oge Safe use of liquid nitrogen By www.safetyandhealthmagazine.com Published On :: Sun, 25 Jun 2023 00:00:00 -0400 Liquid nitrogen is the colorless, odorless, clear liquefied form of nitrogen. It can be extremely dangerous to work around. Full Article
oge S.T.O.P. Carcinogens at Work: EU-OSHA launches website By www.safetyandhealthmagazine.com Published On :: Tue, 01 Oct 2024 00:00:00 -0400 Bilbao, Spain — When carcinogens are present in the workplace, “employers must do everything in their power to prevent workers from coming into contact with them,” the European Agency for Safety and Health at Work says. Full Article
oge Safety board calls for an OSHA standard on liquid nitrogen By www.safetyandhealthmagazine.com Published On :: Tue, 23 Jan 2024 00:00:00 -0500 Washington — Chemical facilities that handle hazardous gases or cryogenic asphyxiants such as liquid nitrogen should maintain atmospheric monitoring and alarm systems and educate workers on hazards. Full Article
oge OGeez! Innovative Gummies By www.preparedfoods.com Published On :: Wed, 17 Jan 2024 07:00:00 -0500 Like freshly squeezed juice, live rosin is created through a pressing process. The highest-quality harvested cannabis is frozen and ultimately pressed to extract the all-natural, live rosin oil. Full Article
oge Epogee: Replace Fat By www.preparedfoods.com Published On :: Wed, 15 Mar 2017 00:00:00 -0400 Health conscious consumers soon will be able to enjoy indulgent foods with drastically fewer calories without sacrificing taste or flavor thanks to Epogee™ (esterified propoxylated glycerol) Fat Replacement. Epogee was developed by Choco Finesse LLC. Full Article
oge EPOGEE: Alternative Fat By www.preparedfoods.com Published On :: Fri, 19 Jun 2020 11:00:00 -0400 Epogee LLC said that its revolutionary new alternative fat, EPG, has achieved additional GRAS (Generally Recognized As Safe) status by the United States Food and Drug Administration (FDA). Full Article
oge Epogee: Keep Flavor, Cut Calories By www.preparedfoods.com Published On :: Tue, 14 Jul 2020 00:00:00 -0400 Epogee LLC used the virtual 2020 Institute of Food Technologists Annual Meeting and Food Expo to introduce EPG, a low-calorie alternative fat technology made from GMO-free plant-based oil. Full Article
oge Epogee: Alternative Fat By www.preparedfoods.com Published On :: Wed, 03 Mar 2021 14:15:00 -0500 Titled “Cooking up a fat revolution with EPG,” this new resource discusses consumer dynamics and highlights EPG, an alternative fat technology—labelled as a GMO-free modified plant-based oil—that helps manufacturers dramatically lower calories without compromising the taste, texture or functionality of a wide variety of food and beverage applications. Full Article
oge Epogee: Cut Calories By www.preparedfoods.com Published On :: Mon, 17 May 2021 13:00:00 -0400 Epogee unveiled a completely redesigned website at www.epogee.com. It give food and beverage manufacturers an informative and efficient experience that is easy to navigate. The site showcases EPG, an alternative fat technology that appears on ingredient labels as “GMO-free modified plant-based oil.” Full Article
oge Epogee: Full Taste, Fewer Calories By www.preparedfoods.com Published On :: Mon, 21 Jun 2021 06:00:00 -0400 Gatsby’s breakthrough product delivers melt-in-your mouth indulgence and achieves unheard-of calorie reduction—thanks to Epogee’s EPG GMO-free, plant-based fat alternative technology. The result is a deliciously satisfying chocolate experience with significantly less calories. Full Article
oge Soupergirl Wins Business Competition Run by Kroger By www.preparedfoods.com Published On :: Thu, 19 Aug 2021 00:00:00 -0400 Soupergirl—the plant-based soup and gazpacho company based in Washington, DC—was one of five winning contestants of Kroger’s new "Go Fresh & Local Supplier Accelerator," a national competition that ended with a Sharktank-like business presentation in front of a panel of judges in Cincinnati. Full Article
oge SternLife: Ketogenic Nutrition By www.preparedfoods.com Published On :: Fri, 18 Jan 2019 00:00:00 -0500 One example that is becoming more and more popular is ketogenic nutrition. This diet consists of 75% fat, 20% protein and only 5% carbohydrate. It brings about in changes in energy metabolism. Because of the reduced carbohydrates, there is no longer enough glucose available as a supply of energy. Full Article
oge Laird Superfood Instant Lattes with Adaptogens, Prebiotic Daily Greens By www.preparedfoods.com Published On :: Wed, 05 Apr 2023 07:00:00 -0400 Laird Superfood has revitalized several products to make them more functional, and they are launching on the Laird Superfood website and at retail partners. This new brand look and the Force of Nature campaign were created to reflect the passion of our consumers and deliver on Laird Superfood's mission. Full Article
