Mohamad Navab
Sep 1, 2000; 41:1495-1508
Articles

Mohamad Navab
Sep 1, 2000; 41:1481-1494
Articles

S Eisenberg
Oct 1, 1984; 25:1017-1058
Reviews

JM Dietschy
Oct 1, 1993; 34:1637-1659
Reviews

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

Expert

Fossil Fuels Expert Roundtable: How Solar is Shaping the Energy Transition 1 June 2018 — 9:00AM TO 10:30AM Anonymous (not verified) 22 May 2018 Chatham House, London

As global temperatures rise and extreme weather events multiply, doubts over the reality and imminence of climate change have dissipated. Despite this, there is a clear lack of urgency by governments to the approaching crisis. At this event, Prem Shankar Jha will set out what he believes are the three main causes for this inaction.

Furthermore, he will argue that catastrophic climate change is imminent, but even if it weren’t, the risk is too great to ignore. Only a complete shift from fossil fuels by 2070 at the latest would provide reasonable certainty of avoiding irreversible consequences. This transition is not only possible but the technologies to enable it were harnessed four to nine decades ago – and all of them draw their primary energy from the sun. These technologies are already capable of delivering electricity, transport fuels, and petrochemicals at prices that are competitive with the current delivered cost of electricity in the US and Western Europe. So what is holding up the energy shift?

Attendance at this event is by invitation only.

Energy transitions

Analysing and understanding the implications of the global energy transition, and what it means for states, communities and people facing these changes.

The world is undergoing an energy transformation, and at its heart is the need to reduce energy-related carbon emissions to limit climate change. But decarbonization of the energy sector – moving away from fossil fuels towards low carbon sources of energy – requires urgent action on a global scale.

Our work focuses on three primary components:

• Clean and renewable energy
• Energy access
• Extractives

This transition will be enabled by technological innovations, the market, improvements to policy and regulatory frameworks, and by increasing awareness – and actions – from consumers all over the world.

Carnosine (β-alanyl-l-histidine) and anserine (β-alanyl-3-methyl-l-histidine) are abundant peptides in the nervous system and skeletal muscle of many vertebrates. Many in vitro and in vivo studies demonstrated that exogenously added carnosine can improve muscle contraction, has antioxidant activity, and can quench various reactive aldehydes. Some of these functions likely contribute to the proposed anti-aging activity of carnosine. However, the physiological role of carnosine and related histidine-containing dipeptides (HCDs) is not clear. In this study, we generated a mouse line deficient in carnosine synthase (Carns1). HCDs were undetectable in the primary olfactory system and skeletal muscle of Carns1-deficient mice. Skeletal muscle contraction in these mice, however, was unaltered, and there was no evidence for reduced pH-buffering capacity in the skeletal muscle. Olfactory tests did not reveal any deterioration in 8-month-old mice lacking carnosine. In contrast, aging (18–24-month-old) Carns1-deficient mice exhibited olfactory sensitivity impairments that correlated with an age-dependent reduction in the number of olfactory receptor neurons. Whereas we found no evidence for elevated levels of lipoxidation and glycation end products in the primary olfactory system, protein carbonylation was increased in the olfactory bulb of aged Carns1-deficient mice. Taken together, these results suggest that carnosine in the olfactory system is not essential for information processing in the olfactory signaling pathway but does have a role in the long-term protection of olfactory receptor neurons, possibly through its antioxidant activity.

Intrinsically disordered protein domains often have multiple binding partners. It is plausible that the strength of pairing with specific partners evolves from an initial low affinity to a higher affinity. However, little is known about the molecular changes in the binding mechanism that would facilitate such a transition. We previously showed that the interaction between two intrinsically disordered domains, NCBD and CID, likely emerged in an ancestral deuterostome organism as a low-affinity interaction that subsequently evolved into a higher-affinity interaction before the radiation of modern vertebrate groups. Here we map native contacts in the transition states of the low-affinity ancestral and high-affinity human NCBD/CID interactions. We show that the coupled binding and folding mechanism is overall similar but with a higher degree of native hydrophobic contact formation in the transition state of the ancestral complex and more heterogeneous transient interactions, including electrostatic pairings, and an increased disorder for the human complex. Adaptation to new binding partners may be facilitated by this ability to exploit multiple alternative transient interactions while retaining the overall binding and folding pathway.

