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The paper assesses the potential for adopting sustainable urban drainage systems (SUDS) in Myanmar to mitigate flood risks related to urbanisation. Fieldwork in commercial and industrial developments and informal settlements was undertaken to identify flood problems, understand causes and assess the potential for SUDS in Yangon. Hydrological modelling was used to assess the benefits in terms of flood risk mitigation from a quantitative perspective and engagement with key stakeholders facilitated a consideration of the practical implications of SUDS adoption. The results demonstrate that on-site source control technologies can play a key role in mitigating flood risks for storm events with return frequencies of one in 10 years. Based on simulation results, the existing situation shows extensive flooding with 45% of the area flooding to a depth of 0.25 m, the SUDS scenario reduces this from 30 to 15% of the modelled catchment area. SUDS need to be adopted at scale for the benefits to be realised but the adoption of SUDS in existing developments is seen to be constrained due to practical and financial considerations. Therefore, green field sites offer the greatest potential for SUDS and a three-stage procedure based on flood risk and drainage impact assessments were developed to be incorporated in the existing planning applications process.

Oncohistones represent compelling evidence for a causative role of epigenetic perturbations in cancer. Giant cell tumours of bone (GCTs) are characterised by a mutated histone H3.3 as the sole genetic driver present in bone-forming osteoprogenitor cells but absent from abnormally large bone-resorbing osteoclasts which represent the hallmark of these neoplasms. While these striking features imply a pathogenic interaction between mesenchymal and myelomonocytic lineages during GCT development, the underlying mechanisms remain unknown. We show that the changes in the transcriptome and epigenome in the mesenchymal cells caused by the H3.3-G34W mutation contribute to increase osteoclast recruitment in part via reduced expression of the TGFβ-like soluble factor, SCUBE3. Transcriptional changes in SCUBE3 are associated with altered histone marks and H3.3G34W enrichment at its enhancer regions. In turn, osteoclasts secrete unregulated amounts of SEMA4D which enhances proliferation of mutated osteoprogenitors arresting their maturation. These findings provide a mechanism by which GCTs undergo differentiation in response to denosumab, a drug that depletes the tumour of osteoclasts. In contrast, hTERT alterations, commonly found in malignant GCT, result in the histone-mutated neoplastic cells being independent of osteoclasts for their proliferation, predicting unresponsiveness to denosumab. We provide a mechanism for the initiation of GCT, the basis of which is dysfunctional cross-talk between bone-forming and bone-resorbing cells. The findings highlight the role of tumour/microenvironment bidirectional interactions in tumorigenesis and how this is exploited in the treatment of GCT.

PlzA is a c-di-GMP-binding protein crucial for adaptation of the Lyme disease spirochete Borrelia ( Borreliella) burgdorferi during its enzootic life cycle. Unliganded apo-PlzA is important for vertebrate infection, while liganded holo-PlzA is important for tick acquisition; however, the biological function of PlzA has remained enigmatic. Here we report that PlzA has RNA chaperone activity that is inhibited by c-di-GMP binding. Holo- and apo-PlzA bind RNA and accelerate RNA annealing, while only apo-PlzA can strand displace and unwind double-stranded RNA. Guided by the crystal structure of PlzA, we identified several key aromatic amino acids protruding from the N- and C-terminal domains that are required for RNA binding and unwinding activity. Our findings illuminate c-di-GMP as a switch controlling the RNA chaperone activity of PlzA and we propose that complex RNA-mediated modulatory mechanisms allow PlzA to regulate gene expression during both the vector and host phases of the B. burgdorferi life cycle.

Transactions of the Leicestershire Archaeological and Historical Society, 61, 24-33, The eighteenth century slate engravers of Leicestershire are a neglected school of craftsmen. They appeared in response to a demand from a population steadily growing in affluence. In the Middle Ages only the very rich or the very holy were buried inside the church, and commemorated by splendid tombs and tombstones: the rest of the population were buried outside in the churchyard, and if they were commemorated at all, it would have been in wood. Such memorials do not survive the centuries, although there are some indications that they existed. But after the Wars of the Roses, England steadily built up its strength, and new classes of people became affluent enough to afford more permanent memorials of their dead.

