bluuebunny/crossref_metadata_2025 huggingface dataset:
Microstructure, Mechanical, and Tribological Characteristics of Heat-Treated AA7075 Composite Reinforced With High-Entropy Alloy Particles
Authors: Verma Pradip Kumar , Singh Alok , Bais Uday Pratap Singh , Kumar Akshay , Malik Nisha
Published: December 2024

This research examines the microstructural, mechanical, and tribological characteristics of an AA7075 alloy composite reinforced with high-entropy alloy (HEA) particulates, synthesized through advanced stir-squeeze casting techniques. To enhance grain refinement and optimize mechanical properties, the composite undergoes T6 heat treatment. Advanced characterization methods, including optical microscopy, scanning electron microscopy (SEM), and optical profilometry, are utilized to investigate microstructural features and worn surface morphology. Microstructural analysis reveals a homogeneous distribution of HEA particles within the AA7075 matrix, promoting a refined grain structure. Mechanical assessments indicate improvements in microhardness and compressive strength with the increasing HEA content. Tribological analysis shows that the wear-rate of the composite decreases with the increase in HEA particles, reaching a maximum reduction with 8 wt% HEA reinforcement. SEM observations of the worn surfaces reveal features such as pronounced grooves, adhesive wear, ploughing effects, wear debris, and microcracking.
Supercritical Carbon Dioxide Lubricated Hybrid Journal Bearing: Computational Fluid Dynamics Analysis and Optimization
Authors: Ali MD Shujan , Shin Dongil , Palazzolo Alan
Published: December 2024

Supercritical CO2 (SCO2) power cycles offer significant advantages in terms of thermal efficiency, cost-effectiveness, and environmental benefits. However, the successful implementation of these cycles depends on the design and analysis of bearings that can operate at high speeds and temperatures. Despite their importance, critical aspects like supporting bearings have received limited attention. This study addresses these gaps by developing sophisticated 3D computational fluid dynamics (CFD) models to accurately predict static characteristics like load capacity and leakage rate of SCO2-lubricated hybrid bearings. These bearings use SCO2 as the lubricating fluid due to the difficulty in maintaining separation between oil and the process fluid in oil-based bearings operating at extreme temperatures and pressures. An optimization tool, response surface optimization along with a 3D CFD model has been utilized to determine the bearing equilibrium point. After validation of the CFD model against available experimental measurements, a parametric study has been conducted to evaluate the effects of various geometric and operating parameters on bearing performance. The hybrid bearing geometry has been optimized based on the findings of the parametric study. The optimized bearing designs achieved a significant boost in load capacity while substantially reducing the leakage rate. This study introduces a new design/optimization process for SCO2-lubricated bearings using a 3D CFD model. The results indicate a strong correlation between load capacity, leakage rate, and variables such as orifice diameter, supply pressure, recess height, and recess length. These insights provide valuable guidance for practical SCO2-lubricated hybrid bearing design and optimization.
Local Calculation of Load-Dependent Gear Power Losses of Cylindrical Gears
Authors: Paschold Constantin , Lohner Thomas , Stahl Karsten
Published: December 2024

The primary design criteria for gearboxes are (i) power density and load capacity; (ii) noise, vibration, and harshness; and (iii) efficiency and heat balance. To meet these design criteria, it is essential to use accurate calculation models throughout the design process. The total power loss can be divided into portions of gears, bearings, seals, and other machine elements, of which the load-dependent gear power loss often makes up the most significant portion. The existing literature provides a number of calculation methods with varying levels of detail for mesh-local models that promise high accuracy; however, these are rarely used, partly due to a lack of validation. This study systematically compares mesh-averaged and mesh-local calculation models using experimental results from a twin-disk tribometer and various cylindrical gears. The study includes a wide range of operating conditions and different gear oils. Three calculation levels I, II, and III are defined. The results show good agreement between the calculated and measured load-dependent gear power losses, with the mesh-local models showing high accuracy. When comparing results for an internal gear, the mesh-local calculation model calculates 30% lower load-dependent gear power losses than the mesh-averaged calculation model, which aligns with initial experimental results. The findings of this study suggest that mesh-local models are viable for wider application.
Microstructure and Friction Characteristics of SiC/Ni60 Coatings by Different Directed Energy Deposition Laser Powers
Authors: Li Wanyang , Liu Weiwei , Ma Zongyu , Liu Huanqiang , Song Jianrong , Li Tao , Wang Fengtao , Zhao Yue , Zhang Hongchao
Published: December 2024

