What is COP29 and why is it important? Explainer jon.wallace 17 October 2024

The COP29 summit will see negotiators try to agree how to finance the climate action the world urgently needs.

COP29, the 29th UN annual conference on climate change, takes place in Baku, Azerbaijan from 11–22 November 2024.

Every COP conference is an important opportunity for international collaboration on climate change. COP29 will have a particular focus on how to make finance available to developing countries for climate action.

COP29 is already contentious, because Azerbaijan’s economy is highly dependent on fossil fuels, the main cause of climate change. That means that Azerbaijan’s government, which will preside over the summit, has a strong incentive to avoid rapid multilateral progress towards phasing out fossil fuels. 

It’s urgent that progress is made at COP29. Climate action lags far behind both what has been promised by countries, and what scientists agree is needed. The impacts of climate change are also rapidly escalating, while backlash against government policies to reduce fossil fuel use is being seen in many places around the world. 

What is a ‘COP’?

The ‘Conference of the Parties’ or ‘COP’ is an annual event that brings together the governments which have signed up to environmental action under the United Nations (UN). 

Governments or ‘parties’ attend the climate change COP if they are part of the United Nations Framework Convention on Climate Change, or the international environmental treaties the Kyoto Protocol (1997) or the landmark and legally binding Paris Agreement (2015).

World leaders, ministers, and negotiators convene at the COP to negotiate and rubber stamp plans to jointly address climate change and its impacts. 

Civil society, businesses, international organizations and the media normally ‘observe’ proceedings to bring transparency, accountability and wider perspectives to the process.

‘Mission 1.5°C’ 

COP28, the 2023 climate conference held in Dubai, was the first of three consecutive COP summits intended to ‘reset’ global climate action – what the UN calls the ‘Roadmap to Mission 1.5°C’ – the ambition to keep global temperatures from rising more than 1.5°C above pre-industrial levels. 

To support continuity and progress across the three COPs, the UAE (COP28), Azerbaijan (COP29) and Brazil (COP30) have formed a COP presidential ‘Troika’ or group of three.

In 2023 the first ‘global stocktake’ of international action to address climate change indicated that the world was far off track for targets set by the Paris Agreement. The ‘UAE Consensus’ agreement, which formed the main output of COP28, set out how parties should respond. 

COP29, the second of the three COPs, is intended to get the finance in place to enable this response. COP30, to be held in Brazil in 2025, will then try to agree how a new round of nationally determined climate plans or ‘contributions’ to global climate efforts (NDCs) should be put into action.

COP29 will be the third consecutive COP held in an authoritarian state, and the second consecutive COP hosted by a petro-state. Taken together, the ‘Troika’ hosts make up the world’s 4th largest oil producer, after the United States, Russia and Saudi Arabia. 

This presents both an opportunity and a risk: the countries are well placed to understand and tackle the core issue of fossil fuel extraction and use. But they also have strong incentives to stall, distract and deflect the negotiations away from phasing out fossil fuels.

Key issues at COP29

Finance – money on the table, and a New Collective Quantified Goal

COP29 has a remit to secure funding for a ‘course correction’ on global climate action. Countries’ revised climate plans (NDCs) are due in February 2025. For developing countries to deliver new ambitious NDCs, however, COP29 must first make clear what finance will be available to help them.

Climate finance is one of the thorniest issues in the negotiations. The previous climate finance goal, of $100 billion per year from developed to developing countries between 2020-25, was symbolic (being a fraction of the sum actually needed) and contentious (developed countries did not meet the target until 2022, and then only with accusations of double-counting). 

A New Collective Quantified Goal (NCQGs), to be agreed at COP29, will need to reflect developing countries’ needs and priorities. Estimates vary, but it is accepted that the scale will be trillions, not billions. To bridge this enormous gap, private finance will need to be mobilized and broader reforms made to global financial architecture. Issues such as subsidies, fossil fuel profits and ‘solidarity levies’ will also need to be on the table. 

Little progress has been made in the run-up to COP29. Parties disagree on who should pay, how much should be paid, what forms the funding should take (loans or grants) and how the funds should be accessed. 

Also up for debate is how funds should be directed – towards mitigating the impacts of climate change (preventing climate change becoming worse), adapting to its effects, or supporting countries to manage loss and damage (climate impacts that have already happened or cannot be avoided).  

In discussions of the NCQG to date, developed countries have consistently called for higher income developing countries, such as China and India, to contribute. 

Such countries have pushed back forcefully against this. For a new goal to be agreed, such divisions will need to be resolved.

Enhanced transparency?

