review Review: The Cultural Revolution still haunts China By www.chathamhouse.org Published On :: Mon, 30 Jan 2023 13:01:21 +0000 Review: The Cultural Revolution still haunts China The World Today mhiggins.drupal 30 January 2023 Tania Branigan’s searching ‘Red Memory’ reveals the costs to Chinese society of not addressing that upheaval’s lingering injustices, writes Nathan Law. Red Memory: Living, Remembering and Forgetting China’s Cultural RevolutionTania Branigan, Faber, £20 The Cultural Revolution, a decade-long socio-political upheaval initiated by Chairman Mao Zedong in 1966, caused as many as two million deaths and reshaped China. Under the influence of Mao’s personality cult, an entire nation was mobilized to purge the ‘reactionary elements’ in society and the Chinese Communist Party through public denunciation and demolition of traditional heritages. Children turned on their parents; pupils murdered their teachers, and those who survived the summary public trials were often banished – as a young Xi Jinping himself was, living in a cave for seven years, after his father fell from favour. Impossible moral choices In her engaging and sensitive narrative account of the revolution’s upheaval and its consequences, Tania Branigan, the Guardian’s China correspondent between 2008 and 2015, speaks to some of those who survived those terrible years, considers their impossible moral choices and explores the far-reaching legacy of the revolution in present-day China. Mao urged the party to cleanse itself of its ‘class enemies’: ‘capitalists’ such as landowners and shopkeepers, but also artists, farmers and university professors. Often their family members were tainted by association and persecuted. Branigan captures the awful sense of intimate betrayal and tragedy nowhere more than in the testimony of Zhang Hongbing, a lawyer turned zealous Red Guard. What I did to my mother was worse even than to an animal Zhang Hongbing, former Red Guard Zhang denounced his mother, a hospital worker, as a ‘counter-revolutionary’ because her father owned land. She was eventually executed but not before her son struck her twice during her arrest to show his party loyalty. ‘What I did to my mother was worse even than to an animal,’ the remorseful Zhang tells Branigan. Zhang points out that his actions were far from uncommon: ‘The whole country was doing it.’ This unreconciled sense of betrayal and fear still blights China: ‘Our society is ethically hollow. If we trace these problems to their roots, we are likely to find them in the Cultural Revolution,’ one survivor is quoted as writing. Branigan encapsulates the difficulties around reconciliation and remembering in the story of Song Binbin. As a schoolgirl in 1966, she and two classmates were the first to pin up a poster attacking teachers for urging students to focus on their work instead of the revolution. Song’s classmates then beat the school vice principal Bian Zhongyun to death in the playground. The case was never properly investigated, and the death was dismissed as an accident. The pain of remembering In 2014, Song apologized publicly for the poster and expressed a sense of guilt for not intervening on Bian’s behalf. But Bian’s widower rejected the apology. Song did not speak to Branigan herself, instead allowing her friends to speak in her defence. ‘They had spoken of truth and reconciliation, but not once of justice. Every remark brought them towards closure, not accountability,’ Branigan writes. The inability to come to terms with the past pervades the book, most of whose interviewees express feelings of resentment, fear and shame about the Cultural Revolution. I sensed the same emotions when, as a boy, I talked to a neighbour in Hong Kong who was then in his 70s. He escaped from China in the late 1960s due to political and economic strains. He simply nodded and fell silent when I asked him to elaborate. The Cultural Revolution warrants no more than a few paragraphs in official textbooks As Branigan writes: ‘Most Cultural Revolution survivors had learnt to bend with the will of the time; not only to do as they were told but to imply that doing so was their own idea. It was better – safer – to stay silent or lie.’ This collective trauma is exacerbated by official unwillingness to address the past. The Cultural Revolution warrants no more than a few paragraphs in official textbooks with no mention of the suffering it unleashed. Documents of the period that might tarnish the CCP remain unavailable; any attempts to interrogate the Cultural Revolution are condemned as ‘historical nihilism’ by the party. Full Article
review Independent Thinking: UK Integrated Review, Georgia protests By www.chathamhouse.org Published On :: Thu, 16 Mar 2023 19:26:37 +0000 Independent Thinking: UK Integrated Review, Georgia protests Audio NCapeling 16 March 2023 Episode 19 of our weekly podcast examines the AUKUS deal, UK defence priorities, and the state of Georgia’s democracy following anti-government protests. The UK and Australia will soon be building nuclear submarines together, but is the UK’s tilt to the Indo-Pacific sustainable? Two years on from the last Integrated Review, has the UK finally clarified its foreign policy priorities on Russia, China, and on defence? And is the money there to do it all? Also on the show, the panel discusses Georgia following recent anti-government protests in Tbilisi. Following the Rose revolution in 2003, Georgia seemed to be on a path towards closer ties with NATO and the European Union (EU). But the country’s government has recently moved closer to Russia and Vladimir Putin. What is the state of Georgia’s democracy and where is the country heading? Joining Bronwen Maddox from Chatham House is Creon Butler, director of our Global Economy and Finance programme, Professor Andrew Dorman, editor of the International Affairs journal, and Alice Billon-Galland, research fellow in our Europe Programme. They are joined by Natia Seskuria, associate fellow with the Royal United Services Institute (RUSI) and Arthur Snell, former diplomat and host of the podcast Doomsday Watch. About Independent Thinking A weekly podcast hosted by Chatham House director Bronwen Maddox, in conversation with leading policymakers, journalists, and Chatham House experts providing insight on the latest international issues. Full Article
review Thematic review series: Lipid Posttranslational Modifications. Protein palmitoylation by a family of DHHC protein S-acyltransferases By www.jlr.org Published On :: 2006-06-01 David A. MitchellJun 1, 2006; 47:1118-1127Thematic Reviews Full Article
review Thematic Review Series: Glycerolipids. DGAT enzymes and triacylglycerol biosynthesis By www.jlr.org Published On :: 2008-11-01 Chi-Liang Eric YenNov 1, 2008; 49:2283-2301Thematic Reviews Full Article
review Thematic review series: The Pathogenesis of Atherosclerosis The oxidation hypothesis of atherogenesis: the role of oxidized phospholipids and HDL By www.jlr.org Published On :: 2004-06-01 Mohamad NavabJun 1, 2004; 45:993-1007Thematic Reviews Full Article
review Fish oils and plasma lipid and lipoprotein metabolism in humans: a critical review By www.jlr.org Published On :: 1989-06-01 WS HarrisJun 1, 1989; 30:785-807Reviews Full Article
review Thematic review series: Brain Lipids. Cholesterol metabolism in the central nervous system during early development and in the mature animal By www.jlr.org Published On :: 2004-08-01 John M. DietschyAug 1, 2004; 45:1375-1397Thematic Reviews Full Article
review Thematic review series: The Pathogenesis of Atherosclerosis. Effects of infection and inflammation on lipid and lipoprotein metabolism mechanisms and consequences to the host By www.jlr.org Published On :: 2004-07-01 Weerapan KhovidhunkitJul 1, 2004; 45:1169-1196Thematic Reviews Full Article
review Thematic review series: Adipocyte Biology. The perilipin family of structural lipid droplet proteins: stabilization of lipid droplets and control of lipolysis By www.jlr.org Published On :: 2007-12-01 Dawn L. BrasaemleDec 1, 2007; 48:2547-2559Thematic Reviews Full Article
review The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function By www.jlr.org Published On :: 1992-02-01 JP SegrestFeb 1, 1992; 33:141-166Reviews Full Article