oge Purely Elizabeth Adaptogenic Grain-Free Superfood Bars By www.preparedfoods.com Published On :: Tue, 06 Mar 2018 00:00:00 -0500 The bars are powered by Reishi - a known adaptogenic superfood that helps the body balance stress and supports healthy immune function, detoxification, and overall health - as well as nutrient-rich, elevated ingredients including cashew butter, coconut oil, hemp seeds, cashews, pumpkin seeds, almonds, and chia seeds. Full Article
oge Toodaloo Adaptogenic Trail Mixes By www.preparedfoods.com Published On :: Wed, 18 Aug 2021 14:15:00 -0400 Toodaloo, a new snack brand dedicated to healing the mind, body, spirit and planet, launched a line of adaptogenic trail mixes. Available in five varieties, each trail mix is crafted with care and infused with adaptogenic herbs and superfoods that restore balance. Full Article
oge heywell Sparkling Adaptogenic Water By www.preparedfoods.com Published On :: Wed, 20 Dec 2023 06:15:00 -0500 heywell's functional beverages are made with adaptogens, antioxidants and organic caffeine to support energy, immunity, focus, hydration and stress. Full Article
oge Preliminary Results on the Ecology of Human Pathogens in the Southwest Environment Released By www.foodengineeringmag.com Published On :: Fri, 07 Jun 2024 09:41:16 -0400 The study sought to better understand the ecology of human pathogens in the environment in the Southwest agricultural region, particularly how pathogens survive, move and possibly contaminate produce prior to harvest Full Article
oge Mohawk Group Introduces Creative Terrain Homogenous Vinyl Tile By www.floortrendsmag.com Published On :: Tue, 14 Dec 2021 00:00:00 -0500 The terrazzo-inspired visuals are constructed in 18” x 36” format with color selections specifically curated for healthcare, education and office environments. Full Article
oge Schluter's New Ditra-PS Uncoupling Membrane and Primer-PS Work Together to Simplify Tile Installation By www.floortrendsmag.com Published On :: Wed, 16 Oct 2024 11:00:00 -0400 Schluter-Systems introduces Schluter-Ditra-PS peel and stick uncoupling membrane and Schluter-Primer-PS, a brand-new primer specifically designed for use with Schluter peel and stick membranes. Full Article
oge Linde to Showcase Cryogenic Freezing Capabilities at PACK EXPO By www.foodengineeringmag.com Published On :: Thu, 12 Sep 2024 11:19:00 -0400 Linde works with food processors to optimize their use of liquid nitrogen and/or liquid carbon dioxide in cryogenic freezing and chilling applications. Full Article
oge New Ideas for Steam: Superheat it to Kill Pathogens on Contact By www.foodengineeringmag.com Published On :: Wed, 01 Feb 2023 12:20:52 -0500 A new cleaning tool has been under development at Cornell University, which uses superheated steam to kill bacteria on production surfaces. Full Article
oge In it together! Cultivating space for intergenerational dialogue, empathy and hope in a climate of uncertainty. By ezproxy.scu.edu.au Published On :: Sun, 01 Oct 2023 00:00:00 -0400 Children's Geographies; 10/01/2023(AN 173035614); ISSN: 14733285Academic Search Premier Full Article UNITED Kingdom EMPATHY CLIMATE change TRUST HOPE FINANCIAL crises OCCUPATIONAL mobility
oge Talking with Focus about Families Stuck at Home Together By jonathanmckeewrites.com Published On :: Fri, 17 Apr 2020 07:17:44 +0000 Today I’ll be on Focus on the Family’s Daily Broadcast talking about what families can do while stuck home together. Focus President Jim Daly and I talk about some specific ways moms and dads can be proactive about helping their kids through these strange times. If you turn on your radio to your nearest Christian radio … Continue reading "Talking with Focus about Families Stuck at Home Together" The post Talking with Focus about Families Stuck at Home Together appeared first on Jonathan's Blog From The Source. Full Article Parenting
oge Exploratory Studies to Investigate Mechanisms of HIV infection, Replication, Latency, and/or Pathogenesis in the Context of Substance Use Disorders (R01 Clinical Trial Not Allowed) [Letter of Intent Due Date: July 14] By ifp.nyu.edu Published On :: Mon, 28 Oct 2024 03:39:40 +0000 The post Exploratory Studies to Investigate Mechanisms of HIV infection, Replication, Latency, and/or Pathogenesis in the Context of Substance Use Disorders (R01 Clinical Trial Not Allowed) [Letter of Intent Due Date: July 14] was curated by information for practice. Full Article Funding
oge More than half of European heat-related deaths in summer 2022 attributed to anthropogenic warming By ifp.nyu.edu Published On :: Sat, 02 Nov 2024 11:03:24 +0000 According to the research, 38,154 of the 68,593 heat-related deaths in the summer of 2022 would not have occurred without anthropogenic warming. The post More than half of European heat-related deaths in summer 2022 attributed to anthropogenic warming was curated by information for practice. Full Article News
oge Together but still alone – A qualitative study exploring how family members of persons with incurable oesophageal or gastric cancer manage everyday life By ifp.nyu.edu Published On :: Sat, 02 Nov 2024 03:43:16 +0000 Cancer affects not only the person with the disease but those around them. Being a family member is described as strenuous and, often, associated with stress, anxiety and feelings of loneliness. There is a hei… Read the full article › The post Together but still alone – A qualitative study exploring how family members of persons with incurable oesophageal or gastric cancer manage everyday life was curated by information for practice. Full Article Open Access Journal Articles
