bluuebunny/crossref_metadata_2025 huggingface dataset:
Serial Metamorphic Manipulator Dynamics Formulation Implementing Screw Theory Tools
Authors: Stravopodis N. , Moulianitis V. C.
Published: September 2024

In this work, a framework is proposed for the analytical formulation of dynamic equations for serial metamorphic manipulators using screw theory tools. The integration of structure reconfiguration is achieved in a compact and comprehensive manner. Based on the previously proposed modular structure representation, additional statements are provided to strictly define the metamorphic structure assembly. To validate the precision of the extracted dynamics, two simulations are performed for paths defined in Cartesian space. The generated trajectory is evaluated by comparing the dynamic matrices produced by the proposed method with those from an established dynamic modeling algorithm. Additionally, the trajectory is simulated in an open-source simulator, and the torques extracted from system dynamics are compared with the corresponding simulator torques under the same kinematic constraints.
Immersion and Invariance Adaptive Control Through Polynomial Adaptation
Authors: Zhou Xingyu , Ahn Hyunjin , Shen Heran , Kung Yung-Chi , Wang Junmin
Published: September 2024

In conventional immersion and invariance (I&I) adaptive control design, control parameter adaptation is typically linear with respect to the parameter error-induced perturbation, resulting in quadratic rate dissipation of energy associated with the off-the-manifold variable. Departing from such a convention, this article contributes a novel strategy—polynomial adaptation. As the name suggests, control parameter adaptation in this approach takes the form of a general polynomial in relation to the perturbation. Accordingly, this new design induces polynomial rate energy dissipation, which is faster than the quadratic one in the conventional scheme, thereby enhancing closed-loop control performance. The theoretical underpinnings of the new approach are demonstrated through the design of an I&I adaptive tracking control law for a general nth-order, single-input–single-output, parametrically uncertain, nonlinear system in the controllable canonical form. In addition, a numerical study of the proposed method on the second-order forced Duffing oscillator shows its improved transient performance in comparison to a baseline controller developed with the standard I&I adaptive control technique.
The Effect of Heterogeneous Natural Gas–Hydrogen Input Into F-Class Gas Turbine Combustor As a Combustion Optimization Method
Authors: Park Jungkeuk , Shin Jugon , Park Seik , Lee Sanghyup , Choi Nakjeong
Published: September 2024

The global push to combat climate change by transitioning to clean power generation is accelerating. One promising avenue involves using hydrogen in place of natural gas in gas turbine-based power plants. While the development of new hydrogen combustors shows potential, advancements in operational technologies are needed to ensure higher hydrogen cofiring with existing combustion systems. In our study, we propose a novel approach called heterogeneous natural gas–hydrogen input: varying hydrogen content between different nozzle groups in gas turbine combustors. Using a full-scale combustor of an F-class gas turbine model, we experimentally investigated the impact of heterogeneous hydrogen concentrations at the center and outer nozzles on combustion dynamics and emissions, comparing these with homogeneous fuel supply cases of 100% natural gas and natural gas–hydrogen mixtures. While hydrogen cofiring did not change the maximum amplitude of combustion dynamic pressure across the total frequency range, peak amplitudes in the 125–245 Hz domain were linearly proportional to the hydrogen cofiring ratio, with a 41.2% increase at 30% cofiring identified as a possible limiting factor. Our findings revealed a significant correlation between NOx emissions and combustion stability under varying levels of heterogeneity. Higher heterogeneity with intensive hydrogen input into the center nozzle improved cofiring performance, reducing the peak amplitude in the limiting frequency domain by 22% for a 25% cofiring ratio, potentially extending the critical hydrogen cofiring ratio. Implementing heterogeneous natural gas-hydrogen inputs emerges as a promising method to enhance combustion stability and enable effective hydrogen cofiring.
A Large Eddy Simulation Study on Hydrogen Microjets in Hot Vitiated Crossflow
Authors: Broumand Mohsen , Yun Sean , Hong Zekai
Published: September 2024

In this paper, the results of a large eddy simulation (LES) study on hydrogen microjets (dj ∼ 0.5 mm) injected into a hot (1600 K) vitiated crossflow at different angles, namely, normal (90 deg) and inclined jet (30 deg), are presented. The goal is to explore the effects of injection angle on coherent turbulent structure formations, flame–vortex interactions, and wall heat flux contributions. The LES identifies the presence of the horseshoe vortex, the shear layer vortices (SLV), and the counter-rotating vortex pair (CVP), along with the shedding of spanwise-symmetry hairpin vortices in both the normal and inclined jets. The structures in the latter, however, appear more convoluted. In the near field, the SLV-induced flow is found to play a key role in the mixing and flame propagation in the windward side of the jet that is stabilized through the auto-ignition process along the front edge of both the normal and inclined jets close to their exits. The flame-shear layer offset phenomenon is also noticed on the windward side of the jets. In the far field, the CVP is found to be the dominating mechanism in the entrainment of the hot vitiated crossflow by the reacting jet and large-scale mixing. Its induced counter-rotating flow field give rises to the flame propagation and the heat and species transfer from the windward to the leeward side of the jet near the injection wall. In the wake region, the combustion and its byproducts persist in closer proximity to the jet exit of the normal case because of the presence of a much stronger recirculation zone behind the jet. Accordingly, higher wall heat fluxes are obtained in this region for the normal jet. The mean wall heat flux values of both the normal and inclined jets decrease and approach each other with moving away from the jet exit in the streamwise direction. The findings indicate that the CVP-induced flow drastically increases heat transfer to the near wall region, resulting in a spanwise-symmetry heat flux profile with double peaks in downstream. The results of the present LES study are compared to the experimental data available in the literature by considering instantaneous hydroxide (OH) fields and mean wall heat fluxes.
Modeling Periodic Asymmetric Light Transmitting Nanostructures for Luminescent Solar Concentrators Using COMSOL Multiphysics Wave Optics Module
Authors: Arnow Hannah , Oliveto Vincent , Smith Duncan , Hughes Michael , Borca-Tasciuc Diana-Andra
Published: September 2024

