An engineered N-acyltransferase-LOV2 domain fusion protein enables light-inducible allosteric control of enzymatic activity.

Transferases are ubiquitous across all known life. While much work has been done to understand and describe these essential enzymes, there have been minimal efforts to exert tight and reversible control over their activity for various biotechnological applications. Here, we apply a rational, computation-guided methodology to design and test a transferase-class enzyme allosterically regulated by light-oxygen-voltage 2 sensing domain. We utilize computational techniques to determine the intrinsic allosteric networks within N-acyltransferase (Orf11/∗Dbv8) and identify potential allosteric sites on the protein's surface. We insert light-oxygen-voltage 2 sensing domain at the predicted allosteric site, exerting reversible control over enzymatic activity. We demonstrate blue-light regulation of N-acyltransferase (Orf11/∗Dbv8) function. Our study for the first time demonstrates optogenetic regulation of a transferase-class enzyme as a proof-of-concept for controllable transferase design. This successful design opens the door for many future applications in metabolic engineering and cellular programming.

Demonstration of quantum-enhanced rangefinding robust against classical jamming.

We demonstrate a quantum-enhanced lidar capable of performing confident target detection and rangefinding in the presence of strong, time-varying classical noise whilst operating with over five orders of magnitude separation between signal and background levels and target reflectivities down to -52 dB. We use a log-likelihood-based framework to introduce a new protocol for dynamic background tracking, verifying resilience of our system to both fast- and slow-modulation jamming in regimes where a classical illumination-based system fails to find a target. These results demonstrate the advantage of exploiting quantum correlations for lidar applications, providing a clear route to implementation in real-world scenarios.

High-Resolution Depth-Discrete Analysis of PFAS Distribution and Leaching for a Vadose-Zone Source at an AFFF-Impacted Site.

The long-term leaching of polyfluoroalkyl substances (PFAS) within the vadose zone of an AFFF application site for which the depth to groundwater is approximately 100 m was investigated by characterizing the vertical distribution of PFAS in a high spatial resolution. The great majority (99%) of PFAS mass resides in the upper 3 m of the vadose zone. The depths to which each PFAS migrated, quantified by moment analysis, is an inverse function of molar volume, demonstrating chromatographic separation. The PFAS were operationally categorized into three chain-length groups based on the three general patterns of retention observed. The longest-chain (>∼335 cm3/mol molar volume) PFAS remained within the uppermost section of the core, exhibiting minimal leaching. Conversely, the shortest-chain (<∼220 cm3/mol) PFAS accumulated at the bottom of the interval, which coincides with the onset of a calcic horizon. PFAS with intermediate-chain lengths were distributed along the length of the core, exhibiting differential magnitudes of leaching. The minimal or differential leaching observed for the longest- and intermediate-chain-length PFAS, respectively, demonstrates that retention processes significantly impacted migration. The accumulation of shorter-chain PFAS at the bottom of the core is hypothesized to result from limited deep infiltration and potential-enhanced retention associated with the calcic horizon.

Randomized Benchmarking Using Nondestructive Readout in a Two-Dimensional Atom Array.

Neutral atoms are a promising platform for scalable quantum computing, however, prior demonstration of high fidelity gates or low-loss readout methods have employed restricted numbers of qubits. Using randomized benchmarking of microwave-driven single-qubit gates, we demonstrate average gate errors of 7(2)×10^{-5} on a 225 site atom array using conventional, destructive readout. We further demonstrate a factor of 1.7 suppression of the primary measurement errors via low-loss, nondestructive, and state-selective readout on 49 sites while achieving gate errors of 2(9)×10^{-4}.

Demonstration of a Quantum Gate Using Electromagnetically Induced Transparency.

We demonstrate a native CNOT gate between two individually addressed neutral atoms based on electromagnetically induced transparency. This protocol utilizes the strong long-range interactions of Rydberg states to enable conditional state transfer on the target qubit when operated in the blockade regime. An advantage of this scheme is it enables implementation of multiqubit CNOT^{k} gates using a pulse sequence independent of qubit number, providing a simple gate for efficient implementation of digital quantum algorithms and stabilizer measurements for quantum error correction. We achieve a loss corrected gate fidelity of F_{CNOT}^{cor}=0.82(6), and prepare an entangled Bell state with F_{Bell}^{cor}=0.66(5), limited at present by laser power. We present a number of technical improvements to advance this to a level required for fault-tolerant scaling.