oge One Size Does Not Fit All: Unraveling Item Response Process Heterogeneity Using the Mixture Dominance-Unfolding Model (MixDUM) By ifp.nyu.edu Published On :: Tue, 05 Nov 2024 04:09:24 +0000 Organizational Research Methods, Ahead of Print. When modeling responses to items measuring non-cognitive constructs that require introspection (e.g., personality, attitude), most studies have assumed that respondents follow the same item response process—either a dominance or an unfolding one. Nevertheless, the results are not equivocal, as some preliminary evidence suggests that some people use an unfolding […] The post One Size Does Not Fit All: Unraveling Item Response Process Heterogeneity Using the Mixture Dominance-Unfolding Model (MixDUM) was curated by information for practice. Full Article Journal Article Abstracts
oge Good Morning, News: Rep. Marie Gluesenkamp Perez Defeats Alt-Right Contender for House Seat, “Keeping Families Together” Struck Down, and What Are Your Plans for Martian New Year's? By www.portlandmercury.com Published On :: Fri, 08 Nov 2024 08:46:00 -0800 by Suzette Smith The Mercury provides its readers with interesting and useful news & culture reporting every single day. If you appreciate that, consider making a small monthly contribution to support our editorial team. If you read something you like, something you don't like but are glad to know about, and/or something you can't find anywhere else consider a one-time tip. It all goes in the same pot and it all goes to the editorial team. Thanks for your support! Good Morning, Portland! We're still "turning and turning in the widening gyre" over here, and we may be for quite some time. IN LOCAL NEWS:• Last night's round of election results arrived without any notable changes in the Portland City Council races. News editor Courtney Vaughn writes: "With Keith Wilson securing the mayor’s seat the day prior, results in City Council districts largely held firm." • While the national election results have been [understatement incoming] pretty distressing, local races are lined with silver. The Columbian reports Rep. Marie Gluesenkamp Perez has maintained her lead over far-right, perennial challenger Joe Kent. The Oregonian has a good breakdown of the race and history of Gluesenkamp Perez's hard-fought win. • PCC Automotive Service Technology Program instructor Jay Kuykendall has been named this year's Educator of the Year by the North American Council of Automotive Teachers, Portland Tribune reports. "Kuykendall oversees the auto shop lab and teaches engine performance classes, along with elective courses like Subaru U, electrified vehicles and light-duty diesel." • Beloved local coffee chain Jim and Patty's Coffee announced earlier this week that it will close its remaining two locations, in Beaverton and in Portland, on November 11. "Thank you all from the bottom of our hearts for your support..." owner Patty Roberts wrote. "Now I will need to find a job. If anyone has any ideas for an old lady who has been off the job market for over 40 years, let me know!" ???? For more backstory, check out this Mercury piece about the struggling coffee shops from October. • There was once a time in Portland when one could easily—well, depending on connection issues—rent a cheery little blue and white hybrid car to drive. The little smart cars were great for unforgiving rain showers and surprisingly solid in the snow. Car2Go merged with Reachnow in 2018, then tanked in 2019. In 2021, Free2Move announced it would drop a "fleet of 200 Jeep Renegades" for Portland consumers to rent, but the cumbersome cars departed once more in 2023. This week MSN reposted that story from 2023, so some people have been letting us know about it. Sorry about MSN, and this all happened last year. Still fun to revisit this tweet: so let me get this straightcar2go joins sharenow, while reachnow becomes reachnow pic.twitter.com/gJi7R6YZ8e — Cabel Sasser (@cabel) March 4, 2019 • Politicians are politicians, but I find Sen. Jeff Merkley's vibe calming: View this post on Instagram A post shared by Senator Jeff Merkley (@senjeffmerkley) • Every week, the Mercury gives out free tickets to local shows and this week we've got sweet tix for Reverend Horton Heat, Des Demonas, Karina Rykman and moooore—check'm out and win with our Free Ticket Thursday giveaway! IN NATIONAL / INTERNATIONAL NEWS:• I can't immediately find who said this, but I think it's a valid concern: As we watch the transition back to a Trump administration presidency, the cabinet appointments are probably going to feel like being repeatedly punched in the face. President-elect Donald Trump named Florida strategist Susie Wiles as his White House chief of staff on