Chondrosarcoma (CS) is a rare tumour type and the most common primary malignant bone cancer in adults. The prognosis, currently based on tumour grade, imaging and anatomical location, is not reliable, and more objective biomarkers are required. We aimed to determine whether the level of circulating tumour DNA (ctDNA) in the blood of CS patients could be used to predict outcome. In this multi‐institutional study, we recruited 145 patients with cartilaginous tumours, of which 41 were excluded. ctDNA levels were assessed in 83 of the remaining 104 patients, whose tumours harboured a hotspot mutation in IDH1/2 or GNAS. ctDNA was detected pre‐operatively in 31/83 (37%) and in 12/31 (39%) patients postoperatively. We found that detection of ctDNA was more accurate than pathology for identification of high‐grade tumours and was associated with a poor prognosis; ctDNA was never associated with CS grade 1/atypical cartilaginous tumours (ACT) in the long bones, in neoplasms sited in the small bones of the hands and feet or in tumours measuring less than 80 mm. Although the results are promising, they are based on a small number of patients, and therefore, introduction of this blood test into clinical practice as a complementary assay to current standard‐of‐care protocols would allow the assay to be assessed more stringently and developed for a more personalised approach for the treatment of patients with CS., In this multi‐institutional study, we detected the amount of circulating tumour DNA (ctDNA) in the blood of patients with chondrosarcoma. We recruited 145 patients, and ctDNA levels were assessed in patients with tumours carrying IDH1/2 or GNAS mutations. We found that ctDNA levels offered a more accurate identification of high‐grade tumours than pathology and were additionally associated with poor prognosis.

A numerical investigation is undertaken on the development of linear disturbances in the rotating disk boundary layer, in which a time-periodic modulation is applied to the disk rotation rate. The model gives a prototypical example of a three-dimensional oscillatory boundary layer, by adding a Stokes layer to the von Kármán flow that develops on a steady disk. The study extends the Floquet analysis of Morgan et al. (J. Fluid Mech., vol. 925, 2021, A20), who showed that disk modulation stabilises the stationary convective instabilities found on the steady rotating disk. Using a radial homogeneous flow approximation, whereby the radial dependence of the basic state is ignored, disturbance development is simulated for several modulation settings, with flow conditions matched to both convective and absolute forms of linear instability. Disturbances excited via a stationary periodic wall forcing display behaviour consistent with that found using Floquet theory; time-periodic modulation stabilises the cross-flow instability by reducing the radial growth rate. In addition, convective and absolute instabilities, generated by an impulsive wall forcing, are both stabilised by the introduction of modulation to the disk rotation rate. Modulation establishes a significant reduction in both the temporal growth rate and the disturbance amplitude as it propagates away from the impulse origin. Moreover, greater stabilising control benefits are realised as the modulation amplitude increases.

The industry has become increasingly aware of the threat posed by selective seam weld corrosion (SSWC). This has been driven by changes made to gas transmission regulation in 2020 and an increased focus on SSWC as a significant threat in both gas and liquid pipelines. A number of historical publications exist, which provide guidance on how corrosion interacting with the long seam can be addressed. However, there has been very little presented in recent years to encompass current understanding of how corrosion on the long seam, and specifically SSWC, can be managed amid present regulation requirements. Operators have recent experience that can be used to develop an optimized approach that includes technology improvements and a much more informed knowledge of how SSWC differs from coincident corrosion. The aim of this paper is to build on existing guidance and present an optimized approach for managing corrosion interacting with the long seam, with particular attention on differentiating SSWC from coincident corrosion crossing the long seam and defining how both can be assessed to create effective remediation plans. The flow chart considers both types of corrosion and leans on existing guidance and models that can be used to assess anomalies. A key part of the process is to consider susceptibility, material properties and appropriate in-line inspection (ILI) assessments in order to define the most suitable approach based on data and a thorough understanding of the individual pipeline system. Examples will be used to illustrate how the approach can be implemented and on what basis decisions can be made to move through to an optimized remediation plan.

