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Addressing genome scale design tradeoffs in Pseudomonas putida for bioconversion of an aromatic carbon source
Genome-scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling and pairing product formation with substrate utilization and can improve strain performance beyond levels typically accessible using traditional strain engineering approaches. However, sustainable feedstocks pose a challenge due to incomplete high-resolution metabolic data for non-canonical carbon sources required to curate GSMM and identify implementable designs. Here we address a four-gene deletion design in the Pseudomonas putida KT2440 strain for the lignin-derived non-sugar carbon source, p-coumarate (p-CA), that proved challenging to implement. We examine the performance of the fully implemented design for p-coumarate to glutamine, a useful biomanufacturing intermediate. In this study glutamine is then converted to indigoidine, an alternative sustainable pigment and a model heterologous product that is commonly used to colorimetrically quantify glutamine concentration. Through proteomics, promoter-variation, and growth characterization of a fully implemented gene deletion design, we provide evidence that aromatic catabolism in the completed design is rate-limited by fumarase hydratase (FUM) enzyme activity in the citrate cycle and requires careful optimization of another fumarate hydratase protein (PP_0897) expression to achieve growth and production. A double sensitivity analysis also confirmed a strict requirement for fumarate hydratase activity in the strain where all genes in the growth coupling design have been implemented. Metabolic cross-feeding experiments were used to examine the impact of complete removal of the fumarase hydratase reaction and revealed an unanticipated nutrient requirement, suggesting additional functions for this enzyme. While a complete implementation of the design was achieved, this study highlights the challenge of completely inactivating metabolic reactions encoded by under-characterized proteins, especially in the context of multi-gene edits.
Unveiling four decades of intensifying precipitation from tropical cyclones using satellite measurements
Increases in precipitation rates and volumes from tropical cyclones (TCs) caused by anthropogenic warming are predicted by climate modeling studies and have been identified in several high intensity storms occurring over the last half decade. However, it has been difficult to detect historical trends in TC precipitation at time scales long enough to overcome natural climate variability because of limitations in existing precipitation observations. We introduce an experimental global high-resolution climate data record of precipitation produced using infrared satellite imagery and corrected at the monthly scale by a gauge-derived product that shows generally good performance during two hurricane case studies but estimates higher mean precipitation rates in the tropics than the evaluation datasets. General increases in mean and extreme rainfall rates during the study period of 1980–2019 are identified, culminating in a 12–18%/40-year increase in global rainfall rates. Overall, all basins have experienced intensification in precipitation rates. Increases in rainfall rates have boosted the mean precipitation volume of global TCs by 7–15% over 40 years, with the starkest rises seen in the North Atlantic, South Indian, and South Pacific basins (maximum 59–64% over 40 years). In terms of inland rainfall totals, year-by-year trends are generally positive due to increasing TC frequency, slower decay over land, and more intense rainfall, with an alarming increase of 81–85% seen from the strongest global TCs. As the global trend in precipitation rates follows expectations from warming sea surface temperatures (11.1%/°C), we hypothesize that the observed trends could be a result of anthropogenic warming creating greater concentrations of water vapor in the atmosphere, though retrospective studies of TC dynamics over the period are needed to confirm.
R-matrix analysis of 22 Ne structure in the energy range 11.7–13.38 MeV
An R-matrix analysis of the old high energy resolution experimental data [4, 5] in the excitation region of 11.7–13.78 MeV of 22 Ne was performed.