Thursday. Wiles has run his political operation for nearly four years, making her one of the few people to survive at his side for any length of time. What's Wiles deal? Nepo baby. Ronald Reagan campaign staffer. Wiles has been credited with putting Rick Scott in Florida's governor’s office. Associated Press has a nice, long profile on her this morning. Is she going to tear the tampon machine out of the White House bathroom again? We're watching. • A Biden administration initiative known as “Keeping Families Together” was struck down by a Texas-based US District judge yesterday; Judge J. Campbell Barker argued that the Biden administration had overstepped its authority with its attempt to lessen barriers to citizenship for undocumented immigrants married to US citizens. • Soccer fans did violence again, but this time it might be motivated by cultural and political friction. NPR reports that "leading political figures in the Netherlands have condemned the violence that followed a match between a Dutch team Ajax and Tel Aviv's Maccabi. According to NPR, "Dutch police said 62 people have been arrested following several clashes." Amsterdam mayor Femke Halsema described local men seeking out Israeli fans on scooters. Dutch police chief Peter Holla said fans of Tel Aviv Maccabi had "set a Palestinian flag on fire in the city and attacked a taxi." Dutch authorities have banned demonstrations through the weekend. • Happy Martian New Year... soon! In Scientific American Phil Plait writes: "Why would anyone pick November 12 as New Year’s Day for Mars? And why does our official reckoning of Martian time set the eons-old Red Planet only in its 38th year? The answer involves a combination of natural cycles and the human need to impose order via somewhat arbitrary timekeeping—pretty much like on Earth." • And now we part—wishing a fine weekend to my naysayers and hatchet men in the fight against violence. Full Article Good Morning News!
oge Alone together: Robyn's 'Dancing On My Own' opens the corners of community By minnesota.publicradio.orghttps Published On :: Mon, 10 Jun 2019 14:40:24 -0500 The magic of Robyn's millennial anthem is its bait and switch: It's a fun, energetic dance song about being lonely and heartbroken. And yet, the minute you hear it, you instantly feel less alone. Full Article
oge Fearless Cat Rides on Her Human’s Back While They’re Skateboarding Together By laughingsquid.com Published On :: Tue, 12 Nov 2024 14:40:58 +0000 A fearless cat named Callie who was found as a kitten by her human Sam Wallace loves to sit on their back while skateboarding. Full Article Blog
oge John Rhys-Davies narrates 'Scrooge' podcast; talks connection with Tolkien's Gimli: 'We all carry our chains' By www.christianpost.com Published On :: Tue, 12 Nov 2024 08:30:25 -0500 Actor John Rhys-Davies narrates a reimagined audio drama of "A Christmas Carol," drawn by the story’s themes of transformation, compassion and redemption, which he likens to the journeys of both Scrooge and his Rings character, Gimli, as they overcome prejudice and open their hearts to others. Full Article
oge Adrian Rogers' pastoral legacy: Passing on dedication to an inerrant Holy Scripture and equipping of local church pastors By www.christianpost.com Published On :: Fri, 18 Aug 2023 09:11:54 -0400 In one of the last public addresses Dr. Adrian Rogers delivered before his untimely demise at the age of 74, he warned pastors of the mortal threat presented to their ministries by the sins of lust and pride. Full Article
oge ISTA European Packaging Symposium will bring together global transport packaging leaders to focus on e-commerce, sustainability and more By www.retailtechnologyreview.com Published On :: The International Safe Transit Association (ISTA), the industry developer of pre-shipment performance testing standards for packaged products, has announced programming for its annual European Packaging Symposium, which will be held 8-9 October at the Le Méridien Frankfurt in Frankfurt, Germany. Full Article Internet Retailing Exhibitions and Events
oge Study reveals connection between estrogen levels and a risk of dementia By english.pravda.ru Published On :: Thu, 07 Apr 2022 14:41:00 +0300 A research group from the George Institute for Global Health in Australia found out that the estrogen levels can be an indicator of a woman's risk of developing dementia. The researchers suggest that some of the reproductive factors (early or late menstruation, early menopause) are a sign of a higher risk of certain neurological problems connected with cognitive and social skills. According to the PloS Medicine journal, pregnancy and abortion are connected with the lower risk of dementia and other neurological problems. Full Article Health
oge First Case of Highly Pathogenic AI This Fall Confirmed in Gangwon Province By world.kbs.co.kr Published On :: Wed, 30 Oct 2024 17:18:54 +0900 [Domestic] : The nation has confirmed its first case of highly pathogenic avian influenza so far this fall season at a poultry farm in Gangwon Province. Quarantine authorities said Wednesday that the birds at the farm in Donghae had the highly pathogenic H5N1 strain of the virus. The farm, which raises some 700 ...[more...] Full Article Domestic
