The open reading frame 5A of foxtail mosaic virus is expressed in vivo and is dispensable for systemic infection

Infectious transcripts were successfully derived from full-length cDNA clones of foxtail mosaic potexvirus (FoMV). Full-length clones were constructed by RT-PCR whereby 50 and 30 genomic segments of 2.7 and 3.4 kb, respectively, were ligated into Bluescript II KS. The in vitro RNA transcripts were infectious to moncotyledonous (barley) and dicotyledonous (Chenopodium amaranticolor) plant species. Individual mutation studies on clones of each of the five major ORFs confirmed predicted gene function for the polymerase, TGB (triple gene block), and coat protein (CP) genes. Protoplast studies on expression of a unique open reading frame, ORF 5A, which initiates 143 nts upstream of the CP before it “reads through” the CP, revealed that the 5A protein was produced in vivo. Mutation analysis of the 5A ORF indicated, however, that it was not required for either replication or for productive infection of plants. However, the nucleic acid sequences encoding the extended CP segment were shown to be important for CP expression. Additional mutations in 5A had no effect on FoMV replication in protoplasts but rendered the virus noninfectious to plants. A correlation with diminished CP production from both mutant clones implies that synthesis of subgenomic CP mRNA was compromised, and this limited systemic infection

Calcite–magnesite solid solutions : using genetic algorithms to understand non-ideality

We show how a genetic algorithm (GA) generates efficiently the energy landscape of the equimolar calcite–magnesite (CaCO3—MgCO3) solid solution. Starting from a random configuration of cations and a supercell containing 480 atoms, the lowest energy form of ordered dolomite was found in all runs, in 94% of which it was located with less than 20,000 fitness evaluations. Practical implementation and operation of the GA are discussed in detail. The method can also generate both low-lying and high-lying excited states. Detailed analysis of the energy-minimised structures of the different configurations reveals that low energies are associated with reduction of strain associated with rotation of the carbonate groups, a mechanism possible only when a carbonate layer lies between a layer of just Ca and a layer of just Mg. Such strain relief is not possible in the equimolar MgO–CaO solid solution despite the similarity of the crystal structures of these binary oxides to calcite–magnesite, and therefore, the enthalpy of mixing is very high. Implications for thermodynamic configurational averaging over the minima in the energy landscape are briefly considered. Overall, the genetic algorithm is shown to be a powerful tool in probing non-ideality in solid solutions and revealing the ordering patterns that give rise to such behaviour

Probing the edge between integrability and quantum chaos in interacting few-atom systems

[EN] Interacting quantum systems in the chaotic domain are at the core of various ongoing studies of many-body physics, ranging from the scrambling of quantum information to the onset of thermalization. We propose a minimum model for chaos that can be experimentally realized with cold atoms trapped in onedimensional multi-well potentials. We explore the emergence of chaos as the number of particles is increased, starting with as few as two, and as the number of wells is increased, ranging from a double well to a multi-well Kronig-Penney-like system. In this way, we illuminate the narrow boundary between integrability and chaos in a highly tunable few-body system. We show that the competition between the particle interactions and the periodic structure of the confining potential reveals subtle indications of quantum chaos for 3 particles, while for 4 particles stronger signatures are seen. The analysis is performed for bosonic particles and could also be extended to distinguishable fermions.The authors thank M. Olshanii, T. Busch, A. Fabra and M. Boubakour for insights on integrability and conversations about chaos. TF acknowledges support from JSPS KAKENHI-21K13856 and the Okinawa Institute of Science and Technology Graduate University. We are grateful for the help and support provided by the Scientific Computing and Data Analysis section of Research Support Division at OIST. LFS was supported by the NSF grant No. DMR-1936006. M.A.G.M. acknowledges funding from the Spanish Ministry of Education and Vocational Training (MEFP) through the Beatriz Galindo program 2018 (BEAGAL18/00203) and Spanish Ministry MINECO (FIDEUA PID2019106901GBI00/10.13039/501100011033).Fogarty, T.; Garcia March, MA.; Santos, LF.; Harshman, N. (2021). Probing the edge between integrability and quantum chaos in interacting few-atom systems. Quantum. 5:1-22. https://doi.org/10.22331/q-2021-06-29-486122

First evidence of industrial fly-ash in an Antarctic ice core

Spheroidal carbonaceous particles (SCPs) are a component of fly-ash, the particulate by-product of industrial high temperature combustion of fuel-oil and coal-series fuels. We provide the first evidence that these indelible markers of industrialisation have been deposited in Antarctic ice, thousands of kilometres from any potential source. The earliest observed particle was deposited in an ice layer from 1936 CE. While depositional fluxes are low, chemical analysis of individual SCPs indicates a coal combustion origin

Attachment disorders diagnosed by community practitioners:a replication and extension

