Mutation of the conserved Asp-Asp pair impairs the structure, function, and inhibition of CTX-M Clas
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Kemp, M. Trent↗
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AmeriFlux FLUXNET-1F US-Mo1 LTAR CMRB Field 1 (CMRB ASP)
This is the AmeriFlux Management Project (AMP) created FLUXNET-1F version of the carbon flux data for the site US-Mo1 LTAR CMRB Field 1 (CMRB ASP). This is the FLUXNET version of the carbon flux data for the site US-Mo1 LTAR CMRB Field 1 (CMRB ASP) produced by applying the standard ONEFlux (1F) software. Site Description - Site is in a 36 ha agricultural research field near Centralia, MO on a broad, slightly sloped landscape. Currently farmed in a corn-soybean-wheat-hay rotation. Used for research since 1991; prior to that was managed for commercial crop production.
Schreiner-McGraw, Adam↗
AmeriFlux US-Mo1 LTAR CMRB Field 1 (CMRB ASP)
This is the AmeriFlux version of the carbon flux data for the site US-Mo1 LTAR CMRB Field 1 (CMRB ASP). Site Description - Site is in a 36 ha agricultural research field near Centralia, MO on a broad, slightly sloped landscape. Currently farmed in a corn-soybean-wheat-hay rotation. Used for research since 1991; prior to that was managed for commercial crop production.
Schreiner-McGraw, Adam↗
AmeriFlux US-LMA Mississippi ARS Arant ASP
This is the AmeriFlux version of the carbon flux data for the site US-LMA Mississippi ARS Arant ASP. Site Description - Field
Witthaus, Lindsey [USDA ARS]↗
Comparison of Response Times for the Thermo ASP-2S1/NRD and Ludlum 30-7B Neutron Instruments
Health Physics Services (HPS) received feedback from a customer service survey regarding the difference in response times between the Thermo ASP-2S1/NRD (Thermo) and Ludlum Model 30-7B (Ludlum). In response to the feedback, tests were performed in the field and duplicated in a laboratory to evaluate and compare each instrument’s response time to reach an applied exposure. The results of the tests showed that optimizing its screen refresh rate by updating the Ludlum’s firmware improves response time, making it more comparable to the Thermo.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Structure and Function of the β-Asp-Arg Polymerase Cyanophycin Synthetase 2
Not provided.
Biochemistry & Molecular Biology↗
ASP (Adaptive Splines for Prediction) [SWR-22-66]
This software package provides functionality to fit piecewise cubic splines to model the relationship between a univariate X (independent variable) and a univariate Y (dependent variable). The output is akin to linear regression but has higher "capacity" in that it can learn more complicated relationships despite leveraging only a single predictor. It thus can learn very reasonable relationships between X and Y with minimal effort. The canonical intended use case is for predicting electric demand (Y) from temperature (X). There can be complicated, non-linear relationships between these two variables, but these can be reasonably approximated by the sum of: 1) an "aggregate" relationship between daily average temperature and daily average demand, and 2) intra-day patterns represented as hourly offsets from the daily average load. The spline functionality is used for learning a robust "aggregate" relationship without the inconvenience of manual feature engineering while still ensuring robust results. The model fitting workhorse is R's built-in smooth.spline. This package provides a suite of options for controlling how smooth.spline fits a spline to the data. In particular, it is designed to return a model with a single critical point (i.e., a single location along the domain/support where the first derivative is zero). This is to ensure that predicted changes in electric demand are always positive as temperatures become more extreme. This helps to prevent overfitting, particularly when the input data has few observations or has significant uncertainty from other sources.
Murphy, Sinnott↗
Performance evaluation of CMIP6 models on the Arctic-Siberian Plain teleconnection affecting the East Asian heat waves
The frequency and intensity of summer heat waves in East Asia have increased sharply in recent decades, significantly impacting public health and the economy. The Arctic-Siberian Plain (ASP) teleconnection pattern has been identified as a key driver, with ASP warming amplifying atmospheric circulation patterns conducive to extreme temperatures. This study evaluates the ability of Coupled Model Inter-comparison Project phase 6 models to simulate the ASP pattern across interannual variability (IAV) and intra-seasonal variability (ISV) timescales using the Common Basis Function method. The multi-model mean shows statistically significant pattern correlations with ERA5 reanalysis, with correlation coefficients of 0.90 and 0.99 for IAV and ISV, respectively. While the ASP pattern is generally well captured, models exhibit substantial inter-model diversity in the intensity and position of anticyclonic anomalies over the ASP and East Asia. Models with ASP pattern variability similar to reanalysis better reproduce extreme East Asian temperatures, whereas those over- or underestimating ASP variability exhibit lower skill. These performance differences are related to differences in simulating key variables associated with the development of the ASP pattern. Our findings highlight the role of the ASP pattern in modulating extreme heat events, as models with improved ASP simulations align more closely with observed temperature extremes. Refining ASP representations in models could enhance seasonal heat wave predictions, improving climate adaptation strategies.