oge Funding awarded for study on hydrogen storage potential in the East Midlands - British Geological Survey By news.google.com Published On :: Mon, 19 Aug 2024 07:00:00 GMT Funding awarded for study on hydrogen storage potential in the East Midlands British Geological Survey Full Article
oge Structure of the outer membrane porin OmpW from the pervasive pathogen Klebsiella pneumoniae By journals.iucr.org Published On :: 2024-01-01 Conjugation is the process by which plasmids, including those that carry antibiotic-resistance genes, are mobilized from one bacterium (the donor) to another (the recipient). The conjugation efficiency of IncF-like plasmids relies on the formation of mating-pair stabilization via intimate interactions between outer membrane proteins on the donor (a plasmid-encoded TraN isoform) and recipient bacteria. Conjugation of the R100-1 plasmid into Escherichia coli and Klebsiella pneumoniae (KP) recipients relies on pairing between the plasmid-encoded TraNα in the donor and OmpW in the recipient. Here, the crystal structure of K. pneumoniae OmpW (OmpWKP) is reported at 3.2 Å resolution. OmpWKP forms an eight-stranded β-barrel flanked by extracellular loops. The structures of E. coli OmpW (OmpWEC) and OmpWKP show high conservation despite sequence variability in the extracellular loops. Full Article text
oge Structural and biochemical characterization of the M405S variant of Desulfovibrio vulgaris formate dehydrogenase By journals.iucr.org Published On :: 2024-05-01 Molybdenum- or tungsten-dependent formate dehydrogenases have emerged as significant catalysts for the chemical reduction of CO2 to formate, with biotechnological applications envisaged in climate-change mitigation. The role of Met405 in the active site of Desulfovibrio vulgaris formate dehydrogenase AB (DvFdhAB) has remained elusive. However, its proximity to the metal site and the conformational change that it undergoes between the resting and active forms suggests a functional role. In this work, the M405S variant was engineered, which allowed the active-site geometry in the absence of methionine Sδ interactions with the metal site to be revealed and the role of Met405 in catalysis to be probed. This variant displayed reduced activity in both formate oxidation and CO2 reduction, together with an increased sensitivity to oxygen inactivation. Full Article text
oge Glucose-6-phosphate dehydrogenase and its 3D structures from crystallography and electron cryo-microscopy By journals.iucr.org Published On :: 2024-09-11 Glucose-6-phosphate dehydrogenase (G6PD) is the first enzyme in the pentose phosphate pathway. It has been extensively studied by biochemical and structural techniques. 13 X-ray crystal structures and five electron cryo-microscopy structures in the PDB are focused on in this topical review. Two F420-dependent glucose-6-phosphate dehydrogenase (FGD) structures are also reported. The significant differences between human and parasite G6PDs can be exploited to find selective drugs against infections such as malaria and leishmaniasis. Furthermore, G6PD is a prognostic marker in several cancer types and is also considered to be a tumour target. On the other hand, FGD is considered to be a target against Mycobacterium tuberculosis and possesses a high biotechnological potential in biocatalysis and bioremediation. Full Article text
oge Specific radiation damage to halogenated inhibitors and ligands in protein–ligand crystal structures By journals.iucr.org Published On :: This article reports an investigation into the effects of specific radiation damage to halogenated ligands in crystal structures of protein-inhibitor complexes. Full Article text
oge A thermal deformation optimization method for cryogenically cooled silicon crystal monochromators under high heat load By journals.iucr.org Published On :: 2024-01-22 A method to optimize the thermal deformation of an indirectly cryo-cooled silicon crystal monochromator exposed to intense X-rays at a low-emittance diffraction-limited synchrotron radiation source is presented. The thermal-induced slope error of the monochromator crystal has been studied as a function of heat transfer efficiency, crystal temperature distribution and beam footprint size. A partial cooling method is proposed, which flattens the crystal surface profile within the beam footprint by modifying the cooling contact area to optimize the crystal peak temperature. The optimal temperature varies with different photon energies, which is investigated, and a proper cooling strategy is obtained to fulfil the thermal distortion requirements over the entire photon energy range. At an absorbed power up to 300 W with a maximum power density of 44.8 W mm−2 normal incidence beam from an in-vacuum undulator, the crystal thermal distortion does not exceed 0.3 µrad at 8.33 keV. This method will provide references for the monochromator design on diffraction-limited synchrotron radiation or free-electron laser light sources. Full Article text