The microstructure and tribological characteristics of SiC/Ni60 composite coatings manufactured using directed energy deposition (DED) technology are investigated. The influence of different laser powers on the composites is studied. The evolution characteristics of the microstructure, the stepped variation pattern of microhardness, and the formation mechanism of wear resistance induced by different laser powers are observed in SiC/Ni60 composite coatings. Laser power variations emerged as crucial factors for improving the structure and performance of the composites. The relationship between microstructure, phase identification, and laser power is clarified using scanning electron microscopy (SEM), energy-dispersive spectroscopy (EDS), electron back-scattered diffraction (EBSD), and X-ray diffractometer (XRD). The best laser power is determined to be 3000 W based on microhardness and tribological characteristics. Additionally, the friction coefficient, wear rate, and wear behavior provide insights into the tribological features. Appropriate laser power parameters can suppress severe abrasive and adhesive wear and reduce the area of oxidative wear, resulting in a 51.99% reduction in wear rate. From the results obtained, it is evident that selecting the appropriate laser power provides a valuable direction for improving the performance of the composite coatings. The present work is expected to be applied to components such as crankshafts, where enhanced wear resistance is required.
Assessment of Tool Condition and Surface Quality Using Hybrid Deep Neural Network: CNN-LSTM-Based Segmentation and Statistical Analysis
Authors: Rao K. Venkata
Published: December 2024

Effective and precise prediction of tool wear plays a key role in improving machining efficiency, and product quality and reducing production cost. The majority of earlier studies have depended on limited experimental data, which may not be sufficient to estimate tool wear and surface quality. Aiming at these issues, the present study proposed a convolutional neural network (CNN)-long short-term memory (LSTM) hybrid deep neural network model that directly utilizes heterogeneous data including timely captured tool images, working conditions, vibration data, surface roughness, flank wear length, and wear depth. First, experiments were conducted on AISI D2 steel at three levels of spindle speed and feed/tooth, and experimental results for wear length, wear depth, surface roughness, and vibration signals were collected. The time domain vibration signals were processed with a fast Fourier transformer and converted to the frequency domain, and 13 and 5 features were extracted from the time and frequency domain, respectively, and integrated with the heterogeneous data. Second, tool images were annotated using Roboflow software, and wear region information was collected using YOLOv8 and added to heterogeneous data. Third, the CNN-LSTM network was trained with heterogeneous data containing spatial and time-dependent features. The performance and accuracy of the proposed methodology were validated using experimental data collected at different working conditions. The results show that the CNN-LSTM model effectively predicted the tool wear length on the flank, with the root mean square error (RMSE) value of 0.219 mm, and the determination coefficient R2 value of 0.974; wear depth with the RMSE value of 0.018 mm and R2 value of 0.943; surface roughness with the RMSE value of 0.216 μm and R2 value of 0.956. The proposed methodology has significance in metal-cutting applications and provides a solution to predict tool conditions and surface quality accurately.
A New Multi-Criteria Decision-Making Tool for Subsea Oil and Gas Asset Decommissioning
Authors: Caprace Jean-David , de Souza Marcelo I. L. , Violante Ferreira Claudio , Ribeiro Nicolosi Eduardo
Published: December 2024

The decommissioning of offshore oil and gas (O&G) facilities poses significant challenges due to high costs, operational risks, social impacts, and environmental protection concerns. Multi-criteria decision analysis (MCDA) emerges as a vital tool to navigate these complexities, enabling stakeholders to evaluate diverse decommissioning alternatives against a broad set of criteria. Existing literature lacks extensive documentation on the application of MCDA in decommissioning decisions, particularly in quantitatively evaluating the performance of different decommissioning strategies against a comprehensive set of criteria. This study introduces a novel MCDA model tailored for the decommissioning of subsea O&G assets, aiming to improve decision-making by providing a quantitative ranking of decommissioning alternatives. Employing the Preference Ranking Organization Method for Enrichment Evaluations method, the model considers 37 attributes across six criteria (safety, environment, waste management, technical, social, and economic) to evaluate several decommissioning alternatives for the Brazilian Espadarte Field. Weightings and scenarios are defined through expert consultation, enhancing the model’s adaptability and relevance to real-world contexts. The model’s application demonstrated significant efficacy, with the selected top-ranked decommissioning alternative achieving a performance indicator of 58%, corresponding to the removal of 50% of the pipeline length considered. This result underscores the model’s capacity to identify optimal compromises between competing criteria. The study contributes to the field by filling the gap in the quantitative evaluation of decommissioning alternatives, offering a robust, transparent decision-making tool that accommodates complex, multi-criteria decisions. The model provides a significant advancement in the rationalization of decommissioning strategies for O&G assets.
Validation of a Frequency-Dependent Morison Force Formulation for a Large Monopile in Severe Irregular Seas
Authors: Dadmarzi Fatemeh H. , Bachynski-Polić Erin E. , Pakozdi Csaba , Thys Maxime
Published: December 2024

Motivated by the increased interest in renewable energy and the need for validated hydrodynamic load models, a rigid monopile and a fully flexible large monopile wind turbine have been tested experimentally at a 1:50 model scale in irregular waves. Furthermore, a new engineering load model combining the conventional Morison equation for slender bodies with a frequency-dependent mass coefficient based on the first-order MacCamy and Fuchs solution has been developed and compared to Rainey’s load model and the model test results. Nonlinear wave kinematics based on the results of the nonlinear potential code REEF3D::FNPF have been applied as input to the numerical models. The new model better estimates the response of the monopile in the frequency range relevant for ringing events. The experimentally obtained 90th percentile bending moment response near the first natural frequency of the monopile is estimated within 2% by the new model with frequency-dependent mass coefficient, while a traditional Morison approach or the Rainey model overestimate the response by 47% and 74%, respectively.
Simulation of Rock-Breaking Ability of Polycrystalline Diamond Compact Cutter Based on Rock Mechanics Experiment After Heat Treatment
Authors: Yin Qishuai , Wen Zhiliang , Ren Laiao , Qu Ximo , Li Qianyu , Zhou Bo
Published: December 2024