The increasing prevalence of Neisseria gonorrhoeae strains exhibiting decreased susceptibility to extended-spectrum cephalosporins (ESCs) presents a challenge for the successful treatment of gonorrhea infections. To address this challenge, we evaluated a panel of 23 cephalosporins against penicillin-binding protein 2 (PBP2) from the ESC-resistant (ESCR) N. gonorrhoeae strain H041 to determine which molecular features are important for antimicrobial activity. Structure-activity relationships (SARs) developed from acylation rate constants against PBP2 and antimicrobial susceptibilities against the H041 strain of N. gonorrhoeae, and interpreted against docking models, reveal that cephalosporins possessing large, lipophilic R1 side chains and electronegative R2 side chains with planar groups are associated with higher acylation rates against PBP2, but also that these same amphipathic features can lower antimicrobial activity. Based on these studies, we tested cefoperazone, one of the most effective ESCs for targeting PBP2, in the female mouse model infected with H041 and showed that it was equally or more effective than ceftriaxone or gentamicin for clearing infections. Taken together, our results reveal that two U.S. Food and Drug Administration (FDA)-approved agents (cefoperazone, ceftaroline) and one FDA-qualified infectious disease product (ceftobiprole) have potential as first-line treatments for gonorrhea and provide a framework for the future design of cephalosporins with improved activity against ESC-resistant N. gonorrhoeae.

Aim: Osteosarcoma (OS) is the most common primary bone tumour in children and adolescents. Circulating free (cfDNA) and circulating tumour DNA (ctDNA) are promising biomarkers for disease surveillance and prognostication in several cancer types; however, few such studies are reported for OS. The purpose of this study was to discover and validate methylation-based biomarkers to detect plasma ctDNA in patients with OS and explore their utility as prognostic markers. Methods: Candidate CpG markers were selected through analysis of methylation array data for OS, non-OS tumours and germline samples. Candidates were validated in two independent OS datasets (n = 162, n = 107) and the four top-performing markers were selected. Methylation-specific digital droplet PCR (ddPCR) assays were designed and experimentally validated in OS tumour samples (n = 20) and control plasma samples. Finally, ddPCR assays were applied to pre-operative plasma and where available post-operative plasma from 72 patients with OS, and findings correlated with outcome. Results: Custom ddPCR assays detected ctDNA in 69% and 40% of pre-operative plasma samples (n = 72), based on thresholds of one or two positive markers respectively. ctDNA was detected in 5/17 (29%) post-operative plasma samples from patients, which in four cases were associated with or preceded disease relapse. Both pre-operative cfDNA levels and ctDNA detection independently correlated with overall survival (p = 0.0015 and p = 0.0096, respectively). Conclusion: Our findings illustrate the potential of mutation-independent methylation-based ctDNA assays for OS. This study lays the foundation for multi-institutional collaborative studies to explore the utility of plasma-derived biomarkers in the management of OS.

The global incidence of the sexually transmitted disease gonorrhea is expected to rise due to the spread of Neisseria gonorrhoeae strains with decreased susceptibility to extended-spectrum cephalosporins (ESCs). ESC resistance is conferred by mosaic variants of penicillin-binding protein 2 (PBP2) that have diminished capacity to form acylated adducts with cephalosporins. To elucidate the molecular mechanisms of ESC resistance, we conducted a biochemical and high-resolution structural analysis of PBP2 variants derived from the decreased-susceptibility N. gonorrhoeae strain 35/02 and ESC-resistant strain H041. Our data reveal that mutations both lower affinity of PBP2 for ceftriaxone and restrict conformational changes that normally accompany acylation. Specifically, we observe that a G545S substitution hinders rotation of the β3 strand necessary to form the oxyanion hole for acylation and also traps ceftriaxone in a noncanonical configuration. In addition, F504L and N512Y substitutions appear to prevent bending of the β3–β4 loop that is required to contact the R1 group of ceftriaxone in the active site. Other mutations also appear to act by reducing flexibility in the protein. Overall, our findings reveal that restriction of protein dynamics in PBP2 underpins the ESC resistance of N. gonorrhoeae.