Building Integrated Photovoltaics (BIPVs) have been developed to aid in meeting new net-zero legislation. BIPVs incorporating Luminescent Solar Concentrators (LSC) are actively investigated to improve utilization of solar cells on vertical walls. However, LSCs suffer from low efficiency due to escape cone losses. One way to increase LSC efficiency is by using Asymmetric Light Transmission (ALT) interfaces that prevent light from escaping the LSC at angles around normal incidence. ALT interfaces consisting of trapezoidal alumina pyramids have been shown effective at light trapping when added to the light-entering surface of a polymethyl methacrylate (PMMA)-based LSC. However, the previous study overlooked the effect of azimuth angle of incidence. Given the geometry of the nanostructured interface, azimuth angle is anticipated to play a role in ALT interface performance. The goal of this paper is to investigate this aspect. Forward and backward transmission data and Poynting vector directional data were collected from COMSOLs Multiphysics Wave Optics Module for a trapezoidal pyramid ALT interface at varying azimuth angles. This data was then used with an in-house Monte Carlo Ray Tracing code to simulate light propagation within the LSC with the ALT interface and calculate the optical efficiency. Average transmission difference for increasing azimuth angles increased at lower polar angles yet decreased at higher polar angles. It was found that the optical efficiency for the ALT interface LSC improves in performance at higher azimuth angles compared to an LSC with a plain interface. This suggests that a horizontal orientation for the ALT interface LSC would be best for optimal performance.
Powering a TLUD Biomass Pyrolyzer Using its Own Waste Heat and Thermoelectric Devices
Authors: Nasef Ziad , Nugen Nathan , Leal-Quiros Edbertho , Diaz Gerardo
Published: September 2024

The escalating severity and frequency of climate change events, including prolonged droughts, extensive wildfire seasons, rising sea levels, and devastating floods, calls for urgent greenhouse gas (GHG) emission reduction policies. Waste heat utilization emerges as one potential strategy for climate change mitigation. Controlled thermochemical processes such as biomass pyrolysis offer a climate-friendly alternative approach in the face of biomass decay or open burning, which contribute to emissions of methane and other harmful pollutants to the environment. Biomass pyrolysis can also produce electric power or industrial heat without adding carbon to the atmosphere and providing a stable form of carbon sequestration in the form of biochar. In response to environmental concerns, California’s San Joaquin Valley Air Pollution Control District is set to prohibit open burning of biomass starting in January 2025. This paper deals with the potential application of thermoelectric generators to harness waste heat from a Top-Lit Up-Draft (TLUD) biomass pyrolyzer. Thermoelectric generator plates were studied and characterized, where the amount of voltage generation and the effect of external cooling were investigated. The contribution of this paper is to use the thermoelectric generator plates to recover some of the waste heat that is lost during biomass pyrolysis. The electric power produced can be used to replace the external power source required in TLUD pyrolyzers.
4E Assessment on Heat Transfer and Optimization of a Novel Cooling-Heating- Power Cogeneration Brayton System
Authors: Wang Yiming , Xie Gongnan , Rowe Andrew
Published: September 2024

High-temperature gas-cooled fast reactors are fourth generation nuclear systems offering ultra-high heat source temperature and advanced safety features. When used in applications such as marine propulsion, delivery of cooling and hot water may be achieved by utilizing reactor heat rejection. The supercritical CO2 Brayton cycle is considered suitable for coupling with the fourth-generation nuclear systems due to the excellent thermophysical properties of supercritical CO2. In this study, a novel cooling-heating-power cogeneration Brayton system that can fully recover the reactor cooling heat is described. The prototype ALLEGRO demonstrator reactor operating conditions are used to design the supercritical CO2 combined cycle. The use of advanced, double-sided etched printed circuit heat exchanger with elliptical channel geometry is examined. Initially, the key thermodynamic and cost metrics are analyzed using energy, exergy, economy, and environment (4E) assessment. Subsequently, multi-objective optimization of the Brayton system is carried out using the 4E metrics. The results show that the economic and environment costs of the combined cycle can be reduced by 2.9% and 49.5%, respectively with respect to the base-case design.
A Model Reduction Method for Conduction-Based Thermal Analysis of a Complex System to Obtain an Equivalent Numerical Model
Authors: Usul Yener , Özkökdemir Emir
Published: September 2024