Background: While considered a rare diagnosis, reactive attachment disorder (RAD) is simultaneously the subject of considerable debate. A recent report suggested that RAD is overdiagnosed in community settings and that conduct problems may be used to make a diagnosis of RAD (Woolgar & Baldock, Child and Adolescent Mental Health, 20, 2015, 34–40). This study seeks to replicate and extend these findings. Method: Clinical assessment data from 100 consecutive admissions of maltreated foster and adopted children (ages 3–17) to a specialty treatment clinic in the United States were reviewed. Measures included semi-structured interviews of RAD and disinhibited social engagement disorder (DSED) symptoms and caregiver-report questionnaires of emotional problems, conduct problems, and the quality of the parent–child relationship. Results: Of the 100 cases reviewed, 39 presented with a diagnostic history of RAD, DSED, or ‘attachment disorder’. Of these cases, three were diagnosed in-clinic with DSED; no cases met diagnostic criteria for RAD according to DSM-5 criteria. However, analyses found that those diagnosed with RAD by community-based clinicians were significantly more likely to display conduct problems and to be adopted (as opposed to in foster care). Conclusions: These findings confirm those of Woolgar and Baldock (Child and Adolescent Mental Health, 20, 2015, 34–40). It appears that the diagnostic criteria of RAD are commonly being inaccurately applied in general community-based practice. Clarification of diagnostic criteria for RAD in recent revisions of diagnostic taxonomies, the accumulation of empirical data on RAD, and improved instrumentation are either poorly disseminated or inadequately implemented in community-based practice settings

The UK risk assessment scheme for all non-native species

1. A pest risk assessment scheme, adapted from the EPPO (European and Mediterranean Plant Protection Organisation) scheme, was developed to assess the risks posed to UK species, habitats and ecosystems by non-native taxa. 2. The scheme provides a structured framework for evaluating the potential for non-native organisms, whether intentional or unintentional introductions, to enter, establish, spread and cause significant impacts in all or part of the UK. Specialist modules permit the relative importance of entry pathways, the vulnerability of receptors and the consequences of policies to be assessed and appropriate risk management options to be selected. Spreadsheets for summarising the level of risk and uncertainty, invasive attributes and economic impact were created. In addition, new methods for quantifying economic impact and summarising risk and uncertainty were explored. 3. Although designed for the UK, the scheme can readily be applied elsewhere

Comparative Assessment of ESI‐MS Softness for Inorganic Complexes: How Soft Is Your ESI‐MS?

Electrospray ionization mass spectrometry (ESI-MS) is a powerful tool for identifying and characterizing organometallic and coordination compounds. However, detection of fragile structures bound by weaker intermolecular forces can be significantly limited in ESI-MS owing to the use of relatively harsh instrument conditions and configurations. In this study, a set of tests was developed to assess the softness of ESI-MS systems. Two variants are presented: positive ion mode, utilizing a mixture of sodium ions and triphenylphosphine oxide producing [Na(OPPh3)n]+ ions (n=1–4), and negative ion mode utilizing Pd(PPh3)4 and sulfonated triphenylphosphine producing [Pd(L)(PPh3)n]− ions (n=0–2), where softer instrument conditions preserve a higher proportion of the high-coordinate ions and harsher conditions will result in increased detection of products of ion fragmentation. The results revealed notable variations in instrument softness, which were influenced by a combination of instrument design and experimental parameters. Meticulously optimizing experimental conditions and ESI-MS parameters is essential to achieving the softest ionization possible, ensuring reliable analysis where applicable. This study offers valuable insight through straightforward tests that can be employed to assess the suitability of an instrument for specific research needs

Spin dependence in high pT2p^{2}_{T} elastic pp and np scattering

Using the polarized proton capability of the Argonne ZGS the authors recently made 90 degrees /sub cm/ measurements of elastic pp scattering from 6 to 11.75 GeV/c, determining the parallel and anti- parallel pure initial spin state cross sections and the associated spin-spin parameter A/sub nn/ with the spins normal to the scattering plane. They find that the parallel to anti-parallel cross section ratio rises dramatically from 1.2+or-.06 at p/sub t//sup 2/=3.3 (GeV /c)/sup 2/ to 3.2+or-.4 at 4.8 (GeV/c)/sup 2/, similar to the p/sub T //sup 2/ dependence previously observed at the fixed laboratory momentum of 11.75 GeV/c. They have also extended the measurements at 6 GeV/c and find that A/sub nn/ has a small but sharp rise at 90 degrees /sub cm/. In addition a month of 12 GeV/c polarized deuteron acceleration in the ZGS enabled them to measure two A/sub nn/ at two points at 6 GeV/c for np elastic scattering: A/sub nn/=-.17+or-.04 at p/sub T//sup 2/=.8, A/sub nn/=-.19+or-.05 at P/sub T//sup 2/=1.0. These values are opposite in sign from the pp results at the same momentum. (4 refs)

A synthetic biology approach to probing nucleosome symmetry

The repeating subunit of chromatin, the nucleosome, includes two copies of each of the four core histones, and several recent studies have reported that asymmetrically-modified nucleosomes occur at regulatory elements in vivo. To probe the mechanisms by which histone modifications are read out, we designed an obligate pair of H3 heterodimers, termed H3X and H3Y, which we extensively validated genetically and biochemically. Comparing the effects of asymmetric histone tail point mutants with those of symmetric double mutants revealed that a single methylated H3K36 per nucleosome was sufficient to silence cryptic transcription in vivo. We also demonstrate the utility of this system for analysis of histone modification crosstalk, using mass spectrometry to separately identify modifications on each H3 molecule within asymmetric nucleosomes. The ability to generate asymmetric nucleosomes in vivo and in vitro provides a powerful and generalizable tool to probe the mechanisms by which H3 tails are read out by effector proteins in the cell