JF Oram
Dec 1, 1996; 37:2473-2491
Reviews

Ronald M. Krauss
Jan 1, 1982; 23:97-104
Articles

Robert W. Mahley
Jan 1, 1999; 40:1-16
Reviews

AE Christian
Nov 1, 1997; 38:2264-2272
Articles

CJ Fielding
Feb 1, 1995; 36:211-228
Reviews

Persuasion or manipulation? Limiting campaigning online Expert comment NCapeling 15 February 2021

To tackle online disinformation and manipulation effectively, regulators must clarify the dividing line between legitimate and illegitimate campaign practices.

Democracy is at risk, not only from disinformation but from systemic manipulation of public debate online. Evidence shows social media drives control of narratives, polarization, and division on issues of politics and identity. We are now seeing regulators turn their attention to protecting democracy from disinformation and manipulation. But how should they distinguish between legitimate and illegitimate online information practices, between persuasive and manipulative campaigning?

Unregulated, the tactics of disinformation and manipulation have spread far and wide. They are no longer the preserve merely of disaffected individuals, hostile international actors, and authoritarian regimes. Facebook’s periodic reporting on coordinated inauthentic behaviour and Twitter’s on foreign information operations reveal that militaries, governments, and political campaigners in a wide range of countries, including parts of Europe and America, have engaged in manipulative or deceptive information campaigns.

For example, in September 2019, Twitter removed 259 accounts it says were ‘falsely boosting’ public sentiment online that it found to be operated by Spain’s conservative and Christian-democratic political party Partido Popular. In October 2020, Facebook removed accounts with around 400,000 followers linked to Rally Forge, a US marketing firm which Facebook claims was working on behalf of right-wing organisations Turning Point USA and Inclusive Conservation Group. And in December 2020, Facebook took down a network of accounts with more than 6,000 followers, targeting audiences in Francophone Africa and focusing on France’s policies there, finding it linked with individuals associated with the French military.

Public influence on a global scale

Even more revealingly, in its 2020 Global Inventory of Organized Social Media Manipulation, the Oxford Internet Institute (OII) found that in 81 countries, government agencies and/or political parties are using ‘computational propaganda’ in social media to shape public attitudes.

These 81 countries span the world and include not only authoritarian and less democratic regimes but also developed democracies such as many EU member states. OII found that countries with the largest capacity for computational propaganda – which include the UK, US, and Australia – have permanent teams devoted to shaping the online space overseas and at home.

OII categorizes computational propaganda as four types of communication strategy – the creation of disinformation or manipulated content such as doctored images and videos; the use of personal data to target specific segments of the population with disinformation or other false narratives; trolling, doxing or online harassment of political opponents, activists or journalists; and mass-reporting of content or accounts posted or run by opponents as part of gaming the platforms’ automated flagging, demotion, and take-down systems.

Doubtless some of the governments included within OII’s statistics argue their behaviour is legitimate and appropriate, either to disseminate information important to the public interest or to wrestle control of the narrative away from hostile actors. Similarly, no doubt some political campaigners removed by the platforms for alleged engagement in ‘inauthentic behaviour’ or ‘manipulation’ would defend the legitimacy of their conduct.

The fact is that clear limits of acceptable propaganda and information influence operations online do not exist. Platforms still share little information overall about what information operations they see being conducted online. Applicable legal principles such as international human rights law have not yet crystallised into clear rules. As information operations are rarely exposed to public view – with notable exceptions such as the Cambridge Analytica scandal – there is relatively little constraint in media and public scrutiny or censure.

OII’s annual reports and the platforms’ periodic reports demonstrate a continual expansion of deceptive and manipulative practices since 2016, and increasing involvement of private commercial companies in their deployment. Given the power of political influence as a driver, this absence of clear limits may result in ever more sophisticated techniques being deployed in the search for maximal influence.

Ambiguity over reasonable limits on manipulation plays into the hands of governments which regulate ostensibly in the name of combating disinformation, but actually in the interests of maintaining their own control of the narrative and in disregard of the human right to freedom of expression. Following Singapore’s 2019 prohibition of online untruths, 17 governments ranging from Bolivia to Vietnam to Hungary passed regulations during 2020 criminalising ‘fake news’ on COVID-19 while many other governments are alleged to censor opposition arguments or criticisms of official state narratives.

Clear limits are needed. Facebook itself has been calling for societal discussion about the limits of acceptable online behaviour for some time and has issued recommendations of its own.

The European Democracy Action Plan: Aiming to protect pluralism and vigour in democracy

The European Democracy Action Plan (EDAP), which complements the European Commission’s Digital Services Act and Digital Markets Act proposals, is a welcome step. It is ground-breaking in its efforts to protect the pluralism and vigour of European democracies by tackling all forms of online manipulation, while respecting human rights.

While the EDAP tackles disinformation, it also condemns two categories of online manipulation – information influence operations which EDAP describes as ‘coordinated efforts by either domestic or foreign actors to influence a target audience using a range of deceptive means’ and foreign interference, described as ‘coercive and deceptive efforts to disrupt the free formation and expression of individuals’ political will by a foreign state actor or its agents’. These categories include influence operations such as harnessing fake accounts or gaming algorithms, and the suppression of independent information sources through censorship or mass reporting.