review Review: Decolonization and its discontents By www.chathamhouse.org Published On :: Mon, 01 Aug 2022 08:27:03 +0000 Review: Decolonization and its discontents The World Today mhiggins.drupal 1 August 2022 Jenna Marshall on a lively if flawed argument to find a way forward in a debate that has descended ‘into acrimony’. Against Decolonization: Taking African Agency SeriouslyOlufemi Taiwo, Hurst, £14.99 Decolonization was once heralded as a moment of potential and possibility for the formerly imperial world to chart a new way forward no longer tied to the apparatus of empire. It marked a period of transition to nation states – and an expansion of a rights-based international community that would dispense with the morally bankrupt regime of racism, dispossession and subjugation that characterized colonialism. The descent of the decolonization debate Half a century later, the debate surrounding decolonization has descended into acrimony. Some factions cast the issue of decolonization as a sustained attack on British and western culture writ large; other disparate voices coalesce around related social justice issues such as inequality, climate change and education. Decolonization has become ubiquitous in the public domain – and its ubiquity is the problem Decolonization has become ubiquitous in the public domain – and its ubiquity is the problem. In Against Decolonization, Olufemi Taiwo renounces a concept he conceives as having been emptied of serious study and analytical purchase; one incapable of addressing the complexities of modern global politics and more importantly, Africa’s place in it. Although the book attacks the inexhaustible ways in which the ‘trope of decolonization’ has been deployed, Taiwo is less bothered by the purported failures of scholars he deems ‘decolonizers’ and focuses his attention instead on the political landscape of African countries, past and present. Central to the book’s argument are two distinct scholarly strands on decolonization. The first, legal focus, centres on the political and economic forces of state-building. The second essays an ‘ideology’ of decolonization that rests on ‘forcing an ex-colony to forswear on pain of being forever under the yoke of colonization any and every cultural, political, intellectual, social and linguistic artefact, idea, process, institution and practice that retains even the slightest whiff of the colonial past’. Whether one should characterize the latter as simply a field of study or a potential set of policy arrangements remains unclear – yet what is certain is that it is too nebulous, too elastic, too open-ended to offer any substantive model or mechanism to understand postcolonial Africa. Correcting Eurocentric narcissism The decolonization research agenda in Africa came to prominence during the Cold War period of national liberation struggles. The intellectual project that followed centred on dismantling Eurocentrism as colonial subjugation through its promotion of the West as the crucible of legitimate and scientific knowledge. Since then, scholars have argued that decolonization itself has become compromised by its enduringly Eurocentric gaze at the expense of the agency of African thinkers, creatives and statesmen and women. Taiwo seeks to correct this narcissism – and the omissions left in its wake – by introducing lesser-known Africans and pan-African scholars and cultural figures. These voices, he hopes, will illuminate issues often ignored by ‘decolonizers’ and spark a ‘renewed interest in an appreciation of the many different ways in which African thinkers have responded to the colonial experience’. The decolonization of language Taiwo challenges the decolonization of language as an oversold promise. Romanticizing an imagined, pristine African pre-colonial past, he says, ultimately leads to nativism and atavism. As a case in point, Taiwo highlights bureaucratic instances of ‘language policy planning’ to deploy African languages in places such as Niger, Mali, Cameroon, Senegal and Nigeria that were hindered by multilingualism, education and high rates of illiteracy. The abstract language of decolonization allows western scholars to engage with the concept without considering their own complicity in upholding systems of exclusion The author goes on to confront the abstract language of decolonization, which, he says, allows western scholars to unproblematically engage with the concept without any serious consideration of their own complicity in upholding systems of exclusion. It entrenches their own institutional power within the academy, amplifies their perspectives at the expense of others, and limits the possibilities for understanding the problems of world politics with deleterious effects on policy. It is a serious claim, but there are issues to be addressed: Taiwo assumes there is coherence among scholars of decolonization, which is not the case. When Taiwo approaches how to foster political systems that cater to the needs of their citizens he dismantles the binary of ‘West as modern’ v ‘Africa as traditional’. Chieftaincies as traditional African governance, he points out, were the product of colonial anthropology, not Africans themselves. From the Fanti Confederation of 1871 to the Egba United Government in what is now Nigeria, Taiwo demonstrates that there has been a sustained tradition towards demands for democratic values. As he concedes an intellectual neglect of African philosophers that underlies the design and operations of Africa’s political institutions, Taiwo’s initial dismissal of the significance of cultural decolonization deserves another look. How should political and economic drives toward self-determination be advanced in the absence of knowledge shaped and mediated through African lived experiences? In this respect, the tale of two decolonizations – the legal alongside the ideological – suggest an unhelpful, if not false, binary. The problem of reconciling modernity and colonialism What resonates throughout the book is the idea that Europe cannot profess to hold an exclusive intellectual claim to modernity. Its universal aspirations are open to all of humanity, allowing those who have historically been marginalized to be worldmakers. The idea that modernity and colonialism are irreconcilable is problematic. For instance, Taiwo argues that the curtailment of capitalism in Africa by restricting the growth of the middle classes while limiting competition between African capitalists and the metropole is the consequence of colonialism. Capitalism not only requires inequality for it to function but that race – as a mechanism for producing ‘difference’ – enshrines it Yet the celebrated cultural anthropologist Sidney Mintz established an understanding that the matter for debate is not whether non-westerners were part of the modern system, but how and to what degree they were included and able to actualise its ideals. The emerging capitalist world economy needed non-western lands and labour, and so they were conscripted to this end. Recent abolitionist and black radical scholarship has built on this argument to maintain that capitalism not only requires inequality for it to function but that race – as a mechanism for producing ‘difference’ – enshrines it. Acknowledging the unacknowledged In the end, Taiwo communicates a palpable frustration at the state of academic discourses on contemporary Africa under the guise of emancipatory and radical scholarship. He offers an alternative approach whereby African students might rid themselves of a faddism that is ‘at best unsatisfactory’ and at worst produces ‘confusion, obscurantism, if not outright distortion and falsification’. Yet out of this irritation, Taiwo’s greatest contribution in Against Decolonization might be to urge an acknowledgement of how and to what degree decolonization has become subdued and its political possibilities curtailed. He ultimately urges us to reconsider the purpose of the decolonization academic movement as an ethics to abide by rather than a social theory of the postcolonial world. This requires those ‘decolonizers’ on whose careers the term is built to adopt greater intellectual humility – to resist the posture of the anarchist radical scholar armed for the ‘good fight’. Instead, they should apply a scholarly curiosity to genuinely engage with those already on the battlefield, so to speak; those ‘doing the work’ in practice, but who have been unacknowledged until now. Full Article
review Review: the rise of Africa’s superwomen By www.chathamhouse.org Published On :: Mon, 01 Aug 2022 09:53:38 +0000 Review: the rise of Africa’s superwomen The World Today mhiggins.drupal 1 August 2022 From foster care in England to colonialism’s legacy in Zimbabwe, this set of essays on race, feminism and identity is searingly honest, says Masiyaleti Mbewe. Black and FemaleTsitsi Dangarembga, Faber, £9.99 The 1988 novel Nervous Conditions by the Zimbabwean author Tsitsi Dangarembga is considered one of Africa’s finest literary exports. It won the Commonwealth Writers’ Prize and alongside The Book of Not (2006) and This Mournable Body (2018), shortlisted for the 2020 Booker Prize, forms a trilogy of semi-autobiographical novels that grapple with the gendered colonial oppression of young black girls and women from Southern Rhodesia through to Zimbabwe. In Black and Female, Dangarembga continues the interrogation of these intersections in an unflinchingly honest and personal, if occasionally dense, collection of essays. Along the way, she examines the sheer magnitude of colonialism’s effects on African people, and how they ripple through her early childhood in England and her formative years as a writer, filmmaker and feminist activist in post-independence Zimbabwe. ‘Writing While Black and Female’ In 1961 Dangarembga’s parents relocated from Southern Rhodesia to the UK. While they worked and studied in London, they put their two-year-old daughter, her older brother and, later, her younger sister into private foster care in Dover, Kent (as many Africans did – a fact that was new to me). The first essay, ‘Writing While Black and Female’, takes a painful look at the four years she spent with her foster parents, Mummy-Gran and Daddy Henry. Blackness, she learned in those years, was a consequence of her non-whiteness. So Dangarembga writes of the momentary elation she felt when a stranger addressed her as a ‘lovely little piccaninny’, giving her ‘a category I could wield against the void of no longer being’. To cope with this sort of racialization and her abandonment, the young Dangarembga turned to disassociation and self-harm. Blackness is a condition imposed on me, rather than being an experienced identity Tsitsi Dangarembga As she writes: ‘Blackness is a condition imposed on me, rather than being an experienced identity.’ Instead of ‘black’ people, therefore, Dangarembga prefers the term ‘highly melanated people’. It is a resonant phrase, highlighting the inherently ridiculous nature of racism. Dangarembga’s ‘Africanness’ shifts into focus upon her return to Rhodesia in 1965. At first, other children refused to play with her and her siblings, calling them ‘varungu’ (white people). As she describes it: ‘The dance of my identities … became frenetic’. In ‘Black, Female and the Superwoman Black Feminist’, the second essay, Dangarembga is adamant about the urgent necessity of a black feminist practice that is centred on action to provide real, material change. Along the way, she makes a distinction – a slightly uneasy one to my mind – between the patriarchy that western colonization imposed, based on private ownership, and the patriarchy of pre-colonial African society with its foundations in kinship that devolved power to an extent. Dangarembga’s discussion of a more accommodating, pre-colonial patriarchy is nuanced, but it jars a little ‘Hence women could and did become rulers and warriors, and royal spirit mediums called mhondoro,’ Dangarembga writes approvingly. She is making a nuanced point; but the idea of a more accommodating sort of patriarchy jars a little nonetheless. While independence may have arrived for Zimbabwe more than 40 years ago, Dangarembga argues strongly that the subjugation of women and feminists at the hands of the ruling Zanu-PF government continues as an extension of colonial rule. Indeed, beyond Zimbabwe, black feminists remain ‘a small, often embattled group’ across Africa, believes Dangarembga. Pointedly, she criticizes global feminism’s greater focus on optics than on practical activism As a young black feminist who is part of this ‘small, embattled group’, I should say we have been able to foster large communities digitally and otherwise to work around the hostility we are often faced with. Despite internet shutdowns and restrictions, we resist – an act Dangarembga encourages. Resistance, she says, starts with establishing community despite these difficulties. At the nucleus of Dangarembga’s argument is the ‘superwoman’ of the essay’s title, the African woman who doesn’t require external factors to be inspired to action but who continuously draws on what Dangarembga calls ‘internal agency’ that derives from ‘an unrelenting fight for survival and dignity’. Pointedly, she criticizes global feminism’s greater focus on optics than activism in the practical sense. One only has to observe the performative allyship and ‘Instagram activism’ rampant on the internet today to see her point. The complexities of decolonization In the final essay, ‘Decolonization as Revolutionary Imagining’, Dangarembga turns her gaze upon the ‘highly stratified’ European societies that outsourced their violent inequality to their empires and ‘the work of decolonization’. However, decolonial discourse is complex, and it is here that the writing occasionally gets bogged down. Fewer recommendations with more elaboration perhaps would have helped. She herself acknowledges the difficulties of decolonization. Centuries of the Enlightenment and its logic of ‘racism, slavery, genocide and colonization’ are hard to uproot ‘whatever one’s melanin concentration’, she writes. Nevertheless, Dangarembga concludes with the radical determination to dismantle that is evident throughout this searing yet hopeful collection: ‘The trajectory of current and future generations depends on that uprooting.’ Full Article
review A review of phosphatidate phosphatase assays By www.jlr.org Published On :: 2020-12-01 Prabuddha DeyDec 1, 2020; 61:1556-1564Reviews Full Article
review Problem Notes for SAS®9 - 66524: SAS Visual Data Builder uses the wrong SAS Application Server for previewing and scheduling By Published On :: Mon, 31 Aug 2020 12:14:44 EST If you have configured more than one SAS Application Server, then SAS Visual Data Builder might unexpectedly use the wrong application server when you preview or schedule queries. This problem occurs even though you h Full Article VISANLYTBNDL+SAS+Visual+Analytics
review WITHDRAWN: The Fundamental And Pathological Importance Of Oxysterol Binding Protein And Its Related Proteins [Thematic Reviews] By www.jlr.org Published On :: 2018-10-15T08:42:37-07:00 This article has been withdrawn by the authors as part of this review overlapped with the contents of Pietrangelo A and Ridgway ND. 2018. Cellular and Molecular Life Sciences. 75; 3079-98. Full Article
review Fatty acid oxidation and photoreceptor metabolic needs [Thematic Reviews] By www.jlr.org Published On :: 2020-02-24T12:30:36-08:00 Photoreceptors have high energy-demands and a high density of mitochondria that produce adenosine triphosphate (ATP) through oxidative phosphorylation (OXPHOS) of fuel substrates. Although glucose is the major fuel for central nervous system (CNS) brain neurons, in photoreceptors (also CNS), most glucose is not metabolized through OXPHOS but is instead metabolized into lactate by aerobic glycolysis. The major fuel sources for photoreceptor mitochondria remained unclear for almost six decades. Similar to other tissues (like heart and skeletal muscle) with high metabolic rates, photoreceptors were recently found to metabolize fatty acids (palmitate) through OXPHOS. Disruption of lipid entry into photoreceptors leads to extracellular lipid accumulation, suppressed glucose transporter expression, and a duel lipid/glucose fuel shortage. Modulation of lipid metabolism helps restore photoreceptor function. However, further elucidation of the types of lipids used as retinal energy sources, the metabolic interaction with other fuel pathways, as well as the crosstalk among retinal cells to provide energy to photoreceptors is not yet known. In this review, we will focus on the current understanding of photoreceptor energy demand and sources, and potential future investigations of photoreceptor metabolism. Full Article
review Bisretinoid phospholipid and vitamin A aldehyde: Shining a light [Thematic Reviews] By www.jlr.org Published On :: 2020-05-05T13:30:26-07:00 Vitamin A aldehyde covalently bound to opsin protein is embedded in a phospholipid-rich membrane that supports photon absorption and phototransduction in photoreceptor cell outer segments. Following absorption of a photon, the 11-cis-retinal chromophore of visual pigment in photoreceptor cells isomerizes to all-trans-retinal. To maintain photosensitivity 11-cis-retinal must be replaced. At the same time, however, all-trans-retinal has to be handled so as to prevent nonspecific aldehyde activity. Some molecules of retinaldehyde upon release from opsin are efficiently reduced to retinol. Other molecules are released into the lipid phase of the disc membrane where they form a conjugate (N-retinylidene-PE, NRPE) through a Schiff base linkage with phosphatidylethanolamine (PE). The reversible formation of NRPE serves as a transient sink for retinaldehyde that is intended to return retinaldehyde to the visual cycle. However, if instead of hydrolyzing to PE and retinaldehyde, NRPE reacts with a second molecule of retinaldehyde a synthetic pathway is initiated that leads to the formation of multiple species of unwanted bisretinoid fluorophores. We report on recently identified members of the bisretinoid family some of which differ with respect to the acyl chains associated with the glycerol backbone. We discuss processing of the lipid moieties of these fluorophores in lysosomes of retinal pigment epithelial (RPE) cells, their fluorescence characters and new findings related to light and iron-associated oxidation of bisretinoids. Full Article
review Retinoids in the visual cycle: Role of the retinal G protein-coupled receptor [Thematic Reviews] By www.jlr.org Published On :: 2020-06-03T16:30:29-07:00 Driven by the energy of a photon, the visual pigments in rod and cone photoreceptor cells isomerize 11-cis-retinal to the all-trans configuration. This photochemical reaction initiates the signal transduction pathway that eventually leads to the transmission of a visual signal to the brain and leaves the opsins insensitive to further light stimulation. For the eye to restore light sensitivity, opsins require recharging with 11-cis-retinal. This trans–cis back conversion is achieved through a series of enzymatic reactions composing the retinoid (visual) cycle. Although it is evident that the classical retinoid cycle is critical for vision, the existence of an adjunct pathway for 11-cis-retinal regeneration has been debated for many years. Retinal pigment epithelium (RPE)–retinal G protein-coupled receptor (RGR) has been identified previously as a mammalian retinaldehyde photoisomerase homologous to retinochrome found in invertebrates. Using pharmacological, genetic, and biochemical approaches, researchers have now established the physiological relevance of the RGR in 11-cis-retinal regeneration. The photoisomerase activity of RGR in the RPE and Müller glia explains how the eye can remain responsive in daylight. In this review, we will focus on retinoid metabolism in the eye and visual chromophore regeneration mediated by RGR. Full Article
