Crystal structure and stability of gyrase–fluoroquinolone cleaved complexes from Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) infects one-third of the world’s population and in 2013 accounted for 1.5 million deaths. Fluoroquinolone antibacterials, which target DNA gyrase, are critical agents used to halt the progression from multidrug-resistant tuberculosis to extensively resistant disease; however, fluoroquinolone resistance is emerging and new ways to bypass resistance are required. To better explain known differences in fluoroquinolone action, the crystal structures of the WT Mtb DNA gyrase cleavage core and a fluoroquinolone-sensitized mutant were determined in complex with DNA and five fluoroquinolones. The structures, ranging from 2.4- to 2.6-Å resolution, show that the intrinsically low susceptibility of Mtb to fluoroquinolones correlates with a reduction in contacts to the water shell of an associated magnesium ion, which bridges fluoroquinolone–gyrase interactions. Surprisingly, the structural data revealed few differences in fluoroquinolone–enzyme contacts from drugs that have very different activities against Mtb. By contrast, a stability assay using purified components showed a clear relationship between ternary complex reversibility and inhibitory activities reported with cultured cells. Collectively, our data indicate that the stability of fluoroquinolone/DNA interactions is a major determinant of fluoroquinolone activity and that moieties that have been appended to the C7 position of different quinolone scaffolds do not take advantage of specific contacts that might be made with the enzyme. These concepts point to new approaches for developing quinolone-class compounds that have increased potency against Mtb and the ability to overcome resistance

Recognition of DNA Supercoil Geometry by Mycobacterium tuberculosis Gyrase

Mycobacterium tuberculosis encodes only a single type II topoisomerase, gyrase. As a result, this enzyme likely carries out the cellular functions normally performed by canonical gyrase and topoisomerase IV, both in front of and behind the replication fork. In addition, it is the sole target for quinolone antibacterials in this species. Because quinolone-induced DNA strand breaks generated on positively supercoiled DNA ahead of replication forks and transcription complexes are most likely to result in permanent genomic damage, the actions of M. tuberculosis gyrase on positively supercoiled DNA were investigated. Results indicate that the enzyme acts rapidly on overwound DNA and removes positive supercoils much faster than it introduces negative supercoils into relaxed DNA. Canonical gyrase and topoisomerase IV distinguish supercoil handedness differently during the DNA cleavage reaction: while gyrase maintains lower levels of cleavage complexes on overwound DNA, topoisomerase IV maintains similar levels of cleavage complexes on both over- and underwound substrates. M. tuberculosis gyrase maintained lower levels of cleavage complexes on positively supercoiled DNA in the absence and presence of quinolone-based drugs. By retaining this important feature of canonical gyrase, the dual function M. tuberculosis type II enzyme remains a safe enzyme to act in front of replication forks and transcription complexes. Finally, the N-terminal gate region of the enzyme appears to be necessary to distinguish supercoil handedness during DNA cleavage, suggesting that the capture of the transport segment may influence how gyrase maintains cleavage complexes on substrates with different topological states

High-throughput shoot phenotyping reveals temporal growth responses to nitrogen and inorganic and organic phosphorus sources in tomato

Advance access publication 8 March 2023High-throughput phenotyping was used to track real-time plant growth of tomato plants and their responses to nutrients supplied from different sources and rates of phosphorus (P). The results suggest that the combined use of P-rich chicken litter (organic matter) and inorganic P sources can be used to close the growth gap between the sole use of organic fertilizer and the use of conventional P fertilizer. Furthermore, organic P fertilizers could reduce the need for additional nitrogen fertilizer.Hue T. T. Ngo, Timothy R. Cavagnaro, Nathaniel Jewell, Christopher J Brien, Bettina Berger and Stephanie J. Watts-William

Acoustic Events in the Solar Atmosphere from Hinode/SOT NFI observations

We investigate the properties of acoustic events (AEs), defined as spatially concentrated and short duration energy flux, in the quiet sun using observations of a 2D field of view (FOV) with high spatial and temporal resolution provided by the Solar Optical Telescope (SOT) onboard \textit{Hinode}. Line profiles of Fe \textsc{i} 557.6 nm were recorded by the Narrow band Filter Imager (NFI) on a $82" \times 82"$ FOV during 75 min with a time step of 28.75 s and 0.08$"$ pixel size. Vertical velocities were computed at three atmospheric levels (80, 130 and 180 km) using the bisector technique allowing the determination of energy flux in the range 3-10 mHz using two complementary methods (Hilbert transform and Fourier power spectra). Horizontal velocities were computed using local correlation tracking (LCT) of continuum intensities providing divergences. The net energy flux is upward. In the range 3-10 mHz, a full FOV space and time averaged flux of 2700 W m$^{-2}$ (lower layer 80-130 km) and 2000 W m$^{-2}$ (upper layer 130-180 km) is concentrated in less than 1% of the solar surface in the form of narrow (0.3$"$) AE. Their total duration (including rise and decay) is of the order of $10^{3}$ s. Inside each AE, the mean flux is $1.6 10^{5}$ W m$^{-2}$ (lower layer) and $1.2 10^{5}$ W m$^{-2}$ (upper). Each event carries an average energy (flux integrated over space and time) of $2.5 10^{19}$ J (lower layer) to $1.9 10^{19}$ J (upper). More than $10^{6}$ events could exist permanently on the Sun, with a birth and decay rate of 3500 s$^{-1}$. Most events occur in intergranular lanes, downward velocity regions, and areas of converging motions.Comment: 18 pages, 10 figure