Hair analysis is capable of determining both an individual's long-term drug history and a single exposure to a drug, which can be particularly important for corroborating incidents of drug-facilitated crimes. As a source of forensic evidence that may be used in a court of law, it must be credible, impartial and reliable, yet the pathways of drug and metabolite entry into hair are still uncertain. Many variables may influence drug analysis results, most of which are outside of the control of an analyst. An individual's pharmacokinetic and metabolic responses, hair growth rates, drug incorporation routes, axial migration, ethnicity, age and gender, for example, all display interpersonal variability. At present there is little standardization of the analytical processes involved with hair analysis. Both false positives and negative results for drugs are frequently encountered, regardless of whether a person has consumed a drug or not. In this regard, we have categorized these variables and proposed a three-stage analytical approach to facilitate forensic toxicologists, hair analysis experts, judiciaries and service users in the analytical and interpretation process. [Abstract copyright: © 2020 John Wiley & Sons, Ltd.]

Auxin treatment of grape (Vitis vinifera L.) berries delays ripening by inducing changes in gene expression and cell wall metabolism and could combat some deleterious climate change effects. Auxins are inhibitors of grape berry ripening and their application may be useful to delay harvest to counter effects of climate change. However, little is known about how this delay occurs. The expression of 1892 genes was significantly changed compared to the control during a 48 h time-course where the auxin 1-naphthaleneacetic acid (NAA) was applied to pre-veraison grape berries. Principal component analysis showed that the control and auxin-treated samples were most different at 3 h post-treatment when approximately three times more genes were induced than repressed by NAA. There was considerable cross-talk between hormone pathways, particularly between those of auxin and ethylene. Decreased expression of genes encoding putative cell wall catabolic enzymes (including those involved with pectin) and increased expression of putative cellulose synthases indicated that auxins may preserve cell wall structure. This was confirmed by immunochemical labelling of berry sections using antibodies that detect homogalacturonan (LM19) and methyl-esterified homogalacturonan (LM20) and by labelling with the CMB3a cellulose-binding module. Comparison of the auxin-induced changes in gene expression with the pattern of these genes during berry ripening showed that the effect on transcription is a mix of changes that may specifically alter the progress of berry development in a targeted manner and others that could be considered as non-specific changes. Several lines of evidence suggest that cell wall changes and associated berry softening are the first steps in ripening and that delaying cell expansion can delay ripening providing a possible mechanism for the observed auxin effects.

The burden of nosocomial SARS-CoV-2 infection remains poorly defined. We report on the outcomes of 2508 adults with molecularly-confirmed SARS-CoV-2 admitted across 18 major hospitals, representing over 60% of those hospitalised across Wales between 1 March and 1 July 2020. Inpatient mortality for nosocomial infection ranged from 38% to 42%, consistently higher than participants with community-acquired infection (31%–35%) across a range of case definitions. Those with hospital-acquired infection were older and frailer than those infected within the community. Nosocomial diagnosis occurred a median of 30 days following admission (IQR 21–63), suggesting a window for prophylactic or postexposure interventions, alongside enhanced infection control measures.