COPs act as showcases for international agreement, but many processes rumble on behind the scenes. COP29 will be an important moment for transparency under the Paris Agreement, as the Parties’ first Biennial Enhanced Transparency Reports (BTRs) are due in December 2024. 

BTRs are an important tool in the Paris Agreement, requiring countries to provide a snapshot of their progress in cutting emissions, setting climate policies, and providing resources for national and international climate action. 

BTRs are meant to build the evidence base for strong NDCs, build trust and promote ambitious climate action. They are also meant to help developing countries showcase achievements and attract climate finance. 

The COP29 presidency has launched the Baku Global Climate Transparency Platform to encourage participation, and support countries in finalising their BTRs. The Platform is meant to provide space for collaboration between government, NGO and private sector stakeholders. 

This is one of the areas in which COP29 host, Azerbaijan, runs into criticism. The country ranks highly on indexes of corruption, and has repeatedly restricted space for NGOs and wider civil society actors through a series of escalating government crackdowns, including imprisonment of environmental activists, in the run-up to the conference.

Members' question time: What has COP29 achieved? 25 November 2024 — 1:00PM TO 1:45PM Anonymous (not verified) 8 November 2024 Online

Join us and ask our senior research fellow, Ruth Townend anything about the outcome from COP29. Submit your questions in advance.

As COP29 prepares to conclude in Baku, Azerbaijan, this year’s conference has taken place against a backdrop of ever worsening climate impacts and escalating financial needs for developing countries. Being hosted by Azerbaijan has been significant, a country whose economy is heavily reliant on fossil fuels. As delegates and officials prepare to leave, the urgency for global climate action intensifies.

Join us as Ruth Townend, our Senior Research Fellow for the Environment and Society Centre to provide the latest insight and analysis from COP. She will give an overview of the key developments from Baku, new global commitments that have been agreed and how this sets up COP 30 in Brazil in 2025.

Submit your questions to Ruth Townend in advance of the event. Your questions will drive the conversation.

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.

Climate finance and conflict dynamics on the road to COP27 21 September 2022 — 1:00PM TO 2:00PM Anonymous (not verified) 9 September 2022 Online

Stakeholders discuss the role of conflict and conflict sensitivity in climate finance and action.

With climate change, fragility and conflict challenges worsening, the role of international climate finance is more urgent than ever.

From the implementation of climate finance and who it reaches to the rush for renewable energy, the inclusion of conflict analysis and conflict sensitivity principles often remain absent from climate finance discussions and planning.

With COP27 around the corner and for the occasion of International Peace Day, stakeholders ranging from government representatives to climate activists discuss their perspectives on the role of conflict and conflict sensitivity as part of climate finance and action.

This event was organized in partnership with International Alert.

What happened at COP27? 23 November 2022 — 12:00PM TO 1:00PM Anonymous (not verified) 14 November 2022 Online

Is the world getting back on track for staying within a 1.5°C temperature rise?

The COP27 summit closes out another year marked by record-breaking floods, deadly heatwaves and other extreme weather events, on top of global energy and food shortages and a cost-of-living crisis.

Remarkable geopolitical shifts including Russia’s invasion of Ukraine have weakened commitments to climate goals and led many to worry that governments are backtracking on their climate pledges.

UN officials have urged countries to show up to COP27 with greater ambition but instead of new pledges, the focus is expected to be on whether countries are following through on commitments made at COP26.

This event explored whether COP27 has met the challenge of truly moving the needle, and whether the world is getting back on track for staying within the 1.5°C temperature rise, or for loss and damage and climate justice.

Our expert panel discusses the summit’s overall success and impact on delivering in key areas: climate finance, mitigation, adaptation, loss and damage, nature and biodiversity and the just transition.

This event is part of the Waddesdon Club Webinar Series. The Waddesdon Club is a Chatham House initiative to encourage climate leadership in financial and economic policymaking. Since 2016, it has proved a highly successful forum for convening senior policymakers and leading climate scientists with future leaders in finance ministries, central banks and other public sector economic and financial organizations from around the world.

The initiative is supported by Ikea Foundation, KR Foundation and the Rothschild Foundation.

Kadian Morgan was overwhelmed with grief as she leaned against a wall outside her gate on Jackson Lane, East Kingston, yesterday, tears streaming down her face. Her 19-year-old son, Kayshan 'Bem Bem' Smith, was lying in the morgue after being...