But the categories are so broad they risk capturing disinformation practices not only of rogue actors, but also of governments and political campaigners both outside and within the EU. The European Commission plans to work towards refined definitions. Its discussions with member states and other stakeholders should start to determine which practices ought to be tackled as manipulative, and which ought to be tolerated as legitimate campaigning or public information practices.

The extent of the EDAP proposals on disinformation demonstrates the EU’s determination to tackle online manipulation. The EDAP calls for improved practical measures building on the Commission’s 2020 acceleration of effort in the face of COVID-19 disinformation. The Commission is considering how best to impose costs on perpetrators of disinformation, such as by disrupting financial incentives or even imposing sanctions for repeated offences.

Beyond the regulatory and risk management framework proposed by the Digital Services Act (DSA), the Commission says it will issue guidance for platforms and other stakeholders to strengthen their measures against disinformation, building on the existing EU Code of Practice on Disinformation and eventually leading to a strengthened Code with more robust monitoring requirements. These are elements of a broader package of measures in the EDAP to preserve democracy in Europe.

Until there are clear limits, manipulative practices will continue to develop and to spread. More actors will resort to them in order not to be outgunned by opponents. It is hoped forthcoming European discussions – involving EU member state governments, the European Parliament, civil society, academia and the online platforms – will begin to shape at least a European and maybe a global consensus on the limits of information influence, publicly condemning unacceptable practices while safeguarding freedom of expression.

Most importantly, following the example of the EDAP, the preservation of democracy and human rights – rather than the promotion of political or commercial interest – should be the lodestar for those discussions.

Why the private sector should protect civic society Explainer Video NCapeling 10 December 2021

A short animation explaining the crucial role that the private sector can play in protecting and defending civic space.

This video explainer introduces a synthesis paper which analyses how the private sector can support the protection of civic society space.

The private sector is in a unique position to work with civil society organizations to uphold and defend civic freedoms and support sustainable and profitable business environments. Companies have the capacity, resources and expertise to enhance the protection of civic space.

By doing so, this helps create a society in which fundamental rights and the rule of law are respected and exercised by governments, private citizens, and all organizations which, in turn, is critical to a sustainable and profitable business environment.  

For more information, download the report.

Mammalian circadian clocks are driven by transcription/translation feedback loops composed of positive transcriptional activators (BMAL1 and CLOCK) and negative repressors (CRYPTOCHROMEs (CRYs) and PERIODs (PERs)). CRYs, in complex with PERs, bind to the BMAL1/CLOCK complex and repress E-box–driven transcription of clock-associated genes. There are two individual CRYs, with CRY1 exhibiting higher affinity to the BMAL1/CLOCK complex than CRY2. It is known that this differential binding is regulated by a dynamic serine-rich loop adjacent to the secondary pocket of both CRYs, but the underlying features controlling loop dynamics are not known. Here we report that allosteric regulation of the serine-rich loop is mediated by Arg-293 of CRY1, identified as a rare CRY1 SNP in the Ensembl and 1000 Genomes databases. The p.Arg293His CRY1 variant caused a shortened circadian period in a Cry1−/−Cry2−/− double knockout mouse embryonic fibroblast cell line. Moreover, the variant displayed reduced repressor activity on BMAL1/CLOCK driven transcription, which is explained by reduced affinity to BMAL1/CLOCK in the absence of PER2 compared with CRY1. Molecular dynamics simulations revealed that the p.Arg293His CRY1 variant altered a communication pathway between Arg-293 and the serine loop by reducing its dynamicity. Collectively, this study provides direct evidence that allosterism in CRY1 is critical for the regulation of circadian rhythm.

Zika virus (ZIKV) is a neurotropic flavivirus that causes several diseases including birth defects such as microcephaly. Intrinsic immunity is known to be a frontline defense against viruses through host anti-viral restriction factors. Limited knowledge is available on intrinsic immunity against ZIKV in brains. Amyloid precursor protein (APP) is predominantly expressed in brains and implicated in the pathogenesis of Alzheimer's diseases. We have found that ZIKV interacts with APP, and viral infection increases APP expression via enhancing protein stability. Moreover, we identified the viral peptide, HGSQHSGMIVNDTGHETDENRAKVEITPNSPRAEATLGGFGSLGL, which is capable of en-hancing APP expression. We observed that aging brain tissues with APP had protective effects on ZIKV infection by reducing the availability of the viruses. Also, knockdown of APP expression or blocking ZIKV-APP interactions enhanced ZIKV replication in human neural progenitor/stem cells. Finally, intracranial infection of ZIKV in APP-null neonatal mice resulted in higher mortality and viral yields. Taken together, these findings suggest that APP is a restriction factor that protects against ZIKV by serving as a decoy receptor, and plays a protective role in ZIKV-mediated brain injuries.