The recent structural elucidation of ex vivo Drosophila Orb2 fibrils revealed a novel amyloid formed by interdigitated Gln and His residue side chains belonging to the prion-like domain. However, atomic-level details on the conformational transitions associated with memory consolidation remain unknown. Here, we have characterized the nascent conformation and dynamics of the prion-like domain (PLD) of Orb2A using a nonconventional liquid-state NMR spectroscopy strategy based on 13C detection to afford an essentially complete set of 13Cα, 13Cβ, 1Hα, and backbone 13CO and 15N assignments. At pH 4, where His residues are protonated, the PLD is disordered and flexible, except for a partially populated α-helix spanning residues 55–60, and binds RNA oligos, but not divalent cations. At pH 7, in contrast, His residues are predominantly neutral, and the Q/H segments adopt minor populations of helical structure, show decreased mobility and start to self-associate. At pH 7, the His residues do not bind RNA or Ca2+, but do bind Zn2+, which promotes further association. These findings represent a remarkable case of structural plasticity, based on which an updated model for Orb2A functional amyloidogenesis is suggested.

24 July 2020

18 August 2020

Towards just transition in Africa: Green financing for urban energy solutions and job creation 9 June 2022 — 7:30AM TO 11:00AM Anonymous (not verified) 18 May 2022 Nairobi and online

This event explores the major openings and potential impediments to the development of a just transition policy in Africa.

Global climate policies towards a ‘just transition’ under the Paris Agreement should also align with and support African states’ national sustainable development priorities. In particular, the need for decent and fair job creation and the establishment of sufficient, resilient and sustainable power supply, accessible to all, and efficient energy use.

Achieving green growth requires innovative and more accessible financing models, especially as wealthy nations’ financial pledges have fallen short. Ahead of the ‘African COP27’ set to take place in Egypt in November 2022, there is a need for transformational strategic thinking and context-specific action from African governments, civil society, businesses and financiers in their green financing demands and national implementation plans.

Sustainable urban energy solutions represent a critical zone of opportunity for the development of new and more reliable green finance pathways. Africa’s rapidly expanding cities present a significant economic opportunity and source of growth. However, urban centres are also where income and energy inequalities are at their starkest. The acceleration of sustainable energy generation and use could have a transformative impact on SMEs and livelihoods across value chains.

At this event, participants will discuss the major openings and potential impediments to the development of a credible ‘just transition’ policy in Africa towards net zero goals, with a particular focus on establishing and enhancing links between green financing innovation, employment creation, sustainable power supply and generation, and sustainable energy usage and consumption in an urban environment.

This event is held in partnership with the Pan African Climate Justice Alliance (PACJA). It is part of a series on Towards Just Transition: Connecting Green Financing and Sustainable Job Creation in Africa, supported by the Chatham House Sustainability Accelerator.

This event will be held in English and French with simultaneous interpretation.

Towards just transition in Africa: Green financing for nature-based solutions and rural resilience 21 July 2022 — 9:30AM TO 1:00PM Anonymous (not verified) 30 June 2022 Libreville and online

This hybrid event in Libreville explores just transition policy and green financing for nature-based solutions, with a particular focus on the integration of job creation priorities in conservation and rural resilience.

Global climate policies towards a ‘just transition’ under the Paris Agreement should align with and support African states’ national sustainable development priorities – in particular, the need for decent and fair job creation, as well as resilient and sustainable land, environment, and ecosystem management policies.

Achieving green growth requires innovative and more accessible financing models, especially as wealthy nations’ financial pledges have fallen short. Ahead of the ‘African COP27’ set to take place in Egypt in November 2022, there is a need for transformational strategic thinking and context-specific action from African governments, civil society, businesses and financiers, in their green financing demands and national implementation plans.

Preservation of biodiversity and nature is not only critical in the global fight against climate change but is also vital for conservation-based economic development. Natural capital stocks, such as terrestrial and marine ecosystems and biodiversity, produce benefits that support societal and individual well-being and economic prosperity, such as clean air, fresh water, regulation of water flows and pollination of crops – while also acting as important carbon sinks. Financing environmental protection must go beyond compensation and contribute to creating fair social and economic conditions for incentivizing conservation.

