Molecular Basis of C–N Bond Cleavage by the Glycyl Radical Enzyme Choline Trimethylamine-Lyase

Deamination of choline catalyzed by the glycyl radical enzyme choline trimethylamine-lyase (CutC) has emerged as an important route for the production of trimethylamine, a microbial metabolite associated with both human disease and biological methane production. Here, we have determined five high-resolution X-ray structures of wild-type CutC and mechanistically informative mutants in the presence of choline. Within an unexpectedly polar active site, CutC orients choline through hydrogen bonding with a putative general base, and through close interactions between phenolic and carboxylate oxygen atoms of the protein scaffold and the polarized methyl groups of the trimethylammonium moiety. These structural data, along with biochemical analysis of active site mutants, support a mechanism that involves direct elimination of trimethylamine. This work broadens our understanding of radical-based enzyme catalysis and will aid in the rational design of inhibitors of bacterial trimethylamine production.National Science Foundation (U.S.) (Grant 0645960

The class III ribonucleotide reductase from Neisseria bacilliformis can utilize thioredoxin as a reductant

The class III anaerobic ribonucleotide reductases (RNRs) studied to date couple the reduction of ribonucleotides to deoxynucleotides with the oxidation of formate to CO[subscript 2]. Here we report the cloning and heterologous expression of the Neisseria bacilliformis class III RNR and show that it can catalyze nucleotide reduction using the ubiquitous thioredoxin/thioredoxin reductase/NADPH system. We present a structural model based on a crystal structure of the homologous Thermotoga maritima class III RNR, showing its architecture and the position of conserved residues in the active site. Phylogenetic studies suggest that this form of class III RNR is present in bacteria and archaea that carry out diverse types of anaerobic metabolism.Singapore. Agency for Science, Technology and ResearchNational Science Foundation (U.S.). Graduate Research Fellowship Program (Grant 0645960)United States. Dept. of Energy. Office of Basic Energy Sciences (Contract DE-AC02-06CH11357)National Institutes of Health (U.S.) (Grant GM29595

Warming of the Indian Ocean Threatens Eastern and Southern Africa, but could be Mitigated by Agricultural Development

Since 1980, the number of undernourished people in eastern and southern Africa has more than doubled. Rural development stalled and rural poverty expanded during the 1990s. Population growth remains very high and declining per capita agricultural capacity retards progress towards Millennium Development goals. Analyses of in situ station data and satellite observations of precipitation identify another problematic trend. Main growing season rainfall receipts have diminished by approximately 15% in food insecure countries clustered along the western rim of the Indian Ocean. Occurring during the main growing seasons in poor countries dependent on rain fed agriculture, these declines are societally dangerous. Will they persist or intensify? Tracing moisture deficits upstream to an anthropogenically warming Indian Ocean leads us to conclude that further rainfall declines are likely. We present analyses suggesting that warming in the central Indian Ocean disrupts onshore moisture transports, reducing continental rainfall. Thus late 20th century anthropogenic Indian Ocean warming has probably already produced societally dangerous climate change by creating drought and social disruption in some of the world's most fragile food economies. We quantify the potential impacts of the observed precipitation and agricultural capacity trends by modeling millions of undernourished people as a function of rainfall, population, cultivated area, seed and fertilizer use. Persistence of current tendencies may result in a 50% increase in undernourished people. On the other hand, modest increases in per capita agricultural productivity could more than offset the observed precipitation declines. Investing in agricultural development can help mitigate climate change while decreasing rural poverty and vulnerability

Biophysical Characterization of Fluorotyrosine Probes Site-Specifically Incorporated into Enzymes:

Fluorinated tyrosines (F[subscript n]Y's, n = 2 and 3) have been site-specifically incorporated into E. coli class Ia ribonucleotide reductase (RNR) using the recently evolved M. jannaschii Y-tRNA synthetase/tRNA pair. Class Ia RNRs require four redox active Y's, a stable Y radical (Y·) in the β subunit (position 122 in E. coli), and three transiently oxidized Y's (356 in β and 731 and 730 in α) to initiate the radical-dependent nucleotide reduction process. F[subscript n]Y (3,5; 2,3; 2,3,5; and 2,3,6) incorporation in place of Y₁₂₂-β and the X-ray structures of each resulting β with a diferric cluster are reported and compared with wt-β2 crystallized under the same conditions. The essential diferric-F[subscript n]Y· cofactor is self-assembled from apo F[subscript n]Y-β2, Fe ²⁺, and O₂ to produce ∼1 Y·/β2 and ∼3 Fe ³⁺ /β2. The F[subscript n]Y· are stable and active in nucleotide reduction with activities that vary from 5% to 85% that of wt-β2. Each F[subscript n] Y·-β2 has been characterized by 9 and 130 GHz electron paramagnetic resonance and high-field electron nuclear double resonance spectroscopies. The hyperfine interactions associated with the 19 F nucleus provide unique signatures of each F[subscript n]Y· that are readily distinguishable from unlabeled Y·'s. The variability of the abiotic F[subscript n]Y pK a 's (6.4 to 7.8) and reduction potentials (-30 to +130 mV relative to Y at pH 7.5) provide probes of enzymatic reactions proposed to involve Y·'s in catalysis and to investigate the importance and identity of hopping Y·'s within redox active proteins proposed to protect them from uncoupled radical chemistry.National Institutes of Health (U.S.) (Grant GM29595)National Science Foundation (U.S.) (Grant 0645960

Exploring Author Gender in Book Rating and Recommendation

Collaborative filtering algorithms find useful patterns in rating and consumption data and exploit these patterns to guide users to good items. Many of the patterns in rating datasets reflect important real-world differences between the various users and items in the data; other patterns may be irrelevant or possibly undesirable for social or ethical reasons, particularly if they reflect undesired discrimination, such as gender or ethnic discrimination in publishing. In this work, we examine the response of collaborative filtering recommender algorithms to the distribution of their input data with respect to a dimension of social concern, namely content creator gender. Using publicly-available book ratings data, we measure the distribution of the genders of the authors of books in user rating profiles and recommendation lists produced from this data. We find that common collaborative filtering algorithms differ in the gender distribution of their recommendation lists, and in the relationship of that output distribution to user profile distribution

Resource-aware Research on Universe and Matter: Call-to-Action in Digital Transformation

Given the urgency to reduce fossil fuel energy production to make climate tipping points less likely, we call for resource-aware knowledge gain in the research areas on Universe and Matter with emphasis on the digital transformation. A portfolio of measures is described in detail and then summarized according to the timescales required for their implementation. The measures will both contribute to sustainable research and accelerate scientific progress through increased awareness of resource usage. This work is based on a three-days workshop on sustainability in digital transformation held in May 2023.Comment: 20 pages, 2 figures, publication following workshop 'Sustainability in the Digital Transformation of Basic Research on Universe & Matter', 30 May to 2 June 2023, Meinerzhagen, Germany, https://indico.desy.de/event/3748

Methods for specifying the target difference in a randomised controlled trial : the Difference ELicitation in TriAls (DELTA) systematic review

Peer reviewedPublisher PD

The ASTRO-H X-ray Observatory

The joint JAXA/NASA ASTRO-H mission is the sixth in a series of highly successful X-ray missions initiated by the Institute of Space and Astronautical Science (ISAS). ASTRO-H will investigate the physics of the high-energy universe via a suite of four instruments, covering a very wide energy range, from 0.3 keV to 600 keV. These instruments include a high-resolution, high-throughput spectrometer sensitive over 0.3-2 keV with high spectral resolution of Delta E < 7 eV, enabled by a micro-calorimeter array located in the focal plane of thin-foil X-ray optics; hard X-ray imaging spectrometers covering 5-80 keV, located in the focal plane of multilayer-coated, focusing hard X-ray mirrors; a wide-field imaging spectrometer sensitive over 0.4-12 keV, with an X-ray CCD camera in the focal plane of a soft X-ray telescope; and a non-focusing Compton-camera type soft gamma-ray detector, sensitive in the 40-600 keV band. The simultaneous broad bandpass, coupled with high spectral resolution, will enable the pursuit of a wide variety of important science themes.Comment: 22 pages, 17 figures, Proceedings of the SPIE Astronomical Instrumentation "Space Telescopes and Instrumentation 2012: Ultraviolet to Gamma Ray