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Introduction COVID-19 showed that countries must strengthen their operational readiness (OPR) capabilities to respond to an imminent pandemic threat rapidly and proactively. We conducted a rapid scoping evidence review to understand the definition and critical elements of OPR against five core sub-systems of a new framework to strengthen the global architecture for Health Emergency Preparedness Response and Resilience (HEPR).Methods We searched MEDLINE, Embase, and Web of Science, targeted repositories, websites, and grey literature databases for publications between 1 January 2010 and 29 September 2021 in English, German, French or Afrikaans. Included sources were of any study design, reporting OPR, defined as immediate actions taken in the presence of an imminent threat, from groups who led or responded to a specified health emergency. We used prespecified and tested methods to screen and select sources, extract data, assess credibility and analyse results against the HEPR framework.Results Of 7005 sources reviewed, 79 met the eligibility criteria, including 54 peer-reviewed publications. The majority were descriptive reports (28%) and qualitative analyses (30%) from early stages of the COVID-19 pandemic. Definitions of OPR varied while nine articles explicitly used the term ‘readiness’, others classified OPR as part of preparedness or response. Applying our working OPR definition across all sources, we identified OPR actions within all five HEPR subsystems. These included resource prepositioning for early detection, data sharing, tailored communication and interventions, augmented staffing, timely supply procurement, availability and strategic dissemination of medical countermeasures, leadership, comprehensive risk assessment and resource allocation supported by relevant legislation. We identified gaps related to OPR for research and technology-enabled manufacturing platforms.Conclusions OPR is in an early stage of adoption. Establishing a consistent and explicit framework for OPRs within the context of existing global legal and policy frameworks can foster coherence and guide evidence-based policy and practice improvements in health emergency management.

Intratumoral B cell responses are associated with more favorable clinical outcomes in human pancreatic ductal adenocarcinoma (PDAC). However, the antigens driving these B cell responses are largely unknown. We sought to discover these antigens by using single-cell RNA sequencing (scRNA-Seq) and immunoglobulin (Ig) sequencing of tumor-infiltrating immune cells from 7 primary PDAC samples. We identified activated T and B cell responses and evidence of germinal center reactions. Ig sequencing identified plasma cell (PC) clones expressing isotype-switched and hypermutated Igs, suggesting the occurrence of T cell–dependent B cell responses. We assessed the reactivity of 41 recombinant antibodies that represented the products of 235 PCs and 12 B cells toward multiple cell lines and PDAC tissues and observed frequent staining of intracellular self-antigens. Three of these antigens were identified: the filamentous actin (F-actin), the nucleic protein RuvB like AAA ATPase 2 (RUVBL2), and the mitochondrial protein heat shock protein family D (Hsp60) member 1 (HSPD1). Antibody titers against F-actin and HSPD1 were substantially elevated in the plasma of patients with PDAC compared with healthy donors. Thus, PCs in PDAC produce autoantibodies reacting with intracellular self-antigens, which may result from promotion of preexisting, autoreactive B cell responses. These observations indicate the chronic inflammatory microenvironment of PDAC can support the adaptive immune response.

Abstract Background Lung cancer remains the major cause of cancer‐related deaths worldwide. Early stages of lung cancer are characterized by long asymptomatic periods that are ineffectively identified with the current screening programs. This deficiency represents a lost opportunity to improve the overall survival of patients. Serum biomarkers are among the most effective strategies for cancer screening and follow up. Methods Using bead‐based multiplexing assays we screened plasma and tumours of the KrasG12D/+; Lkb1f/f (KL) mouse model of lung cancer for cytokines that could be used as biomarkers. We identified tissue inhibitor of metalloproteinase 1 (TIMP1) as an early biomarker and validated this finding in the plasma of lung cancer patients. We used immunohistochemistry (IHC), previously published single‐cell RNA‐seq and bulk RNA‐seq data to assess the source and expression of TIMP1in the tumour. The prognostic value of TIMP1 was assessed using publicly available human proteomic and transcriptomic databases. Results We found that TIMP1 is a tumour‐secreted protein with high sensitivity and specificity for aggressive cancer, even at early stages in mice. We showed that TIMP1 levels in the tumour and serum correlate with tumour burden and worse survival in mice. We validated this finding using clinical samples from our institution and publicly available human proteomic and transcriptomic databases. These data support the finding that high tumour expression of TIMP1 correlates with an unfavorable prognosis in lung cancer patients. Conclusion TIMP1 is a suitable biomarker for lung cancer detection.