Climate-Related Trends of Within-Storm Intensities Using Dimensionless Temporal-Storm Distributions
Huff curves are probabilistic time distributions of rainfall expressed as dimensionless cumulative percentages of storm depth and duration. Previous studies have documented development factors, spatial robustness, and the utility of Huff curves in practical applications. However, the effects of trending rainfall on Huff curve intensity patterns have not yet been studied. As such, the goal of this paper is to fill this gap by studying Huff curve patterns in a watershed with demonstrated increasing trends of temperature and precipitation, with the intention that it can be generalized to other areas in the US and the world. To achieve this goal, the high temporal resolution precipitation data collected from a high spatial density, 72-year precipitation-gauge network on the 4.25-km 2 North Appalachian Experimental Watershed in east-central Ohio were used. Seasonal storm pattern trends from 1939 to 2010 were investigated using dimensionless depth (with the frequency of 50%, $d_{50}$) and the curve variability $(V = d_{80} - d_{20})$ at three dimensionless within-storms time periods (three verticals). The Spearman rank correlation procedure (correlation coefficient, ρ and significance probability, p) was used to statistically determine trends over time using 8 periods of 4-season sets of Huff curves over the 72 years. Two averages of ρ and p were computed: (1) by averaging the individual ρ and p obtained from 10 gauges (AvgI); and (2) by grouped averaging of all individual gauge values of $d_{50}$ and V and then computing ρ and p (AvgG). The test results of individual gauges showed that 4 cases for $d_{50}$ and 23 cases for V were significant for all seasons and verticals (total of 120 cases for each variable). The test results of AvgI for $d_{50}$ and V and AvgG for $d_{50}$ showed no significant trends in all seasons and verticals. Only the AvgG for V led to a significant trend for V in spring and fall at different times within storm patterns. The data do not provide sufficient evidence at the p=0.05 significance level to reject the null hypothesis of unchanging position of the dimensionless depth of the 50% Huff curves for individual or averages for all seasons and verticals. Also, there is insufficient evidence to reject the null hypothesis of unchanging variability, V, using the average ρ of individual gauges (AvgI for V) for all seasons and verticals. AvgG results showed a significant trend in V; however, this analysis may be affected by the nonindependence of storm data. The results suggest that it is likely that there is little if any effect of trending climate over approximately 70 years on Huff curve patterns. The results of this study add to the robustness characteristics of Huff curves and to their potential use in hydrological practice as design storms, as the foundation of stochastic storm generation, and for storm disaggregation, and they deserve further investigation. These different forms of inputs to watershed models have the potential to improve runoff estimation. The results suggest that, if verified in other studies, they have applicability to provide useful stationary precipitation patterns across the US and other areas of the world in areas of nonstationary climate. Also, individual rain gauge data may not be representative of trends even over small areas, and seasonal differences were noticeable as found in other studies. Recommendations are provided.
Efficient formulation of multitime generalized quantum master equations: Taming the cost of simulating 2D spectra
Modern 4-wave mixing spectroscopies are expensive to obtain experimentally and computationally. In certain cases, the unfavorable scaling of quantum dynamics problems can be improved using a generalized quantum master equation (GQME) approach. However, the inclusion of multiple (light–matter) interactions complicates the equation of motion and leads to seemingly unavoidable cubic scaling in time. In this paper, we present a formulation that greatly simplifies and reduces the computational cost of previous work that extended the GQME framework to treat arbitrary numbers of quantum measurements. Specifically, we remove the time derivatives of quantum correlation functions from the modified Mori–Nakajima–Zwanzig framework by switching to a discrete-convolution implementation inspired by the transfer tensor approach. We then demonstrate the method’s capabilities by simulating 2D electronic spectra for the excitation-energy-transfer dimer model. In our method, the resolution of data can be arbitrarily coarsened, especially along the t2 axis, which mirrors how the data are obtained experimentally. Even in a modest case, this demands O(103) fewer data points. We are further able to decompose the spectra into one-, two-, and three-time correlations, showing how and when the system enters a Markovian regime where further measurements are unnecessary to predict future spectra and the scaling becomes quadratic. This offers the ability to generate long-time spectra using only short-time data, enabling access to timescales previously beyond the reach of standard methodologies.
High-resolution climate model datasets for energy infrastructure planning in a renewable-dependent future
Electrification and renewables deployment efforts are amplifying the interdependence of the climate and energy systems. Increases in climate model resolution, which is now approaching that of reanalysis datasets and operational weather forecast models, present a unique opportunity to use future climate projections for energy infrastructure planning. In this Perspective, we review recent developments in high-resolution climate modeling, which have been driven by increased computing power and advanced software tools. We then look ahead to discuss how high-resolution climate data can be used to plan for a renewable-dependent future, and envision a unified climate-energy model framework that captures the two-way feedbacks between these interdependent systems.