review Signaling roles of phosphoinositides in the retina [Thematic Reviews] By www.jlr.org Published On :: 2020-06-15T14:33:05-07:00 The field of phosphoinositide signaling has expanded significantly in recent years. Phosphoinositides (PIs) are universal signaling molecules that directly interact with membrane proteins or with cytosolic proteins containing domains that directly bind phosphoinositides and are recruited to cell membranes. Through the activities of PI kinases and PI phosphatases, seven distinct phosphoinositide lipid molecules are formed from the parent molecule phosphatidylinositol. PI signals regulate a wide range of cellular functions, including cytoskeletal assembly, membrane binding and fusion, ciliogenesis, vesicular transport, and signal transduction. Given the many excellent reviews on phosphoinositide kinases, phosphoinositide phosphatases, and PIs in general, in this review, we discuss recent studies and advances in PI lipid signaling in the retina. We specifically focus on PI lipids from vertebrate (e.g. bovine, rat, mice, toad, and zebrafish) and invertebrate (e.g. drosophila, horseshoe crab, and squid) retinas. We also discuss the importance of PIs revealed from animal models and human diseases, and methods to study PI levels both in vitro and in vivo. We propose that future studies should investigate the function and mechanism of activation of PI-modifying enzymes/phosphatases and further unravel PI regulation and function in the different cell types of the retina. Full Article
review Lipid Conformational Order and the Etiology of Cataract and Dry Eye [Thematic Reviews] By www.jlr.org Published On :: 2020-06-18T14:30:29-07:00 Lens and tear film lipids are as unique as the systems they reside in. The major lipid of the human lens is dihydrosphingomylein, found in quantity only in the lens. The lens contains a cholesterol to phospholipid molar ratio as high as 10:1, more than anywhere in the body. Lens lipids contribute to maintaining lens clarity, and alterations in lens lipid composition due to age are likely to contribute to cataract. Lens lipid composition reflects adaptations to the unique characteristics of the lens: no turnover of lens lipids or proteins; the lowest amount of oxygen than any other tissue and contains almost no intracellular organelles. The tear film lipid layer (TFLL) is also unique. The TFLL is a thin, 100 nm layer of lipid on the surface of tears covering the cornea that contributes to tear film stability. The major lipids of the TFLL are wax esters and cholesterol esters that are not found in the lens. The hydrocarbon chains associated with the esters are longer than those found anywhere in the body, as long as 32 carbons, and many are branched. Changes in the composition and structure of the 30,000 different moieties of TFLL contribute to the instability of tears. The focus of the current review is how spectroscopy has been used to elucidate the relationships between lipid composition, conformational order and function and the etiology of cataract and dry eye. Full Article
review FH through the Retrospectoscope [Thematic Reviews] By www.jlr.org Published On :: 2020-07-10T14:36:31-07:00 AbstractAfter training as a gastroenterologist in the UK the author became interested in lipidology while he was a research fellow in the USA and switched careers after returning home. Together with Nick Myant he introduced the use of plasma exchange to treat FH homozygotes and undertook non-steady state studies of LDL kinetics, which showed that the fractional catabolic rate of LDL remained constant irrespective of pool size. Subsequent steady-state turnover studies showed that FH homozygotes had an almost complete lack of receptor-mediated LDL catabolism, providing in vivo confirmation of the Nobel Prize-winning discovery by Goldstein and Brown that LDL receptor dysfunction was the cause of FH. Further investigation of metabolic defects in FH revealed that a significant proportion of LDL in homozygotes and heterozygotes was produced directly via a VLDL-independent pathway.Management of heterozygous FH has been greatly facilitated by statins and PCSK9 inhibitors but remains dependent upon lipoprotein apheresis in homozygotes. In a recent analysis of a large cohort treated with a combination of lipid-lowering measures survival was markedly enhanced in homozygotes in the lowest quartile of on-treatment serum cholesterol. Emerging therapies could further improve the prognosis of homozygous FH whereas in heterozygotes the current need is better detection. Full Article
review The emerging roles of the macular pigment carotenoids throughout the lifespan and in prenatal supplementation [Thematic Reviews] By www.jlr.org Published On :: 2020-07-24T07:33:25-07:00 Since the publication of the Age-Related Eye Disease Study (AREDS2) in 2013, the macular pigment carotenoids lutein and zeaxanthin have become well known to both the eye care community and the public. It is a fascinating aspect of evolution that primates have repurposed photoprotective pigments and binding proteins from plants and insects to protect and enhance visual acuity. Moreover, utilization of these plant-derived nutrients has been widely embraced for preventing vision loss from age-related macular degeneration (AMD). More recently, there has been growing awareness that these nutrients can also play a role in improving visual performance in adults. On the other hand, the potential benefits of lutein and zeaxanthin supplementation at very young ages have been underappreciated. In this review, we examine the biochemical mechanisms and supportive data for lutein and zeaxanthin supplementation throughout the lifespan, with particular emphasis on prenatal supplementation. We propose that prenatal nutritional recommendations may aim at improving maternal and infant carotenoid status. Prenatal supplementation with lutein and zeaxanthin might enhance infant visual development and performance and may even prevent retinopathy of prematurity, possibilities that should be examined in future clinical studies. Full Article
review Docosanoid signaling modulates corneal nerve regeneration: effect on tear secretion, wound healing, and neuropathic pain [Thematic Reviews] By www.jlr.org Published On :: 2020-08-11T12:36:10-07:00 The cornea is densely innervated, mainly by sensory nerves of the ophthalmic branch of the trigeminal ganglia (TG). These nerves are important to maintain corneal homeostasis, and nerve damage can lead to a decrease in wound healing, an increase in corneal ulceration and dry eye disease (DED), and neuropathic pain. Pathologies, such as diabetes, aging, viral and bacterial infection, as well as prolonged use of contact lenses and surgeries to correct vision can produce nerve damage. There are no effective therapies to alleviate DED (a multifunctional disease) and several clinical trials using -3 supplementation show unclear and sometimes negative results. Using animal models of corneal nerve damage, we show that treating corneas with pigment epithelium-derived factor (PEDF) plus docosahexaenoic acid (DHA) increases nerve regeneration, wound healing, and tear secretion. The mechanism involves the activation of a calcium-independent phospholipase A2 (iPLA2) that releases the incorporated DHA from phospholipids and enhances the synthesis of docosanoids neuroprotectin D1 (NPD1) and a new resolvin stereoisomer RvD6i. NPD1 stimulates the synthesis of brain-derived neurotrophic factor (BDNF), nerve growth factor (NGF), and of semaphorin 7A (Sema7A). RvD6i treatment of injured corneas modulates gene expression in the TG resulting in enhanced neurogenesis; decreased neuropathic pain and increased sensitivity. Taken together, these results represent a promising therapeutic option to re-establish the homeostasis of the cornea. Full Article
review Sphingolipids as Critical Players in Retinal Physiology and Pathology [Thematic Reviews] By www.jlr.org Published On :: 2020-09-18T07:36:30-07:00 Sphingolipids have emerged as bioactive lipids involved in the regulation of many physiological and pathological processes. In the retina, they have been established to participate in numerous processes, such as neuronal survival and death, proliferation and migration of neuronal and vascular cells, inflammation, and neovascularization. Dysregulation of sphingolipids is, therefore, crucial in the onset and progression of retinal diseases. This review examines the involvement of sphingolipids in retinal physiology and diseases. Ceramide (Cer) emerges as a common mediator of inflammation and death of neuronal and retinal pigment epithelium cells in animal models of retinopathies such as glaucoma, age-related macular degeneration (AMD), and retinitis pigmentosa. Sphingosine-1-phosphate (S1P) has opposite roles, preventing photoreceptor and ganglion cell degeneration but also promoting inflammation, fibrosis, and neovascularization in AMD, glaucoma, and pro-fibrotic disorders. Alterations in Cer, S1P, and ceramide-1-phosphate may also contribute to uveitis. Notably, use of inhibitors that either prevent Cer increase or modulate S1P signaling, such as Myriocin, desipramine, and Fingolimod (FTY720), preserves neuronal viability and retinal function. These findings underscore the relevance of alterations in the sphingolipid metabolic network in the etiology of multiple retinopathies and highlight the potential of modulating their metabolism for the design of novel therapeutic approaches. Full Article
