QM/MM simulations as an assay for carbapenemase activity in class A β-lactamases

Carbapenemases are distinguished from carbapenem-inhibited β-lactamases with a protocol involving QM/MM free energy simulations of acyl–enzyme deacylation, requiring only the enzyme 3D structure as input.</p

QM/MM Simulations Reveal the Determinants of Carbapenemase Activity in Class A β-lactamases

[Image: see text] β-lactam antibiotic resistance in Gram-negative bacteria, primarily caused by β-lactamase enzymes that hydrolyze the β-lactam ring, has become a serious clinical problem. Carbapenems were formerly considered “last resort” antibiotics because they escaped breakdown by most β-lactamases, due to slow deacylation of the acyl-enzyme intermediate. However, an increasing number of Gram-negative bacteria now produce β-lactamases with carbapenemase activity: these efficiently hydrolyze the carbapenem β-lactam ring, severely limiting the treatment of some bacterial infections. Here, we use quantum mechanics/molecular mechanics (QM/MM) simulations of the deacylation reactions of acyl-enzyme complexes of eight β-lactamases of class A (the most widely distributed β-lactamase group) with the carbapenem meropenem to investigate differences between those inhibited by carbapenems (TEM-1, SHV-1, BlaC, and CTX-M-16) and those that hydrolyze them (SFC-1, KPC-2, NMC-A, and SME-1). QM/MM molecular dynamics simulations confirm the two enzyme groups to differ in the preferred acyl-enzyme orientation: carbapenem-inhibited enzymes favor hydrogen bonding of the carbapenem hydroxyethyl group to deacylating water (DW). QM/MM simulations of deacylation give activation free energies in good agreement with experimental hydrolysis rates, correctly distinguishing carbapenemases. For the carbapenem-inhibited enzymes, free energies for deacylation are significantly higher than for the carbapenemases, even when the hydroxyethyl group was restrained to prevent interaction with the DW. Analysis of these simulations, and additional simulations of mutant enzymes, shows how factors including the hydroxyethyl orientation, the active site volume, and architecture (conformations of Asn170 and Asn132; organization of the oxyanion hole; and the Cys69-Cys238 disulfide bond) collectively determine catalytic efficiency toward carbapenems

Mg/Ca-Temperature Calibration of Polar Benthic foraminifera species for reconstruction of bottom water temperatures on the Antarctic shelf

Benthic foraminifera Mg/Ca is a well-established bottom water temperature (BWT) proxy used in paleoclimate studies. The relationship between Mg/Ca and BWT for numerous species has been determined using core-top and culturing studies. However, the scarcity of calcareous microfossils in Antarctic shelf sediments and poorly defined calibrations at low temperatures has limited the use of the foraminiferal Mg/Ca paleothermometer in ice proximal Antarctic sediments. Here we present paired ocean temperature and modern benthic foraminifera Mg/Ca data for three species, Trifarina angulosa, Bulimina aculeata, and Globocassidulina subglobosa, but with a particular focus on Trifarina angulosa. The core-top data from several Antarctic sectors span a BWT range of −1.7 to +1.2 °C and constrain the relationship between Mg/Ca and cold temperatures. We compare our results to published lower-latitude core-top data for species in the same or related genera, and in the case of Trifarina angulosa, produce a regional calibration. The resulting regional equation for Trifarina angulosa is Temperature (°C) = (Mg/Ca −1.14 ± 0.035)/0.069 ± 0.033). Addition of our Trifarina angulosa data to the previously published Uvigerina spp. dataset provides an alternative global calibration, although some data points appear to be offset from this relationship and are discussed. Mg-temperature relationships for Bulimina aculeata and Globocassidulina subglobosa are also combined with previously published data to produce calibration equations of Temperature (°C) = (Mg/Ca-1.04 ± 0.07)/0.099 ± 0.01 and Temperature (°C) = (Mg/Ca-0.99 ± 0.03)/0.087 ± 0.01, respectively. These refined calibrations highlight the potential utility of benthic foraminifera Mg/Ca-paleothermometry for reconstructing past BWT in Antarctic margin settings

Tuning charge-assisted and weak hydrogen bonds in molecular complexes of the proton sponge DMAN by acid co-former substitution