Repurposed dihydroorotate dehydrogenase inhibitors with efficacy against drug-resistant Acinetobacter baumannii
New antimicrobials are needed for the treatment of extensively drug-resistantAcinetobacter baumannii. The de novo pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase (DHODH) is a validated drug target for malaria and human autoimmune diseases. Here, we provide genetic evidence thatA. baumanniiDHODH (AbDHODH) is essential for bacterial survival in rodent infection models. We chemically validate the target by repurposing a unique library of ~450 triazolopyrimidine/imidazopyrimidine analogs developed for our malaria DHODH program to identify 21 compounds with submicromolar activity onAbDHODH. The most potent (DSM186, DHODH IC 50 28 nM) had a minimal inhibitory concentration of ≤1 µg/ml against geographically diverseA. baumanniistrains, including meropenem-resistant isolates. A structurally related analog (DSM161) with a long in vivo half-life conferred significant protection in the neutropenic mouse thigh infection model. Encouragingly, the development of resistance to these compounds was not identified in vitro or in vivo. Lastly, the X-ray structure ofAbDHODH bound to DSM186 was solved to 1.4 Å resolution. These data support the potential ofAbDHODH as a drug target for the development of antimicrobials for the treatment ofA. baumanniiand potentially other high-risk bacterial infections.
Resolved Resonance Evaluation for Neutron Interactions with 103 Rh up to 8 keV
A neutron cross-section evaluation for the n + 103 Rh reaction in the resolved resonance region was carried out in the energy range 10−5 eV to 8 keV encompassing thermal energy at 0.0253 eV. The scope of this work is to generate resonance parameters and resonance parameter covariances based on the Reich-Moore reduced R-matrix formalism using the code SAMMY. Some features of the new evaluation are the inclusion of high-resolution capture data in the SAMMY evaluation process and the extension of the resolved resonance range from 4 to 8 keV. Furthermore, the evaluation employs more accurate resonance parameter representation by exploring the use of the LRF = 7 ENDF feature and also the use of the LCOMP = 2 compact format for resonance parameter covariance representation. Included in the SAMMY evaluation are transmission data, capture cross-section data, and neutron scattering length information. Thermal cross-section values listed in the literature, as well as capture resonance integrals, were also incorporated into the evaluation process.
Isospin mixing and the cubic isobaric multiplet mass equation in the lowest T=2, A=32 quintet
The isobaric multiplet mass equation (IMME) is known to break down in the first T=2,A=32 isospin quintet. In this work we combine high-resolution experimental data with state-of-the-art shell-model calculations to investigate isospin mixing as a possible cause for this violation. The experimental data are used to validate isospin-mixing matrix elements calculated with newly developed shell-model Hamiltonians. Our analysis shows that isospin mixing with nonanalog T=1 states contributes to the IMME breakdown, making the requirement of an anomalous cubic term inevitable for the multiplet.