When drilling in geothermal and deep formations, the rock-breaking mechanism of high-temperature formations is not clear. In this work, mechanical tests of rocks subjected to high temperatures were carried out, and rock-breaking models of bottom hole thermal stress dispersion and polycrystalline diamond compact (PDC) cutter were established. Aiming at efficient rock breaking pursued by drilling in high-temperature formation, rock-breaking simulations of PDC cutters with different front rake angles under the condition of temperature and confining pressure changes were carried out based on critical penetration depth. The mechanism of rock breaking is analyzed from the point of view of stress variation in the process of brittle rock breaking. The study shows that rock plasticity is enhanced after high temperature, and the temperature difference between the drilling fluid and bottom hole will make the outer part of the bottom hole shrink obviously. Under the conditions of this study, the optimal rock-breaking angle of the PDC cutter is 20 deg. The confining pressure of deep high-temperature formation will hinder rock breaking at a lower value range, and rocks under high confining pressure are more prone to brittle fracture. The increase of rotational speed has an obvious promotion stage for efficient rock breaking, and too large rotational speed will result in low brittle rock-breaking efficiency. These works are helpful in understanding the efficient brittle rock-breaking mechanism in high-temperature drilling, and can provide references for tooth design and rotational speed optimization of PDC bits.
Online Measurement of Impedance Spectroscopy of Lithium-Ion Batteries Based on Equalized Current Harmonic Injection
Authors: Chen Long , Chen Haisen , Liao Li , Jiang Jiuchun , Wang Lujun
Published: December 2024

Impedance spectroscopy can characterize a variety of states within a battery and shows great potential for application in safety warning and condition assessment, but there is a lack of an effective online monitoring method. Therefore, this article proposes a method for online measurement of impedance spectroscopy based on harmonic injection of equalization currents, which superimposes different frequency sinusoidal perturbation signals on the original equalization currents through process reconstruction and collaborative control, and realizes real-time impedance spectroscopy monitoring at the level of single cell without additional hardware. In order to verify the validity of the method proposed in this article, a hardware experimental platform was constructed. First, a four-switch buck-boost (FSBB) converter is used to perform energy equalization of a six-cell Li-ion battery pack under different working conditions, and the experimental results show that the Li-ion battery pack can be equalized by the active equalization circuit under the states of resting, charging, and discharging in about 60 min, 75 min, and 100 min, respectively. Then, the impedance spectroscopy in the frequency range of 0.2 Hz–800 Hz is achieved through the collaborative control of active equalization and impedance spectroscopy. Finally, in order to verify the reliability of the measured data, the measured impedance spectroscopy data were evaluated by the Kramers–Kronig (K-K) transforms, and the data measured at the initial stage were compared and analyzed with the data measured by a professional electrochemical workstation, which verified the validity of the method proposed in this article.
Effects of heat stresses on fitness of three commercial predatory mites
Authors: Hao Xuemin , Wang Endong , Yan Hong , Zhao Peipei , Sheng Fujing , Ren Qin , Liu Meike , Zhang Bo , Xu Xuenong
Published: December 2024

Predatory mites are important biocontrol agents in controlling small pests in the greenhouse. However, extreme high temperatures often occur during the daytime in greenhouses due to solar radiation in spring and summer. To explore the performances of predatory mites under high temperatures, we selected three popular commercial species Amblyseius orientalis, Neoseiulus californicus, and Neoseiulus barkeri to investigate the survival rate, development duration, and fecundity after their eggs and female adults were treated with high temperatures. The results showed that both eggs and adults of N. barkeri and N. californicus were more tolerant to heat stress than A. orientalis. Compared with 25 °C, the developmental periods and longevity of all three species of predator mites were shortened, and the fecundity was also reduced at 39°C. The total fecundity and longevity of N. californicus reduced by 27% and 29%, respectively. For N. barkeri, the total fecundity reduced by 30% and the longevity decreased by 23%. All A. orientalis died at 40 °C, which also cut half longevity of N. californicus and N. barkeri. Our study confirmed that the N. barkeri and N. californicus had stronger tolerances to high temperatures, while A. orientalis was more heat-sensitive during the egg stage and adult stage. In sum, understanding of the heat resistance of commercial predatory mites can improve the application of biocontrol agents when selecting predator species for pest control in the greenhouse.
Estimating received level in behavioral response studies through the use of ancillary data
Authors: Schick Robert S. , Cioffi William R. , Foley Heather J. , Joseph John , Kaney Nicholas A. , Margolina Tetyana , Swaim Zachary T. , Zheng Larry , Southall Brandon L.
Published: December 2024