review Cholesterol homeostasis in the vertebrate retina: Biology and pathobiology [Thematic Reviews] By www.jlr.org Published On :: 2020-10-20T09:30:27-07:00 Cholesterol is a quantitatively and biologically significant constituent of all mammalian cell membrane, including those that comprise the retina. Retinal cholesterol homeostasis entails the interplay between de novo synthesis, uptake, intra-retinal sterol transport, metabolism and efflux. Defects in these complex processes are associated with several congenital and age-related disorders of the visual system. Herein, we provide an overview of the following topics: a) cholesterol synthesis in the neural retina; b) lipoprotein uptake and intraretinal sterol transport in the neural retina and the retinal pigment epithelium (RPE); c) cholesterol efflux from the neural retina and the RPE; and d) biology and pathobiology of defects in sterol synthesis and sterol oxidation in the neural retina and the RPE. We focus, in particular, on studies involving animal models of monogenic disorders pertinent to the above topics, as well as in vitro models using biochemical, metabolic, and omic approaches. We also identify current knowledge gaps as well as opportunities in the field that beg further research in this topic area. Full Article
review Overview of how N32 and N34 elovanoids sustain sight by protecting retinal pigment epithelial cells and photoreceptors [Thematic Reviews] By www.jlr.org Published On :: 2020-10-26T14:30:21-07:00 The essential fatty acid DHA (22:6, omega-3 or n-3) is enriched in and required for the membrane biogenesis and function of photoreceptor cells (PRC), synapses, mitochondria, etc. of the CNS. PRC DHA becomes an acyl chain at the sn-2 of phosphatidylcholine (PC), amounting to more than 50% of the PRC outer segment phospholipids, where phototransduction takes place. Very long chain PUFAs (VLC-PUFAs,n-3, ≥ 28 carbons) are at the sn-1 of this PC molecular species and interact with rhodopsin. PRC shed their tips (DHA-rich membrane disks) daily, which in turn are phagocytized by the retinal pigment epithelium (RPE), where DHA is recycled back to PRC inner segments to be used for the biogenesis of new photoreceptor membranes. Here, we review the structures and stereochemistry of novel elovanoid (ELV)-N32 and ELV-N34 to be ELV-N32: (14Z,17Z,20R,21E,23E,25Z,27S,29Z)-20,27-dihydroxydo-triaconta-14,17,21,23,25,29-hexaenoic acid; ELV-N34: (16Z,19Z,22R,23E,25E,27Z,29S,31Z)-22,29-dihydroxytetra-triaconta-16,19,23,25,27,31-hexaenoic acid. ELVs are low-abundance, high-potency, protective mediators. Their bioactivity includes enhancing of anti-apoptotic and pro-survival protein expression with concomitant downregulation of pro-apoptotic proteins when RPE is confronted with uncompensated oxidative stress (UOS). ELVs also target PRC/RPE senescence gene programming, the senescence secretory phenotype in the interphotoreceptor matrix (IPM), as well as inflammaging (chronic, sterile, low-grade inflammation). An important lesson on neuroprotection is highlighted by the ELV mediators that target the terminally differentiated PRC and RPE, sustaining a beautifully synchronized renewal process. The role of ELVs in PRC and RPE viability and function uncovers insights on disease mechanisms and the development of therapeutics for age-related macular degeneration (AMD), Alzheimer’s disease (AD), and other pathologies. Full Article
review Lipid metabolism dysregulation in diabetic retinopathy [Thematic Reviews] By www.jlr.org Published On :: 2020-12-23T12:30:44-08:00 Lipid metabolic abnormalities have emerged as potential risk factors for the development and progression of diabetic complications, including diabetic retinopathy (DR). This review article provides an overview of the results of clinical trials evaluating the potential benefits of lipid lowering drugs, such as fibrates, omega 3 fatty acids, and statins, for the prevention and treatment of DR. Although several clinical trials demonstrated that treatment with fibrates leads to improvement of DR, there is a dissociation between the protective effects of fibrates in the retina, and the intended blood lipid classes, including plasma triglycerides, total cholesterol or HDL/LDL cholesterol ratio. Guided by these findings, plasma lipid and lipoprotein-independent mechanisms are addressed based on clinical, cell culture and animal model studies. Potential retinal-specific effects of fatty acids oxidation products, cholesterol, and ceramide, as well as lipid independent effects of PPAR alpha activation are summarized based on current literature. Overall, this review highlights promising potential of lipid-based treatment strategies further enhanced by the new knowledge of intra-retinal lipids and lipoproteins in DR. Full Article
review Chemoprevention of colorectal cancer in individuals with previous colorectal neoplasia: systematic review and network meta-analysis By www.bmj.com Published On :: Monday, December 5, 2016 - 14:46 Full Article
review Chylomicronemia from GPIHBP1 autoantibodies [Reviews] By www.jlr.org Published On :: 2020-11-01T00:05:43-07:00 Some cases of chylomicronemia are caused by autoantibodies against glycosylphosphatidylinositol-anchored HDL binding protein 1 (GPIHBP1), an endothelial cell protein that shuttles LPL to the capillary lumen. GPIHBP1 autoantibodies prevent binding and transport of LPL by GPIHBP1, thereby disrupting the lipolytic processing of triglyceride-rich lipoproteins. Here, we review the "GPIHBP1 autoantibody syndrome" and summarize clinical and laboratory findings in 22 patients. All patients had GPIHBP1 autoantibodies and chylomicronemia, but we did not find a correlation between triglyceride levels and autoantibody levels. Many of the patients had a history of pancreatitis, and most had clinical and/or serological evidence of autoimmune disease. IgA autoantibodies were present in all patients, and IgG4 autoantibodies were present in 19 of 22 patients. Patients with GPIHBP1 autoantibodies had low plasma LPL levels, consistent with impaired delivery of LPL into capillaries. Plasma levels of GPIHBP1, measured with a monoclonal antibody–based ELISA, were very low in 17 patients, reflecting the inability of the ELISA to detect GPIHBP1 in the presence of autoantibodies (immunoassay interference). However, GPIHBP1 levels were very high in five patients, indicating little capacity of their autoantibodies to interfere with the ELISA. Recently, several GPIHBP1 autoantibody syndrome patients were treated successfully with rituximab, resulting in the disappearance of GPIHBP1 autoantibodies and normalization of both plasma triglyceride and LPL levels. The GPIHBP1 autoantibody syndrome should be considered in any patient with newly acquired and unexplained chylomicronemia. Full Article
review A review of phosphatidate phosphatase assays [Reviews] By www.jlr.org Published On :: 2020-12-01T00:05:39-08:00 Phosphatidate phosphatase (PAP) catalyzes the penultimate step in the synthesis of triacylglycerol and regulates the synthesis of membrane phospholipids. There is much interest in this enzyme because it controls the cellular levels of its substrate, phosphatidate (PA), and product, DAG; defects in the metabolism of these lipid intermediates are the basis for lipid-based diseases such as obesity, lipodystrophy, and inflammation. The measurement of PAP activity is required for studies aimed at understanding its mechanisms of action, how it is regulated, and for screening its activators and/or inhibitors. Enzyme activity is determined through the use of radioactive and nonradioactive assays that measure the product, DAG, or Pi. However, sensitivity and ease of use are variable across these methods. This review summarizes approaches to synthesize radioactive PA, to analyze radioactive and nonradioactive products, DAG and Pi, and discusses the advantages and disadvantages of each PAP assay. Full Article
review Proteomics and Metaproteomics Add Functional, Taxonomic and Biomass Dimensions to Modeling the Ecosystem at the Mucosal-luminal Interface [Review] By www.mcponline.org Published On :: 2020-09-01T00:05:24-07:00 Recent efforts in gut microbiome studies have highlighted the importance of explicitly describing the ecological processes beyond correlative analysis. However, we are still at the early stage of understanding the organizational principles of the gut ecosystem, partially because of the limited information provided by currently used analytical tools in ecological modeling practices. Proteomics and metaproteomics can provide a number of insights for ecological studies, including biomass, matter and energy flow, and functional diversity. In this Mini Review, we discuss proteomics and metaproteomics-based experimental strategies that can contribute to studying the ecology, in particular at the mucosal-luminal interface (MLI) where the direct host-microbiome interaction happens. These strategies include isolation protocols for different MLI components, enrichment methods to obtain designated array of proteins, probing for specific pathways, and isotopic labeling for tracking nutrient flow. Integration of these technologies can generate spatiotemporal and site-specific biological information that supports mathematical modeling of the ecosystem at the MLI. Full Article