In this study, we focus on an electronic unit within a complex system for numerical thermal analysis, which must be analyzed for each design iteration. There are heat sources inside and outside the system. The electronic unit itself is also a heat source due to the heat dissipating electronic components. That is to say, there may be a positive or negative heat transfer through the electronic unit from the rest of the system. The first step in the model reduction process employed in this study involves removing regions distant from the unit of interest from the analysis model and simplifying the geometry of regions near the unit. Then, the equivalent thermal properties of the simplified region as well as the corresponding boundary conditions, are estimated. This estimation is carried out iteratively by adjusting the parameters related to the simplified model using the main analysis model results as a reference for predetermined analysis scenarios. Consequently, the analysis model is mathematically reduced while preserving the physical phenomena associated with the unit of interest within an acceptable margin of error.
Advancement in Lithium-Ion Battery Pack Thermal Modeling Based on Electrochemical Principles
Authors: Ferreira Patryck , Tang Shu-Xia
Published: September 2024

This study introduces an advanced thermal model for lithiumion battery packs, examining cell and module-level heat dynamics. Heat within cells originates from complex electrochemical reactions described by Fick’s second law. The Single Particle Model (SPM) utilizes two Partial Differential Equations (PDEs) to analyze electrode dynamics, considering electric power generation via Ohm’s law and subsequent heat generation from Joule’s effect. Conduction interactions within cells and the battery casing are assessed using a thermal resistance model. Convective heat within the liquid electrolyte is also considered in the cell heat analysis. This cumulative heat is averaged per cell within a module to determine total module heat. A transient heat equation, employing PDEs, analyzes internal module temperatures, incorporating the heat exchange system as boundary conditions, creating a system of PDEs for each module. This approach, distinct from computational fluid dynamics studies, focuses on detailed cell-level modeling using PDEs, extending to module-level heat analysis with boundary conditions. The study’s novelty lies in its method of employing multiple PDEs to model module temperature within battery packs, improving accuracy and safety assessment.
Prediction of Critical Heat Flux for Liquid Helium Using Machine Learning Models Assisted by Physics-Based Correlation
Authors: Li Jiayuan , Kharangate Chirag R.
Published: September 2024

Liquid helium plays an important role in fields such as superconductivity, quantum computing, medical cryopreservation, and space exploration. Prediction of pool boiling heat transfer, especially the critical heat flux, is crucial for all these applications. To date, no effective tool is available to give accurate predictions of critical heat flux specific for liquid helium. In this study, we use both traditional machine learning models and physics-assisted machine learning models to predict critical heat flux of liquid helium with 585 data sourced from 22 studies. While the traditional machine learning models possess no information on critical heat flux, the physics-assisted machine learning models obtain physical information of critical heat flux from Zuber [2]’s correlation by predicting the multiplier of the hydrodynamic instability term. Recursive feature elimination and stepwise selection are used to remove the redundant features while multivariate adaptive regression splines, support vector machine, random forest, and extreme gradient boosting are used for modeling. Support vector machine, random forest, and extreme gradient boosting result in better performance than traditional correlations. Physics-assisted extreme gradient boosting model achieves the best result with 14% mean absolute percentage error. This work is the first attempt in reported literatures to predict critical heat flux for liquid helium using machine learning models.
Design of a Continuous Suspension Freeze Crystallizer for Desalination Brine Treatment
Authors: El Kadi Khadije , Al Aghbari Anas , Janajreh Isam
Published: September 2024

Freeze crystallization presents an innovative thermal desalination technology whereby water is separated from salts in brine solution through freezing, commonly known as freeze desalination (FD). This work presents a comprehensive Computational Fluid Dynamics (CFD) investigation aimed at optimizing the design of a Continuous Suspension Freeze Crystallizer (CSFC) for seawater brine treatment. The approach involves a dual-level methodology, comprising non-isothermal geometrical optimization and ice crystallization evaluation. Geometrical optimization explores parameters such as crystallizer height, channel diameter, and the number of inlets/outlets across different residence times. Results demonstrate that increasing crystallizer height, diameter, residence time, and the number of inlets/outlets positively impact heat transfer, leading to a notable enhancement in the outlet-to-inlet temperature difference. This adjustment creates conducive conditions to attain less temperature polarization within the crystallizer. Nonetheless, implementation of solidification modeling revealed heterogeneous ice crystallization at the CSFC walls, especially at higher residence times. The results underscore the potential need for external agitation or ultrasonic power to address temperature polarization near the wall.
Optimisation of Energy Usage in Some Senior High Schools in Tarkwa and its Environs
Authors: Simons Anthony , Offei Daniel
Published: September 2024