For steady flows, the Briggs (Electron-Stream Interaction with Plasmas. MIT Press, 1964) method is a well-established approach for classifying disturbances as either convectively or absolutely unstable. Here, the framework of the Briggs method is adapted to temporally periodic flows, with Floquet theory utilised to account for the time periodicity of the Stokes layer. As a consequence of the antiperiodicity of the flow, symmetry constraints are established that are used to describe the pointwise evolution of the disturbance, with the behaviour governed by harmonic and subharmonics modes. On coupling the symmetry constraints with a cusp-map analysis, multiple harmonic and subharmonic cusps are found for each Reynolds number of the flow. Therefore, linear disturbances experience subharmonic growth about fixed spatial locations. Moreover, the growth rate associated with the pointwise development of the disturbance matches the growth rate of the disturbance maximum. Thus, the onset of the Floquet instability (Blennerhassett & Bassom, J. Fluid Mech., vol. 464, 2002, pp. 393–410) coincides with the onset of absolutely unstable behaviour. Stability characteristics are consistent with the spatio-temporal disturbance development of the family-tree structure that has hitherto only been observed numerically via simulations of the linearised Navier–Stokes equations (Thomas et al., J. Fluid Mech., vol. 752, 2014, pp. 543–571; Ramage et al., Phys. Rev. Fluids, vol. 5, 2020, 103901).

Tetracyclines are a broad-spectrum class of antibiotics that have unclear actions with potentially lasting effects on bone metabolism. Initially isolated from Streptomyces, tetracycline proved to be an effective treatment for Gram +/− infections. The emergence of resistant bacterial strains commanded the development of later generation agents, including minocycline, doxycycline, tigecycline, sarecycline, omadacycline, and eravacycline. In 1957, it was realized that tetracyclines act as bone fluorochrome labels due to their high affinity for the bone mineral matrix. Over the course of the next decade, researchers discerned that these compounds are retained in the bone matrix at high levels after the termination of antibiotic therapy. Studies during this period provided evidence that tetracyclines could disrupt prenatal and early postnatal skeletal development. Currently, tetracyclines are most commonly prescribed as a long-term systemic therapy for the treatment of acne in healthy adolescents and young adults. Surprisingly, the impact of tetracyclines on physiologic bone modeling/remodeling is largely unknown. This article provides an overview of the pharmacology of tetracycline drugs, summarizes current knowledge about the impact of these agents on skeletal development and homeostasis, and reviews prior work targeting tetracyclines’ effects on bone cell physiology. The need for future research to elucidate unclear effects of tetracyclines on the skeleton is addressed, including drug retention/release mechanisms from the bone matrix, signaling mechanisms at bone cells, the impact of newer third generation tetracycline antibiotics, and the role of the gut-bone axis.

The treatment options for central chondrosarcoma are limited, and prognoses are generally unreliable. The presence and absence of mutations in IDH1, and IDH2 are defining events, and TERT mutations have been recently been associated with poor outcome. Despite this, molecular biomarkers are lacking. Here, analysing data from 356 patients, comprising results from whole genome sequencing (n=68), digital droplet PCR (n=346), and methylation arrays (n=57), we present a comprehensive genetic analysis of chondrosarcoma and suggest its clinical utility. Methylation profiles, TERT promoter mutations, genome doubling with prior haploidisation, and age at diagnosis of high grade, distinguish IDH1-mutant, IDH2-mutant and IDH wildtype tumours. The majority of IDH2-mutant tumours harbour TERT mutations, though a significant reduction in survival is only found in the less common mutational combination of IDH1 and TERT. We suggest that diagnostic testing for IDH1, IDH2 and TERT mutations could guide clinical monitoring and prognostication.

