Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks

Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generates Lys-SDE2^(Ct), the C-terminal SDE2 fragment bearing an N-terminal Lys residue. Lys-SDE2^(Ct) constitutes a short-lived physiological substrate of the Arg/N-end rule proteolytic pathway, in which UBR1 and UBR2 ubiquitin ligases mediate the degradation. The Arg/N-end rule and VCP/p97^(UFD1-NPL4) segregase cooperate to promote phosphorylation-dependent, chromatin-associated Lys-SDE2^(Ct) degradation upon UVC damage. Conversely, cells expressing the degradation-refractory K78V mutant, Val-SDE2^(Ct), fail to induce RPA phosphorylation and single-stranded DNA formation, leading to defects in PCNA-dependent DNA damage bypass and stalled fork recovery. Together, our study elucidates a previously unappreciated axis connecting the Arg/N-end rule and the p97-mediated proteolysis with the replication stress response, working together to preserve replication fork integrity

Visualization of Strain-Induced Landau Levels in a Graphene - Black Phosphorus Heterostructure

Strain-induced pseudo magnetic fields offer the possibility of realizing zero magnetic field Quantum Hall effect in graphene, possibly up to room temperature, representing a promising avenue for lossless charge transport applications. Strain engineering on graphene has been achieved via random nanobubbles or artificial nanostructures on the substrate, but the highly localized and non-uniform pseudomagnetic fields can make spectroscopic probes of electronic structure difficult. Heterostructure engineering offers an alternative approach: By stacking graphene on top of another van der Waals material with large lattice mismatch at a desired twist angle, it is possible to generate large strain-induced pseudo magnetic fields uniformly over the entire heterostructure. Here, we report using nano-angle resolved photoemission spectroscopy (nano-ARPES) to probe the electronic bandstructure of a graphene/black phosphorus heterostructure (G/BP). By directly measuring the iso-energy contours of graphene and black phosphorus we determine a twist angle of 20-degrees in our heterostructure. High-resolution nano-ARPES of the graphene bands near the Fermi level reveals the emergence of flat bands located within the Dirac cone. The spacing of the flat bands is consistent with Landau level formation in graphene, and corresponds to a pseudo-field of 11.36 T. Our work provides a new way to study quantum Hall phases induced by strain in 2D materials and heterostructures

Conditional degradation of SDE2 by the Arg/N-End rule pathway regulates stress response at replication forks

Multiple pathways counteract DNA replication stress to prevent genomic instability and tumorigenesis. The recently identified human SDE2 is a genome surveillance protein regulated by PCNA, a DNA clamp and processivity factor at replication forks. Here, we show that SDE2 cleavage after its ubiquitin-like domain generates Lys-SDE2^(Ct), the C-terminal SDE2 fragment bearing an N-terminal Lys residue. Lys-SDE2^(Ct) constitutes a short-lived physiological substrate of the Arg/N-end rule proteolytic pathway, in which UBR1 and UBR2 ubiquitin ligases mediate the degradation. The Arg/N-end rule and VCP/p97^(UFD1-NPL4) segregase cooperate to promote phosphorylation-dependent, chromatin-associated Lys-SDE2^(Ct) degradation upon UVC damage. Conversely, cells expressing the degradation-refractory K78V mutant, Val-SDE2^(Ct), fail to induce RPA phosphorylation and single-stranded DNA formation, leading to defects in PCNA-dependent DNA damage bypass and stalled fork recovery. Together, our study elucidates a previously unappreciated axis connecting the Arg/N-end rule and the p97-mediated proteolysis with the replication stress response, working together to preserve replication fork integrity

Commentary on Coram et al. (2021) on the use of Facebook to understand marine mammal stranding issues in Southeast Asia

We reviewed Coram et al. (Biodivers Conserv 30:2341–2359, 2021, https://doi.org/10.1007/s10531-021-02196-6), a paper that highlights the use of social media data to understand marine litter and marine mammals in Southeast Asia. While we commend its intent, we find that the methodology used and conclusions drawn portray an incomplete and inaccurate perception of how strandings, stranding response, and analysis of stranding data have been conducted in the region. By focusing on investigative results revealed by a very limited search of one social media platform (Facebook), using only English keywords, and insuffcient ground-truthing, Coram et al. (2021) have, unintentionally, given the perception that Southeast Asian scientists have not conducted even the bare minimum of investigation required to better understand the issue of marine litter and its impact on marine mammals. In this commentary we provide a more accurate account of strandings research in Asia and include recommendations to improve future studies using social media to assess conservation issues