Dark matter scattering constraints from observations of stars surrounding Sgr A*
High-resolution infrared data have revealed several young stars in close proximity to Sgr A*. These stars may encounter extremely high dark matter densities. We examine scenarios where dark matter scatters on stellar gas, accumulates in stellar cores, and then annihilates. We study the stars S2, S62, S4711, and S4714 and find three observable effects. First, dark matter interactions can inhibit star formation close to Sgr A*, favoring scenarios where these stars migrate into the Galactic Center. Second, dark matter interactions can delay main sequence evolution, making stars older than they appear. Third, very high dark matter densities can inject enough energy to disrupt main sequence stars, allowing S-star observations to constrain the dark matter density near Sgr A*. Published by the American Physical Society 2024
Exploring the $A$-V-Sb landscape beyond $A$$\mathrm{V_3}$ $\mathrm{Sb_5}$: A case study on the $\mathrm{KV_6}$ $\mathrm{Sb_6}$ Kagome compound
Kagome compounds have garnered attention in the past few years for their intriguing magnetic properties arising from spin frustration dictated by the geometry of the Kagome sublattice. In this paper, we highlight the success of the unconventional hydride route for the fast and easy synthesis of the Kagome compound $\mathrm{KV_6}$ $\mathrm{Sb_6}$. Here, high-temperature in situ powder x-ray diffraction (PXRD) studies proved to be useful in hinting at the existence of $\mathrm{KV_6}$ $\mathrm{Sb_6}$, identifying its synthesis conditions, and understanding the reaction mechanism. The crystal structure for $\mathrm{KV_6}$ $\mathrm{Sb_6}$ was determined from high-resolution PXRD data. The compound has a layered structure [$R\overline{3}m, a = 5.5318$ (9) Å, $c = 34.23$ (3)Å 3 $Z = 3$] at room temperature] and features a Kagome bilayer of V atoms. $\mathrm{KV_6}$ $\mathrm{Sb_6}$ is isostructural to the previously reported $\mathrm{RbV_6}$ $\mathrm{Sb_6}$ and $\mathrm{CsV_6}$ $\mathrm{Sb_6}$ compounds. $\mathrm{KV_6}$ $\mathrm{Sb_6}$ is thermally stable in vacuum up to 1173 K, as evident from the high-temperature in situ PXRD and differential scanning calorimetric analysis. Investigation of magnetic properties for $\mathrm{KV_6}$ $\mathrm{Sb_6}$ between 2 and 300 K reveals temperature-independent paramagnetism and an absence of superconductivity, like the Rb and Cs analogs. Furthermore, we compare the magnetic properties of K V 3 Sb 5 , another ternary Kagome compound, synthesized via two different methods: the hydride route and the traditional route from elements. Low-temperature transport property measurements of $\mathrm{KV_6}$ $\mathrm{Sb_6}$ indicate metallic behavior and an intrinsically low thermal conductivity of $\mathrm{1.0 W K^-1}$ $\mathrm{m^-1}$ at 300 K. The layered structure of $\mathrm{KV_6}$ $\mathrm{Sb_6}$ makes it an attractive candidate for deintercalation and doping studies to tune both magnetic and transport properties, laying a foundation for further studies.
Harnessing the power of an X-ray laser for serial crystallography of membrane proteins crystallized in lipidic cubic phase
Serial femtosecond crystallography (SFX) with X-ray free-electron lasers (XFELs) has proven highly successful for structure determination of challenging membrane proteins crystallized in lipidic cubic phase; however, like most techniques, it has limitations. Here we attempt to address some of these limitations related to the use of a vacuum chamber and the need for attenuation of the XFEL beam, in order to further improve the efficiency of this method. Using an optimized SFX experimental setup in a helium atmosphere, the room-temperature structure of the adenosine A 2A receptor (A 2A AR) at 2.0 Å resolution is determined and compared with previous A 2A AR structures determined in vacuum and/or at cryogenic temperatures. Specifically, the capability of utilizing high XFEL beam transmissions is demonstrated, in conjunction with a high dynamic range detector, to collect high-resolution SFX data while reducing crystalline material consumption and shortening the collection time required for a complete dataset. The experimental setup presented herein can be applied to future SFX applications for protein nanocrystal samples to aid in structure-based discovery efforts of therapeutic targets that are difficult to crystallize.
Dynamic molecular architecture of the synaptonemal complex
During meiosis, pairing between homologous chromosomes is stabilized by the assembly of the synaptonemal complex (SC). The SC ensures the formation of crossovers between homologous chromosomes and regulates their distribution. However, how the SC regulates crossover formation remains elusive. We isolated an unusual mutation in Caenorhabditis elegans that disrupts crossover interference but not SC assembly. This mutation alters the unique C terminal domain of an essential SC protein, SYP-4, a likely ortholog of the vertebrate SC protein SIX6OS1. We use three-dimensional stochastic optical reconstruction microscopy (3D-STORM) to interrogate the molecular architecture of the SC from wild-type and mutant C. elegans animals. Using a probabilistic mapping approach to analyze super-resolution image data, we detect changes in the organization of the synaptonemal complex in wild-type animals that coincide with crossover designation. We also found that our syp-4 mutant perturbs SC architecture. Our findings add to growing evidence that the SC is an active material whose molecular organization contributes to chromosome-wide crossover regulation.