Glycosylation alterations are indicative of tissue inflammation and neoplasia, but whether these alterations contribute to disease pathogenesis is largely unknown. To study the role of glycan changes in pancreatic disease, we inducibly expressed human fucosyltransferase 3 and β1,3-galactosyltransferase 5 in mice, reconstituting the glycan sialyl-Lewisa, also known as carbohydrate antigen 19-9 (CA19-9). Notably, CA19-9 expression in mice resulted in rapid and severe pancreatitis with hyperactivation of epidermal growth factor receptor (EGFR) signaling. Mechanistically, CA19-9 modification of the matricellular protein fibulin-3 increased its interaction with EGFR, and blockade of fibulin-3, EGFR ligands, or CA19-9 prevented EGFR hyperactivation in organoids. CA19-9-mediated pancreatitis was reversible and could be suppressed with CA19-9 antibodies. CA19-9 also cooperated with the KrasG12D oncogene to produce aggressive pancreatic cancer. These findings implicate CA19-9 in the etiology of pancreatitis and pancreatic cancer and nominate CA19-9 as a therapeutic target.

We're stuck. The signal innovations of modern times--mass water purification, electricity, automobiles, modern manufacturing processes--are behind us. This slowing of invention presents a problem. We are trapped by the imperative [...]

The importance of studying the mechanistic aspects of long non-coding RNAs is being increasingly emphasized as more and more regulatory RNAs are being discovered. Non-coding RNA sequences directly associate with generic RNA-binding proteins as well as specific proteins, which cooperate in the downstream functions of the RNA and can also be dysregulated in various physiologic states and/or diseases. While current methods exist for identifying RNA–protein interactions, these methods require high quantities of input cells or use pooled capture reagents that may increase non-specific binding. We have developed a method to efficiently capture specific RNAs using less than one million input cells. One single oligonucleotide is used to pull down the target RNA of choice and oligonucleotide selection is driven by sequence accessibility. We perform thermal elution to specifically elute the target RNA and its associated proteins, which are identified by mass spectrometry. Ultimately, two target and control oligonucleotides are used to create an enrichment map of interacting proteins of interest. Graphical abstract Schematic representation of the SOCRATES workflow. SOCRATES utilizes a single 20-mer oligonucleotide for RNA pull down followed by a temperature elution series and liquid chromatography–mass spectrometry (LC-MS)/MS to identify specific RNA–protein interactions.

Introduction Much is known around public health preparedness and response phases. However, between the two phases is operational readiness that comprises the immediate actions needed to respond to a developing risk or hazard. Currently, emergency readiness is embedded in multiple frameworks and policy documents related to the health emergency cycle. However, knowledge about operational readiness’ critical readiness components and actions required by countries to respond to public health eminent threat is not well known. Therefore, we aim to define and identify the critical elements of ‘operational readiness’ for public health emergencies, including COVID-19, and identify lessons learnt from addressing it, to inform the WHO Operational Readiness Framework.Methods and analysis This is a scoping review following the Joanna Briggs Institute guidance. Reporting will be according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews (PRISMA-ScR) checklist. MEDLINE, Embase and Web of Science databases and grey literature will be searched and exported into an online systematic review software (eg, Rayyan in this case) for review. The review team, which apart from scoping review methodological experts include content experts in health systems and public health and emergency medicine, prepared an a priori study protocol in consultation with WHO representatives. ATLAS.ti V.9 will be used to conduct thematic data analysis as well as store, organise and retrieve data. Data analysis and presentation will be carried out by five reviewers.Ethics and dissemination This review will reveal new insights, knowledge and lessons learnt that will translate into an operational framework for readiness actions. In consultation with WHO, findings will be disseminated as appropriate (eg, through professional bodies, conferences and research papers). No ethics approvals are required as no humans will be involved in data collection.Protocol registration This rapid scoping review has been registered on Open Science Framework (doi:10.17605/OSF.IO/6SYAH).

