Tonie Fares and Pascal Lefèvre
Proc. Amer. Math. Soc. 148 (2020), 2487-2496.
Abstract, references and article information

IntroductionThe nucleolus is the central organelle within eukaryotic cells whose primary function is to generate ribosomes, the major protein producing machines within all cells. New roles for the nucleolus are continuously emerging as we explore its molecular intricacies. Despite the central and fundamental role of the nucleolus in cell biology, there has previously been no single official meeting that enables the gathering of scientists whose research converges on the nucleolus. As a result, the community of researchers who study this organelle risks fragmentation across disciplines. The Emerging Roles for the Nucleolus Symposium, which has now taken place twice on a biennial basis, first in 2017 (1) and again in 2019, therefore, represents the first of its kind. The overarching goals of this symposium are (a) to convene researchers who study the nucleolus across model systems (yeast, nematodes, fruit flies, mouse, human cell lines) and biological perspectives (structural, biophysical, molecular, cellular, pathophysiology), (b) to share and disseminate the latest research breakthroughs in nucleolar biology, (c) to promote interaction, engagement, and collaboration centered on the nucleolus across disciplines, and (d) to provide trainees and early career investigators with an organelle-specific scientific community of support.The second Emerging Roles for the Nucleolus meeting was sponsored by the American Society for Biochemistry and Molecular Biology and was held at the Stowers Institute for Medical Research in Kansas City, MO, from October 24 to October 27, 2019. It was organized by Jennifer Gerton (Stowers Institute), Francesca Duncan (Northwestern University Feinberg School of Medicine), and Craig Pikaard...

VOLUME 285 (2010) PAGES 13742–13747In Fig. 1E, passage 10, the splicing of a non-adjacent lane from the same immunoblot was not marked. This error has now been corrected and does not affect the results or conclusions of this work.jbc;295/16/5533/F1F1F1Figure 1E.

Pyruvate kinase muscle isoform 2 (PKM2) is a key glycolytic enzyme involved in ATP generation and critical for cancer metabolism. PKM2 is expressed in many human cancers and is regulated by complex mechanisms that promote tumor growth and proliferation. Therefore, it is considered an attractive therapeutic target for modulating tumor metabolism. Various stimuli allosterically regulate PKM2 by cycling it between highly active and less active states. Several small molecules activate PKM2 by binding to its intersubunit interface. Serine and cysteine serve as an activator and inhibitor of PKM2, respectively, by binding to its amino acid (AA)-binding pocket, which therefore represents a potential druggable site. Despite binding similarly to PKM2, how cysteine and serine differentially regulate this enzyme remains elusive. Using kinetic analyses, fluorescence binding, X-ray crystallography, and gel filtration experiments with asparagine, aspartate, and valine as PKM2 ligands, we examined whether the differences in the side-chain polarity of these AAs trigger distinct allosteric responses in PKM2. We found that Asn (polar) and Asp (charged) activate PKM2 and that Val (hydrophobic) inhibits it. The results also indicate that both Asn and Asp can restore the activity of Val-inhibited PKM2. AA-bound crystal structures of PKM2 displayed distinctive interactions within the binding pocket, causing unique allosteric effects in the enzyme. These structure-function analyses of AA-mediated PKM2 regulation shed light on the chemical requirements in the development of mechanism-based small-molecule modulators targeting the AA-binding pocket of PKM2 and provide broader insights into the regulatory mechanisms of complex allosteric enzymes.