Central conventional chondrosarcoma (CS) is the most common subtype of primary malignant bone tumour in adults. Treatment options are usually limited to surgery, and prognosis is challenging. These tumours are characterised by the presence and absence of IDH1 and IDH2 mutations, and recently, TERT promoter alterations have been reported in around 20% of cases. The effect of these mutations on clinical outcome remains unclear. The purpose of this study was to determine if prognostic accuracy can be improved by the addition of genomic data, and specifically by examination of IDH1, IDH2, and TERT mutations.In this study, we combined both archival samples and data sourced from the Genomics England 100,000 Genomes Project (n = 356). Mutations in IDH1, IDH2, and TERT were profiled using digital droplet PCR (n = 346), whole genome sequencing (n=68), or both (n = 64). Complex events and other genetic features were also examined, along with methylation array data (n = 84). We correlated clinical features and patient outcomes with our genetic findings.IDH2-mutant tumours occur in older patients and commonly present with high-grade or dedifferentiated disease. Notably, TERT mutations occur most frequently in IDH2-mutant tumours, although have no effect on survival in this group. In contrast, TERT mutations are rarer in IDH1-mutant tumours, yet they are associated with a less favourable outcome in this group. We also found that methylation profiles distinguish IDH1- from IDH2-mutant tumours. IDH wild-type tumours rarely exhibit TERT mutations and tend to be diagnosed in a younger population than those with tumours harbouring IDH1 and IDH2 mutations. A major genetic feature of this group is haploidisation and subsequent genome doubling. These tumours evolve less frequently to dedifferentiated disease and therefore constitute a lower risk group.Tumours with IDH1 or IDH2 mutations or those that are IDHwt have significantly different genetic pathways and outcomes in relation to TERT mutation. Diagnostic testing for IDH1, IDH2, and TERT mutations could therefore help to guide clinical monitoring and prognostication.

An adjoint approach is developed to compute the receptivity of the rotating disc boundary layer to surface roughness. The adjoint linearised Navier–Stokes equations, in cylindrical coordinates, are derived and receptivity characteristics are computed for a broad range of azimuthal mode numbers using a fully equivalent velocity–vorticity formulation. For each set of flow conditions (i.e. azimuthal mode number), the adjoint method only requires that the linear and adjoint solutions be computed once. Thus, the adjoint approach offers significant computational and time advantages over alternative receptivity schemes (i.e. direct linearised Navier–Stokes) as they can be used to instantaneously compute the receptivity of boundary layer disturbances to many environmental mechanisms. Stationary cross-flow disturbances are established by randomly distributed surface roughness that is periodic in the azimuthal direction and modelled via a linearisation of the no-slip condition on the disc surface. Each roughness distribution is scaled on its respective root-mean-square. A Monte-Carlo type uncertainty quantification analysis is performed, whereby mean receptivity amplitudes are computed by averaging over many thousands of roughness realisations with variable length and wavelength filters. The amplitude of the cross-flow instability is significantly larger for roughness distributions near the conditions for neutral linear instability, while roughness elements radially outboard have a negligible effect on the receptivity process. Furthermore, receptivity increases sharply for roughness distributions that encompass wavelength scales equivalent to that associated with the cross-flow instability. Finally, mean receptivity characteristics are used to predict the radial range that stationary cross-flow vortices achieve amplitudes sufficient to invalidate the linear stability assumptions.

The control of stationary convective instabilities in the rotating disk boundary layer via a time-periodic modulation of the disk rotation rate is investigated. The configuration provides an archetypal example of a three-dimensional temporally periodic boundary layer, encompassing both the von Kármán and Stokes boundary layers. A velocity–vorticity formulation of the governing perturbation equations is deployed, together with a numerical procedure that utilises the Chebyshev-tau method. Floquet theory is used to determine the linear stability properties of these time-periodic flows. The addition of a time-periodic modulation to the otherwise steady disk rotation rate establishes a stabilising effect. In particular, for a broad range of modulation frequencies, the growth of the stationary convective instabilities is suppressed and the critical Reynolds number for the onset of both the cross-flow and Coriolis instabilities is raised to larger values than that found for the steady disk without modulation. An energy analysis is undertaken, where it is demonstrated that time-periodic modulation induces a reduction in the Reynolds stress energy production and an increase in the viscous dissipation across the boundary layer. Comparisons are made with other control techniques, including distributed surface roughness and compliant walls.