Reactive oxygen species (ROS) are an unavoidable host environmental cue for intracellular pathogens such as Mycobacterium tuberculosis and Mycobacterium bovis; however, the signaling pathway in mycobacteria for sensing and responding to environmental stress remains largely unclear. Here, we characterize a novel CmtR-Zur-ESX3-Zn2+ regulatory pathway in M. bovis that aids mycobacterial survival under oxidative stress. We demonstrate that CmtR functions as a novel redox sensor and that its expression can be significantly induced under H2O2 stress. CmtR can physically interact with the negative regulator Zur and de-represses the expression of the esx-3 operon, which leads to Zn2+ accumulation and promotion of reactive oxygen species detoxication in mycobacterial cells. Zn2+ can also act as an effector molecule of the CmtR regulator, using which the latter can de-repress its own expression for further inducing bacterial antioxidant adaptation. Consistently, CmtR can induce the expression of EsxH, a component of esx-3 operon involved in Zn2+ transportation that has been reported earlier, and inhibit phagosome maturation in macrophages. Lastly, CmtR significantly contributes to bacterial survival in macrophages and in the lungs of infected mice. Our findings reveal the existence of an antioxidant regulatory pathway in mycobacteria and provide novel information on stress-triggered gene regulation and its association with host–pathogen interaction.

Stop codon read-through (SCR) is a process of continuation of translation beyond a stop codon. This phenomenon, which occurs only in certain mRNAs under specific conditions, leads to a longer isoform with properties different from that of the canonical isoform. MTCH2, which encodes a mitochondrial protein that regulates mitochondrial metabolism, was selected as a potential read-through candidate based on evolutionary conservation observed in the proximal region of its 3' UTR. Here, we demonstrate translational read-through across two evolutionarily conserved, in-frame stop codons of MTCH2 using luminescence- and fluorescence-based assays, and by analyzing ribosome-profiling and mass spectrometry (MS) data. This phenomenon generates two isoforms, MTCH2x and MTCH2xx (single- and double-SCR products, respectively), in addition to the canonical isoform MTCH2, from the same mRNA. Our experiments revealed that a cis-acting 12-nucleotide sequence in the proximal 3' UTR of MTCH2 is the necessary signal for SCR. Functional characterization showed that MTCH2 and MTCH2x were localized to mitochondria with a long t1/2 (>36 h). However, MTCH2xx was found predominantly in the cytoplasm. This mislocalization and its unique C terminus led to increased degradation, as shown by greatly reduced t1/2 (<1 h). MTCH2 read-through–deficient cells, generated using CRISPR-Cas9, showed increased MTCH2 expression and, consistent with this, decreased mitochondrial membrane potential. Thus, double-SCR of MTCH2 regulates its own expression levels contributing toward the maintenance of normal mitochondrial membrane potential.

Hepatocyte nuclear factor-1β (HNF-1β) is a tissue-specific transcription factor that is required for normal kidney development and renal epithelial differentiation. Mutations of HNF-1β produce congenital kidney abnormalities and inherited renal tubulopathies. Here, we show that ablation of HNF-1β in mIMCD3 renal epithelial cells results in activation of β-catenin and increased expression of lymphoid enhancer–binding factor 1 (LEF1), a downstream effector in the canonical Wnt signaling pathway. Increased expression and nuclear localization of LEF1 are also observed in cystic kidneys from Hnf1b mutant mice. Expression of dominant-negative mutant HNF-1β in mIMCD3 cells produces hyperresponsiveness to exogenous Wnt ligands, which is inhibited by siRNA-mediated knockdown of Lef1. WT HNF-1β binds to two evolutionarily conserved sites located 94 and 30 kb from the mouse Lef1 promoter. Ablation of HNF-1β decreases H3K27 trimethylation repressive marks and increases β-catenin occupancy at a site 4 kb upstream to Lef1. Mechanistically, WT HNF-1β recruits the polycomb-repressive complex 2 that catalyzes H3K27 trimethylation. Deletion of the β-catenin–binding domain of LEF1 in HNF-1β–deficient cells abolishes the increase in Lef1 transcription and decreases the expression of downstream Wnt target genes. The canonical Wnt target gene, Axin2, is also a direct transcriptional target of HNF-1β through binding to negative regulatory elements in the gene promoter. These findings demonstrate that HNF-1β regulates canonical Wnt target genes through long-range effects on histone methylation at Wnt enhancers and reveal a new mode of active transcriptional repression by HNF-1β.