pncRNA-D is an irradiation-induced 602-nt long noncoding RNA transcribed from the promoter region of the cyclin D1 (CCND1) gene. CCND1 expression is predicted to be inhibited through an interplay between pncRNA-D and RNA-binding protein TLS/FUS. Because the pncRNA-D–TLS interaction is essential for pncRNA-D–stimulated CCND1 inhibition, here we studied the possible role of RNA modification in this interaction in HeLa cells. We found that osmotic stress induces pncRNA-D by recruiting RNA polymerase II to its promoter. pncRNA-D was highly m6A-methylated in control cells, but osmotic stress reduced the methylation and also arginine methylation of TLS in the nucleus. Knockdown of the m6A modification enzyme methyltransferase-like 3 (METTL3) prolonged the half-life of pncRNA-D, and among the known m6A recognition proteins, YTH domain-containing 1 (YTHDC1) was responsible for binding m6A of pncRNA-D. Knockdown of METTL3 or YTHDC1 also enhanced the interaction of pncRNA-D with TLS, and results from RNA pulldown assays implicated YTHDC1 in the inhibitory effect on the TLS–pncRNA-D interaction. CRISPR/Cas9-mediated deletion of candidate m6A site decreased the m6A level in pncRNA-D and altered its interaction with the RNA-binding proteins. Of note, a reduction in the m6A modification arrested the cell cycle at the G0/G1 phase, and pncRNA-D knockdown partially reversed this arrest. Moreover, pncRNA-D induction in HeLa cells significantly suppressed cell growth. Collectively, these findings suggest that m6A modification of the long noncoding RNA pncRNA-D plays a role in the regulation of CCND1 gene expression and cell cycle progression.

Incorporation of ribonucleotides into DNA can severely diminish genome integrity. However, how ribonucleotides instigate DNA damage is poorly understood. In DNA, they can promote replication stress and genomic instability and have been implicated in several diseases. We report here the impact of the ribonucleotide rATP and of its naturally occurring damaged analog 1,N6-ethenoadenosine (1,N6-ϵrA) on translesion synthesis (TLS), mediated by human DNA polymerase η (hpol η), and on RNase H2–mediated incision. Mass spectral analysis revealed that 1,N6-ϵrA in DNA generates extensive frameshifts during TLS, which can lead to genomic instability. Moreover, steady-state kinetic analysis of the TLS process indicated that deoxypurines (i.e. dATP and dGTP) are inserted predominantly opposite 1,N6-ϵrA. We also show that hpol η acts as a reverse transcriptase in the presence of damaged ribonucleotide 1,N6-ϵrA but has poor RNA primer extension activities. Steady-state kinetic analysis of reverse transcription and RNA primer extension showed that hpol η favors the addition of dATP and dGTP opposite 1,N6-ϵrA. We also found that RNase H2 recognizes 1,N6-ϵrA but has limited incision activity across from this lesion, which can lead to the persistence of this detrimental DNA adduct. We conclude that the damaged and unrepaired ribonucleotide 1,N6-ϵrA in DNA exhibits mutagenic potential and can also alter the reading frame in an mRNA transcript because 1,N6-ϵrA is incompletely incised by RNase H2.

The ribosome biogenesis factor Las1 is an essential endoribonuclease that is well-conserved across eukaryotes and a newly established member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain-containing nuclease family. HEPN nucleases participate in diverse RNA cleavage pathways and share a short HEPN nuclease motif (RφXXXH) important for RNA cleavage. Most HEPN nucleases participate in stress-activated RNA cleavage pathways; Las1 plays a fundamental role in processing pre-rRNA. Underscoring the significance of Las1 function in the cell, mutations in the human LAS1L (LAS1-like) gene have been associated with neurological dysfunction. Two juxtaposed HEPN nuclease motifs create Las1's composite nuclease active site, but the roles of the individual HEPN motif residues are poorly defined. Here using a combination of in vivo experiments in Saccharomyces cerevisiae and in vitro assays, we show that both HEPN nuclease motifs are required for Las1 nuclease activity and fidelity. Through in-depth sequence analysis and systematic mutagenesis, we determined the consensus HEPN motif in the Las1 subfamily and uncovered its canonical and specialized elements. Using reconstituted Las1 HEPN-HEPN' chimeras, we defined the molecular requirements for RNA cleavage. Intriguingly, both copies of the Las1 HEPN motif were important for nuclease function, revealing that both HEPN motifs participate in coordinating the RNA within the Las1 active site. We also established that conformational flexibility of the two HEPN domains is important for proper nuclease function. The results of our work reveal critical information about how dual HEPN domains come together to drive Las1-mediated RNA cleavage.

The Government today said the first batch of subsidies amounting to $5.6 million under two relief measures for recyclers has been disbursed, while $5.6 million in subsidies had been approved under a management sector support scheme.

The two Recycling Fund measures aim to help the recycling industry cope with the current economic situation and recent operational difficulties arising from the COVID-19 epidemic.

The Advisory Committee on Recycling Fund announced in mid-March to reserve $100 million to launch the One-off Recycling Industry Anti-epidemic Scheme.