Tops and Writhing DNA

The torsional elasticity of semiflexible polymers like DNA is of biological significance. A mathematical treatment of this problem was begun by Fuller using the relation between link, twist and writhe, but progress has been hindered by the non-local nature of the writhe. This stands in the way of an analytic statistical mechanical treatment, which takes into account thermal fluctuations, in computing the partition function. In this paper we use the well known analogy with the dynamics of tops to show that when subjected to stretch and twist, the polymer configurations which dominate the partition function admit a local writhe formulation in the spirit of Fuller and thus provide an underlying justification for the use of Fuller's "local writhe expression" which leads to considerable mathematical simplification in solving theoretical models of DNA and elucidating their predictions. Our result facilitates comparison of the theoretical models with single molecule micromanipulation experiments and computer simulations.Comment: 17 pages two figure

Physical and emotional nourishment: Food as the embodied component of loving care of elderly family relatives

Purpose This purpose of this study is to examine the fluidity of family life which continues to attract attention. This is increasingly significant for the intergenerational relationship between adult children and their elderly parents. Using practice theory, the aims are to understand the role of food in elderly families and explore how family practices are maintained when elderly transition into care. Design/methodology/approach A phenomenological research approach was used as the authors sought to build an understanding of the social interactions between family and their lifeworld. Findings This study extends theory on the relationship between the elderly parent and their family and explores through practice theory how families performed their love, how altered routines and long standing rituals provided structure to the elderly relatives and how care practices were negotiated as the elderly relatives transitioned from independence to dependence and towards care. A theoretical framework is introduced that provides guidance for the transition stages and the areas for negotiation. Research limitations/implications This research has implications for food manufacturers and marketers, as the demand for healthy food for the elderly is made more widely available, healthy and easy to prepare. The limitations of the research are due to the sample located in East Yorkshire only. Practical implications This research has implications for brand managers of food manufacturers and supermarkets that need to create product lines that target this segment by producing healthy, convenience food. Social implications It is also important for health and social care policy as the authors seek to understand the role of food, family and community and how policy can be devised to provide stability in this transitional and uncertain lifestage. Originality/value This research extends the body of literature on food and the family by focussing on the elderly cared for and their family. The authors show how food can be construed as loving care, and using practice theory, a theoretical framework is developed that can explain the transitions and how the family negotiates the stages from independence to dependence

Chiral effective field theories of the strong interactions

Effective field theories of the strong interactions based on the approximate chiral symmetry of QCD provide a model-independent approach to low-energy hadron physics. We give a brief introduction to mesonic and baryonic chiral perturbation theory and discuss a number of applications. We also consider the effective field theory including vector and axial-vector mesons.Comment: 22 pages, 9 figures, proceedings of "Many-Body Structure of Strongly Interacting Systems", Mainz, Germany, Feb. 23-25 201

Physical and emotional nourishment: Food as the embodied component of loving care of elderly family relatives

Purpose This purpose of this study is to examine the fluidity of family life which continues to attract attention. This is increasingly significant for the intergenerational relationship between adult children and their elderly parents. Using practice theory, the aims are to understand the role of food in elderly families and explore how family practices are maintained when elderly transition into care. Design/methodology/approach A phenomenological research approach was used as the authors sought to build an understanding of the social interactions between family and their lifeworld. Findings This study extends theory on the relationship between the elderly parent and their family and explores through practice theory how families performed their love, how altered routines and long standing rituals provided structure to the elderly relatives and how care practices were negotiated as the elderly relatives transitioned from independence to dependence and towards care. A theoretical framework is introduced that provides guidance for the transition stages and the areas for negotiation. Research limitations/implications This research has implications for food manufacturers and marketers, as the demand for healthy food for the elderly is made more widely available, healthy and easy to prepare. The limitations of the research are due to the sample located in East Yorkshire only. Practical implications This research has implications for brand managers of food manufacturers and supermarkets that need to create product lines that target this segment by producing healthy, convenience food. Social implications It is also important for health and social care policy as the authors seek to understand the role of food, family and community and how policy can be devised to provide stability in this transitional and uncertain lifestage. Originality/value This research extends the body of literature on food and the family by focussing on the elderly cared for and their family. The authors show how food can be construed as loving care, and using practice theory, a theoretical framework is developed that can explain the transitions and how the family negotiates the stages from independence to dependence