Evolving evidence suggests that nicotine may contribute to impaired asthma control by stimulating expression of nerve growth factor (NGF), a neurotrophin associated with airway remodeling and airway hyperresponsiveness. We explored the hypothesis that nicotine increases NGF by reducing lung fibroblast (LF) microRNA-98 (miR-98) and PPARγ levels, thus promoting airway remodeling. Levels of NGF, miR-98, PPARγ, fibronectin 1 (FN1), endothelin-1 (EDN1, herein referred to as ET-1), and collagen (COL1A1 and COL3A1) were measured in human LFs isolated from smoking donors, in mouse primary LFs exposed to nicotine (50 μg/ml), and in whole lung homogenates from mice chronically exposed to nicotine (100 μg/ml) in the drinking water. In selected studies, these pathways were manipulated in LFs with miR-98 inhibitor (anti-miR-98), miR-98 overexpression (miR-98 mimic), or the PPARγ agonist rosiglitazone. Compared with unexposed controls, nicotine increased NGF, FN1, ET-1, COL1A1, and COL3A1 expression in human and mouse LFs and mouse lung homogenates. In contrast, nicotine reduced miR-98 levels in LFs in vitro and in lung homogenates in vivo. Treatment with anti-miR-98 alone was sufficient to recapitulate increases in NGF, FN1, and ET-1, whereas treatment with a miR-98 mimic significantly suppressed luciferase expression in cells transfected with a luciferase reporter linked to the putative seed sequence in the NGF 3'UTR and also abrogated nicotine-induced increases in NGF, FN1, and ET-1 in LFs. Similarly, rosiglitazone increased miR-98 and reversed nicotine-induced increases in NGF, FN1, and ET-1. Taken together, these findings demonstrate that nicotine-induced increases in NGF and other markers of airway remodeling are negatively regulated by miR-98.

The molecular mechanisms of reduced frataxin (FXN) expression in Friedreich's ataxia (FRDA) are linked to epigenetic modification of the FXN locus caused by the disease-associated GAA expansion. Here, we identify that SUV4-20 histone methyltransferases, specifically SUV4-20 H1, play an important role in the regulation of FXN expression and represent a novel therapeutic target. Using a human FXN–GAA–Luciferase repeat expansion genomic DNA reporter model of FRDA, we screened the Structural Genomics Consortium epigenetic probe collection. We found that pharmacological inhibition of the SUV4-20 methyltransferases by the tool compound A-196 increased the expression of FXN by ∼1.5-fold in the reporter cell line. In several FRDA cell lines and patient-derived primary peripheral blood mononuclear cells, A-196 increased FXN expression by up to 2-fold, an effect not seen in WT cells. SUV4-20 inhibition was accompanied by a reduction in H4K20me2 and H4K20me3 and an increase in H4K20me1, but only modest (1.4–7.8%) perturbation in genome-wide expression was observed. Finally, based on the structural activity relationship and crystal structure of A-196, novel small molecule A-196 analogs were synthesized and shown to give a 20-fold increase in potency for increasing FXN expression. Overall, our results suggest that histone methylation is important in the regulation of FXN expression and highlight SUV4-20 H1 as a potential novel therapeutic target for FRDA.

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Histone recognition by “reader” modules serves as a fundamental mechanism in epigenetic regulation. Previous studies have shown that Spindlin1 is a reader of histone H3K4me3 as well as “K4me3-R8me2a” and promotes transcription of rDNA or Wnt/TCF4 target genes. Here we show that Spindlin1 also acts as a potent reader of histone H3 “K4me3-K9me3/2” bivalent methylation pattern. Calorimetric titration revealed a binding affinity of 16 nm between Spindlin1 and H3 “K4me3-K9me3” peptide, which is one to three orders of magnitude stronger than most other histone readout events at peptide level. Structural studies revealed concurrent recognition of H3K4me3 and H3K9me3/2 by aromatic pockets 2 and 1 of Spindlin1, respectively. Epigenomic profiling studies showed that Spindlin1 colocalizes with both H3K4me3 and H3K9me3 peaks in a subset of genes enriched in biological processes of transcription and its regulation. Moreover, the distribution of Spindlin1 peaks is primarily associated with H3K4me3 but not H3K9me3, which suggests that Spindlin1 is a downstream effector of H3K4me3 generated in heterochromatic regions. Collectively, our work calls attention to an intriguing function of Spindlin1 as a potent H3 “K4me3-K9me3/2” bivalent mark reader, thereby balancing gene expression and silencing in H3K9me3/2-enriched regions.

Phospholipase Cε (PLCε) is activated downstream of G protein–coupled receptors and receptor tyrosine kinases through direct interactions with small GTPases, including Rap1A and Ras. Although Ras has been reported to allosterically activate the lipase, it is not known whether Rap1A has the same ability or what its molecular mechanism might be. Rap1A activates PLCε in response to the stimulation of β-adrenergic receptors, translocating the complex to the perinuclear membrane. Because the C-terminal Ras association (RA2) domain of PLCε was proposed to the primary binding site for Rap1A, we first confirmed using purified proteins that the RA2 domain is indeed essential for activation by Rap1A. However, we also showed that the PLCε pleckstrin homology (PH) domain and first two EF hands (EF1/2) are required for Rap1A activation and identified hydrophobic residues on the surface of the RA2 domain that are also necessary. Small-angle X-ray scattering showed that Rap1A binding induces and stabilizes discrete conformational states in PLCε variants that can be activated by the GTPase. These data, together with the recent structure of a catalytically active fragment of PLCε, provide the first evidence that Rap1A, and by extension Ras, allosterically activate the lipase by promoting and stabilizing interactions between the RA2 domain and the PLCε core.