The scheme provides timely financial support to help with recyclers’ operational costs for six months. The funding limit for each recycler is $20,000 per month from January 1 to June 30, or $120,000 in total maximum subsidy.

The committee has also allocated additional funds to extend the earlier-launched One-off Rental Support Scheme for another six months, providing a total funding of $200 million to fight the virus and help the recycling industry ride out the difficult times.

The rental support scheme, which benefits street-corner recycling shops and recycling sites, originally ran from October to March. It has been extended for six months until September this year, totalling 12 months.

The monthly rental subsidy for each recycler is capped at $25,000, setting the maximum total rental subsidy at $300,000.

Separately, the Anti-epidemic Support Scheme for Property Management Sector has approved 205 applications involving around $5.6 million in subsidies to benefit more than 1,500 building blocks.

The relevant property management companies and owners’ organisations will receive notifications for subsidy disbursement shortly.

The list of properties for which applications have been approved is available online.

Briefing sessions were held earlier to introduce the scheme to the property management sector and owners’ organisations.

The maximum monthly rental subsidy for each recycler under the One-off Rental Support Scheme will be increased from $25,000 to $37,500, the Environmental Protection Department announced today.

To help the recycling industry cope with the current economic situation and operational difficulties due to the COVID-19 epidemic, the Recycling Fund has allocated $50 million in additional funds to raise the scheme’s subsidy level.

The fund has now earmarked up to $250 million in total funding to fight the virus and help the recycling industry ride out difficult times.

On April 15, the Advisory Committee on Recycling Fund agreed to strengthen support under the scheme by increasing the rental assistance from 50% to 75% for the subsidy period from April to September.

The maximum monthly rental subsidy for each recycler will be increased to $37,500, while the maximum total rental subsidy for the 12 months will be increased from $300,000 to $375,000.

The scheme was launched last year to benefit about 500 street-corner recycling shops and 400 recycling sites.

In the face of current economic difficulties, the fund announced in February an extension of the subsidy period from six months to 12 months, lasting until September.     

As of April 9, the scheme has approved 103 applications, involving subsidies of more than $20 million.

The application deadline for the scheme is September 30. Enquiries can be made to 2788 5658 or via email.

Various government departments, together with volunteers today conducted a shoreline clean-up along the remote rocky beach in Kung Pui Wan, Tap Mun to remove two tonnes of refuse.

The Environmental Protection Department, the Food & Environmental Hygiene Department (FEHD) and the Marine Department participated in the operation.

The Inter-departmental Working Group on Marine Environmental Management said the beach, facing the windy and wavy sea, is not easily accessible by working vessels and the rough terrain connecting the rocky beach also increases the difficulty of routine cleaning work.

FEHD cleaners along with the volunteers packed the refuse and delivered it on foot to a nearby pier for temporary storage. FEHD staff then took the refuse to the Marine Department's collection vessel in batches for onward delivery to a rubbish collection point for centralised handling.

To minimise the risk of spreading COVID-19, the operation was carried out in groups of no more than four participants each. They maintained an appropriate distance from each other and paid heed to personal protection, including wearing masks.

The working group thanked the volunteers for taking part and called on the public to keep the countryside and shoreline clean during outings.

For information on clean shorelines, visit the Clean Shorelines facebook and Instagram pages.

Stretching from Sai Kung on the east coast to Tuen Mun in the west, the whopping 100 km-long MacLehose Trail is the longest and first long-distance hiking trail in Hong Kong.

The trail is divided into 10 sections and traverses eight country parks which embrace magnificent natural scenery, interesting historical relics and a wide range of wild fauna and flora, winding past the coastline, rugged mountains, valleys and reservoirs to provide a diverse outdoor experience for hikers.

It was even named as one of the world's 20 dream trails by National Geographic.

A lot of hard work went into building the trail, with Agriculture, Fisheries & Conservation Department workers out in the elements without much shelter, often carrying heavy equipment uphill and downhill over varied terrain.

Building bonds

Wan Keung and Lai Hing joined the department around 40 years ago. They both took part in the MacLehose Trail project which was started in 1979 to promote hiking activities in Hong Kong.