oge Hyperspectral full-field quick-EXAFS imaging at the ROCK beamline for monitoring micrometre-sized heterogeneity of functional materials under process conditions By journals.iucr.org Published On :: 2024-08-23 Full-field transmission X-ray microscopy has been recently implemented at the hard X-ray ROCK–SOLEIL quick-EXAFS beamline, adding micrometre spatial resolution to the second time resolution characterizing the beamline. Benefiting from a beam size versatility due to the beamline focusing optics, full-field hyperspectral XANES imaging has been successfully used at the Fe K-edge for monitoring the pressure-induced spin transition of a 150 µm × 150 µm Fe(o-phen)2(NCS)2 single crystal and the charge of millimetre-sized LiFePO4 battery electrodes. Hyperspectral imaging over 2000 eV has been reported for the simultaneous monitoring of Fe and Cu speciation changes during activation of a FeCu bimetallic catalyst along a millimetre-sized catalyst bed. Strategies of data acquisition and post-data analysis using Jupyter notebooks and multivariate data analysis are presented, and the gain obtained using full-field hyperspectral quick-EXAFS imaging for studies of functional materials under process conditions in comparison with macroscopic information obtained by non-spatially resolved quick-EXAFS techniques is discussed. Full Article text
oge Poly[3-methylpyridinium [(μ2-dihydrogen phosphito)bis(μ3-hydrogen phosphito)dizinc]] By journals.iucr.org Published On :: 2024-04-26 In the title compound, {(C6H8N)[Zn2(HPO3)2(H2PO3)]}n, the constituent ZnO4, HPO3 and H2PO3 polyhedra of the inorganic component are linked into (010) sheets by Zn—O—P bonds (mean angle = 134.4°) and the layers are reinforced by O—H⋯O hydrogen bonds. The protonated templates are anchored to the inorganic sheets via bifurcated N—H⋯(O,O) hydrogen bonds. Full Article text
oge What shapes template-matching performance in cryogenic electron tomography in situ? By journals.iucr.org Published On :: 2024-05-28 The detection of specific biological macromolecules in cryogenic electron tomography data is frequently approached by applying cross-correlation-based 3D template matching. To reduce computational cost and noise, high binning is used to aggregate voxels before template matching. This remains a prevalent practice in both practical applications and methods development. Here, the relation between template size, shape and angular sampling is systematically evaluated to identify ribosomes in a ground-truth annotated data set. It is shown that at the commonly used binning, a detailed subtomogram average, a sphere and a heart emoji result in near-identical performance. These findings indicate that with current template-matching practices macromolecules can only be detected with high precision if their shape and size are sufficiently different from the background. Using theoretical considerations, the experimental results are rationalized and it is discussed why primarily low-frequency information remains at high binning and that template matching fails to be accurate because similarly shaped and sized macromolecules have similar low-frequency spectra. These challenges are discussed and potential enhancements for future template-matching methodologies are proposed. Full Article text
oge High-confidence placement of low-occupancy fragments into electron density using the anomalous signal of sulfur and halogen atoms By journals.iucr.org Published On :: 2024-06-05 Fragment-based drug design using X-ray crystallography is a powerful technique to enable the development of new lead compounds, or probe molecules, against biological targets. This study addresses the need to determine fragment binding orientations for low-occupancy fragments with incomplete electron density, an essential step before further development of the molecule. Halogen atoms play multiple roles in drug discovery due to their unique combination of electronegativity, steric effects and hydrophobic properties. Fragments incorporating halogen atoms serve as promising starting points in hit-to-lead development as they often establish halogen bonds with target proteins, potentially enhancing binding affinity and selectivity, as well as counteracting drug resistance. Here, the aim was to unambiguously identify the binding orientations of fragment hits for SARS-CoV-2 nonstructural protein 1 (nsp1) which contain a combination of sulfur and/or chlorine, bromine and iodine substituents. The binding orientations of carefully selected nsp1 analogue hits were focused on by employing their anomalous scattering combined with Pan-Dataset Density Analysis (PanDDA). Anomalous difference Fourier maps derived from the diffraction data collected at both standard and long-wavelength X-rays were compared. The discrepancies observed in the maps of iodine-containing fragments collected at different energies were attributed to site-specific radiation-damage stemming from the strong X-ray absorption of I atoms, which is likely to cause cleavage of the C—I bond. A reliable and effective data-collection strategy to unambiguously determine the binding orientations of low-occupancy fragments containing sulfur and/or halogen atoms while mitigating radiation damage is presented. Full Article text