Hot topic: Management of cull dairy cows-Consensus of an expert consultation in Canada.

Many cull dairy cows enter the marketing system and travel to widely dispersed and specialized slaughter plants, and they may experience multiple handling events (e.g., loading, unloading, mixing), change of ownership among dealers, and feed and water deprivation during transport and at livestock markets. The objectives of this study were to describe the diverse management of cull dairy cows in Canada and establish consensus on ways to achieve improvements. A 2-day expert consultation meeting was convened, involving farmers, veterinarians, regulators, and experts in animal transport, livestock auction, and slaughter. The 15 participants, recruited from across Canada, discussed regional management practices for cull cattle, related risk factors, animal welfare problems, and recommendations. An audio recording of the meeting was used to extract descriptive data on cull cattle management and identify points of agreement. Eight consensus points were reached: (1) to assemble information on travel times and delays from farm to slaughter; (2) to increase awareness among producers and herd veterinarians of potential travel distances and delays; (3) to promote pro-active culling; (4) to improve the ability of personnel to assess animal condition before loading; (5) to identify local options for slaughter of cull dairy cows; (6) to investigate different management options such as emergency slaughter and mobile slaughter; (7) to ensure that all farms and auctions have, or can access, personnel trained and equipped for euthanasia; and (8) to promote cooperation among enforcement agencies and wider adoption of beneficial regulatory options.

Measuring frailty in clinical practice: a comparison of physical frailty assessment methods in a geriatric out-patient clinic.

BACKGROUND: The objectives of this study were to determine: 1) the prevalence of frailty using Fried's phenotype method and the Short Performance Physical Battery (SPPB), 2) agreement between frailty assessment methods, 3) the feasibility of assessing frailty using Fried's phenotype method and the SPPB. METHODS: This cross-sectional study was conducted at a geriatric out-patient clinic in Hamilton, Canada. A research assistant conducted all frailty assessments. Patients were classified as non-frail, pre-frail or frail according to Fried's phenotype method and the SPPB. Agreement among methods is reported using the Cohen kappa statistic (standard error). Feasibility data included the percent of eligible participants agreeing to attempt the frailty assessments (criterion for feasibility: ≥90% of patients agreeing to the frailty assessment), equipment required, and safety considerations. A p-value of <0.05 is considered significant. RESULTS: A total of 110 participants (92%) and 109 participants (91%) agreed to attempt Fried's phenotype method and SPPB, respectively. No adverse events occurred during any assessments. According to Fried's phenotype method, the prevalence of frailty and pre-frailty was 35% and 56%, respectively, and according to the SPPB, the prevalence of frailty and pre-frailty was 50% and 35%, respectively. There was fair to moderate agreement between methods for determining which participants were frail (0.488 [0.082], p < 0.001) and pre-frail (0.272 [0.084], p = 0.002). CONCLUSIONS: Frailty and pre-frailty are common in this geriatric outpatient population, and there is fair to moderate agreement between Fried's phenotype method and the SPPB. Over 90% of the patients who were eligible for the study agreed to attempt the frailty assessments, demonstrating that according to our feasibility criteria, frailty can be assessed in this patient population. Assessing frailty may help clinicians identify high-risk patients and tailor interventions based on baseline frailty characteristics.

Offering statins to a population attending health checks with a 10-year cardiovascular disease risk between 10% and 20.

BACKGROUND: In 2014 the UK National Institute for Health and Care Excellence recommended reducing the threshold for offering statin therapy to patients from a 10-year modelled risk of cardiovascular disease (CVD) of 20% to 10%. AIM: To describe the response of patients in UK primary care with a CVD risk between 10% and 20% to an invitation to attend a consultation to discuss statins. DESIGN AND SETTING: Review of electronic medical records at one GP practice in the East of England. METHOD: We invited all patients who had attended an NHS Health Check at the practice, had a QRisk(®) score between 10% and 20%, and were not prescribed statins to attend designated clinics in the practice to discuss starting statins. We reviewed the medical records to identify those who had attended the clinics and those who had chosen to start a statin. RESULTS: Of 410 patients invited, 100 (24.4%) patients attended the designated clinics and 45 (11%) chose to start a statin. Those who chose to start a statin were older and with a higher QRisk(®) than those who did not. Among those who attended, individuals who started a statin had a higher QRisk(®) than those who did not and were more likely to be current or ex-smokers. CONCLUSIONS: The proportion choosing to start a statin was substantially lower than previously estimated. Large population-based studies with long-term follow-up are needed to assess the impact on health and workload of this change in guidance.