The project was named after the then-Governor Sir Murray MacLehose - who was himself a keen walker - for his significant efforts to conserve Hong Kong’s countryside.

“I have contributed a lot to the trail. I am happy as it is packed with people now,” said Mr Wan.

While Mr Lai added: “We are going to retire, but the trail will be here for a long time.”

Despite working on the same project, the pair - now in their 60s - only met for the first time recently because they were assigned to different work stations back then. However, they became firm friends instantly.

From setting up the many signposts along the way, to hand-building the heavy stone steps, the two men eagerly shared all the skills and techniques they learnt on the project.

Listening to their conversations now it is hard to imagine that when they first started work, both had little practical knowledge about constructing a trail. They acquired welding, plastering and woodwork skills through hands-on experience and with the support of their seniors. But that was not the biggest challenge they encountered.

“Building the trail was really difficult, as there were so many sections. We were either drowned in sweat or drenched by rain while working,” Mr Lai explained.

One poignant memory for Mr Wan was of working during wildfires that raged through the countryside.

“There was only one thing for it: we stayed until the fire was extinguished. That was really hard.”

Lasting legacy

After nine months’ hard work the MacLehose Trail was finally opened on October 26, 1979.

These days Mr Wan and Mr Lai enjoy the trail for leisure instead of work.

Both said receiving compliments from family and friends or witnessing the sheer enjoyment of hikers on the trail made their hard work worthwhile.

They now hope to pass on their skills to the younger workers, so that a new generation of Hong Kong people can take care of the trail and ensure it lasts for decades to come.

(University of Barcelona) The yellow-legged gull has a high ability to adapt to human activities and benefit from these as a food resource during all year. This is stated in a scientific article published in the journal Ecology and Evolution whose first author is the researcher Francisco Ramírez, from the Faculty of Biology and the Biodiversity Research Institute (IRBio) of the University of Barcelona.

(Clemson University) While the world admires the beauty and fragrance of flowers, most of us are missing out on the extraordinary processes these seemingly delicate life forms are carrying out every moment of the day. Matthew Koski, an assistant professor at Clemson, is not only paying attention, he is advancing his research with a three-year, $455,000 grant from the NSF for a study of flower adaptations titled 'Modifying the floral microenvironment: elevational divergence in floral thermoregulatory mechanisms.'

Patrick Herr
Apr 1, 2020; 19:608-623
Research

Élie Lambert
May 1, 2020; 19:808-827
Research

Karl A. T. Makepeace
Apr 1, 2020; 19:624-639
Research

8 May 2019

This paper sets out a roadmap for how organizations in the civil nuclear sector can explore their options and review their cyber risk exposure.

24 July 2019

Cyberattacks are increasingly challenging critical national infrastructure. This paper considers the security by design approach for civil nuclear power plants and analyses areas of risk and opportunities for the nuclear industry.

This project aims to improve resilience in NATO’s nuclear weapons systems against cyber threats.

This programme of work addresses the conundrum of nuclear weapons as a wicked problem in a complex adaptive system.

20 April 2020

Nuclear deterrence theory, with its roots in the Cold War era, may not account for all eventualities in the 21st century. Researchers at Chatham House have worked with eight experts to produce this collection of essays examining four contested themes in contemporary policymaking on deterrence.

1 May 2020

28 April 2020

This paper aims to assist the region’s local authorities, and their key foreign backers, in understanding how transitional justice can provide alternative avenues for holding local ISIS members to account while contributing to the healing of communities.

1 May 2020

Research Event

Haid Haid, Senior Consulting Fellow, Middle East and North Africa Programme, Chatham House
Sara Kayyali, Syria Researcher, Middle East and North Africa Division, Human Rights Watch
Moderator: Lina Khatib, Director, Middle East and North Africa Programme, Chatham House