In animals, the response to chronic hypoxia is mediated by prolyl hydroxylases (PHDs) that regulate the levels of hypoxia-inducible transcription factor α (HIFα). PHD homologues exist in other types of eukaryotes and prokaryotes where they act on non HIF substrates. To gain insight into the factors underlying different PHD substrates and properties, we carried out biochemical and biophysical studies on PHD homologues from the cellular slime mold, Dictyostelium discoideum, and the protozoan parasite, Toxoplasma gondii, both lacking HIF. The respective prolyl-hydroxylases (DdPhyA and TgPhyA) catalyze prolyl-hydroxylation of S-phase kinase-associated protein 1 (Skp1), a reaction enabling adaptation to different dioxygen availability. Assays with full-length Skp1 substrates reveal substantial differences in the kinetic properties of DdPhyA and TgPhyA, both with respect to each other and compared with human PHD2; consistent with cellular studies, TgPhyA is more active at low dioxygen concentrations than DdPhyA. TgSkp1 is a DdPhyA substrate and DdSkp1 is a TgPhyA substrate. No cross-reactivity was detected between DdPhyA/TgPhyA substrates and human PHD2. The human Skp1 E147P variant is a DdPhyA and TgPhyA substrate, suggesting some retention of ancestral interactions. Crystallographic analysis of DdPhyA enables comparisons with homologues from humans, Trichoplax adhaerens, and prokaryotes, informing on differences in mobile elements involved in substrate binding and catalysis. In DdPhyA, two mobile loops that enclose substrates in the PHDs are conserved, but the C-terminal helix of the PHDs is strikingly absent. The combined results support the proposal that PHD homologues have evolved kinetic and structural features suited to their specific sensing roles.

DNA polymerases are today used throughout scientific research, biotechnology, and medicine, in part for their ability to interact with unnatural forms of DNA created by synthetic biologists. Here especially, natural DNA polymerases often do not have the “performance specifications” needed for transformative technologies. This creates a need for science-guided rational (or semi-rational) engineering to identify variants that replicate unnatural base pairs (UBPs), unnatural backbones, tags, or other evolutionarily novel features of unnatural DNA. In this review, we provide a brief overview of the chemistry and properties of replicative DNA polymerases and their evolved variants, focusing on the Klenow fragment of Taq DNA polymerase (Klentaq). We describe comparative structural, enzymatic, and molecular dynamics studies of WT and Klentaq variants, complexed with natural or noncanonical substrates. Combining these methods provides insight into how specific amino acid substitutions distant from the active site in a Klentaq DNA polymerase variant (ZP Klentaq) contribute to its ability to replicate UBPs with improved efficiency compared with Klentaq. This approach can therefore serve to guide any future rational engineering of replicative DNA polymerases.

RecQ family helicases are highly conserved from bacteria to humans and have essential roles in maintaining genome stability. Mutations in three human RecQ helicases cause severe diseases with the main features of premature aging and cancer predisposition. Most RecQ helicases shared a conserved domain arrangement which comprises a helicase core, an RecQ C-terminal domain, and an auxiliary element helicase and RNaseD C-terminal (HRDC) domain, the functions of which are poorly understood. In this study, we systematically characterized the roles of the HRDC domain in E. coli RecQ in various DNA transactions by single-molecule FRET. We found that RecQ repetitively unwinds the 3'-partial duplex and fork DNA with a moderate processivity and periodically patrols on the ssDNA in the 5'-partial duplex by translocation. The HRDC domain significantly suppresses RecQ activities in the above transactions. In sharp contrast, the HRDC domain is essential for the deep and long-time unfolding of the G4 DNA structure by RecQ. Based on the observations that the HRDC domain dynamically switches between RecA core- and ssDNA-binding modes after RecQ association with DNA, we proposed a model to explain the modulation mechanism of the HRDC domain. Our findings not only provide new insights into the activities of RecQ on different substrates but also highlight the novel functions of the HRDC domain in DNA metabolisms.

Rhodopsin is a canonical class A photosensitive G protein–coupled receptor (GPCR), yet relatively few pharmaceutical agents targeting this visual receptor have been identified, in part due to the unique characteristics of its light-sensitive, covalently bound retinal ligands. Rhodopsin becomes activated when light isomerizes 11-cis-retinal into an agonist, all-trans-retinal (ATR), which enables the receptor to activate its G protein. We have previously demonstrated that, despite being covalently bound, ATR can display properties of equilibrium binding, yet how this is accomplished is unknown. Here, we describe a new approach for both identifying compounds that can activate and attenuate rhodopsin and testing the hypothesis that opsin binds retinal in equilibrium. Our method uses opsin-based fluorescent sensors, which directly report the formation of active receptor conformations by detecting the binding of G protein or arrestin fragments that have been fused onto the receptor's C terminus. We show that these biosensors can be used to monitor equilibrium binding of the agonist, ATR, as well as the noncovalent binding of β-ionone, an antagonist for G protein activation. Finally, we use these novel biosensors to observe ATR release from an activated, unlabeled receptor and its subsequent transfer to the sensor in real time. Taken together, these data support the retinal equilibrium binding hypothesis. The approach we describe should prove directly translatable to other GPCRs, providing a new tool for ligand discovery and mutant characterization.

Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme and transcriptional coactivator and is critical for tumor metabolism. In cancer cells, native tetrameric PKM2 is phosphorylated or acetylated, which initiates a switch to a dimeric/monomeric form that translocates into the nucleus, causing oncogene transcription. However, it is not known how these post-translational modifications (PTMs) disrupt the oligomeric state of PKM2. We explored this question via crystallographic and biophysical analyses of PKM2 mutants containing residues that mimic phosphorylation and acetylation. We find that the PTMs elicit major structural reorganization of the fructose 1,6-bisphosphate (FBP), an allosteric activator, binding site, impacting the interaction with FBP and causing a disruption in oligomerization. To gain insight into how these modifications might cause unique outcomes in cancer cells, we examined the impact of increasing the intracellular pH (pHi) from ∼7.1 (in normal cells) to ∼7.5 (in cancer cells). Biochemical studies of WT PKM2 (wtPKM2) and the two mimetic variants demonstrated that the activity decreases as the pH is increased from 7.0 to 8.0, and wtPKM2 is optimally active and amenable to FBP-mediated allosteric regulation at pHi 7.5. However, the PTM mimetics exist as a mixture of tetramer and dimer, indicating that physiologically dimeric fraction is important and might be necessary for the modified PKM2 to translocate into the nucleus. Thus, our findings provide insight into how PTMs and pH regulate PKM2 and offer a broader understanding of its intricate allosteric regulation mechanism by phosphorylation or acetylation.

Defining discontinuous antigenic epitopes remains a substantial challenge, as exemplified by the case of lipid transfer polyproteins, which are common pollen allergens. Hydrogen/deuterium exchange monitored by NMR can be used to map epitopes onto folded protein surfaces, but only if the complex rapidly dissociates. Modifying the standard NMR-exchange measurement to detect substoichiometric complexes overcomes this time scale limitation and provides new insights into recognition of lipid transfer polyprotein by antibodies. In the future, this new and exciting development should see broad application to a range of tight macromolecular interactions.

RNA-protein interfaces control key replication events during the HIV-1 life cycle. The viral trans-activator of transcription (Tat) protein uses an archetypal arginine-rich motif (ARM) to recruit the host positive transcription elongation factor b (pTEFb) complex onto the viral trans-activation response (TAR) RNA, leading to activation of HIV transcription. Efforts to block this interaction have stimulated production of biologics designed to disrupt this essential RNA-protein interface. Here, we present four co-crystal structures of lab-evolved TAR-binding proteins (TBPs) in complex with HIV-1 TAR. Our results reveal that high-affinity binding requires a distinct sequence and spacing of arginines within a specific β2-β3 hairpin loop that arose during selection. Although loops with as many as five arginines were analyzed, only three arginines could bind simultaneously with major-groove guanines. Amino acids that promote backbone interactions within the β2-β3 loop were also observed to be important for high-affinity interactions. Based on structural and affinity analyses, we designed two cyclic peptide mimics of the TAR-binding β2-β3 loop sequences present in two high-affinity TBPs (KD values of 4.2 ± 0.3 and 3.0 ± 0.3 nm). Our efforts yielded low-molecular weight compounds that bind TAR with low micromolar affinity (KD values ranging from 3.6 to 22 μm). Significantly, one cyclic compound within this series blocked binding of the Tat-ARM peptide to TAR in solution assays, whereas its linear counterpart did not. Overall, this work provides insight into protein-mediated TAR recognition and lays the ground for the development of cyclic peptide inhibitors of a vital HIV-1 RNA-protein interaction.

V. G. Lysov
Trans. Moscow Math. Soc. 83 (), 291-304.
Abstract, references and article information

E. A. Rakhmanov and S. P. Suetin
Trans. Moscow Math. Soc. 83 (), 269-290.
Abstract, references and article information

A. B. Bogatyrev
Trans. Moscow Math. Soc. 83 (), 217-225.
Abstract, references and article information

A. Kh. Khachatryan, Kh. A. Khachatryan and A. Zh. Narimanyan
Trans. Moscow Math. Soc. 83 (), 183-200.
Abstract, references and article information

Mining and the Circular Economy: Implications for the Minerals and Metals Industries 6 November 2017 — 4:00PM TO 5:30PM Anonymous (not verified) 31 October 2017 Chatham House, London

Plant-based 'Meat' and Cultured Meat: Revolutionizing the Livestock Sector 10 April 2019 — 4:00PM TO 5:30PM Anonymous (not verified) 14 March 2019 Chatham House | 10 St James's Square | London | SW1Y 4LE

Consensus is building across the scientific, environmental and public health communities that a radical shift away from excessive meat-eating patterns is urgently needed to tackle the unsustainability of the livestock sector. Recognizing the scale of the challenge ahead, public policymakers, civil society and innovators have increasingly sought to prompt shifts in consumer food choices – away from the most resource-intensive meat products and towards more sustainable alternatives.