At this hybrid event in Libreville, participants will discuss green financing for nature-based solutions, particularly the integration of plans for job creation in conservation and rural resilience within just transition planning.

This event is part of a series on Towards Just Transition: Connecting Green Financing and Sustainable Job Creation in Africa, supported by the Chatham House Sustainability Accelerator.

This event will be held in French and English with simultaneous interpretation.

This event will also be broadcast live on the Chatham House Africa Programme’s Facebook page.

Towards democracy in Sudan: Reflections on the transitional period 20 September 2022 — 2:00PM TO 4:00PM Anonymous (not verified) 31 August 2022 Online

In this webinar, panellists discuss the key outcomes of the evaluation workshop and reflect on how the experience of the transition to date should inform the realization of Sudan’s democratic aspirations going forward.

The military coup on 25 October 2021 halted Sudan’s transition to democracy and prospects for sustainable peace. Since then, members of the former regime have regained political influence, with many reinstated to senior positions.

The coup has provoked a strong reaction from the country’s pro-democracy movement and youth-led resistance committees who have led continuous peaceful protests demanding civilian democratic transition, despite a brutal crackdown by state security forces.

Those supportive of the coup have blamed the Forces of Freedom and Change (FFC), a wide coalition of pro-democracy political and civilian groups, for the mistakes of the transitional government.

However, the country’s political, security and economic situation has sharply deteriorated since the military’s action, and the progress achieved by the transitional government has been reversed, leading to an accelerating economic crisis, increased food insecurity and political instability.

The FFC, which played a key role in appointing the transitional government, has acknowledged its errors. In July 2022, it held a workshop in Khartoum, which was broadcast on social media, to evaluate its performance and identify lessons learned, in discussion with civil society actors and activists.

In this webinar, leading pro-democracy movement figures and independent experts discuss the key outcomes of the evaluation workshop and reflect on how the experience of the transition to date should inform the realization of Sudan’s democratic aspirations going forward.

This event is part of a Chatham House Africa programme project on supporting Sudan’s civilian-led democratic transition.

Towards just transition in Africa: Continental coordination on green financing and job creation 6 October 2022 — 7:00AM TO 3:30PM Anonymous (not verified) 8 September 2022 Addis Ababa and online

At this hybrid conference in Addis Ababa, speakers take stock of preparations ahead of the ‘African COP27’ in November and discuss the key priorities for streamlining continental cooperation on policy approaches to just transition.

At this hybrid conference in Addis Ababa, speakers will take stock of policy efforts and preparations ahead of the ‘African COP27’ in November and discuss the key priorities for streamlining continental cooperation on policy approaches to just transition.

Global climate policies towards a ‘just transition’ under the Paris Agreement should align with and support African states’ national sustainable development priorities – in particular, the need for decent and fair job creation, as well as resilient and sustainable land, environment and ecosystem management policies.

They must also be cognizant of African nations’ urgent requirements for sustainable and accessible energy to underpin economic development. Achieving green growth requires innovative and more accessible financing models, especially as wealthy nations’ financial pledges have fallen short. It also requires clarity and cooperation to unlock investment in both renewable and transitional energy.

African countries face collective climate and employment-related challenges. However, policymaking often remains regionally siloed according to differing political, energy sector and ecological realities. There is a need for transformational strategic thinking and context-specific action from African governments, civil society, businesses and financiers, in their green financing demands and national implementation plans.

At this hybrid conference in Addis Ababa, speakers will take stock of policy efforts and preparations ahead of the ‘African COP27’ in November and discuss the key priorities for streamlining continental cooperation on policy approaches to just transition, job creation and green financing.

This event is the third in a series on Towards just transition: Connecting green financing and sustainable job creation in Africa, supported by the Chatham House Sustainability Accelerator.

Towards just transition in Africa Interview Video NCapeling 23 December 2022

Highlighting key interventions from African policymakers, business leaders, researchers, and civil society voices on green financing and implementation plans.

African countries face collective climate and employment-related challenges. However, policymaking often remains regionally siloed according to differing political, energy sector, and ecological realities.

There is a need for transformational strategic thinking and context-specific action from African governments, civil society, businesses, and financiers, in their green financing demands and national implementation plans.