review Single-cell Proteomics: Progress and Prospects [Review] By www.mcponline.org Published On :: 2020-11-01T00:05:37-07:00 MS-based proteome profiling has become increasingly comprehensive and quantitative, yet a persistent shortcoming has been the relatively large samples required to achieve an in-depth measurement. Such bulk samples, typically comprising thousands of cells or more, provide a population average and obscure important cellular heterogeneity. Single-cell proteomics capabilities have the potential to transform biomedical research and enable understanding of biological systems with a new level of granularity. Recent advances in sample processing, separations and MS instrumentation now make it possible to quantify >1000 proteins from individual mammalian cells, a level of coverage that required an input of thousands of cells just a few years ago. This review discusses important factors and parameters that should be optimized across the workflow for single-cell and other low-input measurements. It also highlights recent developments that have advanced the field and opportunities for further development. Full Article
review Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation [Review] By www.mcponline.org Published On :: 2020-06-23T08:35:15-07:00 Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification. Full Article
review Recent advances in software tools for more generic and precise intact glycopeptide analysis [Review] By www.mcponline.org Published On :: 2020-07-01T15:38:41-07:00 Intact glycopeptide identification has long been known as a key and challenging barrier to the comprehensive and accurate understanding the role of glycosylation in an organism. Intact glycopeptide analysis is a blossoming field that has received increasing attention in recent years. Mass spectrometry (MS)-based strategies and relative software tools are major drivers that have greatly facilitated the analysis of intact glycopeptides, particularly intact N-glycopeptides. This manuscript provides a systematic review of the intact glycopeptide identification process using mass spectrometry data generated in shotgun proteomic experiments, which typically focus on N-glycopeptide analysis. Particular attention is paid to the software tools that have been recently developed in the last decade for the interpretation and quality control of glycopeptide spectra acquired using different MS strategies. The review also provides information about the characteristics and applications of these software tools, discusses their advantages and disadvantages, and concludes with a discussion of outstanding tools. Full Article
review Meta-heterogeneity: evaluating and describing the diversity in glycosylation between sites on the same glycoprotein [Review] By www.mcponline.org Published On :: 2020-07-31T13:35:11-07:00 Mass spectrometry-based glycoproteomics has gone through some incredible developments over the last few years. Technological advances in glycopeptide enrichment, fragmentation methods, and data analysis workflows have enabled the transition of glycoproteomics from a niche application, mainly focused on the characterization of isolated glycoproteins, to a mature technology capable of profiling thousands of intact glycopeptides at once. In addition to numerous biological discoveries catalyzed by the technology, we are also observing an increase in studies focusing on global protein glycosylation and the relationship between multiple glycosylation sites on the same protein. It has become apparent that just describing protein glycosylation in terms of micro- and macro-heterogeneity, respectively the variation and occupancy of glycans at a given site, is not sufficient to describe the observed interactions between sites. In this perspective we propose a new term, meta-heterogeneity, to describe a higher level of glycan regulation: the variation in glycosylation across multiple sites of a given protein. We provide literature examples of extensive meta-heterogeneity on relevant proteins such as antibodies, erythropoietin, myeloperoxidase and a number of serum and plasma proteins. Furthermore, we postulate on the possible biological reasons and causes behind the intriguing meta-heterogeneity observed in glycoproteins. Full Article
review Calculating glycoprotein similarities from mass spectrometric data [Review] By www.mcponline.org Published On :: 2020-09-03T11:35:14-07:00 Complex protein glycosylation occurs through biosynthetic steps in the secretory pathway that create macro- and microheterogeneity of structure and function. Required for all life forms, glycosylation diversifies and adapts protein interactions with binding partners that underpin interactions at cell surfaces and pericellular and extracellular environments. Because these biological effects arise from heterogeneity of structure and function, it is necessary to measure their changes as part of the quest to understand nature. Quite often, however, the assumption behind proteomics that post-translational modifications are discrete additions that can be modeled using the genome as a template does not apply to protein glycosylation. Rather, it is necessary to quantify the glycosylation distribution at each glycosite and to aggregate this information into a population of mature glycoproteins that exist in a given biological system. To date, mass spectrometric methods for assigning singly glycosylated peptides are well-established. But it is necessary to quantify glycosylation heterogeneity accurately in order to gauge the alterations that occur during biological processes. The task is to quantify the glycosylated peptide forms as accurately as possible and then apply appropriate bioinformatics algorithms to the calculation of micro- and macro-similarities. In this review, we summarize current approaches for protein quantification as they apply to this glycoprotein similarity problem. Full Article
review Developments in Mass Spectrometry for Glycosaminoglycan Analysis: A Review [Review] By www.mcponline.org Published On :: 2020-09-16T09:35:59-07:00 This review covers recent developments in glycosaminoglycan (GAG) analysis via mass spectrometry (MS). GAGs participate in a variety of biological functions, including cellular communication, wound healing, and anticoagulation, and are important targets for structural characterization. GAGs exhibit a diverse range of structural features due to the variety of O- and N-sulfation modifications and uronic acid C-5 epimerization that can occur, making their analysis a challenging target. Mass spectrometry approaches to the structure assignment of GAGs have been widely investigated, and new methodologies remain the subject of development. Advances in sample preparation, tandem MS techniques (MS/MS), on-line separations and automated analysis software have advanced the field of GAG analysis. These recent developments have led to remarkable improvements in the precision and time efficiency for the structural characterization of GAGs. Full Article
review Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites [Review] By www.mcponline.org Published On :: 2020-09-16T09:35:59-07:00 O-GlcNAcylation, the addition of a single N-acetylglucosamine residue to serine and threonine residues of cytoplasmic, nuclear, or mitochondrial proteins, is a widespread regulatory post-translational modification. It is involved in response to nutritional status and stress and its dysregulation is associated with diseases ranging from Alzheimer’s to diabetes. While the modification was first detected over thirty-five years ago, research into the function of O-GlcNAcylation has accelerated dramatically in the last ten years due to the development of new enrichment and mass spectrometry techniques that facilitate its analysis. This article summarizes methods for O-GlcNAc enrichment, key mass spectrometry instrumentation advancements, particularly those that allow modification site localization, and software tools that allow analysis of data from O-GlcNAc modified peptides. Full Article
review A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-based Glycoproteomics [Review] By www.mcponline.org Published On :: 2020-09-16T09:35:59-07:00 Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry (MS)-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography (HILIC) and its derivatives, porous graphitic carbon (PGC), reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as MS instrumentation and software improve, so this review aims to help equip researchers with necessary information to choose appropriate enrichment strategies that best complement these efforts. Full Article
review Glycomics, Glycoproteomics and Glycogenomics: an Inter-Taxa Evolutionary Perspective [Review] By www.mcponline.org Published On :: 2020-09-29T11:35:15-07:00 Glycosylation is a highly diverse set of co- and post-translational modification of proteins. For mammalian glycoproteins, glycosylation is often site-, tissue- and species-specific, and diversified by microheterogeneity. Multitudinous biochemical, cellular, physiological and organismic effects of their glycans have been revealed, either intrinsic to the carrier proteins or mediated by endogenous reader proteins with carbohydrate recognition domains. Furthermore, glycans frequently form the first line of access by or defense from foreign invaders, and new roles for nucleocytoplasmic glycosylation are blossoming. We now know enough to conclude that the same general principles apply in invertebrate animals and unicellular eukaryotes – different branches of which spawned the plants or fungi and animals. The two major driving forces for exploring the glycomes of invertebrates and protists are (i) to understand the biochemical basis of glycan-driven biology in these organisms, especially of pathogens, and (ii) to uncover the evolutionary relationships between glycans, their biosynthetic enzyme genes, and biological functions for new glycobiological insights. With an emphasis on emerging areas of protist glycobiology, here we offer an overview of glycan diversity and evolution, to promote future access to this treasure trove of glycobiological processes. Full Article