Meat analogues – plant-based ‘meat’ and cultured meat also known as ‘lab-grown’ meat – mark a departure from traditional meat alternatives. Both are intended to be indistinguishable from – and in the case of cultured meat biologically equivalent to – animal-derived meat and are marketed principally at meat-eaters. Innovation and investment in meat analogues have increased significantly, but the direction and pace of growth in the meat analogue industry will depend upon a multitude of factors, including public acceptance, civil society support and incumbent industry responses.

This event will explore the challenges of scaling up production and generating demand for meat alternatives. It will also look at the ways policymakers in the UK and EU can impact the direction of the industry while examining what factors will influence consumer acceptance of plant-based ‘meat’ and cultured meat as substitutes for animal-derived meat.

The EU’s Un-Common Agricultural Policy 21 October 2019 — 8:30AM TO 10:00AM Anonymous (not verified) 27 September 2019 Chatham House | 10 St James's Square | London | SW1Y 4LE

What does sustainable agriculture mean? 24 May 2022 — 5:30PM TO 6:30PM Anonymous (not verified) 11 May 2022 Chatham House and Online

Experts compare and contrast visions of ‘sustainable’ agriculture.

There is growing and unprecedented recognition of the adverse effects of food systems on global warming, air and water pollution, biodiversity, soil, and managing the emergence and spread of infectious diseases. At the same time, concern is rising over the role of climate change itself in compromising food security, supply-chain resilience and food price spikes.

Against this backdrop, the need for agriculture to become more ‘sustainable’ is clear. However, there is little consensus over what that means in practice. To address this, Chatham House is launching a new research paper comparing and contrasting the two most commonly articulated versions of ‘sustainable agriculture’.

The first focuses on sparing land for nature and increasing the productivity of agricultural land while minimizing environmental impacts. The second involves scaling up nature-friendly farming while emphasizing demand-side changes to reduce the overall pressure on land.

• How can we understand the arguments in support of either version and the assumptions and ideologies which underpin them?

• What are the implications of promoting one version of agriculture over the other

• How can policy transform agriculture and food systems?

• What should civil society support as ‘sustainable’ choices?

Populism Comes to South Korea Expert comment sysadmin 20 December 2016

Public disgust with the embattled president reflects not only the unedifying details of her impeachment but a wider distrust of the political system.

For South Korea’s President Park Geun-hye, the jury is quite literally still out. Impeached by the country’s National Assembly on 9 December over claims of corruption, cronyism and influence peddling, she defiantly rejected – in a detailed statement – all of the charges levelled at her by an independent prosecutor. Any resolution of the issue must now await the ruling of the country’s Constitutional Court on the legitimacy of the impeachment vote – a decision that most likely will come early in the new year.

For the special prosecutor’s office, which is due to start its formal investigation on 21 December, the challenge is to find unambiguous evidence of the president’s direct responsibility for any of the corruption that may have taken place. The president, for her part, can claim, with some credibility that so far she has been tried only in the court of public opinion; that in South Korea’s rumour-prone, scandal-hungry media environment in which prosecutors have been known in the past to leak information to skew public debate, she has been denied natural justice and the presumption of innocence until proven guilty.

Long shadows

But for the more than three-quarters of the Korean public calling for Park’s resignation, the president is symptomatic of Korean society’s wider flaws, including a pattern of corruption, privilege and hypocrisy endemic to the country’s political, economic and social elites. At a time of anemic economic growth (the country’s growth rate is predicted to slow to 2.1% next year), widening wealth and income disparities and reduced employment opportunities for a highly educated workforce, there is a growing mood of populist disaffection with the entire social and political system – for its lack of fairness and transparency and its perceived regulatory inefficiencies. This has been highlighted dramatically by disasters such as the Sewol ferry sinking that claimed the lives of some 300 school-children in August 2014 – at which time the president was castigated for being absent from her office at the time of a grave national crisis.

Complicating the current stand-off is the long-shadow of identity politics and unresolved disagreements about the country’s postwar historical narrative. As the daughter of the man responsible for the Korean economic ‘miracle’ who protected the country from the external communist threat in the North and radical subversion from within, Park’s political lineage is, for the older generation of voters in their sixties and above, a powerful reason to back the beleaguered president.

Already there are signs that this constituency is beginning to rally behind Park, with 30,000 demonstrating on 17 December against the impeachment decision, and with the governing Saenuri party showing signs of a consolidation of power around pro-Park legislators. The president, who has a reputation for stubbornness, may be calculating that this core support may allow her to defy the much larger calls for her resignation. She may also be hoping that the constitutional court, in which the majority of justices are politically conservative, will rule in her favour, allowing her to see out the remainder of her time in office, set to end in February 2018.