Connexin (Cx) protein forms hemichannels and gap junctional channels, which play diverse and profound roles in human physiology and diseases. Gap junctions are arrays of intercellular channels formed by the docking of two hemichannels from adjacent cells. Each hexameric hemichannel contains the same or different Cx isoform. Although homomeric Cxs forms have been largely described functionally and structurally, the stoichiometry and arrangement of heteromeric Cx channels remain unknown. The latter, however, are widely expressed in human tissues and variation might have important implications on channel function. Investigating properties of heteromeric Cx channels is challenging considering the high number of potential subunit arrangements and stoichiometries, even when only combining two Cx isoforms. To tackle this problem, we engineered an HA tag onto Cx26 or Cx30 subunits and imaged hemichannels that were liganded by Fab-epitope antibody fragments via atomic force microscopy. For Cx26-HA/Cx30 or Cx30-HA/Cx26 heteromeric channels, the Fab-HA binding distribution was binomial with a maximum of three Fab-HA bound. Furthermore, imaged Cx26/Cx30-HA triple liganded by Fab-HA showed multiple arrangements that can be derived from the law of total probabilities. Atomic force microscopy imaging of ringlike structures of Cx26/Cx30-HA hemichannels confirmed these findings and also detected a polydisperse distribution of stoichiometries. Our results indicate a dominant subunit stoichiometry of 3Cx26:3Cx30 with the most abundant subunit arrangement of Cx26-Cx26-Cx30-Cx26-Cx30-Cx30. To our knowledge, this is the first time that the molecular architecture of heteromeric Cx channels has been revealed, thus providing the basis to explore the functional effect of these channels in biology.

COP27: Navigating a difficult road to Sharm El-Sheikh Expert comment NCapeling 6 July 2022

Against a backdrop of rising urgency, COP27 in Egypt will bring all aspects of climate action into the spotlight – but especially the role of the host country.

As COP26 drew to a close in Glasgow, Egyptian officials announced their priorities for COP27, emphasizing climate finance and climate adaptation – a new approach given previous COPs mainly focused on mitigation, reducing emissions to limit climate damage.

This was followed by the COP27 presidency outlining its vision at MENA Climate Week 2022 to achieve ‘substantive and equal progress’ on all aspects of the negotiations, and Egypt emphasizing its intention to focus on implementing existing carbon reduction targets rather than pushing for further carbon cuts.

Egypt argues it is hosting COP27 on behalf of African nations and that, while it is promoting the interests of the developing world, it will be an impartial arbiter. However it is also useful to consider its priorities from the Egyptian government’s perspective.

Agenda drivers

Egypt has long prioritized climate finance and adaptation because it remains in need of technical and financial support to adapt, especially in agriculture and tourism.

It plans to expand its access to climate funding and investment, an area in which Egypt has been relatively successful as it currently receives 27 per cent of all multilateral climate finance in the MENA region and has issued the region’s first sovereign green bonds.

With public debt currently 94 per cent of GDP, Egyptian officials have also called for debt relief for Egypt and other developing countries.

Egypt’s Climate Change Strategy reflects this approach, aiming to enhance Egypt’s rank on the Climate Change Performance Index in order to ‘attract more investments and acquire more climate funding’.

Limiting the mitigation scope and the focus on finance also echoes Egypt’s own reluctance to make carbon reduction commitments. The Egyptian nationally determined contribution (NDC) – its 2030 pledge under the Paris Agreement – does not include any quantifiable emission reduction targets.

Egypt is one of only a few countries which failed to submit an updated NDC in 2021 and its upcoming update will not include an economy-wide carbon reduction target.

Egypt has also never published a long-term strategy and has no decarbonization plans despite independent estimates it should cut rising emissions by one-quarter by 2030, and by two-thirds by 2050 to be aligned with the Paris Agreement. This partly explains why observers rate Egypt’s climate action as highly insufficient.

Furthermore, Egypt’s championing of ‘moving from pledges to implementation’ without having quantifiable carbon reduction pledges of its own effectively exempts it from both pledging and implementation.

As a developing country, Egypt’s negotiating position is supported by UNFCCC provisions which recognize differentiated responsibilities and respective capabilities of nations.

Its proposal to focus COP27 on the implementation of climate action and finance pledges is important in consolidating progress. But not pushing for more emission reductions at this critical moment risks derailing global decarbonization momentum and undermining global climate action.

According to optimistic estimates, if current climate pledges were implemented the world would still remain on track for 2°C of warming by the end of the century, with far worse impacts than if warming was curbed at 1.5°C.

Under a 2°C scenario, 37 per cent of the global population could regularly be exposed to extreme heat waves compared to 14 per cent in a 1.5°C warmer world, with developing countries expected to be worst-affected.