Nine new molecular complexes of the proton sponge 1,8-bis(dimethylamino)naphthalene (DMAN) with substituted benzoic acid co-formers have been engineered with varying component stoichiometries (1?:?1, 1?:?2 or 1?:?3). These complexes are all ionic in nature, following proton transfer between the acid co-former and DMAN; the extracted proton is held by DMAN in all instances in an intramolecular [N–H?N]+ hydrogen bond. A number of structural features are common to all complexes and are found to be tunable in a predictable way using systematic acid co-former substitution. These features include charge-assisted hydrogen bonds formed between acid co-formers in hydrogen bonding motifs consistent with complex stoichiometry, and weak hydrogen bonds which facilitate the crystal packing of DMAN and acid co-former components into a regular motif. Possible crystal structure tuning by co-former substitution can aid the rational design of such materials, offering the potential to target solid-state properties that may be influenced by these interactions

Orbit size and estimated eye size in dinosaurs and other archosaurs and their implications for the evolution of visual capabilities

Vision is one of the most important senses for animals, allowing them to interact with their environment and with further implications for evolutionary histories. However, relevant soft tissues, such as the eye and associated structures, are not preserved in fossil vertebrates, limiting our knowledge of their visual capabilities. Here, we quantified absolute and relative orbit size for 400 species of dinosaurs and other extinct archosaurs using linear measurements of the preserved skeletal elements as a proxy for visual capabilities. Our results demonstrate that the orbit makes up on average 20% of skull size with a strong and consistent correlation across all sampled groups. This trend is largely independent of temporal distribution, species richness, and phylogeny. In fact, relative orbit size is narrowly constrained and did not surpass 45% of skull size, suggesting physiological and functional controls. Estimated eye size was found to be absolutely larger in herbivores, whereas carnivores tended to have smaller eyes absolutely and compared with skull size. Relatively large eyes only occurred in small-bodied species and vice versa. However, eye size alone was not sufficient to discriminate between different activity patterns or to characterize visual capabilities in detail.</p

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

TNPO2 variants associate with human developmental delays, neurologic deficits, and dysmorphic features and alter TNPO2 activity in Drosophila

Transportin-2 (TNPO2) mediates multiple pathways including non-classical nucleocytoplasmic shuttling of >60 cargoes, such as developmental and neuronal proteins. We identified 15 individuals carrying de novo coding variants in TNPO2 who presented with global developmental delay (GDD), dysmorphic features, ophthalmologic abnormalities, and neurological features. To assess the nature of these variants, functional studies were performed in Drosophila. We found that fly dTnpo (orthologous to TNPO2) is expressed in a subset of neurons. dTnpo is critical for neuronal maintenance and function as downregulating dTnpo in mature neurons using RNAi disrupts neuronal activity and survival. Altering the activity and expression of dTnpo using mutant alleles or RNAi causes developmental defects, including eye and wing deformities and lethality. These effects are dosage dependent as more severe phenotypes are associated with stronger dTnpo loss. Interestingly, similar phenotypes are observed with dTnpo upregulation and ectopic expression of TNPO2, showing that loss and gain of Transportin activity causes developmental defects. Further, proband-associated variants can cause more or less severe developmental abnormalities compared to wild-type TNPO2 when ectopically expressed. The impact of the variants tested seems to correlate with their position within the protein. Specifically, those that fall within the RAN binding domain cause more severe toxicity and those in the acidic loop are less toxic. Variants within the cargo binding domain show tissue-dependent effects. In summary, dTnpo is an essential gene in flies during development and in neurons. Further, proband-associated de novo variants within TNPO2 disrupt the function of the encoded protein. Hence, TNPO2 variants are causative for neurodevelopmental abnormalities

Clinical and cost-effectiveness of contingency management for cannabis use in early psychosis: the CIRCLE randomised clinical trial