A group of long non-coding RNAs (lncRNAs), Mammary Tumor Associated RNA s 1-30 (MaTARs 1-30), are differentially expressed between mammary tumor cells and normal mammary epithelial cells. Here the authors report that MaTAR25 plays a role in breast cancer cell proliferation, migration and invasion by regulating the expression of the Tensin1 gene in trans.

We present the development of a multiphase adjoint for the Community Multiscale Air Quality (CMAQ) model, a widely used chemical transport model. The adjoint model provides location- and time-specific gradients that can be used in various applications such as backward sensitivity analysis, source attribution, optimal pollution control, data assimilation, and inverse modeling. The science processes of the CMAQ model include gas-phase chemistry, aerosol dynamics and thermodynamics, cloud chemistry and dynamics, diffusion, and advection. Discrete adjoints are implemented for all the science processes, with an additional continuous adjoint for advection. The development of discrete adjoints is assisted with algorithmic differentiation (AD) tools. Particularly, the Kinetic PreProcessor (KPP) is implemented for gas-phase and aqueous chemistry, and two different automatic differentiation tools are used for other processes such as clouds, aerosols, diffusion, and advection. The continuous adjoint of advection is developed manually. For adjoint validation, the brute-force or finite-difference method (FDM) is implemented process by process with box- or column-model simulations. Due to the inherent limitations of the FDM caused by numerical round-off errors, the complex variable method (CVM) is adopted where necessary. The adjoint model often shows better agreement with the CVM than with the FDM. The adjoints of all science processes compare favorably with the FDM and CVM. In an example application of the full multiphase adjoint model, we provide the first estimates of how emissions of particulate matter (PM2.5) affect public health across the US.

Pancreatic cancer is one of the most lethal malignancies due to its late diagnosis and limited response to treatment. Tractable methods to identify and interrogate pathways involved in pancreatic tumorigenesis are urgently needed. We established organoid models from normal and neoplastic murine and human pancreas tissues. Pancreatic organoids can be rapidly generated from resected tumors and biopsies, survive cryopreservation, and exhibit ductal- and disease-stage-specific characteristics. Orthotopically transplanted neoplastic organoids recapitulate the full spectrum of tumor development by forming early-grade neoplasms that progress to locally invasive and metastatic carcinomas. Due to their ability to be genetically manipulated, organoids are a platform to probe genetic cooperation. Comprehensive transcriptional and proteomic analyses of murine pancreatic organoids revealed genes and pathways altered during disease progression. The confirmation of many of these protein changes in human tissues demonstrates that organoids are a facile model system to discover characteristics of this deadly malignancy.

Oncogenic RAS (H-RAS(V12)) induces premature senescence in primary cells by triggering production of reactive oxygen species (ROS), but the molecular role of ROS in senescence remains elusive. We investigated whether inhibition of protein tyrosine phosphatases by ROS contributed to H-RAS(V12)-induced senescence. We identified protein tyrosine phosphatase 1B (PTP1B) as a major target of H-RAS(V12)-induced ROS. Inactivation of PTP1B was necessary and sufficient to induce premature senescence in H-RAS(V12)-expressing IMR90 fibroblasts. We identified phospho-Tyr 393 of argonaute 2 (AGO2) as a direct substrate of PTP1B. Phosphorylation of AGO2 at Tyr 393 inhibited loading with microRNAs (miRNAs) and thus miRNA-mediated gene silencing, which counteracted the function of H-RAS(V12)-induced oncogenic miRNAs. Overall, our data illustrate that premature senescence in H-RAS(V12)-transformed primary cells is a consequence of oxidative inactivation of PTP1B and inhibition of miRNA-mediated gene silencing.