Marine mammals are known to respond to various human noises, including and in certain cases, strongly, to military active sonar. Responses include small and short-term changes in diving behavior, horizontal avoidance of an ensonified area, and mass strandings. Considerable research has been conducted using short-term biologging tags to understand these responses. Yet researchers and managers want a better understanding of responses to sound over longer periods of time in a variety of contexts. The Atlantic Behavioral Response Study examines responses across multiple spatial and temporal scales using vessel-based focal follows, short-term biologging tags, and medium-term satellite transmitting tags. Since the latter do not record sound, we must intersect positions with a sound propagation model to estimate received sound pressure levels. We use all available information from (1) the observed x,y positions from the tag(s) and from focal follow vessels; (2) the discrete depth bin data (z) from the tag; (3) ocean bathymetry; and (4) outputs from sound propagation models. All these disparate streams of data contain varying levels of error in x, y, or z. We account for as much uncertainty as possible and include here a refined approach to better estimate the range of sound levels received by animals.
Nearfield observation of spin-orbit interactions at nanoscale using photoinduced force microscopy
Authors: Dong Yajuan , Wang Yu , He Dengji , Wang Tao , Zeng Jinwei , Wang Jian
Published: December 2024

Optical spin and orbital angular momenta are intrinsic characteristics of light determined by its polarization and spatial degrees of freedom, respectively. At the nanoscale, sharply focused structured light carries coupled spin-orbital angular momenta with complex 3D nearfield structures, crucial for manipulating multidimensional information of light in nanophotonics. However, characterizing these interactions faces challenges with conventional farfield–based methods, which typically lack the essential accuracy and resolution to interrogate the structured nearfield with high fidelity. To address this challenge, we experimentally observe spin-orbit interactions at the nanoscale using photoinduced force microscopy. Such interactions are enabled through sharply focused circularly polarized optical vortices, which are then mapped by nearfield optical forces in high resolution. Because the optical forces can reveal both longitudinal and transverse nearfield structures with high fidelity, the spin-orbit interactions are eventually evaluated quantitatively at the nearfield, as an important inspiration to use the coupled momenta in dense optical nano-device systems.
RNA-dependent RNA polymerase of predominant human norovirus forms liquid-liquid phase condensates as viral replication factories
Authors: Kaundal Soni , Anish Ramakrishnan , Ayyar B. Vijayalakshmi , Shanker Sreejesh , Kaur Gundeep , Crawford Sue E. , Pollet Jeroen , Stossi Fabio , Estes Mary K. , Prasad B. V. Venkataram
Published: December 2024

Many viral proteins form biomolecular condensates via liquid-liquid phase separation (LLPS) to support viral replication and evade host antiviral responses, and thus, they are potential targets for designing antivirals. In the case of nonenveloped positive-sense RNA viruses, forming such condensates for viral replication is unclear and less understood. Human noroviruses (HuNoVs) are positive-sense RNA viruses that cause epidemic and sporadic gastroenteritis worldwide. Here, we show that the RNA-dependent RNA polymerase (RdRp) of pandemic GII.4 HuNoV forms distinct condensates that exhibit all the signature properties of LLPS with sustained polymerase activity and the capability of recruiting components essential for viral replication. We show that such condensates are formed in HuNoV-infected human intestinal enteroid cultures and are the sites for genome replication. Our studies demonstrate the formation of phase-separated condensates as replication factories in a positive-sense RNA virus, which plausibly is an effective mechanism to dynamically isolate RdRp replicating the genomic RNA from interfering with the ribosomal translation of the same RNA.
Extreme longevity may be the rule not the exception in Balaenid whales
Authors: Breed Greg A. , Vermeulen Els , Corkeron Peter
Published: December 2024

We fit ongoing 40+-year mark-recapture databases from the thriving southern right whale (SRW),
Eubalaena australis
, and highly endangered North Atlantic right whale (NARW),
Eubalaena glacialis
, to candidate survival models to estimate their life spans. Median life span for SRW was 73.4 years, with 10% of individuals surviving past 131.8 years. NARW life spans were likely anthropogenically shortened, with a median life span of just 22.3 years, and 10% of individuals living past 47.2 years. In the context of extreme longevity recently documented in other whale species, we suggest that all balaenid and perhaps most great whales have an unrecognized potential for great longevity that has been masked by the demographic disruptions of industrial whaling. This unrecognized longevity has profound implication for basic biology and conservation of whales.
Nutrient management offsets the effect of deoxygenation and warming on nitrous oxide emissions in a large US estuary
Authors: Tang Weiyi , Da Fei , Tracey John C. , Intrator Naomi , Kunes Moriah A. , Lee Jenna A. , Wan Xianhui Sean , Jayakumar Amal , Friedrichs Marjorie A. M. , Ward Bess B.
Published: December 2024