oge A structural role for tryptophan in proteins, and the ubiquitous Trp Cδ1—H⋯O=C (backbone) hydrogen bond By journals.iucr.org Published On :: 2024-06-28 Tryptophan is the most prominent amino acid found in proteins, with multiple functional roles. Its side chain is made up of the hydrophobic indole moiety, with two groups that act as donors in hydrogen bonds: the Nɛ—H group, which is a potent donor in canonical hydrogen bonds, and a polarized Cδ1—H group, which is capable of forming weaker, noncanonical hydrogen bonds. Due to adjacent electron-withdrawing moieties, C—H⋯O hydrogen bonds are ubiquitous in macromolecules, albeit contingent on the polarization of the donor C—H group. Consequently, Cα—H groups (adjacent to the carbonyl and amino groups of flanking peptide bonds), as well as the Cɛ1—H and Cδ2—H groups of histidines (adjacent to imidazole N atoms), are known to serve as donors in hydrogen bonds, for example stabilizing parallel and antiparallel β-sheets. However, the nature and the functional role of interactions involving the Cδ1—H group of the indole ring of tryptophan are not well characterized. Here, data mining of high-resolution (r ≤ 1.5 Å) crystal structures from the Protein Data Bank was performed and ubiquitous close contacts between the Cδ1—H groups of tryptophan and a range of electronegative acceptors were identified, specifically main-chain carbonyl O atoms immediately upstream and downstream in the polypeptide chain. The stereochemical analysis shows that most of the interactions bear all of the hallmarks of proper hydrogen bonds. At the same time, their cohesive nature is confirmed by quantum-chemical calculations, which reveal interaction energies of 1.5–3.0 kcal mol−1, depending on the specific stereochemistry. Full Article text
oge Roodmus: a toolkit for benchmarking heterogeneous electron cryo-microscopy reconstructions By journals.iucr.org Published On :: 2024-10-15 Conformational heterogeneity of biological macromolecules is a challenge in single-particle averaging (SPA). Current standard practice is to employ classification and filtering methods that may allow a discrete number of conformational states to be reconstructed. However, the conformation space accessible to these molecules is continuous and, therefore, explored incompletely by a small number of discrete classes. Recently developed heterogeneous reconstruction algorithms (HRAs) to analyse continuous heterogeneity rely on machine-learning methods that employ low-dimensional latent space representations. The non-linear nature of many of these methods poses a challenge to their validation and interpretation and to identifying functionally relevant conformational trajectories. These methods would benefit from in-depth benchmarking using high-quality synthetic data and concomitant ground truth information. We present a framework for the simulation and subsequent analysis with respect to the ground truth of cryo-EM micrographs containing particles whose conformational heterogeneity is sourced from molecular dynamics simulations. These synthetic data can be processed as if they were experimental data, allowing aspects of standard SPA workflows as well as heterogeneous reconstruction methods to be compared with known ground truth using available utilities. The simulation and analysis of several such datasets are demonstrated and an initial investigation into HRAs is presented. Full Article text
oge Synthesis, crystal structure and hydrogenation properties of MgxLi3 − xB48 − y (x = 1.11, y = 0.40) By journals.iucr.org Published On :: 2024-01-01 The ternary magnesium/lithium boride, MgxLi3 − xB48 − y (x = 1.11, y = 0.40, idealized formula MgLi2B48), crystallizes as its own structure type in P43212, which is closely related to the structural family comprising α-AlB12, Be0.7Al1.1B22 and tetragonal β-boron. The asymmetric unit of title structure contains two statistical mixtures Mg/Li in Wyckoff sites 8b with relative occupancies Mg:Li = 0.495 (9):0.505 (9) and 4a with Mg:Li = 0.097 (8):0.903 (8). The boron atoms occupy 23 8b sites and two 4a sites. One of the latter sites has a partial occupancy factor of 0.61 (2). Both unique Mg/Li atoms adopt a twelvefold coordination environment in the form of truncated tetrahedra (Laves polyhedra). These polyhedra are connected by triangular faces to four [B12] icosahedra. The boron atoms exhibit four kinds of polyhedra, namely pentagonal pyramid (coordination number CN = 6), distorted tetragonal pyramid (CN = 5), bicapped hexagon (CN = 8) and gyrobifastigium (CN = 8). At the gas hydrogenation of MgLi2B48 alloy, formation of the eutectic composite hydride LiBH4+Mg(BH4)2 and amorphous boron is observed. In the temperature range 543–623 K, the hydride eutectics decompose, forming MgH2, LiH, MgB4, B and H2. Full Article text