Background Cannabis is the most commonly used illicit substance among people with psychosis. Continued cannabis use following the onset of psychosis is associated with poorer functional and clinical outcomes. However, finding effective ways of intervening has been very challenging. We examined the clinical and cost-effectiveness of adjunctive contingency management (CM), which involves incentives for abstinence from cannabis use, in people with a recent diagnosis of psychosis. Methods CIRCLE was a pragmatic multi-centre randomised controlled trial. Participants were recruited via Early Intervention in Psychosis (EIP) services across the Midlands and South East of England. They had had at last one episode of clinically diagnosed psychosis (affective or non-affective); were aged 18 to 36; reported cannabis use in at least 12 out of the previous 24 weeks; and were not currently receiving treatment for cannabis misuse, or subject to a legal requirement for cannabis testing. Participants were randomised via a secure web-based service 1:1 to either an experimental arm, involving 12 weeks of CM plus a six-session psychoeducation package, or a control arm receiving the psychoeducation package only. The total potential voucher reward in the CM intervention was £240. The primary outcome was time to acute psychiatric care, operationalised as admission to an acute mental health service (including community alternatives to admission). Primary outcome data were collected from patient records at 18 months post-consent by assessors masked to allocation. The trial was registered with the ISRCTN registry, number ISRCTN33576045. Results: 551 participants were recruited between June 2012 and April 2016. Primary outcome data were obtained for 272 (98%) in the CM (experimental) group and 259 (95%) in the control group. There was no statistically significant difference in time to acute psychiatric care (the primary outcome) (HR 1.03, 95% CI 0.76, 1.40) between groups. By 18 months, 90 (33%) of participants in the CM group, and 85 (30%) of the control groups had been admitted at least once to an acute psychiatric service. Amongst those who had experienced an acute psychiatric admission, the median time to admission was 196 days (IQR 82, 364) in the CM group and 245 days (IQR 99,382) in the control group. Cost-effectiveness analyses suggest that there is an 81% likelihood that the intervention was cost-effective, mainly resulting from higher mean inpatient costs for the control group compared with the CM group, however the cost difference between groups was not statistically significant. There were 58 adverse events, 27 in the CM group and 31 in the control group. Conclusions Overall, these results suggest that CM is not an effective intervention for improving the time to acute psychiatric admission or reducing cannabis use in psychosis, at least at the level of voucher reward offered

ICDP workshop on the Lake Tanganyika Scientific Drilling Project: a late Miocene–present record of climate, rifting, and ecosystem evolution from the world's oldest tropical lake

The Neogene and Quaternary are characterized by enormous changes in global climate and environments, including global cooling and the establishment of northern high-latitude glaciers. These changes reshaped global ecosystems, including the emergence of tropical dry forests and savannahs that are found in Africa today, which in turn may have influenced the evolution of humans and their ancestors. However, despite decades of research we lack long, continuous, well-resolved records of tropical climate, ecosystem changes, and surface processes necessary to understand their interactions and influences on evolutionary processes. Lake Tanganyika, Africa, contains the most continuous, long continental climate record from the mid-Miocene (∼10 Ma) to the present anywhere in the tropics and has long been recognized as a top-priority site for scientific drilling. The lake is surrounded by the Miombo woodlands, part of the largest dry tropical biome on Earth. Lake Tanganyika also harbors incredibly diverse endemic biota and an entirely unexplored deep microbial biosphere, and it provides textbook examples of rift segmentation, fault behavior, and associated surface processes. To evaluate the interdisciplinary scientific opportunities that an ICDP drilling program at Lake Tanganyika could offer, more than 70 scientists representing 12 countries and a variety of scientific disciplines met in Dar es Salaam, Tanzania, in June 2019. The team developed key research objectives in basin evolution, source-to-sink sedimentology, organismal evolution, geomicrobiology, paleoclimatology, paleolimnology, terrestrial paleoecology, paleoanthropology, and geochronology to be addressed through scientific drilling on Lake Tanganyika. They also identified drilling targets and strategies, logistical challenges, and education and capacity building programs to be carried out through the project. Participants concluded that a drilling program at Lake Tanganyika would produce the first continuous Miocene–present record from the tropics, transforming our understanding of global environmental change, the environmental context of human origins in Africa, and providing a detailed window into the dynamics, tempo and mode of biological diversification and adaptive radiations.© Author(s) 2020. This open access article is distributed under the Creative Commons Attribution 4.0 License