Storage and control of optical photons using Rydberg polaritons.

We use a microwave field to control the quantum state of optical photons stored in a cold atomic cloud. The photons are stored in highly excited collective states (Rydberg polaritons) enabling both fast qubit rotations and control of photon-photon interactions. Through the collective read-out of these pseudospin rotations it is shown that the microwave field modifies the long-range interactions between polaritons. This technique provides a powerful interface between the microwave and optical domains, with applications in quantum simulations of spin liquids, quantum metrology and quantum networks.

Deconstructing maize population structure.

Association studies have rarely been used in plant genetics, in part because of the risk of false positives caused by population structure. A study of flowering time in maize makes the first use of recent 'structured association' methods-statistical approaches that use independent loci to control for the effects of structure and admixture.

The roles of the cation transporters CHX21 and CHX23 in the development of Arabidopsis thaliana.

The Arabidopsis thaliana genome encodes a family of 28 proteins whose members have been associated with the transport of monovalent cations across membranes. Experiments have been performed to elucidate the biochemical function and the role in plant development of two closely related members of this CHX family. A genotype carrying a knockout of the AtCHX23 gene (At1g05580) showed no phenotype when grown in glasshouse conditions. In particular, it did not exhibit the reduced root growth phenotype observed for a knockout of its homologue AtCHX21 when exposed to elevated sodium concentration. However, it was not possible to produce plants that were homozygous knockout for both AtCHX21 and AtCHX23. Reverse transcription-PCR (RT-PCR) experiments revealed that both genes are highly expressed in flower buds, flowers, and pollen. However, examination of pollen grain viability and pollen tube growth through excised styles did not reveal a phenotypic difference between the chx21(-)chx23(-) condition and other haplotypes. Crosses between selected mutants and wild-type plants in which the chx21(-)chx23(-) haplotype was produced by either the male or female parent demonstrated unequivocally that the chx21(-)chx23(-) haplotype could not pass through the female line. This suggests that the genes share a critical function in the development and/or function of the female gametophyte and that this function cannot be provided by other members of the AtCHX gene family. Experiments were carried out using the heterologous expression of AtCHX23 in Saccharomyces cerevisiae genotypes carrying combinations of deletions of genes involved in the transport of sodium or potassium across membranes. The results show that CHX23 would only complement the poor colony growth phenotype associated with the deletion of the yeast gene kha1. The conclusion is that both AtCHX21 and AtCHX23 act in potassium homeostasis within the female gametophyte and this is discussed in terms of the diversification of gene sequence and function within the CHX gene family.

Ankle fractures do not predict osteoporotic fractures in women with or without diabetes.

UNLABELLED: It is not clear whether ankle fractures predict future osteoporotic fractures in women, and whether diabetes influences this relationship. We found that a prior ankle fracture does not predict subsequent osteoporotic fractures in women with or without diabetes. INTRODUCTION: We aimed to determine: (1) whether a prior ankle fracture was a risk factor for a subsequent major osteoporotic fracture in older women; (2) whether this risk was modified by the presence of diabetes; (3) the risk factors for ankle fracture in older women. METHODS: We identified 3,054 women age 50 years and older with diabetes and 9,151 matched controls using the Manitoba Bone Density Program database. Multivariable regression models were used to examine factors associated with prior ankle fracture, and the importance of prior ankle fracture as a predictor of subsequent major osteoporotic fracture during a mean 4.8 years of observation. RESULTS: A prior ankle fracture was not a significant predictor of subsequent major osteoporotic fracture for women with diabetes (hazard ratio [HR] 1.13; 95% confidence interval [CI], 0.68-1.83; p = 0.623) or women without diabetes (HR 1.16; 95% CI, 0.79-1.71; p = 0.460), and there was no interaction between diabetes and ankle fracture after pooling all women in the cohort (p = 0.971). The presence of diabetes was not independently associated with prior ankle fracture (adjusted odds ratio [OR] 1.14 [95% CI, 0.93-1.38], p = 0.200), whereas higher body mass index (adjusted OR 1.04 per standard deviation increase [95% CI, 1.03-1.06], p < 0.001), previous major osteoporotic fracture (adjusted OR 1.40 [95% CI, 1.13-1.75], p = 0.002), and multiple comorbidities (>6 ambulatory diagnostic groups) (adjusted OR 1.81 [95% CI, 1.40-2.36], p < 0.001) were related to prior ankle fracture. CONCLUSIONS: Ankle fracture was not a significant predictor of major osteoporotic fracture in women, and a diagnosis of diabetes did not influence the relationship.