Oncogenic RAS (H-RAS V12 ) induces premature senescence in primary cells by triggering production of reactive oxygen species (ROS), but the molecular role of ROS in senescence remains elusive. We investigated whether inhibition of protein tyrosine phosphatases by ROS contributed to H-RAS V12 -induced senescence. We identified protein tyrosine phosphatase 1B (PTP1B) as a major target of H-RAS V12 -induced ROS. Inactivation of PTP1B was necessary and sufficient to induce premature senescence in H-RAS V12 -expressing IMR90 fibroblasts. We identified phospho-Tyr 393 of argonaute 2 (AGO2) as a direct substrate of PTP1B. Phosphorylation of AGO2 at Tyr 393 inhibited loading with microRNAs (miRNAs) and thus miRNA-mediated gene silencing, which counteracted the function of H-RAS V12 -induced oncogenic miRNAs. Overall, our data illustrate that premature senescence in H-RAS V12 -transformed primary cells is a consequence of oxidative inactivation of PTP1B and inhibition of miRNA-mediated gene silencing. © 2014 Elsevier Inc. All rights reserved.

Abstract Background Approximately 2.9 million deaths are attributed to ambient fine particle air pollution around the world each year (PM2.5). In general, cohort studies of mortality and outdoor PM2.5 concentrations have limited information on individuals exposed to low levels of PM2.5 as well as covariates such as smoking behaviours, alcohol consumption, and diet which may confound relationships with mortality. This study provides an updated and extended analysis of the Canadian Community Health Survey-Mortality cohort: a population-based cohort with detailed PM2.5 exposure data and information on a number of important individual-level behavioural risk factors. We also used this rich dataset to provide insight into the shape of the concentration-response curve for mortality at low levels of PM2.5. Methods Respondents to the Canadian Community Health Survey from 2000 to 2012 were linked by postal code history from 1981 to 2016 to high resolution PM2.5 exposure estimates, and mortality incidence to 2016. Cox proportional hazard models were used to estimate the relationship between non-accidental mortality and ambient PM2.5 concentrations (measured as a three-year average with a one-year lag) adjusted for socio-economic, behavioural, and time-varying contextual covariates. Results In total, 50,700 deaths from non-accidental causes occurred in the cohort over the follow-up period. Annual average ambient PM2.5 concentrations were low (i.e. 5.9 μg/m3, s.d. 2.0) and each 10 μg/m3 increase in exposure was associated with an increase in non-accidental mortality (HR = 1.11; 95% CI 1.04–1.18). Adjustment for behavioural covariates did not materially change this relationship. We estimated a supra-linear concentration-response curve extending to concentrations below 2 μg/m3 using a shape constrained health impact function. Mortality risks associated with exposure to PM2.5 were increased for males, those under age 65, and non-immigrants. Hazard ratios for PM2.5 and mortality were attenuated when gaseous pollutants were included in models. Conclusions Outdoor PM2.5 concentrations were associated with non-accidental mortality and adjusting for individual-level behavioural covariates did not materially change this relationship. The concentration-response curve was supra-linear with increased mortality risks extending to low outdoor PM2.5 concentrations.

Hepatocellular carcinoma, the most common type of liver malignancy, is one of the most lethal forms of cancer. We identified a long non-coding RNA, Gm19705, that is overexpressed in hepatocellular carcinoma and mouse embryonic stem cells. We named this RNA Pluripotency and Hepatocyte Associated RNA Overexpressed in HCC, or PHAROH. Depletion of PHAROH impacts cell proliferation and migration, which can be rescued by ectopic expression of PHAROH. RNA-seq analysis of PHAROH knockouts revealed that a large number of genes with decreased expression contain a Myc motif in their promoter. MYC is decreased in knockout cells at the protein level, but not the mRNA level. RNA-antisense pulldown identified nucleolysin TIAR, a translational repressor, to bind to a 71-nt hairpin within PHAROH, sequestration of which increases MYC translation. In summary, our data suggest that PHAROH regulates MYC translation by sequestering TIAR and as such represents a potentially exciting diagnostic or therapeutic target in hepatocellular carcinoma.