Resistance to the extended-spectrum cephalosporin ceftriaxone in the pathogenic bacteria Neisseria gonorrhoeae is conferred by mutations in penicillin-binding protein 2 (PBP2), the lethal target of the antibiotic, but how these mutations exert their effect at the molecular level is unclear. Using solution NMR, X-ray crystallography, and isothermal titration calorimetry, we report that WT PBP2 exchanges dynamically between a low-affinity state with an extended β3–β4 loop conformation and a high-affinity state with an inward β3–β4 loop conformation. Histidine-514, which is located at the boundary of the β4 strand, plays an important role during the exchange between these two conformational states. We also find that mutations present in PBP2 from H041, a ceftriaxone-resistant strain of N. gonorrhoeae, increase resistance to ceftriaxone by destabilizing the inward β3–β4 loop conformation or stabilizing the extended β3–β4 loop conformation to favor the low-affinity drug-binding state. These observations reveal a unique mechanism for ceftriaxone resistance, whereby mutations in PBP2 lower the proportion of target molecules in the high-affinity drug-binding state and thus reduce inhibition at lower drug concentrations.

In the tick-borne pathogens, Borreliella burgdorferi and Borrelia hermsii, c-di-GMP is produced by a single diguanylate cyclase (Rrp1). In these pathogens, the Plz proteins (PlzA, B and C) are the only c-di-GMP receptors identified to date and PlzA is the sole c-di-GMP receptor found in all Borreliella isolates. Bioinformatic analyses suggest that PlzA has a unique PilZN3-PilZ architecture with the relatively uncommon xPilZ domain. Here, we present the crystal structure of PlzA in complex with c-di-GMP (1.6 Å resolution). This is the first structure of a xPilz domain in complex with c-di-GMP to be determined. PlzA has a two-domain structure, where each domain comprises topologically equivalent PilZ domains with minimal sequence identity but remarkable structural similarity. The c-di-GMP binding site is formed by the linker connecting the two domains. While the structure of apo PlzA could not be determined, previous fluorescence resonance energy transfer data suggest that apo and holo forms of the protein are structurally distinct. The information obtained from this study will facilitate ongoing efforts to identify the molecular mechanisms of PlzA-mediated regulation in ticks and mammals., Here, the authors present a high-resolution structure of the Borreliella burgdorferi PlzA protein complexed with c-di-GMP.

The generalised Proca (GP) theory is a modified gravity model in which the acceleration of the cosmic expansion rate can be explained by self interactions of a cosmological vector field. In this paper we study a particular sub-class of the GP theory, with up to cubic order Lagrangian, known as the cubic vector Galileon (cvG) model. This model is similar to the cubic scalar Galileon (csG) in many aspects, including a fifth force and the Vainshtein screening mechanism, but with the additional flexibility that the strength of the fifth force depends on an extra parameter -- interpolating between zero and the full strength of the csG model -- while the background expansion history is independent of this parameter. It offers an interesting alternative to LambdaCDM in explaining the cosmic acceleration, as well as a solution to the tension between early- and late-time measurements of the Hubble constant H_0. To identify the best ways to test this model, in this paper we conduct a comprehensive study of the phenomenology of this model in the nonlinear regime of large-scale structure formation, using a suite of N-body simulations run with the modified gravity code ECOSMOG. By inspecting thirteen statistics of the dark matter field, dark matter haloes and weak lensing maps, we find that the fifth force in this model can have particularly significant effects on the large-scale velocity field and lensing potential at late times, which suggest that redshift-space distortions and weak lensing can place strong constraints on it., 32 pages, 15 figures, version to appear in JCAP