In line with the worldwide efforts to reduce carbon emissions and promote sustainability in energy generation, renewable energy sources offer the most advantageous option. This work explores optimisation of energy consumption in four Senior High Schools within the Tarkwa Nsuaem and Prestea Huni-Valley Municipalities in the Western Region of Ghana. A comprehensive energy audit used the ASHRAE standards to identify areas for improvement in the electricity usage of these schools. Replacing CFLs and incandescent lamps with LED bulbs, along with changing old refrigerators with higher energy consumption, reduced the general energy consumption by an average of 40 % in the selected schools. The study went further to assess the feasibility of implementing solar energy technology options for power generation on the gable roof which is predominant in Ghanaian schools. Comparison of solar technologies favored grid-connected PV for its cost-effectiveness. A prototype of solar tracking system designed specifically for the gable roof was fabricated to increase solar panel efficiency. This new design collected 31 % more solar power compared to another installation which did not track the varying position of the sun in the sky. It was recommended that exclusive use of LED bulbs in Senior High Schools should be encouraged, and government should continue to support the usage of renewable energy to achieve sustainable energy goals. This study emphasises the vital role of energy efficiency and renewable energy in educational institutions to reduce the cost of purchasing energy (a direct function of the rate of energy consumption) and for climate change mitigation.
Numerical Analysis of Surface Coatings Performances for In-Flight Icing Device Performance Enhancement
Authors: Croce Giulio , Suzzi Nicola
Published: September 2024

Recent developments in manufacturing techniques offer a wide range of high-performance coatings designed to improve heat and mass transfer processes. Superhydrophobic surfaces may enhance the performances of anti and de-icing devices for in-flight ice applications. Numerical modeling of the effect of such devices requires the analysis of the behavior of an ensemble of individual droplets, rather than assuming a continuous film as in standard icing codes. Here an individual-based method (IBM) is adopted. Droplets are assumed as the smaller element of the simulations, and phenomenological sub-models describe their behavior through impact on the surface, possible rebound, growth via coalescence or phase change (either freezing or evaporation), transition from still droplet to moving ones, the transition from running droplets to rivulets. The model is validated versus literature experimental data, showing the capability of the approach. It appears that hydrophobicity is not yet enough to build a passive anti-icing system but can significantly enhance the performances of typical thermal devices.
An Embedded Microfluidic Approach for Direct Cooling of Copper Windings in Printed Circuit Boards
Authors: Moguel Daniel A. , Pekarek Steven D. , Weibel Justin A.
Published: September 2024

Increasing the current density of electric machine windings is a means to increase the torque density, and thus the power density, of an electric machine. The peak achievable current density is governed by the ability to remove heat from the windings subject to material temperature constraints. Traditional thermal management schemes use external cooling jackets or other approach where the coolant indirectly interfaces with the windings. However, recent studies have shown the use of printed circuit boards (PCB) as a shared substrate for both cooling channels as well as copper traces, with demonstrations of planar inductor coil current densities that exceed those in traditional power-dense machinery. In view of this application need, this study explores an approach to increase the achievable current densities to > 100 A/mm2 in windings using direct liquid cooling of copper traces on PCBs. This is enabled by fabricating multi-layer board stacks having embedded microchannels for cooling with a dielectric fluid that is in direct contact with internal copper winding traces.
Adaptive Determination of the Damping Coefficient of the Levenberg-Marquardt Algorithm Using Type-2 Fuzzy in Inverse Heat Transfer Problems
Authors: Sajedi Ramin , Faraji Javad , Samadi Forooza , Kowsary Farshad
Published: September 2024

In this study, a combination of the Levenberg-Marquardt algorithm and the type-2 fuzzy method is used to solve an inverse heat transfer problem. Considering the essential role of the damping factor in the stability and efficiency of the Levenberg-Marquardt algorithm in solving ill-posed problems, a new method based on fuzzy logic theory is used to update the value of this parameter in the iteration of the solution. A cubic polynomial test case is estimated using classical, type-1, and type-2 fuzzy Levenberg-Marquardt methods for the boundary heat flux in a one-dimensional heat transfer problem. The evaluation criteria chosen are convergence speed and robustness. The results show that the use of the new method increases the speed of convergence. The robustness and the accuracy of the estimates is improved by using this new method compared to the conventional Levenberg-Marquardt method.
Validating the Use of Continuous Glucose Monitors With Nondiabetic Recreational Runners
Authors: Mason Lesley J. , Hartwig Timothy , Greene David
Published: September 2024