Abstract Background Abiotic stress reduces photosynthetic yield and plant growth, negatively impacting global crop production and is a major constraint faced by agriculture. However, the knowledge on the impact on plants under extremely high irradiance is limited. We present the first in-depth proteomics analysis of plants treated with a method developed by our research group to generate a light gradient using an extremely intense light. Methods The method consists of utilizing light emitting diodes (LED) to create a single spot at 24,000 μmol m− 2 s− 1 irradiance, generating three light stress levels. A light map and temperature profile were obtained during the light experiment. The proteins expressed in the treated tomato (Solanum lycopersicum, Heinz H1706) leaves were harvested 10 days after the treatment, allowing for the detection of proteins involved in a long-term recovery. A multiplex labeled proteomics method (iTRAQ) was analyzed by LC-MS/MS. Results A total of 3994 proteins were identified at 1% false discovery rate and matched additional quality filters. Hierarchical clustering analysis resulted in four types of patterns related to the protein expression, with one being directly linked to the increased LED irradiation. A total of 37 proteins were found unique to the least damaged leaf zone, while the medium damaged zone had 372 proteins, and the severely damaged presented unique 1003 proteins. Oxygen evolving complex and PSII complex proteins (PsbH, PsbS, PsbR and Psb28) were found to be abundant in the most damaged leaf zone. This leaf zone presented a protein involved in the salicylic acid response, while it was not abundant in the other leaf zones. The mRNA level of PsbR was significantly lower (1-fold) compared the control in the most damaged zone of the leaf, while Psb28 and PsbH were lower (1-fold) in the less damaged leaf zones. PsbS mRNA abundance in all leaf zones tested presented no statistically significant change from the control. Conclusions We present the first characterization of the proteome changes caused by an extreme level of high-light intensity (24,000 μmol m− 2 s− 1). The proteomics results show the presence of specific defense responses to each level of light intensity, with a possible involvement of proteins PsbH, Psb28, PsbR, and PsbS.

Phenotypic responses to biotic stresses are often studied as the interactions between two species; however, in the phytobiome, these responses frequently result from complex interactions involving several organisms. Here, we show that variation in chlorosis caused by Russian wheat aphid (Diuraphis noxia) feeding is determined, in part, by aphid-associated bacteria. Proteomic analysis of fluids injected into a sterile medium by the aphid during feeding indicate that 99% of the proteins are of bacterial origin. Of these, the greatest proportion are produced by bacteria in the order Enterobacteriales. Bacteria from five genera in four families that have the capacity to produce these proteins were isolated directly from aphids as well as from wheat leaves only after D. noxia feeding. By themselves or in combination, these bacteria were not virulent to wheat, even at high inoculum levels. Metagenomic analysis showed that the same five D. noxia-associated genera dominated the non-Buchnera component of the aphid microbiome, and that representation of these genera was reduced in aphids from colonies established after isolation of newborn nymphs from their mothers prior to feeding (isolated aphids). Isolation or treatment with antibiotics reduced bacterial numbers, and these aphids caused less feeding damage on wheat than non-isolated or non-antibiotic-treated aphids. Our data show that bacterial proteins are a significant component of Russian wheat aphid saliva, that the bacteria producing these proteins are associated with aphids and plants fed upon by aphids, and that these aphid-associated bacteria facilitate aphid virulence to wheat.

Summary: A hallmark of advanced prostate cancer (PC) is the concomitant loss of PTEN and p53 function. To selectively eliminate such cells, we screened cytotoxic compounds on Pten−/−;Trp53−/− fibroblasts and their Pten-WT reference. Highly selective killing of Pten-null cells can be achieved by deguelin, a natural insecticide. Deguelin eliminates Pten-deficient cells through inhibition of mitochondrial complex I (CI). Five hundred-fold higher drug doses are needed to obtain the same killing of Pten-WT cells, even though deguelin blocks their electron transport chain equally well. Selectivity arises because mitochondria of Pten-null cells consume ATP through complex V, instead of producing it. The resulting glucose dependency can be exploited to selectively kill Pten-null cells with clinically relevant CI inhibitors, especially if they are lipophilic. In vivo, deguelin suppressed disease in our genetically engineered mouse model for metastatic PC. Our data thus introduce a vulnerability for highly selective targeting of incurable PC with inhibitors of CI. : Naguib et al. find that Pten-null cells are highly vulnerable to mitochondrial complex I inhibition under conditions in which Pten-WT cells remain perfectly viable. They suggest that such an approach could serve as a blueprint for selective targeting of lethal Pten-deficient metastatic prostate cancer. Keywords: Pten, mitochondria, deguelin, prostate cancer, complex I, ATP synthase, metabolism, glucose, RapidCaP, ATP

An amendment to this paper has been published and can be accessed via a link at the top of the paper.