Arctic-Siberian Plain (ASP)↗
Regulation of L - and D -Aspartate Transport and Metabolism in Acinetobacter baylyi ADP1
Here, the regulated uptake and consumption of d-amino acids by bacteria remain largely unexplored, despite the physiological importance of these compounds. Unlike other characterized bacteria, such as Escherichia coli, which utilizes only l-Asp, Acinetobacter baylyi ADP1 can consume both d-Asp and l-Asp as the sole carbon or nitrogen source. As described here, two LysR-type transcriptional regulators (LTTRs), DarR and AalR, control d- and l-Asp metabolism in strain ADP1. Heterologous expression of A. baylyi proteins enabled E. coli to use d-Asp as the carbon source when either of two transporters (AspT or AspY) and a racemase (RacD) were coexpressed. A third transporter, designated AspS, was also discovered to transport Asp in ADP1. DarR and/or AalR controlled the transcription of aspT, aspY, racD, and aspA (which encodes aspartate ammonia lyase). Conserved residues in the N-terminal DNA-binding domains of both regulators likely enable them to recognize the same DNA consensus sequence (ATGC-N7-GCAT) in several operator-promoter regions. In strains lacking AalR, suppressor mutations revealed a role for the ClpAP protease in Asp metabolism. In the absence of the ClpA component of this protease, DarR can compensate for the loss of AalR. ADP1 consumed l- and d-Asn and l-Glu, but not d-Glu, as the sole carbon or nitrogen source using interrelated pathways.
59 BASIC BIOLOGICAL SCIENCES↗
Discovery of cyanophycin dipeptide hydrolase enzymes suggests widespread utility of the natural biopolymer cyanophycin
Cyanophycin is a bacterial polymer mainly used for nitrogen storage. It is composed of a peptide backbone of L-aspartate residues with L-arginines attached to their side chains through isopeptide bonds. Cyanophycin is degraded in two steps: Cyanophycinase cleaves the polymer into β-Asp-Arg dipeptides, which are hydrolyzed into free Asp and Arg by enzymes possessing isoaspartyl dipeptide hydrolase activity. Two unrelated enzymes with this activity, isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA) have been shown to degrade β-Asp-Arg dipeptides, but bacteria which encode cyanophycin-metabolizing genes can lack iaaA and iadA genes. In this study, we investigate a previously uncharacterized enzyme whose gene can cluster with cyanophycin-metabolizing genes. This enzyme, which we name cyanophycin dipeptide hydrolase (CphZ), is specific for dipeptides derived from cyanophycin degradation. Accordingly, a co-complex structure of CphZ and β-Asp-Arg shows that CphZ, unlike IadA or IaaA, recognizes all portions of its β-Asp-Arg substrate. Bioinformatic analyses showed that CphZ is found in very many proteobacteria and is homologous to an uncharacterized protein encoded in the “arginine/ornithine transport” (aot) operon of many pseudomonas species, including Pseudomonas aeruginosa . In vitro assays show that AotO is indeed a CphZ, and in cellulo growth experiments show that this enzyme and the aot operon allow P. aeruginosa to take up and use β-Asp-Arg as a sole carbon and nitrogen source. Together the results establish the novel, highly specific enzyme subfamily of CphZs, suggesting that cyanophycin is potentially used by a much wider range of bacteria than previously appreciated.
Science & Technology - Other Topics↗
Simulation of adiabatic quantum computing for molecular ground states
Quantum computation promises to provide substantial speedups in many practical applications with a particularly exciting one being the simulation of quantum many-body systems. Adiabatic state preparation (ASP) is one way that quantum computers could recreate and simulate the ground state of a physical system. In this paper, we explore a novel approach for classically simulating the time dynamics of ASP with high accuracy and with only modest computational resources via an adaptive sampling configuration interaction scheme for truncating the Hilbert space to only the most important determinants. We verify that this truncation introduces negligible error and use this new approach to simulate ASP for sets of small molecular systems and Hubbard models. Furthermore, we examine two approaches to speeding up ASP when performed on quantum hardware: (i) using the complete active space configuration interaction (CASCI) wave function instead of the Hartree–Fock initial state and (ii) a nonlinear interpolation between the initial and target Hamiltonians. We find that starting with a CASCI wave function with a limited active space yields substantial speedups for many of the systems examined, while nonlinear interpolation does not. In additional, we observe interesting trends in the minimum gap location (based on the initial state) as well as how state preparation time can depend on certain molecular properties, such as the number of valence electrons. Importantly, we find that the required state preparation times do not show an immediate exponential wall that would preclude an efficient run of ASP on actual hardware.