review Chromatin proteomics to study epigenetics - challenges and opportunities [Review] By www.mcponline.org Published On :: 2020-10-15T08:35:17-07:00 Regulation of gene expression is essential for the functioning of all eukaryotic organisms. Understanding gene expression regulation requires determining which proteins interact with regulatory elements in chromatin. Mass spectrometry-based analysis of chromatin has emerged as a powerful tool to identify proteins associated with gene regulation, as it allows studying protein function and protein complex formation in their in vivo chromatin-bound context. Total chromatin isolated from cells can be directly analysed using mass spectrometry or further fractionated into transcriptionally active and inactive chromatin prior to MS-based analysis. Newly formed chromatin that is assembled during DNA replication can also be specifically isolated and analysed. Furthermore, capturing specific chromatin domains facilitates the identification of previously unknown transcription factors interacting with these domains. Finally, in recent years, advances have been made towards identifying proteins that interact with a single genomic locus of interest. In this review, we highlight the power of chromatin proteomics approaches and how these provide complementary alternatives compared to conventional affinity purification methods. Furthermore, we discuss the biochemical challenges that should be addressed to consolidate and expand the role of chromatin proteomics as a key technology in the context of gene expression regulation and epigenetics research in health and disease. Full Article
review Accelerating the field of epigenetic histone modification through mass spectrometry-based approaches [Review] By www.mcponline.org Published On :: 2020-11-17T10:35:13-08:00 Histone post-translational modifications (PTMs) are one of the main mechanisms of epigenetic regulation. Dysregulation of histone PTMs leads to many human diseases, such as cancer. Due to its high-throughput, accuracy, and flexibility, mass spectrometry (MS) has emerged as a powerful tool in the epigenetic histone modification field, allowing the comprehensive and unbiased analysis of histone PTMs and chromatin-associated factors. Coupled with various techniques from molecular biology, biochemistry, chemical biology and biophysics, MS has been employed to characterize distinct aspects of histone PTMs in the epigenetic regulation of chromatin functions. In this review we will describe advancements in the field of MS that have facilitated the analysis of histone PTMs and chromatin biology. Full Article
review Proteome Turnover in the Spotlight: Approaches, Applications & Perspectives [Review] By www.mcponline.org Published On :: 2020-11-30T16:35:18-08:00 In all cells, proteins are continuously synthesized and degraded in order to maintain protein homeostasis and modify gene expression levels in response to stimuli. Collectively, the processes of protein synthesis and degradation are referred to as protein turnover. At steady state, protein turnover is constant to maintain protein homeostasis, but in dynamic responses, proteins change their rates of synthesis and degradation in order to adjust their proteomes to internal or external stimuli. Thus, probing the kinetics and dynamics of protein turnover lends insight into how cells regulate essential processes such as growth, differentiation, and stress response. Here we outline historical and current approaches to measuring the kinetics of protein turnover on a proteome-wide scale in both steady-state and dynamic systems, with an emphasis on metabolic tracing using stable-isotope-labeled amino acids. We highlight important considerations for designing proteome turnover experiments, key biological findings regarding the conserved principles of proteome turnover regulation, and future perspectives for both technological and biological investigation. Full Article
review The peptide vaccine of the future [Review] By www.mcponline.org Published On :: 2020-12-07T10:40:19-08:00 The approach of peptide-based anti-cancer vaccination has proven the ability to induce cancer-specific immune responses in multiple studies for various cancer entities. However, clinical responses remain so far limited to single patients and broad clinical applicability was not achieved. Therefore, further efforts are required to improve peptide vaccination in order to integrate this low side effect therapy into the clinical routine of cancer therapy. To design clinically effective peptide vaccines in the future, different issues have to be addressed and optimized comprising antigen target selection as well as choice of optimal adjuvants and vaccination schedules. Furthermore, the combination of peptide-based vaccines with other immuno- and molecular targeted therapies as well as the development of predictive biomarkers could further improve efficacy. In this review, current approaches in the development of peptide-based vaccines and critical implications for optimal vaccine design are discussed. Full Article
review The role of Data-Independent Acquisition for Glycoproteomics [Review] By www.mcponline.org Published On :: 2020-12-28T12:35:13-08:00 Data independent acquisition (DIA) is now an emerging method in bottom-up proteomics and capable of achieving deep proteome coverage and accurate label-free quantification. However, for post-translational modifications (PTM), such as glycosylation, DIA methodology is still in the early stage of development. The full characterization of glycoproteins requires site specific glycan identification as well as subsequent quantification of glycan structures at each site. The tremendous complexity of glycosylation represents a significant analytical challenge in glycoproteomics. This review focuses on the development and perspectives of DIA methodology for N- and O- glycoproteomics and posits that DIA-based glycoproteomics could be a method of choice to address some of the challenging aspects of glycoproteomics. First, the current challenges in glycoproteomics and the basic principles of DIA is briefly introduced. DIA based glycoproteomics is then summarized and described into four aspects based on the actual samples. Lastly, we discussed the important challenges and future perspectives in the field. We believe that DIA can significantly facilitate glycoproteomic studies and contribute to the development of future advanced tools and approaches in the field of glycoproteomics. Full Article
review Annual Review 2017-18 By www.chathamhouse.org Published On :: Wed, 18 Jul 2018 07:19:06 +0000 Annual Review 2017-18 Other resource sysadmin 18 July 2018 Explore the institute’s output, activities and achievements from the past year examining how to make the world more secure in uncertain times; new thinking on how societies can flourish and be prosperous; and how to contribute to a more just society. Director’s statement I wrote a year ago that the world has entered one of the most politically turbulent periods in the modern era. This rings even more true now, as relations have seriously deteriorated between the US administration and its European allies, while instability persists across the Middle East, and China and Russia increase their strategic influence. Over the past year, Chatham House has assessed these changes and proposed ways to manage the associated risks, while seeking out opportunities to expand prosperity and security across the world. Adam Ward, our deputy director, led the publication of the first Chatham House Expert Perspectives report on risks and opportunities in international affairs, to coincide with our fifth annual London Conference on 21–22 June 2018. The conference was attended by over 450 participants from 71 countries. Furthermore, using our new simulation centre on the Stavros Niarchos Foundation (SNF) Floor, our research teams are ‘stress-testing’ their ideas in exercises involving both practitioners and experts. For example, in June 2017 the Centre on Global Health Security and the Africa Programme hosted our first scenario exercise, which explored how to respond to a humanitarian emergency that required landmine clearance. Since then, we have hosted other simulation and scenario planning exercises, including on cyberattacks, Brexit ‘futures’ and the rise of the populist parties in Europe. We have also used the new facilities to host events supported by modern audiovisual systems; to stress-test our own communications strategy; and even to conduct a round of scenario-based interactive job interviews. The new media studio and editing facilities have led us to create more multimedia content, which has, in turn, enabled us to reach expanded and more diverse audiences for our work. The new SNF Floor has also provided staff with an open, multifunctional meeting area and has alleviated some of the space pressures which had been created by our growing staff