This video highlights key interventions from policymakers, business leaders, researchers, and civil society voices at a series of events hosted by the Chatham House Africa programme in Nairobi, Libreville, and Addis Ababa in the lead-up to COP27.

The events series, Towards just transition: Connecting green financing and sustainable job creation in Africa, was supported by the Chatham House Sustainability Accelerator and the United Nations Development Programme.

Africa Aware: Towards just transition in Africa Audio NCapeling 1 March 2023

African countries face collective climate and job creation-related challenges, yet policymaking often remains regionally siloed.

This podcast reflects on the key policy messages from the Africa programme’s series on Towards just transition: Connecting green financing and sustainable job creation in Africa.

African countries face collective climate and job creation-related challenges. Yet policymaking often remains regionally siloed according to differing political, energy sector and ecological realities.

This output is part of a stream of work supported by the Chatham House Sustainability Accelerator and the United Nations Development Programme (UNDP). 

A critical juncture for Sudan’s democratic transition Expert comment LJefferson 28 March 2023

International pressure is essential to reach an agreement that establishes a credible civilian government.

The signing of the Framework Agreement (FA) on 5 December 2022 between Sudan’s military leaders and its leading pro-democracy parties is a major step to reversing the damage done by the disastrous military coup in October 2021.

The FA removes any formal role for the military in Sudan’s politics. A civilian head of state and prime minister will select the cabinet and chair the Defence and Security Council. The armed forces will be prohibited from non-military business activities and security sector reform will lead to a unified, professional and non-partisan national army. Elections are due to take place at the end of a two-year transitional period. 

Signatories included General Abdel Fatah Al Burhan, chair of the Sovereign Council and head of the Sudanese Armed Forces (SAF), General Mohamed Hamdan Dagalo (known as Hemedti), his deputy and Commander of the paramilitary Rapid Support Forces (RSF) and more than 40 civilian entities, including the Forces of Freedom and Change- Central Council (FFC-CC), a few other political parties, former armed movements, civil society organizations and professional associations. However, the agreement has faced criticism from the street for not being sufficiently radical, has been overshadowed at times by heightened tension between the two military leaders, and has seen sabotage attempts by supporters of the Bashir regime.

Building consensus on the Framework Agreement

The agreement meets most of the demands of the anti-coup camp, at least on paper. Yet doubts persist as to whether the military are genuine about handing over power, particularly among the neighbourhood-based resistance committees – the heart of the youth-led mobilization that forced the military to recognize the failure of their power grab. Peaceful protests against the coup have seen 125 killed and over 8,000 injured by government security forces. Many want to see Burhan and Hemedti held accountable.

Recognizing the need to expand popular support, FFC-CC leaders have been reaching out to other pro-democracy forces to build a united civilian front. They report increased buy-in from some resistance committees in the last few months, recognizing that street protests alone were not sufficient to overthrow the coup, and that engagement with the military is necessary to find a way out of the impasse.

The FA offers the only currently available path to embedding civilian politics in Sudan and has received active diplomatic support from UNITAMS, AU and IGAD (who form the Tripartite Mechanism), the Troika of the US, UK and Norway, alongside the EU, as well as Saudi Arabia and the UAE (who are members of ‘the Quad’ with the US and UK).

Broader public participation has also been developed through a series of conferences, facilitated by the Tripartite Mechanism, on five contentious issues – dismantling the old regime, the Juba Peace Agreement, Eastern Sudan, Transitional Justice and Security Sector Reform. Recommendations will be incorporated in a final political agreement. 

The political process has been overshadowed by increasingly visible tension between Burhan and Hemedti, seen in parallel foreign visits, conflicting public statements, and a heavy military presence in Khartoum. But concerns that SAF and the RSF were heading towards confrontation appear to have been assuaged thanks to international pressure and preliminary agreements reached between military and civilian signatories of the FA on security sector reform and integration. In a significant breakthrough, both sides have now agreed to draft the final agreement and transitional constitution, with the aim of forming a civilian government by 11 April.  

Potential spoilers and interests from Sudan’s regions

Progress has been made, but significant challenges remain, notably from supporters of the former Bashir regime in ‘the deep state’ and from Sudan’s historically marginalized peripheries. Old regime elements have been intensifying social media campaigns to derail the agreement and drive a wedge between the SAF and RSF, and have been accused of deliberately inciting instability in the peripheries to undermine the democratic transition. 