Resistance of Neisseria gonorrhoeae to extended-spectrum cephalosporins (ESCs) has become a major threat to human health. The primary mechanism by which N. gonorrhoeae becomes resistant to ESCs is by acquiring a mosaic penA allele, encoding penicillin-binding protein 2 (PBP2) variants containing up to 62 mutations compared with WT, of which a subset contribute to resistance. To interpret molecular mechanisms underpinning cephalosporin resistance, it is necessary to know how PBP2 is acylated by ESCs. Here, we report the crystal structures of the transpeptidase domain of WT PBP2 in complex with cefixime and ceftriaxone, along with structures of PBP2 in the apo form and with a phosphate ion bound in the active site at resolutions of 1–7-1.9 Å. These structures reveal that acylation of PBP2 by ESCs is accompanied by rotation of the Thr-498 side chain in the KTG motif to contact the cephalosporin carboxylate, twisting of the β3 strand to form the oxyanion hole, and rolling of the β3–β4 loop toward the active site. Recognition of the cephalosporin carboxylate appears to be the key trigger for formation of an acylation-competent state of PBP2. The structures also begin to explain the impact of mutations implicated in ESC resistance. In particular, a G545S mutation may hinder twisting of β3 because its side chain hydroxyl forms a hydrogen bond with Thr-498. Overall, our data suggest that acylation is initiated by conformational changes elicited or trapped by binding of ESCs and that these movements are restricted by mutations associated with resistance against ESCs.

Background and Aims The climate‐change driven uncoupling of grape (Vitis vinifera L.) berry ‘sugar‐ripeness’ and ‘flavour‐ripeness’ necessitates an improved understanding of the sugar/flavour nexus. Methods and Results Analysis of grape metabolites and wine volatiles derived from Riesling berries of peduncle‐girdled and Control bunches over the course of 30 days provided time‐dependent insights into changes to grape and wine composition associated with phloem import. Girdling resulted in stable berry mass and concentration of sugar and cytokinin and in reduced concentration of amino acids. Such changes to grape composition correlated with a lasting increase in wine monoterpenoids and a transient reduction in fermentation‐derived wine volatiles. Conclusions Oxidative stress and restricted amino acid import, not sugar accumulation, were identified as possible elicitors for the increased accumulation of varietal wine aroma compounds in Riesling. Significance of the Study The concentration and composition of berry amino acids and cytokinin concentration in grapes during the later stages of rapid sugar accumulation may represent potential targets for vineyard management strategies and grapevine breeding to counter climate‐change driven modifications to the wine volatile profile of aromatic cultivars.

Pyruvate kinases (PKs) synthesize ATP as the final step of glycolysis in the three domains of life. PKs from most bacteria and eukarya are allosteric enzymes that are activated by sugar phosphates; for example, the feed-forward regulator fructose-1,6-bisphosphate, or AMP as a sensor of energy charge. Archaea utilize unusual glycolytic pathways, but the allosteric properties of PKs from these species are largely unknown. Here, we present an analysis of 24 PKs from most archaeal clades with respect to allosteric properties, together with phylogenetic analyses constructed using a novel mode of rooting protein trees. We find that PKs from many Thermoproteales, an order of crenarchaeota, are allosterically activated by 3-phosphoglycerate (3PG). We also identify five conserved amino acids that form the binding pocket for 3PG. 3PG is generated via an irreversible reaction in the modified glycolytic pathway of these archaea and therefore functions as a feed-forward regulator. We also show that PKs from hyperthermophilic Methanococcales, an order of euryarchaeota, are activated by AMP. Phylogenetic analyses indicate that 3PG-activated PKs form an evolutionary lineage that is distinct from that of sugar-phosphate activated PKs, and that sugar phosphate-activated PKs originated as AMP-regulated PKs in hyperthermophilic Methanococcales. Since the phospho group of sugar phosphates and 3PG overlap in the allosteric site, our data indicate that the allostery in PKs first started from a progenitor phosphate-binding site that evolved in two spatially distinct directions: one direction generated the canonical site that responds to sugar phosphates and the other gave rise to the 3PG site present in Thermoproteales. Overall, our data suggest an intimate connection between the allosteric properties and evolution of PKs.