Kremenetski, Vladimir↗
Examining Interactions of Uranyl(VI) Ions with Amino Acids in the Gas Phase
Gas-phase experiments, using electrospray ionization quadrupole ion trap mass spectrometry (ESI-QIT/MS), were conducted to probe basic interactions of the uranyl(VI) ion, UO 2 2+ , with selected natural amino acids, namely, L-cysteine (Cys), L-histidine (His), and L-aspartic acid (Asp), which strongly bind to metal ions. The simplest amino acid, glycine (Gly), was also studied for comparison. Cys, His, and Asp have additional potentially coordinating groups beyond the amino and carboxylic acid functional groups, specifically thiol in Cys, imidazole in His, and a second carboxylate in Asp. Gas-phase experiments comprised collision-induced dissociation (CID) of uranyl–amino acid complexes and competitive CID to assess the relative binding strength of different amino acids in the same uranyl complex. Reactivity of selected uranyl–amino acid complexes with water provided further insights into relative stabilities. In positive ion mode, CID and ensuing reactions with water suggested that uranyl–neutral AA binding strength decreased in the order His > Asp > Cys > Gly, which is similar to amino acid proton affinities. In negative ion mode, CID revealed a decreasing dissociation tendency in the order Gly >> His ≈ Cys > Asp, presumably reflecting a reverse enhanced binding to uranyl of the doubly deprotonated amino acids formed in CID.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Bioinformatics of cyanophycin metabolism genes and characterization of promiscuous isoaspartyl dipeptidases that catalyze the final step of cyanophycin degradation
Cyanophycin is a bacterial biopolymer used for storage of fixed nitrogen. It is composed of a backbone of L-aspartate residues with L-arginines attached to each of their side chains. Cyanophycin is produced by cyanophycin synthetase 1 (CphA1) using Arg, Asp and ATP, and is degraded in two steps. First, cyanophycinase breaks down the backbone peptide bonds, releasing β-Asp-Arg dipeptides. Then, these dipeptides are broken down into free Asp and Arg by enzymes with isoaspartyl dipeptidase activity. Two bacterial enzymes are known to possess promiscuous isoaspartyl dipeptidase activity: isoaspartyl dipeptidase (IadA) and isoaspartyl aminopeptidase (IaaA). We performed a bioinformatic analysis to investigate whether genes for cyanophycin metabolism enzymes cluster together or are spread around the microbial genomes. Many genomes showed incomplete contingents of known cyanophycin metabolizing genes, with different patterns in various bacterial clades. Cyanophycin synthetase and cyanophycinase are usually clustered together when recognizable genes for each are found within a genome. Cyanophycinase and isoaspartyl dipeptidase genes typically cluster within genomes lacking cphA1. About one-third of genomes with genes for CphA1, cyanophycinase and IaaA show these genes clustered together, while the proportion is around one-sixth for CphA1, cyanophycinase and IadA. We used X-ray crystallography and biochemical studies to characterize an IadA and an IaaA from two such clusters, in Leucothrix mucor and Roseivivax halodurans, respectively. The enzymes retained their promiscuous nature, showing that being associated with cyanophycin-related genes did not make them specific for β-Asp-Arg dipeptides derived from cyanophycin degradation.
59 BASIC BIOLOGICAL SCIENCES↗
RrA, an enzyme from Rhodospirillum rubrum , is a prototype of a new family of short‐chain L‐asparaginases
Abstract L‐Asparaginases (ASNases) catalyze the hydrolysis of L‐Asn to L‐Asp and ammonia. Members of the ASNase family are used as drugs in the treatment of leukemia, as well as in the food industry. The protomers of bacterial ASNases typically contain 300–400 amino acids (typical class 1 ASNases). In contrast, the chain of ASNase from Rhodospirillum rubrum , reported here and referred to as RrA, consists of only 172 amino acid residues. RrA is homologous to the N‐terminal domain of typical bacterial class 1 ASNases and exhibits millimolar affinity for L‐Asn. In this study, we demonstrate that RrA belongs to a unique family of cytoplasmic, short‐chain ASNases (scASNases). These proteins occupy a distinct region in the sequence space, separate from the regions typically assigned to class 1 ASNases. The scASNases are present in approximately 7% of eubacterial species, spanning diverse bacterial lineages. They seem to be significantly enriched in species that encode for more than one class 1 ASNase. Here, we report biochemical, biophysical, and structural properties of RrA, a member of scASNases family. Crystal structures of the wild‐type RrA, both with and without bound L‐Asp, as well as structures of several RrA mutants, reveal topologically unique tetramers. Moreover, the active site of one protomer is complemented by two residues (Tyr21 and Asn26) from another protomer. Upon closer inspection, these findings clearly outline scASNases as a stand‐alone subfamily of ASNases that can catalyze the hydrolysis of L‐Asn to L‐Asp despite the lack of the C‐terminal domain that is present in all ASNases described structurally to date.