The Popular Defence Forces, established by the National Islamic Front in the 1990s, have been reactivated under different names in several parts of the country and there are reports of mobilization and recruitment of armed militias in Darfur. The recent public appearance of Ali Karti, the Secretary-General of the Islamic Movement, who has close relations with Islamists in SAF, has also caused renewed concern.

Two Darfuri armed movement leaders who signed the October 2020 Juba Peace Agreement (JPA) and are members of the current military-led government, have not signed the FA, allegedly due to concerns about their representation in the next government.

Despite intensive efforts to bring them on board, there is continuing disagreement over the inclusion of other members of ‘the Democratic Bloc’, a political alliance backed by Sudan’s influential neighbour Egypt, which is reportedly angry at being excluded from the Quad. The FFC-CC say that the door is open for the two Darfuri leaders and some other political parties, but they will not allow the agreement to be ‘diluted’ with political forces who intend to torpedo the transition, including by imposing a weak prime minister.

Both Burhan and Hemedti have courted support from the regions. Burhan used the 2020 SAF takeover of Al Fashaga in the contested eastern border region with Ethiopia to boost his national standing and secure backing from local tribal leaders; while Hemedti has sought to position himself as a champion of the peripheries, particularly in his Darfur heartlands, while simultaneously advancing his business interests.

Competition between them in building domestic powerbases, as well as alliances with neighbouring states, risks reigniting tensions, particularly given deep grievances and contrasting ambitions between and among Sudan’s diverse regional leaders and communities.

Eugen Netz
Dec 1, 2020; 19:2157-2167
Technological Innovation and Resources

Philipp Emanuel Geyer
Dec 17, 2020; 0:RA120.002359v1-mcp.RA120.002359
Research

Post-transcriptional modifications of pre-mRNAs expand the diversity of proteomes in higher eukaryotes. In the brain, these modifications diversify the functional output of many critical neuronal signal molecules. In this study, we identified a brain-specific A-to-I RNA editing that changed glutamine to arginine (Q/R) at exon 20 and an alternative splicing of exon 4 in Tmem63b, which encodes a ubiquitously expressed osmosensitive cation channel. The channel isoforms lacking exon 4 occurred in ∼80% of Tmem63b mRNAs in the brain but were not detected in other tissues, suggesting a brain-specific splicing. We found that the Q/R editing was catalyzed by Adar2 (Adarb1) and required an editing site complementary sequence located in the proximal 5' end of intron 20. Moreover, the Q/R editing was almost exclusively identified in the splicing isoform lacking exon 4, indicating a coupling between the editing and the splicing. Elimination of the Q/R editing in brain-specific Adar2 knockout mice did not affect the splicing efficiency of exon 4. Furthermore, transfection with the splicing isoform containing exon 4 suppressed the Q/R editing in primary cultured cerebellar granule neurons. Thus, our study revealed a coupling between an RNA editing and a distant alternative splicing in the Tmem63b pre-mRNA, in which the splicing plays a dominant role. Finally, physiological analysis showed that the splicing and the editing coordinately regulate Ca2+ permeability and osmosensitivity of channel proteins, which may contribute to their functions in the brain.

Genta Kakiyama
Dec 1, 2020; 61:1629-1644
Research Articles

Roux-en-Y gastric bypass (RYGB) is one of the most commonly performed weight-loss procedures, but how severe obesity and RYGB affects circulating HDL-associated microRNAs (miRNAs) remains unclear. Here, we aim to investigate how HDL-associated miRNAs are regulated in severe obesity and how weight loss after RYGB surgery affects HDL-miRNAs. Plasma HDL were isolated from patients with severe obesity (n=53) before, 6 and 12 months after RYGB by immunoprecipitation using goat anti-human apoA-I microbeads. HDL were also isolated from 18 healthy participants. miRNAs were extracted from isolated HDL and levels of miR-24, miR-126, miR-222 and miR-223 were determined by TaqMan miRNA assays. We found that HDL-associated miR-126, miR-222 and miR-223 levels, but not miR-24 levels, were significantly higher in patients with severe obesity when compared with healthy controls. There were significant increases in HDL-associated miR-24, miR-222 and miR-223 at 12 months after RYGB. Additionally, cholesterol efflux capacity and paraoxonase (PON1) activity were increased and intracellular adhesion molecule-1 (ICAM-1) levels decreased. The increases in HDL-associated miR-24 and miR-223 were positively correlated with increase in cholesterol efflux capacity (r=0.326, P=0.027 and r=0.349, P=0.017 respectively). An inverse correlation was observed between HDL-associated miR-223 and ICAM-1 at baseline. Together, these findings show that HDL-associated miRNAs are differentially regulated in healthy versus patients with severe obesity and are altered after RYGB. These findings provide insights into how miRNAs are regulated in obesity before and after weight reduction, and may lead to the development of novel treatment strategies for obesity and related metabolic disorders.