A 2°C trajectory also runs the risk of tipping points such as the melting of ice sheets in Antarctica and Greenland, triggering runaway climate change. Time to change the warming trajectory is running out as the latest IPCC assessment warns the window of opportunity is now ‘brief and rapidly closing’, and the UN Secretary General recently called for faster carbon cuts by the end of 2022 to avoid a ‘climate catastrophe’.

A different energy transition

Egypt opted not to join any of the voluntary sectoral coalitions at COP26 on reducing methane, clean energy transition, transition to zero-emissions vehicles, or moving beyond oil and gas.

This position is explained by its growing role as an exporter and advocate for fossil gas in the energy transition. Egypt is the second-largest producer of natural gas in Africa and is emerging as a fossil gas hub for the eastern Mediterranean, which is shaping its domestic energy policy.

Its 59GW electricity generation capacity is almost double the peak demand and is dominated by gas-powered electricity generation, which currently represents 42 per cent of all Africa’s gas generation.

Egypt’s climate policy is also shaped by fossil gas, and its national Climate Change Strategy encourages the expansion of gas use by promoting a transition to compressed natural gas for vehicles, the expansion of its domestic natural gas network – despite having universal access to electricity – and shifting to a gas-fuelled shipping sector.

Egypt also voiced support for other African countries to extract and deploy fossil gas and oil resources, making it one of the protagonists of the ‘great fossil gas pushback’. These advocates defend the right of developing countries to deploy fossil gas as a ‘transition fuel’ and champion its necessity to solve energy poverty.

But their position is not shared by all African and developing countries, and is rejected by some civil society groups, who argue it risks locking in greenhouse gases and local emissions for decades as well as delaying future development of low carbon energy systems.

Egypt’s huge spare generation capacity has contributed to a slowdown in renewable energy projects over the past two years. With renewables representing just 6GW, Egypt is expected to miss its renewable energy target for 2022, set at 20 per cent of generating capacity.

Engaging Egypt better

But these positions are more malleable than they seem, and Egypt is open to dialogue – not just on refining the COP27 agenda but also on reviewing its own climate priorities and leveraging its energy sector for a more ambitious transition.

Toma Keser
Dec 29, 2020; 0:RA120.002433v1-mcp.RA120.002433
Research

Zilu Ye
Dec 28, 2020; 0:R120.002204v1-mcp.R120.002204
Review

Abstract

After 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.

Mass spectrometry has become an indispensable tool for the characterization of glycosylation across biological systems. Our ability to generate rich fragmentation of glycopeptides has dramatically improved over the last decade yet our informatic approaches still lag behind. Although glycoproteomic informatics approaches using glycan databases have attracted considerable attention, database independent approaches have not. This has significantly limited high throughput studies of unusual or atypical glycosylation events such as those observed in bacteria. As such, computational approaches to examine bacterial glycosylation and identify chemically diverse glycans are desperately needed. Here we describe the use of wide-tolerance (up to 2000 Da) open searching as a means to rapidly examine bacterial glycoproteomes. We benchmarked this approach using N-linked glycopeptides of Campylobacter fetus subsp. fetus as well as O-linked glycopeptides of Acinetobacter baumannii and Burkholderia cenocepacia revealing glycopeptides modified with a range of glycans can be readily identified without defining the glycan masses before database searching. Using this approach, we demonstrate how wide tolerance searching can be used to compare glycan use across bacterial species by examining the glycoproteomes of eight Burkholderia species (B. pseudomallei; B. multivorans; B. dolosa; B. humptydooensis; B. ubonensis, B. anthina; B. diffusa; B. pseudomultivorans). Finally, we demonstrate how open searching enables the identification of low frequency glycoforms based on shared modified peptides sequences. Combined, these results show that open searching is a robust computational approach for the determination of glycan diversity within bacterial proteomes.

Synaptic transmission leading to release of neurotransmitters in the nervous system is a fast and highly dynamic process. Previously, protein interaction and phosphorylation have been thought to be the main regulators of synaptic transmission. Here we show that sialylation of N-linked glycosylation is a novel potential modulator of neurotransmitter release mechanisms by investigating depolarization-dependent changes of formerly sialylated N-linked glycopeptides. We suggest that negatively charged sialic acids can be modulated, similarly to phosphorylation, by the action of sialyltransferases and sialidases thereby changing local structure and function of membrane glycoproteins. We characterized site-specific alteration in sialylation on N-linked glycoproteins in isolated rat nerve terminals after brief depolarization using quantitative sialiomics. We identified 1965 formerly sialylated N-linked glycosites in synaptic proteins and found that the abundances of 430 glycosites changed after 5 s depolarization. We observed changes on essential synaptic proteins such as synaptic vesicle proteins, ion channels and transporters, neurotransmitter receptors and cell adhesion molecules. This study is to our knowledge the first to describe ultra-fast site-specific modulation of the sialiome after brief stimulation of a biological system.