Many estuaries experience eutrophication, deoxygenation and warming, with potential impacts on greenhouse gas emissions. However, the response of N
2
O production to these changes is poorly constrained. Here we applied nitrogen isotope tracer incubations to measure N
2
O production under experimentally manipulated changes in oxygen and temperature in the Chesapeake Bay—the largest estuary in the United States. N
2
O production more than doubled from nitrification and increased exponentially from denitrification when O
2
was decreased from >20 to <5 micromolar. Raising temperature from 15° to 35°C increased N
2
O production 2- to 10-fold. Developing a biogeochemical model by incorporating these responses, N
2
O emissions from the Chesapeake Bay were estimated to decrease from 157 to 140 Mg N year
−1
from 1986 to 2016 and further to 124 Mg N year
−1
in 2050. Although deoxygenation and warming stimulate N
2
O production, the modeled decrease in N
2
O emissions, attributed to decreased nutrient inputs, indicates the importance of nutrient management in curbing greenhouse gas emissions, potentially mitigating climate change.
Simultaneous noninvasive quantification of redox and downstream glycolytic fluxes reveals compartmentalized brain metabolism
Authors: Patel Saket , Porcari Paola , Coffee Elizabeth , Kim Nathaniel , Berishaj Marjan , Peyear Thasin , Zhang Guannan , Keshari Kayvan R.
Published: December 2024

Brain metabolism across anatomic regions and cellular compartments plays an integral role in many aspects of neuronal function. Changes in key metabolic pathway fluxes, including oxidative and reductive energy metabolism, have been implicated in a wide range of brain diseases. Given the complex nature of the brain and the need for understanding compartmentalized metabolism noninvasively in vivo, new tools are required. Herein, using hyperpolarized (HP) magnetic resonance imaging coupled with in vivo isotope tracing, we develop a platform to simultaneously probe redox and energy metabolism in the murine brain. By combining HP dehydroascorbate and pyruvate, we are able to visualize increased lactate production in the white matter and increased redox capacity in the deep gray matter. Leveraging positional labeling, we show differences in compartmentalized tricarboxylic acid cycle entry versus downstream flux to glutamate. These findings lay the foundation for clinical translation of the proposed approach to probe brain metabolism.
A combined NMR and deep neural network approach for enhancing the spectral resolution of aromatic side chains in proteins
Authors: Shukla Vaibhav Kumar , Karunanithy Gogulan , Vallurupalli Pramodh , Hansen D. Flemming
Published: December 2024

Nuclear magnetic resonance (NMR) spectroscopy is an important technique for deriving the dynamics and interactions of macromolecules; however, characterizations of aromatic residues in proteins still pose a challenge. Here, we present a deep neural network (DNN), which transforms NMR spectra recorded on simple uniformly
13
C-labeled samples to yield high-quality
1
H-
13
C correlation maps of aromatic side chains. Key to the success of the DNN is the design of NMR experiments that produce data with unique features to aid the DNN produce high-resolution spectra. The methodology was validated experimentally on protein samples ranging from 7 to 40 kDa in size, where it accurately reconstructed multidimensional aromatic
1
H-
13
C correlation maps, to facilitate
1
H-
13
C chemical shift assignments and to quantify kinetics. More generally, we believe that the strategy of designing new NMR experiments in combination with customized DNNs represents a substantial advance that will have a major impact on the study of molecules using NMR in the years to come.
Measuring lost votes by mail
Authors: Meredith Marc , Morse Michael , Madarang Amaya , Steele Katie
Published: December 2024

The rise of mail balloting has led to concerns that procedural requirements can lead to “lost votes by mail.” We theorize how procedural requirements can affect the incidence and form of lost votes and highlight three measurement issues with equating lost votes and rejected mail ballots. First, coverage: Not all rejected mail ballots are documented. Second, substitution: Some people whose mail ballot is rejected may subsequently successfully vote, in particular if they were notified in time to take action. Third, deterrence: Others may not return their mail ballots if they expect them to be rejected. While rejected mail ballots could over- or underestimate lost votes, a case study of Pennsylvania’s 2022 general election reveals at least 47% more lost votes than rejected mail ballots. These lost votes could prove electorally consequential in Pennsylvania given the number of mail ballots cast and the substantial partisan splits on mail versus in-person ballots.
Pneumatic coding blocks enable programmability of electronics-free fluidic soft robots
Authors: Picella Sergio , van Riet Catharina M. , Overvelde Johannes T. B.
Published: December 2024

Decision-making based on environmental cues is a crucial feature of autonomous systems. Embodying this feature in soft robots poses nontrivial challenges on both hardware and software that can undermine the simplicity and autonomy of such devices. Existing pneumatic electronics-free soft robots have so far mostly been approached by using system fluidic circuit architectures analogous to digital electronics. Instead, here we design dedicated pneumatic coding blocks equivalent to
If
,
If...break
, and
For
software control statements, which are based on the analog nature of nonlinear mechanical components. We demonstrate that we can combine these coding blocks into programs to implement sequences and to control an electronics-free autonomous soft gripper that switches between behaviors based on interactions with the environment. As such, our strategy provides an alternative approach to designing complex behavior in soft robotics that is more reminiscent of how functionalities are also encoded in the body of living systems.
Cancer mutations rewire the RNA methylation specificity of METTL3-METTL14
Authors: Zhang Chi , Scott Robyn L. , Tunes Luiza , Hsieh Meng-Hsiung , Wang Ping , Kumar Ashwani , Khadgi Brijesh B. , Yang Yen-Yu , Doxtader Lacy Katelyn A. , Herrell Emily , Zhang Xunzhi , Evers Bret , Wang Yinsheng , Xing Chao , Zhu Hao , Nam Yunsun
Published: December 2024