The analysis of T cell lipid raft proteome is challenging due to the highly dynamic nature of rafts and the hydrophobic character of raft-resident proteins. We explored an innovative strategy for bottom-up lipid raftomics based on suspension-trapping (S-Trap) sample preparation. Mouse T cells were prepared from splenocytes by negative immunoselection, and rafts were isolated by a detergent-free method and OptiPrep gradient ultracentrifugation. Microdomains enriched in flotillin-1, LAT, and cholesterol were subjected to proteomic analysis through an optimized protocol based on S-Trap and high pH fractionation, followed by nano-LC-MS/MS. Using this method, we identified 2,680 proteins in the raft-rich fraction and established a database of 894 T cell raft proteins. We then performed a differential analysis on the raft-rich fraction from nonstimulated versus anti-CD3/CD28 T cell receptor (TCR)-stimulated T cells. Our results revealed 42 proteins present in one condition and absent in the other. For the first time, we performed a proteomic analysis on rafts from ex vivo T cells obtained from individual mice, before and after TCR activation. This work demonstrates that the proposed method utilizing an S-Trap-based approach for sample preparation increases the specificity and sensitivity of lipid raftomics.

NAFLD is an important public health issue closely associated with the pervasive epidemics of diabetes and obesity. Yet, despite NAFLD being among the most common of chronic liver diseases, the biological factors responsible for its transition from benign nonalcoholic fatty liver (NAFL) to NASH remain unclear. This lack of knowledge leads to a decreased ability to find relevant animal models, predict disease progression, or develop clinical treatments. In the current study, we used multiple mouse models of NAFLD, human correlation data, and selective gene overexpression of steroidogenic acute regulatory protein (StarD1) in mice to elucidate a plausible mechanistic pathway for promoting the transition from NAFL to NASH. We show that oxysterol 7α-hydroxylase (CYP7B1) controls the levels of intracellular regulatory oxysterols generated by the "acidic/alternative" pathway of cholesterol metabolism. Specifically, we report data showing that an inability to upregulate CYP7B1, in the setting of insulin resistance, results in the accumulation of toxic intracellular cholesterol metabolites that promote inflammation and hepatocyte injury. This metabolic pathway, initiated and exacerbated by insulin resistance, offers insight into approaches for the treatment of NAFLD.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most aggressive cancers and known for its extensive genetic heterogeneity, high therapeutic resistance, and strong variation in intrinsic radiosensitivity. To understand the molecular mechanisms underlying radioresistance, we screened the phenotypic response of 38 PDAC cell lines to ionizing radiation. Subsequent phosphoproteomic analysis of two representative sensitive and resistant lines led to the reproducible identification of 7,800 proteins and 13,000 phosphorylation sites (p-sites). Approximately 700 p-sites on 400 proteins showed abundance changes after radiation in all cell lines regardless of their phenotypic sensitivity. Apart from recapitulating known radiation response phosphorylation markers such as on proteins involved in DNA damage repair, the analysis uncovered many novel members of a radiation-responsive signaling network that was apparent only at the level of protein phosphorylation. These regulated p-sites were enriched in potential ATM substrates and in vitro kinase assays corroborated 10 of these. Comparing the proteomes and phosphoproteomes of radiosensitive and -resistant cells pointed to additional tractable radioresistance mechanisms involving apoptotic proteins. For instance, elevated NADPH quinine oxidoreductase 1 (NQO1) expression in radioresistant cells may aid in clearing harmful reactive oxygen species. Resistant cells also showed elevated phosphorylation levels of proteins involved in cytoskeleton organization including actin dynamics and focal adhesion kinase (FAK) activity and one resistant cell line showed a strong migration phenotype. Pharmacological inhibition of the kinases FAK by Defactinib and of CHEK1 by Rabusertib showed a statistically significant sensitization to radiation in radioresistant PDAC cells. Together, the presented data map a comprehensive molecular network of radiation-induced signaling, improves the understanding of radioresistance and provides avenues for developing radiotherapeutic strategies.