Fast and Accurate Intersections on a Sphere
We introduce a fast, high-precision algorithm for calculating intersections between great circle arcs and lines of constant latitude on the unit sphere. We first propose a simplified intersection point formula with improved speed and numerical robustness over the ones traditionally implemented in geoscience software. We then show how algorithms based on the concept of error-free transformations (EFT) can be applied to evaluate this formula within a relative error bound that is on the order of machine precision. Here, we demonstrate that, with a vectorized and parallelized implementation, this enhanced accuracy is achieved with no compute time overhead compared to a direct calculation in hardware floating point, making our algorithm suitable for performance-sensitive applications like regridding of high-resolution climate data. In contrast, evaluating our formula using high-precision data types like quadruple precision and arbitrary precision, or using the robust intersection computation routines from the Computational Geometry Algorithms Library, leads to significant computational overhead, especially since these alternatives inhibit vectorization. More generally, our work demonstrates how EFT techniques can be combined and extended to implement nontrivial geometric calculations with high accuracy and speed.
Satellite-Based Ranking of the World’s Hottest and Coldest Cities Reveals Inequitable Distribution of Temperature Extremes
The identification of the world’s hottest and coldest cities fascinates both the public and the scientific community. However, the ranking of city temperatures, especially from the perspective of human discomfort, has been difficult. Here we estimated the monthly mean maximum and minimum 1-km resolution urban temperatures of 13,135 cities worldwide (2003–19) from the thermal discomfort perspective by combining in situ measurements, satellite-based land surface temperatures, fine-resolution intracity data, and reanalysis data. Manama, Bahrain, was identified as the hottest city (48.18° ± 1.31°C) and Yakutsk, Russia (–42.96° ± 0.72°C), as the coldest city. The global city temperatures followed a power-law pattern, characterized by cities with <0.3 million inhabitants covering 80% of the top 20% global cities with extreme temperatures. Our study reveals an inequitable pattern of global city temperature extremes and highlights the urgency of developing appropriate strategies to reduce climate change risks in small- and medium-sized cities with low development levels.
Object-Based Evaluation of Dynamical and Statistical Downscaled Precipitation Products over CONUS
High-resolution precipitation data, generated through dynamical downscaling (DD) or statistical downscaling (SD) of global climate model output, provide critical information for regional climate assessment and adaptation planning. Most downscaling development and validation have focused on accurate gridscale precipitation construction and ignored the spatial structure of precipitation across model grids and at the event scale. However, many applications, e.g., hydrologic modeling and the analysis using the downscaled precipitation, require a reasonable representation of the spatial structure of precipitation within watersheds. Therefore, a set of standard metrics to evaluate the representation of the spatial structure of individual storms across diverse downscaled precipitation products is desired. To address this need, we conducted an object-based evaluation of precipitation in decades-long DD and SD products over the contiguous United States (CONUS). Specifically, we evaluate their ability to reproduce various features of precipitation objects in the observations: total volume, precipitation area, peak intensity, and spatial structure. Multiple metrics (bias, Perkins score, and nonparametric statistical tests) are used to quantify model performance. Our evaluation reveals notable variations in performance among individual products across different climate zones and seasons, as well as between extreme and nonextreme events. In general, most DD products exhibit balanced performance across the four precipitation object features, while SD products vary more significantly in their performance across products. Based on this comprehensive evaluation, we provide guidance on choosing downscaled products for specific regions, seasons, and precipitation object features. These findings and recommendations can inform precipitation-relevant modeling and analysis over CONUS, guide future downscaling technique developments, and provide actionable information for climate impact assessment and adaptation.