 forms a scaffold for paraspeckles, nuclear bodies located in the interchromatin space, must likely remain unspliced for paraspeckle assembly and is up-regulated in HSV-1 and IAV infection. We show that NEAT1_2 splicing and up-regulation can be induced by ectopic co-expression of the HSV-1 immediate-early proteins ICP22 and ICP27, potentially linking increased expression and splicing of NEAT1_2. To identify other conditions with NEAT1_2 splicing, we performed a large-scale screen of published RNA-seq data. This uncovered both induction of NEAT1_2 splicing and poly(A) read-through similar to HSV-1 and IAV infection in cancer cells upon inhibition or knockdown of CDK7 or the MED1 subunit of the Mediator complex phosphorylated by CDK7. In summary, our study reveals induction of novel circular and linear NEAT1_2 splicing isoforms as a common characteristic of HSV-1 and IAV infection and highlights a potential role of CDK7 in HSV-1 or IAV infection.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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