Cross-linking MS (XL-MS) has been recognized as an effective source of information about protein structures and interactions. In contrast to regular peptide identification, XL-MS has to deal with a quadratic search space, where peptides from every protein could potentially be cross-linked to any other protein. To cope with this search space, most tools apply different heuristics for search space reduction. We introduce a new open-source XL-MS database search algorithm, OpenPepXL, which offers increased sensitivity compared with other tools. OpenPepXL searches the full search space of an XL-MS experiment without using heuristics to reduce it. Because of efficient data structures and built-in parallelization OpenPepXL achieves excellent runtimes and can also be deployed on large compute clusters and cloud services while maintaining a slim memory footprint. We compared OpenPepXL to several other commonly used tools for identification of noncleavable labeled and label-free cross-linkers on a diverse set of XL-MS experiments. In our first comparison, we used a data set from a fraction of a cell lysate with a protein database of 128 targets and 128 decoys. At 5% FDR, OpenPepXL finds from 7% to over 50% more unique residue pairs (URPs) than other tools. On data sets with available high-resolution structures for cross-link validation OpenPepXL reports from 7% to over 40% more structurally validated URPs than other tools. Additionally, we used a synthetic peptide data set that allows objective validation of cross-links without relying on structural information and found that OpenPepXL reports at least 12% more validated URPs than other tools. It has been built as part of the OpenMS suite of tools and supports Windows, macOS, and Linux operating systems. OpenPepXL also supports the MzIdentML 1.2 format for XL-MS identification results. It is freely available under a three-clause BSD license at https://openms.org/openpepxl.

The goal of clinical proteomics is to identify, quantify, and characterize proteins in body fluids or tissue to assist diagnosis, prognosis, and treatment of patients. In this way, it is similar to more mature omics technologies, such as genomics, that are increasingly applied in biomedicine. We argue that, similar to those fields, proteomics also faces ethical issues related to the kinds of information that is inherently obtained through sample measurement, although their acquisition was not the primary purpose. Specifically, we demonstrate the potential to identify individuals both by their characteristic, individual-specific protein levels and by variant peptides reporting on coding single nucleotide polymorphisms. Furthermore, it is in the nature of blood plasma proteomics profiling that it broadly reports on the health status of an individual – beyond the disease under investigation. Finally, we show that private and potentially sensitive information, such as ethnicity and pregnancy status, can increasingly be derived from proteomics data. Although this is potentially valuable not only to the individual, but also for biomedical research, it raises ethical questions similar to the incidental findings obtained through other omics technologies. We here introduce the necessity of - and argue for the desirability for - ethical and human rights-related issues to be discussed within the proteomics community. Those thoughts are more fully developed in our accompanying manuscript. Appreciation and discussion of ethical aspects of proteomic research will allow for deeper, better-informed, more diverse, and, most importantly, wiser guidelines for clinical proteomics.

Africa and Europe: Cooperation on digital transitions and new technologies 26 May 2022 — 8:00AM TO 12:30PM Anonymous (not verified) 12 May 2022 Online

The 11th Africa Day International Conference takes place under the auspices of the president of the Republic of Slovenia, HE Mr Borut Pahor, and within the framework of the Bled Strategic Forum.

Slovenia’s annual high-level Africa event seeks to improve policy outcomes for citizens in Europe and Africa as a result of a mutual understanding and strengthened cooperation between the two regions.

The event is co-hosted by the Ministry of Foreign Affairs of the Republic of Slovenia, the Chatham House Africa Programme and the European Commission.

Expert discussions at this year’s edition will examine collaborative links between Africa and Europe in promoting responsible innovation and governance of emerging technologies, as well as the role of technology in shaping creative and cultural economies.