Chemical modification of RNAs is important for posttranscriptional gene regulation. The METTL3-METTL14 complex generates most
N
6
-methyladenosine (m
6
A) modifications in messenger RNAs (mRNAs), and dysregulated methyltransferase expression has been linked to cancers. Here we show that a changed sequence context for m
6
A can promote oncogenesis. A gain-of-function missense mutation from patients with cancer, METTL14
R298P
, increases malignant cell growth in culture and transgenic mice without increasing global m
6
A levels in mRNAs. The mutant methyltransferase preferentially modifies noncanonical sites containing a GGAU motif, in vitro and in vivo. The m
6
A in GGAU context is detected by the YTH family of readers similarly to the canonical sites but is demethylated less efficiently by an eraser, ALKBH5. Combining the biochemical and structural data, we provide a model for how the cognate RNA sequences are selected for methylation by METTL3-METTL14. Our work highlights that sequence-specific m
6
A deposition is important and that increased GGAU methylation can promote oncogenesis.
Trapped-ion quantum simulation of electron transfer models with tunable dissipation
Authors: So Visal , Duraisamy Suganthi Midhuna , Menon Abhishek , Zhu Mingjian , Zhuravel Roman , Pu Han , Wolynes Peter G. , Onuchic José N. , Pagano Guido
Published: December 2024

Electron transfer is at the heart of many fundamental physical, chemical, and biochemical processes essential for life. The exact simulation of these reactions is often hindered by the large number of degrees of freedom and by the essential role of quantum effects. Here, we experimentally simulate a paradigmatic model of molecular electron transfer using a multispecies trapped-ion crystal, where the donor-acceptor gap, the electronic and vibronic couplings, and the bath relaxation dynamics can all be controlled independently. By manipulating both the ground-state and optical qubits, we observe the real-time dynamics of the spin excitation, measuring the transfer rate in several regimes of adiabaticity and relaxation dynamics. Our results provide a testing ground for increasingly rich models of molecular excitation transfer processes that are relevant for molecular electronics and light-harvesting systems.
NK cells restrain cytotoxic CD8
+
T cells in the submandibular gland via PD-1–PD-L1
Authors: Borys Samantha M. , Reilly Shanelle P. , Magill Ian , Zemmour David , Brossay Laurent
Published: December 2024

The increasing use of anti–programmed cell death 1 (PD-1) immune checkpoint blockade has led to the emergence of immune-related adverse events (irAEs), including dysfunction of the submandibular gland (SMG). In this study, we investigated the immunoregulatory mechanism contributing to the susceptibility of the SMG to irAEs. We found that the SMGs of PD-1–deficient mice and anti–programmed cell death ligand 1 (PD-L1)–treated mice harbor an expanded population of CD8
+
T cells. We demonstrate that natural killer (NK) cells expressing PD-L1 tightly regulate CD8
+
T cells in the SMG. When this immunoregulation is disrupted, CD8
+
T cells clonally expand and acquire a unique transcriptional profile consistent with T cell receptor (TCR) activation. These clonally expanded cells phenotypically overlapped with cytotoxic GzmK
+
CD8
+
T autoimmune cells identified in patients with primary Sjögren’s syndrome. Understanding how NK cells modulate CD8
+
T cell activity in the SMG opens new avenues for preventing irAEs in patients undergoing checkpoint blockade therapies.
Microbiome composition and turnover in the face of complex lifecycles and bottlenecks: insights through the study of dung beetles
Authors: Jones Joshua A. , Newton Irene Garcia , Moczek Armin P.
Published: December 2024

Microbiome composition and function often change throughout a host’s life cycle, reflecting shifts in the ecological niche of the host. The mechanisms that establish these relationships are therefore important dimensions of host ecology and evolution; yet, their nature remains poorly understood. Here, we sought to investigate the microbial communities associated with the complex life cycle of the dung beetle
Onthophagus taurus
and the relative contributions of host life stage, sex, and environment in determining microbiome assembly. We find that
O. taurus
plays host to a diverse microbiota that undergo drastic community shifts throughout host development, influenced by host life stage, environmental microbiota, and, to a lesser degree, sex. Contrary to predictions, we found that egg and pupal stages—despite the absence of a digestive tract or defined microbe-storing organs—do not constrain microbial maintenance, while host-constructed environments, such as a maternally derived fecal pellet or the pupal chamber constructed by late larvae, may still serve as complementary microbial refugia for select taxa. Lastly, we identify a small community of putative core microbiota likely to shape host development and fitness. Our results provide important insights into mechanisms employed by solitary organisms to assemble, maintain, and adjust beneficial microbiota to confront life-stage-specific needs and challenges.