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.

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.

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.

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.

Glycopeptides in peptide or digested protein samples pose a number of analytical and bioinformatics challenges beyond those posed by unmodified peptides or peptides with smaller posttranslational modifications. Exact structural elucidation of glycans is generally beyond the capability of a single mass spectrometry experiment, so a reasonable level of identification for tandem mass spectrometry, taken by several glycopeptide software tools, is that of peptide sequence and glycan composition, meaning the number of monosaccharides of each distinct mass, for example HexNAc(2)Hex(5) rather than man5. Even at this level, however, glycopeptide analysis poses challenges:  finding glycopeptide spectra when they are a tiny fraction of the total spectra; assigning spectra with unanticipated glycans, not in the initial glycan database; and finding, scoring, and labeling diagnostic peaks in tandem mass spectra.  Here we discuss recent improvements to Byonic, a glycoproteomics search program, that address these three issues. Byonic now supports filtering spectra by m/z peaks, so that the user can limit attention to spectra with diagnostic peaks, for example, at least two out of three of 204.087 for HexNAc, 274.092 for NeuAc (with water loss), and 366.139 for HexNAc-Hex, all within a set mass tolerance, for example, ± 0.01 Daltons. Also new is glycan "wildcard" search, which allows an unspecified mass within a user-set mass range to be applied to N- or O-linked glycans and enables assignment of spectra with unanticipated glycans. Finally the next release of Byonic supports user-specified peak annotations from user-defined posttranslational modifications. We demonstrate the utility of these new software features by finding previously unrecognized glycopeptides in publicly available data, including glycosylated neuropeptides from rat brain.

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.

Sparkling wine is an alcoholic beverage enjoyed around the world. The sensory properties of sparkling wine depend on a complex interplay between the chemical and biochemical components in the final product. Glycoproteins have been linked to positive and negative qualities in sparkling wine, but the glycosylation profiles of sparkling wine have not been previously investigated in detail. We analysed the glyco/proteome of sparkling wines using protein- and glycopeptide-centric approaches. We developed an automated workflow that created ion libraries to analyse Sequential Window Acquisition of all THeoretical mass spectra (SWATH) Data Independent Acquisition (DIA) mass spectrometry data based on glycopeptides identified by Byonic. We applied our workflow to three pairs of experimental sparkling wines to assess the effects of aging on lees and of different yeast strains used in the Liqueur de Tirage for secondary fermentation. We found that aging a cuvée on lees for 24 months compared to 8 months led to a dramatic decrease in overall protein abundance and an enrichment in large glycans at specific sites in some proteins. Secondary fermentation of a Riesling wine with Saccharomyces cerevisiae yeast strain Siha4 produced more yeast proteins and glycoproteins than with S. cerevisiae yeast strain DV10. The abundance and glycosylation profiles of grape glycoproteins were also different between grape varieties. This work represents the first in-depth study into protein- and peptide-specific glycosylation in sparkling wines and describes a quantitative glycoproteomic SWATH/DIA workflow that is broadly applicable to other sample types.

Many cell surface and secreted proteins are modified by the covalent addition of glycans that play an important role in the development of multicellular organisms. These glycan modifications enable communication between cells and the extracellular matrix via interactions with specific glycan-binding lectins and the regulation of receptor-mediated signaling. Aberrant protein glycosylation has been associated with the development of several muscular diseases suggesting essential glycan- and lectin-mediated functions in myogenesis and muscle development but our molecular understanding of the precise glycans, catalytic enzymes and lectins involved remain only partially understood. Here, we quantified dynamic remodeling of the membrane-associated proteome during a time-course of myogenesis in cell culture. We observed wide-spread changes in the abundance of several important lectins and enzymes facilitating glycan biosynthesis. Glycomics-based quantification of released N-linked glycans confirmed remodeling of the glycome consistent with the regulation of glycosyltransferases and glycosidases responsible for their formation including a previously unknown di-galactose-to-sialic acid switch supporting a functional role of these glycoepitopes in myogenesis. Furthermore, dynamic quantitative glycoproteomic analysis with multiplexed stable isotope labelling and analysis of enriched glycopeptides with multiple fragmentation approaches identified glycoproteins modified by these regulated glycans including several integrins and growth factor receptors. Myogenesis was also associated with the regulation of several lectins most notably the up-regulation of galectin-1 (LGALS1). CRISPR/Cas9-mediated deletion of Lgals1 inhibited differentiation and myotube formation suggesting an early functional role of galectin-1 in the myogenic program. Importantly, similar changes in N-glycosylation and the up-regulation of galectin-1 during postnatal skeletal muscle development were observed in mice. Treatment of new-born mice with recombinant adeno-associated viruses to overexpress galectin-1 in the musculature resulted in enhanced muscle mass. Our data form a valuable resource to further understand the glycobiology of myogenesis and will aid the development of intervention strategies to promote healthy muscle development or regeneration.

