Structural and mechanistic analysis of ATPase inhibitors targeting mycobacterial DNA gyrase

Objectives To evaluate the efficacy of two novel compounds against mycobacteria and determine the molecular basis of their action on DNA gyrase using structural and mechanistic approaches. Methods Redx03863 and Redx04739 were tested in antibacterial assays, and also against their target, DNA gyrase, using DNA supercoiling and ATPase assays. X-ray crystallography was used to determine the structure of the gyrase B protein ATPase sub-domain from Mycobacterium smegmatis complexed with the aminocoumarin drug novobiocin, and structures of the same domain from Mycobacterium thermoresistibile complexed with novobiocin, and also with Redx03863. Results Both compounds, Redx03863 and Redx04739, were active against selected Gram-positive and Gram-negative species, with Redx03863 being the more potent, and Redx04739 showing selectivity against M. smegmatis. Both compounds were potent inhibitors of the supercoiling and ATPase reactions of DNA gyrase, but did not appreciably affect the ATP-independent relaxation reaction. The structure of Redx03863 bound to the gyrase B protein ATPase sub-domain from M. thermoresistibile shows that it binds at a site adjacent to the ATP- and novobiocin-binding sites. We found that most of the mutations that we made in the Redx03863-binding pocket, based on the structure, rendered gyrase inactive. Conclusions Redx03863 and Redx04739 inhibit gyrase by preventing the binding of ATP. The fact that the Redx03863-binding pocket is distinct from that of novobiocin, coupled with the lack of activity of resistant mutants, suggests that such compounds could have potential to be further exploited as antibiotics

The effectiveness and cost-effectiveness of minimal access surgery amongst people with gastro-oesophageal reflux disease – a UK collaborative study