IMPORTANCE

As the influence of symbionts on host ecology, evolution, and development has become more apparent so has the importance of understanding how hosts facilitate the reliable maintenance of their interactions with these symbionts. A growing body of work has thus begun to identify diverse behaviors and physiological mechanisms underpinning the selective colonization of beneficial symbionts across a range of host taxa. Yet, how organisms with complex life cycles, such as holometabolous insects, establish and maintain key symbionts remains poorly understood. This is particularly interesting considering the drastic transformations of both internal and external host morphology, and the ecological niche shifts in diet and environment, that are the hallmark of metamorphosis. This work investigates the dynamic changes of the microbiota associated with the complex life cycle and host-constructed environments of the bull-headed dung beetle,
Onthophagus taurus
, a useful model for understanding how organisms may maintain and modulate their microbiota across development.
Chlorine disinfectant significantly changed microfauna habitat, community structure, and colonization mode in wastewater treatment plants
Authors: Zhong Yuening , Zhang Yibo , Meng Qiyue , Zhang Haoyu , Wu Zhenbing , Dang Chenyuan , Fu Jie
Published: December 2024

During the coronavirus disease 2019 epidemic, excessive chlorine disinfectants have been used to block the spread of severe acute respiratory syndrome-coronavirus 2, resulting in large amounts of residual disinfectants entering wastewater treatment plants (WWTPs) through sewage systems. So far, no relevant research has been conducted on the impact of chlorine disinfectants on microfauna, an important microbial component in activated sludge treatment systems. This study comprehensively investigated the changes in microfauna habitat, community structure, and colonization mode under the chlorine stress by combining the full-scale WWTP survey and laboratory-scale sequencing batch reactor experiments. The results showed that chlorine disinfectants significantly changed the community structure of microfauna, including decrease in sedentary ciliates and increase in free-living ciliates, amoebas, and flagellates. Besides the disinfection effect of chlorine disinfectants, the microfauna community was also influenced by changes in habitat and bacterial community. The loose structure and excessive extracellular polymeric substance (EPS) of activated sludge caused by chlorination would impact the colonization of sedentary ciliates, while it was conducive to the survival of free-living ciliates due to their predation on EPS as the nutrients. Bacteria in the activated sludge had strong interactions with protozoa, and their changes under chlorine stress directly affected the protozoan community and even indirectly affected the micro-metazoa community through the food chain.

IMPORTANCE

This study revealed that chlorine disinfectant significantly changed microfauna habitat, community structure, and colonization mode in wastewater treatment plants during the coronavirus disease 2019 pandemic. Chlorine disinfectant could destroy the structure and stability of sludge flocs, reduce the abundance of beneficial microfauna in activated sludge, and even affect the colonization of sedentary ciliates on sludge. In addition, chlorine disinfectants might induce environmental and ecological risks related to microfauna, such as elevated suspended solids and release of bacteria and microfauna in the effluents.
Conformational changes in and translocation of small proteins: insights into the ejection mechanism of podophages
Authors: Zheng Jing , Xiao Hao , Pang Hao , Wang Li , Song Jingdong , Chen Wenyuan , Cheng Lingpeng , Liu Hongrong
Published: December 2024

Podophage tails are too short to span the cell envelope during infection. Consequently, podophages initially eject the core proteins within the head for the formation of an elongated trans-envelope channel for DNA ejection. Although the core proteins of bacteriophage T7 have been resolved at near-atomic resolution, the mechanisms of core proteins and DNA ejection remain to be fully elucidated. In this study, we provided improved structures of core proteins in mature T7 and the portal–tail complex in lipopolysaccharide-induced DNA-ejected T7 to resolutions of approximately 3 Å. Using these structures, we identified three small proteins, namely gp14, gp6.7, and gp7.3, and illustrated the conformational changes in and translocation of these proteins from the mature to DNA-ejected states. Our structures indicate that gp6.7, which participates in the assembly of the core and trans-envelope channel, is a core protein, and that gp7.3 serves as a structural scaffold to assist the assembly of the nozzle into the adaptor.

IMPORTANCE

Podophage T7 core proteins form an elongated trans-envelope channel for genomic DNA delivery into the host cell. The structures of the core proteins within the mature T7 and assembled in the periplasmic tunnel form in the DNA-ejected T7 have been resolved previously. Here, we resolved the structures of two new structural proteins (gp6.7 and gp7.3) within mature T7 and receptor-induced DNA-ejected T7. The gp6.7 protein participates in the assembly of the core complex within mature T7 and the trans-envelope channel during T7 infection; therefore, gp6.7 is a core protein. Before T7 infection, gp7.3 plays a role in promoting the assembly of the nozzle into the adaptor.
Progression of
ampC
amplification during
de novo
amoxicillin resistance development in
E. coli
Authors: Nong Luyuan , Jonker Martijs , de Leeuw Wim , Wortel Meike T. , ter Kuile Benno
Published: December 2024

Beta-lactam antibiotics are the most applied antimicrobials in human and veterinarian health care. Hence, beta-lactam resistance is a major health problem. Gene amplification of AmpC beta-lactamase is a main contributor to
de novo
β-lactam resistance in
Escherichia coli
. However, the time course of amplification and the accompanying DNA mutations are unclear. Here, we study the progression of
ampC
amplification and
ampC
promoter mutations during the evolution of resistance induced by stepwise increasing amoxicillin concentrations.
AmpC
promoter mutations occurred by day 2, while the approximately eight-fold amplification occurred after more than 6 days of amoxicillin exposure. The combination of the amplification and the promoter mutations increased the
ampC
mRNA level by an average factor of 200 after 22 days. An IS
1
insertion is identified in the amplification junction after resistance induction in the wild type (WT) and the
ampC
gene complementation strain (CompA), but not in ∆
ampC
, suggesting that the amplification depends on mobile genetic element transposition. In order to elucidate the correlation between gene mutations and
ampC
amplification, the DNA mutations acquired during resistance evolution by the WT, ∆
ampC
, and CompA were analyzed. Compared to evolved ∆
ampC
, several resistance-causing mutations are absent in evolved WT, while more mutations accumulated in stress response. The amoxicillin-resistant ∆
ampC
did not show amplification of the fragment around the original
ampC
position but exhibited a large duplication or triplication at another position, suggesting the essential role of the duplicated genes in resistance development.