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.

Paramphistomosis, caused by the rumen fluke, Calicophoron daubneyi, is a parasitic infection of ruminant livestock which has seen a rapid rise in prevalence throughout Western Europe in recent years. Following ingestion of metacercariae (parasite cysts) by the mammalian host, newly-excysted juveniles (NEJs) emerge and invade the duodenal submucosa which causes significant pathology in heavy infections. The immature larvae then migrate upwards, along the gastrointestinal tract, and enter the rumen where they mature and begin to produce eggs. Despite their emergence, and sporadic outbreaks of acute disease, we know little about the molecular mechanisms used by C. daubneyi to establish infection, acquire nutrients and to avoid the host immune response. Here, transcriptome analysis of four intra-mammalian life-cycle stages, integrated with secretome analysis of the NEJ and adult parasites (responsible for acute and chronic disease respectively), revealed how the expression and secretion of selected families of virulence factors and immunomodulators are regulated in accordance with fluke development and migration. Our data show that whilst a family of cathepsins B with varying S2 sub-site residues (indicating distinct substrate specificities) are differentially secreted by NEJs and adult flukes, cathepsins L and F are secreted in low abundance by NEJs only. We found that C. daubneyi has an expanded family of aspartic peptidases, which is up-regulated in adult worms, although they are underrepresented in the secretome. The most abundant proteins in adult fluke secretions were helminth defence molecules (HDMs) that likely establish an immune environment permissive to fluke survival and/or neutralise pathogen-associated molecular patterns (PAMPs) such as bacterial lipopolysaccharide in the microbiome-rich rumen. The distinct collection of molecules secreted by C. daubneyi allowed the development of the first coproantigen-based ELISA for paramphistomosis which, importantly, did not recognise antigens from other helminths commonly found as co-infections with rumen fluke.

The complexity and dynamics of the immensely heterogeneous glycoproteome of the prostate cancer (PCa) tumour micro-environment remain incompletely mapped, a knowledge gap that impedes our molecular-level understanding of the disease. To this end, we have used sensitive glycomics and glycoproteomics to map the protein-, cell- and tumour grade-specific N- and O-glycosylation in surgically-removed PCa tissues spanning five histological grades (n = 10/grade) and tissues from patients with benign prostatic hyperplasia (n = 5). Quantitative glycomics revealed PCa grade-specific alterations of the oligomannosidic-, paucimannosidic- and branched sialylated complex-type N-glycans, and dynamic remodelling of the sialylated core 1- and core 2-type O-glycome. Deep quantitative glycoproteomics identified ~7,400 unique N-glycopeptides from 500 N-glycoproteins and ~500 unique O-glycopeptides from nearly 200 O-glycoproteins. With reference to a recent Tissue and Blood Atlas, our data indicate that paucimannosidic glycans of the PCa tissues arise mainly from immune cell-derived glycoproteins. Further, the grade-specific PCa glycosylation arises primarily from dynamics in the cellular makeup of the PCa tumour microenvironment across grades involving increased oligomannosylation of prostate-derived glycoproteins and decreased bisecting GlcNAcylation of N-glycans carried by the extracellular matrix proteins. Further, elevated expression of several oligosaccharyltransferase subunits and enhanced N-glycoprotein site occupancy were observed associated with PCa progression. Finally, correlations between the protein-specific glycosylation and PCa progression were observed including increased site-specific core 2-type O-glycosylation of collagen VI. In conclusion, integrated glycomics and glycoproteomics have enabled new insight into the complexity and dynamics of the tissue glycoproteome associated with PCa progression generating an important resource to explore the underpinning disease mechanisms.

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.