Correlated photon emission from multiatom Rydberg dark States.

We consider three-level atoms driven by two resonant light fields in a ladder scheme where the upper level is a highly excited Rydberg state. We show that the dipole-dipole interactions between Rydberg excited atoms prevents the formation of single particle dark states and leads to strongly correlated photon pairs from atoms separated by distances large compared to the emission wavelength. For a pair of atoms, this enables realization of an efficient photon-pair source with on average one pair every 30 µs.

Is photosynthetic enhancement sustained through three years of elevated CO2 exposure in 175-year-old Quercus robur?

Current carbon cycle models attribute rising atmospheric CO2 as the major driver of the increased terrestrial carbon sink, but with substantial uncertainties. The photosynthetic response of trees to elevated atmospheric CO2 is a necessary step, but not the only one, for sustaining the terrestrial carbon uptake, but can vary diurnally, seasonally and with duration of CO2 exposure. Hence, we sought to quantify the photosynthetic response of the canopy-dominant species, Quercus robur, in a mature deciduous forest to elevated CO2 (eCO2) (+150 µmol mol-1 CO2) over the first 3 years of a long-term free air CO2 enrichment facility at the Birmingham Institute of Forest Research in central England (BIFoR FACE). Over 3000 measurements of leaf gas exchange and related biochemical parameters were conducted in the upper canopy to assess the diurnal and seasonal responses of photosynthesis during the 2nd and 3rd year of eCO2 exposure. Measurements of photosynthetic capacity via biochemical parameters, derived from CO2 response curves, (Vcmax and Jmax) together with leaf nitrogen concentrations from the pre-treatment year to the 3rd year of eCO2 exposure, were examined. We hypothesized an initial enhancement in light-saturated net photosynthetic rates (Asat) with CO2 enrichment of ≈37% based on theory but also expected photosynthetic capacity would fall over the duration of the study. Over the 3-year period, Asat of upper-canopy leaves was 33 ± 8% higher (mean and standard error) in trees grown in eCO2 compared with ambient CO2 (aCO2), and photosynthetic enhancement decreased with decreasing light. There were no significant effects of CO2 treatment on Vcmax or Jmax, nor leaf nitrogen. Our results suggest that mature Q. robur may exhibit a sustained, positive response to eCO2 without photosynthetic downregulation, suggesting that, with adequate nutrients, there will be sustained enhancement in C assimilated by these mature trees. Further research will be required to understand the location and role of the additionally assimilated carbon.

Serum 25-hydroxyvitamin D concentrations and mortality in dogs with blastomycosis.

Blastomycosis is a prominent fungal disease in the United States. Vitamin D status has been found to be altered in critical illness and various infectious diseases. The objectives of this study were to compare serum 25-hydroxyvitamin D (25[OH]D) concentrations in dogs with blastomycosis and healthy controls, to assess the change in serum 25(OH)D concentrations in dogs with blastomycosis after 30 days of treatment, and to determine if baseline serum 25(OH)D concentrations in dogs with blastomycosis were associated with in-hospital, 30-day, or end-of-study mortality. In this prospective cohort study, 19 dogs newly diagnosed with blastomycosis had serum 25(OH)D concentrations measured with a commercially available validated radioimmunoassay at the time of diagnosis and 30 days after start of treatment. These values were compared to 24 healthy control dogs. Serum 25(OH)D concentrations at the time of diagnosis were lower in dogs with blastomycosis (median, 203 nmol/L; range, 31-590 nmol/L) than in clinically healthy control dogs (259.5 nmol/L, 97-829 nmol/L; P = 0.01). Despite clinical improvement, there was no significant change in serum 25(OH)D concentrations from baseline to 30-day follow-up. Dogs with baseline serum 25(OH)D concentrations <180.5nmol/L had a greater odds of death during hospitalization (odds ratio [OR], 15.0; 95% confidence interval [CI], 1.4-191.3; P = 0.04) and at 30 days follow-up (OR, 30.0; 95% CI, 2.5-366.7; P = 0.006). These findings highlight the need for further studies evaluating the prognostic value of vitamin D status in dogs with blastomycosis at diagnosis and throughout treatment and remission.

