Genome Stability: A Self-Sufficient DNA Repair Machine

AbstractThe repair of DNA double-strand breaks often requires the broken ends to be processed prior to religation. New results describe a bacterial enzyme with processing and rejoining activities encoded in a single polypeptide chain

Genome Sequencing: And Then There Were Six

AbstractThe genome of the fission yeast Schizosaccharomyces pombe has been sequenced, bringing the number of sequenced eukaryotic genomes to six. Analysis of the sequence predicts only 4824 protein coding genes, the smallest number yet recorded for a free-living eukaryote

Biochemical characterisation of LigN, an NAD(+)-dependent DNA ligase from the halophilic euryarchaeon Haloferax volcanii that displays maximal in vitro activity at high salt concentrations

BACKGROUND: DNA ligases are required for DNA strand joining in all forms of cellular life. NAD(+)-dependent DNA ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. Among the archaeal NAD(+)-dependent DNA ligases is the LigN enzyme of the halophilic euryarchaeon Haloferax volcanii, the gene for which was apparently acquired by Hfx.volcanii through lateral gene transfer (LGT) from a halophilic eubacterium. Genetic studies show that the LGT-acquired LigN enzyme shares an essential function with the native Hfx.volcanii ATP-dependent DNA ligase protein LigA. RESULTS: To characterise the enzymatic properties of the LigN protein, wild-type and three mutant forms of the LigN protein were separately expressed in recombinant form in E.coli and purified to apparent homogeneity by immobilised metal ion affinity chromatography (IMAC). Non-isotopic DNA ligase activity assays using λ DNA restriction fragments with 12 bp cos cohesive ends were used to show that LigN activity was dependent on addition of divalent cations and salt. No activity was detected in the absence of KCl, whereas maximum activity could be detected at 3.2 M KCl, close to the intracellular KCl concentration of Hfx.volcanii cells. CONCLUSION: LigN is unique amongst characterised DNA ligase enzymes in displaying maximal DNA strand joining activity at high (> 3 M) salt levels. As such the LigN enzyme has potential both as a novel tool for biotechnology and as a model enzyme for studying the adaptation of proteins to high intracellular salt levels

ATP-dependent DNA ligases

By catalyzing the joining of breaks in the phosphodiester backbone of duplex DNA, DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Three related classes of ATP-dependent DNA ligase are readily apparent in eukaryotic cells. Enzymes of each class comprise catalytic and non-catalytic domains together with additional domains of varying function. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis, as well as for several DNA-repair pathways; these functions are mediated, at least in part, by interactions between DNA ligase I and the sliding-clamp protein PCNA. DNA ligase III, which is unique to vertebrates, functions both in the nucleus and in mitochondria. Two distinct isoforms of this enzyme, differing in their carboxy-terminal sequences, are produced by alternative splicing: DNA ligase IIIα has a carboxy-terminal BRCT domain that interacts with the mammalian DNA-repair factor XrccI, but both α and β isoforms have an amino-terminal zinc-finger motif that appears to play a role in the recognition of DNA secondary structures that resemble intermediates in DNA metabolism. DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV forms a tight complex with Xrcc4 through an interaction motif located between a pair of carboxy-terminal BRCT domains in the ligase. Recent structural studies have shed light on the catalytic function of DNA ligases, as well as illuminating protein-protein interactions involving DNA ligases IIIα and IV

Thickness dependence of spin-orbit torques generated by WTe2

We study current-induced torques in WTe2/permalloy bilayers as a function of WTe2 thickness. We measure the torques using both second-harmonic Hall and spin-torque ferromagnetic resonance measurements for samples with WTe2 thicknesses that span from 16 nm down to a single monolayer. We confirm the existence of an out-of-plane antidamping torque, and show directly that the sign of this torque component is reversed across a monolayer step in the WTe2. The magnitude of the out-of-plane antidamping torque depends only weakly on WTe2 thickness, such that even a single-monolayer WTe2 device provides a strong torque that is comparable to much thicker samples. In contrast, the out-of-plane field-like torque has a significant dependence on the WTe2 thickness. We demonstrate that this field-like component originates predominantly from the Oersted field, thereby correcting a previous inference drawn by our group based on a more limited set of samples.Comment: 8 pages, 8 figure

Social Defense: An Evolutionary-Developmental Model of Children’s Strategies for Coping with Threat in the Peer Group

Navigating the ubiquitous conflict, competition, and complex group dynamics of the peer group is a pivotal developmental task of childhood. Difficulty negotiating these challenges represents a substantial source of risk for psychopathology. Evolutionary developmental psychology offers a unique perspective with the potential to reorganize the way we think about the role of peer relationships in shaping how children cope with the everyday challenges of establishing a social niche. To address this gap, we utilize the ethological reformulation of the emotional security theory as a guide to developing an evolutionary framework for advancing an understanding of the defense strategies children use to manage antagonistic peer relationships and protect themselves from interpersonal threat (Davies and Sturge-Apple, 2007). In this way, we hope to illustrate the value of an evolutionary developmental lens in generating unique theoretical insight and novel research directions into the role of peer relationships in the development of psychopathology