The conference will be broadcast live on this website, on the Slovenian Ministry of Foreign Affairs website and on the Africa Programme Facebook page.

Unspecific bone uptake (UBU) related to [¹⁸F]PSMA-1007 PET/CT imaging represents a clinical challenge. We aimed to assess whether a combination of clinical, biochemical, and imaging parameters could predict skeletal metastases in patients with [¹⁸F]PSMA-1007 bone focal uptake, aiding in result interpretation. Methods: We retrospectively analyzed [¹⁸F]PSMA-1007 PET/CT performed in hormone-sensitive prostate cancer (PCa) patients at 3 tertiary-level cancer centers. A fourth center was involved in performing an external validation. For each, a volume of interest was drawn using a threshold method to extract SUV_max, SUV_mean, PSMA tumor volume, and total lesion PSMA. The same volume of interest was applied to CT images to calculate the mean Hounsfield units (HU_mean) and maximum Hounsfield units. Clinical and laboratory data were collected from electronic medical records. A composite reference standard, including follow-up histopathology, biochemistry, and imaging data, was used to distinguish between PCa bone metastases and UBU. PET readers with less (n = 2) or more (n = 2) experience, masked to the reference standard, were asked to visually rate a subset of focal bone uptake (n = 178) as PCa metastases or not. Results: In total, 448 bone [¹⁸F]PSMA-1007 focal uptake specimens were identified in 267 PCa patients. Of the 448 uptake samples, 188 (41.9%) corresponded to PCa metastases. Ongoing androgen deprivation therapy at PET/CT (P < 0.001) with determination of SUV_max (P < 0.001) and HU_mean (P < 0.001) independently predicted bone metastases. A composite prediction score, the bone uptake metastatic probability (BUMP) score, achieving an area under the receiver-operating-characteristic curve (AUC) of 0.87, was validated through a 10-fold internal and external validation (n = 89 bone uptake, 51% metastatic; AUC, 0.92). The BUMP score’s AUC was significantly higher than that of HU_mean (AUC, 0.62) and remained high among lesions with HU_mean in the first tertile (AUC, 0.80). A decision-curve analysis showed a higher net benefit with the score. Compared with the visual assessment, the BUMP score provided added value in terms of specificity in less-experienced PET readers (88% vs. 54%, P < 0.001). Conclusion: The BUMP score accurately distinguished UBU from bone metastases in PCa patients with [¹⁸F]PSMA-1007 focal bone uptake at PET imaging, offering additional value compared with the simple assessment of the osteoblastic CT correlate. Its use could help clinicians interpret imaging results, particularly those with less experience, potentially reducing the risk of patient overstaging.

The historic ocean liner SS United States, whose fate had been in limbo for years, will begin its transition into the world's largest sunken artificial reef beginning this week in Philadelphia, its owner says.

Haiti's ruling transitional council has fired Prime Minister Garry Conille, six months after the doctor and former UNICEF Latin America head was appointed to lead the troubled nation.

Jenni Farley discusses her directorial debut "Devon," streaming and on video-on-demand Tuesday, and how she applied her love of horror movies to making one.

These tools encourage school administrators to gather as much information as possible about the students who will be entering kindergarten and the early-learning offerings in their communities.

DeVos slammed for remarks on HBCU's, a new Senate measure could overturn Obama-era ESSA rules on accountability, and more.

Social protection and decent jobs are cornerstones of agrifood systems transformation, but they require strong political commitment

Transitions: Photographs by Robert Creamer

The Solar Dynamics Observatory captured this epic footage of Venus crossing the face of the sun on June 5, 2012

Building highways isn't the only solution to the growing problem of traffic congestion in and around the Halifax Regional Municipality, says the head of an organization that advocates for rail-based public transit.

The Surrey Police Service is less than three weeks from taking over from the RCMP to manage policing in British Columbia's second most populous municipality, but there's still no formal deal on how responsibilities will be split between the two forces.

Several firearms, body armour, diamonds and fentanyl shaped like dog treats were among the items seized in a recent bust, say Metro Vancouver Transit Police.

OC Transpo is short $120 million for next year, and Wednesday's draft budget will shed light on who can expect to pay the bill.

A Transform 2012 Dancelink team in Mondim, Portugal, clears the way for a Transform Transit team to see the Gospel bear fruit four months later.