Cooperative atom-light interaction in a blockaded Rydberg ensemble.

By coupling a probe transition to a Rydberg state using electromagnetically induced transparency (EIT) we map the strong dipole-dipole interactions onto an optical field. We characterize the resulting cooperative optical nonlinearity as a function of probe strength and density. We demonstrate good quantitative agreement between the experiment and an N-atom cooperative model for N=3 atoms per blockade sphere and the n=60 Rydberg state. The measured linewidth of the EIT resonance places an upper limit on the dephasing rate of the blockade spheres of <110 kHz.

Veterinary pharmaceuticals and antibiotic resistance of Escherichia coli isolates in poultry litter from commercial farms and controlled feeding trials.

Veterinary pharmaceuticals are commonly used in poultry farming to prevent and treat microbial infections as well as to increase feed efficiency, but their use has created public and environmental health concerns. Poultry litter contains antimicrobial residues and resistant bacteria; when applied as fertilizer, the level and effects of these pharmaceuticals and antimicrobial-resistant bacteria in the environment are of concern. The purpose of this study was to investigate poultry litter for veterinary pharmaceuticals and resistance patterns of Escherichia coli. Litter samples were collected from controlled feeding trials and from commercial farms. Feed additives bacitracin, chlortetracycline, monensin, narasin, nicarbazin, penicillin, salinomycin, and virginiamycin, which were present in the feed on commercial farms and added to the feed in the controlled trials, were extracted in methanol and analyzed by liquid chromatography-mass spectrometry techniques. Sixty-nine E. coli were isolated and identified by API 20E. The susceptibility of the isolates to antibiotics was determined using Avian plates and the Sensititer automated system. This study confirmed the presence of antimicrobial residues in broiler litter from controlled environments as well as commercial farms, ranging from 0.07 to 66 mg/L depending on the compound. Concentrations of individual residues were higher in litter from controlled feeding trials than those from commercial farms. All E. coli isolates from commercial farms were multiresistant to at least 7 antibiotics. Resistance to beta-lactam antibiotics (amoxicillin, ceftiofur), tetracyclines, and sulfonamides was the most prevalent. This study concluded that broiler litter is a source of antimicrobial residues and represents a reservoir of multiple antibiotic-resistant E. coli.

An approximate likelihood for genetic data under a model with recombination and population splitting.

We describe a new approximate likelihood for population genetic data under a model in which a single ancestral population has split into two daughter populations. The approximate likelihood is based on the 'Product of Approximate Conditionals' likelihood and 'copying model' of Li and Stephens [Li, N., Stephens, M., 2003. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165 (4), 2213-2233]. The approach developed here may be used for efficient approximate likelihood-based analyses of unlinked data. However our copying model also considers the effects of recombination. Hence, a more important application is to loosely-linked haplotype data, for which efficient statistical models explicitly featuring non-equilibrium population structure have so far been unavailable. Thus, in addition to the information in allele frequency differences about the timing of the population split, the method can also extract information from the lengths of haplotypes shared between the populations. There are a number of challenges posed by extracting such information, which makes parameter estimation difficult. We discuss how the approach could be extended to identify haplotypes introduced by migrants.

Ancient Mammalian and Plant DNA from Late Quaternary Stalagmite Layers at Solkota Cave, Georgia.

Metagenomic analysis is a highly promising technique in paleogenetic research that allows analysis of the complete genomic make-up of a sample. This technique has successfully been employed to archaeological sediments, but possible leaching of DNA through the sequence limits interpretation. We applied this technique to the analysis of ancient DNA (aDNA) from Late Quaternary stalagmites from two caves in Western Georgia, Melouri Cave and Solkota. Stalagmites form closed systems, limiting the effect of leaching, and can be securely dated with U-series. The analyses of the sequence data from the Melouri Cave stalagmite revealed potential contamination and low preservation of DNA. However, the two Solkota stalagmites preserved ancient DNA molecules of mammals (bear, roe deer, bats) and plants (chestnut, hazelnut, flax). The aDNA bearing layers from one of the two Solkota stalagmites were dated to between ~84 ka and ~56 ka BP by U-series. The second Solkota stalagmite contained excessive detrital clay obstructing U-series dating, but it also contained bear bones with a minimum age of ~50 BP uncalibrated years and ancient DNA molecules. The preservation of authentic ancient DNA molecules in Late Quaternary speleothems opens up a new paleogenetic archive for archaeological, paleontological and paleoenvironmental research.