Oxygenated sunflower biodiesel: spectroscopic and emissions quantification under reacting swirl spray conditions

The spray combustion characteristics of sunflower (Helianthus annuus) biodiesel/methyl esters (SFME) and 50% SFME/diesel blend and diesel were investigated via a liquid swirl flame burner. The swirl flame was established at atmospheric condition by using a combined twin-fluid atomiser-swirler configuration at varied atomising air-to-liquid ratios (ALR) of 2.0–2.5. Diesel flame showed a sooty flame brush downstream of the main reaction zone, as opposed to the biodiesel flame which showed a non-sooty, bluish flame core. Biodiesel flame exhibited a more intense flame spectra with higher OH* radicals as compared to diesel. Higher preheating main swirl air temperature led to higher NO emission, while CO correspondingly decreased. Sunflower-derived biodiesel generally exhibited slightly higher NO and CO levels than diesel when compared at the same power output, mostly due to higher flame temperature and fuel chemistry effect. By increasing ALR, a significant reduction of NO and CO for both fuel types were concurrently achieved, presenting a strategy to control emissions and atomise biodiesel with higher viscosity under swirl combustion mode

Quality assessment of an interferon-gamma release assay for tuberculosis infection in a resource-limited setting

<p>Abstract</p> <p>Background</p> <p>When a test for diagnosis of infectious diseases is introduced in a resource-limited setting, monitoring quality is a major concern. An optimized design of experiment and statistical models are required for this assessment.</p> <p>Methods</p> <p>Interferon-gamma release assay to detect tuberculosis (TB) infection from whole blood was tested in Hanoi, Viet Nam. Balanced incomplete block design (BIBD) was planned and fixed-effect models with heterogeneous error variance were used for analysis. In the first trial, the whole blood from 12 donors was incubated with nil, TB-specific antigens or mitogen. In 72 measurements, two laboratory members exchanged their roles in harvesting plasma and testing for interferon-gamma release using enzyme linked immunosorbent assay (ELISA) technique. After intervention including checkup of all steps and standard operation procedures, the second trial was implemented in a similar manner.</p> <p>Results</p> <p>The lack of precision in the first trial was clearly demonstrated. Large within-individual error was significantly affected by both harvester and ELISA operator, indicating that both of the steps had problems. After the intervention, overall within-individual error was significantly reduced (<it>P </it>< 0.0001) and error variance was no longer affected by laboratory personnel in charge, indicating that a marked improvement could be objectively observed.</p> <p>Conclusion</p> <p>BIBD and analysis of fixed-effect models with heterogeneous variance are suitable and useful for objective and individualized assessment of proficiency in a multistep diagnostic test for infectious diseases in a resource-constrained laboratory. The action plan based on our findings would be worth considering when monitoring for internal quality control is difficult on site.</p

Liquid biofuels production and emissions performance in gas turbines: A review

The increasing demand for clean and sustainable energy sources provides the impetus for the development of alternative fuels. Recent development of fuel-flexible gas turbine technologies enables the use of alternative non-fossil fuels that could play key roles in contributing to the global efforts in meeting emissions targets. This review highlights the current state-of-the-art production and properties of alternative fuels such as straight vegetable oil (SVO), biodiesel, bioethanol, bio-oil, hydrogenated vegetable oil (HVO) and Fischer-Tropsch (FT) fuel. This is followed by the evaluation of combustion performances in gas turbines. All of the alternative liquid biofuels have shown their potentials in reducing regulated emissions such as NOx, CO and soot under favourable operating conditions. Both HVO and FT fuels show comparable performance as that of jet fuel and can be used in aviation gas turbines, although the present day high production cost restricts the large-scale adoption, limiting its utility. They also have considerably higher cetane number than the rest, making it easier for the fuel to ignite. As for stationary power generation gas turbines that need not carry payloads, the other four alternative biofuels of biodiesel, bioethanol, bio-oil and SVO are possible candidates despite the physics-chemical properties variations when compared to fossil fuels. Amongst them, the use of SVO and bio-oil in gas turbines would require the parallel development of fuel supply systems and atomisation technologies to improve the combustion of the fuels. In all, the alternative liquid fuels reviewed provides realistic opportunities for cleaner and more sustainable operation of aviation and power generation gas turbines. Profound understanding on the fundamental combustion characteristics of the fuels are essential to expedite their mass adoption in gas turbine applications