Purpose: Continuous glucose monitors (CGMs) are becoming increasingly popular among endurance athletes despite unconfirmed accuracy. We assessed the concurrent validity of the FreeStyle Libre 2 worn on 2 different sites at rest, during steady-state running, and postprandial. Methods: Thirteen nondiabetic, well-trained recreational runners (age = 40 [8] y, maximal aerobic oxygen consumption = 46.1 [6.4] mL·kg–1·min–1) wore a CGM on the upper arm and chest while treadmill running for 30, 60, and 90 minutes at intensities corresponding to 50%, 60%, and 70% of maximal aerobic oxygen consumption, respectively. Glucose was measured by manually scanning CGMs and obtaining a finger-prick capillary blood glucose sample. Mean absolute relative difference, time in range, and continuous glucose Clarke error grid analysis were used to compare paired CGM and blood glucose readings. Results: Across all intensities of steady-state running, we found a mean absolute relative difference of 13.8 (10.9) for the arm and 11.4 (9.0) for the chest. The coefficient of variation exceeded 70%. Approximately 47% of arm and 50% of chest paired glucose measurements had an absolute difference ≤10%. Continuous glucose Clarke error grid analysis indicated 99.8% (arm) and 99.6% (chest) CGM data fell in clinically acceptable zones A and B. Time-in-range analysis showed reduced accuracy at lower glucose levels. However, CGMs accurately detected trends in mean glucose readings over time. Conclusions: CGMs are not valid for point glucose monitoring but appear to be valid for monitoring glucose trends during steady-state exercise. Accuracy is similar for arm and chest. Further research is needed to determine whether CGMs can detect important events such as hypoglycemia during exercise.
Zebrafish as an effective model for evaluating phage therapy in bacterial infections: a promising strategy against human pathogens
Authors: Plumet Lucile , Costechareyre Denis , Lavigne Jean-Philippe , Kissa Karima , Molle Virginie
Published: September 2024

The escalating prevalence of antibiotic-resistant bacterial infections necessitates urgent alternative therapeutic strategies. Phage therapy, which employs bacteriophages to specifically target pathogenic bacteria, emerges as a promising solution. This review examines the efficacy of phage therapy in zebrafish models, both embryos and adults, which are proven and reliable for simulating human infectious diseases. We synthesize findings from recent studies that utilized these models to assess phage treatments against various bacterial pathogens, including
Enterococcus faecalis
,
Pseudomonas aeruginosa
,
Mycobacterium abscessus
,
Staphylococcus aureus
,
Klebsiella pneumoniae
,
Acinetobacter baumannii
, and
Escherichia coli
. Methods of phage administration, such as circulation injection and bath immersion, are detailed alongside evaluations of survival rates and bacterial load reductions. Notably, combination therapies of phages with antibiotics show enhanced efficacy, as evidenced by improved survival rates and synergistic effects in reducing bacterial loads. We also discuss the transition from zebrafish embryos to adult models, emphasizing the increased complexity of immune responses. This review highlights the valuable contribution of the zebrafish model to advancing phage therapy research, particularly in the face of rising antibiotic resistance and the urgent need for alternative treatments.
Characterization of 2-phenanthroate:CoA ligase from the sulfate-reducing, phenanthrene-degrading enrichment culture TRIP
Authors: Kaplieva-Dudek I. , Samak Nadia A. , Bormann Jenny , Kaschani Farnusch , Kaiser Markus , Meckenstock Rainer U.
Published: September 2024

Polycyclic aromatic hydrocarbons (PAHs) are chemically stable pollutants that are poorly degraded by microorganisms in anoxic sediments. The anaerobic degradation pathway of PAHs such as phenanthrene starts with a carboxylation reaction forming phenanthroic acid. In this study, we identified and characterized the next enzyme in the pathway, the 2-phenanthroate:CoA ligase involved in the ATP-dependent formation of 2-phenanthroyl-CoA from cell-free extracts of the sulfate-reducing enrichment culture TRIP grown anaerobically with phenanthrene. The identified gene sequence indicated that 2-phenanthroate:CoA ligase belongs to the phenylacetate:CoA ligase-like enzyme family. Based on the sequence, we predict a two-domain structure of the 2-phenanthroate:CoA ligase with a typical large N-terminal and a smaller C-terminal domain. Partial purification of 2-phenanthroate:CoA ligase allowed us to identify the coding gene in the genome. 2-Phenanthroate:CoA ligase gene was heterologously expressed in
Escherichia coli
. Characterization of the 2-phenanthroate:CoA ligase was performed using the partially purified enzyme from cell-free extract and the purified recombinant enzyme. Testing all possible phenanthroic acid isomers as substrate for the ligase reaction showed that 2-phenanthroic acid is the preferred substrate and only 3-phenanthroic acid can be utilized to a minor extent. This also suggests that the product of the prior carboxylase reaction is 2-phenanthroic acid. 2-Phenanthroate:CoA ligase has an optimal activity at pH 7.5 and is oxygen-insensitive, analogous to other aryl-CoA ligases. In contrast to aryl-Coenzyme A ligases reported in the literature, which need Mg
2+
as cofactor, 2-phenanthroate:CoA ligase showed greatest activity with a combination of 5 mM MgCl
2
and 5 mM KCl. Furthermore, a substrate inhibition was observed at ATP concentrations above 1 mM and the enzyme was also active with ADP.