59 BASIC BIOLOGICAL SCIENCES↗
Hydrogen Mitigation Process Testing at Nevada Solar One
The National Renewable Energy Laboratory (NREL) and Acciona Solar Power (ASP) developed and installed a process that addresses the issue of hydrogen buildup in Acciona's Nevada Solar One power plant. Our method selectively removes hydrogen from the expansion tanks of the power plant to control hydrogen levels in the circulating heat-transfer fluid (HTF). During previous work, we developed a sensor that measures hydrogen partial pressure in the expansion-tank headspace gas. We demonstrated that our sensor measures hydrogen levels over a wide range of partial pressure from 10 mbar down to 0.003 mbar. More recently, we conceived and developed an integrated process module that performs both hydrogen sensing and separating functions. The sensor/separator measures hydrogen partial pressure in the headspace gas in the same way as our original sensor design. Additionally, the integrated module separates hydrogen from the headspace gas to reduce hydrogen to the level needed to maintain the performance of receivers in the collector field. Laboratory testing at NREL showed that the sensor function had an accuracy of +/-7%, and the hydrogen extraction rate for separator function was consistent with our modeling predictions. The primary benefit of this module is its simple design, both in terms of function and incorporation into the HTF subsystem of the power plant. Most recently, NREL and ASP completed installation and initial testing of a mitigation process at ASP's Nevada Solar One power plant in Boulder City, Nevada. In this paper, we report on the completed installation, initial testing, and plans to bring the process to full automation, so that it can be operated unattended on a daily schedule.
chemical elements↗
Cheaper and more noise-resilient quantum state preparation using eigenvector continuation
Subspace methods are powerful, noise-resilient methods that can effectively prepare ground states on quantum computers. The challenge is to get a subspace with a small condition number that spans the states of interest using minimal quantum resources. In this work, we will use eigenvector continuation to build a subspace from the low-lying states of a set of Hamiltonians. The basis vectors are prepared using truncated versions of standard state preparation methods such as imaginary-time evolution (ITE), adiabatic state preparation (ASP), and variational quantum eigensolver. By using these truncated methods combined with eigenvector continuation, we can directly improve upon them, obtaining more accurate ground-state energies at a reduced cost. We use several spin systems to demonstrate convergence even when methods like ITE and ASP fail, such as ASP in the presence of level crossings and ITE with vanishing energy gaps. We also showcase the noise resilience of this approach beyond the gains already made by having shallower quantum circuits. Furthermore, our findings suggest that eigenvector continuation can be used to improve existing state preparation methods in the near term.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Identification of residues involved in allosteric signal transmission from amino acid binding site of pyruvate kinase muscle isoform 2
PKM2 is a rate-limiting enzyme in the glycolytic process and is involved in regulating tumor proliferation. Several amino acids (AAs) such as Asn, Asp, Val, and Cys have been shown to bind to the AA binding pocket of PKM2 and modulate its oligomeric state, substrate binding affinity, and activity. Although previous studies have attributed that the main chain and side chain of bound AAs are responsible for initiating signal to regulate PKM2, the signal transduction pathway remains elusive. To identify the residues involved in signal transfer process, N70 and N75 located at two ends of a β strand connecting the active site and AA binding pocket were altered. Biochemical studies of these variants with various AA ligands (Asn, Asp, Val, and Cys), illustrate that N70 and N75, along with β1 connecting these residues are part of the signal transduction pathway between the AA binding pocket and the active site. The results demonstrate that mutation of N70 to D prevents the transfer of the inhibitory signal mediated by Val and Cys, whereas N75 to L alteration blocks the activating signal initiated by Asn and Asp. Taken together, this study confirms that N70 is one of the residues responsible for transmitting the inhibitory signal and N75 is involved in the activation signal flow.
36 MATERIALS SCIENCE↗