numbers. As you will read in the following pages, our research is currently centred around three themes: making the world more secure in uncertain times; offering new ideas on how societies can flourish and be prosperous; and contributing to a more just society. A growing number of cross-cutting projects enable us to address topics within each of these themes, including cyberthreats, transatlantic relations, the future of the EU–China economic relationship, regulating data, vulnerabilities in global food trade and implementing universal health coverage. Our ability to do so has been enhanced by the appointment of several new senior research staff: Hans Kundnani as senior fellow in the Europe Programme; Champa Patel as head of the Asia- Pacific Programme; and Leslie Vinjamuri as head of the US and the Americas Programme and dean of the Queen Elizabeth II Academy for Leadership in International Affairs. In addition, Bernice Lee will take over as the new research director of our Global Economy and Finance Department, alongside her continuing role as executive director of the Hoffmann Centre for Sustainable Resource Economy. During the coming months, we will lay the foundations to mark the institute’s centenary in the summer of 2020. In doing so, we will draw on our archives to acknowledge the institute’s unique achievements over the past 100 years, recognize those many individuals who have supported us along the way, and set out our objectives for the future. In preparation, we have already launched a series of members’ events with a historical focus, examining how the lessons from the past can inform international affairs and policy thinking today. In closing, I would like to pay tribute and offer my sincere thanks to Stuart Popham, who steps down this year after six years as chair of the institute and 13 years between 2005 and 2018 as a member of Council. Stuart has been a tremendous support and guide to me, and to the institute as a whole, during this period. His measured advice to management and collegiate leadership of Council have been invaluable during a period in which the institute has more than doubled in size, and in which it has thrived despite the increasingly competitive environment for policy convening, analysis and ideas. We look forward to welcoming Stuart back to Chatham House as a highly engaged individual member, and wish him all the best for the future. Robin Niblett CMG 2018-07-18-annual-review (PDF) Full Article
review Annual Review 2018-19 By www.chathamhouse.org Published On :: Wed, 24 Jul 2019 11:59:47 +0000 Annual Review 2018-19 Other resource sysadmin 24 July 2019 Explore the institute’s output, activities and achievements from the past year examining how to make the world more stable in uncertain times, new thinking on how societies can promote prosperity, and how to contribute to a more just society. Chair’s statement I was delighted to be elected chair of Chatham House last year. It is an honour to lead such a remarkable institution and to have the opportunity to build on the legacy left by Stuart Popham, who stepped down last year as chair and whom I thank and pay tribute to. My ambition is to ensure that the institute has an even better future than its illustrious past. We are living in unpredictable times, and I want us to be at the centre of the drive to guide the world to a healthier place both politically and economically. Chatham House possesses world-leading convening power, which – when combined with our capacity to deliver leading, cross-cutting research – gives us a unique advantage in the field of international relations. I want us to harness these assets and better combine the strengths of our research teams so that we can address the big global challenges around economic growth; avoiding geopolitical tensions; and developing new governance systems (as outlined on page 7). This will enable us to improve our impact and effect more policy change. I also want Chatham House to be an exciting place that attracts younger, more diverse, international audiences. We need to drive more engagement with the next generation of members and others to draw on their enthusiasm, energy and ideas. Our Common Futures Conversations project, for example, is engaging young people from 13 countries across Africa and Europe to identify their shared concerns, and is enabling them to work together to identify solutions via online communities. This initiative, and indeed all of our activities, would not be possible without funding and support. As noted in more detail in the Honorary Treasurer’s report (page 32), 2018/19 was a challenging year financially, with income totalling £16,381,000, slightly below the level recorded in 2017/18. Although total net assets at 31 March 2019 were 3 per cent down year on year, the balance sheet remain strong and there was an inflow of cash, with the level of forward income received and pledged increasing significantly. In this context, I am delighted to note the award of the transformational £10 million grant to facilitate the creation of the Stavros Niarchos Foundation Wing, which will help facilitate research, host our Queen Elizabeth II Academy for Leadership in International Affairs and establish a new collaboration space – the ‘CoLab’ – for engaging our new audiences. All of Chatham House’s supporters, and not least our members, remain indispensable to our success. Without their engagement, enthusiasm and input, the institute could not fulfil its mission. I am indebted to my colleagues on Council for their support, engagement and expertise. I can say with confidence that they are actively involved in their governance responsibilities at this time when the operational, as well as financial, pressures on all charitable institutions are more intense than ever. I would like to pay tribute to Alistair Burnett, Martin Fraenkel and Barbara Ridpath, who step down from Council this year after a total of 15 years’ service. I would also like to thank and acknowledge Robin Niblett and his team for their dedication and hard work. Some of the outcomes of their labours are highlighted on the following pages. Lord Jim O’Neill 264415_Chatham_AR19_Text-HR (PDF) Full Article
review Annual Review 2021–22 By www.chathamhouse.org Published On :: Mon, 11 Jul 2022 10:56:39 +0000 Annual Review 2021–22 Other resource NCapeling 11 July 2022 Explore highlights from our work over the past year, including research, events, and next generation initiatives. Chair’s statement The past 12 months have seen new levels of instability injected into international affairs. The consequences of the COVID-19 pandemic, the continued fracturing of the international system and Russia’s war on Ukraine, which triggered the largest movement of refugees since the Second World War, have had severe impacts on trade, prices and people around the world. Chatham House’s Russia and Eurasia Programme and its Ukraine Forum have advised allied governments on their response to the war on Ukraine, and secured the participation of Ukrainian president Volodymyr Zelenskyy in the most watched event of the institute’s history. The challenge now is to ensure Chatham House can bring together its diverse areas of research and offer influential ideas on how to respond to the uncertain future. Council has supported the push to define clear priorities for the institute’s work, and the launch of two new research centres covering sustainability and global governance. Drawing out the best from the institute’s expertise in the changed geopolitical landscape will be a top priority for Bronwen Maddox when she takes over as director at the end of August. Council is delighted to have found such a worthy successor to Robin Niblett. Robin’s 15 years of inspiring leadership have seen the institute more than triple in size of staff and budget. New areas of research under his tenure include cyber policy, digital governance, global health, the US and the Americas, and the UK in the world post-Brexit. Robin also launched the Queen Elizabeth II Academy for Leadership in International Affairs, providing the base for many initiatives to engage the next generation. He also leaves the institute with a rebuilt balance sheet after securing some major long-term gifts; expanded and renovated premises; and a strong communications and digital infrastructure that has raised the profile of Chatham House with our audiences. Council places on record the institute’s debt to Robin and to his wife, Trisha de Borchgrave. Chatham House’s supporters around the world were delighted to see Robin awarded a knighthood in HM The Queen’s Birthday Honours 2022. I pay tribute also to my predecessor, Jim O’Neill, and I am grateful to Simon Fraser, deputy chair, and to the other four retiring members of Council (Mimi Ajibadé, Heide Baumann, Kenneth Cukier and Tim Willasey-Wilsey) for their dedication and counsel. Council will continue to focus on strengthening the impact of the institute’s work and on improving governance, as well as providing continuity during the leadership transition. We will act as a strategic partner for Bronwen as she takes Chatham House forward. Central to this will be implementing the institute’s plan to strengthen equality, diversity and inclusion across the board. Finally, I thank the staff for their commitment through this period of transformation. Sir Nigel Sheinwald GCMG Annual Review 2021–22 (PDF) Full Article
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