IMPORTANCE

Polycyclic aromatic hydrocarbons (PAHs) constitute a class of very toxic and persistent pollutants in the environment. However, the anaerobic degradation of three-ring PAHs such as phenanthrene is barely investigated. The initial degradation step starts with a carboxylation followed by a CoA‑thioesterification reaction performed by an aryl-CoA ligase. The formation of a CoA-thioester is an important step in the degradation pathway of aromatic compounds because the CoA-ester is needed for all downstream biochemical reactions in the pathway. Furthermore, we provide biochemical proof for the identification of the first genes for anaerobic phenanthrene degradation. Results presented here provide information about the biochemical and structural properties of the purified 2‑phenanthroate:CoA ligase and expand our knowledge of aryl-CoA ligases.
Molecular, structural, and functional characterization of delta subunit of T-complex protein-1 from
Leishmania donovani
Authors: Anand Apeksha , Gautam Gunjan , Srivastava Gaurava , Yadav Shailendra , Ramalingam Karthik , Siddiqi Mohammad Imran , Goyal Neena
Published: September 2024

Chaperonins/Heat shock protein 60 are ubiquitous multimeric protein complexes that assist in the folding of partially and/or misfolded proteins using metabolic energy into their native stage. The eukaryotic group II chaperonin, also referred as T-complex protein-1 ring complex (TRiC)/T-complex protein-1 (TCP1)/chaperonin containing T-complex protein (CCT), contains 8–9 paralogous subunits, arranged in each of the two rings of hetero-oligomeric complex. In
Leishmania
, till date, only one subunit, LdTCP1γ, has been well studied. Here, we report the molecular, structural, and functional characterization of TCP1δ subunit of
Leishmania donovani
(LdTCP1δ), the causative agent of Indian kala-azar. LdTCP1δ gene exhibited only 27.9% identity with LdTCP1γ and clustered in a separate branch in the phylogenic tree of LdTCP1 subunits. The purified recombinant protein formed a high molecular weight complex (0.75 MDa), arranged into 16-mer assembly, and performed
in vitro
chaperonin activity as assayed by ATP-dependent luciferase folding. LdTCP1δ exhibits 1.8-fold upregulated expression in metabolically active, rapidly dividing log phase promastigotes. Over-expression of LdTCP1δ in promastigotes results in increased infectivity and rate of multiplication of intracellular amastigotes. The study thus establishes the existence of an individual functionally active homo-oligomeric complex of LdTCP1δ chaperonin with its role in parasite infectivity and multiplication.
Conformations of membrane human immunodeficiency virus (HIV-1) envelope glycoproteins solubilized in Amphipol A18 lipid-nanodiscs
Authors: Zhang Shijian , Anang Saumya , Zhang Zhiqing , Nguyen Hanh T. , Ding Haitao , Kappes John C. , Sodroski Joseph
Published: September 2024

Upon binding to the host cell receptor, CD4, the pretriggered (State-1) conformation of the human immunodeficiency virus (HIV-1) envelope glycoprotein (Env) trimer undergoes transitions to downstream conformations important for virus entry. State 1 is targeted by most broadly neutralizing antibodies (bNAbs), whereas downstream conformations elicit immunodominant, poorly neutralizing antibody (pNAb) responses. Extraction of Env from the membranes of viruses or Env-expressing cells disrupts the metastable State-1 Env conformation, even when detergent-free approaches like styrene-maleic acid lipid nanoparticles (SMALPs) are used. Here, we combine three strategies to solubilize and purify mature membrane Envs that are antigenically native (i.e., recognized by bNAbs and not pNAbs): (1) solubilization of Env with a novel amphipathic copolymer, Amphipol A18; (2) use of stabilized pretriggered Env mutants; and (3) addition of the State-1-stabilizing entry inhibitor, BMS-806. Amphipol A18 was superior to the other amphipathic copolymers tested (SMA and AASTY 11–50) for preserving a native Env conformation. A native antigenic profile of A18 Env-lipid-nanodiscs was maintained for at least 7 days at 4°C and 2 days at 37°C in the presence of BMS-806 and was also maintained for at least 1 h at 37°C in a variety of adjuvants. The damaging effects of a single cycle of freeze-thawing on the antigenic profile of the A18 Env-lipid-nanodiscs could be prevented by the addition of 10% sucrose or 10% glycerol. These results underscore the importance of the membrane environment to the maintenance of a pretriggered (State-1) Env conformation and provide strategies for the preparation of lipid-nanodiscs containing native membrane Envs.

IMPORTANCE

The human immunodeficiency virus (HIV-1) envelope glycoproteins (Envs) mediate virus entry into the host cell and are targeted by neutralizing antibodies elicited by natural infection or vaccines. Detailed studies of membrane proteins like Env rely on purification procedures that maintain their natural conformation. In this study, we show that an amphipathic copolymer A18 can directly extract HIV-1 Env from a membrane without the use of detergents. A18 promotes the formation of nanodiscs that contain Env and membrane lipids. Env in A18-lipid nanodiscs largely preserves features recognized by broadly neutralizing antibodies (bNAbs) and conceals features potentially recognized by poorly neutralizing antibodies (pNAbs). Our results underscore the importance of the membrane environment to the native conformation of HIV-1 Env. Purification methods that bypass the need for detergents could be useful for future studies of HIV-1 Env structure, interaction with receptors and antibodies, and immunogenicity.
Identification of amino acid residue in the
Cronobacter sakazakii
LamB responsible for the receptor compatibility of polyvalent coliphage CSP1
Authors: Kim Moosung , Kim Minsik , Ryu Sangryeol
Published: September 2024