Mapping and mutation of the conserved DNA polymerase interaction motif (DPIM) located in the C-terminal domain of fission yeast DNA polymerase δ subunit Cdc27

BACKGROUND: DNA polymerases α and δ play essential roles in the replication of chromosomal DNA in eukaryotic cells. DNA polymerase α (Pol α)-primase is required to prime synthesis of the leading strand and each Okazaki fragment on the lagging strand, whereas DNA polymerase δ (Pol δ) is required for the elongation stages of replication, a function it appears capable of performing on both leading and lagging strands, at least in the absence of DNA polymerase ε (Pol ε). RESULTS: Here it is shown that the catalytic subunit of Pol α, Pol1, interacts with Cdc27, one of three non-catalytic subunits of fission yeast Pol δ, both in vivo and in vitro. Pol1 interacts with the C-terminal domain of Cdc27, at a site distinct from the previously identified binding sites for Cdc1 and PCNA. Comparative protein sequence analysis identifies a protein sequence motif, called the DNA polymerase interaction motif (DPIM), in Cdc27 orthologues from a wide variety of eukaryotic species, including mammals. Mutational analysis shows that the DPIM in fission yeast Cdc27 is not required for effective DNA replication, repair or checkpoint function. CONCLUSIONS: The absence of any detectable phenotypic consequences arising from mutation of the DPIM suggests that despite its evolutionary conservation, the interaction between the two polymerases mediated by this motif is a non-essential one

Electrical Control of 2D Magnetism in Bilayer CrI3

The challenge of controlling magnetism using electric fields raises fundamental questions and addresses technological needs such as low-dissipation magnetic memory. The recently reported two-dimensional (2D) magnets provide a new system for studying this problem owing to their unique magnetic properties. For instance, bilayer chromium triiodide (CrI3) behaves as a layered antiferromagnet with a magnetic field-driven metamagnetic transition. Here, we demonstrate electrostatic gate control of magnetism in CrI3 bilayers, probed by magneto-optical Kerr effect (MOKE) microscopy. At fixed magnetic fields near the metamagnetic transition, we realize voltage-controlled switching between antiferromagnetic and ferromagnetic states. At zero magnetic field, we demonstrate a time-reversal pair of layered antiferromagnetic states which exhibit spin-layer locking, leading to a remarkable linear dependence of their MOKE signals on gate voltage with opposite slopes. Our results pave the way for exploring new magnetoelectric phenomena and van der Waals spintronics based on 2D materials.Comment: To appear in Nature Nanotechnolog

Do temperature changes cause eczema flares? An English cohort study.

BACKGROUND: It is unclear if ambient temperature changes affect eczema. It is also unclear if people with worse disease are more susceptible to weather-related flares, or specific types of emollient offer protection. Substantiating these links may help inform action plans and patients self-management. OBJECTIVE: To investigate the effect of short-term temperature variations on eczema symptoms in children. METHODS: Data from a UK cohort of 519 children (6 months-12 years) with at least mild eczema, participating in a randomised trial comparing four types of emollients on eczema symptoms, were combined with observed temperature data from the Hadley Centre's Integrated Surface Database.Hot & cold weeks were defined by average regional temperature >75th or <25th percentile, January 2018-February 2020. Eczema flares were defined as ≥3 point change in patient-oriented eczema measure (POEM). Random effects logistic regression models were used to estimate the odds ratios of flares in hot & cold weeks (reference group: temperate weeks). The likelihood ratio test assessed for evidence of effect modification by disease severity and emollient type. RESULTS: The baseline mean age was 4.9 years (SD 3.2) and POEM score was 9.2 (SD 5.5), indicating moderate eczema. 90% of participants lived within 20 km of their nearest weather station. From the 519 participants there were 6,796 consecutively paired POEMs and 1,082 flares.Seasonal variation in POEM scores was observed, suggesting symptoms worsening with colder weather in winter and improving with warmer weather in summer. Odds ratios of flares were: 1.15 (p = 0.136, 95%CI 0.96-1.39) in cold weeks, 0.85 (p = 0.045, 95%CI 0.72-1.00) in hot weeks. Likelihood ratio test showed no evidence of this differing by disease severity (p = 0.53) or emollient type used (p = 0.55). CONCLUSIONS: Our findings are consistent with previous studies demonstrating either improvements in eczema symptoms or reduced flares in hot weather. Worse disease and different emollient types did not increase susceptibility or provide protection against temperature changes. Further work should investigate the role of sunlight, humidity, air pollution and other environmental factors