Alpha-1-acid glycoprotein (AGP) is an acute phase glycoprotein in blood, which is primarily synthetized in the liver and whose biological role is not completely understood. It consists of 45% carbohydrates that are present in the form of five N-linked complex glycans. AGP N-glycosylation was shown to be changed in many different diseases and some changes appear to be disease-specific, thus it has a great diagnostic and prognostic potential. However, AGP glycosylation was mainly analyzed in small cohorts and without detailed site-specific glycan information. Here, we developed a cost-effective method for a high-throughput and site-specific N-glycosylation LC-MS analysis of AGP which can be applied on large cohorts, aid in search for novel disease biomarkers and enable better understanding of AGP’s role and function in health and disease. The method does not require isolation of AGP with antibodies and affinity chromatography, but AGP is enriched by acid precipitation from 5 μl of bloodplasma in a 96 well format. After trypsinization, AGP glycopeptides are purified using a hydrophilic interaction chromatography based solid-phase extraction and analyzed by RP-LC-ESI-MS. We used our method to show for the first time that AGP N-glycan profile is stable in healthy individuals (14 individuals in 3 time points), which is a requirement for evaluation of its diagnostic potential. Furthermore, we tested our method on a population including individuals with registered hyperglycemia in critical illness (59 cases and 49 controls), which represents a significantly increased risk of developing type 2 diabetes. Individuals at higher risk of diabetes presented increased N-glycan branching on AGP’s second glycosylation site and lower sialylation of N-glycans on AGP’s third and AGP1’s fourth glycosylation site. Although this should be confirmed on a larger prospective cohort, it indicates that site-specific AGP N-glycan profile could help distinguish individuals who are at risk of type 2 diabetes.

COP26: What happened, what does this mean, and what happens next? Chatham House briefing NCapeling 15 November 2021

Analysing a crucial opportunity for enhancing ambitions on climate finance, adaptation, and ‘loss and damage’, and the implementation of the Paris Agreement.

Key findings

Raising the ambition of national emission reduction targets (nationally determined contributions – NDCs) was a critical task for COP26. On this front, governments fell short: although over 120 parties have submitted new or updated NDCs, the new targets only narrow the gap to 1.5°C by 15–17 per cent, and are, if fully implemented (and this is far from certain), projected to result in warming of 2.4°C by the end of the century.

If warming is to be limited to 1.5°C above pre-industrial levels, additional emissions reductions before 2030, over and above current NDC pledges, will need to equate to reducing emissions by the equivalent of two years of current annual emissions. To keep warming to 2°C, the equivalent reductions would be needed of one year’s total emissions.

The Glasgow Climate Pact – the main political outcome of COP26 – requests governments to revisit and strengthen their NDCs before the end of 2022 to bring these in line with the Paris Agreement’s temperature goal. To keep 1.5°C within reach, it will be absolutely essential that governments return to the table with significantly enhanced offers ahead of COP27, which will take place at Sharm El-Sheikh, Egypt, in 2022.

Another key feature of the Glasgow Climate Pact is the reference to ‘accelerating efforts towards the phasedown of unabated coal power and phase-out of inefficient fossil fuel subsidies’. Although the language was watered down over the course of the negotiations, COP26 marks the first time ever reducing fossil fuels is mentioned in a COP decision.

Discussions around climate finance, adaptation, and loss and damage were centre stage in Glasgow, and were critical points of contention. Although the Glasgow Climate Pact urges developed countries to ‘fully’ deliver on the $100 billion annual climate finance pledge through to 2025, it remains unclear when this sum will actually be raised in full – and if a total of $500 billion will be mobilized between 2020 and 2025 to make up for initial shortfalls.

And while the Pact urges developed countries to double their adaptation finance by 2025, and establishes a dialogue on loss and damage finance, much more will need to be done to address the needs of climate-vulnerable developing countries. 

COP26 saw a flurry of plurilateral deals on key issues such as phasing out various forms of fossil fuels and ending deforestation. These initiatives have the potential to accelerate decarbonization, but monitoring their implementation and holding governments and other institutions to account will be critical. Future COPs provide a platform for doing this, and governments should seek to incorporate the pledges made outside the formal remits of the UNFCCC process in their NDCs.

While some progress was made at COP26, the next 12 months will be crucial in determining if the formal agreements reached in Glasgow provide grounds for optimism that 1.5°C remains firmly in sight, and are sufficient to build trust between countries and between citizens and governments.

Read the full analysis

The road to COP27: In conversation with US Special Presidential Envoy for Climate John Kerry 27 October 2022 — 3:00PM TO 4:00PM Anonymous (not verified) 20 October 2022 Chatham House and Online

What will progress on climate change look like at COP27?

With global attention zeroing in on COP27, policymakers and world leaders will meet in Egypt to take the next step in the fight against the climate crisis. The planet is on course to warm well beyond 1.5°C and climate hazards are increasing our exposure to climate risk. Violent and unpredictable weather events increasingly leave devastation among communities, particularly in vulnerable countries.