*Corresponding author randomised arm of the trial (178 allocated to surgical management,179 allocated to continued, but optimised,medical management) and 453 recruited to the parallel non-randomised preference arm (261 chose surgical management, 192 chose to continue with best medical management). The type of fundoplication was left to the discretion of the surgeon. Main outcome measures: Participants completed a baseline reflux questionnaire, developed specifically for this study, containing a disease-specific outcome measure, the Short Form with 36 Items (SF-36), the EuroQol-5 Dimensions (EQ-5D) and the Beliefs about Medicines and Surgery questionnaires (BMQ/BSQ).Postal questionnaires were completed at participant specific time intervals after joining the trial (equivalent to approximately 3 and 12 months after surgery).Intraoperative data were recorded by the surgeons and all other in-hospital data were collected by the research nurse. At the end of the study period, participants completed a discrete choice experiment questionnaire. Results: The randomised groups were well balanced at entry. Participants had been taking GORD medication for a median of 32 months; the mean age of participants was 46 years and 66% were men. Of 178 randomised to surgery, 111 (62%) actually had fundoplication.There was a mixture of clinical and personal reasons why some patients did not have surgery, sometimes Objectives: To evaluate the clinical effectiveness, costeffectiveness and safety of a policy of relatively early laparoscopic surgery compared with continued medical management amongst people with gastro-oesophageal reflux disease (GORD) judged suitable for both policies. Design: Relative clinical effectiveness was assessed by a randomised trial (with parallel non-randomised preference groups) comparing a laparoscopic surgerybased policy with a continued medical management policy. The economic evaluation compared the costeffectiveness of the two management policies in order to identify the most efficient provision of future care and describe the resource impact that various policies for fundoplication would have on the NHS.Setting: A total of 21 hospitals throughout the UK with a local partnership between surgeon(s) and gastroenterologist(s) who shared the secondary care of patients with GORD.Participants: The 810 participants, who were identified retrospectively or prospectively via their participating clinicians, had both documented evidence of GORD (endoscopy and/or manometry/24-hour pH monitoring) and symptoms for longer than 12 months. In addition,the recruiting clinician(s) was clinically uncertain about which management policy was best.Intervention: Of the 810 eligible patients who consented to participate, 357 were recruited to the related to long waiting times. A total or partial wrap procedure was performed depending on surgeon preference. Complications were uncommon and there were no deaths associated with surgery. By the equivalent of 12 months after surgery, 38% in the randomised surgical group (14% amongst those who had surgery) were taking reflux medication compared with 90% in the randomised medical group. There were substantial differences (one-third to one-half standard deviation) favouring the randomised surgical group across the health status measures, the size depending on assumptions about the proportion that actually had fundoplication. These differences were the same or somewhat smaller than differences observed at 3 months. The lower the reflux score, the worse the symptoms at trial entry and the larger the benefit observed after surgery. The preference surgical group had the lowest reflux scores at baseline. These scores improved substantially after surgery, and by 12 months they were better than those in the preference medical group. The BMQ/BSQ and discrete choice experiment did distinguish the preference groups from each other and from the randomised groups. The latter indicated that the risk of serious complications was the most important single attribute of a treatment option. A within trial cost-effectiveness analysis suggested that the surgery policy was more costly (mean £2049) but also more effective [+0.088 quality-adjusted life-years (QALYs)]. The estimated incremental cost per QALY was £19,000–£23,000, with a probability between 46% (when 62% received surgery) and 19% (when all received surgery) of cost-effectiveness at a threshold of £20,000 per QALY. Modelling plausible longer-term scenarios (such as lifetime benefit after surgery) indicated a greater likelihood (74%) of costeffectiveness at a threshold of £20,000, but applying a range of alternative scenarios indicated wide uncertainty.The expected value of perfect information was greatest for longer-term quality of life and proportions of surgical patients requiring medication.Conclusions: Amongst patients requiring long-term medication to control symptoms of GORD, surgical management significantly increases general and refluxspecific health-related quality of life measures, at least up to 12 months after surgery. Complications of surgery were rare. A surgical policy is, however, more costly than continued medical management. At a threshold of £20,000 per QALY it may well be cost-effective, especially when putative longer-term benefits are taken into account, but this is uncertain.The more troublesome the symptoms, the greater the potential benefit from surgery. Uncertainty about cost-effectiveness would be greatly reduced by more reliable information about relative longer-term costs and benefits of surgical and medical policies. This could be through extended follow-up of the reflux trial cohorts or of other cohorts of fundoplication patients.Peer reviewedPublisher PD

InterPro in 2022.

The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. Here, we report recent developments with InterPro (version 90.0) and its associated software, including updates to data content and to the website. These developments extend and enrich the information provided by InterPro, and provide a more user friendly access to the data. Additionally, we have worked on adding Pfam website features to the InterPro website, as the Pfam website will be retired in late 2022. We also show that InterPro's sequence coverage has kept pace with the growth of UniProtKB. Moreover, we report the development of a card game as a method of engaging the non-scientific community. Finally, we discuss the benefits and challenges brought by the use of artificial intelligence for protein structure prediction

The Gemini Planet Imager View of the HD 32297 Debris Disk

We present new H-band scattered light images of the HD 32297 edge-on debris disk obtained with the Gemini Planet Imager. The disk is detected in total and polarized intensity down to a projected angular separation of 0.?15, or 20 au. On the other hand, the large-scale swept-back halo remains undetected, likely a consequence of its markedly blue color relative to the parent body belt. We analyze the curvature of the disk spine and estimate a radius of ?100 au for the parent body belt, smaller than past scattered light studies but consistent with thermal emission maps of the system. We employ three different flux-preserving post-processing methods to suppress the residual starlight and evaluate the surface brightness and polarization profile along the disk spine. Unlike past studies of the system, our high-fidelity images reveal the disk to be highly symmetric and devoid of morphological and surface brightness perturbations. We find the dust scattering properties of the system to be consistent with those observed in other debris disks, with the exception of HR 4796. Finally, we find no direct evidence for the presence of a planetary-mass object in the system