Objective: To develop a novel approach to generate individual maps of white matter (WM) innate immune cell activation using ¹⁸F-DPA-714 translocator protein (TSPO) positron emission tomography (PET), and to explore the relationship between these maps and individual trajectories of disability worsening in patients with multiple sclerosis (MS). Methods: Patients with MS (n = 37), whose trajectories of disability worsening over the 2 years preceding study entry were calculated, and healthy controls (n = 19) underwent magnetic resonance magnetic and ¹⁸F-DPA-714 PET. A threshold of significant activation of ¹⁸F-DPA-714 binding was calculated with a voxel-wise randomized permutation-based comparison between patients and controls, and used to classify each WM voxel in patients as characterized by a significant activation of innate immune cells (DPA+) or not. Individual maps of innate immune cell activation in the WM were employed to calculate the extent of activation in WM regions-of-interests and to classify each WM lesion as "DPA-active", "DPA-inactive" or "unclassified". Results: Compared with the WM of healthy controls, patients with MS had a significantly higher percentage of DPA+ voxels in the normal-appearing WM, (NAWM in patients=24.9±9.7%; WM in controls=14.0±7.8%, p<0.001). In patients with MS, the percentage of DPA+ voxels showed a significant increase from NAWM, to perilesional areas, T2 hyperintense lesions and T1 hypointense lesions (38.1±13.5%, 45.0±17.9%, and 51.9±22.9%, respectively, p<0.001). Among the 1379 T2 lesions identified, 512 were defined as DPA-active and 258 as DPA-inactive. A higher number of lesions classified as DPA-active (OR=1.13, P = 0.009), a higher percentage of DPA+ voxels in the NAWM (OR=1.16, P = 0.009) and in T1-spin-echo lesions (OR=1.06, P = 0.036), were significantly associated with a retrospective more severe clinical trajectory in patients with MS. Conclusion: A more severe trajectory of disability worsening in MS is associated with an innate immune cells activation inside and around WM lesions. ¹⁸F-DPA-714 PET may provide a promising biomarker to identify patients at risk of severe clinical trajectory.

Background: Radiopharmaceutical dosimetry depends on the localization in space and time of radioactive sources and requires the estimation of the amount of energy emitted by the sources deposited within targets. In particular, when computing resources are not accessible, this task can be carried out using precomputed tables of Specific Absorbed Fractions (SAFs) or S values based on dosimetric models. The OpenDose collaboration aims to generate and make freely available a range of dosimetric data and tools. Methods: OpenDose brings together resources and expertise from 18 international teams to produce and compare traceable dosimetric data using 6 of the most popular Monte Carlo codes in radiation transport (EGSnrc/EGS++, FLUKA, GATE, Geant4, MCNP/MCNPX and PENELOPE). SAFs are uploaded, together with their associated statistical uncertainties, in a relational database. S values are then calculated from mono-energetic SAFs, based on the radioisotope decay data presented in the International Commission on Radiological Protection (ICRP) publication 107. Results: The OpenDose collaboration produced SAFs for all source regions and targets combinations of the two ICRP 110 adult reference models. SAFs computed from the different Monte Carlo codes were in good agreement at all energies, with standard deviations below individual statistical uncertainties. Calculated S values were in good agreement with OLINDA 2 (commercial) and IDAC 2.1 (free) software. A dedicated website (www.opendose.org) has been developed to provide easy and open access to all data. Conclusion: The OpenDose website allows the display and download of SAFs and the corresponding S values for 1252 radionuclides. The OpenDose collaboration, open to new research teams, will extend data production to other dosimetric models and implement new free features, such as online dosimetric tools and patient-specific absorbed dose calculation software, together with educational resources.

Radionuclide imaging of myocardial perfusion, function, and viability has been established for decades and remains a robust, evidence-based and broadly available means for clinical workup and therapeutic guidance in ischemic heart disease. Yet, powerful alternative modalities have emerged for this purpose, and their growth has resulted in increasing competition. But the potential of the tracer principle goes beyond the assessment of physiology and function, towards the interrogation of biology and molecular pathways. This is a unique selling point of radionuclide imaging, which has been under-recognized in cardiovascular medicine until recently. Now, molecular imaging methods for the detection of myocardial infiltration, device infection and cardiovascular inflammation are successfully gaining clinical acceptance. This is further strengthened by the symbiotic quest of cardiac imaging and therapy for an increasing implementation of molecular-targeted procedures, where specific therapeutic interventions require specific diagnostic guidance towards the most suitable candidates. This review will summarize the current advent of clinical cardiovascular molecular imaging and highlight its transformative contribution to the evolution of cardiovascular therapy beyond mechanical interventions and broad "blockbuster" medication, towards a future of novel, individualized molecular targeted and molecular imaging-guided therapies.