Polyvalent bacteriophages show the feature of infecting bacteria across multiple species or even orders. Infectivity of a polyvalent phage is variable depending on the host bacteria, which can disclose differential inhibition of bacteria by the phage. In this study, a polyvalent phage CSP1 infecting both
Cronobacter sakazakii
ATCC 29544 and
Escherichia coli
MG1655 was isolated. CSP1 showed higher growth inhibition and adsorption rate in
E. coli
compared to
C. sakazakii
, and identification of host receptors revealed that CSP1 uses
E. coli
LamB (LamB
E
) as a receptor but that CSP1 requires both
C. sakazakii
LamB (LamB
C
) and lipopolysaccharide (LPS) core for
C. sakazakii
infection. The substitution of LamB
C
with LamB
E
in
C. sakazakii
enhanced CSP1 susceptibility and made
C. sakazakii
LPS core no more essential for CSP1 infection. Comparative analysis of LamB
C
and LamB
E
disclosed that the extra proline at amino acid residue 284 in LamB
C
made a structural distinction by forming a longer loop and that the deletion of 284P in LamB
C
aligns its structure and makes LamB
C
function like LamB
E
, enhancing CSP1 adsorption and growth inhibition of
C. sakazakii
. These results suggest that 284P of LamB
C
plays a critical role in determining the CSP1-host bacteria interaction. These findings could provide insight into the elucidation of molecular determinants in the interaction between polyvalent phages and host bacteria and help us to understand the phage infectivity for efficient phage application.

IMPORTANCE

Polyvalent phages have the advantage of a broader host range, overcoming the limitation of the narrow host range of phages. However, the limited molecular biological understanding on the host bacteria-polyvalent phage interaction hinders its effective application. Here, we revealed that the ability of the polyvalent phage CSP1 to infect
Cronobacter sakazakii
ATCC 29544 is disturbed by a single proline residue in the LamB protein and that lipopolysaccharide is used as an auxiliary receptor for CSP1 to support the adsorption and the subsequent infection of
C. sakazakii
. These results can contribute to a better understanding of the interaction between polyvalent phages and host bacteria for efficient phage application.
High-throughput screening identification of apigenin that reverses the colistin resistance of mcr-1-positive pathogens
Authors: Tang Feng , Peng Wenjing , Kou Xu , Chen Zeliang , Zhang Libo
Published: September 2024

The plasmid-mediated gene mcr-1 that makes bacteria resistant to the antibiotic colistin is spreading quickly, which means that colistin is no longer working well to treat Gram-negative bacterial infections. Herein, we utilized a computer-aided high-throughput screening drugs method to identify the natural product apigenin, a potential
mcr
-protein inhibitor, which effectively enhanced the antimicrobial activity of colistin. Several assays, including a checkerboard minimum inhibitory concentration assay, a time-kill assay, the combined disk test, molecular simulation dynamics, and animal infection models assay, were conducted to verify whether apigenin enhanced the ability of colistin to fight Gram-negative bacterial infections. The results showed that apigenin improved the antimicrobial activity of colistin against multidrug-resistant
Enterobacteriaceae
infection. Moreover, apigenin not only did not increase the toxic effect of colistin but also had the ability to effectively inhibit the frequency of bacterial resistance mutations to colistin. Studies clearly elucidated that apigenin could interfere with the thermal stability of the protein by binding to the
mcr
-1 protein. Additionally, the combination of apigenin and colistin could exert multiple effects, including disrupting bacterial membranes, the generation of bacterial nitric oxide and reactive oxygen species, as well as inhibiting bacterial adenosine triphosphate production. Furthermore, the addition of apigenin was able to significantly inhibit colistin-stimulated high expression levels of the bacterial mcr-1 gene. Finally, apigenin exhibited a characteristic anti-inflammatory effect while enhancing the antimicrobial activity of colistin against mcr-1-positive
Escherichia coli
(
E. coli
) infected animals. In conclusion, as a potential lead compound, apigenin is promising in combination with colistin in the future treatment of mcr-1-positive
E. coli
infections.

IMPORTANCE

This study found that apigenin was able to inhibit the activity of the
mcr
-1 protein using a high-throughput virtual screening method. Apigenin effectively enhanced the antimicrobial activity of colistin against multidrug-resistant
Enterobacteriaceae
, including mcr-1-positive strains,
in vitro
and
in vivo
. This study will provide new options and strategies for the future treatment of multidrug-resistant pathogen infections.
The effects of
Pinus sylvestris
L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment
Authors: Maitra Pulak , Hrynkiewicz Katarzyna , Szuba Agnieszka , Niestrawska Adrianna , Mucha Joanna
Published: September 2024

Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of
Pinus sylvestris
L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different
P. sylvestris
origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within
P. sylvestris
also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments.