Debris Disk Results from the Gemini Planet Imager Exoplanet Survey\u27s Polarimetric Imaging Campaign

We report the results of a ∼4 yr direct imaging survey of 104 stars to resolve and characterize circumstellar debris disks in scattered light as part of the Gemini Planet Imager (GPI) Exoplanet Survey. We targeted nearby (≲150 pc), young (≲500 Myr) stars with high infrared (IR) excesses (L IR/L ∗ \u3e 10-5), including 38 with previously resolved disks. Observations were made using the GPI high-contrast integral field spectrograph in H-band (1.6 μm) coronagraphic polarimetry mode to measure both polarized and total intensities. We resolved 26 debris disks and 3 protoplanetary/transitional disks. Seven debris disks were resolved in scattered light for the first time, including newly presented HD 117214 and HD 156623, and we quantified basic morphologies of five of them using radiative transfer models. All of our detected debris disks except HD 156623 have dust-poor inner holes, and their scattered-light radii are generally larger than corresponding radii measured from resolved thermal emission and those inferred from spectral energy distributions. To assess sensitivity, we report contrasts and consider causes of nondetections. Detections were strongly correlated with high IR excess and high inclination, although polarimetry outperformed total intensity angular differential imaging for detecting low-inclination disks (≲70°). Based on postsurvey statistics, we improved upon our presurvey target prioritization metric predicting polarimetric disk detectability. We also examined scattered-light disks in the contexts of gas, far-IR, and millimeter detections. Comparing H-band and ALMA fluxes for two disks revealed tentative evidence for differing grain properties. Finally, we found no preference for debris disks to be detected in scattered light if wide-separation substellar companions were present

‘Caution! The Bread is Poisoned’: The Hong Kong Mass Poisoning of January 1857

This article examines the Hong Kong mass poisoning of 15 January 1857, in which bread from a Chinese bakery that supplied the colonial community was adulterated with arsenic. Even though there is a wealth of printed and manuscript documentation available many vital aspects of the poisoning remain unclear. What kind of incident was it: an act of terrorism and attempted mass murder, a war crime, a criminal conspiracy, an act of commercial sabotage, an accident or even an imagined or imaginary event? Throughout, our focus remains firmly fixed on the central act of the poisoning itself and on what it reveals about the precarious nature of early colonial Hong Kong. Interpretations have swarmed over the available ‘facts'. Equally ironic is what happened to the afterlife of how the event was understood. This article seeks to rescue the Hong Kong poisoning from being a freakish and isolated footnote of only local interest. Accepting this historical verdict would be a mistake as it is of significance not only at a local level, but geopolitically in Britain and across the empire

Intertidal No. 1

For the first year ever, Intertidal has surfaced to showcase the art of Cal Poly\u27s students and faculty. An \u27intertidal zone\u27 is an area where the ocean meets the land--hidden during the high tide and exposed during the low. Our journal embodies the moment where the tide recedes, revealing stories previously hidden

Target 2035-update on the quest for a probe for every protein

Twenty years after the publication of the first draft of the human genome, our knowledge of the human proteome is still fragmented. The challenge of translating the wealth of new knowledge from genomics into new medicines is that proteins, and not genes, are the primary executers of biological function. Therefore, much of how biology works in health and disease must be understood through the lens of protein function. Accordingly, a subset of human proteins has been at the heart of research interests of scientists over the centuries, and we have accumulated varying degrees of knowledge about approximately 65% of the human proteome. Nevertheless, a large proportion of proteins in the human proteome (∼35%) remains uncharacterized, and less than 5% of the human proteome has been successfully targeted for drug discovery. This highlights the profound disconnect between our abilities to obtain genetic information and subsequent development of effective medicines. Target 2035 is an international federation of biomedical scientists from the public and private sectors, which aims to address this gap by developing and applying new technologies to create by year 2035 chemogenomic libraries, chemical probes, and/or biological probes for the entire human proteome