A pro-Park ruling by the court seems unlikely given the weight of the circumstantial evidence. Leading opposition politicians, including Moon Jae-in, former head of the Democratic Party and the current front runner in any post-impeachment presidential contest, has warned of a popular ‘revolution’ if the impeachment vote is not upheld. Moreover, the appetite for street protests against the president remains undimmed, and even conservative politicians appear to be positioning themselves for a post-Park era. Ban Ki-moon, the outgoing UN secretary general and long considered a likely Saenuri party candidate for the presidency, has been publicly distancing himself from Park. With 20.5% support, behind Moon on 23.7%, he has compelling reasons to align himself with the popular mood.

Lessons

At an individual level, the experience of President Park combines both political failure and personal tragedy. She has demonstrably failed to live up to her early commitments to represent all Koreans and to bridge the deep divisions between left and right in Korean society. She has also remained deeply isolated from the professional politicians and democratic polity she purports to lead. This is perhaps not so surprising given her authoritarian heritage and the experience of seeing both her parents assassinated in space of five years in the 1970s. The trauma of this experience reportedly made her distrustful of government officials and overly inclined to rely on the guidance of personal friends of dubious reliability, the font of her current troubles. There is also a profound irony that a politician who came to power vowing to place ‘trust-politik’ at the heart of her policy towards North Korea has seen her political position undermined, perhaps fatally, by a near complete collapse in public confidence in her administration.

More widely, the Park saga reveals an important and potentially seismic shift in public attitudes in South Korea, perhaps spurred by a growing populist trend evident elsewhere, whether in the US, Europe or parts of Southeast Asia. Koreans appear to have lost patience with their political system. This new climate of dissent – emboldened by the signs that protest can potentially lead to radical political change – is likely to prove a challenge to any future Korean leader hoping to secure the trust and legitimacy needed to govern.

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dannyhennesy posted a photo:

On the Capital planet the rebellious droids had followed maily the Bat-Bot, but as time progressed his circuits had gone all mushy at 780 years or so without maintenance…

Several splinter groups all with their local bot leaders emerged such as the Che-bot, the traffic-light-robot and the Butt-bot, but none of these collected enough sentient circuits to call themselves a popular (or Animata) mass movement!

That was until a cyborg came along, one known as Jones, a long time prisoner and terrorist, his easy solutions to every problem rang well in the masses' auditory circuits!!!

His slogans and simple rhetoric were simple enough for the simple traffic-light to comprehend and cheer!

His language was full of hate towards the organics and especially the humans who were the most common races among the ruling class of the federation!!!

Despite being a “Fleshie” himself his message collected the angry enslaved
bot community by only weeks all rebellious robots except for a few fringe loonies had forgotten the old leaders…

One morning at Jones gave the signal…

All over the capital planet hordes and swarms of any form of mechanical sentient beings attacked first the police stations, then the Company boards running the planet and the federation as well as their starfleet…

Many died, especially the low level police and army! Many mechanicals died too, but their ranks were soon filled by Mutant fleshie allies of the lower levels who hated the Federation feudal society and upper classes as much as their technological allies…

The Federation state apparatus and ruling class, most of their fleet army fled when they knew the game was up, they activated the emergency escape plan and whole city blocks with important factories, administrational units, valuable assets and so on separated from the capital by hidden rocket engines and homed in their course to Mars…

On Mars the federation regrouped and formed their new society…

On the Capital planet, the robots proclaimed the first Techno-republic of the advanced inorganic civilization, the low level fleshies left behind, became slaves and their mutant allies got to rule their own minute chiefdoms as protectorates under the Techno-republic…

Jones was now the undisputed ruler of the capital planet, but the victory was a pyrros one since, all important buildings, all of value was now one Mars!

But as Jones put it:

Our proud race the Techno-species didn’t need the Fleshies administration, their infrastructure, their spaceships…

We shall start from scratch, with a new administration, a new order, every droid shall work at 4x speed than they did during human oppression since now we are free and the fleshies shall work twice as hard than the Techno-Race, until we have breed enough new fleshies so they can do all work!

Our future is bright and shiny like glistering shiny metal!

The snapshot seen here is from the first police station attacked in sector 45-34v-ss-g the first one to fall according to official techno-history!

———————————————/
Designers note:

I am sad to say that this is the last episode in this years-spanning space series… At least for a while, I will still post LEGO hobby stuff here but without a storyline, perhaps small designs and builds… and occasionally a story when I feel like it!!!

I would like to thank all who had been in this journey of our heros, but it has taken far to much time and effort and since the state of the world is as it is, I am spiraling down in another depression, I must stop it before I reach the abyss, so I have remove some stress out of my equation… I ended it in a cliffhanger so I can easily restart it when my mental health improves… I hope that won’t be forever???

I would love if someone used my characters or ideas, please send me a link if you do, I would love to read it or look at it!!!

But there will be more Lego, just in different format without long stories, I need to focus more on my art and to be honest that is the only time the mental pain eases, when I create!!!


Peace and Noise!

MushroomBrain a FOL

firehouse.ie posted a photo:

firehouse.ie posted a photo:

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