IMPORTANCE

Amoxicillin is the most used antimicrobial against bacterial infections. DNA fragments containing
ampC
are amplified upon prolonged and stepwise increasing exposure to amoxicillin, causing resistance. These
ampC
-containing fragments have been identified in extended-spectrum beta-lactamase plasmids, which are considered the main cause of beta-lactam resistance. In this study, we document the time course of two important factors for
ampC
transcription enhancement,
ampC
amplification and
ampC
promoter mutations, during
de novo
amoxicillin resistance evolution. We propose that the transposon IS
1
contributes to the amplification
ampC
region, that the sigma factor 70 regulates
ampC
overexpression, and that these combined form the backbone of a putative mechanism for
ampC
amplification.
Genome sequence of
Vibrio harveyi
strain TUMSAT-2019, isolated from kuruma shrimp,
Penaeus japonicus
Authors: Yuasa Hajime , Koiwai Keiichiro , Konishi Kayo , Furukawa Miho , Nozaki Reiko , Kondo Hidehiro , Hirono Ikuo
Published: December 2024

The Gram-negative bacterium
Vibrio harveyi
is a serious shrimp pathogen. Here, we present the genome sequence of
Vibrio harveyi
TUMSAT-2019, which was isolated from a kuruma shrimp (
Penaeus japonicus
) that originated from a shrimp farm in Okinawa Prefecture. The assembly totaled 5.7 Mbp, consisting of two chromosomes with no plasmid.
mtlA,
a novel typing gene offering enhanced resolution for pandemic
Vibrio
species
Authors: Zhou Lei , Liu Danlei , Zhang Zilong , Zhu Yongqiang , Zheng Huajun
Published: December 2024

The gene
mtlA
, encoding the mannitol transporter subunit IICBA of the phosphotransferase system, was the core gene with the greatest variability in
Vibrio parahaemolyticus
and could be used as a new typing marker in
Vibrio parahaemolyticus
. To expand its application, we performed an evolutionary analysis and found that the
mtlA
gene was present in nine phyla, 371 genera, and 1,662 species of bacteria. It is commonly found in pathogenic species of
Vibrio
, followed by
Paenibacillus
,
Mycolicibacterium
, etc. To investigate whether the
mtlA
gene could serve as a novel typing gene for whole
Vibrio
species, we compared the typing effect of the
mtlA
gene with multilocus sequence type (MLST) in 13 common pathogenic
Vibrio
species. The results revealed that the
mtlA
gene was present in all common pathogenic species, providing comparable or even higher typing resolution than MLST, especially in
Vibrio cholerae
,
Vibrio alginolyticus
,
Vibrio harveyi
, and
Vibrio anguillarum
, enabling accurate typing and traceability; however, many species lacked allelic profiles of MLST genes, making it impossible to obtain accurate STs. In summary, these findings validated the potential typing application of the
mtlA
gene in
Vibrio
species.

IMPORTANCE

Vibrio
is a collection of gram-negative bacteria characterized by possessing two chromosomes, which exhibit numerous shared biological and genomic traits. Around 13 species of
Vibrio
are known to cause infections in humans. Without appropriate medical interventions, the consequences of these infections can escalate to become life-threatening. Therefore, based on the prevalent characteristics of pathogenic
Vibrio
, it is imperative for us to classify and trace various
Vibrio
species that cause human illness and prescribe medication rationally to control the spread of diseases. In our investigation, we explored the prevalence and typing accuracy of the
mtlA
gene in
Vibrio
. Our findings revealed its ubiquitous presence across typical pathogenic
Vibrio
species, offering superior typing efficacy compared with MLST and more extensive implications.
Supplemental Material: Geochemical transition from Miocene–Pliocene to Quaternary arc volcanism in the northern Sierra Nevada, California
Authors: Stoffers Albert J.
Published: December 2024

Supplemental File S1: Map showing locations of previous K-Ar and 40Ar/39Ar age determinations on volcanic rocks; Supplemental File S2: Sagehen Volcanic Center Rock unit descriptions (Fig. 3 map units); Supplemental File S3: 40Ar/39Ar ages, Sagehen Field Station Area, with plateau and isochron diagrams; Supplemental File S4: Analytical techniques at Washington State University and University of Kansas Radiogenic Isotope Laboratory analytical procedures; Supplemental File S5: All samples; Supplemental File S6: Major, trace element, and radiogenic isotope data for Mesozoic Sierra Nevada granitoids of the North Sierra segment; and Supplemental File S7: Estimates of analytical precision from repeat analyses of internal and international rock standards. 