At the same time, the ripple effects of the conflict in Ukraine will have wide-ranging economic, social and geopolitical consequences for years to come. Whilst some finance is being made available, more is needed to properly address the damage caused by climate change and fund the transition to net zero worldwide. These challenges have become more acute as the world grapples with a growing energy crisis, the war in Ukraine and a troubling economic outlook.

Joined by US Special Presidential Envoy for Climate John Kerry, the following questions are considered:

• Is ‘1.5 degrees’ still on track?

• How can countries better collaborate to move to net zero faster?

• How can we achieve progress on adaptation, climate finance, and loss and damage?

As with all members events, questions from the audience drive the conversation.

Read the transcript. 

The U.S. Navy began its deep-sea search this week for the remains of an MH-60S Sea Hawk helicopter and the remains of five sailors who died after the aircraft crashed into waters off the San Diego coast on Aug. 31.

New blood tests screen for colorectal cancer in a much less invasive way than colonoscopy, but deaths will increase if many people choose this alternative, a new study indicates.

The U.S. Department of Veterans Affairs announced plans Monday to eliminate copayments for all VA telehealth services, while expanding online emergency care access for rural veterans.

Lionsgate announced Monday that "Megalopolis" will be available for a $19.99 rental on video-on-demand Tuesday.

Suboxone is a medicine prescribed to treat opioid use disorder. But in recent times, it has gained a poor reputation for contributing to severe side effects, such as dental damage and decay. Many patients have had to undergo costly dental repair surgery to treat the gum and tooth issues they faced. But the side effects […]

The post How To Cope With the Psychological Symptoms of Suboxone Withdrawal first appeared on What is Psychology?.

In the aftermath of last month’s killing of an unarmed Minneapolis man in police custody, school systems are re-examining their own contracts with local police agencies.

In the aftermath of last month’s killing of an unarmed Minneapolis man in police custody, school systems are re-examining their own contracts with local police agencies.

This year at COP28, FAO will be advocating for global action on climate, agriculture and food security

For more than a year now, the world has been treated to breathtaking images of the outer reaches of our universe from the NASA instrument. But how does it even work? --- For more videos from Smithsonian Magazine: https://www.smithsonianmag.com/videos/ Digital Editorial Director: Brian Wolly Supervising Producer & Scriptwriter: Michelle Mehrtens Video Editor: Sierra Theobald

Some researchers initially dismissed the remains of Palaeopascichnus lineari as teeny turds from a bygone era

A new exhibition in New York City uses more than 200 texts and artifacts to contemplate Lincoln's rise to the nation's highest office

A new analysis suggests that the piece was created by several artists working in the Italian Renaissance painter's studio—and that Botticelli himself may have worked on important details

The final 3D atlas of the sky will help scientists study dark matter and dark energy, which make up 96 percent of the universe but remain mysterious

Winners of the Nikon Small World Photomicrography Competition captured insects, cancer cells, cat claws and more

The technique of visualizing axon pathways in the embryonic ventral nerve cord using antibody labeling has been fundamental to our understanding of the genetic and developmental mechanisms underlying nervous system wiring in Drosophila. High-resolution microscopic examination of the ventral nerve cord remains an essential component of many experiments in Drosophila developmental neuroscience. Although it is possible to examine the ventral nerve cord in intact whole-mount embryos, to collect the highest-quality images it is often useful to isolate the nervous system away from the other embryonic tissues through embryo dissection. This protocol describes methods for dissecting ventral nerve cords from Drosophila embryos that have been fixed and stained via immunofluorescence or horseradish peroxidase (HRP) immunohistochemistry. The process of making fine dissection needles for this purpose from electrolytically sharpened tungsten wire is also described. Dissected and mounted ventral nerve cords can be examined and imaged using a variety of microscopy techniques including differential interference contrast (DIC) optics, epifluorescence, or confocal microscopy.

The crowning achievement at last year's COP climate conference in Dubai was a global consensus on the need to "transition away from fossil fuels." This year, the conference had not even started yet before BBC News exposed senior organizers of using the event to arrange potential deals for fossil fuel expansion. The recent election of Donald Trump in the U.S. has added an additional layer of uncertainty to this year's meeting.

3D CAD software fuels cool aircraft design innovation, while halving design time and cutting costs

Relies on SolidWorks Simulation Software to Ensure Flight Worthiness, Safety

Minister of the DFFE Dion George is off to Azerbaijan with one of the onerous responsibilities of our time.