IMPORTANCE

This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (
Pinus sylvestris
). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant–microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.
Penicillin susceptibility among
Staphylococcus aureus
skin and soft tissue infections at a children’s hospital
Authors: McNeil J. Chase , Sommer Lauren M. , Joseph Marritta , Hulten Kristina G. , Kaplan Sheldon L.
Published: September 2024

Shortly after its introduction into clinical practice,
Staphylococcus aureus
isolates gained resistance to penicillin via the acquisition of β-lactamases. A number of centers have recently described an increase in the proportion of invasive methicillin-susceptible
S. aureus
(MSSA), which are also susceptible to penicillin (PSSA). Little data are available regarding the prevalence or impact of PSSA in skin and soft tissue infections (SSTI). Community-acquired MSSA SSTI isolates were obtained through a surveillance study at Texas Children’s Hospital from January 2017 to December 2021. A total of 200 random isolates underwent PCR for
blaZ
β-lactamase;
blaZ
-negative isolates then underwent penicillin susceptibility testing using macrobroth dilution. Isolates which were
blaZ
negative and had a penicillin MIC ≤0.125 µg/mL were regarded as PSSA with the remainder regarded as penicillin-resistant MSSA (PR-MSSA). All PSSA underwent multilocus sequence typing. Medical records were reviewed. The median age of subjects was 4.2 years (IQR: 1.6–10.5). PSSA accounted for 9% of isolates during the study period. PSSA and PR-MSSA cases were similar with respect to age, demographics, and rates of prior antibiotic exposure. PSSA isolates less often had vancomycin MIC ≥1.5 µg/mL. Furthermore, 39% of PSSA were variants of sequence type 1. In multivariable analyses, penicillin susceptibility was independently associated with both hospital admission and surgical intervention. PSSA account for a small but significant proportion of MSSA SSTI in children. Clinically distinguishing patients with PSSA and PR-MSSA SSTI is challenging. However, PSSA SSTI were independently associated with higher rates of hospital admission as well as the need for surgical intervention suggesting a significant clinical impact.

IMPORTANCE

The vast majority of
Staphylococcus aureus
in the US are penicillin resistant with most clinical labs no longer reporting penicillin susceptibility for this organism. A number of centers, however, have reported increasing penicillin susceptibility among invasive
S. aureus
infections. Skin and soft tissue infections (SSTI) are far more common than invasive infections, yet the frequency and impact of penicillin-susceptible
S. aureus
(PSSA) in this population are uncertain. Through active surveillance at a children’s hospital, we found that 9% of methicillin-susceptible
S. aureus
SSTI isolates were PSSA. PSSA were independently associated with hospital admission for the management of SSTI as well as the need for debridement in the operating room. Given that most SSTI are managed in the outpatient setting, these findings suggest a clinical impact of this phenotype and the need for a reassessment of the value in susceptibility testing and potentially even treatment with penicillin.
The timing of Missoula floods: Implications for the age of Grand Coulee (eastern Washington, USA)
Authors: Lehnigk Karin E. , Larsen Isaac J. , Quirk Brendon J. , David Scott R.
Published: September 2024

The Channeled Scabland of eastern Washington (USA) was formed by outburst floods from glacial Lake Missoula. Despite chronological advances, the timing of erosion in the main flood channels is unresolved. In particular, it is still uncertain whether upper Grand Coulee, the largest canyon in the Channeled Scabland, was incised during or prior to the last glaciation. We report 10Be exposure ages from erratics in upper Grand Coulee, glacial Lake Columbia, and surrounding flood routes. Flood-transported boulders on the high-elevation east rim of Grand Coulee date to ca. 17–15 ka. Ages from boulders on the floor of Grand Coulee indicate later flooding at ca. 14 ka, which post-dated canyon incision and occurred after inundation of the Telford-Crab Creek scabland at ca. 15–14.5 ka. Prior hydraulic modeling and dating suggest the entrance to Grand Coulee was blocked by rock and that canyon incision was incomplete at ca. 17 ka; hence, we interpret the 17–15 ka exposure ages on the east rim to coincide with flow over a retreating cataract during canyon incision. Our results indicate incision of Grand Coulee was completed between 17 ka and 14 ka. The short duration of canyon incision suggests that glacial Lake Missoula generated some of the most erosive outburst floods in Earth's history.
Supplemental Material: Deep marine records of Deccan Trap volcanism before the Cretaceous–Paleogene (K–Pg) mass extinction
Authors: Sinnesael Matthias , al. et
Published: September 2024

Newly measured Hg concentrations, PGE, and Os isotope data. 
Thermodynamic Properties of NaH2PO4⋅2H2O and K2HPO4⋅3H2O Crystal Hydrates
Authors: Novikov A. A. , Yongxu Luo , Tiflova L. A. , Kurdakova S. V. , Kovalenko N. A. , Uspenskaya I. A.
Published: September 2024

NaH2PO4⋅2H2O and K2HPO4⋅3H2О crystal hydrates are synthesized from aqueous solutions at room temperature. The resulting samples are identified using X-ray structural analysis (XSA) and thermogravimetry (TG). The enthalpies of dissolution in water at 298.15 K are determined through the calorimetry of dissolution, and the standard enthalpies of formation for the crystal hydrates of sodium dihydrophosphate and potassium hydrophosphate are calculated. A comparison of the estimated and experimentally obtained values of the enthalpy of formation for NaH2PO4⋅2H2O and K2HPO4⋅3H2О shows they are within the limits of the error of determination.