oge Crystal structures of sixteen phosphane chalcogenide complexes of gold(I) chloride, bromide and iodide By journals.iucr.org Published On :: 2024-01-01 The structures of 16 phosphane chalcogenide complexes of gold(I) halides, with the general formula R13-nR2nPEAuX (R1 = t-butyl; R2 = isopropyl; n = 0 to 3; E = S or Se; X = Cl, Br or I), are presented. The eight possible chlorido derivatives are: 1a, n = 3, E = S; 2a, n = 2, E = S; 3a, n = 1, E = S; 4a, n = 0, E = S; 5a, n = 3, E = Se; 6a, n = 2, E = Se; 7a, n = 1, E = Se; and 8a, n = 0, E = Se, and the corresponding bromido derivatives are 1b–8b in the same order. However, 2a and 2b were badly disordered and 8a was not obtained. The iodido derivatives are 2c, 6c and 7c (numbered as for the series a and b). All structures are solvent-free and all have Z' = 1 except for 6b and 6c (Z' = 2). All molecules show the expected linear geometry at gold and approximately tetrahedral angles P—E—Au. The presence of bulky ligands forces some short intramolecular contacts, in particular H⋯Au and H⋯E. The Au—E bond lengths have a slight but consistent tendency to be longer when trans to a softer X ligand, and vice versa. The five compounds 1a, 5a, 6a, 1b and 5b form an isotypic set, despite the different alkyl groups in 6a. Compounds 3a/3b, 4b/8b and 6b/6c form isotypic pairs. The crystal packing can be analysed in terms of various types of secondary interactions, of which the most frequent are `weak' hydrogen bonds from methine hydrogen atoms to the halogenido ligands. For the structure type 1a, H⋯X and H⋯E contacts combine to form a layer structure. For 3a/3b, the packing is almost featureless, but can be described in terms of a double-layer structure involving borderline H⋯Cl/Br and H⋯S contacts. In 4a and 4b/8b, which lack methine groups, Cmethyl—H⋯X contacts combine to form layer structures. In 7a/7b, short C—H⋯X interactions form chains of molecules that are further linked by association of short Au⋯Se contacts to form a layer structure. The packing of compound 6b/6c can conveniently be analysed for each independent molecule separately, because they occupy different regions of the cell. Molecule 1 forms chains in which the molecules are linked by a Cmethine⋯Au contact. The molecules 2 associate via a short Se⋯Se contact and a short H⋯X contact to form a layer structure. The packing of compound 2c can be described in terms of two short Cmethine—H⋯I contacts, which combine to form a corrugated ribbon structure. Compound 7c is the only compound in this paper to feature Au⋯Au contacts, which lead to twofold-symmetric dimers. Apart from this, the packing is almost featureless, consisting of layers with only translation symmetry except for two very borderline Au⋯H contacts. Full Article text
oge Crystal structures of ten phosphane chalcogenide complexes of gold(III) chloride and bromide By journals.iucr.org Published On :: 2024-03-12 The structures of ten phosphane chalcogenide complexes of gold(III) halides, with general formula R13–nR2nPEAuX3 (R1 = t-butyl; R2 = i-propyl; n = 0 to 3; E = S or Se; X = Cl or Br) are presented. The eight possible chlorido derivatives are: 9a, n = 3, E = S; 10a, n = 2, E = S; 11a, n = 1, E = S; 12a, n = 0, E = S; 13a, n = 3, E = Se; 14a, n = 2, E = Se; 15a, n = 1, E = Se; and 16a, n = 0, E = Se, and the corresponding bromido derivatives are 9b–16b in the same order. Structures were obtained for 9a, 10a (and a second polymorph 10aa), 11a (and its deuterochloroform monosolvate 11aa), 12a (as its dichloromethane monosolvate), 14a, 15a (as its deuterochloroform monosolvate 15aa, in which the solvent molecule is disordered over two positions), 9b, 11b, 13b and 15b. The structures of 11a, 15a, 11b and 15b form an isotypic set, and those of compounds 10aa and 14a form an isotypic pair. All structures have Z' = 1. The gold(III) centres show square-planar coordination geometry and the chalcogenide atoms show approximately tetrahedral angles (except for the very wide angle in 12a, probably associated with the bulky t-butyl groups). The bond lengths at the gold atoms are lengthened with respect to the known gold(I) derivatives, and demonstrate a considerable trans influence of S and Se donor atoms on a trans Au—Cl bond. Each compound with an isopropyl group shows a short intramolecular contact of the type C—Hmethine⋯Xcis; these may be regarded as intramolecular ‘weak’ hydrogen bonds, and they determine the orientation of the AuX3 groups. The molecular packing is analysed in terms of various short contacts such as weak hydrogen bonds C—H⋯X and contacts between the heavier atoms, such as X⋯X (9a, 10aa, 11aa, 15aa and 9b), S⋯S (10aa, 11a and 12a) and S⋯Cl (10a). The packing of the polymorphs 10a and 10aa is thus quite different. The solvent molecules take part in C—H⋯Cl hydrogen bonds; for 15aa, a disordered solvent region at z ≃ 0 is observed. Structure 13b involves unusual inversion-symmetric dimers with Se⋯Au and Se⋯Br contacts, further connected by Br⋯Br contacts. Full Article text